Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006328.1 Hibiscus syriacus cultivar Beakdansim tig00015125_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: 139913
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4411 original size:24 final size:24
Alignment explanation
Indices: 4384--4435 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
4374 ATAATAAACA
4384 AACACAAA-CAATCGAACATAAATG
1 AACACAAATCAA-CGAACATAAATG
* *
4408 AACACAAATGAACGAGCATAAATG
1 AACACAAATCAACGAACATAAATG
4432 AACA
1 AACA
4436 TAAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.58, C:0.19, G:0.12, T:0.12
Consensus pattern (24 bp):
AACACAAATCAACGAACATAAATG
Found at i:31188 original size:9 final size:8
Alignment explanation
Indices: 31172--31197 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31162 CGTAAATACA
31172 TATTTTTT
1 TATTTTTT
31180 TATTTTTT
1 TATTTTTT
31188 TATTTTTT
1 TATTTTTT
31196 TA
1 TA
31198 GAAATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:32809 original size:44 final size:48
Alignment explanation
Indices: 32737--32833 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 48
32727 TTATTTTCGT
*
32737 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCAAGCGAACTAGATATCATGCGGTTAGGATTTA
* *
32784 TTTTT-GAAT-AA-GCAAGCGAATTAGATATCATGCGGTTAGGATTTC
1 TTTTTCGAATAAATGCAAGCGAACTAGATATCATGCGGTTAGGATTTA
32829 TTTTT
1 TTTTT
32834 ATGGATAACA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
44 27 0.59
45 10 0.22
46 4 0.09
47 5 0.11
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (48 bp):
TTTTTCGAATAAATGCAAGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:42505 original size:18 final size:16
Alignment explanation
Indices: 42478--42543 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 16
42468 AAGAAGAAAT
42478 AAAA-GAGAAAAAATGA
1 AAAATGAGAAAAAA-GA
42494 GAAAATGAGAAAAAAGA
1 -AAAATGAGAAAAAAGA
42511 AAAATGATGGAAAAAACG-
1 AAAATGA--GAAAAAA-GA
42529 AAAA-G-GAAAAAAGA
1 AAAATGAGAAAAAAGA
42543 A
1 A
42544 GAAAAAATGG
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.02
14 8 0.18
16 7 0.16
17 7 0.16
18 20 0.45
19 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (16 bp):
AAAATGAGAAAAAAGA
Found at i:42557 original size:19 final size:19
Alignment explanation
Indices: 42529--42570 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
42519 GGAAAAAACG
42529 AAAA-GGAAAAAAGAAGAA
1 AAAATGGAAAAAAGAAGAA
**
42547 AAAATGGAAAAGGGAAGAA
1 AAAATGGAAAAAAGAAGAA
42566 AAAAT
1 AAAAT
42571 AAAAATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (19 bp):
AAAATGGAAAAAAGAAGAA
Found at i:42582 original size:14 final size:14
Alignment explanation
Indices: 42563--42621 Score: 61
Period size: 13 Copynumber: 4.4 Consensus size: 14
42553 GAAAAGGGAA
*
42563 GAAAAAATAAAAAT
1 GAAAAAAGAAAAAT
42577 G-AAAAAGAAAAAT
1 GAAAAAAGAAAAAT
42590 -AAAAAGAGAAAAAT
1 GAAAAA-AGAAAAAT
* *
42604 GGAAAAAGAGAAAT
1 GAAAAAAGAAAAAT
42618 -AAAA
1 GAAAA
42622 GGAGGGTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 18 0.47
14 16 0.42
15 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (14 bp):
GAAAAAAGAAAAAT
Found at i:42611 original size:16 final size:14
Alignment explanation
Indices: 42571--42616 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 14
42561 AAGAAAAAAT
*
42571 AAAAATGAAAA-AG
1 AAAAATAAAAAGAG
42584 AAAAATAAAAAGAG
1 AAAAATAAAAAGAG
42598 AAAAATGGAAAAAGAG
1 AAAAAT--AAAAAGAG
42614 AAA
1 AAA
42617 TAAAAGGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 10 0.34
14 8 0.28
16 11 0.38
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAAATAAAAAGAG
Found at i:43974 original size:51 final size:51
Alignment explanation
Indices: 43913--44369 Score: 734
Period size: 51 Copynumber: 8.9 Consensus size: 51
43903 AAATTCGTTT
43913 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
43964 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
44015 GTTGAAGATTGAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
44066 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
44117 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAATTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
*
44168 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGAAGCGGACAAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* *
