Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008944.1 Hibiscus syriacus cultivar Beakdansim tig00112265_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: 190011
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3864 original size:35 final size:37
Alignment explanation
Indices: 3818--3897 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
3808 TTTGATAATT
*
3818 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
3853 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
3890 TGGTGATG
1 TGGTGATG
3898 GAAATAGTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:8543 original size:11 final size:11
Alignment explanation
Indices: 8529--8553 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
8519 CAAAAAAAAA
8529 GAAGTGCAAGT
1 GAAGTGCAAGT
8540 GAAGTGCAAGT
1 GAAGTGCAAGT
8551 GAA
1 GAA
8554 AAAAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:8601 original size:22 final size:26
Alignment explanation
Indices: 8574--8627 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
8564 AAAATCAGCA
*
8574 AAGAAA-TTG-AAGCACT-CAAAA-G
1 AAGAAATTTGTAAGCACTAAAAAATG
8596 AAGAAATTTGTAAGCACTAAAAAATG
1 AAGAAATTTGTAAGCACTAAAAAATG
8622 AAGAAA
1 AAGAAA
8628 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 6 0.22
23 3 0.11
24 7 0.26
25 4 0.15
26 7 0.26
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (26 bp):
AAGAAATTTGTAAGCACTAAAAAATG
Found at i:15513 original size:30 final size:30
Alignment explanation
Indices: 15479--15535 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
15469 GATGTAGGAG
* *
15479 TCTTTTTCT-TTTCTTTTTGTTTTTGTTCTT
1 TCTTTTTCTCTTT-TTGTTGCTTTTGTTCTT
15509 TCTTTTTCTCTTTTTGTTGCTTTTGTT
1 TCTTTTTCTCTTTTTGTTGCTTTTGTT
15536 GCAGCACTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.00, C:0.14, G:0.09, T:0.77
Consensus pattern (30 bp):
TCTTTTTCTCTTTTTGTTGCTTTTGTTCTT
Found at i:15749 original size:10 final size:10
Alignment explanation
Indices: 15736--15761 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15726 AAGAAAAAAG
15736 GAAATGGATA
1 GAAATGGATA
15746 GAAATGGATA
1 GAAATGGATA
15756 GAAATG
1 GAAATG
15762 TTATCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (10 bp):
GAAATGGATA
Found at i:19312 original size:45 final size:44
Alignment explanation
Indices: 19235--19339 Score: 108
Period size: 50 Copynumber: 2.3 Consensus size: 44
19225 AGGATTATAT
* *
19235 TTATTATTTTATTAGGAATTAAGGTTGGGTTAAAATATTATCTTTAG-TTA
1 TTATTATTTTATTAGGAATTAA-G--GAGTT--AAGA-TAT-TTTAGTTTA
19285 TTATTATTTTATTAGGAATT-A-GAGTTAAGATATTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGAGTTAAGATATTTTAGTTTA
19327 TTATTATTTTATT
1 TTATTATTTTATT
19340 CATTAGTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
41 5 0.10
42 19 0.37
43 3 0.06
45 4 0.08
49 1 0.02
50 20 0.38
ACGTcount: A:0.31, C:0.01, G:0.13, T:0.54
Consensus pattern (44 bp):
TTATTATTTTATTAGGAATTAAGGAGTTAAGATATTTTAGTTTA
Found at i:20122 original size:8 final size:8
Alignment explanation
Indices: 20104--20178 Score: 105
Period size: 8 Copynumber: 8.8 Consensus size: 8
20094 CTAATTTTTT
20104 AAAACAAAC
1 AAAA-AAAC
20113 AAAAAAAC
1 AAAAAAAC
20121 AAAAAAAGGC
1 AAAAAAA--C
20131 AAAAAAAAAC
1 --AAAAAAAC
20141 AAAAAAAC
1 AAAAAAAC
20149 AAAAAAAC
1 AAAAAAAC
20157 AAAAAAAC
1 AAAAAAAC
20165 AAAAAAAC
1 AAAAAAAC
20173 AAAAAA
1 AAAAAA
20179 GCCAAAATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
8 49 0.79
9 4 0.06
10 2 0.03
12 7 0.11
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:20135 original size:1 final size:1
Alignment explanation
Indices: 20131--20178 Score: 51
Period size: 1 Copynumber: 48.0 Consensus size: 1
20121 AAAAAAAGGC
* * * * *
20131 AAAAAAAAACAAAAAAACAAAAAAACAAAAAAACAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
20179 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:20143 original size:28 final size:25
