Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000726.1 Hibiscus syriacus cultivar Beakdansim tig00001412_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: 96706
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:9736 original size:232 final size:228
Alignment explanation
Indices: 9311--9969 Score: 743
Period size: 227 Copynumber: 2.9 Consensus size: 228
9301 TTATAAGTGA
* * * * * *
9311 AAAAATGATAAAAGTTTCACATTTAAATCTAAAAATGGAAATTGTTGGAAAGCAAGAAAAGTTTC
1 AAAAATGAAAAAAGTTTCTCATTTAAATCTAAAAAT-TAAATTTTTGAAAAGTAAGAAAAGTTTC
* * * * *
9376 TTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCAGCCAATCAAT-AGTTTTTCGAGCATG
65 TTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCGGCC-ATCAGTAAGTCTTTCGAGCATG
* * * * *
9440 ATGCTTAAATCATTTGGGTCATATGTAAGTCTTTCAAGCAAGATGATAAGCCCTTCAAGCCATCC
129 ATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCC
* * ** *
9505 ATAATACCTTTTGGC-ATGATGTTTTCACATGTCTCCTG
194 ATAAGACATTCGGGCGA-GAT-TTTT-ACATGT-TCCTC
* *
9543 AAAAATGAGAAATGTTTCTCATTTAAATCTAAAAATTAAAATTTTTGAAAAGTAAGAAAAGTTTC
1 AAAAATGAAAAAAGTTTCTCATTTAAATCTAAAAATT-AAATTTTTGAAAAGTAAGAAAAGTTTC
* ** *
9608 TTACCTAATAAACTATTTTCAAAGTCAGTAAGTCATTCGGTCCATCAGTAAGTCTTTCGAGCATA
65 TTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCGG-CCATCAGTAAGTCTTTCGAGCATG
* * * * *
9673 ATGCTTAAACCCTTCGGGTCATCTGTAAGTTTTTCGAGCAAGATGATAA-TTCTTCTGGCCATCC
129 ATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCC
**
9737 ATAAGACATTCGGGCGAGATTTTTACATGTTTTTC
194 ATAAGACATTCGGGCGAGATTTTTACATGTTCCTC
* * * * *
9772 AAAACA--AAAAAAGTTTCTCAGTTAAATCTGAAAATTGATTTTTTAAAAAGTAAGAAAAGTTTC
1 AAAA-ATGAAAAAAGTTTCTCATTTAAATCTAAAAATTAAATTTTTGAAAAGTAAGAAAAGTTTC
* * * *
9835 TTACCTAGTAAACTATTCTCAAATTTGGTAAGTCTTTCGACCCATCAGTAAGTCTTTCGAGCATG
65 TTACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCG-GCCATCAGTAAGTCTTTCGAGCATG
* * * * * * *
9900 ATGTTTAAATCATTCGGATCATCTATAAGACTCTCGAGCAAGATGATAAGTCCTTCGGGTCATCC
129 ATGCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCC
9965 ATAAG
194 ATAAG
9970 TTCTTCGGGC
Statistics
Matches: 361, Mismatches: 59, Indels: 18
0.82 0.13 0.04
Matches are distributed among these distances:
227 121 0.34
228 43 0.12
229 6 0.02
230 7 0.02
231 4 0.01
232 121 0.34
233 59 0.16
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (228 bp):
AAAAATGAAAAAAGTTTCTCATTTAAATCTAAAAATTAAATTTTTGAAAAGTAAGAAAAGTTTCT
TACCTAGTAAACTATTTTCAAAGTTGGTAAGTCATTCGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCATTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCAGGCCATCCAT
AAGACATTCGGGCGAGATTTTTACATGTTCCTC
Found at i:16485 original size:23 final size:23
Alignment explanation
Indices: 16459--16519 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
16449 CTCGTATAAA
*
16459 TGCACCAAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
16482 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
16505 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
16520 TATAAGATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:17233 original size:64 final size:66
Alignment explanation
Indices: 17162--17322 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 66
17152 CCCTTGACGG
*
17162 GTGCATCGATACACTATCTAT-T-CATCGATACA-TAAATCCCATTCGATGTTTGTATTTTAAGG
1 GTGCATCGATACACTATCTATGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAAG
*
17224 GC
65 GA
* * ** *
17226 GTGCATCGATGCACTA-CT-TGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAGG
1 GTGCATCGATACACTATCTATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAGG
17289 A
66 A
*
17290 GTGTATCGATACACT-TC-ATGTGCATCGATACAC
1 GTGCATCGATACACTATCTATGTGCATCGATACAC
17323 CTTGAACAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 3 0.04
64 78 0.94
65 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (66 bp):
GTGCATCGATACACTATCTATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAGG
A