44219 GTTGAAGATTGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAGTTC
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * ** *
44270 GTTGAAGATTGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTGTTT
1 GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
* * * * *
44321 ATTGAAGATTTTTCGAGTTCTATACTCTCTGAAGGAAGAGAGAGCGGAC
1 GTTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGAC
44370 CCGTTTTATT
Statistics
Matches: 381, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
51 349 0.92
54 2 0.01
55 30 0.08
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (51 bp):
GTTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTC
Found at i:44402 original size:56 final size:56
Alignment explanation
Indices: 43923--44476 Score: 288
Period size: 51 Copynumber: 10.6 Consensus size: 56
43913 GTTGAAGATT
* * * ** **
43923 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
43974 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* ** **
44025 GAGTCTTATACTCTCTGAAGGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
44076 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
44127 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGA-CAATTTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * ** **
44178 GAGTCCTATACTCTCTGAATGAATAG-GAAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAG-AGCGGACCCGTTTTATTGAAGATTGTTC
* * ** **
44229 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * *
44280 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACCTG-TTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* *
44335 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * *
44391 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
44446 GAGTCTTATACT-TCCTGAAGGAATAGAGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
44477 AGGCTCGTCA
Statistics
Matches: 459, Mismatches: 32, Indels: 20
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.00
51 331 0.72
52 2 0.00
54 3 0.01
55 69 0.15
56 51 0.11
57 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:44477 original size:55 final size:55
Alignment explanation
Indices: 44229--44478 Score: 230
Period size: 55 Copynumber: 4.6 Consensus size: 55
44219 GTTGAAGATT
* * * * **
44229 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACTAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
* * * * * *
44280 GAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACC-TGTTTATTGAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGT-TTTATTGAAGATTGTTC
* * *
44335 GAGT-TCTATACTCTCTGAAGGAAGAGAGAGCGGACCCGTTTTATTAAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CCGTTTTATTGAAGATTGTTC
* *
44391 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACGTTTTA-TGAAGATTGTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-CGTTTTATTGAAGATTGTTC
44446 GAGTCTTATACT-TCCTGAAGGAATAGAGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
44479 GCTCGTCATT
Statistics
Matches: 168, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
51 42 0.25
54 3 0.02
55 69 0.41
56 52 0.31
57 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (55 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCGTTTTATTGAAGATTGTTC
Found at i:61321 original size:216 final size:217
Alignment explanation
Indices: 61026--62286 Score: 1208
Period size: 216 Copynumber: 5.9 Consensus size: 217
61016 AAAATAGTAG
* * * *
61026 CCTCAATTTTACCAATTCTCTCACCTTTTTCCTCAGCACCACTATTTTCTTCCTCCTCCAGTTTA
1 CCTCAATTTTACCAATTCTCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
* * * * *
61091 ACACTATAGGGAACTTCACTTTTGGAACCAGACTCTGAAGCAGCTAGTTC-ATTCCTAATTTCAC
66 ACACTGTGGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTAGTTCGATT-CTAACTTCAC
* *
61155 TTTCAATAGCAAGAGCTGCCAATGGAGGAGAAACCTGTTCTACATCAGGAACTAAATTTATCTTA
130 TTTCAATAGCAGGAGCTGCCAATGGAGGAGAAACCTGTTCTACATCAGGAACTAAATCTATCTTA
* **
61220 G-GCTCGTTATTTGAAGTGGTAC
195 GCCCTCCATATTTGAAGTGGTAC
* *
61242 CCTCAATTATACCAATTCTCTCCCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
1 CCTCAATTTTACCAATTCTCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
* * * * * * *
61307 ACACTGTGGGGAACTTCTCTTTTGGAAATAGAATCTGCAGAAGCTAATTCGGTTCTAGCTTCACT
66 ACACTGTGGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTAGTTCGATTCTAACTTCACT
* *
61372 TCCAATAGCAGGAGCTGCCAATGGAGGAGCAACCTGTTCTACATCAGGAACTAAATCTATCTTAG
