Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008485.1 Hibiscus syriacus cultivar Beakdansim tig00111319_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: 259404
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:11197 original size:2 final size:2
Alignment explanation
Indices: 11192--11229 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11182 AGAGTCAGAA
11192 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
11230 GGGTTAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26616 original size:14 final size:14
Alignment explanation
Indices: 26597--26627 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
26587 CATAGCAAAA
26597 AAAGAATAAAAAGG
1 AAAGAATAAAAAGG
26611 AAAGAATAAAAAGG
1 AAAGAATAAAAAGG
26625 AAA
1 AAA
26628 TAATCTCTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.06
Consensus pattern (14 bp):
AAAGAATAAAAAGG
Found at i:28679 original size:21 final size:21
Alignment explanation
Indices: 28655--28704 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
28645 GATGTAGGAA
28655 TTTCAGCAATGGCTGTAAGAT
1 TTTCAGCAATGGCTGTAAGAT
* * *
28676 TTTCAGTAGTGGCTGTATGAT
1 TTTCAGCAATGGCTGTAAGAT
*
28697 TTTTAGCA
1 TTTCAGCA
28705 GGTTTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (21 bp):
TTTCAGCAATGGCTGTAAGAT
Found at i:57529 original size:17 final size:17
Alignment explanation
Indices: 57507--57554 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
57497 TTTCAACACT
57507 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
57524 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
57541 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
57555 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:61784 original size:2 final size:2
Alignment explanation
Indices: 61777--61818 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
61767 TTGAAGCAGC
61777 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
61819 TGATAGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70339 original size:18 final size:18
Alignment explanation
Indices: 70316--70352 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
70306 GCTTAGATCC
70316 TGCCTTTTGGTTTCACAT
1 TGCCTTTTGGTTTCACAT
70334 TGCCTTTTGGTTTCACAT
1 TGCCTTTTGGTTTCACAT
70352 T
1 T
70353 AAAAAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.11, C:0.22, G:0.16, T:0.51
Consensus pattern (18 bp):
TGCCTTTTGGTTTCACAT
Found at i:77766 original size:31 final size:31
Alignment explanation
Indices: 77730--77794 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
77720 ATGAATGAAT
* *
77730 AATGCAAAATATTATATGTTCCTGTTGGTTA
1 AATGCAAAATATTATATATTCCTGTTGATTA
** * *
77761 AATGCATGATGTTATATATTCTTGTTGATTA
1 AATGCAAAATATTATATATTCCTGTTGATTA
77792 AAT
1 AAT
77795 ATATGATGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (31 bp):
AATGCAAAATATTATATATTCCTGTTGATTA
Found at i:77801 original size:31 final size:31
Alignment explanation
Indices: 77741--77804 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
77731 ATGCAAAATA
* * *
77741 TTATATGTTCCTGTTGGTTAAATGCATGATG
1 TTATATATTCCTGTTGATTAAATACATGATG
* *
77772 TTATATATTCTTGTTGATTAAATATATGATG
1 TTATATATTCCTGTTGATTAAATACATGATG
77803 TT
1 TT
77805 TTTTGTACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.50
Consensus pattern (31 bp):
TTATATATTCCTGTTGATTAAATACATGATG
Found at i:80833 original size:21 final size:21
Alignment explanation
Indices: 80812--80900 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
80802 GAAGTGCCAT
*
80812 ATAATTGTCCCAAATGACCAT
1 ATAATTGTCCCAAATGACCAC
* * *
80833 ATAGGTTTGTACCAAA-GTTCCAC
1 ATA--ATTGTCCCAAATG-ACCAC
* * *
80856 ATATTTGTCCCGAAGGACCAC
1 ATAATTGTCCCAAATGACCAC
*
80877 ATAATTGTCCCGAATGACCAC
1 ATAATTGTCCCAAATGACCAC
80898 ATA
1 ATA
80901 GACCCTCGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
21 38 0.69
22 2 0.04
23 15 0.27
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.27
Consensus pattern (21 bp):
ATAATTGTCCCAAATGACCAC
Found at i:81707 original size:55 final size:55
Alignment explanation
Indices: 81623--81764 Score: 203
Period size: 55 Copynumber: 2.6 Consensus size: 55