Found at i:22924 original size:230 final size:230
Alignment explanation
Indices: 22521--22934 Score: 557
Period size: 230 Copynumber: 1.8 Consensus size: 230
22511 AAATTGTTGG
** *
22521 AAAGTAAGTAAAGTTTATTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCAGACCATCAG
1 AAAGTAAAAAAAGTTTATTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCAGACCATCAA
* * * * * *
22586 TAAGTCTTTCGAGCATTGTGTTTAAACCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATCATA
66 TAAGTCTTTCGAGCATTGTGCTTAAACCCTTCAGGTCATCTATAAGCCTCTCGAGCAAGATAATA
* * * * *
22651 AGTTTTTCGGGTCATCCATAAGACCTTAGGGCGGGATGTTTTCACATGTTTTTCAAAAAAAAAGT
131 AGTATTTCGGGTCATACATAAGACATTAGGGCAGGATGTTTTCACATGATTTTCAAAAAAAAAGT
22716 TTCTTAGTTAAATCTGAAAATTGATTTTTTTAAAA
196 TTCTTAGTTAAATCTGAAAATTGATTTTTTTAAAA
* * * *
22751 AAAGTAAAAAAAGTTTATTACCTAGTAGACTA-TTCTCAAATTTGGTAAGTTCTTCAGCCCATCA
1 AAAGTAAAAAAAGTTTATTACCTAGTAAACTATTTC-CAAAGTTGGTAAGTCCTTCAGACCATCA
* *
22815 ATAAGTCTTTCGAGCA-TGATGCTTAAATCCTTCAGGTCATCTATAAGCCTCTCGAGTAAGATAA
65 ATAAGTCTTTCGAGCATTG-TGCTTAAACCCTTCAGGTCATCTATAAGCCTCTCGAGCAAGATAA
* * *
22879 TAAGTCATTT-GGGTCATACATAA-ATCATTCGTGCATGATGTTTTCACATGATTTTC
129 TAAGT-ATTTCGGGTCATACATAAGA-CATTAGGGCAGGATGTTTTCACATGATTTTC
22935 TGAAAAATGA
Statistics
Matches: 157, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
229 6 0.04
230 148 0.94
231 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (230 bp):
AAAGTAAAAAAAGTTTATTACCTAGTAAACTATTTCCAAAGTTGGTAAGTCCTTCAGACCATCAA
TAAGTCTTTCGAGCATTGTGCTTAAACCCTTCAGGTCATCTATAAGCCTCTCGAGCAAGATAATA
AGTATTTCGGGTCATACATAAGACATTAGGGCAGGATGTTTTCACATGATTTTCAAAAAAAAAGT
TTCTTAGTTAAATCTGAAAATTGATTTTTTTAAAA
Found at i:23406 original size:134 final size:132
Alignment explanation
Indices: 23262--23678 Score: 516
Period size: 134 Copynumber: 3.1 Consensus size: 132
23252 TTTAAAGAAT
* * * * * *
23262 AGTGGAATGAATCAATGTCCCCATATCTGATTTTCTCTCAAGAAGAAGTGGAACAAATCCATCTC
1 AGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATCCCTCTC
* * *
23327 TTTCAAAGATTTGATATTCCCTGAGTAACAATGGAACAAATCTGGCTCGATTCAATCTTCCT-TA
66 TTTC-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCTGTA
23391 AGAA
130 AG-A
* * * *
23395 ACGTGGAATGAATCAACGTCCCCAGATTTAATTTTCCCTCAGGAAGAAGTGAAACAGATCCCCCT
1 A-GTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATCCCTCT
* *
23460 CTTGCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCTATTCAATCTTTCCTGA
65 CTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATC-TTCCT--
23525 GTAAGA
127 GTAAGA
* * * *
23531 A-TGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTCAAGAAGAAGCGCAACAGGTCCCTCTC
1 AGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATCCCTCTC
* * * *
23595 TTTCAAGATTTGGTATTCTCTGAGTAACAGTGGAACAAGTCTGCCTTGATTTAATCTTCCCTGT-
66 TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTT-CCTGTA
23659 AGAA
130 AG-A
*
23663 CAGTGGAATGAGTCAA
1 -AGTGGAATGAATCAA
23679 TATTTCTCGA
Statistics
Matches: 245, Mismatches: 30, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
131 2 0.01
132 3 0.01
133 52 0.21
134 182 0.74
136 2 0.01
137 4 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (132 bp):
AGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATCCCTCTC
TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCGATTCAATCTTCCTGTAA
GA
Found at i:23691 original size:134 final size:131
Alignment explanation
Indices: 23257--23725 Score: 444
Period size: 134 Copynumber: 3.5 Consensus size: 131
23247 TTTTCTTTAA
* * * * *
23257 AGAATAGTGGAATGAATC-AATGTCCCCATATCTGATTTTCTCTCAAGAAGAAGTGGAACAAATC
1 AGAA-AGTGGAATGAATCAAAT-TCCTC-GATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATC
* * * * *
23321 CATCTCTTTCAAAGATTTGATATTCCCTGAGTAACAATGGAACAAATCTGGCTCGATTCAATCTT
63 CCTCTCTTTC-AAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTTGATTCAATCTT
23386 CCT-T
127 CCTGT
** * * * *
23390 AAGAAACGTGGAATGAATCAACGTCCCCAGATTTAATTTTCCCTCAGGAAGAAGTGAAACAGATC