Alignment explanation
Indices: 20104--20178 Score: 107
Period size: 28 Copynumber: 2.9 Consensus size: 25
20094 CTAATTTTTT
*
20104 AAAACAAACAAAAAAACAAAAAAAGGC
1 AAAAAAAACAAAAAAACAAAAAAA--C
20131 AAAAAAAAACAAAAAAACAAAAAAAC
1 -AAAAAAAACAAAAAAACAAAAAAAC
20157 -AAAAAAACAAAAAAACAAAAAA
1 AAAAAAAACAAAAAAACAAAAAA
20179 GCCAAAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
24 22 0.48
26 1 0.02
28 23 0.50
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (25 bp):
AAAAAAAACAAAAAAACAAAAAAAC
Found at i:32857 original size:35 final size:37
Alignment explanation
Indices: 32788--32867 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
32778 ATATTATTTC
*
32788 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
32825 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
32860 TATCACCA
1 CATCACCA
32868 AATTCTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:34639 original size:19 final size:20
Alignment explanation
Indices: 34615--34657 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
34605 AGCATTTATC
*
34615 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
34634 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
34654 TTCA
1 TTCA
34658 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:37718 original size:35 final size:37
Alignment explanation
Indices: 37649--37728 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
37639 ATACTATTTC
*
37649 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
37686 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
37721 CATCACCA
1 CATCACCA
37729 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:38137 original size:20 final size:21
Alignment explanation
Indices: 38103--38152 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 21
38093 AAAGTGCTAC
*
38103 AAAAAAAAAGCAACAAAAAAGAAG
1 AAAAAAAAA-CAA-AAAGAA-AAG
38127 AAAAAAAAACAAAAAGAAAAG
1 AAAAAAAAACAAAAAGAAAAG
38148 AAAAA
1 AAAAA
38153 GACTCTTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 8 0.32
22 5 0.20
23 3 0.12
24 9 0.36
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAAGAAAAG
Found at i:38209 original size:14 final size:15
Alignment explanation
Indices: 38178--38219 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38168 TTTGGAGTGC
38178 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
38193 AAAAG-AAGAATA-A
1 AAAAGAAAGAAAAGA
38206 AAAAGCAAAGAAAA
1 AAAAG-AAAGAAAA
38220 AGTGAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:38417 original size:24 final size:25
Alignment explanation
Indices: 38373--38422 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
38363 TTACTATTTC
*
38373 ATTTCATTTTCTTTCATATTTTCTT
1 ATTTCATTTACTTTCATATTTTCTT
38398 ATTTCA-TTACTTT-ATCATTTTCTT
1 ATTTCATTTACTTTCAT-ATTTTCTT
38422 A
1 A
38423 ACCTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATATTTTCTT
Found at i:42386 original size:33 final size:32
Alignment explanation
Indices: 42322--42386 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
42312 CTTGTTGATG
*
42322 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
42354 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
42387 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:46212 original size:38 final size:37
Alignment explanation
Indices: 46140--46214 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
46130 GAAAAAGGTT
*
46140 AAGAAAAAGGATAAAGTAATGAAATAAGAAAAGATGA
1 AAGAAAAAGGATAAAGAAATGAAATAAGAAAAGATGA
* **
46177 AAGAAAAAGGA-AATGAAATAGTAAATAAGTGAAGATGA
1 AAGAAAAAGGATAAAGAAAT-G-AAATAAGAAAAGATGA
46215 CTTACAACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 12 0.38
38 14 0.44
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.15
Consensus pattern (37 bp):
AAGAAAAAGGATAAAGAAATGAAATAAGAAAAGATGA
Found at i:46831 original size:33 final size:32
Alignment explanation