81613 TACTTAGGGA
* * *
81623 TATCGATACACTCCTCAGTGTACCGATACACAAATAGTACTCGATGTTTTGAGAG
1 TATCGATACACTCCTCAGTGTACCGATACACAAAGAGCACTCGATGTTTTAAGAG
* * * * *
81678 TATCGATACACTCTTCAGTATACCGATACAAAAAGAGCATTCGATGTTTTAAGGG
1 TATCGATACACTCCTCAGTGTACCGATACACAAAGAGCACTCGATGTTTTAAGAG
*
81733 TATCGATACACTCCTCAGTGTACTGATACACA
1 TATCGATACACTCCTCAGTGTACCGATACACA
81765 CTCATACAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (55 bp):
TATCGATACACTCCTCAGTGTACCGATACACAAAGAGCACTCGATGTTTTAAGAG
Found at i:82305 original size:4 final size:4
Alignment explanation
Indices: 82296--82320 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
82286 AGGCAAGAAG
82296 AAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA A
82321 GAGCTTCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:86352 original size:21 final size:21
Alignment explanation
Indices: 86327--86460 Score: 96
Period size: 21 Copynumber: 6.3 Consensus size: 21
86317 CATCGAAGTG
86327 CCACATAATTGTCCCAAATGA
1 CCACATAATTGTCCCAAATGA
* *
86348 CCACATAGGTT-TGCACCGAAGTG-
1 CCACATA-ATTGT-C-CC-AAATGA
* *
86371 CCACATATTTGTCCTGAAA-GA
1 CCACATAATTGTCC-CAAATGA
* *
86392 CCA-AAAATTGTCCCGAATGA
1 CCACATAATTGTCCCAAATGA
* * * *
86412 CCACATAATTATCTCGAAGGA
1 CCACATAATTGTCCCAAATGA
*
86433 CCACATAATTGTCCCGAATGA
1 CCACATAATTGTCCCAAATGA
86454 CCACATA
1 CCACATA
86461 GACCCTCGAC
Statistics
Matches: 88, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.02
20 14 0.16
21 52 0.59
22 6 0.07
23 10 0.11
24 4 0.05
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (21 bp):
CCACATAATTGTCCCAAATGA
Found at i:87281 original size:41 final size:41
Alignment explanation
Indices: 87224--87301 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
87214 CAAATAGCAC
* *
87224 TCGATGTTTTGAGGGTATCGATACACTCTTTAGTGTATCAT
1 TCGATGTTTTGAGGGTATCGATACACTCCTCAGTGTATCAT
87265 TCGATGTTTTGAGGGTATCGATACACTCCTCAGTGTA
1 TCGATGTTTTGAGGGTATCGATACACTCCTCAGTGTA
87302 CCGATACACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (41 bp):
TCGATGTTTTGAGGGTATCGATACACTCCTCAGTGTATCAT
Found at i:87283 original size:21 final size:22
Alignment explanation
Indices: 87224--87286 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 22
87214 CAAATAGCAC
87224 TCGATGTTTTGAGGGTATCGAT
1 TCGATGTTTTGAGGGTATCGAT
* * *
87246 AC-ACT-CTTT-AGTGTATC-AT
1 TCGA-TGTTTTGAGGGTATCGAT
87265 TCGATGTTTTGAGGGTATCGAT
1 TCGATGTTTTGAGGGTATCGAT
87287 ACACTCCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
19 4 0.13
20 11 0.37
21 11 0.37
22 4 0.13
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.41
Consensus pattern (22 bp):
TCGATGTTTTGAGGGTATCGAT
Found at i:91157 original size:15 final size:15
Alignment explanation
Indices: 91137--91166 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
91127 AAAATATGAC
91137 ATGAGCTATGTGATA
1 ATGAGCTATGTGATA
91152 ATGAGCTATGTGATA
1 ATGAGCTATGTGATA
91167 TAAGTTATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
ATGAGCTATGTGATA
Found at i:91177 original size:14 final size:15
Alignment explanation
Indices: 91140--91178 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
91130 ATATGACATG
*
91140 AGCTATGTGATAATG
1 AGCTATGTGATAATA
91155 AGCTATGTGAT-ATA
1 AGCTATGTGATAATA
*
91169 AGTTATGTGA
1 AGCTATGTGA
91179 ACTGTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (15 bp):
AGCTATGTGATAATA
Found at i:91294 original size:23 final size:22
Alignment explanation
Indices: 91267--91343 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
91257 CTACGCAGTC
91267 CTTCGGGATAATTCTACGTGGT
1 CTTCGGGATAATTCTACGTGGT
* *
91289 CATTCGGGATAATTTTACGCTGTT
1 C-TTCGGGATAATTCTACG-TGGT
* * *
91313 CTTCAGGATAATACTATGTGGT
1 CTTCGGGATAATTCTACGTGGT
91335 CCTTCGGGA
1 -CTTCGGGA
91344 CATTTCTATG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.09
23 36 0.82
24 4 0.09
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (22 bp):
CTTCGGGATAATTCTACGTGGT
Found at i:93408 original size:5 final size:5
Alignment explanation
Indices: 93364--93407 Score: 70
Period size: 5 Copynumber: 8.8 Consensus size: 5
93354 GAAAAGTAAA
* *
93364 TAATG TAATG TAATG TAATG TAATG TAATG TAATA TAATA TAAT
