Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009012.1 Hibiscus syriacus cultivar Beakdansim tig00112400_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: 359633
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:244471 original size:24 final size:25
Alignment explanation
Indices: 244419--244471 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
244409 TTCTGGATAA
244419 ATATGTGGCACTTCGGTGCAAAACT
1 ATATGTGGCACTTCGGTGCAAAACT
*
244444 -TATGTGGCACTTCGGTG-TAAACT
1 ATATGTGGCACTTCGGTGCAAAACT
244467 ATATG
1 ATATG
244472 GTCCTTCGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (25 bp):
ATATGTGGCACTTCGGTGCAAAACT
Found at i:246040 original size:33 final size:33
Alignment explanation
Indices: 246003--246083 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
245993 TTTAGTGTAG
* * *
246003 TTTGGTTCGAACAATACA-GAAAAATAGTGCAAT
1 TTTGGTTCGAACAAGA-AGGAAAAACAATGCAAT
* *
246036 TTTGGTTCGAACGAGAAGGAAACACAATGCAAT
1 TTTGGTTCGAACAAGAAGGAAAAACAATGCAAT
246069 TTTGGATTCGAACAA
1 TTTGG-TTCGAACAA
246084 AAAAAACAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.77
34 8 0.20
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (33 bp):
TTTGGTTCGAACAAGAAGGAAAAACAATGCAAT
Found at i:247750 original size:22 final size:23
Alignment explanation
Indices: 247718--247767 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
247708 TTTTTAGAAT
247718 AGTGATGAACAGTA-CCATGAAC
1 AGTGATGAACAGTACCCATGAAC
*
247740 AGTGATTAACAGTACCCATGAAC
1 AGTGATGAACAGTACCCATGAAC
247763 AGTGA
1 AGTGA
247768 CTGTACCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 13 0.50
23 13 0.50
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (23 bp):
AGTGATGAACAGTACCCATGAAC
Found at i:248546 original size:56 final size:55
Alignment explanation
Indices: 248422--248550 Score: 150
Period size: 56 Copynumber: 2.3 Consensus size: 55
248412 ATAAGCACCG
** * **
248422 TAGTGCTATCCCGTATGACACATAAGGTCGTGTCCACCATCTGTACTGCTATCCTT
1 TAGTG-TATCCCGTATGACACATAAGGTCGTACCCACCATATACACTGCTATCCTT
* * * *
248478 AAGTATAGTCCCGTATGGCACATAAGGTCGTACCCACCATATACACTAGGTATCCTT
1 TAGTGTA-TCCCGTATGACACATAAGGTCGTACCCACCATATACACT-GCTATCCTT
248535 TAGTGTATCCCGTATG
1 TAGTGTATCCCGTATG
248551 CAACCTGTTG
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
55 2 0.03
56 45 0.75
57 13 0.22
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (55 bp):
TAGTGTATCCCGTATGACACATAAGGTCGTACCCACCATATACACTGCTATCCTT
Found at i:250051 original size:30 final size:30
Alignment explanation
Indices: 249990--250054 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
249980 ATTTTGGTCC
* * * *
249990 CTAAACTTTTCAAAGTTTATACTTTGGTCA
1 CTAAACTTTCCAAAGTGTATAATTTGATCA
250020 CTAAACTTTACCAAA-TGTATAATTTGATCA
1 CTAAACTTT-CCAAAGTGTATAATTTGATCA
250050 CTAAA
1 CTAAA
250055 TAGATCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 26 0.87
31 4 0.13
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (30 bp):
CTAAACTTTCCAAAGTGTATAATTTGATCA
Found at i:255727 original size:2 final size:2
Alignment explanation
Indices: 255720--255752 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
255710 TACACTCGTG
255720 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
255753 CTTACACATA
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:258756 original size:41 final size:43
Alignment explanation
Indices: 258587--259065 Score: 206
Period size: 43 Copynumber: 11.0 Consensus size: 43
258577 TCAGGGTCCC
* * * *
258587 CATTTTTTATCTTTATAATT-A-GCTCCTTAATTTTTTTAAATCT
1 CATTTTTTAACTTTATAATTAAGGC-CCCTAA-TTTTATCAATCT
* * *** * *
258630 TATTTTTT-ACATTTATAATTGA-TATCCTAATATTATTCAATTT
1 CATTTTTTAAC-TTTATAATTAAGGCCCCTAATTTTA-TCAATCT
* * * * *
258673 TATTTTTTATCTTTATAATTGAA-GTCTCTAATTTTTTCAATCT
1 CATTTTTTAACTTTATAATT-AAGGCCCCTAATTTTATCAATCT
* *
258716 C-TTTTTTACCTTTATAATTAAGGCCCCTGATTTTAT-AATCT
1 CATTTTTTAACTTTATAATTAAGGCCCCTAATTTTATCAATCT
* * **** *
258757 CACTTTTTAACTCTATAATTAAGGATTTTAAGTTTTTTCAATCT
1 CATTTTTTAACTTTATAATTAAGGCCCCTAA-TTTTATCAATCT
* * *
258801 CATTTTCT-ACTTTTTCAATTGAGGCCCCTAAGTTTT-TCAATCT
1 CATTTTTTAACTTTAT-AATTAAGGCCCCTAA-TTTTATCAATCT
* * * * * * * * *
258844 CAATTTCTACCTTTATAATTGAGGCCCTTATTTTTTTTAATCC
1 CATTTTTTAACTTTATAATTAAGGCCCCTAATTTTATCAATCT
* ** * **
258887 CACTTTTTTAACTTTATAATTGAGGCCATTAAGTTTTTTTTATCT
1 CA-TTTTTTAACTTTATAATTAAGGCCCCTAA-TTTTATCAATCT
* ** * *
258932 CACTTTTTAACTTTCGAATTGAGGCCCCTAATTTT-T-AATTCC
1 CATTTTTTAACTTTATAATTAAGGCCCCTAATTTTATCAA-TCT
* * * * * *
258974 CACTTTTTAAACTTTAAAATTGAGGCCCTTAAGTTTTTTTTAATCT
1 CA-TTTTTTAACTTTATAATTAAGGCCCCTAA--TTTTATCAATCT
* * * * * *
259020 CACTTTATAACTTTCTAATTGAGGCCCCTAAGTTTTTTCGATCT
1 CATTTTTTAACTTTATAATTAAGGCCCCTAA-TTTTATCAATCT
259064 CA
1 CA
259066 ATTATACCTT
Statistics
Matches: 337, Mismatches: 79, Indels: 39
0.74 0.17 0.09
Matches are distributed among these distances:
41 9 0.03
42 61 0.18
43 120 0.36
44 101 0.30
45 39 0.12
46 5 0.01
47 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.50
Consensus pattern (43 bp):
CATTTTTTAACTTTATAATTAAGGCCCCTAATTTTATCAATCT
Found at i:258833 original size:44 final size:44
Alignment explanation
Indices: 258700--259114 Score: 232
Period size: 44 Copynumber: 9.6 Consensus size: 44
258690 ATTGAAGTCT
* * * * *
258700 CTAA-TTTTTTCAATCTC-TTTTTTACCTTTATAATTAAGGCCC
1 CTAAGTTTTTTTAATCTCATTTTCTAACTTTTTAATTGAGGCCC
* * * * * ***
258742 CT--GATTTTATAATCTCACTTTT-TAACTCTATAATTAAGGATT
1 CTAAGTTTTTTTAATCTCA-TTTTCTAACTTTTTAATTGAGGCCC
* *
258784 TTAAGTTTTTTCAATCTCATTTTCT-ACTTTTTCAATTGAGGCCC
1 CTAAGTTTTTTTAATCTCATTTTCTAACTTTTT-AATTGAGGCCC
* * * *
258828 CTAAG-TTTTTCAATCTCAATTTCTACCTTTATAATTGAGG-CC
1 CTAAGTTTTTTTAATCTCATTTTCTAACTTTTTAATTGAGGCCC
* * * * * *
258870 CTTATTTTTTTTAATCCCACTTTTTTAACTTTATAATTGAGGCCA
1 CTAAGTTTTTTTAATCTCA-TTTTCTAACTTTTTAATTGAGGCCC
* * **
258915 TTAAGTTTTTTTTATCTCACTTTT-TAACTTTCGAATTGAGGCCC
1 CTAAGTTTTTTTAATCTCA-TTTTCTAACTTTTTAATTGAGGCCC
* **
258959 CTAA---TTTTTAATTCCCACTTTT-TAAACTTTAAAATTGAGGCCC
1 CTAAGTTTTTTTAA-TCTCA-TTTTCT-AACTTTTTAATTGAGGCCC
* * * *
259002 TTAAGTTTTTTTTAATCTCACTTTATAACTTTCTAATTGAGGCCC