131 TTCAATAGCAGGAGCTGCCAATGGAGGAGAAACCTGTTCTACATCAGGAACTAAATCTATCTTAG
61437 ACCCCTCCATATTTGAAGTGGTAC
196 --CCCTCCATATTTGAAGTGGTAC
* * * * ** * * * *
61461 CCTCAATTTTACCAGTTATCTCTCCATTTTCCTC--CTCCAG-CTTAAC--ACT-GTCGGGAACT
1 CCTCAATTTTACCAATTCTCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTC--CAGCT
* ** * ** * * **
61520 T--CTCT-TTTGGAAATAGAC-TCTGCAGAAGCTA-ATTC-G--G-TTCTAG--C--TTC--ACT
64 TAACACTGTGGGGAACTTCACTTTTG--GAA-CTAGACTCTGAAGAAGCTAGTTCGATTCTAACT
* ** ** * * * * * *
61570 TCCAATAGCAGGAGCTGCCA-ATG--GA-GGA--C-CAACCTGTTCTACATCAGGAACTAAATCT
126 T-CACTTTCAATAGCAG-GAGCTGCCAATGGAGGAGAAACCTGTTCTACATCAGGAACTAAATCT
61628 ATCTTAGACCCCTCCATATTTGAAGTGGTAC
189 ATCTTAG--CCCTCCATATTTGAAGTGGTAC
*
61659 CCTCAATTTTACC-AGTCATCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTT
1 CCTCAATTTTACCAATTC-TCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTT
* * * * * * *
61723 AACACTCTGGGGAACTTCACTTTTAGAACTAAACTCTGCAGAAGCTAATTCGGTTCTAGCTTCAC
65 AACACTGTGGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTAGTTCGATTCTAACTTCAC
* * **
61788 TTTCAATAGCAGGAGCTTCCAATGGAGGA-ACGACCTGTTCTACAAGAGGAACTAAATCTATCTT
130 TTTCAATAGCAGGAGCTGCCAATGGAGGAGA-AACCTGTTCTACATCAGGAACTAAATCTATCTT
61852 AGATCCCTCCATATTTGAAGTGGTAC
194 AG--CCCTCCATATTTGAAGTGGTAC
* * * *
61878 CCTCAATTTTACCAATTATCTCTCCATTTTCCTCAGCGCCGGTATTTCCTTCCTCCTCCAGCTTA
1 CCTCAATTTTACCAATTCTCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
* * * *
61943 ACACTGTGGGAAACTTCGCTTTTGGAACTAGACTCTGGAGAAGCTAGTTC-AGTCCTAA-TTCCA
66 ACACTGTGGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTAGTTCGA-TTCTAACTT-CA
* * * *
62006 CTTTCCATAGCAGGAGCTGCCAATGGAGGAGAAGCCTGTTCTACATCAGGAACGAAATTTATCTT
129 CTTTCAATAGCAGGAGCTGCCAATGGAGGAGAAACCTGTTCTACATCAGGAACTAAATCTATCTT
* *
62071 AG-ACTCCATATTTGGAGTGGTAC
194 AGCCCTCCATATTTGAAGTGGTAC
* *
62094 CCTCAGTTTTACCAATTCTCTCCCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
1 CCTCAATTTTACCAATTCTCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
* * * * * **
62159 ACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTAAAGAAGCTAGTTCAATTGTAATTTCAGG
66 ACACTGTGGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTAGTTCGATTCTAACTTCACT
* * * * * * * *
62224 TTCAGTAGCAGAAGCTTCCAGTGGAGGAGAAACCT-TTTTAATATCAGGAACGAAATCAATCTT
131 TTCAATAGCAGGAGCTGCCAATGGAGGAGAAACCTGTTCT-ACATCAGGAACTAAATCTATCTT
62287 TGATACCAAA
Statistics
Matches: 850, Mismatches: 148, Indels: 94
0.78 0.14 0.09
Matches are distributed among these distances:
197 1 0.00
198 89 0.10
200 5 0.01
201 6 0.01
202 5 0.01
203 8 0.01
204 22 0.03
205 13 0.02
206 2 0.00
207 2 0.00
208 3 0.00
209 3 0.00
210 2 0.00
211 3 0.00
212 12 0.01
213 21 0.02
214 7 0.01
215 8 0.01
216 357 0.42
217 10 0.01
218 2 0.00
219 266 0.31
220 3 0.00
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (217 bp):
CCTCAATTTTACCAATTCTCTCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTA
ACACTGTGGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTAGTTCGATTCTAACTTCACT
TTCAATAGCAGGAGCTGCCAATGGAGGAGAAACCTGTTCTACATCAGGAACTAAATCTATCTTAG
CCCTCCATATTTGAAGTGGTAC
Found at i:61629 original size:198 final size:198
Alignment explanation
Indices: 61291--61911 Score: 900
Period size: 198 Copynumber: 3.0 Consensus size: 198
61281 CAGTATTTTC
*
61291 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCTCTTTTGGAAATAGAATCTGCAGAAGCTAATT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAATT
*
61356 CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGAGCAACCTGTTCTACATCAGGA
66 CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGAACAACCTGTTCTACATCAGGA
61421 ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAGTTATCTCTCC
131 ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAGTTATCTCTCC
61486 ATT
196 ATT
*
61489 TTCCTCCTCCAGCTTAACACTGTCGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAATT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAATT
*
61554 CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGACCAACCTGTTCTACATCAGGA
66 CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGAACAACCTGTTCTACATCAGGA
61619 ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAGTCATCTCTCC
131 ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAG-----T-T--
*
61684 ATTTTCCTCAGCACCAGTATTTT