1 TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAATG TAAT
93408 AAAAACGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (5 bp):
TAATG
Found at i:93447 original size:21 final size:21
Alignment explanation
Indices: 93423--93463 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
93413 CGATATAACA
* * *
93423 TATATTATATTTTTCAAAAAC
1 TATATAATATGTTTAAAAAAC
93444 TATATAATATGTTTAAAAAA
1 TATATAATATGTTTAAAAAA
93464 AATTATATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
TATATAATATGTTTAAAAAAC
Found at i:93514 original size:2 final size:2
Alignment explanation
Indices: 93509--93541 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
93499 TTAAAAAAAC
93509 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
93542 GTTTTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93587 original size:37 final size:38
Alignment explanation
Indices: 93529--93615 Score: 131
Period size: 37 Copynumber: 2.3 Consensus size: 38
93519 TATATATATA
* *
93529 TATATATATATATGTTTTCAAAAATGTGTTTTCAAAAC
1 TATATATATATACGCTTTCAAAAATGTGTTTTCAAAAC
93567 TATATAT-TATACGCTTTCAAAAATGTGTTTTCAAAAC
1 TATATATATATACGCTTTCAAAAATGTGTTTTCAAAAC
*
93604 CATATCATATAT
1 TATAT-ATATAT
93616 GTTTTCCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 32 0.73
38 9 0.20
39 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (38 bp):
TATATATATATACGCTTTCAAAAATGTGTTTTCAAAAC
Found at i:99453 original size:18 final size:18
Alignment explanation
Indices: 99430--99464 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
99420 GTTCTTAAGG
99430 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
99448 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
99465 AATATACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:107616 original size:21 final size:21
Alignment explanation
Indices: 107590--107629 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
107580 CAGAACCCCA
*
107590 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
107611 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
107630 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:113929 original size:18 final size:18
Alignment explanation
Indices: 113903--113937 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
113893 GTTCTTAAGG
*
113903 AGTGGTCCTTCGGGACAT
1 AGTGATCCTTCGGGACAT
113921 AGTGATCCTTCGGGACA
1 AGTGATCCTTCGGGACA
113938 AATATATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
AGTGATCCTTCGGGACAT
Found at i:118039 original size:19 final size:19
Alignment explanation
Indices: 118012--118059 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
118002 GCAATTAGTA
*
118012 CATCGATGCGTAAAGAGTG
1 CATCGATGCATAAAGAGTG
* *
118031 CATCAATGCATAAGGAGTG
1 CATCGATGCATAAAGAGTG
118050 CATCGATGCA
1 CATCGATGCA
118060 CCCCCTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (19 bp):
CATCGATGCATAAAGAGTG
Found at i:118894 original size:18 final size:17
Alignment explanation
Indices: 118871--118919 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
118861 GGGATAAATC
*
118871 AGTGGTACTTCAGGACAT
1 AGTGGTCCTTC-GGACAT
118889 AGTGGTCCTTCGGAACAT
1 AGTGGTCCTTCGG-ACAT
118907 AGTGGTCCTTCGG
1 AGTGGTCCTTCGG
118920 GACAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (17 bp):
AGTGGTCCTTCGGACAT
Found at i:119335 original size:21 final size:21
Alignment explanation
Indices: 119311--119350 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
119301 TAATTCAAGG
119311 AAAAGG-TATATAGATAAGTAT
1 AAAAGGATAT-TAGATAAGTAT
119332 AAAAGGATATTAGATAAGT
1 AAAAGGATATTAGATAAGT
119351 TGTGCAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.53, C:0.00, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAAGGATATTAGATAAGTAT
Found at i:136483 original size:24 final size:24
Alignment explanation
Indices: 136456--136574 Score: 168
Period size: 24 Copynumber: 5.0 Consensus size: 24
136446 TTCGATTTGA
*
136456 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
136480 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
* * *
136504 ATTATGATTTGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