1 CTAAG-TTTTTTTAATCTCATTTTCTAACTTTTTAATTGAGGCCC
** * * * * *
259047 CTAAGTTTTTTCGATCTCA-ATTATACCTTTTACAATTGAGACCC
1 CTAAGTTTTTTTAATCTCATTTTCTAACTTTT-TAATTGAGGCCC
* *
259091 CT-A-TTTTTTTAATATCAATTTCTA
1 CTAAGTTTTTTTAATCTCATTTTCTA
259115 CCTCTATAAT
Statistics
Matches: 292, Mismatches: 61, Indels: 39
0.74 0.16 0.10
Matches are distributed among these distances:
41 16 0.05
42 44 0.15
43 84 0.29
44 92 0.32
45 44 0.15
46 5 0.02
47 7 0.02
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.48
Consensus pattern (44 bp):
CTAAGTTTTTTTAATCTCATTTTCTAACTTTTTAATTGAGGCCC
Found at i:258932 original size:131 final size:129
Alignment explanation
Indices: 258700--259143 Score: 429
Period size: 131 Copynumber: 3.4 Consensus size: 129
258690 ATTGAAGTCT
* * * *
258700 CTAATTTTTTCAATCTC-TTTTTTACCTTTATAATTAAGGCCCCTGA--TTTTATAATCTCACTT
1 CTAATTTTTTCAATCTCAATTTCTACCTTTATAATTAAGG-CCCTTATTTTTTTTAATCTCACTT
* * ***
258762 TTTAACTCTATAATTAAGGATTTTAAGTTTTTTCAATCTCATTTTCTACTTTTTCAATTGAGGCC
65 TTTAACTTTATAATTGAGGCCATTAAGTTTTTTCAATCTCATTTT-TACTTTTTCAATTGAGGCC
258827 C
129 C
* * *
258828 CTAAGTTTTTCAATCTCAATTTCTACCTTTATAATTGAGGCCCTTATTTTTTTTAATCCCACTTT
1 CTAATTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCCCTTATTTTTTTTAATCTCAC-TT
**
258893 TTTAACTTTATAATTGAGGCCATTAAGTTTTTTTTATCTCACTTTTTAAC--TTTCGAATTGAGG
65 TTTAACTTTATAATTGAGGCCATTAAGTTTTTTCAATCTCA-TTTTT-ACTTTTTC-AATTGAGG
258956 CCC
127 CCC
* * * * * *
258959 CTAA-TTTTT-AATTCCCACTTTTTAAACTTTAAAATTGAGGCCCTTAAGTTTTTTTTAATCTCA
1 CTAATTTTTTCAA-TCTCAATTTCT-ACCTTTATAATTAAGGCCCTT-A-TTTTTTTTAATCTCA
* * ** * * * *
259022 CTTTATAACTTTCTAATTGAGGCCCCTAAGTTTTTTCGATCTCAATTATACCTTTTACAATTGAG
62 CTTTTTAACTTTATAATTGAGGCCATTAAGTTTTTTCAATCTCATTTTTA-CTTTTTCAATTGAG
*
259087 ACCC
126 GCCC
* * *
259091 CT-ATTTTTTTAATATCAATTTCTACCTCTATAATTAAGG-CCTCTATTTTTTTT
1 CTAATTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCCCT-TATTTTTTTT
259144 TCGATTTAAT
Statistics
Matches: 261, Mismatches: 38, Indels: 33
0.79 0.11 0.10
Matches are distributed among these distances:
128 21 0.08
129 29 0.11
130 34 0.13
131 89 0.34
132 68 0.26
133 20 0.08
ACGTcount: A:0.25, C:0.19, G:0.08, T:0.48
Consensus pattern (129 bp):
CTAATTTTTTCAATCTCAATTTCTACCTTTATAATTAAGGCCCTTATTTTTTTTAATCTCACTTT
TTAACTTTATAATTGAGGCCATTAAGTTTTTTCAATCTCATTTTTACTTTTTCAATTGAGGCCC
Found at i:258952 original size:88 final size:88
Alignment explanation
Indices: 258877--259056 Score: 292
Period size: 87 Copynumber: 2.1 Consensus size: 88
258867 GCCCTTATTT
* * *
258877 TTTTTAA-TCCCACTTTTTTAACTTTATAATTGAGGCCATTAAGTTTTTTTT-ATCTCACTTTTT
1 TTTTTAATTCCCACTTTTTAAACTTTAAAATTGAGGCCATTAAGTTTTTTTTAATCTCACTTTAT
258940 AACTTTCGAATTGAGGCCCCTAA
66 AACTTTCGAATTGAGGCCCCTAA
*
258963 TTTTTAATTCCCACTTTTTAAACTTTAAAATTGAGGCCCTTAAGTTTTTTTTAATCTCACTTTAT
1 TTTTTAATTCCCACTTTTTAAACTTTAAAATTGAGGCCATTAAGTTTTTTTTAATCTCACTTTAT
*
259028 AACTTTCTAATTGAGGCCCCTAA
66 AACTTTCGAATTGAGGCCCCTAA
259051 GTTTTT
1 -TTTTT
259057 TCGATCTCAA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
86 7 0.08
87 41 0.48
88 33 0.38
89 5 0.06
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (88 bp):
TTTTTAATTCCCACTTTTTAAACTTTAAAATTGAGGCCATTAAGTTTTTTTTAATCTCACTTTAT
AACTTTCGAATTGAGGCCCCTAA
Found at i:259071 original size:43 final size:44
Alignment explanation
Indices: 258676--259065 Score: 325
Period size: 44 Copynumber: 9.0 Consensus size: 44
258666 TCAATTTTAT
* * * * *
258676 TTTTTATCTTTATAATTGAAGTCTCTAA-TTTTTTCAATCTC-T
1 TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAC
* * * *
258718 TTTTTACCTTTATAATTAAGGCCCCTGA-TTTTAT-AATCTCAC
1 TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAC
* * ****
258760 TTTTTAACTCTATAATTAAGGATTTTAAGTTTTTTCAATCTCA-
1 TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAC
* *
258803 TTTTCT-ACTTTTTCAATTGAGGCCCCTAAG-TTTTTCAATCTCAA
1 TTTT-TAACTTTAT-AATTGAGGCCCCTAAGTTTTTTCAATCTCAC
* * * * * *
258847 TTTCTACCTTTATAATTGAGG-CCCTTATTTTTTTTAATCCCAC
1 TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAC
** **
258890 TTTTTTAACTTTATAATTGAGGCCATTAAGTTTTTTTTATCTCAC
1 -TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAC
** *
258935 TTTTTAACTTTCGAATTGAGGCCCCTAA--TTTTT-AATTCCCAC
1 TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAA-TCTCAC
* * *
258977 TTTTTAAACTTTAAAATTGAGGCCCTTAAGTTTTTTTTAATCTCAC
1 TTTTT-AACTTTATAATTGAGGCCCCTAAG-TTTTTTCAATCTCAC
* * *
259023 TTTATAACTTTCTAATTGAGGCCCCTAAGTTTTTTCGATCTCA
1 TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCA
259066 ATTATACCTT
Statistics
Matches: 277, Mismatches: 55, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
41 7 0.03
42 68 0.25
43 67 0.24
44 82 0.30
45 37 0.13
46 14 0.05
47 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.48
Consensus pattern (44 bp):
TTTTTAACTTTATAATTGAGGCCCCTAAGTTTTTTCAATCTCAC
Found at i:265097 original size:20 final size:19
Alignment explanation
Indices: 265060--265098 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
265050 TGTGTTTTAA
* *
265060 ATTTTTTAATAATTTTTTT
1 ATTTTTTAAAAATATTTTT
265079 ATTTTTTAAGAAATATTTTT
1 ATTTTTTAA-AAATATTTTT
265099 TCAAAATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
ATTTTTTAAAAATATTTTT
Found at i:271312 original size:21 final size:21
Alignment explanation
Indices: 271286--271327 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
271276 TCAAATATTA
271286 TTGCACCTAATTTTGACATTG
1 TTGCACCTAATTTTGACATTG
271307 TTGCACCTAATTTTGACATTG
1 TTGCACCTAATTTTGACATTG
271328 CAATATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (21 bp):
TTGCACCTAATTTTGACATTG
Found at i:275962 original size:21 final size:21
Alignment explanation
Indices: 275932--275979 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
275922 TAATTTTCAA
*
275932 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
275953 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
275974 ACATTG
1 ACATTG
275980 CAATATTATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:276983 original size:28 final size:29
Alignment explanation