1 -AGAAA-GTGGAATGAATCAAATTCCTC-GATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATC
* *
23455 CCCCTCTTGCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCT-ATTCAATCTT
63 CCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCT-TGATTCAATC-T
23519 TCCTG-
126 TCCTGT
* * * * * * *
23524 AGTAAGAATGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTCAAGAAGAAGCGCAACAGGTC
1 AG-AA-AGTGGAATGAATCAA-ATTCCTCGATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATC
* * *
23589 CCTCTCTTTCAAGATTTGGTATTCTCTGAGTAACAGTGGAACAAGTCTGCCTTGATTTAATCTTC
63 CCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTTGATTCAATCTT-
23654 CCTGT
127 CCTGT
* * * * * * *
23659 AGAACAGTGGAATGAGTCAATATTTCTCGATCTGATCTACCCTGAAGAA-ACAGTGGAACAAATC
1 AGAA-AGTGGAATGAATCAA-ATTCCTCGATCTGATTTTCCCTCAAGAAGA-AGTGAAACAGATC
23723 CCT
63 CCT
23726 TATCAGATTT
Statistics
Matches: 275, Mismatches: 48, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
133 54 0.20
134 215 0.78
135 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (131 bp):
AGAAAGTGGAATGAATCAAATTCCTCGATCTGATTTTCCCTCAAGAAGAAGTGAAACAGATCCCT
CTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTTGATTCAATCTTCCTG
T
Found at i:23860 original size:3 final size:3
Alignment explanation
Indices: 23852--23936 Score: 134
Period size: 3 Copynumber: 28.0 Consensus size: 3
23842 GTCTGAACCG
23852 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
23900 TTA CTA TTA TTA TTA TTA TTA ATA ATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
23937 ATGCAGACCA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
3 74 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:26970 original size:101 final size:101
Alignment explanation
Indices: 26784--27092 Score: 465
Period size: 101 Copynumber: 3.0 Consensus size: 101
26774 TACTTATTCA
* * * * * *
26784 ATTAAGATTTTAAATAAAATTGACTTAATAAGAAGATTTCTCTTTTCTTAATTAAGTTAACACTC
1 ATTATGATTTTAAATATAATTGACTTAGTAAGAAGATTACTCTATTC-----TCAGTTAACACTC
*
26849 GATTAACCAATAACGTCAACTCAATCAAAATTTAAGGGAAT
61 GATTAACCAATAACGCCAACTCAATCAAAATTTAAGGGAAT
*
26890 ATTATGATTTTAAATATAATTGACTTGGTAAGAAGATTACTCTATTCTCAGTTAACACTCGATTA
1 ATTATGATTTTAAATATAATTGACTTAGTAAGAAGATTACTCTATTCTCAGTTAACACTCGATTA
26955 ACCAATAACGCCAACTCAATCAAAATTTAAGGGAAT
66 ACCAATAACGCCAACTCAATCAAAATTTAAGGGAAT
** *
26991 AACATGATTTTAAACATAATTGACTTAGTAAGAAGATTACTCTATTCTCAGTTAACACTCGATTA
1 ATTATGATTTTAAATATAATTGACTTAGTAAGAAGATTACTCTATTCTCAGTTAACACTCGATTA
*
27056 ACCAATAACGCCAACTCAATCAAAATTTAAAGGAAT
66 ACCAATAACGCCAACTCAATCAAAATTTAAGGGAAT
27092 A
1 A
27093 AAATCAAAAT
Statistics
Matches: 190, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
101 149 0.78
106 41 0.22
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (101 bp):
ATTATGATTTTAAATATAATTGACTTAGTAAGAAGATTACTCTATTCTCAGTTAACACTCGATTA
ACCAATAACGCCAACTCAATCAAAATTTAAGGGAAT
Found at i:30732 original size:39 final size:39
Alignment explanation
Indices: 30689--30767 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
30679 AAATATGAAA
*
30689 ACTCCAAGAATGCATGGCGTCTTCAGGCAAA-TGAAGAAG
1 ACTCCAAGAATACATGGCGTCTTCAGGCAAATTG-AGAAG
* * *
30728 ACTCCACGACTATATGGCGTCTTCAGGCAAATTGAGAAG
1 ACTCCAAGAATACATGGCGTCTTCAGGCAAATTGAGAAG
30767 A
1 A
30768 TTCGAGGAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (39 bp):
ACTCCAAGAATACATGGCGTCTTCAGGCAAATTGAGAAG
Found at i:31034 original size:14 final size:14
Alignment explanation
Indices: 31015--31053 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
31005 TAATGGGGAG
31015 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
31029 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
31043 GAATCTCTGCA
1 TAATCCCTGCA
31054 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:31909 original size:2 final size:2
Alignment explanation
Indices: 31902--31936 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
