Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006023.1 Hibiscus syriacus cultivar Beakdansim tig00014213_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: 1315283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:295236 original size:16 final size:16
Alignment explanation
Indices: 295215--295247 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
295205 AAAAAAATTT
295215 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
295231 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
295247 T
1 T
295248 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:295836 original size:54 final size:54
Alignment explanation
Indices: 295770--295885 Score: 135
Period size: 54 Copynumber: 2.1 Consensus size: 54
295760 TATTCACCCA
* * *
295770 AAAAAATTGCTACAATGAAAAAGGTGTGATTACAAACCGTCTTAACTATTCAC-
1 AAAAAATAGCTACAATGAAAAAGGTGCGATTACAAACCGTCTTAACTAATCACT
* * * * * *
295823 AAAAAATGAGCTACAATGAAGACGTTGCGATTACAACCCGTCTTCATTAATCACT
1 AAAAAAT-AGCTACAATGAAAAAGGTGCGATTACAAACCGTCTTAACTAATCACT
295878 AAAAAATA
1 AAAAAATA
295886 ATTAAAAAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
53 7 0.13
54 38 0.73
55 7 0.13
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (54 bp):
AAAAAATAGCTACAATGAAAAAGGTGCGATTACAAACCGTCTTAACTAATCACT
Found at i:300293 original size:38 final size:38
Alignment explanation
Indices: 300224--300298 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
300214 TACATATTAT
*
300224 AGAAAACCATATAAAACACATACATATCAAAATATCAC
1 AGAAAACCATATAAAACACATACATAACAAAATATCAC
* **
300262 AGAAAACCTTATAAAACATTTACGA-AACAAAATATCA
1 AGAAAACCATATAAAACACATAC-ATAACAAAATATCA
300299 GTAATACAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.57, C:0.19, G:0.04, T:0.20
Consensus pattern (38 bp):
AGAAAACCATATAAAACACATACATAACAAAATATCAC
Found at i:306845 original size:38 final size:38
Alignment explanation
Indices: 306775--306850 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
306765 ATACATATTT
* *
306775 TAGAAAACCATATAAAACACATACATATCAAAATATCA
1 TAGAAAACCATATAAAACACATACAGAACAAAATATCA
* ** *
306813 TAGAAAACCTTATAAAACATTTACGGAACAAAATATCA
1 TAGAAAACCATATAAAACACATACAGAACAAAATATCA
306851 GTAATATGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.22
Consensus pattern (38 bp):
TAGAAAACCATATAAAACACATACAGAACAAAATATCA
Found at i:311188 original size:60 final size:60
Alignment explanation
Indices: 311062--311188 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 60
311052 TATTACAATT
** * *
311062 ATATTAATATTTCTCAACAATCAAACTAACTATATAATATAGTAAAAATTTTCTACATAA
1 ATATTAATATTTCTCAACAATCAAACTAACTATATAATATAGTAAAAATTTTAAAAACAA
* *
311122 ATATTAATA-TTCATCAACAATCAAATTAACTATAATAA-ATAATTTAAAAA-TTTAAAAACAA
1 ATATTAATATTTC-TCAACAATCAAACTAACTAT-ATAATAT-A-GTAAAAATTTTAAAAACAA
311183 A-ATTAA
1 ATATTAA
311189 AAATTCTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
59 3 0.05
60 35 0.61
61 13 0.23
62 6 0.11
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.35
Consensus pattern (60 bp):
ATATTAATATTTCTCAACAATCAAACTAACTATATAATATAGTAAAAATTTTAAAAACAA
Found at i:311301 original size:254 final size:260
Alignment explanation
Indices: 310844--311356 Score: 758
Period size: 254 Copynumber: 2.0 Consensus size: 260
310834 TATAACATGC
* * *
310844 AAAATTTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACAATAATATATAATTTTAA
1 AAAAATTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACAATAATAAATAATTTAAA
310909 AATTAAAAACAAAATTAATGATATAATATTACTTAATTAAAAATTAAAATATACACATACTTACA
66 AATTAAAAACAAAATT-ATGATATAATATTACTTAATTAAAAATTAAAATATACACATACTTACA
* * *
310974 AATATTTTCTCCTTCTTATTCCTTCTTCTTCTTGTTCTTCTTTTACAATTTTTTATTATTCTCAA
130 AATATTTTCTCCTTCTTATTCCTTCTTCTCCTTCTTCTTCCTTTACAATTTTTTATTATTCTCAA
* *
311039 ATTACATGCATAATATTACA-ATTATATTAATATTTCTCAACAATCAAACTAACTATATAATATA
195 ACTACATGCATAATATTA-ATATTATATTAACATTTCTCAACAATCAAACTAACTATATAATATA
311103 GT
259 GT
*
311105 AAAAATTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACTATAATAAATAATTTAAA
1 AAAAATTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACAATAATAAATAATTTAAA
*
311170 AATTTAAAAACAAAA-T-T-A-A-AA-ATT-CTTAATTAAAAATTAAAATATACATC-TACTTAT
66 AA-TTAAAAACAAAATTATGATATAATATTACTTAATTAAAAATTAAAATATACA-CATACTTAC
* * * * *
311227 TAATATTTTCTCCTTCTTCTTTCTTTTTCTCCTTCTT-TTCCTTTACAATTTTTTCATTCTTCTC
129 AAATATTTTCTCCTTCTTATTCCTTCTTCTCCTTCTTCTTCCTTTACAATTTTTT-ATTATTCTC
* *
311291 AAACTACATGCATAATTTTAATATTATATTAACATTTCTCAACAATCAAACTAGCTATATAATAT
193 AAACTACATGCATAATATTAATATTATATTAACATTTCTCAACAATCAAACTAACTATATAATAT
311356 A
258 A
311357 TCATTTAAAA
Statistics
Matches: 231, Mismatches: 17, Indels: 15
0.88 0.06 0.06
Matches are distributed among these distances:
253 17 0.07
254 129 0.56
255 4 0.02
256 2 0.01
257 1 0.00
258 1 0.00
259 1 0.00
261 64 0.28
262 12 0.05
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.42
Consensus pattern (260 bp):
AAAAATTTTCTACATAAATATTAATATTCATCAACAATCAAATTAACAATAATAAATAATTTAAA
AATTAAAAACAAAATTATGATATAATATTACTTAATTAAAAATTAAAATATACACATACTTACAA
ATATTTTCTCCTTCTTATTCCTTCTTCTCCTTCTTCTTCCTTTACAATTTTTTATTATTCTCAAA
CTACATGCATAATATTAATATTATATTAACATTTCTCAACAATCAAACTAACTATATAATATAGT
Found at i:311462 original size:203 final size:201
Alignment explanation
Indices: 311132--311611 Score: 502
Period size: 208 Copynumber: 2.4 Consensus size: 201
311122 ATATTAATAT
* * * *
311132 TCATCAACAATCAAATTAACTATAATAAATAATTTAAAAATTTAAAAACAAAATT----A-A-AA
1 TCATCAACAATCAAACTAACTACAATATATAACTTAAAAA-TTAAAAACAAAATTAACAATATAA
* * * *
311191 -ATT-CTTAATTAAAAATTAAAATATACATCTACTTATTAATATTTTCTCCTTCTTCT-TTCTTT
65 TATTACTTAATTAAAAAATAAAATATACATCTACTTATTAATAATTTCTACTTCTTCTCTTCTTC
* *
311253 TTCTCCTTCTT-TTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAATTTTAATATTA
130 TCCT-CTTCTTATTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAA--TTAAAATT-
*
311317 TATTAACATT-
191 TAATAACATTA
* * * * * **
311327 TC-TCAACAATCAAACTAGCTATATAATATATCATTTAAAAATTAAAAACAAAGTTAACGTTATA
1 TCATCAACAATCAAACTAAC--TACAATATATAACTTAAAAATTAAAAACAAAATTAACAATATA
*
311391 ATTTTACTTAATTAAAAAATAAAATATACATCTACTTACTAGTAGA-AATTTCTACTTCTTC-CT
64 ATATTACTTAATTAAAAAATAAAATATACATCTACTTA-T--TA-ATAATTTCTACTTCTTCTCT
* * *
311454 TCTTCTCCTTTTTCTTCTTATTCTTTTACAATTTTTTCCTTCTTCTCAAATTACATGCATAATTA
125 TCTTCTCC----TCTTCTTATTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAATTA
311519 AAATTTAATAACATTCA
186 AAATTTAATAACATT-A
*
311536 TCATCAACAATCAAATTAACTACAATATATAACTTAAAAATTAAAAACAAAATTAACAATATAAT
1 TCATCAACAATCAAACTAACTACAATATATAACTTAAAAATTAAAAACAAAATTAACAATATAAT
*
311601 ATTACGTAATT
66 ATTACTTAATT
311612 TCTACTTACT
Statistics
Matches: 235, Mismatches: 27, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
194 15 0.06
195 15 0.06
196 18 0.08
200 1 0.00
201 2 0.01
202 2 0.01
203 31 0.13
204 1 0.00
206 22 0.09
207 10 0.04
208 55 0.23
209 8 0.03
210 55 0.23
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (201 bp):
TCATCAACAATCAAACTAACTACAATATATAACTTAAAAATTAAAAACAAAATTAACAATATAAT
ATTACTTAATTAAAAAATAAAATATACATCTACTTATTAATAATTTCTACTTCTTCTCTTCTTCT
CCTCTTCTTATTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAATTAAAATTTAATA
ACATTA
Found at i:311546 original size:210 final size:199
Alignment explanation
Indices: 311131--311611 Score: 531
Period size: 210 Copynumber: 2.4 Consensus size: 199
311121 AATATTAATA
311131 TTCATCAACAATCAAATTAACTATAATAA-ATA-ATTTAAAAATTTAAAAACAAAATTAA--A-A
1 TTCATCAACAATCAAATTAACTAT-ATAATATATATTTAAAAA-TTAAAAACAAAATTAACTATA
* * *
311191 A-TT-CTTAATTAAAAATTAAAATATACATCTACTTATTAATATTTTCTCCTTCTTCTTTCTTTT
64 ATTTACTTAATTAAAAAATAAAATATACATCTACTTATTAAAATTTTCTCCTTCTTCTTTCCTTT
*
311254 TCTCCTTCTTTTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAATTTTAATATTATA
129 TCTCCTTCTTTTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAA-TTTAAAATTATA
*
311319 TTAACAT
193 ATAACAT
* * *
311326 TTC-TCAACAATCAAACTAGCTATATAATATATCATTTAAAAATTAAAAACAAAGTTAACGTTAT
1 TTCATCAACAATCAAATTAACTATATAATATAT-ATTTAAAAATTAAAAACAAAATTAAC--TAT
*
311390 AATTTTACTTAATTAAAAAATAAAATATACATCTACTTACTAGTAGAAATTTCTACTTCTTCCTT
63 AA-TTTACTTAATTAAAAAATAAAATATACATCTACTTA-T--TA-AAATTT-T-CTCCTT-CTT
* * *
311455 CTTCTCCTTTT-T-CTTCTTATTCTTTTACAATTTTTTCCTTCTTCTCAAATTACATGCATAA-T
120 CTT-TCCTTTTCTCCTTCTT-TTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAATT
311517 TAAAATT-TAATAACAT
183 TAAAATTATAATAACAT
* *
311533 TCATCATCAACAATCAAATTAAC--TACAATATATAACTTAAAAATTAAAAACAAAATTAACAAT
1 T--TCATCAACAATCAAATTAACTATATAATATAT-ATTTAAAAATTAAAAACAAAATTAAC--T
*
311596 ATAATATTACGTAATT
61 ATAAT-TTACTTAATT
311612 TCTACTTACT
Statistics
Matches: 241, Mismatches: 21, Indels: 35
0.81 0.07 0.12
Matches are distributed among these distances:
193 4 0.02
194 21 0.09
195 18 0.07
196 9 0.04
199 1 0.00
200 2 0.01
202 2 0.01
203 31 0.13
204 1 0.00
206 2 0.01
207 15 0.06
208 55 0.23
209 13 0.05
210 61 0.25
211 6 0.02
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (199 bp):
TTCATCAACAATCAAATTAACTATATAATATATATTTAAAAATTAAAAACAAAATTAACTATAAT
TTACTTAATTAAAAAATAAAATATACATCTACTTATTAAAATTTTCTCCTTCTTCTTTCCTTTTC
TCCTTCTTTTCCTTTACAATTTTTTCATTCTTCTCAAACTACATGCATAATTTAAAATTATAATA
ACAT
Found at i:313407 original size:47 final size:48
Alignment explanation
Indices: 313356--313548 Score: 180
Period size: 47 Copynumber: 3.9 Consensus size: 48
313346 GACTCTGGAC
* *
313356 CTCATCT-AATGTCTAGTGTATATTCCTGATGCTATGTGACCCCATGT
1 CTCATCTGAATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGT
* * * *
313403 CTCAT-TCG-ATGTCGGGTGTACGTTCCTGATGTTGTGTGACCCCAAT-T
1 CTCATCT-GAATGTCGAGTGTACATTCCTGATGCTATGTGACCCC-ATGT
*
313450 CTCATCTGAGGATGGATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGC
1 CTCATCT---GA---ATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGT
* * *
313504 CTCACCTGATTG-CTGAGTGTACATTCCTGATGTTATGTGACCCCA
1 CTCATCTGAATGTC-GAGTGTACATTCCTGATGCTATGTGACCCCA
313549 AACCTCACTT
Statistics
Matches: 119, Mismatches: 15, Indels: 23
0.76 0.10 0.15
Matches are distributed among these distances:
46 1 0.01
47 41 0.34
48 35 0.29
50 1 0.01
51 2 0.02
53 2 0.02
54 37 0.31
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (48 bp):
CTCATCTGAATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGT
Found at i:313541 original size:48 final size:47
Alignment explanation
Indices: 313464--313591 Score: 159
Period size: 48 Copynumber: 2.7 Consensus size: 47
313454 TCTGAGGATG
* **
313464 GATGTCGAGTGTACATTCCTGATGCTATGTGACCCCATGCCTCACCT
1 GATGCCGAGTGTACATTCCTGATGCTATGTGACCCCAAACCTCACCT
* * *
313511 GATTGCTGAGTGTACATTCCTGATGTTATGTGACCCCAAACCTCACTT
1 GA-TGCCGAGTGTACATTCCTGATGCTATGTGACCCCAAACCTCACCT
* *
313559 GATGCCG-GATATACGTTCCTGATGCTATGTGAC
1 GATGCCGAG-TGTACATTCCTGATGCTATGTGAC