Indices: 276930--276987 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 29
276920 TTCATACGAT
*
276930 AAACATATATATAAATCGAAAAACCGTGTA
1 AAACATATACATAAATCGAAAAACCG-GTA
276960 AAACATATACA-AAA-C-AAAATACCGGTA
1 AAACATATACATAAATCGAAAA-ACCGGTA
276987 A
1 A
276988 TACAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
27 8 0.31
28 5 0.19
29 3 0.12
30 10 0.38
ACGTcount: A:0.57, C:0.16, G:0.09, T:0.19
Consensus pattern (29 bp):
AAACATATACATAAATCGAAAAACCGGTA
Found at i:278347 original size:30 final size:30
Alignment explanation
Indices: 278313--278382 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
278303 TAATTTGGAT
* *
278313 TCAAATTTAATCAAAATTTCACTATGATCC
1 TCAAATTTAATCAAAATTTCAATATAATCC
** *
278343 TCAAATTTAATTTAAATTTCAATTTAATCC
1 TCAAATTTAATCAAAATTTCAATATAATCC
278373 TCACAATTTA
1 TCA-AATTTA
278383 TTTTAAGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 28 0.82
31 6 0.18
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.41
Consensus pattern (30 bp):
TCAAATTTAATCAAAATTTCAATATAATCC
Found at i:279027 original size:6 final size:6
Alignment explanation
Indices: 279018--279051 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
279008 TGGAAAAGAG
* *
279018 GATGAA GATGAA GATGAA GATGAA TAGGAA GATG
1 GATGAA GATGAA GATGAA GATGAA GATGAA GATG
279052 CTATTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.35, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:279157 original size:6 final size:6
Alignment explanation
Indices: 279146--279170 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
279136 GTCGGTCTCC
279146 ACCACT ACCACT ACCACT ACCACT A
1 ACCACT ACCACT ACCACT ACCACT A
279171 GTAATAGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
ACCACT
Found at i:280923 original size:11 final size:11
Alignment explanation
Indices: 280907--280931 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
280897 TAAAATTATG
280907 TAATATATTTT
1 TAATATATTTT
280918 TAATATATTTT
1 TAATATATTTT
280929 TAA
1 TAA
280932 AGAATGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TAATATATTTT
Found at i:284441 original size:30 final size:30
Alignment explanation
Indices: 284407--284496 Score: 180
Period size: 30 Copynumber: 3.0 Consensus size: 30
284397 CACGAATGAC
284407 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
284437 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
284467 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
284497 ACTGTCCATA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:286376 original size:12 final size:12
Alignment explanation
Indices: 286358--286388 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
286348 TGGTTGTTTT
286358 CTCTGATCTCTG
1 CTCTGATCTCTG
*
286370 TTCTGATCTCTG
1 CTCTGATCTCTG
286382 CTCTGAT
1 CTCTGAT
286389 TTCTAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.29, G:0.16, T:0.45
Consensus pattern (12 bp):
CTCTGATCTCTG
Found at i:286498 original size:31 final size:31
Alignment explanation
Indices: 286463--286567 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 31
286453 ACACTCTGGC
* *
286463 AGGTTCAGTCGCTGTTGGTAATTCCTTGTAT
1 AGGTTCAGTCGCTGCTGGTAATTCCTTATAT
* * * *
286494 AGGTTTAG-CACTGACTGGTAATTCCTATCTCT
1 AGGTTCAGTCGCTG-CTGGTAATTCCT-TATAT
286526 GGCAGGTTCAGTCGCTGCTGGTAATTCCTTATAT
1 ---AGGTTCAGTCGCTGCTGGTAATTCCTTATAT
286560 AGGTTCAG
1 AGGTTCAG
286568 CACCGACTGG
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
30 4 0.07
31 26 0.44
32 3 0.05
34 3 0.05
35 19 0.32
36 4 0.07
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (31 bp):
AGGTTCAGTCGCTGCTGGTAATTCCTTATAT
Found at i:286547 original size:35 final size:34
Alignment explanation
Indices: 286456--286555 Score: 109
Period size: 35 Copynumber: 3.0 Consensus size: 34
286446 GGTATGAACA
*
286456 CTCTGGCAGGTTCAGTCGCTGTTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTT
* * * *
286490 GTAT---AGGTTTAG-CACTGACTGGTAATTCCTAT
1 CTCTGGCAGGTTCAGTCGCTG-CTGGTAATTCCT-T
286522 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTT
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTT
286556 ATATAGGTTC
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
30 4 0.08
31 18 0.35
32 3 0.06
34 3 0.06
35 19 0.37
36 4 0.08
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (34 bp):
CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTT
Found at i:286562 original size:66 final size:66
Alignment explanation
Indices: 286456--286582 Score: 218
Period size: 66 Copynumber: 1.9 Consensus size: 66
286446 GGTATGAACA
* * * *
286456 CTCTGGCAGGTTCAGTCGCTGTTGGTAATTCCTTGTATAGGTTTAGCACTGACTGGTAATTCCTA
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTATATAGGTTCAGCACCGACTGGTAATTCCTA
286521 T
66 T
286522 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTATATAGGTTCAGCACCGACTGGTAATT
1 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTATATAGGTTCAGCACCGACTGGTAATT
286583 ACTTATGGAC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.35
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTTATATAGGTTCAGCACCGACTGGTAATTCCTA
T
Found at i:286578 original size:31 final size:31
Alignment explanation
Indices: 286478--286588 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
286468 CAGTCGCTGT
* *
286478 TGGTAATTCCTTGTATAGGTTTAGCACTGAC
1 TGGTAATTCCTTATATAGGTTCAGCACTGAC
* * *
286509 TGGTAATTCCTATCTCTGGCAGGTTCAGTCGCTG-C
1 TGGTAATTCCT-TATAT---AGGTTCAG-CACTGAC
*
286544 TGGTAATTCCTTATATAGGTTCAGCACCGAC
1 TGGTAATTCCTTATATAGGTTCAGCACTGAC
*
286575 TGGTAATTACTTAT
1 TGGTAATTCCTTAT
286589 GGACTTAAGG
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
30 3 0.05
31 33 0.51
32 3 0.05
34 3 0.05
35 19 0.29
36 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
TGGTAATTCCTTATATAGGTTCAGCACTGAC
Found at i:287153 original size:22 final size:22
Alignment explanation
Indices: 287125--287180 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
287115 ACTTTGGCCC
287125 AGTATCGATACTAGGTACCCTG
1 AGTATCGATACTAGGTACCCTG
*
287147 AGTATCGATCCTAGGTACCCTG
1 AGTATCGATACTAGGTACCCTG
287169 AGTATCGATACT
1 AGTATCGATACT