31892 GACTGGAAAA
31902 AT AT AT AT -T GAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
31937 AAGAATCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33420 original size:37 final size:36
Alignment explanation
Indices: 33378--33462 Score: 98
Period size: 38 Copynumber: 2.2 Consensus size: 36
33368 TATTAAACCT
*
33378 TTTTATATTTTCAATTTTGTAAAAAAAATTATATAAA
1 TTTTATATTTTAAATTTTGTAAAAAAAA-TATATAAA
* * *
33415 TTTTATGAATTTAAATTTTTTAAAGAAAATATATAAA
1 TTTTAT-ATTTTAAATTTTGTAAAAAAAATATATAAA
33452 TATCTTATATT
1 T-T-TTATATT
33463 AATATTATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
37 15 0.38
38 21 0.52
39 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTTATATTTTAAATTTTGTAAAAAAAATATATAAA
Found at i:33882 original size:23 final size:23
Alignment explanation
Indices: 33822--33884 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
33812 TTATAAATTC
*
33822 TAATTATC-AAACTTA-TATAAA
1 TAATCATCAAAACTTATTATAAA
* **
33843 TAATCATTAAATTTTATTATAAA
1 TAATCATCAAAACTTATTATAAA
33866 -ATATCATCAAAACTTATTA
1 TA-ATCATCAAAACTTATTA
33885 AATTATTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 6 0.19
22 6 0.19
23 20 0.62
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATCATCAAAACTTATTATAAA
Found at i:34530 original size:41 final size:41
Alignment explanation
Indices: 34483--34599 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
34473 TTTACATCAA
* *
34483 TAATTATAATTGATAATAT-TTATTATAATTCTAAATATATT
1 TAATTATAATTG-TAATTTATTATTATAATTATAAATATATT
* *
34524 TTATTAT-ATGTTTAATTTATTATTATAATTATAAATATATT
1 TAATTATAAT-TGTAATTTATTATTATAATTATAAATATATT
* *
34565 TAACTATATATT-TAATTTATTATTATAATTGTAAA
1 TAATTATA-ATTGTAATTTATTATTATAATTATAAA
34600 ACTTCGTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
40 7 0.11
41 55 0.85
42 1 0.02
43 2 0.03
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (41 bp):
TAATTATAATTGTAATTTATTATTATAATTATAAATATATT
Found at i:34588 original size:12 final size:13
Alignment explanation
Indices: 34517--34594 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 13
34507 ATAATTCTAA
*
34517 ATATATTTTA-TT
1 ATATATTTAATTT
*
34529 ATATGTTTAATTT
1 ATATATTTAATTT
34542 AT-TATTATAATTAT
1 ATATATT-TAATT-T
*
34556 AAATATATTTAA-CT
1 --ATATATTTAATTT
34570 ATATATTTAATTT
1 ATATATTTAATTT
34583 AT-TATTATAATT
1 ATATATT-TAATT
34595 GTAAAACTTC
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
12 25 0.47
13 17 0.32
14 2 0.04
16 5 0.09
17 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (13 bp):
ATATATTTAATTT
Found at i:45180 original size:22 final size:22
Alignment explanation
Indices: 45124--45182 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
45114 CTGTTAACTG
45124 TTGTTATT-AAAATAATGATATA
1 TTGTT-TTAAAAATAATGATATA
* *
45146 TTG-TATAACAAATAATTATATA
1 TTGTTTTAA-AAATAATGATATA
45168 TTGTTTTAAAAATAA
1 TTGTTTTAAAAATAA
45183 CCTTAAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 24 0.77
23 4 0.13
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (22 bp):
TTGTTTTAAAAATAATGATATA
Found at i:47449 original size:23 final size:22
Alignment explanation
Indices: 47414--47457 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
47404 TAATTATTTT
47414 AAAAAATTAAATAAAAAATATC
1 AAAAAATTAAATAAAAAATATC
*
47436 AAAAATATTTAATAAAAAATAT
1 AAAAA-ATTAAATAAAAAATAT
47458 TTTTTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATATC
Found at i:47938 original size:17 final size:16
Alignment explanation
Indices: 47917--47947 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47907 CTTCTAATTT
*
47917 TTTTTTTAGTTCAAGC
1 TTTTTTGAGTTCAAGC
47933 TTTTTTGAGTTCAAG
1 TTTTTTGAGTTCAAG
47948 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (16 bp):
TTTTTTGAGTTCAAGC
Found at i:49103 original size:31 final size:31
Alignment explanation
Indices: 49038--49111 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
49028 GAGATAATAA