188 A---T-CT---CTCC---A--TT
* * * * *
61707 CTTCCTCCTCCAGCTTAACACTCTGGGGAACTTCACTTTTAGAACTAAACTCTGCAGAAGCTAAT
1 -TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAAT
* * * **
61772 TCGGTTCTAGCTTCACTTTCAATAGCAGGAGCTTCCAATGGAGGAACGACCTGTTCTACAAGAGG
65 TCGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGAACAACCTGTTCTACATCAGG
* *
61837 AACTAAATCTATCTTAGATCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTATCTCTC
130 AACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAGTTATCTCTC
61902 CATT
195 CATT
61906 TTCCTC
1 TTCCTC
61912 AGCGCCGGTA
Statistics
Matches: 383, Mismatches: 19, Indels: 42
0.86 0.04 0.09
Matches are distributed among these distances:
198 188 0.49
199 2 0.01
201 1 0.00
203 1 0.00
204 4 0.01
206 1 0.00
207 2 0.01
208 1 0.00
209 1 0.00
210 2 0.01
211 1 0.00
213 4 0.01
214 1 0.00
216 1 0.00
218 2 0.01
219 171 0.45
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (198 bp):
TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAATT
CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGAACAACCTGTTCTACATCAGGA
ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAGTTATCTCTCC
ATT
Found at i:61846 original size:417 final size:418
Alignment explanation
Indices: 61071--62204 Score: 1525
Period size: 417 Copynumber: 2.7 Consensus size: 418
61061 GCACCACTAT
* * * *
61071 TTTCTTCCTCCTCCAGTTTAACACTATAGGGAACTTCACTTTTGGAACCAGACTCTGAAGCAGCT
1 TTTCTTCCTCCTCCAGCTTAACACTGT-GGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCT
* * *
61136 AGTTCATTCCTAATTTCACTTTCAATAGCAAGAGCTGCCAATGGAGGAGAAACCTGTTCTACATC
65 AGTTCGTT-CTAA-TTCACTTCCAATAGCAGGAGCTGCCAATGGAGGA-AAACCTGTTCTACATC
* ** *
61201 AGGAACTAAATTTATCTTAGGCTCGTTATTTGAAGTGGTACCCTCAATTATACCAATTCTCTCCC
127 AGGAACTAAATTTATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCC
*
61266 CATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCTCTTTTG
192 CATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCACTTTTG
*
61331 GAAATAGAA-TCTGCAGAAGCTAATTCGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATG
257 GAACTA-AACTCTGCAGAAGCTAATTCGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATG
* *
61395 GAGGAGCAACCTGTTCTACATCAGGAACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTA
321 GAGGAACAACCTGTTCTACAACAGGAACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTA
*
61460 CCCTCAATTTTACCAGTTA-T-C-T-CT-CC-A
386 CCCTCAATTTTACCAATTACTCCTTCCTCCCGA
* * *
61487 -TT-TTCCTCCTCCAGCTTAACACTGTCGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCT
1 TTTCTTCCTCCTCCAGCTTAACACTGT-GGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCT
* * *
61550 AATTCGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGACCAACCTGTTCTACATC
65 AGTTC-GTTCTA-ATTCACTTCCAATAGCAGGAGCTGCCAATGGAGGA-AAACCTGTTCTACATC
* *
61615 AGGAACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACC-AGTCATC
127 AGGAACTAAATTTATCTTAGA---CTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTC-TC
* *
61679 TCTCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTCTGGGGAACTTCACT
188 TCCCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCACT
* * *
61744 TTTAGAACTAAACTCTGCAGAAGCTAATTCGGTTCTAGCTTCACTTTCAATAGCAGGAGCTTCCA
253 TTTGGAACTAAACTCTGCAGAAGCTAATTCGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCA
* * *
61809 ATGGAGGAACGACCTGTTCTACAAGAGGAACTAAATCTATCTTAGATCCCTCCATATTTGAAGTG
318 ATGGAGGAACAACCTGTTCTACAACAGGAACTAAATCTATCTTAGACCCCTCCATATTTGAAGTG
61874 GTACCCTCAATTTTACCAATTATCTCTCCATTTTCCTCAGCGCCGGTA
383 GTACCCTCAATTTTACCAATTA---CTCC---TTCCT---C-CC-G-A
* *
61922 TTTCCTTCCTCCTCCAGCTTAACACTGTGGGAAACTTCGCTTTTGGAACTAGACTCTGGAGAAGC
1 TTT-CTTCCTCCTCCAGCTTAACACTGTGGG-AACTTCACTTTTGGAACTAGACTCTGAAGAAGC
* *
61987 TAGTTCAGTCCTAATTCCACTTTCC-ATAGCAGGAGCTGCCAATGGAGGAGAAGCCTGTTCTACA
64 TAGTTC-GTTCTAATT-CAC-TTCCAATAGCAGGAGCTGCCAATGGAGGA-AAACCTGTTCTACA
* * *
62051 TCAGGAACGAAATTTATCTTAGACTCCATATTTGGAGTGGTACCCTCAGTTTTACCAATTCTCTC
125 TCAGGAACTAAATTTATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTC
*
62116 CCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTT
190 CCCATTTTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCACTTT
* **
62181 TGGAACTAGACTCTAAAGAAGCTA
255 TGGAACTAAACTCTGCAGAAGCTA
62205 GTTCAATTGT
Statistics
Matches: 630, Mismatches: 56, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