287181 CTCCATATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (22 bp):
AGTATCGATACTAGGTACCCTG
Found at i:293587 original size:38 final size:36
Alignment explanation
Indices: 293521--293604 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 36
293511 TGTTCGGGTT
293521 GGGTC-GGGTTTTTTAAGTGATATTCGGGTC-GAGTC
1 GGGTCAGGGTTTTTTAAGTGATATTCGGGTCGGA-TC
*
293556 GGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCGGATC
1 GGGTCAGGGTTTTTTAA--GTGATATTCGGGTCGGATC
293594 GGGTTCAGGGT
1 GGG-TCAGGGT
293605 GAAAAAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
35 5 0.12
36 10 0.24
38 19 0.45
39 8 0.19
ACGTcount: A:0.14, C:0.11, G:0.38, T:0.37
Consensus pattern (36 bp):
GGGTCAGGGTTTTTTAAGTGATATTCGGGTCGGATC
Found at i:293804 original size:38 final size:38
Alignment explanation
Indices: 293747--293830 Score: 145
Period size: 38 Copynumber: 2.2 Consensus size: 38
293737 GTTCGGGTAT
293747 GGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-GAGTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAG-GTCG
293784 GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCG
1 GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCG
293822 GGTCGGGTT
1 GGTCGGGTT
293831 CAAGTTTAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 7 0.16
38 37 0.82
39 1 0.02
ACGTcount: A:0.12, C:0.11, G:0.39, T:0.38
Consensus pattern (38 bp):
GGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCG
Found at i:294432 original size:16 final size:18
Alignment explanation
Indices: 294407--294452 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
294397 TATGGAATTG
294407 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
*
294423 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
294441 GATTCCAATTCC
1 GATTCCAATTCC
294453 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:303627 original size:32 final size:32
Alignment explanation
Indices: 303588--303660 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
303578 TTAAACCGGT
303588 TGAACCGTTATTAGTGAACCGGCCAGAACCGC
1 TGAACCGTTATTAGTGAACCGGCCAGAACCGC
303620 TGAACCGTTATTAGTGAACCGGCCAGAACCGC
1 TGAACCGTTATTAGTGAACCGGCCAGAACCGC
303652 TGAACCGTT
1 TGAACCGTT
303661 CAAACCGGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (32 bp):
TGAACCGTTATTAGTGAACCGGCCAGAACCGC
Found at i:303673 original size:32 final size:32
Alignment explanation
Indices: 303588--303674 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
303578 TTAAACCGGT
* **
303588 TGAACCGTTATTAGTGAACCGGCCAGAACCGC
1 TGAACCGTTATAACCGAACCGGCCAGAACCGC
* **
303620 TGAACCGTTATTAGTGAACCGGCCAGAACCGC
1 TGAACCGTTATAACCGAACCGGCCAGAACCGC
*
303652 TGAACCGTTCA-AACCGGACCGGC
1 TGAACCGTT-ATAACCGAACCGGC
303675 TGAAAACCGG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 49 0.98
33 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (32 bp):
TGAACCGTTATAACCGAACCGGCCAGAACCGC
Found at i:309787 original size:105 final size:105
Alignment explanation
Indices: 309651--310725 Score: 1943
Period size: 105 Copynumber: 10.2 Consensus size: 105
309641 TTTGTCGGAT
* ** * *
309651 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
309716 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
309756 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* *
309821 GGAACATGCTCTTCTCATTACGAACCCTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
309861 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
309926 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
309966 GAGTTCTTCTCATTATGAACTCTTCTGGAAAAGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
310031 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
310071 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
310136 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
310176 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
310241 GGAACAAGCTCTTCTCATTACGAACCTTCTCATTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
310281 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* *
310346 GGAACAAGTTTTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
310386 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* *
310451 GGAACAAGTTTTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
310491 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
310556 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
310596 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
310661 GGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
310701 GAGTTCTTCTCATTATGAACTCTTC
1 GAGTTCTTCTCATTATGAACTCTTC
310726 ATTTGAAATA
Statistics
Matches: 946, Mismatches: 24, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 946 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:311597 original size:54 final size:55
Alignment explanation
Indices: 311526--312380 Score: 963
Period size: 54 Copynumber: 15.7 Consensus size: 55
311516 AAAGTTTTAA
* ** * * * * *
311526 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAA-TTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
** * * * * *
311580 AAAACATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTG--AACGTTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAC-CTCATTTG
* *
311634 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTT-AAAA-CACATTTG
1 A-AAACATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * * *
311688 AAAAGCGTCAAGAAACTTCTAAAAACCAGACTTAGTTTCTTT-AAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * * *
311743 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * *
311797 AAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* *
311851 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * * *
311906 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * *
311960 AAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * *
312014 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAA-CTTATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * *
312069 AAATCATCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTT-AAAACCTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* * *
