Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397297.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_236.0, 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: 298872
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.22
Warning! 106566 characters in sequence are not A, C, G, or T
Found at i:16438 original size:14 final size:14
Alignment explanation
Indices: 16419--16450 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16409 TTAAATTGTA
16419 CTTTTGTAGGTGTG
1 CTTTTGTAGGTGTG
16433 CTTTTGTAGGTGTG
1 CTTTTGTAGGTGTG
16447 CTTT
1 CTTT
16451 AAAGAAGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.09, G:0.31, T:0.53
Consensus pattern (14 bp):
CTTTTGTAGGTGTG
Found at i:33103 original size:29 final size:29
Alignment explanation
Indices: 33054--33226 Score: 137
Period size: 29 Copynumber: 6.2 Consensus size: 29
33044 NNNNNNNNNN
* *
33054 GCACCGTTTGAACTTTATTAGGTGCCTTA
1 GCACCTTTTGAACTTTGTTAGGTGCCTTA
* *
33083 GTACCTTTTGAACTTTGTTAGGTGCTTTA
1 GCACCTTTTGAACTTTGTTAGGTGCCTTA
* * *
33112 GCACCTATAGAACTTTGTAAGGTG---T-
1 GCACCTTTTGAACTTTGTTAGGTGCCTTA
* * * *
33137 GTACCTTTTAAACATTGTTAAGTGCCTTA
1 GCACCTTTTGAACTTTGTTAGGTGCCTTA
* **
33166 GCACCGTTTG-ACTTTAG-TAGGCACCTTA
1 GCACCTTTTGAACTTT-GTTAGGTGCCTTA
* *
33194 GCACC-TTTGAACTTTG-TAAGTGCCATA
1 GCACCTTTTGAACTTTGTTAGGTGCCTTA
33221 GCACCT
1 GCACCT
33227 ATGGATTTTG
Statistics
Matches: 111, Mismatches: 26, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
25 17 0.15
26 1 0.01
27 17 0.15
28 23 0.21
29 53 0.48
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (29 bp):
GCACCTTTTGAACTTTGTTAGGTGCCTTA
Found at i:43376 original size:28 final size:27
Alignment explanation
Indices: 43305--43384 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
43295 CAAAATCCAT
* *
43305 AGGTGCTATGGCACTTACAAAGTTCAA
1 AGGTGCTAAGGCACCTACAAAGTTCAA
** *
43332 AGGTGCTAAGGTGCCTATTAAAG-TCAA
1 AGGTGCTAAGGCACCTA-CAAAGTTCAA
43359 ACGGTGCTAAGGCACCTAACAAAGTT
1 A-GGTGCTAAGGCACCT-ACAAAGTT
43385 TAAAAGGTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
27 18 0.44
28 21 0.51
29 2 0.05
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (27 bp):
AGGTGCTAAGGCACCTACAAAGTTCAA
Found at i:52807 original size:25 final size:25
Alignment explanation
Indices: 52779--52872 Score: 89
Period size: 25 Copynumber: 3.6 Consensus size: 25
52769 GTGGTCACAA
* * *
52779 CCACCTATATCAACTCGTGGCCTAG
1 CCACGTATAACAACCCGTGGCCTAG
*
52804 CCACGTATAACAACCCGTGGCCTTG
1 CCACGTATAACAACCCGTGGCCTAG
* *
52829 CCACGTATAATCACATACCGTGCCCTAG
1 CCACGTATAA-CA-A-CCCGTGGCCTAG
* *
52857 CCATGTCTAACAACCC
1 CCACGTATAACAACCC
52873 CTAGGTGACC
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
25 33 0.59
26 3 0.05
27 3 0.05
28 17 0.30
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.21
Consensus pattern (25 bp):
CCACGTATAACAACCCGTGGCCTAG
Found at i:69282 original size:125 final size:125
Alignment explanation
Indices: 69060--69292 Score: 331
Period size: 125 Copynumber: 1.9 Consensus size: 125
69050 GATGAGAGAA
*
69060 AGAGAGGGGAGGAAAAATAGTAATTCCTTCCTTTCCTTTCTTTGGTGAGAAAAACTAGGAGGAGA
1 AGAGAGGGGAGGAAAAATAGTAATTCCTTCCTTTCCTTTCTTTGGTGAAAAAAACTAGGAGGAGA
* ********** *
69125 GAAGGANNNNNNNNNNATTTGCATTGATTCCTTCCTTTTAAATCTAATCCTTTTAAATTG
66 AAAGGAAAATGCATGAATTTGAATTGATTCCTTCCTTTTAAATCTAATCCTTTTAAATTG
* *
69185 AGAGAGTGGAGGGAAAATAGTAATTCCTTCCTTTCCTTTCTTTGGTGAAAAAAACTAGGAGGAGA