136528 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
136552 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
136575 AATTATGTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:136751 original size:43 final size:43
Alignment explanation
Indices: 136690--136784 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
136680 GGGCCTTACT
*
136690 TGGTGTGTTGGTGGGTGTATGATTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGATTCTGGGAAACCTACACATTA
*
136733 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGATTCTGGGAAACCTACACATTA
136776 TGGTGTGTT
1 TGGTGTGTT
136785 CGGTTGGAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGATTCTGGGAAACCTACACATTA
Found at i:138907 original size:13 final size:13
Alignment explanation
Indices: 138889--138931 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
138879 TCATAACCCG
138889 ACCCGACCCGTTT
1 ACCCGACCCGTTT
*
138902 ACCCGACCCATTT
1 ACCCGACCCGTTT
*
138915 ACCCGACCCGTTG
1 ACCCGACCCGTTT
138928 ACCC
1 ACCC
138932 ATTGACTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.19, C:0.49, G:0.14, T:0.19
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:141523 original size:24 final size:24
Alignment explanation
Indices: 141496--141612 Score: 173
Period size: 24 Copynumber: 4.9 Consensus size: 24
141486 TTCGATTTGA
141496 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
141520 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
141544 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
141568 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
141592 ATTTTGATATGATACTTGACA
1 ATTCTGATCTGATACTTGACA
141613 GGAATTATGT
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:141791 original size:43 final size:43
Alignment explanation
Indices: 141730--141824 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
141720 GGGCCTTACT
141730 TGGTGTGTTGATGGGTGTATGATTCTAGGG-AACCTACACATTA
1 TGGTGTGTTGATGGGTGTATGATTCT-GGGAAACCTACACATTA
*
141773 TGGTGTGTTGATGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGATGGGTGTATGATTCTGGGAAACCTACACATTA
141816 TGGTGTGTT
1 TGGTGTGTT
141825 CGGTTGGAGG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 3 0.06
43 47 0.94
ACGTcount: A:0.20, C:0.11, G:0.33, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGATGGGTGTATGATTCTGGGAAACCTACACATTA
Found at i:143939 original size:26 final size:27
Alignment explanation
Indices: 143910--143971 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
143900 ACCTTATCTA
143910 ATATAATATAATATATAAT-AAAAACT
1 ATATAATATAATATATAATCAAAAACT
* **
143936 ATATAACAT-ATATATTTTCAAAAACT
1 ATATAATATAATATATAATCAAAAACT
*
143962 ATAGAATATA
1 ATATAATATA
143972 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (27 bp):
ATATAATATAATATATAATCAAAAACT
Found at i:143992 original size:22 final size:21
Alignment explanation
Indices: 143943--143993 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
143933 ACTATATAAC
143943 ATATATATTTTCAAAAACTAT
1 ATATATATTTTCAAAAACTAT
* *
143964 AGAATATATTTTCAAAAAAT-T
1 A-TATATATTTTCAAAAACTAT
143985 ATATATATT
1 ATATATATT
143994 ATATATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 7 0.27
21 3 0.12
22 16 0.62
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATATTTTCAAAAACTAT
Found at i:144053 original size:43 final size:42
Alignment explanation
Indices: 143972--144066 Score: 113
Period size: 41 Copynumber: 2.2 Consensus size: 42
143962 ATAGAATATA
* *
143972 TTTTCAAAAAATTATATATATTATATATTTTTTCAAAAATCG
1 TTTTCAAAAAATTATATATATTATATATATATTCAAAAATCG
*
144014 TTTT-AAAAAATTATATATATATATGTATATATATT-AAAAATGTG
1 TTTTCAAAAAATTATATATAT-TA--TATATATATTCAAAAAT-CG
144058 TTTTCAAAA
1 TTTTCAAAA
144067 CTATATATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
41 16 0.36
42 6 0.13
43 6 0.13
44 13 0.29
45 4 0.09
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (42 bp):
TTTTCAAAAAATTATATATATTATATATATATTCAAAAATCG
Found at i:144074 original size:37 final size:38
Alignment explanation
Indices: 144031--144112 Score: 125
Period size: 37 Copynumber: 2.2 Consensus size: 38
144021 AAATTATATA
*
144031 TATATATGTATATATATT-AAAAATGTGTTTTCAAAAC