312123 AAAATCGTCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTT-AAAAGCTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
*** * *
312178 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTG-AAAGCTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
*** * * *
312232 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTG-AAAGCTCATTTA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
* *
312286 AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAGCTCATTTA
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
*
312341 AAAATCATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
312381 AAAAAAATAC
Statistics
Matches: 716, Mismatches: 64, Indels: 41
0.87 0.08 0.05
Matches are distributed among these distances:
52 2 0.00
53 15 0.02
54 413 0.58
55 280 0.39
56 6 0.01
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (55 bp):
AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTG
Found at i:311675 original size:109 final size:109
Alignment explanation
Indices: 311526--312380 Score: 1028
Period size: 109 Copynumber: 7.9 Consensus size: 109
311516 AAAGTTTTAA
* ** * * * * *
311526 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAA-TTCATTTGAAAA-CATCA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAACCTCATTTGAAAATCATCA
** * * * * * * *
311589 AGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* * * *
311634 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTTAAAA-CACATTTGAAAAGCGTC
1 A-AAACATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATC
* * *
311697 AAGAAACTTCTAAAAACCAGACTTAGTTTCTTTAAAAACTCATTTG
64 AAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* * * *
311743 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTG-AAATCATCA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAACCTCATTTGAAAATCATCA
* *
311806 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* *
311851 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTG-AAATCATCA
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATCA
* * *
311915 TGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAAGCTCATTTG
* * * *
311960 AAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTGAAAATCATCAT
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATCAA
* *
312025 GAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAA-CTTATTTG
66 GAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAAGCTCATTTG
* * * *
312069 AAATCATCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAACCTCACTTGAAAATCGTCAA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATCAA
*
312134 GAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAGCTCATTTG
66 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*** * * * **
312178 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTG-AAATTGTCAA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATCAA
* * *
312242 GAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTA
66 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* *
312286 AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTAAAAATCATCA
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATCA
*
312351 AGAAACTTCTGAAGATCAGACTTAGTTTCT
65 AGAAACTTCTGAAAATCAGACTTAGTTTCT
312381 AAAAAAATAC
Statistics
Matches: 665, Mismatches: 70, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
108 211 0.32
109 413 0.62
110 41 0.06
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (109 bp):
AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAACCTCATTTGAAAATCATCAA
GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
Found at i:311854 original size:163 final size:163
Alignment explanation
Indices: 311531--312380 Score: 1118
Period size: 163 Copynumber: 5.2 Consensus size: 163
311521 TTTAAAAAAA
** * * * * * * *
311531 ATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAATTCATTTGAAAACATCAAGAAACC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* * * * * * **
311596 CCTAAAAATTAGGCTTAATTTCTTTG--AACGTTCATTTGAGAAAAATCAAGAAACTT-TCGAAA
66 TCTGAAAATCAGACTTAGTTTCGTTGAAAAC-TT-ATTTGA-AATCATCAAGAAACTTCT-GAAA
* *
311658 ATCAGACTTAGTTTCTTT-AAAACACATTTGAAAAGC
127 ATCAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * * *
311694 GTCAAGAAACTTCTAAAAACCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCATGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
311759 TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATCA
66 TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATCA
*
311824 GACTTAGTTTCTTTAAAAACTCACTTGAAAATC
131 GACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * *
311857 ATCATGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCATGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
311922 TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATCA
66 TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATCA
*
311987 GACTTAGTTTCTTTAAAAACTCACTTGAAAATC
131 GACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * *
312020 ATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* * * * *
312085 TCTGAAAATAAGACTTAGTTTC-TTTAAAACCTCACTTGAAAATCGTCAAGAAACTTCTGAAAAT
66 TCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTG-AAATCATCAAGAAACTTCTGAAAAT
* * *
312149 AAGACTTAGTTTCTTTAAAAGCTCATTTG-AAATT
129 CAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * **
312183 GTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTGAAATTGTCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* * * * *
312248 TCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCTGAAAATC
66 TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTT-GAAATCATCAAGAAACTTCTGAAAATC
* *
312313 AGACTTAGTTTCTTTAAAAGCTCATTTAAAAATC
130 AGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
*
312347 ATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
312381 AAAAAAATAC
Statistics
Matches: 617, Mismatches: 61, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
162 42 0.07
163 480 0.78
164 92 0.15
165 3 0.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.33
Consensus pattern (163 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATCA
GACTTAGTTTCTTTAAAAACTCATTTGAAAATC
Found at i:314383 original size:25 final size:25
Alignment explanation
Indices: 314349--314426 Score: 103
Period size: 23 Copynumber: 3.3 Consensus size: 25
314339 TCCATTTCTT
314349 TCTTTTTTTTCTTTTTTTTTTTTTC
1 TCTTTTTTTTCTTTTTTTTTTTTTC
*
314374 TCTTTCTTTTC--TTTTTTTTTTTC
1 TCTTTTTTTTCTTTTTTTTTTTTTC
*
314397 TGTTTTTTTT-TTTTTTTTTTTTT-
1 TCTTTTTTTTCTTTTTTTTTTTTTC
314420 T-TTTTTT
1 TCTTTTTT
314427 GTGTTTTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 6 0.12
23 21 0.44
24 11 0.23
25 10 0.21
ACGTcount: A:0.00, C:0.09, G:0.01, T:0.90
Consensus pattern (25 bp):
TCTTTTTTTTCTTTTTTTTTTTTTC
Found at i:314434 original size:1 final size:1
Alignment explanation
Indices: 314351--314426 Score: 89
Period size: 1 Copynumber: 76.0 Consensus size: 1
314341 CATTTCTTTC
* * * * * * *
314351 TTTTTTTTCTTTTTTTTTTTTTCTCTTTCTTTTCTTTTTTTTTTTCTGTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
314416 TTTTTTTTTTT
1 TTTTTTTTTTT
314427 GTGTTTTTAT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.08, G:0.01, T:0.91
Consensus pattern (1 bp):
T
Found at i:315844 original size:21 final size:23
Alignment explanation
Indices: 315803--315853 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
315793 ATGCACATGC
315803 AAATG-AAAAGATACAAAAATGG
1 AAATGCAAAAGATACAAAAATGG
* *
315825 GAATGCAAAA-ATAC-AAAATGT
1 AAATGCAAAAGATACAAAAATGG
315846 AAATGCAA
1 AAATGCAA
315854 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (23 bp):
AAATGCAAAAGATACAAAAATGG
Found at i:320201 original size:6 final size:6
Alignment explanation
Indices: 320190--320228 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
320180 AGTTCTAGTC
320190 TAAAAT TAAAAT TAAAAT TAAAA- -AAAAT TATAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TA-AAAT TAAA
320229 GATCAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
TAAAAT
Found at i:320218 original size:16 final size:17
Alignment explanation
Indices: 320197--320228 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
320187 GTCTAAAATT
320197 AAAATTA-AAATTAAAA
1 AAAATTATAAATTAAAA
320213 AAAATTATAAATTAAA
1 AAAATTATAAATTAAA
320229 GATCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAATTATAAATTAAAA
Found at i:327352 original size:16 final size:16
Alignment explanation
Indices: 327327--327364 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
327317 AAATAACCAA
327327 AAAC-GAAATATAAAT
1 AAACTGAAATATAAAT
327342 AAACTGAAATATAAAT
1 AAACTGAAATATAAAT
327358 AAACTGA
1 AAACTGA
327365 TTTTTTAACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (16 bp):
AAACTGAAATATAAAT
Found at i:327469 original size:31 final size:31
Alignment explanation
Indices: 327433--327491 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
327423 AACTTAAAAG
* *
327433 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAAAACTGAAATTTAAATAATTTT
327464 AGTTTTACAAAACTGAAATTTAAATAAT
1 AGTTTTACAAAACTGAAATTTAAATAAT
327492 CCATACAACT
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:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (31 bp):
AGTTTTACAAAACTGAAATTTAAATAATTTT
Found at i:327923 original size:61 final size:62
Alignment explanation
Indices: 327819--327942 Score: 169
Period size: 61 Copynumber: 2.0 Consensus size: 62
327809 AACACCACCT
* *
327819 AAGTGTTTAGAAGCGATTTCAGTTAATGGATAGAAAAAATGAGTGACTTTCATTCTTAGAGG
1 AAGTGTTTAGAAGCGATTTCAGTTAATAGATAGAAAAAATGAGTGACTTTCATTCTTAAAGG
** * * **
327881 AAGTGTTTAGAAG-GATTTTGGTTAGTAGATAGCAAATGTGAGTGACTTTCATTCTTAAAGG
1 AAGTGTTTAGAAGCGATTTCAGTTAATAGATAGAAAAAATGAGTGACTTTCATTCTTAAAGG
327942 A
1 A
327943 TGAACATGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
61 41 0.76
62 13 0.24
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.34
Consensus pattern (62 bp):
AAGTGTTTAGAAGCGATTTCAGTTAATAGATAGAAAAAATGAGTGACTTTCATTCTTAAAGG
Found at i:334195 original size:35 final size:35
Alignment explanation
Indices: 334155--334232 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 35
334145 TACACAGATG
*
334155 CATAGATAGTGCATCGATGCACCCGTCAAGGGATC
1 CATAGATAGTGCATCGATGCACCCATCAAGGGATC
*
334190 CATAGATAGTGCATCGATGCACCCATCAAGGGATG
1 CATAGATAGTGCATCGATGCACCCATCAAGGGATC
*
334225 CATCGATA
1 CATAGATA
334233 CATGGTGTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (35 bp):
CATAGATAGTGCATCGATGCACCCATCAAGGGATC
Found at i:335804 original size:23 final size:23
Alignment explanation
Indices: 335771--335838 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
335761 AATCTTGTAT
335771 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
335794 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
335817 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
335839 AGCTATGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:341590 original size:105 final size:105
Alignment explanation
Indices: 341454--342423 Score: 1769
Period size: 105 Copynumber: 9.2 Consensus size: 105
341444 TTTGTCGGAT
* ** * *
341454 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
341519 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
341559 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* *
341624 GGAACATGCTCTTCTCATTACGAACCCTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
341664 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
341729 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
341769 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
341834 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
341874 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
341939 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
341979 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
342044 GGAACAAGCTCTTCTCATTACGAACCTTCTCATTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
342084 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* * *
342149 GGAACAAGTTTTTCTCATTACAAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
342189 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
342254 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