313592 TTAAGGCCTC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 1 0.01
47 27 0.39
48 41 0.59
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (47 bp):
GATGCCGAGTGTACATTCCTGATGCTATGTGACCCCAAACCTCACCT
Found at i:313951 original size:31 final size:31
Alignment explanation
Indices: 313817--313944 Score: 168
Period size: 31 Copynumber: 4.1 Consensus size: 31
313807 TCATGGATGA
*
313817 GTAGGTGAATGATAACATGCTTAAGCAGCGT
1 GTAGGTGAATGATAACATGCTTAAGTAGCGT
*
313848 GTAGGTGAATGATAACATGCTTGAA-TAGTGT
1 GTAGGTGAATGATAACATGCTT-AAGTAGCGT
* * **
313879 GTAGGTAAATGATAAAATGCTTAAGTAATGT
1 GTAGGTGAATGATAACATGCTTAAGTAGCGT
* *
313910 GTATGTGAATGATAACATGCTTGAGTAGCGT
1 GTAGGTGAATGATAACATGCTTAAGTAGCGT
313941 GTAG
1 GTAG
313945 ACGAATGTTG
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
30 2 0.02
31 79 0.95
32 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (31 bp):
GTAGGTGAATGATAACATGCTTAAGTAGCGT
Found at i:314546 original size:23 final size:22
Alignment explanation
Indices: 314487--314547 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
314477 ACAAATATAT
314487 CAAACTAACATATTAC-A-ACA
1 CAAACTAACATATTACAATACA
* *
314507 -AAAATAACA-ATCCACAATACA
1 CAAACTAACATAT-TACAATACA
314528 CCAAACTAACATATTACAAT
1 -CAAACTAACATATTACAAT
314548 CATCCCTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
18 2 0.06
19 10 0.32
20 1 0.03
21 3 0.10
23 13 0.42
24 2 0.06
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.20
Consensus pattern (22 bp):
CAAACTAACATATTACAATACA
Found at i:315638 original size:2 final size:2
Alignment explanation
Indices: 315631--315663 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
315621 CTAATAAGAC
315631 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
315664 TTCTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:320748 original size:60 final size:60
Alignment explanation
Indices: 320654--320806 Score: 166
Period size: 60 Copynumber: 2.5 Consensus size: 60
320644 GATGACTCTG
* ** * * * *
320654 GGGATGAAAAT-GAAATATTCAAAAGTTTGGGGACTGATTTAGAAA-GAGGGTCATAGTTTA
1 GGGATGAAATTAG-AATATTCAAAAGTTTAAGGACTAATTTA-AAATGAGAGTCACAATTTA
* * *
320714 TGGATGAAATTAGAATGTTCAAAATTTTAAGGACTAATTTAAAATGAGAGTCACAATTTA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCACAATTTA
**
320774 GGGATGGCATTAGAATATTCAAAAGTTTAAGGA
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGA
320807 TCAATATAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
59 3 0.04
60 72 0.95
61 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.30
Consensus pattern (60 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAAAATGAGAGTCACAATTTA
Found at i:326402 original size:30 final size:29
Alignment explanation
Indices: 326366--326441 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
326356 TATTGGCGAT
* *
326366 TTTCCCGATATATCACTGGTGAATAATATA
1 TTTCCCGATATAACACCGGT-AATAATATA
* * *
326396 TTTCCCGATCTAACACCGGTCATATTATA
1 TTTCCCGATATAACACCGGTAATAATATA
*
326425 TTTCCCGATCTAACACC
1 TTTCCCGATATAACACC
326442 CTTAGCAGTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 24 0.59
30 17 0.41
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (29 bp):
TTTCCCGATATAACACCGGTAATAATATA
Found at i:332868 original size:51 final size:51
Alignment explanation
Indices: 332717--332871 Score: 181
Period size: 51 Copynumber: 3.1 Consensus size: 51
332707 CCCCCTGCAC
* * * * *
332717 CGCGCTATACCCCACGTGTCAG--ATATCAAGGTATAGCGCGCTGCAGGGGC
1 CGCGCTATACCCCACGTGAC-GCCAAATCAACGTATAGCGCGGTGCAGGGGG
* * *
332767 CGCGCTATA-CCCACGTGTATGCCAGATCACCGTATAGCGCGGTGCAGGGGG
1 CGCGCTATACCCCACGTG-ACGCCAAATCAACGTATAGCGCGGTGCAGGGGG
* *
332818 CGCGCTATACCCCACGTGGCGCCAAATCATCGTATAGCGCGGTGCAGGGGG
1 CGCGCTATACCCCACGTGACGCCAAATCAACGTATAGCGCGGTGCAGGGGG
332869 CGC
1 CGC
332872 TTTACTGCTA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
49 9 0.10
50 9 0.10
51 64 0.71
52 8 0.09
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (51 bp):
CGCGCTATACCCCACGTGACGCCAAATCAACGTATAGCGCGGTGCAGGGGG
Found at i:340218 original size:15 final size:14
Alignment explanation
Indices: 340184--340218 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
340174 TTATTAATTC
340184 TTTAAAATTATTTT
1 TTTAAAATTATTTT
340198 TTTAAAATTATTTT
1 TTTAAAATTATTTT
340212 TTATAAA
1 TT-TAAA
340219 TTTTATGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTAAAATTATTTT
Found at i:340380 original size:13 final size:14
Alignment explanation
Indices: 340335--340379 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
340325 TGAAAATTTC
*
340335 TAAATTATAGTGAG
1 TAAAATATAGTGAG
* *
340349 TGAAATA-AGAGAG
1 TAAAATATAGTGAG
340362 TAAAATATAGTGAG
1 TAAAATATAGTGAG
340376 TAAA
1 TAAA
340380 TTTATAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (14 bp):
TAAAATATAGTGAG
Found at i:344476 original size:38 final size:38
Alignment explanation
Indices: 344407--344529 Score: 142
Period size: 37 Copynumber: 3.3 Consensus size: 38
344397 TATTCCACTT
** *
344407 GAATATAAATTTGT-AATAATATATTCATATTTTAATT
1 GAATATAAATTCATAAATAATATATTCATATTTTAATC
* * **
344444 GAATATAAGTTCATAAATTATATATTTGTA-TTTAATC
1 GAATATAAATTCATAAATAATATATTCATATTTTAATC
* * *
344481 AAATATAAATTCATAAATAATATATTCCTATTTCAATC
1 GAATATAAATTCATAAATAATATATTCATATTTTAATC
344519 GAATATAAATT
1 GAATATAAATT
344530 TGTAATTTTA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
37 42 0.60
38 28 0.40
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (38 bp):
GAATATAAATTCATAAATAATATATTCATATTTTAATC
Found at i:357454 original size:20 final size:19
Alignment explanation
Indices: 357382--357460 Score: 52
Period size: 20 Copynumber: 3.8 Consensus size: 19
357372 TTGGTGCAGA
*
357382 GGGAATCGA-TCCCCCCATG
1 GGGAACCGATTCCCCCCA-G
357401 AGGGAACCGATTCCCCCTTTGCAG
1 -GGGAACCGATTCCCCC----CAG
*
357425 AGGAACCGATTCCCCCACAG
1 GGGAACCGATTCCCCC-CAG
* *
357445 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
357461 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 24 0.50
21 6 0.12
23 15 0.31
24 1 0.02
25 2 0.04
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.15
Consensus pattern (19 bp):
GGGAACCGATTCCCCCCAG
Found at i:357460 original size:43 final size:44
Alignment explanation
Indices: 357376--357461 Score: 106
Period size: 43 Copynumber: 2.0 Consensus size: 44
357366 AGCATTTTGG
* *
357376 TGCAGAGGGAATCGATCCCCCCATGAGGGAACCGATTCCCCCTT
1 TGCAGAGGGAACCGATCCCCCCATGAGGGAACCGATACCCCCTT
*
357420 TGCAGA-GGAACCGATTCCCCCACA-G-GGGAATCGATACCCCCT
1 TGCAGAGGGAACCGA-TCCCCC-CATGAGGGAACCGATACCCCCT
357462 GGGGTTCTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 22 0.59
44 13 0.35
45 2 0.05
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.16
Consensus pattern (44 bp):
TGCAGAGGGAACCGATCCCCCCATGAGGGAACCGATACCCCCTT
Found at i:359719 original size:9 final size:9
Alignment explanation
Indices: 359705--359732 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
359695 AGAGTGTGTG
359705 TTTTTAAAA
1 TTTTTAAAA
359714 TTTTTAAAA
1 TTTTTAAAA
359723 TTTTTAAAA
1 TTTTTAAAA
359732 T
1 T
359733 GATAAATGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:361390 original size:38 final size:38
Alignment explanation
Indices: 361323--361449 Score: 161
Period size: 37 Copynumber: 3.4 Consensus size: 38
361313 ATTCCACTTT
*
361323 AATATAAATTCGT-AATAATATATTCGTATTTTAATTG
1 AATATAAATTCATAAATAATATATTCGTATTTTAATTG
* *
361360 AATATAAATTCATAAATTATATATTTGTA--TTAATTG
1 AATATAAATTCATAAATAATATATTCGTATTTTAATTG
* * * *
361396 AAATATAAATTTATAAATAATATATTCCTATTTCAATAG
1 -AATATAAATTCATAAATAATATATTCGTATTTTAATTG
361435 AATATAAATTCATAA
1 AATATAAATTCATAA
361450 TTTTAATTGA
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
36 7 0.09
37 37 0.49
38 27 0.36
39 5 0.07
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (38 bp):
AATATAAATTCATAAATAATATATTCGTATTTTAATTG
Found at i:361703 original size:20 final size:20
Alignment explanation
Indices: 361638--361709 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
361628 TCTGAACAAG
* *
361638 TAGTACTGATACTATTCTTA
1 TAGTACCGATACTATTCATA
* * *
361658 CAGTATCGATACTATATGA-A
1 TAGTACCGATACTAT-TCATA
361678 TAGTACCGATACTATTCATA
1 TAGTACCGATACTATTCATA
*
361698 TGGTACCGATAC
1 TAGTACCGATAC
361710 AAAAGGTAAG
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
19 2 0.05
20 38 0.93
21 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (20 bp):
TAGTACCGATACTATTCATA
Found at i:361853 original size:20 final size:21
Alignment explanation
Indices: 361828--361867 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
361818 CTTTACATAG
361828 TAGTATCGATACCAT-AGACT
1 TAGTATCGATACCATCAGACT
361848 TAGTATCGATACCATCAGAC
1 TAGTATCGATACCATCAGAC
361868 CCAACAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGACT
Found at i:371219 original size:22 final size:23
Alignment explanation
Indices: 371159--371224 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 23
371149 TTCTCAATAA
* *
371159 TTCTGCATTTGTGACACATTTT-
1 TTCTGCCTTTGTGGCACATTTTC
*
371181 TT-TGTCTTTGTGGCACATTTTC
1 TTCTGCCTTTGTGGCACATTTTC
371203 TTCTGCCTTT-TGGCACATTTTC
1 TTCTGCCTTTGTGGCACATTTTC
371225 GATCATTTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.42
22 16 0.42
23 6 0.16
ACGTcount: A:0.12, C:0.21, G:0.15, T:0.52
Consensus pattern (23 bp):
TTCTGCCTTTGTGGCACATTTTC
Found at i:379263 original size:17 final size:18
Alignment explanation
Indices: 379224--379270 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
379214 TATTTCTGAT
379224 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
379242 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
379259 GGAATTGGAATC
1 GGAATTGGAATC
379271 CAATTCCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:379344 original size:44 final size:44
Alignment explanation
Indices: 379260--379344 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
379250 AATCTGTCAG
*
379260 GAATTGGAATCCAATTCCATATTCTGTTTGGTTGGCAGAAAATT
1 GAATTGGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAAATT
*
379304 GAATTGGAATCCAATTCCATATTCTGTTTGGTTCGTAGAAA
1 GAATTGGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAA
379345 TGTCAGATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.36
Consensus pattern (44 bp):
GAATTGGAATCCAATTCCATATTCTGTTTGGTTCGCAGAAAATT
Found at i:382181 original size:59 final size:59
Alignment explanation
Indices: 382088--382207 Score: 181
Period size: 59 Copynumber: 2.0 Consensus size: 59
382078 GCCCAACGAC
382088 TAGTAACAGCTAGTTTTATTTAAAAATAAAAAAGGAAGTA-CTGATACTCCATGTAGGAG
1 TAGTAACAGCTAGTTTTATTTAAAAATAAAAAAGGAAGTATC-GATACTCCATGTAGGAG
* * *
382147 TAGTAAC-GACTAGTTTTATTTAAAAATAACAAAGGCAGTATCGATACTCCGTGTAGGAG
1 TAGTAACAG-CTAGTTTTATTTAAAAATAAAAAAGGAAGTATCGATACTCCATGTAGGAG