49038 GGGACCACTGTGAAAAGAAATAAAAAAAGGAG
1 GGGACCACTGTGAAAAGAAAT-AAAAAAGGAG
* *
49070 GGGACCTCTGTGAAAAGTAAT-AAAAAGGAAG
1 GGGACCACTGTGAAAAGAAATAAAAAAGG-AG
49101 GGGA--ACTGTGA
1 GGGACCACTGTGA
49112 TAATTATCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 6 0.16
30 7 0.18
31 6 0.16
32 19 0.50
ACGTcount: A:0.46, C:0.09, G:0.31, T:0.14
Consensus pattern (31 bp):
GGGACCACTGTGAAAAGAAATAAAAAAGGAG
Found at i:49421 original size:2 final size:2
Alignment explanation
Indices: 49407--49463 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
49397 ATTTTCGTCC
*
49407 AT AT AT A- AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49448 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
49464 TATTTAAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:50848 original size:14 final size:16
Alignment explanation
Indices: 50829--50860 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
50819 ATATTTTTTC
50829 TTTATTTC-TT-TATT
1 TTTATTTCATTCTATT
50843 TTTATTTCATTCTATT
1 TTTATTTCATTCTATT
50859 TT
1 TT
50861 GTTTATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTATTTCATTCTATT
Found at i:50905 original size:21 final size:21
Alignment explanation
Indices: 50879--50921 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
50869 ATTTTACTTG
50879 TTTTATT-TTATTTATTTATTA
1 TTTTATTGTTATTTATTT-TTA
*
50900 TTTTATTGTTTTTTATTTTTA
1 TTTTATTGTTATTTATTTTTA
50921 T
1 T
50922 GATGTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTATTGTTATTTATTTTTA
Found at i:50921 original size:16 final size:15
Alignment explanation
Indices: 50879--50918 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
50869 ATTTTACTTG
50879 TTTTATTTTATT-TAT
1 TTTTATTTTATTGT-T
50894 TTATTATTTTATTGTT
1 TT-TTATTTTATTGTT
50910 TTTTATTTT
1 TTTTATTTT
50919 TATGATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.39
16 13 0.57
17 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (15 bp):
TTTTATTTTATTGTT
Found at i:51515 original size:2 final size:2
Alignment explanation
Indices: 51508--51536 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
51498 CCAATATGAC
51508 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51537 TCTCATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:51633 original size:9 final size:9
Alignment explanation
Indices: 51619--51666 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
51609 CACTTAACCG
51619 ATTAATTAA
1 ATTAATTAA
51628 ATTAATTAA
1 ATTAATTAA
*
51637 ATTTTAATTCA
1 A--TTAATTAA
51648 ATTAATTAA
1 ATTAATTAA
*
51657 TTTAATTAA
1 ATTAATTAA
51666 A
1 A
51667 ATCAAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 25 0.76
11 8 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (9 bp):
ATTAATTAA
Found at i:52022 original size:19 final size:19
Alignment explanation
Indices: 52000--52058 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
51990 AAAAATCGAA
52000 CCGAACCGAACCGAAAAAC
1 CCGAACCGAACCGAAAAAC
*
52019 CCGAACCGTTA---AAAAAC
1 CCGAACCG-AACCGAAAAAC
*
52036 CCGAACCGAACCGAAAAAA
1 CCGAACCGAACCGAAAAAC
52055 CCGA
1 CCGA
52059 TTTCGGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.03
17 14 0.42
19 17 0.52
20 1 0.03
ACGTcount: A:0.47, C:0.34, G:0.15, T:0.03
Consensus pattern (19 bp):
CCGAACCGAACCGAAAAAC
Found at i:52024 original size:14 final size:14
Alignment explanation
Indices: 52005--52045 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
51995 TCGAACCGAA
52005 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
52019 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
52036 CCGAACCGAA
1 CCGAACCGAA
52046 CCGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:52163 original size:5 final size:5
Alignment explanation
Indices: 52153--52179 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
52143 TTTGATAAAA
52153 AACCG AACCG AACCG AACCG AACCG AA
1 AACCG AACCG AACCG AACCG AACCG AA