Indices: 46767--46831 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
46757 CTTGTTGATG
*
46767 AATGAAGGATGATTTAATGGTGATGAAATGGT
1 AATGAAGGATGATTTAATGGCGATGAAATGGT
* *
46799 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
1 AATG-AAGGATGAT-TTAATGGCGATGAAATGGT
46832 GATGGATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.14
33 17 0.61
34 7 0.25
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (32 bp):
AATGAAGGATGATTTAATGGCGATGAAATGGT
Found at i:48284 original size:35 final size:37
Alignment explanation
Indices: 48215--48294 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
48205 ATACTATTTC
*
48215 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
48252 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
48287 CATCACCA
1 CATCACCA
48295 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:48774 original size:14 final size:15
Alignment explanation
Indices: 48743--48784 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48733 TTTGGAGTGC
48743 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
48758 AAAAG-AAGAATA-A
1 AAAAGAAAGAAAAGA
48771 AAAAGCAAAGAAAA
1 AAAAG-AAAGAAAA
48785 AGTGAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:48982 original size:24 final size:25
Alignment explanation
Indices: 48938--48987 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
48928 TTACTATTTA
*
48938 ATTTCATTTTCTTTCATATTTTCTT
1 ATTTCATTTACTTTCATATTTTCTT
48963 ATTTCA-TTACTTT-ATCATTTTCTT
1 ATTTCATTTACTTTCAT-ATTTTCTT
48987 A
1 A
48988 ACCTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATATTTTCTT
Found at i:52355 original size:35 final size:37
Alignment explanation
Indices: 52286--52365 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
52276 ATACTATTTC
*
52286 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
52323 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
52358 CATCACCA
1 CATCACCA
52366 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:55029 original size:19 final size:19
Alignment explanation
Indices: 54989--55030 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
54979 AGCATTTATC
* *
54989 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTAGT
55008 TTCATTTAAAATCATGT-GT
1 TTCA-TTAAAATCATGTAGT
55027 TTCA
1 TTCA
55031 AAGGGATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (19 bp):
TTCATTAAAATCATGTAGT
Found at i:57025 original size:19 final size:20
Alignment explanation
Indices: 57001--57043 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
56991 AGCATTTATC
*
57001 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
57020 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
57040 TTCA
1 TTCA
57044 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:63902 original size:18 final size:17
Alignment explanation
Indices: 63858--63904 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
63848 TTTTTGGCTC
63858 TTTTTTTTTTGCCTTTT
1 TTTTTTTTTTGCCTTTT
*
63875 TTTTAATTTTTGCCTTTT
1 TTTT-TTTTTTGCCTTTT
63893 TTTGTTTTTTTG
1 TTT-TTTTTTTG
63905 AAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 21 0.81
19 1 0.04
ACGTcount: A:0.04, C:0.09, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTGCCTTTT
Found at i:70355 original size:16 final size:16
Alignment explanation
Indices: 70334--70371 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
70324 GAATGGAAAC
70334 AAAGAAATCAAAATGA
1 AAAGAAATCAAAATGA
*
70350 AAAGAAATCAAAATGC
1 AAAGAAATCAAAATGA
70366 AAAGAA
1 AAAGAA
70372 GTGCCACAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.68, C:0.08, G:0.13, T:0.11
Consensus pattern (16 bp):
AAAGAAATCAAAATGA
Found at i:84943 original size:19 final size:20
Alignment explanation
Indices: 84919--84961 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
84909 AGCATTTATC
*
84919 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
84938 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