1 AGAGAGGGGAGGAAAAATAGTAATTCCTTCCTTTCCTTTCTTTGGTGAAAAAAACTAGGAGGAGA
69250 AAAGGAAAATGCATGAATTTGAATTGATTCCTTCCTTTTAAAT
66 AAAGGAAAATGCATGAATTTGAATTGATTCCTTCCTTTTAAAT
69293 TGAGAGGAAG
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
125 93 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.31
Consensus pattern (125 bp):
AGAGAGGGGAGGAAAAATAGTAATTCCTTCCTTTCCTTTCTTTGGTGAAAAAAACTAGGAGGAGA
AAAGGAAAATGCATGAATTTGAATTGATTCCTTCCTTTTAAATCTAATCCTTTTAAATTG
Found at i:83374 original size:11 final size:11
Alignment explanation
Indices: 83358--83393 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
83348 ATGAAATTCC
83358 ATAGTTTGTTA
1 ATAGTTTGTTA
83369 ATAGTTTGTTA
1 ATAGTTTGTTA
83380 ATAGTTTGTTA
1 ATAGTTTGTTA
83391 ATA
1 ATA
83394 AGGCAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.53
Consensus pattern (11 bp):
ATAGTTTGTTA
Found at i:98058 original size:21 final size:21
Alignment explanation
Indices: 98032--98077 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
98022 TATAATAAAC
98032 TCAAAAGAAC-TAACATTACAT
1 TCAAAAG-ACTTAACATTACAT
*
98053 TCAAAAGACTTAACTTTACAT
1 TCAAAAGACTTAACATTACAT
98074 TCAA
1 TCAA
98078 CGAAGCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.48, C:0.20, G:0.04, T:0.28
Consensus pattern (21 bp):
TCAAAAGACTTAACATTACAT
Found at i:165340 original size:14 final size:11
Alignment explanation
Indices: 165306--165334 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
165296 GGCATCAAAT
165306 TATTTTAATAC
1 TATTTTAATAC
165317 TATTTTAATAC
1 TATTTTAATAC
165328 TATTTTA
1 TATTTTA
165335 TTAATAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTTAATAC
Found at i:166524 original size:29 final size:29
Alignment explanation
Indices: 166383--166567 Score: 100
Period size: 29 Copynumber: 6.6 Consensus size: 29
166373 CAAAATCCAC
* * *
166383 AGGTGCCATGGCACCT-ACAAAG-TCTAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
** *
166410 AGGTGCTAAGGTGCCTAATAAAG-TCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* * * * ** *
166438 TGATGATACGAAACCTAACAATGTTCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* * *
166467 A-G-G-T-AGGCATCTAACAAAGTTCCAT
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
*
166492 AGGTGTTAAGGCACCTAACAAAGTTCAAA
1 AGGTGCTAAGGCACCTAACAAAGTTCAAA
* * *
166521 AGGTACTATGGCACCGTATA-TAA-TTCAAA
1 AGGTGCTAAGGCACC-TA-ACAAAGTTCAAA
*
166550 AGGTGCAAAGGCACCTAA
1 AGGTGCTAAGGCACCTAA
166568 GAGGGTTAAA
Statistics
Matches: 116, Mismatches: 34, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
25 15 0.13
26 2 0.02
27 15 0.13
28 26 0.22
29 53 0.46
30 4 0.03
31 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.22
Consensus pattern (29 bp):
AGGTGCTAAGGCACCTAACAAAGTTCAAA
Found at i:172490 original size:25 final size:25
Alignment explanation
Indices: 172426--172509 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
172416 AGACTATGAG
*
172426 ACGTGGCTAGGCCATGGTCTATGATTAT
1 ACGTGGCTAGGCCATGG-GT-TG-TTAT
* *
172454 ATGTGGCAAGGCCATGGGTTGTTAT
1 ACGTGGCTAGGCCATGGGTTGTTAT
* * * *
172479 ACGTGTCTAGGCCACGAGTTGATAT
1 ACGTGGCTAGGCCATGGGTTGTTAT
172504 ACGTGG
1 ACGTGG
172510 TTACAACCAC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
25 28 0.61
26 2 0.04
27 1 0.02
28 15 0.33
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (25 bp):
ACGTGGCTAGGCCATGGGTTGTTAT
Found at i:176341 original size:5 final size:5