1 TATATATGTATACATATTCAAAAATGTGTTTTCAAAAC
*
144068 TATATAT-TATACATTTTCAAAAATGTGTTTTCAAAAC
1 TATATATGTATACATATTCAAAAATGTGTTTTCAAAAC
144105 TAT-TATGT
1 TATATATGT
144113 GTTTTGATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 11 0.27
37 30 0.73
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (38 bp):
TATATATGTATACATATTCAAAAATGTGTTTTCAAAAC
Found at i:145340 original size:16 final size:17
Alignment explanation
Indices: 145319--145354 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
145309 TATAATATTG
145319 AAACTTGAACT-AAAAA
1 AAACTTGAACTCAAAAA
145335 AAACTTGAACTCAAAAA
1 AAACTTGAACTCAAAAA
145352 AAA
1 AAA
145355 TTTAGAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.17
Consensus pattern (17 bp):
AAACTTGAACTCAAAAA
Found at i:147067 original size:16 final size:16
Alignment explanation
Indices: 147046--147092 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
147036 AGGTTTCAGA
*
147046 TTCATATTTTAATTCC
1 TTCATATTCTAATTCC
*
147062 TTCATATTCTAATTCTT
1 TTCATATTCTAATTC-C
147079 TTACATATTCTAAT
1 TT-CATATTCTAAT
147093 AAACATTCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 14 0.52
17 2 0.07
18 11 0.41
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (16 bp):
TTCATATTCTAATTCC
Found at i:153473 original size:3 final size:3
Alignment explanation
Indices: 153465--153542 Score: 95
Period size: 3 Copynumber: 25.3 Consensus size: 3
153455 CATTTAAATT
* * *
153465 TTA TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA T-TA TTA
153512 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
153543 ATATATATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 1 0.02
3 58 0.89
4 6 0.09
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:154825 original size:19 final size:18
Alignment explanation
Indices: 154797--154839 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
154787 ATATTATTTG
154797 TTATTACTTTATATT-TTAA
1 TTATTACTTTA-ATTATT-A
*
154816 TTATTGCTTTAATTATTA
1 TTATTACTTTAATTATTA
154834 TTATTA
1 TTATTA
154840 TCTTAGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATTACTTTAATTATTA
Found at i:155544 original size:20 final size:21
Alignment explanation
Indices: 155521--155572 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
155511 AGAAATTAAA
155521 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
155541 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
155563 -ATT-ATTTATT
1 AATTCATTTATT
155573 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:159291 original size:4 final size:4
Alignment explanation
Indices: 159282--159317 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
159272 TTGTGCAAAA
159282 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
159318 TGTGTTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:162653 original size:83 final size:83
Alignment explanation
Indices: 162514--162768 Score: 483
Period size: 83 Copynumber: 3.1 Consensus size: 83
162504 GTAATTGGGA
162514 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
162579 TTTAGAAGATGAATGTGC
66 TTTAGAAGATGAATGTGC
162597 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
162662 TTTAGAAGATGAATGTGC
66 TTTAGAAGATGAATGTGC
*
162680 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTATACAGAACCAATCATTGAA
1 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
* *
162745 TTTAAAAGATGAATTTGC
66 TTTAGAAGATGAATGTGC
162763 TCATAG
1 TCATAG
162769 GAGAAATAAG
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 169 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (83 bp):
TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACCAATCATTGAA
TTTAGAAGATGAATGTGC
Found at i:165544 original size:22 final size:22
Alignment explanation
Indices: 165476--165555 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
165466 TACATCTGCA
* *
165476 CTTTTTAAAGATAATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
** * * * *
165498 CACTTCAGAGATGACAAATTTT
1 CTTTTCAAAGATGATAGATTCT
*
165520 CTTTTTAAAGATGATAGATTCT
1 CTTTTCAAAGATGATAGATTCT
*
165542 CTTTTCAAAAATGA
1 CTTTTCAAAGATGA
165556 AAGCTTTATG
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (22 bp):