84958 TTCA
1 TTCA
84962 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:86851 original size:19 final size:20
Alignment explanation
Indices: 86827--86869 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
86817 AGCATTTATC
86827 TTCATTAAAAAT-ATGTATT
1 TTCATTAAAAATCATGTATT
*
86846 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
86866 TTCA
1 TTCA
86870 AAGGGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:91454 original size:10 final size:10
Alignment explanation
Indices: 91441--91484 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
91431 AAATTTTGGC
91441 TTTTTTGTTT
1 TTTTTTGTTT
*
91451 TTTTTTGTGT
1 TTTTTTGTTT
**
91461 TTTTTTG-CC
1 TTTTTTGTTT
91470 TTTTTTGTTT
1 TTTTTTGTTT
91480 TTTTT
1 TTTTT
91485 GTAGAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:98199 original size:13 final size:11
Alignment explanation
Indices: 98183--98262 Score: 56
Period size: 11 Copynumber: 6.7 Consensus size: 11
98173 ATACTATTTC
98183 CATCACCATAGT
1 CATCACCATA-T
*
98195 CCATCTTCCATTAT
1 -CATC-ACCA-TAT
98209 CAT-ACCTATAT
1 CATCACC-ATAT
98220 CATCACCATAGTT
1 CATCACCATA--T
98233 CATCACCATAT
1 CATCACCATAT
*
98244 CA-CGCCTATAT
1 CATCACC-ATAT
98255 CATCACCA
1 CATCACCA
98263 AATTCTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
10 3 0.05
11 21 0.38
12 7 0.13
13 18 0.33
14 4 0.07
15 2 0.04
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:98252 original size:35 final size:37
Alignment explanation
Indices: 98183--98262 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
98173 ATACTATTTC
* *
98183 CATCACCATAGTCCATCTTCCATTATCATACCTATAT
1 CATCACCATAGTCCATCTACCATTATCACACCTATAT
* *
98220 CATCACCATAGTTCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAGTCCATCTACCATTATCACACCTATAT
98255 CATCACCA
1 CATCACCA
98263 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (37 bp):
CATCACCATAGTCCATCTACCATTATCACACCTATAT
Found at i:106437 original size:15 final size:15
Alignment explanation
Indices: 106417--106447 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
106407 CTTCATATCT
106417 CCCAATTGAAAAGGA
1 CCCAATTGAAAAGGA
106432 CCCAATTGAAAAGGA
1 CCCAATTGAAAAGGA
106447 C
1 C
106448 ACAAGTACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (15 bp):
CCCAATTGAAAAGGA
Found at i:111850 original size:35 final size:37
Alignment explanation
Indices: 111781--111858 Score: 124
Period size: 35 Copynumber: 2.2 Consensus size: 37
111771 ATACTATTCC
*
111781 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
111818 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
111853 CATCAC
1 CATCAC
111859 GAAATTCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.31, C:0.37, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:112338 original size:14 final size:15
Alignment explanation
Indices: 112307--112348 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
112297 TTTGGAGTGC
112307 AAAAGAAAGAAAAGA
1 AAAAGAAAGAAAAGA
*
112322 AAAAG-AAGAATA-A
1 AAAAGAAAGAAAAGA
112335 AAAAGCAAAGAAAA
1 AAAAG-AAAGAAAA
112349 AGTGAAGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (15 bp):
AAAAGAAAGAAAAGA
Found at i:119682 original size:25 final size:23
Alignment explanation
Indices: 119647--119692 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
119637 TTTTAAAATC
119647 ATTTTCTTTTTCT-TCTTTTCTGA
1 ATTTTCTTTTT-TGTCTTTTCTGA
119670 ATTTTCTTCTTTTTGTCTTTTCT
1 ATTTTC-T-TTTTTGTCTTTTCT
119693 TTCTTTTTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.07, C:0.17, G:0.04, T:0.72
Consensus pattern (23 bp):
ATTTTCTTTTTTGTCTTTTCTGA
Found at i:122222 original size:35 final size:37
Alignment explanation
Indices: 122153--122232 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
122143 ATACTATTCC
*
122153 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
122190 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
