Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007338.1 Hibiscus syriacus cultivar Beakdansim tig00019664_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: 236009
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:155925 original size:19 final size:19
Alignment explanation
Indices: 155885--156013 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
155875 TAGTTTACTT
* *
155885 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
155905 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
155924 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
155943 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
155957 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
155976 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
155990 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
156009 TCGCA
1 TCGCA
156014 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:155964 original size:33 final size:32
Alignment explanation
Indices: 155921--156013 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
155911 CGCGAAACCA
**
155921 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
155953 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
155986 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
156014 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:156011 original size:52 final size:52
Alignment explanation
Indices: 155885--156013 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
155875 TAGTTTACTT
**
155885 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
155937 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
155990 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
156014 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:156031 original size:19 final size:19
Alignment explanation
Indices: 156009--156143 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
155999 GAAACCAAAA
*
156009 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
156028 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
156044 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
156061 TCGCGTTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
156077 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
156094 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
156113 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
156133 TCGTGTTGCGA
1 TCGCGTTGCGA
156144 AAGTAAACTA
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:156050 original size:14 final size:14
Alignment explanation
Indices: 156031--156087 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
156021 TTTCATTTCG
156031 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
156045 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
156062 CGCGTTGCGATTCTGT
1 --CGTTGCGATTCTTT
156078 CGTTGCGATT
1 CGTTGCGATT
156088 TTCATTTCGC
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:0.09, C:0.21, G:0.25, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:156056 original size:33 final size:33
Alignment explanation
Indices: 156014--156106 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
156004 CAAAATCGCA
*
156014 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
156047 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
156080 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
156107 TTGGTTTCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:157989 original size:37 final size:37
Alignment explanation
Indices: 157956--158026 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
157946 ATTGATTGTT
157956 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
*
157993 TTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTGATTGTTTAATTGATTTGTAAAAGTTGATT
158027 TGTAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (37 bp):
TTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
Found at i:158025 original size:14 final size:14
Alignment explanation
Indices: 158008--158043 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
157998 ATTGTTTAAT
158008 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
158022 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
158036 TGATTTGT
1 TGATTTGT
158044 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:158166 original size:19 final size:19
Alignment explanation
Indices: 158150--158270 Score: 189
Period size: 19 Copynumber: 6.6 Consensus size: 19
158140 AAAAATGACT
158150 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
158169 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
158188 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
158207 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
158221 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
158240 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
158260 ATCGCAATGCG
1 ATCGCAATGCG
158271 TTTATAATTT
Statistics
Matches: 94, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 59 0.63
20 19 0.20
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:158229 original size:33 final size:36
Alignment explanation
Indices: 158150--158270 Score: 167
Period size: 33 Copynumber: 3.3 Consensus size: 36
158140 AAAAATGACT
158150 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
158188 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
158221 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