CTTTTCAAAGATGATAGATTCT
Found at i:166462 original size:76 final size:76
Alignment explanation
Indices: 166224--166718 Score: 857
Period size: 76 Copynumber: 6.5 Consensus size: 76
166214 CTATTTCTCA
166224 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
166289 AAAGCCTTCGGGT
64 AAAACCTTCGGGT
* *
166302 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAAAGCCTTCGGTAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
166367 AAAGCCTTCGGGT
64 AAAACCTTCGGGT
166380 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
166445 AACCTTCGGGT
66 AACCTTCGGGT
166456 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
166521 AACCTTCGGGT
66 AACCTTCGGGT
*
166532 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
166597 AGCCTTCGGGT
66 AACCTTCGGGT
166608 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
166673 AACCTTCGGGT
66 AACCTTCGGGT
* * *
166684 CATCTATAAGCCCTTTC-GTGCATGATGTTTTCAAA
1 CATCTGTAAGTCC-TTCAGTGCATGATGTTTCCAAA
166719 CATTTCCATC
Statistics
Matches: 404, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
76 294 0.73
77 3 0.01
78 107 0.26
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:166853 original size:3 final size:3
Alignment explanation
Indices: 166845--166918 Score: 96
Period size: 3 Copynumber: 24.3 Consensus size: 3
166835 CATTTAAATT
* * *
166845 TTA TTA TTA TTA TTA TTA -AA TTTA TTA TTA CTAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA
166891 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
166919 ATATATATAT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 58 0.94
4 3 0.05
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:172339 original size:14 final size:14
Alignment explanation
Indices: 172320--172354 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
172310 GTTAATAATT
172320 TCCAAAAGTTATTC
1 TCCAAAAGTTATTC
172334 TCCAAAAGTTATTC
1 TCCAAAAGTTATTC
172348 TCCAAAA
1 TCCAAAA
172355 ATATAATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (14 bp):
TCCAAAAGTTATTC
Found at i:174533 original size:12 final size:13
Alignment explanation
Indices: 174504--174532 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
174494 AAATCATATG
174504 TTTTAAAAATGAA
1 TTTTAAAAATGAA
174517 TTTTAAAAATGAA
1 TTTTAAAAATGAA
174530 TTT
1 TTT
174533 ATTAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (13 bp):
TTTTAAAAATGAA
Found at i:190846 original size:3 final size:3
Alignment explanation
Indices: 190838--190922 Score: 134
Period size: 3 Copynumber: 27.7 Consensus size: 3
190828 TTTTTACCCA
190838 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* *
190884 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAA TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
190923 AATACATATA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
3 70 0.92
4 6 0.08
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:194598 original size:22 final size:20
Alignment explanation
Indices: 194568--194607 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
194558 GCATTTGTAT
194568 TTTGCATTTGTACATTTTTACG
1 TTTGCA-TT-TACATTTTTACG
*
194590 TTTGTATTTACATTTTTA
1 TTTGCATTTACATTTTTA
194608 AATTTACATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 2 0.12
22 5 0.29
ACGTcount: A:0.20, C:0.10, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTGCATTTACATTTTTACG
Found at i:197970 original size:13 final size:12
Alignment explanation
Indices: 197952--197988 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
197942 AATAAAGAAG
197952 AAAAAAAAGGAA
1 AAAAAAAAGGAA
197964 AAAAAAAAGGAA
1 AAAAAAAAGGAA
197976 AAAAAAAA-GAA
1 AAAAAAAAGGAA
197987 AA
1 AA
197989 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGGAA
Found at i:197988 original size:17 final size:16
Alignment explanation
Indices: 197962--197994 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
197952 AAAAAAAAGG
197962 AAAAAAAAAAGGAAAA
1 AAAAAAAAAAGGAAAA
197978 AAAAAAGAAAAGGAAAA
1 AAAAAA-AAAAGGAAAA
197995 TTGAATCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGGAAAA
Found at i:197994 original size:12 final size:11
Alignment explanation