382206 TA
1 TA
382208 CCCTCTGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
58 1 0.02
59 54 0.96
60 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (59 bp):
TAGTAACAGCTAGTTTTATTTAAAAATAAAAAAGGAAGTATCGATACTCCATGTAGGAG
Found at i:386883 original size:17 final size:17
Alignment explanation
Indices: 386861--386916 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
386851 CCGTTAACTG
*
386861 TTGACCGCCTTTGACCA
1 TTGACCGCCGTTGACCA
* *
386878 TTGACCGTCGTTGACCG
1 TTGACCGCCGTTGACCA
* * *
386895 TTGATCGTCGTTGACCG
1 TTGACCGCCGTTGACCA
386912 TTGAC
1 TTGAC
386917 TTTGACCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.14, C:0.29, G:0.25, T:0.32
Consensus pattern (17 bp):
TTGACCGCCGTTGACCA
Found at i:390290 original size:24 final size:24
Alignment explanation
Indices: 390262--390315 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
390252 TTTTTTTTTC
390262 TGATTTCTGCTCTGAATTCTATTA
1 TGATTTCTGCTCTGAATTCTATTA
* * * *
390286 TGATTTCTTCTTTTAATTCTATTC
1 TGATTTCTGCTCTGAATTCTATTA
390310 TGATTT
1 TGATTT
390316 TTGATATCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (24 bp):
TGATTTCTGCTCTGAATTCTATTA
Found at i:390498 original size:31 final size:31
Alignment explanation
Indices: 390460--390536 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 31
390450 TAAGGCGACC
* * *
390460 CTTGGGTAGGCTCTGCGGCCCTGAGATTTTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAATTAT
* * *
390491 CTTGGGTAAGCCTTTGTGGCCCCGAGAATTAT
1 CTTGGGT-AGGCTCTGCGGCCCCGAGAATTAT
*
390523 CTTAGGTAGGCTCT
1 CTTGGGTAGGCTCT
390537 CATGCCCCAA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.14, C:0.22, G:0.30, T:0.34
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGCGGCCCCGAGAATTAT
Found at i:394900 original size:54 final size:55
Alignment explanation
Indices: 394841--394954 Score: 185
Period size: 56 Copynumber: 2.1 Consensus size: 55
394831 ATATACTATT
*
394841 ATATGTATTTATAATGAGTTC-TTTTGTATAAAATCTTGATATTATATATTATGA
1 ATATGTATTTATAATGAGTTCTTTTTGTATAAAATCTTGATATTATATATTATAA
* *
394895 ATATGTATTTATTATGAGTTCTTTTTTGTATAGAATCTTGATATTATATATTATAA
1 ATATGTATTTATAATGAGTTC-TTTTTGTATAAAATCTTGATATTATATATTATAA
394951 ATAT
1 ATAT
394955 TTTATATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
54 20 0.36
56 35 0.64
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (55 bp):
ATATGTATTTATAATGAGTTCTTTTTGTATAAAATCTTGATATTATATATTATAA
Found at i:395150 original size:8 final size:8
Alignment explanation
Indices: 395137--395165 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
395127 ATTTTAATAA
395137 TTTTTTAT
1 TTTTTTAT
395145 TTTTTTAT
1 TTTTTTAT
395153 TTTTTTAT
1 TTTTTTAT
395161 TTTTT
1 TTTTT
395166 ATATATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:398563 original size:135 final size:137
Alignment explanation
Indices: 398340--398613 Score: 525
Period size: 135 Copynumber: 2.0 Consensus size: 137
398330 ACCTTATAAT
398340 TGAAGCAAAGGAAATCCAAATACAATTGGTATTGTGTTTAGCTATCACATGAACTAAATTAATTA
1 TGAAGCAAAGGAAATCCAAATACAATTGGTATTGTGTTTAGCTATCACATGAACTAAATTAATTA
*
398405 TTGATTTTATTTAATCTGACAGCTTAATATTGAACAAGTTTATGTACAAATTTGTTCTACACTCA
66 TTGATTTTATTTAATCGGACAGCTTAATATTGAACAAGTTTATGTACAAATTTGTTCTACACTCA
398470 ATGAGAA
131 ATGAGAA
398477 TGAAGCAAAGGAAATCCAAATACAATTGGTA-TGTGTTTAGCTATCACATGAACT-AATTAATTA
1 TGAAGCAAAGGAAATCCAAATACAATTGGTATTGTGTTTAGCTATCACATGAACTAAATTAATTA
398540 TTGATTTTATTTAATCGGACAGCTTAATATTGAACAAGTTTATGTACAAATTTGTTCTACACTCA
66 TTGATTTTATTTAATCGGACAGCTTAATATTGAACAAGTTTATGTACAAATTTGTTCTACACTCA
398605 ATGAGAA
131 ATGAGAA
398612 TG
1 TG
398614 TATTAAAAAT
Statistics
Matches: 136, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
135 82 0.60
136 23 0.17
137 31 0.23
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (137 bp):
TGAAGCAAAGGAAATCCAAATACAATTGGTATTGTGTTTAGCTATCACATGAACTAAATTAATTA
TTGATTTTATTTAATCGGACAGCTTAATATTGAACAAGTTTATGTACAAATTTGTTCTACACTCA
ATGAGAA
Found at i:401238 original size:28 final size:29
Alignment explanation
Indices: 401186--401317 Score: 203
Period size: 29 Copynumber: 4.6 Consensus size: 29
401176 CTTTTTTTTT
*
401186 AAATATTTACGAAAATAGCATCTTTTTAA
1 AAATAATTACGAAAATAGCATCTTTTTAA
401215 AAATAATTACGAAAATAGCA-CTTTTTAA
1 AAATAATTACGAAAATAGCATCTTTTTAA
*
401243 AAATAATTACGAAAATAACATCTTTTTAA
1 AAATAATTACGAAAATAGCATCTTTTTAA
* *
401272 AAATAATTACGGAAATAGCACCTTTTTAA
1 AAATAATTACGAAAATAGCATCTTTTTAA
* *
401301 AAATATTTACAAAAATA
1 AAATAATTACGAAAATA
401318 TCACCGGGTC
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
28 27 0.29
29 67 0.71
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (29 bp):
AAATAATTACGAAAATAGCATCTTTTTAA
Found at i:401253 original size:57 final size:58
Alignment explanation
Indices: 401186--401317 Score: 221
Period size: 57 Copynumber: 2.3 Consensus size: 58
401176 CTTTTTTTTT
*
401186 AAATATTTACGAAAATAGCATCTTTTTAAAAATAATTACGAAAATAGCA-CTTTTTAA
1 AAATATTTACGAAAATAACATCTTTTTAAAAATAATTACGAAAATAGCACCTTTTTAA
* *
401243 AAATAATTACGAAAATAACATCTTTTTAAAAATAATTACGGAAATAGCACCTTTTTAA
1 AAATATTTACGAAAATAACATCTTTTTAAAAATAATTACGAAAATAGCACCTTTTTAA
*
401301 AAATATTTACAAAAATA
1 AAATATTTACGAAAATA
401318 TCACCGGGTC
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
57 46 0.67
58 23 0.33
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (58 bp):
AAATATTTACGAAAATAACATCTTTTTAAAAATAATTACGAAAATAGCACCTTTTTAA
Found at i:401359 original size:10 final size:10
Alignment explanation
Indices: 401344--401368 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
401334 ACGGGTCAAC
401344 CCGGTTCAGA
1 CCGGTTCAGA
401354 CCGGTTCAGA
1 CCGGTTCAGA
401364 CCGGT
1 CCGGT
401369 CAAGCCGGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.20
Consensus pattern (10 bp):
CCGGTTCAGA
Found at i:402458 original size:14 final size:14
Alignment explanation
Indices: 402432--402469 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
402422 TTAGTTTATA
402432 TAATTTT-ATATTT
1 TAATTTTGATATTT
*
402445 TGATTTTGATATTT
1 TAATTTTGATATTT
402459 TAATTTTGATA
1 TAATTTTGATA
402470 AAATTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (14 bp):
TAATTTTGATATTT
Found at i:410996 original size:58 final size:58
Alignment explanation
Indices: 410922--411064 Score: 180
Period size: 58 Copynumber: 2.4 Consensus size: 58
410912 TTGAGTTCTT
* * *
410922 CGACCATTAAAAATTACAAAATGATCCATCAACTATAGTTTGATGC-TTGTTAAGTATA
1 CGACTATT-AAAATTACAAAATGATCCATCAACTATAGGTTGATGCTTTGTTAAGTACA
* * * *
410980 CGACTATTAAATATTACAAAATGATCCTTCGACTATAGGTTGTTGCTTTGTTAAGTCCA
1 CGACTATTAAA-ATTACAAAATGATCCATCAACTATAGGTTGATGCTTTGTTAAGTACA
*
411039 CAACTATTAAAAGTTACAAAATGATC
1 CGACTATTAAAA-TTACAAAATGATC
411065 ACTCGACTAT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 3 0.04
58 38 0.51
59 33 0.45
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.34
Consensus pattern (58 bp):
CGACTATTAAAATTACAAAATGATCCATCAACTATAGGTTGATGCTTTGTTAAGTACA
Found at i:411060 original size:59 final size:56
Alignment explanation
Indices: 410931--411074 Score: 180
Period size: 59 Copynumber: 2.5 Consensus size: 56
410921 TCGACCATTA
* * * *
410931 AAAATTACAAAATGATCCATCAACTATAGTTTGATGCTTGTTAAGTATACGACTATT
1 AAAATTACAAAATGATCC-TCGACTATAGGTTGATGCTTGTTAAGTACACAACTATT
* *
410988 AAATATTACAAAATGATCCTTCGACTATAGGTTGTTGCTTTGTTAAGTCCACAACTATT
1 AAA-ATTACAAAATGATCC-TCGACTATAGGTTGATGC-TTGTTAAGTACACAACTATT
411047 AAAAGTTACAAAATGATCACTCGACTAT
1 AAAA-TTACAAAATGATC-CTCGACTAT
411075 TTAGTATGTT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
57 3 0.04
58 31 0.41
59 41 0.54
60 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (56 bp):
AAAATTACAAAATGATCCTCGACTATAGGTTGATGCTTGTTAAGTACACAACTATT
Found at i:419403 original size:20 final size:21
Alignment explanation
Indices: 419378--419437 Score: 86
Period size: 20 Copynumber: 2.8 Consensus size: 21
419368 TTTGGTGCAG
*
419378 AGGGAATCGATTCCCCCTTT-
1 AGGGAACCGATTCCCCCTTTA
419398 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCTTT-A
419420 AGGGGAACCGATTCCCCC
1 A-GGGAACCGATTCCCCC
419438 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.23, T:0.22
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCTTTA
Found at i:419446 original size:21 final size:21
Alignment explanation
Indices: 419420--419459 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
419410 CCCCCTTTGA
*
419420 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
419441 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
419460 TGGGGTTCTG
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:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:422957 original size:21 final size:21
Alignment explanation
Indices: 422933--422983 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
422923 TTCCAAATAC
*
422933 AACTCATTATAAGCAACTTAT
1 AACTCATCATAAGCAACTTAT
*
422954 AACTCATCATAAGCAACTTGT
1 AACTCATCATAAGCAACTTAT
422975 AACTCATCA
1 AACTCATCA
422984 AAAGAATAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.29
Consensus pattern (21 bp):
AACTCATCATAAGCAACTTAT
Found at i:425367 original size:60 final size:60
Alignment explanation
Indices: 425271--425445 Score: 271
Period size: 60 Copynumber: 2.9 Consensus size: 60
425261 AATAGGCGGT
* *
425271 GACCATTTTGTAACTTTTGATAGTCGGAGGACTCAACAATGCAACACCCTATAGTCGAAG
1 GACCATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACCCTATAGTCGAAG
* *
425331 GATCATTTTGTAACTTTTAATAGTCGGATGACTCAACAAAGCAACACCCTATAGTCGAAG
1 GACCATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACCCTATAGTCGAAG
* * *
425391 GACCATTTTGTAACTTTAAATAGTC-GACGGACTCAACAAAGCATCATCCTATAGT
1 GACCATTTTGTAACTTTTAATAGTCGGA-GGACTCAACAAAGCAACACCCTATAGT
425446 ATAGGGACCA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
59 2 0.02
60 103 0.98
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGGAGGACTCAACAAAGCAACACCCTATAGTCGAAG
Found at i:425467 original size:60 final size:60
Alignment explanation
Indices: 425271--425468 Score: 229
Period size: 60 Copynumber: 3.3 Consensus size: 60
425261 AATAGGCGGT
* ** * *
425271 GACCATTTTGTAACTTTTGATAGTCGGAGGACTCAACAATGCAACACCCTATAGTCGAAG
1 GACCATCTTGTAACTTTAAATAGTCGGAGGACTCAACAAAGCAACACCCTATAGTAGAAG
* * * * *
425331 GATCATTTTGTAACTTTTAATAGTCGGATGACTCAACAAAGCAACACCCTATAGTCGAAG
1 GACCATCTTGTAACTTTAAATAGTCGGAGGACTCAACAAAGCAACACCCTATAGTAGAAG
* * * * *
425391 GACCATTTTGTAACTTTAAATAGTC-GACGGACTCAACAAAGCATCATCCTATAGTATAGG
1 GACCATCTTGTAACTTTAAATAGTCGGA-GGACTCAACAAAGCAACACCCTATAGTAGAAG
425451 GACCA-CTTGTATACTTTA
1 GACCATCTTGTA-ACTTTA
425469 CCTTTTTTAT
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
59 7 0.06
60 116 0.94
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (60 bp):
GACCATCTTGTAACTTTAAATAGTCGGAGGACTCAACAAAGCAACACCCTATAGTAGAAG