158260 ATCGCAATGCG
1 ATCGCAATGCG
158271 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
33 29 0.39
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.36
39 14 0.19
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:158323 original size:19 final size:19
Alignment explanation
Indices: 158299--158623 Score: 396
Period size: 19 Copynumber: 18.4 Consensus size: 19
158289 GATTATCTCG
158299 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
158318 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
158337 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
158351 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
158370 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
158389 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
158408 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
158427 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
158446 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
158460 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
158479 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
158498 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
158512 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
158531 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
158550 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
158564 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
158583 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
158597 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
158616 TTGCGATT
1 TTGCGATT
158624 GTATTTTCCG
Statistics
Matches: 268, Mismatches: 12, Indels: 52
0.81 0.04 0.16
Matches are distributed among these distances:
14 35 0.13
15 3 0.01
16 30 0.11
17 28 0.10
18 1 0.00
19 166 0.62
20 5 0.02
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:158374 original size:71 final size:71
Alignment explanation
Indices: 158299--158623 Score: 376
Period size: 71 Copynumber: 4.6 Consensus size: 71
158289 GATTATCTCG
158299 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCG-TTGCGATTTTCA
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGA-TTTCA
158363 TTTCGCA
65 TTTCGCA
* *
158370 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG-ATTGCGA-T
158435 TTCATTTCGCA
61 TTCATTTCGCA
*
158446 TTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-T
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-ATTGCGATT
*
158505 TC-TCTCG--
62 TCATTTCGCA
*
158512 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TTGCGATTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTCAT
158576 TTCCGCA
66 TT-CGCA
* *
158583 TTGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
158624 GTATTTTCCG
Statistics
Matches: 227, Mismatches: 11, Indels: 37
0.83 0.04 0.13
Matches are distributed among these distances:
66 37 0.16
67 3 0.01
68 14 0.06
69 13 0.06
71 121 0.53
73 6 0.03
74 8 0.04
76 25 0.11
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGATTGCGATTTCAT
TTCGCA
Found at i:158568 original size:33 final size:33
Alignment explanation
Indices: 158318--158623 Score: 271
Period size: 33 Copynumber: 8.8 Consensus size: 33
158308 TCATTTCGCA
*
158318 TTGCGATTTTCATTTCGCATTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
158351 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * *
158387 CATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCG
1 --TTGCGATTTTCATTTCGCATTGCGA--TT-CTCTCG
158425 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 --TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
158460 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
158496 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
158531 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
158564 TTGCGA-TTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
158597 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
158624 GTATTTTCCG
Statistics
Matches: 233, Mismatches: 20, Indels: 40
0.80 0.07 0.14
Matches are distributed among these distances:
31 9 0.04
32 13 0.06
33 98 0.42
34 9 0.04
35 12 0.05
36 11 0.05
37 2 0.01
38 67 0.29
39 3 0.01
40 9 0.04
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:158623 original size:52 final size:52
Alignment explanation
Indices: 158277--158595 Score: 541
Period size: 52 Copynumber: 6.0 Consensus size: 52
158267 TGCGTTTATA
*
158277 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
158329 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
* *
158381 ATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTTAATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
158438 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
158490 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
158542 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
158594 AT
1 AT
158596 GTTGGGATTT
Statistics
Matches: 256, Mismatches: 5, Indels: 12
0.94 0.02 0.04
Matches are distributed among these distances:
51 8 0.03
52 190 0.74
54 7 0.03
55 8 0.03
57 43 0.17
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:160940 original size:12 final size:12
Alignment explanation
Indices: 160923--160947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
160913 TCTTCGGGGA
160923 CTTTTTCTTCTT
1 CTTTTTCTTCTT
160935 CTTTTTCTTCTT
1 CTTTTTCTTCTT
160947 C
1 C