52180 TACACCCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.44, C:0.37, G:0.19, T:0.00
Consensus pattern (5 bp):
AACCG
Found at i:66054 original size:10 final size:10
Alignment explanation
Indices: 66039--66068 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
66029 TTTTAGAAAC
66039 ATCCAAACCG
1 ATCCAAACCG
66049 ATCCAAACCG
1 ATCCAAACCG
66059 ATCCAAACCG
1 ATCCAAACCG
66069 TAAACATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.10, T:0.10
Consensus pattern (10 bp):
ATCCAAACCG
Found at i:69611 original size:26 final size:23
Alignment explanation
Indices: 69576--69631 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 23
69566 AAAAATCAAA
69576 ATTTT-ATTTAA-AAATTATCGAATT
1 ATTTTCATTTAACAAA-TAT-G-ATT
69600 ATTTATCATTTAACAAATATGATT
1 ATTT-TCATTTAACAAATATGATT
69624 ATTTTCAT
1 ATTTTCAT
69632 GGCATTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
23 4 0.14
24 11 0.38
25 2 0.07
26 9 0.31
27 3 0.10
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTTTCATTTAACAAATATGATT
Found at i:73974 original size:28 final size:26
Alignment explanation
Indices: 73933--74027 Score: 73
Period size: 28 Copynumber: 3.3 Consensus size: 26
73923 TAAAAAGTTG
*
73933 AATACTTTTGGTACTTATCTCGACAAAA
1 AATA-TTTTAGTACTTAT-TCGACAAAA
73961 AATATTTTATGTACTTATTCTGACCAAAA
1 AATATTTTA-GTACTTATTC-GA-CAAAA
* * * *
73990 ACTAATTTTAGATATTTATTTTGACTAAA
1 AAT-ATTTTAG-TACTTA-TTCGACAAAA
74019 AATATTTTA
1 AATATTTTA
74028 AATATTTGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
27 6 0.11
28 20 0.36
29 14 0.25
30 13 0.24
31 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (26 bp):
AATATTTTAGTACTTATTCGACAAAA
Found at i:74032 original size:28 final size:28
Alignment explanation
Indices: 73958--74034 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 28
73948 TATCTCGACA
** *
73958 AAAAATATTTTATGTACTTATTCTGACC
1 AAAAATATTTTAAATATTTATTCTGACC
* * *
73986 AAAAACTAATTTTAGATATTTATTTTGACT
1 AAAAA-T-ATTTTAAATATTTATTCTGACC
74016 AAAAATATTTTAAATATTT
1 AAAAATATTTTAAATATTT
74035 GAATTAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 17 0.41
29 2 0.05
30 22 0.54
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (28 bp):
AAAAATATTTTAAATATTTATTCTGACC
Found at i:74368 original size:49 final size:49
Alignment explanation
Indices: 74291--74436 Score: 265
Period size: 49 Copynumber: 3.0 Consensus size: 49
74281 CTCAAATCCG
* * *
74291 AGATCTCAAGGAATAACAACAATTCTTTTATTATTGTGGTTACTTGATT
1 AGATCTCAAAGAGTAACAACAATACTTTTATTATTGTGGTTACTTGATT
74340 AGATCTCAAAGAGTAACAACAATACTTTTATTATTGTGGTTACTTGATT
1 AGATCTCAAAGAGTAACAACAATACTTTTATTATTGTGGTTACTTGATT
74389 AGATCTCAAAGAGTAACAACAATACTTTTATTATTGTGGTTACTTGAT
1 AGATCTCAAAGAGTAACAACAATACTTTTATTATTGTGGTTACTTGAT
74437 ACGTGCATCA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 94 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (49 bp):
AGATCTCAAAGAGTAACAACAATACTTTTATTATTGTGGTTACTTGATT
Found at i:81830 original size:18 final size:18
Alignment explanation
Indices: 81807--81842 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
81797 AGCACAAGGC
81807 TCATGTGGCTACATGGAG
1 TCATGTGGCTACATGGAG
81825 TCATGTGGCTACATGGAG
1 TCATGTGGCTACATGGAG
81843 CGATGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
TCATGTGGCTACATGGAG
Found at i:85813 original size:21 final size:21
Alignment explanation
Indices: 85787--85906 Score: 95
Period size: 21 Copynumber: 5.6 Consensus size: 21
85777 TGTGCATATA
85787 GTATCGATACCCCTTAGACT-G
1 GTATCGATACCCCTTAGA-TAG
*
85808 GTATCGATACCCCCTTTGAATAG
1 GTATCGATA-CCCCTTAG-ATAG
*
85831 GTATCAATACCCCTTCA-ATAG
1 GTATCGATACCCCTT-AGATAG
* * *
85852 GTATTGATACCATCCTTGGATGG
1 GTATCGATACC--CCTTAGATAG
*
85875 GTATCGATACCCCCCT-GAT-G
1 GTATCGATA-CCCCTTAGATAG
85895 GTATCGATACCC
1 GTATCGATACCC
85907 TCCACGAGGT
Statistics
Matches: 82, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.04
20 10 0.12
21 25 0.30
22 17 0.21