Found at i:435135 original size:22 final size:23
Alignment explanation
Indices: 435092--435135 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
435082 TCAACGCAAA
*
435092 AAAATAAATCATAAATGAATATT
1 AAAATAAAGCATAAATGAATATT
* *
435115 AAAAT-AAGCATACATGCATAT
1 AAAATAAAGCATAAATGAATAT
435136 GTGGTGATCG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.27
Consensus pattern (23 bp):
AAAATAAAGCATAAATGAATATT
Found at i:436091 original size:74 final size:77
Alignment explanation
Indices: 435971--436159 Score: 257
Period size: 74 Copynumber: 2.5 Consensus size: 77
435961 CCGTTGTACA
* * * *
435971 AGGGGAGAATCGGTACC-CCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTC-GAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
436033 -CAAAACTGTTT
66 CCAAAACCATTT
* *
436044 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
436108 CCAAAACCATTT
66 CCAAAACCATTT
436120 A--GGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTC
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTC
436160 TGAGTAATCT
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
73 15 0.15
74 57 0.55
75 21 0.20
76 10 0.10
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:438755 original size:21 final size:21
Alignment explanation
Indices: 438721--438780 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
438711 AACAGAACCC
438721 CAGGGGGGATATCGATTCCCCT
1 CAGGGGGGA-ATCGATTCCCCT
** *
438743 GTGGGGGGAATCGGTT-CCCT
1 CAGGGGGGAATCGATTCCCCT
438763 CAGGGGGG-ATCGATTCCC
1 CAGGGGGGAATCGATTCCC
438781 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 6 0.19
20 12 0.39
21 6 0.19
22 7 0.23
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (21 bp):
CAGGGGGGAATCGATTCCCCT
Found at i:438774 original size:19 final size:20
Alignment explanation
Indices: 438721--438782 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
438711 AACAGAACCC
438721 CAGGGGGGATATCGATTCCCCT
1 CAGGGGGGA-ATCGATT-CCCT
** *
438743 GTGGGGGGAATCGGTTCCCT
1 CAGGGGGGAATCGATTCCCT
438763 CAGGGGGG-ATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
438782 C
1 C
438783 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
19 11 0.32
20 10 0.29
21 6 0.18
22 7 0.21
ACGTcount: A:0.15, C:0.26, G:0.37, T:0.23
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Found at i:442631 original size:22 final size:21
Alignment explanation
Indices: 442589--442628 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
442579 AAGTTTGTTT
*
442589 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
442610 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
442629 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:444681 original size:77 final size:78
Alignment explanation
Indices: 444551--444761 Score: 295
Period size: 77 Copynumber: 2.8 Consensus size: 78
444541 CCGTTGTACA
* * *
444551 AGGGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGA
**
444614 G-CAAAACTGTTT
66 GCCAAAACCATTT
* *
444626 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGA
444691 GCCAAAACCATTT
66 GCCAAAACCATTT
* * * *
444704 A-GGGGGAATCGGTTCCTCATATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
444762 TTTGGCTTTG
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 19 0.16
76 8 0.07
77 84 0.69
78 10 0.08
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (78 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGA
GCCAAAACCATTT
Found at i:445385 original size:16 final size:17
Alignment explanation
Indices: 445364--445395 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
445354 TCTCTAGTCC
445364 TCATCTCTA-CTCTACA
1 TCATCTCTATCTCTACA
445380 TCATCTCTATCTCTAC
1 TCATCTCTATCTCTAC
445396 TCTAAAGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.22, C:0.38, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATCTCTATCTCTACA
Found at i:445749 original size:21 final size:22
Alignment explanation
Indices: 445710--445762 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
445700 TAGAACAAAA
*
445710 TTAATATGTTTATTCATCTAATT
1 TTAATATATTTATTCATCT-ATT
445733 TTAATATATTT-TT-ATCTATT
1 TTAATATATTTATTCATCTATT
445753 TT-ATA-ATTTA
1 TTAATATATTTA
445763 ATAATAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 5 0.18
21 4 0.14
22 2 0.07
23 10 0.36
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAATATATTTATTCATCTATT
Found at i:451486 original size:16 final size:14
Alignment explanation
Indices: 451436--451482 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
451426 CAGATGCTTC
*
451436 TTTTTCAGTCTGCT
1 TTTTTCAATCTGCT
451450 TTTTTCAATCTGCT
1 TTTTTCAATCTGCT
451464 TTTTTCAATCTGCT
1 TTTTTCAATCTGCT
451478 TTTTT
1 TTTTT
451483 TTCAGTGCCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.11, C:0.19, G:0.09, T:0.62
Consensus pattern (14 bp):
TTTTTCAATCTGCT
Found at i:451965 original size:35 final size:37
Alignment explanation
Indices: 451882--451972 Score: 118
Period size: 35 Copynumber: 2.5 Consensus size: 37
451872 GTTGAACAAA
* *
451882 TTCTTCTCATTATAAACT-TCTCCCTTGTTGGATGAG
1 TTCTTCTCATTATGAACTCTCTCCCTTGTTGGATAAG
*
451918 TTCTTCTAATTATGAACTCTCT-CCTT-TAT-GATAAG
1 TTCTTCTCATTATGAACTCTCTCCCTTGT-TGGATAAG
451953 TTCTTCTCATTATGAACTCT
1 TTCTTCTCATTATGAACTCT
451973 TCATTAGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 25 0.51
36 21 0.43
37 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (37 bp):
TTCTTCTCATTATGAACTCTCTCCCTTGTTGGATAAG
Found at i:452153 original size:130 final size:131
Alignment explanation
Indices: 451919--452240 Score: 463
Period size: 130 Copynumber: 2.4 Consensus size: 131
451909 TTGGATGAGT
* * * *
451919 TCTTCTAATTATGAAC-TCTCTCCT-TTATGATAAGTTCTTCTCATTATGAACTCTTCATTAGAA
1 TCTTCTCATTATGAACTTCTCTCCTCTT-TGATGAGTTCTTCTCATTATGAACTC-TCCTGAGAA
**
451982 ATGTTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACA
64 ATGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACA
452047 AGC
129 AGC
452050 TCTTCTCATTATGAACTTCT-TCCTCGTTTGATGAGTTCTTCTCATTATGAACTCTCCTGA-AAA
1 TCTTCTCATTATGAACTTCTCTCCTC-TTTGATGAGTTCTTCTCATTATGAACTCTCCTGAGAAA
* * *
452113 TGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCGAACAA
65 TGTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACAA
452178 GC
130 GC
*
452180 TCTTCTCATTATGAACTTCTTCTCCCTCTGTTGAATGAGTTTTTCTCATTATGAACTCTCC
1 TCTTCTCATTATGAACTTC-TCT-CCTCT-TTG-ATGAGTTCTTCTCATTATGAACTCTCC
452241 ATTGGAAATG
Statistics
Matches: 173, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
130 84 0.49
131 24 0.14
132 30 0.17
133 9 0.05
134 26 0.15
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (131 bp):
TCTTCTCATTATGAACTTCTCTCCTCTTTGATGAGTTCTTCTCATTATGAACTCTCCTGAGAAAT
GTCAATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGTCAAACAAG
C
Found at i:453141 original size:8 final size:8
Alignment explanation
Indices: 453130--453206 Score: 59
Period size: 8 Copynumber: 9.5 Consensus size: 8
453120 CCTTTTTCTC
453130 TTTTCATT
1 TTTTCATT
453138 TTTTCATT
1 TTTTCATT
*
453146 TTTTCATCA
1 TTTTCAT-T
453155 TTTT--TT
1 TTTTCATT
**
453161 TCATCATT
1 TTTTCATT
453169 TTTTCATTTT
1 TTTTCA--TT
453179 TTTTCATT
1 TTTTCATT
*
453187 TTTTTATT
1 TTTTCATT
* *
453195 TGTTCCTT
1 TTTTCATT
453203 TTTT
1 TTTT
453207 TCCTTCAAGC
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
6 2 0.04
7 1 0.02
8 38 0.72
9 4 0.08
10 8 0.15
ACGTcount: A:0.12, C:0.13, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTCATT
Found at i:453157 original size:11 final size:11
Alignment explanation
Indices: 453141--453185 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
453131 TTTCATTTTT
453141 TCATTTTTTCA
1 TCATTTTTTCA
453152 TCATTTTTTTCA
1 TCA-TTTTTTCA
453164 TCATTTTTTCA
1 TCATTTTTTCA
*
453175 T-TTTTTTTCA
1 TCATTTTTTCA
453185 T
1 T
453186 TTTTTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 9 0.28
11 12 0.38
12 11 0.34
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (11 bp):
TCATTTTTTCA
Found at i:453161 original size:12 final size:12
Alignment explanation
Indices: 453144--453185 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
453134 CATTTTTTCA
453144 TTTTTTCATCAT
1 TTTTTTCATCAT
453156 TTTTTTCATCA-
1 TTTTTTCATCAT
453167 TTTTTTCAT--T
1 TTTTTTCATCAT
453177 TTTTTTCAT
1 TTTTTTCAT
453186 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.31
11 9 0.31
12 11 0.38
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTCATCAT
Found at i:453161 original size:20 final size:19
Alignment explanation
Indices: 453130--453191 Score: 72
Period size: 20 Copynumber: 3.2 Consensus size: 19
453120 CCTTTTTCTC
453130 TTTTCA-TTTTTTCATTTT
1 TTTTCATTTTTTTCATTTT
* *
453148 TTCATCATTTTTTTCATCATT
1 TT-TTCATTTTTTTCAT-TTT
453169 TTTTCATTTTTTTTCATTTT
1 TTTTCA-TTTTTTTCATTTT
453189 TTT
1 TTT
453192 ATTTGTTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.06
19 3 0.08
20 17 0.47
21 14 0.39
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCATTTTTTTCATTTT
Found at i:453167 original size:23 final size:21
Alignment explanation
Indices: 453141--453185 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 21
453131 TTTCATTTTT
453141 TCATTTTTTCATCATTTTTTTCA
1 TCATTTTTTCAT--TTTTTTTCA
453164 TCATTTTTTCATTTTTTTTCA
1 TCATTTTTTCATTTTTTTTCA
453185 T
1 T
453186 TTTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 10 0.45
23 12 0.55
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.69
Consensus pattern (21 bp):
TCATTTTTTCATTTTTTTTCA
Found at i:453171 original size:31 final size:30
Alignment explanation
Indices: 453133--453191 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
453123 TTTTCTCTTT
453133 TCATTTTTTCATTTTTTCATCATTTTTTTCA
1 TCATTTTTTCATTTTTT-ATCATTTTTTTCA
*
453164 TCATTTTTTCATTTTTTTTCATTTTTTT
1 TCATTTTTTCATTTTTTATCATTTTTTT
453192 ATTTGTTCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (30 bp):
TCATTTTTTCATTTTTTATCATTTTTTTCA
Found at i:453178 original size:18 final size:18
Alignment explanation
Indices: 453157--453195 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
453147 TTTCATCATT
453157 TTTTTCATCATTTTTTCA
1 TTTTTCATCATTTTTTCA
** *
453175 TTTTTTTTCATTTTTTTA
1 TTTTTCATCATTTTTTCA
453193 TTT
1 TTT
453196 GTTCCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTCATCATTTTTTCA
Found at i:453190 original size:12 final size:11
Alignment explanation
Indices: 453136--453191 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
453126 TCTCTTTTCA
453136 TTTTTTCATTT
1 TTTTTTCATTT
**
453147 TTTCATCA--T
1 TTTTTTCATTT
**
453156 TTTTTTCATCA
1 TTTTTTCATTT
453167 TTTTTTCA-TT
1 TTTTTTCATTT
453177 TTTTTTCATTT
1 TTTTTTCATTT
453188 TTTT
1 TTTT
453192 ATTTGTTCCT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
9 7 0.20
10 8 0.23
11 20 0.57
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTCATTT
Found at i:455667 original size:22 final size:22
Alignment explanation
Indices: 455642--455687 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
455632 GTTTACAAAT
*
455642 AGGGAATCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
455664 AGGGAACCGATTCCCCTGCTAC
1 AGGGAACCGATTCCCCTGCTAC
455686 AG
1 AG
455688 TACTTCCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCTGCTAC
Found at i:463087 original size:22 final size:22
Alignment explanation
Indices: 463056--463127 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
463046 CTGAGTGGCA
463056 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
* *
463079 TGTGAATTTGTCCCGAATGACC
1 TATGAATTTGTCCCGAAGGACC
*
463101 TATG-AGTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
463122 TATGAA
1 TATGAA
463128 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.44
22 21 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:463112 original size:21 final size:21
Alignment explanation
Indices: 463064--463126 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
463054 CATATGAAAT
* *
463064 TTGTCCCGAAGGACCTGTGAAT
1 TTGTCCCGAAGGACCTATG-AG
*
463086 TTGTCCCGAATGACCTATGAG
1 TTGTCCCGAAGGACCTATGAG
463107 TTGTCCCGAAGGACCTATGA
1 TTGTCCCGAAGGACCTATGA
463127 AACCCTCGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAG
Found at i:476355 original size:15 final size:15
Alignment explanation
Indices: 476335--476369 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
476325 GAACACGTTC
476335 TTCTCATTATGAACT
1 TTCTCATTATGAACT
476350 TTCTCATTATGAACT
1 TTCTCATTATGAACT
476365 TTCTC
1 TTCTC
476370 CTTCTGTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.49
Consensus pattern (15 bp):
TTCTCATTATGAACT
Found at i:480498 original size:3 final size:3
Alignment explanation
Indices: 480479--480570 Score: 76
Period size: 3 Copynumber: 29.3 Consensus size: 3
480469 GGTCAAAAAA
* * * * * * *
480479 TAT TAT TAGT TAC TAT TAT TAT TAAT AAT AAT AAT AAT AAT AAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT
*
480526 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TACT GAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
480571 TTTACATGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
3 69 0.87
4 10 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:480552 original size:28 final size:28
Alignment explanation
Indices: 480479--480570 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
480469 GGTCAAAAAA
*
480479 TATTATTAGTTACTATTATTATTAATAAT
1 TATTATTA-TTATTATTATTATTAATAAT
* * * * * *
480508 AATAATAATAATAATTATTATTAATTAT
1 TATTATTATTATTATTATTATTAATAAT
* *
480536 TATTATTATTATTATTATTATTACTGAT
1 TATTATTATTATTATTATTATTAATAAT
480564 TATTATT
1 TATTATT
480571 TTTACATGTT
Statistics
Matches: 49, Mismatches: 14, Indels: 1
0.77 0.22 0.02
Matches are distributed among these distances:
28 44 0.90
29 5 0.10
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTATTATTATTATTATTATTAATAAT
Found at i:482994 original size:16 final size:17
Alignment explanation
Indices: 482956--482995 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
482946 ACGCAGACCA
482956 GTTTTTATCTTAAAAAT
1 GTTTTTATCTTAAAAAT
* *
482973 GATTTT-TCTTAAAATT
1 GTTTTTATCTTAAAAAT
482989 GTTTTTA
1 GTTTTTA
482996 AAAGACATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (17 bp):
GTTTTTATCTTAAAAAT
Found at i:484271 original size:19 final size:19
Alignment explanation
Indices: 484247--484320 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
484237 TATCTCACAT
484247 AAAATAATATATTTATTAA
1 AAAATAATATATTTATTAA
* *
484266 AAAATATTATTTTTATTCAATA
1 AAAATAATATATTTATT--A-A
* *
484288 AAAATATAGATATTTAATTTA
1 AAAATA-ATATATTT-ATTAA
484309 AAAATAATATAT
1 AAAATAATATAT
484321 ATGGAGATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 15 0.35
20 5 0.12
21 8 0.19
22 7 0.16
23 5 0.12
24 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
AAAATAATATATTTATTAA
Found at i:485459 original size:34 final size:35
Alignment explanation
Indices: 485410--485477 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
485400 CGCAACATTC
485410 TTACATTCCAGTAATCTTATTCTC-AAATGTAATA
1 TTACATTCCAGTAATCTTATTCTCAAAATGTAATA
* *
485444 TTACATTCTATTAATCTTATTCTCAAAATGTAAT
1 TTACATTCCAGTAATCTTATTCTCAAAATGTAAT
485478 CTCACATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 22 0.71
35 9 0.29
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.44
Consensus pattern (35 bp):
TTACATTCCAGTAATCTTATTCTCAAAATGTAATA
Found at i:485485 original size:35 final size:34
Alignment explanation
Indices: 485412--485485 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 34
485402 CAACATTCTT
*
485412 ACATTCCAGTAATCTTATTCTCAAATGTAATATT
1 ACATTCCAGTAATCTTATTCTCAAATGTAATATC
* * *
485446 ACATTCTATTAATCTTATTCTCAAAATGTAATCTC
1 ACATTCCAGTAATCTTATTCTC-AAATGTAATATC
485481 ACATT
1 ACATT
485486 TCGTGAGCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 20 0.57
35 15 0.43
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (34 bp):
ACATTCCAGTAATCTTATTCTCAAATGTAATATC
Found at i:489826 original size:15 final size:15
Alignment explanation
Indices: 489806--489910 Score: 165
Period size: 15 Copynumber: 7.0 Consensus size: 15
489796 TAATAAGGTT
489806 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
489821 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
489836 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
489851 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
489866 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
489881 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
489896 AATTATTATAAAATA
1 ATTTATTTTAAAATA
489911 TGGATTGATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 84 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:489923 original size:22 final size:22
Alignment explanation
Indices: 489898--489948 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
489888 TTAAAATAAA
489898 TTATTATAAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
*
489920 TTATTTTAAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
489942 TTATTAT
1 TTATTAT
489949 TGTAGTTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TTATTATAAAATATGGATTGAT
Found at i:490000 original size:54 final size:54
Alignment explanation
Indices: 489959--490510 Score: 331
Period size: 54 Copynumber: 10.3 Consensus size: 54
489949 TGTAGTTGTG
489959 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
*
490013 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
* ** ** ** * * *
490067 TGAATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGATTTATTTATTTTA-AAATA
* *
490120 TGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
* * * * *
490174 TGGATTGATTTATTATT--GTAGTTGTA-T-GGATTGATTTATTTTAAATAATTTATTAATA
1 TGGATTGATTTATT-TTAAATAATT-TATTAGTATGGATTTA-TTT--AT--TTTA-AAATA
** ** ** * * *
490232 TGGATTGATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATA-ATTTATTAGTATGGA-TTTATTTATTTTA-AAATA
*
490286 TGGATTGATTTATTTT-AA-AA--TA-T-G-A---ATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
* ** * *
490330 TGGATTGATTTATTTTAAATAATTTATTAATATATATTGATTTATTTTTAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
* * * ** * * * * ***
490384 ---ATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTA
1 TGGATTGATTTATTTTAAATAATTTA--TT--AGTATGGATTTATTTA-T-TT-TA-AAATA
* *
490443 TGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
1 TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
490497 TGGATTGATTTATT
1 TGGATTGATTTATT
490511 ATTGTAGTTG
Statistics
Matches: 387, Mismatches: 72, Indels: 78
0.72 0.13 0.15
Matches are distributed among these distances:
44 19 0.05
45 11 0.03
46 3 0.01
48 2 0.01
49 4 0.01
50 1 0.00
51 17 0.04
52 21 0.05
53 41 0.11
54 156 0.40
55 32 0.08
56 4 0.01
57 9 0.02
58 40 0.10
59 9 0.02
60 2 0.01
62 16 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTATGGATTTATTTATTTTAAAATA
Found at i:490002 original size:32 final size:32
Alignment explanation
Indices: 489959--490063 Score: 131
Period size: 32 Copynumber: 3.6 Consensus size: 32
489949 TGTAGTTGTG
489959 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
*
489991 TGGATTTATTTA-TTT---TAA---A--A-TA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
490013 TGGATTGATTTATTTTAAATAATTTATTAGTA
1 TGGATTGATTTATTTTAAATAATTTATTAGTA
490045 TGGATTGATTTATTTTAAA
1 TGGATTGATTTATTTTAAA
490064 ATATGAATTG
Statistics
Matches: 61, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
22 13 0.21
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 32 0.52
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
TGGATTGATTTATTTTAAATAATTTATTAGTA
Found at i:490002 original size:80 final size:82
Alignment explanation
Indices: 489909--490590 Score: 843
Period size: 80 Copynumber: 8.5 Consensus size: 82
489899 TATTATAAAA
*
489909 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTGTGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
489971 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
* *
489989 TATGGATTTATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGAT
490054 TTATTTT-AA-AA--TA-T-G
62 TTATTTTAAATAATTTATTAG
*
490069 -A---ATTGATTTATTTTAAAATATGGATTGATTTATTTAAATAATTTATTAGTATGGATTGATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA-TT-AAT-ATGTATTAGTATGGATTGATT
*
490130 TATTTTAAATAATTTATTTG
63 TATTTTAAATAATTTATTAG
490150 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
*
490212 TTTTAAATAATTTATTAA
65 TTTTAAATAATTTATTAG
*
490230 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGAT
490295 TTATTTT-AA-AA--TA-T-G
62 TTATTTTAAATAATTTATTAG
* * **
490310 -A---ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAATATATATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT-AAT-ATGTATTAGTATGGATTGAT
*
490371 TTATTTTTAAATAATTTATTTG
62 TTA-TTTTAAATAATTTATTAG
490393 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
490455 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
*
490473 TATGAATTGATTTATTTTAAAATATGGATTGATTTATT-AT-TGTAGTT-GTATGGATTGATTTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTA-TTAGTATGGATTGATTTA
490535 TTTTAAATAATTTATTAG
65 TTTTAAATAATTTATTAG
490553 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATT
490591 TTAAATAATT
Statistics
Matches: 546, Mismatches: 19, Indels: 74
0.85 0.03 0.12
Matches are distributed among these distances:
75 35 0.06
76 92 0.17
77 6 0.01
78 2 0.00
79 6 0.01
80 240 0.44
81 22 0.04
82 14 0.03
83 3 0.01
84 11 0.02
85 41 0.08
86 43 0.08
87 31 0.06
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.53
Consensus pattern (82 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTAATATGTATTAGTATGGATTGATTTAT
TTTAAATAATTTATTAG