160948 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:161156 original size:24 final size:24
Alignment explanation
Indices: 161122--161168 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
161112 CTGAAACATC
161122 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
161146 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
161169 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:161867 original size:20 final size:20
Alignment explanation
Indices: 161839--162207 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
161829 AAATTTCAGT
* * * *
161839 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
161859 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
161879 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
161899 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
161919 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
161939 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
161959 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
161979 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
161999 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
162019 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
162039 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
162059 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
162079 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
162099 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
162119 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
162139 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
162159 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
162179 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
162199 GTTGCGATT
1 GTTGCGATT
162208 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:177833 original size:120 final size:119
Alignment explanation
Indices: 177620--177860 Score: 419
Period size: 120 Copynumber: 2.0 Consensus size: 119
177610 CGTGAATCTC
* *
177620 TGTTTCCTTGAACCATTAATTGAATTATTCACCCATCAAGCTAGCAAGCAAGGTAATGGAGGTTG
1 TGTTTCCTTGAACCATTAATTGAAATATTCACCAATCAAGCTAGCAAGCAAGGTAATGGAGGTTG
* *
177685 AGCAATCGATATCAAACTATCCAGAAAAGCTTACAATTATATATCAGACCCCCAT
66 AACAATCGATATCAAACTATCCAGAAAAGCTTACAATTAAATATCAGA-CCCCAT
*
177740 TGTTTCCTTGAACCATTAATTGAAATATTCACCAATCAAGCTAGCATGCAAGGTAATGGAGGTTG
1 TGTTTCCTTGAACCATTAATTGAAATATTCACCAATCAAGCTAGCAAGCAAGGTAATGGAGGTTG
*
177805 AACAATCGATATCGAACTATCCAGAAAAGCTTACAATTAAATATCAGACCCCAT
66 AACAATCGATATCAAACTATCCAGAAAAGCTTACAATTAAATATCAGACCCCAT
177859 TG
1 TG
177861 ATCATCTTGC
Statistics
Matches: 115, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
119 8 0.07
120 107 0.93
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (119 bp):
TGTTTCCTTGAACCATTAATTGAAATATTCACCAATCAAGCTAGCAAGCAAGGTAATGGAGGTTG
AACAATCGATATCAAACTATCCAGAAAAGCTTACAATTAAATATCAGACCCCAT
Found at i:178675 original size:24 final size:24
Alignment explanation
Indices: 178620--178689 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
178610 TTAAGCGGAG
* *
178620 ATATCAGAAATCAAAACAGAATTA
1 ATATCAGAAATCAGAACAGAATCA
* * * *
178644 AGAACAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATCA
178668 ATATCAGAAATCAGAACAGAAT
1 ATATCAGAAATCAGAACAGAAT
178690 TCAGGTCATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.17
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATCA
Found at i:178687 original size:12 final size:12
Alignment explanation
Indices: 178624--178693 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
178614 GCGGAGATAT
*
178624 CAGAAATCAAAA
1 CAGAAATCAGAA
* *
178636 CAGAATTAAGAA
1 CAGAAATCAGAA
*
178648 CAGATATCAGAA
1 CAGAAATCAGAA
* *
178660 CAG-AATCCATAT
1 CAGAAAT-CAGAA
178672 CAGAAATCAGAA
1 CAGAAATCAGAA
*
178684 CAGAATTCAG
1 CAGAAATCAG
178694 GTCATGTATC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.89
13 3 0.07
ACGTcount: A:0.53, C:0.17, G:0.14, T:0.16
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:179888 original size:18 final size:18
Alignment explanation
Indices: 179861--179898 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
179851 TTCCGTCTGA
179861 TCTTACTATTAATTTCAG
1 TCTTACTATTAATTTCAG
* *
179879 TCTTATTATTTATTTCAG
1 TCTTACTATTAATTTCAG
179897 TC
1 TC
179899 ATTTCGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (18 bp):
TCTTACTATTAATTTCAG
Found at i:188905 original size:10 final size:11
Alignment explanation
Indices: 188889--188942 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
188879 TCAATTCTAC
188889 ATTTTAATTAT
1 ATTTTAATTAT
188900 -TTTTAATTAT
1 ATTTTAATTAT
188910 ATATATT-ATTAT
1 AT-T-TTAATTAT
188922 ATTTTAATT-T
1 ATTTTAATTAT
188932 AATTTTAATTA
1 -ATTTTAATTA
188943 CTTGCCATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
10 13 0.35
11 14 0.38
12 8 0.22
13 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTTAATTAT
Found at i:199451 original size:21 final size:21
Alignment explanation
Indices: 199413--199452 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
199403 TTTATTAAAT
*
199413 TATTATAAAATAGCGATAACA
1 TATTATAAAATAACGATAACA
*
199434 TATTATAAAATAATGATAA
1 TATTATAAAATAACGATAA
199453 ATTTTAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TATTATAAAATAACGATAACA
Found at i:199462 original size:21 final size:20
Alignment explanation
Indices: 199408--199463 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