342294 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
342359 GGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
342399 GAGTTCTTCTCATTATGAACTCTTC
1 GAGTTCTTCTCATTATGAACTCTTC
342424 ATTTGAAATA
Statistics
Matches: 843, Mismatches: 22, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 843 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:343236 original size:53 final size:53
Alignment explanation
Indices: 343177--343348 Score: 159
Period size: 54 Copynumber: 3.2 Consensus size: 53
343167 ATTTACAGTT
*
343177 ATCAAGAAACCCCT-AAAATTAGGCTTAGCTTCTTTCAAAAGTT-TTTAAAAAAA
1 ATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTCAAAA-TTATTT-AAAAAA
* ** * * * * *
343230 ATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAATTCATTTGAAAAC
1 ATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTCAAAATT-ATTTAAAAAA
* * ** *
343284 ATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTGAGAAAA
1 ATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTCAAAATT-ATTT-AAAAAA
343339 ATCAAGAAAC
1 ATCAAGAAAC
343349 TTTCGAAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 16 0.16
54 66 0.67
55 16 0.16
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (53 bp):
ATCAAGAAACCCCTAAAAATTAGGCTTAACTTCTTTCAAAATTATTTAAAAAA
Found at i:343288 original size:54 final size:55
Alignment explanation
Indices: 343225--343916 Score: 782
Period size: 54 Copynumber: 12.7 Consensus size: 55
343215 AAGTTTTTAA
* ** * * * * *
343225 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAA-TTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
** * * * * * *
343279 AAAACATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTG-AACGTTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* *
343333 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTT-AAAA-CACATTTG
1 A-AAACATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* * * *
343387 AAAAGCGTCAAGAAACTTCTAAAAACCAGACTTAGTTTCTTT-AAAAACTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* * * *
343442 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* * *
343496 AAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAACTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* * *
343550 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAA-CTTATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* * * *
343605 AAATCATCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTT-AAAACCTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
* *
343659 AAAATCGTCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTT-AAAAGCTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
*** *
343714 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTG-AAAGCTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
*** * *
343768 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTG-AAAGCTCATTTA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
*
343822 AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAGCTCATTTA
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
*
343877 AAAATCATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
343917 AAAAAAATAC
Statistics
Matches: 565, Mismatches: 57, Indels: 31
0.87 0.09 0.05
Matches are distributed among these distances:
53 12 0.02
54 322 0.57
55 227 0.40
56 4 0.01
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (55 bp):
AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTG
Found at i:343372 original size:109 final size:109
Alignment explanation
Indices: 343225--343916 Score: 772
Period size: 109 Copynumber: 6.4 Consensus size: 109
343215 AAGTTTTTAA
** * * * * *
343225 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAA-TTCATTTGAAAACATCAA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAACATCAA
** * * * * * * *
343289 GAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTG
66 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* *
343333 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTT-AAAA-CACATTTGAAAAGCGT
1 A-AAAAATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAA-CAT
* * *
343395 CAAGAAACTTCTAAAAACCAGACTTAGTTTCTTTAAAAACTCATTTG
63 CAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
** * * * *
343442 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CTTATTTGAAATCATCAA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAACATCAA
* *
343506 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTG
66 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* * * * *
343550 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAA-CTTATTTGAAATCATCA
1 AAAA-AATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAACATCA
* * *
343614 AGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAACCTCACTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
** * * ***
343659 AAAATCGTCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTT-AAAAGCTCATTTGAAATTGTCA
1 AAAA-AATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAACATCA
* *
343723 AGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*** * * *
343768 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTG-AAAGCTCATTTAAAAATCATCA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAA-CATCA
343832 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTT-
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*
343876 AAAAATCATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 AAAAA--ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
343917 AAAAAAATAC
Statistics
Matches: 512, Mismatches: 61, Indels: 20
0.86 0.10 0.03
Matches are distributed among these distances:
108 153 0.30
109 328 0.64
110 31 0.06
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (109 bp):
AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACCTCATTTGAAAACATCAA
GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
Found at i:343553 original size:163 final size:163
Alignment explanation
Indices: 343230--343916 Score: 860
Period size: 163 Copynumber: 4.2 Consensus size: 163
343220 TTTAAAAAAA
** * * * * * * *
343230 ATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAATTCATTTGAAAACATCAAGAAACC