23 25 0.30
24 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (21 bp):
GTATCGATACCCCTTAGATAG
Found at i:91947 original size:64 final size:64
Alignment explanation
Indices: 91846--91982 Score: 202
Period size: 64 Copynumber: 2.1 Consensus size: 64
91836 ATAGGTAAAA
* * * *
91846 CTTATATAATAAAATATGTTAATCACTGGAAACATTATCAAACACAATAACACATTAGTTATCG
1 CTTATATAATAAAATAGGTTAATCACTAGAAACATTATCAAACACAATAACACATTAGGTAGCG
* * * *
91910 CTTATATAATAAAATAGGTTAATTACTAGATACATTATCAATCACAATAACATATTAGGTAGCG
1 CTTATATAATAAAATAGGTTAATCACTAGAAACATTATCAAACACAATAACACATTAGGTAGCG
91974 CTTATATAA
1 CTTATATAA
91983 CGTAATAGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.33
Consensus pattern (64 bp):
CTTATATAATAAAATAGGTTAATCACTAGAAACATTATCAAACACAATAACACATTAGGTAGCG
Found at i:91982 original size:23 final size:23
Alignment explanation
Indices: 91956--92002 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
91946 ATCAATCACA
* *
91956 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
* *
91979 ATAACGTAATAGATATCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
92002 A
1 A
92003 ATAAAATACG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:92389 original size:112 final size:111
Alignment explanation
Indices: 92070--92459 Score: 604
Period size: 111 Copynumber: 3.5 Consensus size: 111
92060 ATAACTGGTT
* *
92070 ATTTACCTGATATGTTGAAAGTATCAATCCTTTTTATAAAAAGATCGATAATTTACAATATAACA
1 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAAGATCGATACTTTACAATATAACA
* * **
92135 GGTAAAAATATGGCAAAATTAGTTTCATTATGACAAAACCGATAAA
66 AGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGATAAA
92181 ATTTACCTGATATGTTGAAAGTATCGATCC-TTTTATAAAAAAGATCGATACTTTACAATATAAC
1 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTAT-AAAAAGATCGATACTTTACAATATAAC
* * *
92245 ATGTAAAAATATGACAAAACCAATTTCATTATGACAAAACCGGTAAA
65 AAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGATAAA
*
92292 ATTTACCTGATATGTTGAAAGCATCGATCCTTTTTATAAAAAGGATCGA-ATCTTTACAATATAA
1 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAA-GATCGATA-CTTTACAATATAA
92356 CAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGATAAA
64 CAAGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGATAAA
* * *
92404 ATTTACATGATATGTTGAAAGTATAGATACTTTTTATAAAAATGTATCGATACTTT
1 ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAA-G-ATCGATACTTT
92460 GTTGAAAGTT
Statistics
Matches: 256, Mismatches: 17, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
110 6 0.02
111 131 0.51
112 109 0.43
113 9 0.04
114 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.33
Consensus pattern (111 bp):
ATTTACCTGATATGTTGAAAGTATCGATCCTTTTTATAAAAAGATCGATACTTTACAATATAACA
AGTAAAAATATGACAAAACCAGTTTCATTATGACAAAACCGATAAA
Found at i:92883 original size:87 final size:87
Alignment explanation
Indices: 92779--92982 Score: 354
Period size: 87 Copynumber: 2.3 Consensus size: 87
92769 TCCACAGAGA
* *
92779 TAGCGCTTATATAATAAAATAGGTTAATTACTGAAAACATTATTAAGCACAATAACATATTATGT
1 TAGCGCTTATATAATAAAATATGTTAATTACTGAAAACATTATTAAGCACAATAACATATTAGGT
* * *
92844 ACCGGTTATATAATGTAATAGG
66 AACGCTTATATAACGTAATAGG
*
92866 TAGCGCTTATATAATAAAATATGTTAATTACTGGAAACATTATTAAGCACAATAACATATTAGGT
1 TAGCGCTTATATAATAAAATATGTTAATTACTGAAAACATTATTAAGCACAATAACATATTAGGT
92931 AACGCTTATATAACGTAATAGG
66 AACGCTTATATAACGTAATAGG
92953 TAGCGCTTATATAATAAAATATGTTAATTA
1 TAGCGCTTATATAATAAAATATGTTAATTA
92983 TTTAATTTGT
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 111 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TAGCGCTTATATAATAAAATATGTTAATTACTGAAAACATTATTAAGCACAATAACATATTAGGT
AACGCTTATATAACGTAATAGG
Found at i:92943 original size:23 final size:23
Alignment explanation
Indices: 92917--92966 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
92907 ATTAAGCACA
*
92917 ATAACATATTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