122225 CATCACCA
1 CATCACCA
122233 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:126286 original size:35 final size:37
Alignment explanation
Indices: 126217--126296 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
126207 ATACTATTTC
*
126217 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
126254 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
126289 CATCACCA
1 CATCACCA
126297 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:132428 original size:14 final size:15
Alignment explanation
Indices: 132394--132440 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
132384 AATTTGGAGT
132394 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
132409 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
132423 TCAAAAGTAAAAGAAAA
1 GCAAAAG--AAAGAAAA
132440 G
1 G
132441 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.04
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:136400 original size:35 final size:37
Alignment explanation
Indices: 136331--136410 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
136321 ATACTATTTC
* * *
136331 CATCACTATAATCCATCTTCCATTATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
136368 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
136403 CATCACCA
1 CATCACCA
136411 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 3 0.08
37 15 0.38
ACGTcount: A:0.31, C:0.35, G:0.04, T:0.30
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:139843 original size:19 final size:21
Alignment explanation
Indices: 139819--139870 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
139809 CGGCCAAGAG
*
139819 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
139838 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
139859 CATGTATTTTCA
1 CATGTATTTTCA
139871 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:141239 original size:4 final size:4
Alignment explanation
Indices: 141222--141264 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
141212 AAAGCAACAA
* *
141222 AAAG AAAA AAAG AAAG AAGAG AAAG AAAA AAGAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AA-AG AAAG AAAG AA-AG AAAG AAAG A
141265 CTCCTAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:141248 original size:13 final size:13
Alignment explanation
Indices: 141230--141264 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
141220 AAAAAGAAAA
141230 AAAGAAAGAAGAG
1 AAAGAAAGAAGAG
*
141243 AAAGAAAAAAGAG
1 AAAGAAAGAAGAG
141256 AAAGAAAGA
1 AAAGAAAGA
141265 CTCCTAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAGAG
Found at i:145696 original size:15 final size:15
Alignment explanation
Indices: 145678--145720 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
145668 AAACAACAAA
145678 AAGAAAAAAAGAAAG
1 AAGAAAAAAAGAAAG
*
145693 AAGAAAAACAAAAAAG
1 AAGAAAAA-AAGAAAG
145709 -AGAAAGAAAAGA
1 AAGAAA-AAAAGA
145721 CTCCTACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAAAG
Found at i:148057 original size:28 final size:28
Alignment explanation
Indices: 148025--148159 Score: 100
Period size: 28 Copynumber: 4.9 Consensus size: 28
148015 TGAATTAACT
*
148025 AAACAAATGATGAACTTGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
*
148053 AAACAAATGATGAACATGTTGTTATG--
1 AAACAAATGATGAACATGCTGTTATGCA
** ** * * * *
148079 TGA-ATGTGAGTGCACGTGAAT-TTA-ACA
1 AAACAAATGA-TGAACATG-CTGTTATGCA
* * *
148106 AAACAAATGATAAATATGTTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
148134 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
148160 AACCCCACGA
Statistics
Matches: 77, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
25 4 0.05
26 11 0.14
27 9 0.12
28 53 0.69
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:148141 original size:81 final size:80
Alignment explanation
Indices: 147985--148159 Score: 262
Period size: 81 Copynumber: 2.2 Consensus size: 80