Found at i:490005 original size:22 final size:22
Alignment explanation
Indices: 489989--490103 Score: 95
Period size: 22 Copynumber: 4.8 Consensus size: 22
489979 AATTTATTAG
*
489989 TATGGATTTATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
490011 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
490035 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
*
490065 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
490087 TATGGATTGATTTATTT
1 TATGGATTGATTTATTT
490104 AAATAATTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
22 39 0.52
23 2 0.03
24 2 0.03
25 2 0.03
26 10 0.13
27 2 0.03
28 10 0.13
29 2 0.03
30 2 0.03
31 2 0.03
32 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:490142 original size:32 final size:32
Alignment explanation
Indices: 490087--490170 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
490077 TATTTTAAAA
490087 TATGGATTGATTTA-TTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
490118 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
490150 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
490171 ATATGGATTG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 14 0.27
32 37 0.73
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:490175 original size:22 final size:22
Alignment explanation
Indices: 490150--490348 Score: 92
Period size: 22 Copynumber: 8.0 Consensus size: 22
490140 AATTTATTTG
490150 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
490172 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
490198 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
** *
490222 TTTATTAATATGGATTGATTTATTTTAAAA
1 --TATGGAT-T-GATTTA-TT---TTAAAA
490252 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
490276 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
*
490306 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
490328 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
490349 TAATTTATTA
Statistics
Matches: 134, Mismatches: 19, Indels: 48
0.67 0.09 0.24
Matches are distributed among these distances:
22 42 0.31
23 4 0.03
24 7 0.05
25 7 0.05
26 34 0.25
27 4 0.03
28 20 0.15
29 4 0.03
30 4 0.03
31 4 0.03
32 4 0.03
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:490239 original size:32 final size:32
Alignment explanation
Indices: 490198--490304 Score: 135
Period size: 32 Copynumber: 3.7 Consensus size: 32
490188 ATTGTAGTTG
490198 TATGGATTGATTTATTTTAAATAATTTATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
490230 TATGGATTGATTTA-TTT---T-A---A--AA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
490252 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
490284 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
490305 ATATGAATTG
Statistics
Matches: 64, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
22 16 0.25
23 3 0.05
24 1 0.02
26 1 0.02
27 2 0.03
28 1 0.02
30 1 0.02
31 3 0.05
32 36 0.56
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAA
Found at i:490384 original size:33 final size:33
Alignment explanation
Indices: 490326--490416 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
490316 TTTATTTTAA
*
490326 AATATGGATTGATTTA-TTTTAAATAATTTATT
1 AATATAGATTGATTTATTTTTAAATAATTTATT
*
490358 AATATATATTGATTTATTTTTAAATAATTTATT
1 AATATAGATTGATTTATTTTTAAATAATTTATT
** * *
490391 TGTATGGATTGATTTATTTTAAAATA
1 AATATAGATTGATTTATTTTTAAATA
490417 TGGATTGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 14 0.27
33 37 0.73
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (33 bp):
AATATAGATTGATTTATTTTTAAATAATTTATT
Found at i:490399 original size:109 final size:113
Alignment explanation
Indices: 490250--490496 Score: 371
Period size: 109 Copynumber: 2.2 Consensus size: 113
490240 TTTATTTTAA
*
490250 AATATGGATTGATTTA-TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATT
1 AATATGAATTGATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATT
490314 GATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATT
66 GATTTATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATT
* *
490358 AATAT-ATATTGATTTATTTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGAT
1 AATATGA-ATTGATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAAT
***
490422 TGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATT
65 TGATTTATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATT
* *
490471 AGTATGAATTGATTTATTTTAAAATA
1 AATATGAATTGATTTATTTTTAAATA
490497 TGGATTGATT
Statistics
Matches: 124, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
108 14 0.11
109 52 0.42
110 1 0.01
111 2 0.02
112 2 0.02
113 52 0.42
114 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (113 bp):
AATATGAATTGATTTATTTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATT
GATTTATTATTGTAGAAATATGGATTGATTTATTTTAAATAATTTATT
Found at i:490409 original size:22 final size:22
Alignment explanation
Indices: 490384--490457 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
490374 TTTTTAAATA
490384 ATTTATTTGTATGGATTGATTT
1 ATTTATTTGTATGGATTGATTT
***
490406 ATTT-TAAAATATGGATTGATTTATT
1 ATTTAT-TTGTATGGATTGA--T-TT
*
490431 ATTGTAGTTGTATGGATTGATTT
1 ATT-TATTTGTATGGATTGATTT
490454 ATTT
1 ATTT
490458 TAAATAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
21 1 0.03
22 15 0.38
23 5 0.13
24 2 0.05
25 5 0.13
26 11 0.28
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (22 bp):
ATTTATTTGTATGGATTGATTT
Found at i:490578 original size:22 final size:22
Alignment explanation
Indices: 490553--490595 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
490543 AATTTATTAG
490553 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
490575 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
490596 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:490655 original size:31 final size:31
Alignment explanation
Indices: 490620--490678 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
490610 AGTTGTATGG
* *
490620 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
490651 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
490679 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:490717 original size:16 final size:16
Alignment explanation
Indices: 490696--490738 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
490686 GTTTAAAAAA
490696 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
490712 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
* *
490728 TTAGTTCATTT
1 TCAGTTTATTT
490739 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:491351 original size:65 final size:64
Alignment explanation
Indices: 491282--491441 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 64
491272 GAATAAATTG
* * *
491282 AACATCGAATGCATTTTATGCAACGATGCACATACCATACATCGATGCACTC-AGGGTT-TTATG
1 AACATCGAATGCATTTTATGCATCGATGCACAAACCATACATCGATGCACTCTA-GCTTGTT-TG
491345 AA
64 -A
* ** * * *
491347 AACATCGAATACATTTTATGCATTAAAGCACAAACCATGCATCGATGCGCTCTAGCTTGTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAAACCATACATCGATGCACTCTAGCTTGTTTGA
* *
491411 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
491442 TCCTAGTGCA
Statistics
Matches: 78, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
64 26 0.33
65 49 0.63
66 3 0.04
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAACCATACATCGATGCACTCTAGCTTGTTTGA
Found at i:497303 original size:21 final size:23
Alignment explanation
Indices: 497255--497332 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 23
497245 ACACTTAACA
* * *
497255 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATACA-CTCATTGAAT
*
497279 GTGCATCGATACAC-CA-TGAAG
1 GTGCATCGATACACTCATTGAAT
* *
497300 GTGCACCGATTCACTCATTGAAT
1 GTGCATCGATACACTCATTGAAT
497323 GTGCATCGAT
1 GTGCATCGAT
497333 GCACAAGGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.36
22 3 0.07
23 14 0.31
24 12 0.27
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (23 bp):
GTGCATCGATACACTCATTGAAT
Found at i:500098 original size:65 final size:64
Alignment explanation
Indices: 500028--500169 Score: 214
Period size: 65 Copynumber: 2.2 Consensus size: 64
500018 GAATAAATTG
* *
500028 AACATCCAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAAGG-TTTTATTA
1 AACATCAAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTC-AGGCTTGT-TTA
500092 A
64 A
* * *
500093 AACATCGAATGCATTTTATGCATCGATGTACATACCATGCATCGATGCACTCTGGCTTGTTTAA
1 AACATCAAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTAA
500157 AACATCAAATGCA
1 AACATCAAATGCA
500170 CTAAGGGTCT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 18 0.25
65 53 0.75
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (64 bp):
AACATCAAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTGTTTAA
Found at i:501758 original size:18 final size:18
Alignment explanation
Indices: 501735--501770 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
501725 GAGGGTATCT
*
501735 TAGGCCATTTACATTCTA
1 TAGGCCATTTACACTCTA
501753 TAGGCCATTTACACTCTA
1 TAGGCCATTTACACTCTA
501771 GGGGCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (18 bp):
TAGGCCATTTACACTCTA
Found at i:504402 original size:8 final size:8
Alignment explanation
Indices: 504391--504436 Score: 78
Period size: 8 Copynumber: 6.0 Consensus size: 8
504381 ATATTTCTAA
504391 ATTTTAGT
1 ATTTTAGT
504399 A-TTT-GT
1 ATTTTAGT
504405 ATTTTAGT
1 ATTTTAGT
504413 ATTTTAGT
1 ATTTTAGT
504421 ATTTTAGT
1 ATTTTAGT
504429 ATTTTAGT
1 ATTTTAGT
504437 GTATGCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 3 0.08
7 6 0.17
8 27 0.75
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.63
Consensus pattern (8 bp):
ATTTTAGT
Found at i:504407 original size:22 final size:22
Alignment explanation
Indices: 504382--504435 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
504372 TAAAACCTCA
504382 TATTTCTA-AATTTTAGTATTTG
1 TATTT-TAGAATTTTAGTATTTG
*
504404 TATTTTAGTATTTTAGTATTTTAG
1 TATTTTAGAATTTTAGTA-TTT-G
504428 TATTTTAG
1 TATTTTAG
504436 TGTATGCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 2 0.07
22 14 0.50
23 3 0.11
24 9 0.32
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (22 bp):
TATTTTAGAATTTTAGTATTTG
Found at i:509493 original size:2 final size:2
Alignment explanation
Indices: 509486--509574 Score: 101
Period size: 2 Copynumber: 44.5 Consensus size: 2
509476 TGTAGTCATG
* * ** *
509486 TA TA TA TA TA TA TA TA TA TA -A GTA TT TA TG GG TA TA TGA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA T-A TA TA
509528 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
509570 TA TA T
1 TA TA T
509575 GCATATAAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
1 2 0.03
2 71 0.95
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:522933 original size:12 final size:13