92940 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
92963 ATAA
1 ATAA
92967 TAAAATATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:92973 original size:23 final size:23
Alignment explanation
Indices: 92917--92973 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
92907 ATTAAGCACA
* *
92917 ATAACATATTAGGTAACGCTTAT
1 ATAACAAAATAGGTAACGCTTAT
** *
92940 ATAACGTAATAGGTAGCGCTTAT
1 ATAACAAAATAGGTAACGCTTAT
*
92963 ATAATAAAATA
1 ATAACAAAATA
92974 TGTTAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.32
Consensus pattern (23 bp):
ATAACAAAATAGGTAACGCTTAT
Found at i:93515 original size:113 final size:112
Alignment explanation
Indices: 93210--93670 Score: 716
Period size: 111 Copynumber: 4.1 Consensus size: 112
93200 TATCGCCTAT
93210 AATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
1 AATG-ATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
* * **
93275 CCGGTAAAATTTACCGGATATGTTGAAAGTATAGATCCTTTTTATAAA
65 CCAGTAAAATTTACCTGATATGTTGAAAGTATAGATATTTTTTATAAA
* * *
93323 AATGTATCGATACTTTACAATATAACAAGT--AAGTATGACAAAACCAGTTTCATTATAACAAAA
1 AATG-ATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
* * *
93386 CCGGTAAAATTTACCTGATATGTTGAAAGTATCGATTCTTTTTTATAAA
65 CCAGTAAAATTTACCTGATATGTTGAAAGTATAGA-TATTTTTTATAAA
* *
93435 AATGATCGATACTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAC
1 AATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAC
* *
93500 CAGTAAAATTTACCTGATATGTTGAAAGTATCGATATGTTTTATAAA
66 CAGTAAAATTTACCTGATATGTTGAAAGTATAGATATTTTTTATAAA
*
93547 AAGGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGAC-AAAC
1 AATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAC
*
93611 CAGTAAAATTTA-CTGATATGTTGAAAGTATAGATAATTTTTATAAA
66 CAGTAAAATTTACCTGATATGTTGAAAGTATAGATATTTTTTATAAA
93657 AAT-ATCGATACTTT
1 AATGATCGATACTTT
93671 GTTGAAAGTT
Statistics
Matches: 325, Mismatches: 20, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
109 11 0.03
110 33 0.10
111 104 0.32
112 84 0.26
113 93 0.29
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (112 bp):
AATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAC
CAGTAAAATTTACCTGATATGTTGAAAGTATAGATATTTTTTATAAA
Found at i:93619 original size:224 final size:222
Alignment explanation
Indices: 93210--93670 Score: 714
Period size: 224 Copynumber: 2.1 Consensus size: 222
93200 TATCGCCTAT
93210 AATGTATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
1 AATG-ATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAA
* * *
93275 CCGGTAAAATTTACCGGATATGTTGAAAGTATAGATCCTTTTTATAAAAATGTATCGATACTTTA
65 CCAGTAAAATTTACCGGATATGTTGAAAGTATAGATCATTTTTATAAAAATGGATCGATACTTTA
* *
93340 CAATATAACAAGTAAGTATGACAAAACCAGTTTCATTATAACAAAACCGGTAAAATTTACCTGAT
130 CAATATAACAAGTAAATATGACAAAACCAGTTTCATTATAACAAAACCAGTAAAATTTA-CTGAT
* **
93405 ATGTTGAAAGTATCGATTCTTTTTTATAAA
194 ATGTTGAAAGTATAGA-TAATTTTTATAAA
* *
93435 AATGATCGATACTTTACAATATAACATGTAAAAATATGACAAAATCAGTTTCATTATGACAAAAC
1 AATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAC
* *
93500 CAGTAAAATTTACCTGATATGTTGAAAGTATCGAT-ATGTTTTATAAAAA-GGATCGATACTTTA
66 CAGTAAAATTTACCGGATATGTTGAAAGTATAGATCAT-TTTTATAAAAATGGATCGATACTTTA
* *
93563 CAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGAC-AAACCAGTAAAATTTACTGA
130 CAATATAACAAGT--AAATATGACAAAACCAGTTTCATTATAACAAAACCAGTAAAATTTACTGA
93627 TATGTTGAAAGTATAGATAATTTTTATAAA
193 TATGTTGAAAGTATAGATAATTTTTATAAA
93657 AAT-ATCGATACTTT
1 AATGATCGATACTTT
93671 GTTGAAAGTT
Statistics
Matches: 219, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
221 11 0.05
222 14 0.06
223 46 0.21
224 117 0.53
225 31 0.14
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (222 bp):
AATGATCGATACTTTACAATATAACAGGTAAAAATATGACAAAACCAGTTTCATTATGACAAAAC
CAGTAAAATTTACCGGATATGTTGAAAGTATAGATCATTTTTATAAAAATGGATCGATACTTTAC
AATATAACAAGTAAATATGACAAAACCAGTTTCATTATAACAAAACCAGTAAAATTTACTGATAT
GTTGAAAGTATAGATAATTTTTATAAA
Done.