414 126 0.20
415 4 0.01
416 5 0.01
417 233 0.37
421 1 0.00
422 1 0.00
426 1 0.00
427 2 0.00
432 2 0.00
435 118 0.19
436 5 0.01
437 5 0.01
438 123 0.20
439 4 0.01
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (418 bp):
TTTCTTCCTCCTCCAGCTTAACACTGTGGGAACTTCACTTTTGGAACTAGACTCTGAAGAAGCTA
GTTCGTTCTAATTCACTTCCAATAGCAGGAGCTGCCAATGGAGGAAAACCTGTTCTACATCAGGA
ACTAAATTTATCTTAGACTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCCCCATT
TTCCTCAGCACCAGTATTTTCTTCCTCCTCCAGCTTAACACTGTGGGGAACTTCACTTTTGGAAC
TAAACTCTGCAGAAGCTAATTCGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGA
ACAACCTGTTCTACAACAGGAACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTC
AATTTTACCAATTACTCCTTCCTCCCGA
Found at i:61868 original size:219 final size:218
Alignment explanation
Indices: 61489--62204 Score: 1055
Period size: 219 Copynumber: 3.3 Consensus size: 218
61479 TCTCTCCATT
* * *
61489 TTCCTCCTCCAGCTTAACACTGTCGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAATT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGCAGAAGCTAATT
* * *
61554 CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGACCAACCTGTTCTACATCAGGA
66 CGGTTCTAGCTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAACGACCTGTTCTACATCAGGA
*
61619 ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAGTCATCTCTCC
131 ACTAAATCTATCTTAGA-CCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAATCATCTCTCC
61684 ATTTTCCTCAGCACCAGTATTTTC
195 ATTTTCCTCAGCACCAGTATTTTC
* * * *
61708 TTCCTCCTCCAGCTTAACACTCTGGGGAACTTCACTTTTAGAACTAAACTCTGCAGAAGCTAATT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGCAGAAGCTAATT
* **
61773 CGGTTCTAGCTTCACTTTCAATAGCAGGAGCTTCCAATGGAGGAACGACCTGTTCTACAAGAGGA
66 CGGTTCTAGCTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAACGACCTGTTCTACATCAGGA
*
61838 ACTAAATCTATCTTAGATCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTATCTCTCC
131 ACTAAATCTATCTTAGA-CCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAATCATCTCTCC
* * *
61903 ATTTTCCTCAGCGCCGGTATTTCC
195 ATTTTCCTCAGCACCAGTATTTTC
* * *
61927 TTCCTCCTCCAGCTTAACACTGTGGGAAACTTCGCTTTTGGAACTAGACTCTGGAGAAGCTAGTT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGCAGAAGCTAATT
* * * * *
61992 CAGTCCTA-ATTCCACTTTCCATAGCAGGAGCTGCCAATGGAGGAGAAG-CCTGTTCTACATCAG
66 CGGTTCTAGCTT-CACTTTCAATAGCAGGAGCTGCCAATGGAGGA-ACGACCTGTTCTACATCAG
* * * * *
62055 GAACGAAATTTATCTTAGA--CTCCATATTTGGAGTGGTACCCTCAGTTTTACCAATTC-TCTCC
129 GAACTAAATCTATCTTAGACCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAA-TCATCTCT
62117 CCATTTTCCTCAGCACCAGTATTTTC
193 CCATTTTCCTCAGCACCAGTATTTTC
**
62143 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTAAAGAAGCTA
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGCAGAAGCTA
62205 GTTCAATTGT
Statistics
Matches: 449, Mismatches: 45, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
216 119 0.27
217 1 0.00
218 2 0.00
219 325 0.72
220 2 0.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (218 bp):
TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGCAGAAGCTAATT
CGGTTCTAGCTTCACTTTCAATAGCAGGAGCTGCCAATGGAGGAACGACCTGTTCTACATCAGGA
ACTAAATCTATCTTAGACCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAATCATCTCTCCA
TTTTCCTCAGCACCAGTATTTTC
Found at i:62318 original size:216 final size:214
Alignment explanation
Indices: 61489--62286 Score: 956
Period size: 219 Copynumber: 3.7 Consensus size: 214
61479 TCTCTCCATT
* * * * *
61489 TTCCTCCTCCAGCTTAACACTGTCGGGAACTTCTCTTTTGGAAATAGACTCTGCAGAAGCTAATT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGAAGAAGCTAGTT
* ** * * ** *
61554 CGGTTCTAGCTTCACTTCCAATAGCAGGAGCTGCCAATGGAGGACCAACCTGTTCTACATCAGGA
66 CAGTTCTAATTTCACTTTC-ATAGCAGGAGCTTCCAATGGAGGAGAAACCTGTTCTAAATCAGGA
* *
61619 ACTAAATCTATCTTAGACCCCTCCATATTTGAAGTGGTACCCTCAATTTTACC-AGTCATCTCTC
130 ACGAAATCTATCTTAGA----TCCATATTTGAAGTGGTACCCTCAATTTTACCAATTC-TCTCTC
61683 CATTTTCCTCAGCACCAGTATTTTC
190 CATTTTCCTCAGCACCAGTATTTTC
* * * * * *
61708 TTCCTCCTCCAGCTTAACACTCTGGGGAACTTCACTTTTAGAACTAAACTCTGCAGAAGCTAATT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGAAGAAGCTAGTT
* ** * *
61773 CGGTTCTAGCTTCACTTTCAATAGCAGGAGCTTCCAATGGAGGA-ACGACCTGTTCTACAA-GAG
66 CAGTTCTAATTTCACTTTC-ATAGCAGGAGCTTCCAATGGAGGAGA-AACCTGTTCTA-AATCAG
* *