Alignment explanation
Indices: 176332--176364 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
176322 AAATAAAATA
*
176332 ATATT TTATT -TATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATAT
176365 AGATAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
ATATT
Found at i:181691 original size:29 final size:29
Alignment explanation
Indices: 181646--181727 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
181636 NNNNNNNAAG
* *
181646 TTCAAAAGGTACTAAGGCACCTAATATAA-
1 TTCAAAAGGTGCAAAGGCACCTAATA-AAT
*
181675 TTCAAAAGGTGCAAAGGCACCTCATAAAT
1 TTCAAAAGGTGCAAAGGCACCTAATAAAT
181704 TTCAAAAGGTGCAAAGGCACCTAA
1 TTCAAAAGGTGCAAAGGCACCTAA
181728 CAAGGTTAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.04
29 46 0.96
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.21
Consensus pattern (29 bp):
TTCAAAAGGTGCAAAGGCACCTAATAAAT
Found at i:182796 original size:21 final size:21
Alignment explanation
Indices: 182770--182809 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
182760 AAAGAGAAAT
182770 AATGTGAATGGTGGATTGAGA
1 AATGTGAATGGTGGATTGAGA
* *
182791 AATGTGAATTGTGTATTGA
1 AATGTGAATGGTGGATTGA
182810 AAAGTAAGCA
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:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (21 bp):
AATGTGAATGGTGGATTGAGA
Found at i:210704 original size:19 final size:19
Alignment explanation
Indices: 210659--210696 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
210649 NNTTGTGGGT
210659 AATCTTTGACATATTTTCA
1 AATCTTTGACATATTTTCA
210678 AATCTTTGACATATTTTCA
1 AATCTTTGACATATTTTCA
210697 GCTCTTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.47
Consensus pattern (19 bp):
AATCTTTGACATATTTTCA
Found at i:212258 original size:19 final size:19
Alignment explanation
Indices: 212234--212278 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
212224 ACAATGATCT
212234 TCAAAGAGCTGAAAATATG
1 TCAAAGAGCTGAAAATATG
**
212253 TCAAAGATTTGAAAATATG
1 TCAAAGAGCTGAAAATATG
212272 TCAAAGA
1 TCAAAGA
212279 TTACCCACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (19 bp):
TCAAAGAGCTGAAAATATG
Found at i:212279 original size:19 final size:19
Alignment explanation
Indices: 212243--212280 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
212233 TTCAAAGAGC
212243 TGAAAATATGTCAAAGATT
1 TGAAAATATGTCAAAGATT
212262 TGAAAATATGTCAAAGATT
1 TGAAAATATGTCAAAGATT
212281 ACCCACAANN
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.32
Consensus pattern (19 bp):
TGAAAATATGTCAAAGATT
Found at i:216901 original size:19 final size:17
Alignment explanation
Indices: 216865--216903 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
216855 AATTGAAAAG
*
216865 ATAAAATATTTAGTTAT
1 ATAAAATATTTAGATAT
216882 ATAAAATATATATAGATAT
1 ATAAAATAT-T-TAGATAT
216901 ATA
1 ATA
216904 TAGGTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
ATAAAATATTTAGATAT
Found at i:229967 original size:18 final size:19
Alignment explanation
Indices: 229944--229983 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
229934 CAAGTGAAAA
229944 ATTTTA-CAATAAAATAAT
1 ATTTTATCAATAAAATAAT
* *
229962 ATTTTATTAATAAAATATT
1 ATTTTATCAATAAAATAAT
229981 ATT
1 ATT
229984 AAAATNNNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTATCAATAAAATAAT
Found at i:231242 original size:16 final size:16
Alignment explanation
Indices: 231201--231242 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