147975 GATAATGAAA
* * * * *
147985 AACATGCTGTAAAGTGAATGTGGGTGCACGTGAATTAACTAAACAAATGATGAACTTGCTGTTAT
1 AACATGCTGTTATGTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAATTGCTGTTAT
148050 GCAAAACAAATGATG
66 GCAAAACAAATGATG
* *
148065 AACATGTTGTTATGTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGAT-AAATATGTTGTT
1 AACATGCTGTTATGTGAATGTGAGTGCACGTGAA-TTAACAAAACAAATGATGAAAT-TGCTGTT
148129 ATGCAAAACAAATGATG
64 ATGCAAAACAAATGATG
148146 AACATGCTGTTATG
1 AACATGCTGTTATG
148160 AACCCCACGA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
80 33 0.39
81 52 0.61
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (80 bp):
AACATGCTGTTATGTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAATTGCTGTTAT
GCAAAACAAATGATG
Found at i:152055 original size:38 final size:37
Alignment explanation
Indices: 152004--152078 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
151994 GAGTTGTAAG
*
152004 TCATCTTCACTTATTTACTATTTCATT-TCCTTTTTCTT
1 TCATCTTCACTTATTT-C-ATTACATTATCCTTTTTCTT
** *
152042 TCATCTTTTCTTATTTCATTACTTTATCCTTTTTCTT
1 TCATCTTCACTTATTTCATTACATTATCCTTTTTCTT
152079 AACCTTTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 12 0.38
38 14 0.44
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.63
Consensus pattern (37 bp):
TCATCTTCACTTATTTCATTACATTATCCTTTTTCTT
Found at i:156503 original size:10 final size:10
Alignment explanation
Indices: 156460--156495 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
156450 TTGTTTTAAA
156460 AAAAAAAGGC
1 AAAAAAAGGC
156470 AAAAAAAGGC
1 AAAAAAAGGC
*
156480 AAAAAAAGCC
1 AAAAAAAGGC
156490 AAAAAA
1 AAAAAA
156496 GCTAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.75, C:0.11, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:162494 original size:15 final size:16
Alignment explanation
Indices: 162461--162498 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
162451 TTTATTATCT
162461 TTTATTTCATCTTCCG
1 TTTATTTCATCTTCCG
**
162477 TTTATTT-ATCTTTTG
1 TTTATTTCATCTTCCG
162492 TTTATTT
1 TTTATTT
162499 TATTCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.13, C:0.13, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTATTTCATCTTCCG
Found at i:164522 original size:24 final size:24
Alignment explanation
Indices: 164490--164544 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
164480 TTTTCTTTTC
**
164490 TTTTTTTTAATTTTCGGAATTTGT
1 TTTTTTTTAATTTTCGGAATTCAT
164514 TTTTTTTTAATTTTCGGAATTCAT
1 TTTTTTTTAATTTTCGGAATTCAT
164538 TTTTTTT
1 TTTTTTT
164545 CAAGATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.69
Consensus pattern (24 bp):
TTTTTTTTAATTTTCGGAATTCAT
Found at i:165835 original size:28 final size:28
Alignment explanation
Indices: 165803--165856 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
165793 TGAATTAACT
165803 AAACAAATGATGAAAATGCTGTTATGCA
1 AAACAAATGATGAAAATGCTGTTATGCA
*
165831 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAAAATGCTGTTATG
165857 TGAATGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAAAATGCTGTTATGCA
Found at i:165918 original size:81 final size:80
Alignment explanation
Indices: 165776--165937 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 80
165766 ATGATGTAAA
* * *
165776 GTGAATGTGGGTGCATGTGAATTAACTAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
1 GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
165841 TGAACATGCTGTTAT
66 TGAACATGCTGTTAT
* *
165856 GTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGAT-AAATATTCTGTTATTCAAAACAAAT
1 GTGAATGTGAGTGCACGTGAA-TTAACAAAACAAATGATGAAA-ATGCTGTTATGCAAAACAAAT
165920 GATGAACATGCTGTTAT
64 GATGAACATGCTGTTAT
165937 G
1 G
165938 AATCCCACGA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 22 0.29
81 53 0.71
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (80 bp):
GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
TGAACATGCTGTTAT