61836 GAACTAAATCTATCTTAGATCCCTCCATATTTGAAGTGGTACCCTCAATTTTACCAATTATCTCT
128 GAACGAAATCTATCTTAGA----TCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCT
* * *
61901 CCATTTTCCTCAGCGCCGGTATTTCC
189 CCATTTTCCTCAGCACCAGTATTTTC
* *
61927 TTCCTCCTCCAGCTTAACACTGTGGGAAACTTCGCTTTTGGAACTAGACTCTGGAGAAGCTAGTT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGAAGAAGCTAGTT
* * * * *
61992 CAGTCCTAATTCCACTTTCCATAGCAGGAGCTGCCAATGGAGGAGAAGCCTGTTCTACATCAGGA
66 CAGTTCTAATTTCACTTT-CATAGCAGGAGCTTCCAATGGAGGAGAAACCTGTTCTAAATCAGGA
* * * *
62057 ACGAAATTTATCTTAGACTCCATATTTGGAGTGGTACCCTCAGTTTTACCAATTCTCTCCCCATT
130 ACGAAATCTATCTTAGA-TCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCTCCATT
62122 TTCCTCAGCACCAGTATTTTC
194 TTCCTCAGCACCAGTATTTTC
*
62143 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTAAAGAAGCTAGTT
1 TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGAAGAAGCTAGTT
* * ** * * *
62208 CAATTGTAATTTCAGGTTCAGTAGCAGAAGCTTCCAGTGGAGGAGAAACCT-TTTTAATATCAGG
66 CAGTTCTAATTTCACTTTCA-TAGCAGGAGCTTCCAATGGAGGAGAAACCTGTTCTAA-ATCAGG
*
62272 AACGAAATCAATCTT
129 AACGAAATCTATCTT
62287 TGATACCAAA
Statistics
Matches: 510, Mismatches: 61, Indels: 19
0.86 0.10 0.03
Matches are distributed among these distances:
215 6 0.01
216 181 0.35
218 1 0.00
219 317 0.62
220 5 0.01
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (214 bp):
TTCCTCCTCCAGCTTAACACTGTGGGGAACTTCGCTTTTGGAACTAGACTCTGAAGAAGCTAGTT
CAGTTCTAATTTCACTTTCATAGCAGGAGCTTCCAATGGAGGAGAAACCTGTTCTAAATCAGGAA
CGAAATCTATCTTAGATCCATATTTGAAGTGGTACCCTCAATTTTACCAATTCTCTCTCCATTTT
CCTCAGCACCAGTATTTTC
Found at i:66701 original size:13 final size:13
Alignment explanation
Indices: 66683--66708 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66673 TAAAATCGAA
66683 CCCGACCCGATTC
1 CCCGACCCGATTC
66696 CCCGACCCGATTC
1 CCCGACCCGATTC
66709 AAACAGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.54, G:0.15, T:0.15
Consensus pattern (13 bp):
CCCGACCCGATTC
Found at i:68144 original size:37 final size:37
Alignment explanation
Indices: 68068--68144 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
68058 TTTTTATATT
*
68068 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * * *
68105 TTTAATTTTTTTAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
68142 TTT
1 TTT
68145 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:83829 original size:2 final size:2
Alignment explanation
Indices: 83824--83848 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
83814 ATTGTGTGAT
83824 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 T
83849 TAAAATGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:84321 original size:25 final size:26
Alignment explanation
Indices: 84292--84342 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
84282 TCTATTTTCG
84292 TCTCT-TCTAAAATTTTATAAATTCA
1 TCTCTCTCTAAAATTTTATAAATTCA
*
84317 TCTCTCCTTTAAAATTTTATAAATTC
1 TCTCT-CTCTAAAATTTTATAAATTC
84343 GCCCCTCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.22
27 18 0.78
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (26 bp):
TCTCTCTCTAAAATTTTATAAATTCA
Found at i:85865 original size:6 final size:6
Alignment explanation
Indices: 85854--85880 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
85844 ATCAGCATAA
85854 AACTGC AACTGC AACTGC AACTGC AAC
1 AACTGC AACTGC AACTGC AACTGC AAC
85881 CCCCTCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.37, C:0.33, G:0.15, T:0.15
Consensus pattern (6 bp):
AACTGC
Found at i:96619 original size:20 final size:20
Alignment explanation
Indices: 96596--96651 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
96586 ATTCGCGTTG
*
96596 CATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATTTTC
96616 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
96636 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
96652 AGTCTACAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:96757 original size:6 final size:6
Alignment explanation
Indices: 96746--96838 Score: 186
Period size: 6 Copynumber: 15.5 Consensus size: 6
96736 GACACGTATT
96746 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
96794 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
96839 CGAGACGAGA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 87 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:96849 original size:5 final size:5