231191 AAGAGAGGAG
231201 AGAAAAAAAGGAAGAA
1 AGAAAAAAAGGAAGAA
*
231217 AGAAAGAAAGG-AGAA
1 AGAAAAAAAGGAAGAA
231232 AGAAGAAAAAG
1 AGAA-AAAAAG
231243 ACAAAGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGGAAGAA
Found at i:240518 original size:5 final size:5
Alignment explanation
Indices: 240508--240548 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
240498 CTAGGTAGTC
*
240508 ATCAT ATCAT ATTAT ATCAT ATCAT ATCAT ATCAT ATCAT A
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT A
240549 AAGTGGTCCN
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (5 bp):
ATCAT
Found at i:241385 original size:49 final size:50
Alignment explanation
Indices: 241310--241452 Score: 139
Period size: 49 Copynumber: 2.9 Consensus size: 50
241300 CCACCTATGC
* * *
241310 AACATACGTATCTCACTTCAC-GTCATCATTTGAAATCATCTACAG-ACAG
1 AACATACGTATCTCACATC-CTATCATCATCTGAAATCATCTACAGAACAG
* * * * *
241359 AACATACGTATCTGACATCCTATCATCGTCCGAAATCATCTA-TGAATAG
1 AACATACGTATCTCACATCCTATCATCATCTGAAATCATCTACAGAACAG
* * * * *
241408 AACAGACATATCTCACATCATATCATCATCTGGAATCATATACAG
1 AACATACGTATCTCACATCCTATCATCATCTGAAATCATCTACAG
241453 GTGGAACATA
Statistics
Matches: 74, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
48 2 0.03
49 71 0.96
50 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.28
Consensus pattern (50 bp):
AACATACGTATCTCACATCCTATCATCATCTGAAATCATCTACAGAACAG
Found at i:243155 original size:16 final size:15
Alignment explanation
Indices: 243111--243155 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
243101 CTTTCCTTGT
243111 CTTTTTCTTCTTTCTC
1 CTTTTT-TTCTTTCTC
*
243127 CTTTCTTTCTTTCTTC
1 CTTTTTTTCTTTC-TC
*
243143 CTTTTTTTATTTC
1 CTTTTTTTCTTTC
243156 CTCTCTTCGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (15 bp):
CTTTTTTTCTTTCTC
Found at i:248512 original size:36 final size:35
Alignment explanation
Indices: 248473--248592 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 35
248463 ATTCCTATAA
* *
248473 CAAACGACAGAGTCATGTCACGCCCAATTTCCAAG
1 CAAACGACAGAGTCATGTCAAGCCCAATTACCAAG
* * ** * *
248508 ACAAATGACGGAGTCAAATCATGCCCTATTACCAAG
1 -CAAACGACAGAGTCATGTCAAGCCCAATTACCAAG
* * * * *
248544 CAAACAACAGAGTCTTGTCAAGCCCCATTGCTAAG
1 CAAACGACAGAGTCATGTCAAGCCCAATTACCAAG
*
248579 CAAACGATAGAGTC
1 CAAACGACAGAGTC
248593 TCAAAGTCAT
Statistics
Matches: 65, Mismatches: 19, Indels: 1
0.76 0.22 0.01
Matches are distributed among these distances:
35 37 0.57
36 28 0.43
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.18
Consensus pattern (35 bp):
CAAACGACAGAGTCATGTCAAGCCCAATTACCAAG
Found at i:249165 original size:49 final size:50
Alignment explanation
Indices: 249013--249167 Score: 190
Period size: 49 Copynumber: 3.2 Consensus size: 50
249003 ATCCACCTAT
* * * *
249013 GGAACATACATATCTCACTTCATGTCATCATTCGAAATCATCTACA-AAC
1 GGAACATACATATCTCACATCATATCATCGTCCGAAATCATCTACAGAAC
* * * *
249062 GGAACATACGTATCTGACATCCTATCATCGTCTGAAATCATCTAC-GAAC
1 GGAACATACATATCTCACATCATATCATCGTCCGAAATCATCTACAGAAC
* * *
249111 AGAACATACATATCTCACATCATATCATCGTCCGAAATCATATACAGGA-
1 GGAACATACATATCTCACATCATATCATCGTCCGAAATCATCTACAGAAC
249160 GGAACATA
1 GGAACATA
249168 TTCCTTAACA
Statistics
Matches: 88, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
49 86 0.98
50 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (50 bp):
GGAACATACATATCTCACATCATATCATCGTCCGAAATCATCTACAGAAC