199398 TTGAATTTAT
*
199408 TAAATTATTATAAAATAGCGA
1 TAAATT-TTATAAAATAACGA
* *
199429 TAACATATTATAAAATAATGA
1 TAA-ATTTTATAAAATAACGA
199450 TAAATTTTAATAAA
1 TAAATTTT-ATAAA
199464 TTTAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.14
21 23 0.79
22 2 0.07
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAATTTTATAAAATAACGA
Found at i:203051 original size:32 final size:32
Alignment explanation
Indices: 202998--203091 Score: 84
Period size: 32 Copynumber: 2.9 Consensus size: 32
202988 GTCAATATCT
* *
202998 AGTCGGGTCAATATC-GAATCGGTTGATTTTTG
1 AGTCAGGTCAATACCAG-ATCGGTTGATTTTTG
* * *
203030 GGTCGGGTTAATACCAGATCGGTTAGA-TTTTG
1 AGTCAGGTCAATACCAGATCGGTT-GATTTTTG
* * *
203062 AGTCAGGTCAATATCGGATTGGTTGATTTT
1 AGTCAGGTCAATACCAGATCGGTTGATTTT
203092 CGATTTAGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
31 2 0.04
32 45 0.90
33 3 0.06
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (32 bp):
AGTCAGGTCAATACCAGATCGGTTGATTTTTG
Found at i:203861 original size:16 final size:16
Alignment explanation
Indices: 203833--203890 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
203823 ATTGGGTTAA
203833 AATTTCG-TTCAGGTT
1 AATTTCGATTCAGGTT
203848 AATTTCGATTCAGGTT
1 AATTTCGATTCAGGTT
** * *
203864 TCTTTCGGTTCGGGTT
1 AATTTCGATTCAGGTT
203880 AATTTCGATTC
1 AATTTCGATTC
203891 TAGTTGATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
15 7 0.20
16 28 0.80
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.47
Consensus pattern (16 bp):
AATTTCGATTCAGGTT
Found at i:203902 original size:32 final size:32
Alignment explanation
Indices: 203834--203905 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
203824 TTGGGTTAAA
*
203834 ATTTC-GTTCAGGTTAATTTCGATTCAGGTTT
1 ATTTCGGTTCAGGTTAATTTCGATTCAGGTTG
* *
203865 CTTTCGGTTCGGGTTAATTTCGATTCTA-GTTG
1 ATTTCGGTTCAGGTTAATTTCGATTC-AGGTTG
203897 ATTTCGGTT
1 ATTTCGGTT
203906 TTGCTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 4 0.11
32 30 0.86
33 1 0.03
ACGTcount: A:0.15, C:0.14, G:0.22, T:0.49
Consensus pattern (32 bp):
ATTTCGGTTCAGGTTAATTTCGATTCAGGTTG
Found at i:205999 original size:16 final size:17
Alignment explanation
Indices: 205978--206010 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
205968 ACTATTCACA
205978 TGAATAGTG-AATTTCG
1 TGAATAGTGAAATTTCG
205994 TGAATAGTGAAATTTCG
1 TGAATAGTGAAATTTCG
206011 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (17 bp):
TGAATAGTGAAATTTCG
Found at i:206777 original size:15 final size:16
Alignment explanation
Indices: 206759--206791 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
206749 GTGGCAGATC
206759 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
206774 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
206790 AA
1 AA
206792 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:214194 original size:2 final size:2
Alignment explanation
Indices: 214183--214212 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
214173 TCATGGTTAC
214183 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
214213 TATTACTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:215082 original size:44 final size:44
Alignment explanation
Indices: 215019--215108 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
215009 CTAAAGAAGA
*
215019 TAGAAAAAGTATGGCTATGTTTACGAGAAGCCGATATTTTTGCT
1 TAGAAAAAGTATGGCTATGTTTACGAGAAGCCAATATTTTTGCT
215063 TAGAAAAAGTATGGCTATGTTTACGAGAAGCCAATATTTTTGCT
1 TAGAAAAAGTATGGCTATGTTTACGAGAAGCCAATATTTTTGCT
215107 TA
1 TA
215109 AACTCTCTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (44 bp):
TAGAAAAAGTATGGCTATGTTTACGAGAAGCCAATATTTTTGCT
Found at i:217871 original size:19 final size:20
Alignment explanation
Indices: 217835--217873 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
217825 AAAATTTGAG
*
217835 ATTTGATCTTTCTATTTTTA
1 ATTTGATCCTTCTATTTTTA
217855 ATTTGATCCTT-TATTTTTA
1 ATTTGATCCTTCTATTTTTA
217874 TAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.21, C:0.10, G:0.05, T:0.64
Consensus pattern (20 bp):
ATTTGATCCTTCTATTTTTA
Found at i:218328 original size:14 final size:15
Alignment explanation
Indices: 218304--218340 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
218294 ACTAATTGGT
218304 TAATATTTTAAAATA
1 TAATATTTTAAAATA
218319 TAAT-TTTTAAAAT-
1 TAATATTTTAAAATA
*
218332 TGATATTTT
1 TAATATTTT
218341 TTATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 13 0.65
15 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TAATATTTTAAAATA
Found at i:219247 original size:21 final size:20
Alignment explanation
Indices: 219213--219251 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
219203 ATTAATTATT
219213 TAAAAAATTAAATAAAAATA
1 TAAAAAATTAAATAAAAATA
*
219233 TAAAAACATTTAATAAAAA
1 TAAAAA-ATTAAATAAAAA
219252 AAAGTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAAAATTAAATAAAAATA
Found at i:229186 original size:20 final size:20
Alignment explanation
Indices: 229142--229189 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
229132 TATAGTTTTG
229142 TTTTTGATATAGGTATGTTTA
1 TTTTTGATATA-GTATGTTTA
*
229163 TTTTATGATATA-TATGTATTT
1 TTTT-TGATATAGTATGT-TTA
229184 TTTTTG
1 TTTTTG
229190 TTACCTGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.29
21 10 0.42
22 7 0.29
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (20 bp):
TTTTTGATATAGTATGTTTA
Done.