Alignment explanation
Indices: 96839--96879 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
96829 GACCACGACC
96839 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
96880 GCGGCGGCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.37, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:97365 original size:6 final size:6
Alignment explanation
Indices: 97356--97483 Score: 220
Period size: 6 Copynumber: 21.2 Consensus size: 6
97346 GTCCGTCTCG
97356 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
97404 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
* * *
97452 GGTCGT GGTAGT GGTAGT GGTAGT GGTACGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT-CGT G
97484 TCTTCGACAC
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
6 116 0.97
7 3 0.03
ACGTcount: A:0.03, C:0.14, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:100862 original size:19 final size:20
Alignment explanation
Indices: 100835--100872 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
100825 TATATTTTAT
100835 TTAAAATTTA-AAAATTAAA
1 TTAAAATTTATAAAATTAAA
*
100854 TTAATATTTATAAAATTAA
1 TTAAAATTTATAAAATTAA
100873 TATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAATTTATAAAATTAAA
Found at i:104955 original size:11 final size:11
Alignment explanation
Indices: 104939--105001 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
104929 AAAATTACAT
104939 TATTAAAAATA
1 TATTAAAAATA
104950 TATTAAAAATA
1 TATTAAAAATA
* ***
104961 AATTATTGATA
1 TATTAAAAATA
104972 -ATTATAAAAT-
1 TATTA-AAAATA
104982 T-TTAAAAATA
1 TATTAAAAATA
104992 TATTAAAAAT
1 TATTAAAAAT
105002 TCTATAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:105010 original size:21 final size:21
Alignment explanation
Indices: 104972--105011 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
104962 ATTATTGATA
*
104972 ATTATAAAATTTTAAAAATAT
1 ATTATAAAATTCTAAAAATAT
104993 ATTA-AAAATTCTATAAAAT
1 ATTATAAAATTCTA-AAAAT
105012 TATAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATAAAATTCTAAAAATAT
Found at i:106629 original size:260 final size:260
Alignment explanation
Indices: 105877--106635 Score: 1277
Period size: 258 Copynumber: 2.9 Consensus size: 260
105867 GACCCTTGAA
* * * *
105877 TTCCTCGTCTCCTTTACTTTCTATTGCTGCCACCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCC
1 TTCCTCGTCTCCTTTTCTTTCTATTGCTGTCGCCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCA
105942 TTTCGTTTTCATTAAGATCCG-TCTGGTTTTAGATACTTATACTCGTTTATTCTTCTTTTTAATC
66 TTTCGTTTTCATTAAGATCCGCTCTGGTTTTAGATACTTATACTCGTTTATTCTTCTTTTTAATC
*
106006 TTAAATCTTG----CTTTTCATTTCTCGAATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
131 TTAAATCTTGTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
* *
106067 TATGTTGTTACTTAGCTCTAAAATGATTTTGAATGTGTATTAAATCTTGGTTCCTCAGGTTTGCT
196 TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAGGTTTGCT
* *
106132 TTCCTCATCTCCTTTTCTTTCTATTACTGTCGCCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCA
1 TTCCTCGTCTCCTTTTCTTTCTATTGCTGTCGCCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCA
106197 TTTCGTTTTCATTAAGATCC-CTCTGGTTTTAGATAC-T-TACTCGTTTATTCTTCTTTTTAATC
66 TTTCGTTTTCATTAAGATCCGCTCTGGTTTTAGATACTTATACTCGTTTATTCTTCTTTTTAATC
106259 TTAAATCTTGCTTTCCTTTTCATTTCTCGGATTTTGATT-GAAGTGTGAATGTTTTTAGTACTCA
131 TTAAATCTTG-TTTCCTTTTCATTTCTCGGATTTTG-TTGGAAGTGTGAATGTTTTTAGTACTCA
*
106323 ATTATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAGGTTTG
194 ACTATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAGGTTTG
106388 CT
259 CT
* * *
106390 TTCCTCGTCTCCTTTTCTTTCTATTGCTGTCGTCTTTCTCGGTTCCTCAGGTTTGCCCCTTTCCA
1 TTCCTCGTCTCCTTTTCTTTCTATTGCTGTCGCCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCA
* *
106455 TTTCGTTTTCATTAAGATCCGCT-TGGTTTTAGATACTTATACTTGTTTTTTCTTCTTTTTAATC
66 TTTCGTTTTCATTAAGATCCGCTCTGGTTTTAGATACTTATACTCGTTTATTCTTCTTTTTAATC
106519 TTAAATCTTGTTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAA
131 TTAAATCTTG-TTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAA
*
106584 CTATGATGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGT
195 CTATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGT
106636 ATTGGCTATT
Statistics
Matches: 473, Mismatches: 20, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