Found at i:165922 original size:28 final size:28
Alignment explanation
Indices: 165882--165936 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
165872 GTGAATTTAA
* *
165882 CAAAACAAATGATAAATATTCTGTTATT
1 CAAAACAAATGATAAACATGCTGTTATT
*
165910 CAAAACAAATGATGAACATGCTGTTAT
1 CAAAACAAATGATAAACATGCTGTTAT
165937 GAATCCCACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (28 bp):
CAAAACAAATGATAAACATGCTGTTATT
Found at i:171494 original size:24 final size:23
Alignment explanation
Indices: 171463--171507 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
171453 TTCTTTTCTT
171463 TTTTTTTTTAATTTTCGGAATTG
1 TTTTTTTTTAATTTTCGGAATTG
171486 TTTTTTTTTAATTTTCGGAATT
1 TTTTTTTTTAATTTTCGGAATT
171508 CCTTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.04, G:0.11, T:0.67
Consensus pattern (23 bp):
TTTTTTTTTAATTTTCGGAATTG
Found at i:171513 original size:24 final size:23
Alignment explanation
Indices: 171463--171515 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
171453 TTCTTTTCTT
*
171463 TTTTTTTTTAATTTTCGGAATTG
1 TTTTTTTTTAATTTTCGGAATTC
171486 TTTTTTTTTAATTTTCGGAATTC
1 TTTTTTTTTAATTTTCGGAATTC
*
171509 CTTTTTT
1 TTTTTTT
171516 CAAGATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.15, C:0.08, G:0.09, T:0.68
Consensus pattern (23 bp):
TTTTTTTTTAATTTTCGGAATTC
Found at i:172796 original size:28 final size:28
Alignment explanation
Indices: 172764--172817 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
172754 TGAATTAACT
172764 AAACAAATGATGAAAATGCTGTTATGCA
1 AAACAAATGATGAAAATGCTGTTATGCA
*
172792 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAAAATGCTGTTATG
172818 TGAATGTGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAAAATGCTGTTATGCA
Found at i:172879 original size:81 final size:80
Alignment explanation
Indices: 172737--172898 Score: 254
Period size: 81 Copynumber: 2.0 Consensus size: 80
172727 ATGATGTAAA
* * * *
172737 GTGAATGTGGGTGCATGTGAATTAACTAAACAAATGATGAAAATGCTGTTATGCAAAACAAATGA
1 GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAAATACTGTTATGCAAAACAAATGA
172802 TGAACATGCTGTTAT
66 TGAACATGCTGTTAT
*
172817 GTGAATGTGAGTGCACGTGAATTTAACAAAACAAATGAT-AAATATACTGTTATTCAAAACAAAT
1 GTGAATGTGAGTGCACGTGAA-TTAACAAAACAAATGATGAAA-ATACTGTTATGCAAAACAAAT
172881 GATGAACATGCTGTTAT
64 GATGAACATGCTGTTAT
172898 G
1 G
172899 AATCCCACAA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
80 22 0.29
81 53 0.71
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.29
Consensus pattern (80 bp):
GTGAATGTGAGTGCACGTGAATTAACAAAACAAATGATGAAAATACTGTTATGCAAAACAAATGA
TGAACATGCTGTTAT
Found at i:172883 original size:28 final size:28
Alignment explanation
Indices: 172843--172897 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
172833 GTGAATTTAA
*
172843 CAAAACAAATGATAAATATACTGTTATT
1 CAAAACAAATGATAAACATACTGTTATT
* *
172871 CAAAACAAATGATGAACATGCTGTTAT
1 CAAAACAAATGATAAACATACTGTTAT
172898 GAATCCCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (28 bp):
CAAAACAAATGATAAACATACTGTTATT
Found at i:179080 original size:23 final size:24
Alignment explanation
Indices: 179038--179090 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
179028 TTTATTTCTT
179038 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
179062 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
179085 TTTCTT
1 TTTCTT
179091 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:187389 original size:25 final size:25
Alignment explanation
Indices: 187341--187390 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
187331 TCTTTTTCTT
* *
187341 CTTTTGAGTGCTGTATTTTTTTTTC
1 CTTTTGAGTGCTGTACTTTGTTTTC
187366 CTTTTGAGTGCT-TCACTTTGTTTTC
1 CTTTTGAGTGCTGT-ACTTTGTTTTC
187391 TGATTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 21 0.95
ACGTcount: A:0.08, C:0.16, G:0.16, T:0.60
Consensus pattern (25 bp):
CTTTTGAGTGCTGTACTTTGTTTTC
Done.