Found at i:252718 original size:29 final size:29
Alignment explanation
Indices: 252609--252708 Score: 139
Period size: 29 Copynumber: 3.4 Consensus size: 29
252599 CATAGGTGTT
*
252609 AAGGCACCTAACAAAGTTCAAAAGGTGCT
1 AAGGCACCTAACAAAGTTCAAAAGGTGCA
* *
252638 AAGGCACCTAATATAA-TGCAAAAGGTGCA
1 AAGGCACCTAACA-AAGTTCAAAAGGTGCA
* *
252667 AAAGCACCTAATAAAGTTCAAAAGGTGCA
1 AAGGCACCTAACAAAGTTCAAAAGGTGCA
252696 AAGGCACCTAACA
1 AAGGCACCTAACA
252709 GGGTTAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 2 0.03
29 58 0.94
30 2 0.03
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (29 bp):
AAGGCACCTAACAAAGTTCAAAAGGTGCA
Found at i:254830 original size:16 final size:15
Alignment explanation
Indices: 254800--254841 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
254790 TCCTTGCCTT
254800 TTTC-TTCTTTCTCC
1 TTTCTTTCTTTCTCC
254814 TTTCTTTCTTTCTTCC
1 TTTCTTTCTTTC-TCC
*
254830 TTTTTTTCTTTC
1 TTTCTTTCTTTC
254842 CTCTCTTCGN
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.16
15 7 0.28
16 14 0.56
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTTTCTTTCTCC
Found at i:265115 original size:15 final size:15
Alignment explanation
Indices: 265095--265125 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
265085 CTACGTAGTC
265095 ATCATAGCATATTAT
1 ATCATAGCATATTAT
*
265110 ATCATATCATATTAT
1 ATCATAGCATATTAT
265125 A
1 A
265126 AAGTGGTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (15 bp):
ATCATAGCATATTAT
Found at i:272328 original size:5 final size:5
Alignment explanation
Indices: 272318--272358 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
272308 CTACATAGTC
* *
272318 ATCAT ATCAT ATTAT ATCAT ATCAT GTCAT ATCAT ATCAT A
1 ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT ATCAT A
272359 AACTGGTCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.41
Consensus pattern (5 bp):
ATCAT
Found at i:277070 original size:49 final size:49
Alignment explanation
Indices: 277017--277121 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
277007 TCATCATTTG
* * ** * *
277017 AAATCATCTAC-AGACTGAACATACGTATCTGACATCCTATCATTGTCCA
1 AAATCATCTACTA-ACGGAACATACATATCACACATCATATCATCGTCCA
* *
277066 AAATCATCTACTAACGGAACATACATATCACATATCATATCATCGTTCA
1 AAATCATCTACTAACGGAACATACATATCACACATCATATCATCGTCCA
277115 AAATCAT
1 AAATCAT
277122 ATAGAGGTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 46 0.98
50 1 0.02
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.29
Consensus pattern (49 bp):
AAATCATCTACTAACGGAACATACATATCACACATCATATCATCGTCCA
Found at i:281581 original size:15 final size:16
Alignment explanation
Indices: 281557--281594 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
281547 TCCTTGTCTT
281557 TTTC-TTCTTTC-TCC
1 TTTCTTTCTTTCTTCC
281571 TTTCTTTCTTTCTTCC
1 TTTCTTTCTTTCTTCC
*
281587 TTTTTTTC
1 TTTCTTTC
281595 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 7 0.33
16 10 0.48
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTTTCTTTCTTCC
Found at i:284158 original size:21 final size:21
Alignment explanation
Indices: 284132--284182 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
284122 GTAACCGGCG
284132 AGTAGAATTAGCTAGACACAC
1 AGTAGAATTAGCTAGACACAC
284153 AGTAGAATTAGCTAGACACAC
1 AGTAGAATTAGCTAGACACAC
284174 AGTAGAATT
1 AGTAGAATT
284183 GATAGCGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTAGAATTAGCTAGACACAC
Done.