Alignment explanation
Indices: 522916--523011 Score: 98
Period size: 12 Copynumber: 7.8 Consensus size: 13
522906 TCTTGAAGAA
*
522916 AAAAAAAAGAA-G
1 AAAAAAATGAATG
522928 AAAAAAATGAATG
1 AAAAAAATGAATG
522941 -AAAAAATGAATG
1 AAAAAAATGAATG
522953 AAAAAAATGAATG
1 AAAAAAATGAATG
*
522966 AAAAAAATGGAAAG
1 AAAAAAAT-GAATG
* *
522980 ATAATAA--AAT-
1 AAAAAAATGAATG
522990 -AAAAAATGAATG
1 AAAAAAATGAATG
523002 -AAAAAATGAA
1 AAAAAAATGAA
523012 AAAAAAGAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 4 0.06
11 5 0.07
12 32 0.45
13 21 0.30
14 9 0.13
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.14
Consensus pattern (13 bp):
AAAAAAATGAATG
Found at i:522944 original size:25 final size:26
Alignment explanation
Indices: 522916--522972 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 26
522906 TCTTGAAGAA
522916 AAAAAAAAGAA-GAAAAAAATGAATG
1 AAAAAAAAGAATGAAAAAAATGAATG
*
522941 -AAAAAATGAATGAAAAAAATGAATG
1 AAAAAAAAGAATGAAAAAAATGAATG
522966 AAAAAAA
1 AAAAAAA
522973 TGGAAAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.31
25 14 0.48
26 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (26 bp):
AAAAAAAAGAATGAAAAAAATGAATG
Found at i:523545 original size:13 final size:13
Alignment explanation
Indices: 523527--523552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
523517 AATAAAGAGA
523527 CATTTTCCCTTTT
1 CATTTTCCCTTTT
523540 CATTTTCCCTTTT
1 CATTTTCCCTTTT
523553 ACAAGCATCT
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:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
CATTTTCCCTTTT
Found at i:524112 original size:55 final size:54
Alignment explanation
Indices: 524037--524956 Score: 508
Period size: 55 Copynumber: 16.7 Consensus size: 54
524027 ACGATCATTG
* *
524037 AAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTCA
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * * * *
524092 AAGATTATTCGAGTTCTATACT-TCCTGAAAGAAAGAGGGAGC-GAAACCATT-TGCA
1 AAGATTGTTCGAG-TCTATACTCT-CTG-AAGAAATAGGGAGCAGACACGATTGT-TA
* * * * *
524147 GAGGATTATTCGAGTTCTATACT-TCCTGAAGAAAGAGGGAAC-GAACCCG--T-TTA
1 -AAGATTGTTCGAG-TCTATACTCT-CTGAAGAAATAGGGAGCAG-ACACGATTGTTA
* * * * * * * *
524200 AAGA-AGATGTCTGAGTTCTATACTCCCT-AGAGGAAGAGGGAGCAAACCCGTTTG-AA
1 AAGATTG-T-TC-GAG-TCTATACTCTCTGA-AGAAATAGGGAGCAGACACGATTGTTA
* * * * * * *
524256 GAAGA-TATCCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGC-GAACCCGTTTG-AA
1 -AAGATTGTTCGAG-TCTATACTCTCTGA-AGAAATAGGGAGCAG-ACACGATTGTTA
* *
524310 GAAGA-TGTTCGGGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
1 -AAGATTGTTCGAGTCT-ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * * * *
524365 AATATTGTTCGAGTCTTATACTCTCTGAACAAATATGGAGCAGATACGATTGTTG
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * *
524420 AAGATTGTTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGACATGATTGTTG
1 AAGATTGTTCGAGTCT-ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * * * *
524475 AAGATTATTCGAGTTCTATACT-TCCTGAAAGAAAGAGGGAGC-GAACCCGTTTG-CA
1 AAGATTGTTCGAG-TCTATACTCT-CTG-AAGAAATAGGGAGCAG-ACACGATTGTTA
* * * * * * *
524530 GAGGATTATTCGAGTTCTATACTTTCTGAAGAAAGAGGGAGC-GAACCCGTTTG-AA
1 -AAGATTGTTCGAG-TCTATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTTA
* * * * *
524585 GAAGA-TGTCCGAGTTCTATACTC-CAT-AGAGAAAGAGGGAG-AGAACCCGTTTG-AA
1 -AAGATTGTTCGAG-TCTATACTCTC-TGA-AGAAATAGGGAGCAG-ACACGATTGTTA
* * * * * *
524639 GAAGA-TGTTCGGGTCTCATACTCTCTAAAGAAATAGAGAGAAGACATGATTGTTG
1 -AAGATTGTTCGAGTCT-ATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * * ** * * *
524694 AAGATTGTTAGAGTCTTATACTCTCTGAAGAAAAAGGGGGCAGACGTGACTGGTG
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * * * ** *
524749 AAGATTGCTCGAGTCTTATACTCTCTAAAGAAATAGGGGGAAGACGTGTGATTGTTG
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGAC--ACGATTGTTA
* *
524806 AAGATTGTTCGAGTCTTATACTCTCTGAAGAGATAGGGGGCAGACACGATTGTTA
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * *
524861 AAGATTGTTCGAGTCTTATACTCTCTAAAGAGATAGGGGGCAGACACGATTGTTA
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
* * * *
524916 AAGATTGTTTGAGTCTTATACTCTCTTAAGGACTAGGGAGC
1 AAGATTGTTCGAGTC-TATACTCTCTGAAGAAATAGGGAGC
524957 TGACGCGGTT
Statistics
Matches: 725, Mismatches: 98, Indels: 84
0.80 0.11 0.09
Matches are distributed among these distances:
52 4 0.01
53 12 0.02
54 196 0.27
55 366 0.50
56 93 0.13
57 54 0.07
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (54 bp):
AAGATTGTTCGAGTCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTA
Found at i:524448 original size:110 final size:109
Alignment explanation
Indices: 524034--524941 Score: 599
Period size: 110 Copynumber: 8.3 Consensus size: 109
524024 CCAACGATCA
* * ** *
524034 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTCAAAGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCAGA-ACGATTGTTGAAGATTG
* * *
524099 TTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGC-GAAACCATTTG
65 TTCGAGTCTC-ATACTCT-CT-AAAGAAATAGGGAGCAGACACGA-TTG
** * * * * ***
524145 CAGAGGATTATTCGAGT-TCTATACT-TCCTGAAGAAAGAGGGAAC-GAACCCGTTTAAAGAAGA
1 TTGAAGATTGTTCGAGTCT-TATACTCT-CTGAAGAAAGAGGGAGCAGAA--CGATTGTTGAAGA
* * * * * * *
524207 -TG-TCTGAGT-TCTATACTCCCTAGAGGAAGAGGGAGCAAACCCGTTTG
62 TTGTTC-GAGTCTC-ATACTCTCTAAAGAAATAGGGAGCAGACACGATTG
** * * * * **
524254 AAGAAGA-TATCCGAGT-TCTATACTCCCT-AGAGAAAGAGGGAGC-GAACCCGTTTGAAGAAGA
1 TTGAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAAGAGGGAGCAGAA--CGATTGTTGAAGA
* *
524315 -TGTTCGGGTCTCATACTCTCTGAAGAAATAGGGAGCAGACACGATTG
62 TTGTTCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGATTG
* * * *
524362 TTGAATATTGTTCGAGTCTTATACTCTCTGAACAAATATGGAGCAGATACGATTGTTGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCAGA-ACGATTGTTGAAGATTG
* * *
524427 TTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGACATGATTG
65 TTCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGATTG
* * ** *
524472 TTGAAGATTATTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGC-GAACCCGTTTGCAGAGG
1 TTGAAGATTGTTCGAGTCT-TATACTCT-CTG-AAGAAAGAGGGAGCAGAA--CGATTGTTGAAG
* * * * * *
524534 ATTATTCGAGT-TCTATACTTTCTGAAGAAAGAGGGAGC-GAACCCGTTTG
61 ATTGTTCGAGTCTC-ATACTCTCTAAAGAAATAGGGAGCAG-ACACGATTG
** * * **
524583 AAGAAGA-TGTCCGAGT-TCTATACTC-CAT-AGAGAAAGAGGGAG-AGAACCCGTTTGAAGAAG
1 TTGAAGATTGTTCGAGTCT-TATACTCTC-TGA-AGAAAGAGGGAGCAGAA--CGATTGTTGAAG
* * * *
524643 A-TGTTCGGGTCTCATACTCTCTAAAGAAATAGAGAGAAGACATGATTG
61 ATTGTTCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGATTG
* * * * *
524691 TTGAAGATTGTTAGAGTCTTATACTCTCTGAAGAAAAAGGGGGCAG-ACGTGACTGGTGAAGATT
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCAGAAC--GATTGTTGAAGATT
* * * * **
524755 GCTCGAGTCTTATACTCTCTAAAGAAATAGGGGGAAGACGTGTGATTG
64 GTTCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGAC--ACGATTG
* * * *
524803 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAGATAGGGGGCAGACACGATTGTTAAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCAGA-ACGATTGTTGAAGATTG
* * *
524868 TTCGAGTCTTATACTCTCTAAAGAGATAGGGGGCAGACACGATTG
65 TTCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGATTG
* *
524913 TTAAAGATTGTTTGAGTCTTATACTCTCT
1 TTGAAGATTGTTCGAGTCTTATACTCTCT
524942 TAAGGACTAG
Statistics
Matches: 643, Mismatches: 112, Indels: 85
0.77 0.13 0.10
Matches are distributed among these distances:
107 2 0.00
108 121 0.19
109 133 0.21
110 186 0.29
111 103 0.16
112 96 0.15
114 2 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (109 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAAGAGGGAGCAGAACGATTGTTGAAGATTGT
TCGAGTCTCATACTCTCTAAAGAAATAGGGAGCAGACACGATTG
Found at i:524637 original size:329 final size:327
Alignment explanation
Indices: 524034--524836 Score: 1037
Period size: 329 Copynumber: 2.4 Consensus size: 327
524024 CCAACGATCA
* ** *
524034 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTCAAAGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
* * ** *
524099 TTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGCGAAACCAT--TTGCAGAGGATTATTCGA
66 TTCGAGTCTC-ATACTCT-CTG-AAGAAATAGGGAGC-AGA-CATGATTGTTGAAGATTATTCGA
524160 GTTCTATACTTCCTGAAGAAAGAGGGAACGAACCCGTTTAAAGAAGATGTCTGAGTTCTATACTC
126 GTTCTATACTTCCTGAAGAAAGAGGGAACGAACCCGTTTAAAGAAGATGTCTGAGTTCTATACTC
* *
524225 CCTAGAGGAAGAGGGAGCAAACCCGTTTGAAGAAGATATCCGAGTTCTATACTCCCTAGAGAAAG
191 CCTAGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATATCCGAGTTCTATACTCCATAGAGAAAG
* * * *
524290 AGGGAGCGAACCCGTTTGAAGAAGATGTTCGGGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC
256 AGGGAGAGAACCCGTTTGAAGAAGATGTTCGGGTCTCATACTCTCTAAAGAAATAGAGAGAAGAC
524355 ACGATTG
321 ACGATTG
* * * *
524362 TTGAATATTGTTCGAGTCTTATACTCTCTGAACAAATATGGAGCAGATACGATTGTTGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
*
524427 TTCGAGTCTCATACTCTCTGAAGAAATAGAGAGCAGACATGATTGTTGAAGATTATTCGAGTTCT
66 TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAGATTATTCGAGTTCT
* ** * * **
524492 ATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCAGAGGAT-TATTCGAGTTCTATACTTTC
131 ATACTTCCTG-AAGAAAGAGGGAACGAACCCGTTTAAAGAAGATGT-CT-GAGTTCTATACTCCC
* *
524556 T-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATGTCCGAGTTCTATACTCCATAGAGAAAGA
193 TAG-AGAAAGAGGGAGCAAACCCGTTTGAAGAAGATATCCGAGTTCTATACTCCATAGAGAAAGA
524620 GGGAGAGAACCCGTTTGAAGAAGATGTTCGGGTCTCATACTCTCTAAAGAAATAGAGAGAAGACA
257 GGGAGAGAACCCGTTTGAAGAAGATGTTCGGGTCTCATACTCTCTAAAGAAATAGAGAGAAGACA
*
524685 TGATTG
322 CGATTG
* * * ** * *
524691 TTGAAGATTGTTAGAGTCTTATACTCTCTGAAGAAAAAGGGGGCAGACGTGACTGGTGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
* * * * * * *
524756 CTCGAGTCTTATACTCTCTAAAGAAATAGGGGGAAGACGTGTGATTGTTGAAGATTGTTCGAG-T
66 TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGAC--ATGATTGTTGAAGATTATTCGAGTT
524820 CTTATAC-TCTCTGAAGA
129 C-TATACTTC-CTGAAGA
524837 GATAGGGGGC
Statistics
Matches: 414, Mismatches: 49, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
325 3 0.01
326 2 0.00
327 43 0.10
328 103 0.25
329 226 0.55
330 8 0.02
331 29 0.07
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (327 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTG
TTCGAGTCTCATACTCTCTGAAGAAATAGGGAGCAGACATGATTGTTGAAGATTATTCGAGTTCT
ATACTTCCTGAAGAAAGAGGGAACGAACCCGTTTAAAGAAGATGTCTGAGTTCTATACTCCCTAG
AGAAAGAGGGAGCAAACCCGTTTGAAGAAGATATCCGAGTTCTATACTCCATAGAGAAAGAGGGA
GAGAACCCGTTTGAAGAAGATGTTCGGGTCTCATACTCTCTAAAGAAATAGAGAGAAGACACGAT
TG
Found at i:524660 original size:54 final size:53
Alignment explanation
Indices: 524099--524671 Score: 391
Period size: 54 Copynumber: 10.5 Consensus size: 53
524089 TCAAAGATTA
* * * * * *
524099 TTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAAACCATTTGCAGAGGATTA
1 TTCGAGTTCTATAC-TCCTG-AAGAAAGAGGGAGAGAACCCGTTTGAAGAAGA-TG
*
524155 TTCGAGTTCTATACTTCCTGAAGAAAGAGGGA-ACGAACCCGTTTAAAGAAGATG
1 TTCGAGTTCTATAC-TCCTGAAGAAAGAGGGAGA-GAACCCGTTTGAAGAAGATG
* *
524209 -TCTGAGTTCTATACTCCCT-AGAGGAAGAGGGAGCA-AACCCGTTTGAAGAAGATA
1 TTC-GAGTTCTATACT-CCTGA-AGAAAGAGGGAG-AGAACCCGTTTGAAGAAGATG
* *
524263 TCCGAGTTCTATACTCCCT-AGAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATG
1 TTCGAGTTCTATACT-CCTGA-AGAAAGAGGGAGAGAACCCGTTTGAAGAAGATG
* * * * ** *
524317 TTCG-GGTCTCATACTCTCTGAAGAAATAGGGAGCAG-ACACGATTGTTGAATATTG
1 TTCGAGTTCT-ATACTC-CTGAAGAAAGAGGGAG-AGAACCCGTTTGAAGAAGA-TG
* * * * **
524372 TTCGAG-TCTTATACTCTCTGAACAAATATGGAGCAGATA--CGATTGTTGAAGATTG
1 TTCGAGTTC-TATACTC-CTGAAGAAAGAGGGAG-AGA-ACCCGTTTGAAGAAGA-TG
* * ** * ** *
524427 TTCGAG-TCTCATACTCTCTGAAGAAATAGAGAGCAG-ACATGATTGTTGAAGATTA
1 TTCGAGTTCT-ATACTC-CTGAAGAAAGAGGGAG-AGAACCCGTTTGAAGAAGA-TG
* * * *
524482 TTCGAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCCGTTTGCAGAGGATTA
1 TTCGAGTTCTATAC-TCCTG-AAGAAAGAGGGAGAGAACCCGTTTGAAGAAGA-TG
* *
524538 TTCGAGTTCTATACTTTCTGAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGATG
1 TTCGAGTTCTATAC-TCCTGAAGAAAGAGGGAGAGAACCCGTTTGAAGAAGATG
*
524592 TCCGAGTTCTATACTCCAT-AGAGAAAGAGGGAGAGAACCCGTTTGAAGAAGATG
1 TTCGAGTTCTATACTCC-TGA-AGAAAGAGGGAGAGAACCCGTTTGAAGAAGATG
* *
524646 TTCG-GGTCTCATACTCTCTAAAGAAA
1 TTCGAGTTCT-ATACTC-CTGAAGAAA
524672 TAGAGAGAAG
Statistics
Matches: 439, Mismatches: 49, Indels: 60
0.80 0.09 0.11
Matches are distributed among these distances:
53 17 0.04
54 184 0.42
55 166 0.38
56 71 0.16
57 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (53 bp):
TTCGAGTTCTATACTCCTGAAGAAAGAGGGAGAGAACCCGTTTGAAGAAGATG
Found at i:524820 original size:112 final size:110
Alignment explanation
Indices: 524651--524941 Score: 402
Period size: 112 Copynumber: 2.6 Consensus size: 110
524641 AGATGTTCGG
* * *
524651 GTCTCATACTCTCTAAAGAAATAGAGAGAAGACATGATTGTTGAAGATTGTTAGAGTCTTATACT
1 GTCTTATACTCTCTAAAGAAATAGGGGGAAGACATGATTGTTGAAGATTGTTAGAGTCTTATACT
** *
524716 CTCTGAAGAAAAAGGGGGCAGACGTGACTGGTGAAGATTGCTCGA
66 CTCTGAAGAAAAAGGGGGCAGACACGACTGGTAAAGATTGCTCGA
* *
524761 GTCTTATACTCTCTAAAGAAATAGGGGGAAGACGTGTGATTGTTGAAGATTGTTCGAGTCTTATA
1 GTCTTATACTCTCTAAAGAAATAGGGGGAAGAC--ATGATTGTTGAAGATTGTTAGAGTCTTATA
* * * * *
524826 CTCTCTGAAGAGATAGGGGGCAGACACGATTGTTAAAGATTGTTCGA
64 CTCTCTGAAGAAAAAGGGGGCAGACACGACTGGTAAAGATTGCTCGA
* * * * *
524873 GTCTTATACTCTCTAAAGAGATAGGGGGCAGACACGATTGTTAAAGATTGTTTGAGTCTTATACT
1 GTCTTATACTCTCTAAAGAAATAGGGGGAAGACATGATTGTTGAAGATTGTTAGAGTCTTATACT
524938 CTCT
66 CTCT
524942 TAAGGACTAG
Statistics
Matches: 160, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
110 62 0.39
112 98 0.61
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (110 bp):
GTCTTATACTCTCTAAAGAAATAGGGGGAAGACATGATTGTTGAAGATTGTTAGAGTCTTATACT
CTCTGAAGAAAAAGGGGGCAGACACGACTGGTAAAGATTGCTCGA
Found at i:525353 original size:2 final size:2
Alignment explanation
Indices: 525346--525424 Score: 81
Period size: 2 Copynumber: 39.5 Consensus size: 2
525336 TGTAGTCATG
* * **
525346 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA TT TA TG GG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
525388 TA TGA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
525425 GCATATAAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
1 2 0.03
2 61 0.94
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:525930 original size:19 final size:19
Alignment explanation
Indices: 525906--525948 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
525896 CCAGAGCCCT
525906 GCAAACAAACCAAACGAGA
1 GCAAACAAACCAAACGAGA
*
525925 GCAAACACACCAAACGAGA
1 GCAAACAAACCAAACGAGA
525944 GCAAA
1 GCAAA
525949 AACAGACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.56, C:0.28, G:0.16, T:0.00
Consensus pattern (19 bp):
GCAAACAAACCAAACGAGA
Found at i:529784 original size:2 final size:2
Alignment explanation
Indices: 529777--529825 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
529767 ATAAGAGTTA
529777 AT AT AT AT AT 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
*
529819 AG AT AT A
1 AT AT AT A
529826 GACGCGGAAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:530169 original size:19 final size:19
Alignment explanation
Indices: 530145--530197 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
530135 TAAAATAATA
530145 TATTTATTAAAAATATTTT
1 TATTTATTAAAAATATTTT
530164 TATTTATTAAAAATATTTT
1 TATTTATTAAAAATATTTT
*
530183 TATTTAATAAAAATA
1 TATTTATTAAAAATA
530198 GAGATTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTATTAAAAATATTTT
Found at i:530787 original size:19 final size:19
Alignment explanation
Indices: 530763--530799 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
530753 ATGACCAACA
* *
530763 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
530782 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
530800 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:530871 original size:21 final size:21
Alignment explanation
Indices: 530845--530885 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
530835 ATTTTGACCA
*
530845 TCGCATTGCGATTTTCGAAAT
1 TCGCATTGCGATTTTAGAAAT
530866 TCGCATTGCGATTTTAGAAA
1 TCGCATTGCGATTTTAGAAA
530886 ATGCGAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTAGAAAT
Found at i:531159 original size:22 final size:22
Alignment explanation
Indices: 531088--531165 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
531078 ACTCTCTATG
* *
531088 GCGACATCCGTCCCCATCTC-C
1 GCGAAATCCGTCCCCATCTCTA
* *
531109 GACGAAATCCGTCCCCATTTCTG
1 G-CGAAATCCGTCCCCATCTCTA
531132 GCGAAATCCGTCCCCATCTCTA
1 GCGAAATCCGTCCCCATCTCTA
*
531154 GTGAAATCCGTC
1 GCGAAATCCGTC
531166 TATCTCCATC
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
21 1 0.02
22 47 0.96
23 1 0.02
ACGTcount: A:0.21, C:0.40, G:0.17, T:0.23
Consensus pattern (22 bp):
GCGAAATCCGTCCCCATCTCTA
Found at i:531631 original size:20 final size:20
Alignment explanation
Indices: 531578--531633 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
531568 GTTAGTCAAA
* **
531578 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
531598 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
**
531618 TTTTTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
531634 AAGTCTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.14, G:0.20, T:0.54
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:533608 original size:20 final size:20
Alignment explanation
Indices: 533524--533593 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
533514 AAAAATAGTT
*
533524 GCAACACGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* *
533544 GCAATGTGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
533564 GCAACGCGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
533584 GCAACGCGAA
1 GCAACGCGAA
533594 TTTGATTATT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:533608 original size:40 final size:40
Alignment explanation
Indices: 533522--533608 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
533512 AGAAAAATAG
* *
533522 TTGCAACACGAAAATGACTATCGCAATGTGAAAATGACTA
1 TTGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
* * ** *
533562 TCGCAACGCGAAAATGACTATCGCAACGCGAATTTGATTA
1 TTGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
533602 TTGCAAC
1 TTGCAAC
533609 TGGGTAATCG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (40 bp):
TTGCAACACGAAAATGACTATCGCAACGCGAAAATGACTA
Found at i:533714 original size:33 final size:33
Alignment explanation
Indices: 533672--533766 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
533662 TTTAGTTTCG
533672 CGTTGCGATTTGATTTTCGCATTGTGATTACCC
1 CGTTGCGATTTGATTTTCGCATTGTGATTACCC
*
533705 CGTTGCGATTTGATTTTCGTATTGTGATTACCC
1 CGTTGCGATTTGATTTTCGCATTGTGATTACCC
* * *
533738 CGTTGCGATAGTCATTTTCGCGTTGTGAT
1 CGTTGCGAT-TTGATTTTCGCATTGTGAT
533767 AGTCATTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 41 0.73
34 15 0.27
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTGATTTTCGCATTGTGATTACCC
Found at i:533767 original size:20 final size:20
Alignment explanation
Indices: 533738--533806 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
533728 GTGATTACCC
533738 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
533758 CGTTGTGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
533778 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
533798 TGTTGCGAT
1 CGTTGCGAT
533807 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.14, C:0.17, G:0.26, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:534388 original size:21 final size:21
Alignment explanation
Indices: 534297--534401 Score: 113
Period size: 21 Copynumber: 5.0 Consensus size: 21
534287 GACTCACCTG
*
534297 TCATCGTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
534318 TTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
* *
534339 TCATTC-CTCAAGAGTCCCCTC
1 TCA-TCGTTCAAGAGGCCCCTC
* *
534360 TCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTC
* *
534381 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
534402 CCAACATTCT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.01
21 64 0.96
22 2 0.03
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:534394 original size:42 final size:42
Alignment explanation
Indices: 534293--534399 Score: 126
Period size: 42 Copynumber: 2.5 Consensus size: 42
534283 TCCCGACTCA
* * * *
534293 CCTGTCATCGTTCAAGAGGCCTCTCTTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
* *
534335 CCTATCATTC-CTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
1 CCTGTCA-TCGTTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
*
534377 CCTGTCATCGTTGAAGAGGTCCC
1 CCTGTCATCGTTCAAGA-GTCCC
534400 TCCCAACATT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
41 2 0.04
42 44 0.83
43 7 0.13
ACGTcount: A:0.20, C:0.35, G:0.20, T:0.26
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGTCCCCTCTCACCGTTCAAGAGGCC
Found at i:535980 original size:34 final size:34
Alignment explanation
Indices: 535918--536054 Score: 123
Period size: 34 Copynumber: 3.9 Consensus size: 34
535908 ATCATATTCG
* * *
535918 CGTTGCGATAGTCTAATACACTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCACGTTGCGATTTTCT
* * *
535952 CGTTGCGATAGTCAAATTCCCGTGGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCACGTTGCGAT--T----TTCT
* *
535992 CGTTGCGATAATCAAATTCGCGTTGCGATTTT-T
1 CGTTGCGATAGTCAAATTCACGTTGCGATTTTCT
*
536025 GCTTTGCGATAGTCAAATTCACGTTGCGAT
1 -CGTTGCGATAGTCAAATTCACGTTGCGAT
536055 AGTTAAATTC
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
34 52 0.63
36 1 0.01
38 1 0.01
40 29 0.35
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCACGTTGCGATTTTCT
Done.