Indices: 197952--197988 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
197942 AATAAAGAAG
197952 AAAAAAAAGGAA
1 AAAAAAAAGG-A
197964 AAAAAAAAGGA
1 AAAAAAAAGGA
*
197975 AAAAAAAAAGA
1 AAAAAAAAGGA
197986 AAA
1 AAA
197989 GGAAAATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGGA
Found at i:202950 original size:22 final size:22
Alignment explanation
Indices: 202920--202998 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
202910 ACATCTACAT
*
202920 TCTTCAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
*
202942 TCTTTAAAGATGATAGATTCCC
1 TCTTTAAAGATGATAGATTCTC
* * *
202964 TTTTTAAAGATGACAGATTATC
1 TCTTTAAAGATGATAGATTCTC
202986 T-TTTCAAAGATGA
1 TCTTT-AAAGATGA
202999 AAGTTTTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
21 3 0.06
22 47 0.94
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:203598 original size:113 final size:112
Alignment explanation
Indices: 203435--204638 Score: 1553
Period size: 113 Copynumber: 10.6 Consensus size: 112
203425 GTATCAGTTC
*
203435 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
203500 CAACCTTTTGCTCAAATCCATCATCTGATAGATCAGCTTTTCCAGAAA
66 CAACCTTTTGCTCGAATTCATCAT-TGATGGATCAGCTTTTCCAGAAA
*
203548 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
203613 CAACCTTTTGCTCAAATCCATCATCTGGTGGATCAGCTTTTCCAGAAA
66 CAACCTTTTGCTCGAATTCATCAT-TGATGGATCAGCTTTTCCAGAAA
* * **
203661 AAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
203726 CAACCTTTTGCTCAAATCCATCATTTGATGGATCAGATTTTCCAGAAA
66 CAACCTTTTGCTCGAATTCATCA-TTGATGGATCAGCTTTTCCAGAAA
* **
203774 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
203839 CAACCTTTTGCTCAAATCCATCATTTGATGGATCAGATTTTCCAGAAA
66 CAACCTTTTGCTCGAATTCATCA-TTGATGGATCAGCTTTTCCAGAAA
203887 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-G--GAAGAAGTTCATAAT-AGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
203948 CAACCTTTTAC-CTGAATTCATCAAATTGATGGATTATCTTTTCCAGAAA
66 CAACCTTTTGCTC-GAATTCATC--ATTGATGGATCAGCTTTTCCAGAAA
*
203997 AGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
204062 CAACCTTTTAC-CTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGA
66 CAACCTTTTGCTC-GAATTCATC--ATTGATGGATCAGCTTTTCCAGAAA
* *
204111 AGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
204176 CAACCTTTTAC-CTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGA
66 CAACCTTTTGCTC-GAATTCATC--ATTGATGGATCAGCTTTTCCAGAAA
*
204225 AGGTTCATAATGAGAAG-ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * * *
204289 CAACCTTTTAC-CTGAATTCATCAAATTGATGGATTATCTTTTCCAGAGA
66 CAACCTTTTGCTC-GAATTCATC--ATTGATGGATCAGCTTTTCCAGAAA
* *
204338 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGGAGTTTCATAATGAGAAGAACTTGT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG-TTCATAATGAGAAGAATTTGT
* * * * * *
204403 TCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAGATA
65 TCAACCTTTTGCTCGAATTCATCA-TTGATGGATCAGCTTTTCCAGAAA
* *
204452 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * * * * **
204517 GTTCAATCTTTTGTTTGAATTCATCATTTGATGTATCAACATTGCCAGGTA
63 GTTCAACCTTTTGCTCGAATTCATCA-TTGATGGATCAGCTTTTCCAGAAA
* * * *
204568 GAGTTCATAATGAAAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTT
1 AAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
204633 GTTCAA
63 GTTCAA
204639 TAATTCTATC
Statistics
Matches: 1035, Mismatches: 41, Indels: 27
0.94 0.04 0.02
Matches are distributed among these distances:
108 1 0.00
109 28 0.03
110 66 0.06
111 2 0.00
112 1 0.00
113 486 0.47
114 253 0.24
115 39 0.04
116 137 0.13
117 22 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGCTCGAATTCATCATTGATGGATCAGCTTTTCCAGAAA
Found at i:204971 original size:3 final size:3
Alignment explanation
Indices: 204965--205022 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
204955 TTTTATAATA
* *
204965 ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATC ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
205013 ATT ATT ATT A
1 ATT ATT ATT A
205023 AATATATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:205034 original size:11 final size:10
Alignment explanation