253 35 0.07
254 1 0.00
255 94 0.20
258 202 0.43
259 7 0.01
260 134 0.28
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.49
Consensus pattern (260 bp):
TTCCTCGTCTCCTTTTCTTTCTATTGCTGTCGCCTTTCTTGGTTCCTCAGGTTTGCCCTTTTCCA
TTTCGTTTTCATTAAGATCCGCTCTGGTTTTAGATACTTATACTCGTTTATTCTTCTTTTTAATC
TTAAATCTTGTTTCCTTTTCATTTCTCGGATTTTGTTGGAAGTGTGAATGTTTTTAGTACTCAAC
TATGTTGTTACTTAGCTCTAAAATGTTTTTGAATGTGTATTAAATCTGGGTTCCTCAGGTTTGCT
Found at i:107600 original size:17 final size:17
Alignment explanation
Indices: 107575--107631 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
107565 TAGGTTTAAA
*
107575 TTCGAGCTTGAATTGAG
1 TTCGAGCTTGAATCGAG
*
107592 TTTGAGCTTGAATCGAG
1 TTCGAGCTTGAATCGAG
107609 TTCGAGCTTGAATCGAG
1 TTCGAGCTTGAATCGAG
*
107626 CTCGAG
1 TTCGAG
107632 TCTCGAGCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.32
Consensus pattern (17 bp):
TTCGAGCTTGAATCGAG
Found at i:107674 original size:16 final size:16
Alignment explanation
Indices: 107649--107679 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
107639 CTCTTGAAAT
*
107649 TTTTTTGAGTTCGAGC
1 TTTTTCGAGTTCGAGC
107665 TTTTTCGAGTTCGAG
1 TTTTTCGAGTTCGAG
107680 TCGAGTTTCA
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:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCGAGC
Found at i:108999 original size:18 final size:18
Alignment explanation
Indices: 108976--109013 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
108966 TCTATATGAT
108976 ACATGAGAAAACATACAA
1 ACATGAGAAAACATACAA
* *
108994 ACATGAGATAATATACAA
1 ACATGAGAAAACATACAA
109012 AC
1 AC
109014 TATTATTACA
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:0.58, C:0.16, G:0.11, T:0.16
Consensus pattern (18 bp):
ACATGAGAAAACATACAA
Found at i:117484 original size:76 final size:75
Alignment explanation
Indices: 117400--117547 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
117390 TAAACTCAAA
117400 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
117464 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
117476 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
117541 TTAATTA
66 TTAATTA
117548 GGATTTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 24 0.36
76 43 0.64
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:118235 original size:21 final size:22
Alignment explanation
Indices: 118210--118250 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
118200 CTTTAATTTG
118210 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
118231 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
118251 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:128456 original size:6 final size:6
Alignment explanation
Indices: 128445--128476 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
128435 ACACTAGTAT
128445 GTAGGA GTAGGA GTAGGA GTAGGA GTAGGA GT
1 GTAGGA GTAGGA GTAGGA GTAGGA GTAGGA GT
128477 GAGTGTCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (6 bp):
GTAGGA
Found at i:131361 original size:3 final size:3
Alignment explanation
Indices: 131355--131382 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
131345 GATCTGATGA
131355 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
131383 CGCATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:136687 original size:9 final size:8
Alignment explanation
Indices: 136673--136714 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
136663 AAATAAATAA
136673 ATAAAATT
1 ATAAAATT
136681 ATAAAAATT
1 AT-AAAATT
*
136690 GTAAAATT
1 ATAAAATT
136698 AT-AAATT
1 ATAAAATT
136705 ATTAAAATT
1 A-TAAAATT
136714 A
1 A
136715 AAAGTGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
7 6 0.21
8 10 0.34
9 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
ATAAAATT
Found at i:137838 original size:33 final size:30
Alignment explanation
Indices: 137767--137838 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 30
137757 GGATTTTTTT
137767 AAAAATTTTAATAATATTTTTATTTAAAAA
1 AAAAATTTTAATAATATTTTTATTTAAAAA
*
137797 AAATATTTTAATAATATTTTTATTTTTAAAAA
1 AAAAATTTTAATAATATTTTTA--TTTAAAAA
137829 ATAAAATTTT
1 A-AAAATTTT
137839 TCAAATTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 21 0.57
32 9 0.24
33 7 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
AAAAATTTTAATAATATTTTTATTTAAAAA
Done.