Indices: 205018--205058 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
205008 TTATTATTAT
205018 TATTAAATATA
1 TATTAAATA-A
205029 TATTAAATACA
1 TATTAAATA-A
205040 TATATAAATAA
1 TAT-TAAATAA
205051 TATTAAAT
1 TATTAAAT
205059 TACAAAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:205495 original size:18 final size:17
Alignment explanation
Indices: 205466--205504 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
205456 CTGAAAAAAG
205466 AAAAAAGAAAGAAGACAGA
1 AAAAAAGAAAG-A-ACAGA
205485 AAAAAAG-AAGAACAGA
1 AAAAAAGAAAGAACAGA
205501 AAAA
1 AAAA
205505 CAGAGAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 3 0.15
19 7 0.35
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAGAACAGA
Found at i:205499 original size:16 final size:16
Alignment explanation
Indices: 205468--205515 Score: 64
Period size: 15 Copynumber: 3.1 Consensus size: 16
205458 GAAAAAAGAA
205468 AAAAGAAAGAAG-ACAG
1 AAAA-AAAGAAGAACAG
205484 AAAAAAAGAAGAACAG
1 AAAAAAAGAAGAACAG
*
205500 AAAAACAG-AGAACAG
1 AAAAAAAGAAGAACAG
205515 A
1 A
205516 TCCTAGAGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAGAACAG
Found at i:229775 original size:214 final size:214
Alignment explanation
Indices: 229406--229833 Score: 811
Period size: 214 Copynumber: 2.0 Consensus size: 214
229396 ATATTTATTT
*
229406 TAAAAATAGTATGAATTGTATTGAAATGTGATGGACAGAAATGAAATTTTCATAGTAAGACATGT
1 TAAAAATAGTATGAATTGTATTGAAATGCGATGGACAGAAATGAAATTTTCATAGTAAGACATGT
*
229471 TCAATGGTCACTATTGTTTATAGTTCTTGGCTTTATTTTCTTTTCATCCCATTGACTGAATATGA
66 TCAATGGTCACTACTGTTTATAGTTCTTGGCTTTATTTTCTTTTCATCCCATTGACTGAATATGA
*
229536 TAAAAGGACGTGTGTTAAAATCTTTTTTTCAATATTGCATTCTTAAATGCGTTCGAACCCACGTT
131 TAAAAGGACGTGTGTTAAAATCTTTTTTTCAATATTGCATTCTTAAATGCATTCGAACCCACGTT
229601 CTCTTGGATGTTGCAACAA
196 CTCTTGGATGTTGCAACAA
229620 TAAAAATAGTATGAATTGTATTGAAATGCGATGGACAGAAATGAAATTTTCATAGTAAGACATGT
1 TAAAAATAGTATGAATTGTATTGAAATGCGATGGACAGAAATGAAATTTTCATAGTAAGACATGT
229685 TCAATGGTCACTACTGTTTATAGTTCTTGGCTTTATTTTCTTTTCATCCCATTGACTGAATATGA
66 TCAATGGTCACTACTGTTTATAGTTCTTGGCTTTATTTTCTTTTCATCCCATTGACTGAATATGA
*
229750 TAAAAGGATGTGTGTTAAAATCTTTTTTTCAATATTGCATTCTTAAATGCATTCGAACCCACGTT
131 TAAAAGGACGTGTGTTAAAATCTTTTTTTCAATATTGCATTCTTAAATGCATTCGAACCCACGTT
*
229815 CTTTTGGATGTTGCAACAA
196 CTCTTGGATGTTGCAACAA
229834 CAATGGTGCA
Statistics
Matches: 209, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
214 209 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (214 bp):
TAAAAATAGTATGAATTGTATTGAAATGCGATGGACAGAAATGAAATTTTCATAGTAAGACATGT
TCAATGGTCACTACTGTTTATAGTTCTTGGCTTTATTTTCTTTTCATCCCATTGACTGAATATGA
TAAAAGGACGTGTGTTAAAATCTTTTTTTCAATATTGCATTCTTAAATGCATTCGAACCCACGTT
CTCTTGGATGTTGCAACAA
Found at i:242724 original size:33 final size:34
Alignment explanation
Indices: 242687--242756 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
242677 TTTTTCTAGG
*
242687 AGGGTTAGAGTGT-ATGTGTTTCTTATGTAATTC
1 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
242720 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
1 AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
242754 AGG
1 AGG
242757 TTTATTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 13 0.37
34 22 0.63
ACGTcount: A:0.24, C:0.06, G:0.29, T:0.41
Consensus pattern (34 bp):
AGGGTTAGAGTGTAATGTGTATCTTATGTAATTC
Found at i:247792 original size:18 final size:19
Alignment explanation
Indices: 247756--247796 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
247746 TTCTCAAACA
247756 AAGTCCTAAGACTCTGTTCC
1 AAGTCCTAAGAC-CTGTTCC
247776 AAGTCCTAAGA-CTGTTCC
1 AAGTCCTAAGACCTGTTCC
247794 AAG
1 AAG
247797 CCATAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (19 bp):
AAGTCCTAAGACCTGTTCC
Found at i:256128 original size:29 final size:29
Alignment explanation
Indices: 256093--256174 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
256083 AAGCTAAATT
* *
256093 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
256122 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
256151 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
256175 GTTAGCTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Done.