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* * * * *** **
343295 CCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTGAGAAAAATCAAGAAACTT-TCGAAAAT
66 TCTGAAAATCAGACTTAATTTCTTTGAAAACTCATTTGA-AATCATCAAGAAACTTCT-GAAAAT
* *
343359 CAGACTTAGTTTCTTT-AAAACACATTTGAAAAGC
129 CAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * * *
343393 GTCAAGAAACTTCTAAAAACCAGACTTAGTTTCTTTAAAAACTCATTTGAAATCATCATGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* * *
343458 TCTGAAAATCAGACTTAGTTTCGTTGAAAACTTATTTGAAATCATCAAGAAACTTCTGAAAATCA
66 TCTGAAAATCAGACTTAATTTCTTTGAAAACTCATTTGAAATCATCAAGAAACTTCTGAAAATCA
*
343523 GACTTAGTTTCTTTAAAAACTCACTTGAAAATC
131 GACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * *
343556 ATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAACTTATTTGAAATCATCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* * * *
343621 TCTGAAAATAAGACTTAGTTTCTTT-AAAACCTCACTTGAAAATCGTCAAGAAACTTCTGAAAAT
66 TCTGAAAATCAGACTTAATTTCTTTGAAAA-CTCATTTG-AAATCATCAAGAAACTTCTGAAAAT
* * *
343685 AAGACTTAGTTTCTTTAAAAGCTCATTTG-AAATT
129 CAGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
* * * **
343719 GTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTGAAATTGTCAAGAAACT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
* *
343784 TCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCATCAAGAAACTTCTGAAAATC
66 TCTGAAAATCAGACTTAATTTCTTTGAAAACTCATTT-GAAATCATCAAGAAACTTCTGAAAATC
* *
343849 AGACTTAGTTTCTTTAAAAGCTCATTTAAAAATC
130 AGACTTAGTTTCTTTAAAAACTCATTTGAAAATC
*
343883 ATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
343917 AAAAAAATAC
Statistics
Matches: 453, Mismatches: 64, Indels: 13
0.85 0.12 0.02
Matches are distributed among these distances:
162 40 0.09
163 325 0.72
164 88 0.19
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (163 bp):
ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTGAAATCATCAAGAAACT
TCTGAAAATCAGACTTAATTTCTTTGAAAACTCATTTGAAATCATCAAGAAACTTCTGAAAATCA
GACTTAGTTTCTTTAAAAACTCATTTGAAAATC
Found at i:345935 original size:11 final size:10
Alignment explanation
Indices: 345882--346001 Score: 73
Period size: 11 Copynumber: 11.3 Consensus size: 10
345872 GATCTGTCCA
*
345882 TTTCTTTTTT
1 TTTCTCTTTT
*
345892 TTTAATCTTTT
1 TTT-CTCTTTT
345903 TTT-TC-TTT
1 TTTCTCTTTT
*
345911 TTCCTCTATTT
1 TTTCTCT-TTT
345922 TTTCTCTTTCTTT
1 TTTCTC--T-TTT
345935 TTTCTCTTTCT
1 TTTCTCTTT-T
*
345946 TTTTTCTGTTT
1 TTTCTCT-TTT
* * *
345957 TTTTTCTGTG
1 TTTCTCTTTT
345967 TTTCTCTTTT
1 TTTCTCTTTT
*
345977 TTTTTCTTTT
1 TTTCTCTTTT
345987 TTTCTTTCTTTT
1 TTTC--TCTTTT
345999 TTT
1 TTT
346002 GTGTTTTTTA
Statistics
Matches: 87, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
8 5 0.06
9 4 0.05
10 25 0.29
11 32 0.37
12 11 0.13
13 10 0.11
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTCTCTTTT
Found at i:345972 original size:32 final size:32
Alignment explanation
Indices: 345921--345995 Score: 100
Period size: 31 Copynumber: 2.3 Consensus size: 32
345911 TTCCTCTATT
*
345921 TTTTCTCTTTCT-TTTTTCTCTTTCTTTTTTCTG
1 TTTT-TCTTTCTGTGTTTCTCTTT-TTTTTTCTG
*
345954 TTTTT-TTTCTGTGTTTCTCTTTTTTTTTCTT
1 TTTTTCTTTCTGTGTTTCTCTTTTTTTTTCTG
345985 TTTTTCTTTCT
1 TTTTTCTTTCT
345996 TTTTTTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 18 0.47
32 16 0.42
33 4 0.11
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (32 bp):
TTTTTCTTTCTGTGTTTCTCTTTTTTTTTCTG
Found at i:346000 original size:12 final size:12
Alignment explanation
Indices: 345919--346001 Score: 80
Period size: 12 Copynumber: 6.6 Consensus size: 12
345909 TTTTCCTCTA
345919 TTTTTTCTCTTTC
1 TTTTTT-TCTTTC
345932 TTTTTTCTCTTTC
1 TTTTTT-TCTTTC
*
345945 -TTTTTTCTGTTT
1 TTTTTTTCT-TTC
*
345957 TTTTTCTGTGTTTC
1 TTTTT-T-TCTTTC
345971 TCTTTTTT-TTTC
1 T-TTTTTTCTTTC
345983 TTTTTTTCTTTC
1 TTTTTTTCTTTC
345995 TTTTTTT
1 TTTTTTT
346002 GTGTTTTTTA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
11 9 0.15
12 23 0.38
13 18 0.30
14 5 0.08
15 6 0.10
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTTTC
Found at i:346001 original size:13 final size:13
Alignment explanation
Indices: 345919--346000 Score: 91
Period size: 13 Copynumber: 6.5 Consensus size: 13
345909 TTTTCCTCTA
345919 TTTTTTCTCTTTC
1 TTTTTTCTCTTTC
345932 TTTTTTCTCTTTC
1 TTTTTTCTCTTTC
*
345945 TTTTTTCTGTTT-
1 TTTTTTCTCTTTC
* *
345957 TTTTTCTGTGTTTC
1 TTTTT-TCTCTTTC
345971 TCTTTTT-T-TTTC
1 T-TTTTTCTCTTTC
345983 TTTTTT-TCTTTC
1 TTTTTTCTCTTTC
345995 TTTTTT
1 TTTTTT
346001 TGTGTTTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
11 6 0.10
12 20 0.32
13 31 0.49
14 2 0.03
15 4 0.06
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTTTCTCTTTC
Found at i:346008 original size:19 final size:19
Alignment explanation
Indices: 345947--346008 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
345937 TCTCTTTCTT
345947 TTTTCTGTTTTTTTTCTGTG
1 TTTTCT-TTTTTTTTCTGTG
*
345967 TTTCTCTTTTTTTTTCT-TT
1 TTT-TCTTTTTTTTTCTGTG
345986 TTTTCTTTCTTTTTT-TGTG
1 TTTTCTTT-TTTTTTCTGTG
346005 TTTT
1 TTTT
346009 TTATATATCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
18 6 0.16
19 15 0.41
20 13 0.35
21 3 0.08
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTTTTTTCTGTG
Found at i:346008 original size:20 final size:20
Alignment explanation
Indices: 345946--346009 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
345936 TTCTCTTTCT
345946 TTTTTCTGTTTTTTTTCTGTG
1 TTTTTCT-TTTTTTTTCTGTG
*
345967 TTTCTCTTTTTTTTTCT-T-
1 TTTTTCTTTTTTTTTCTGTG
345985 TTTTTCTTTCTTTTTT-TGTG
1 TTTTTCTTT-TTTTTTCTGTG
346005 TTTTT
1 TTTTT
346010 TATATATCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.24
19 8 0.21
20 15 0.39
21 6 0.16
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTTTTTTCTGTG
Found at i:346025 original size:50 final size:51
Alignment explanation
Indices: 345928--346027 Score: 134
Period size: 50 Copynumber: 2.0 Consensus size: 51
345918 ATTTTTTCTC
* * *
345928 TTTCTTTTTTCTCTTTCTTTTTTCTGTTTTTTTTCTGTGTTTCTCTTTTTT
1 TTTCTTTTTTCTCTTTCTTTTTTCTGTTTTTTTTATATCTTTCTCTTTTTT
345979 TTTCTTTTTT-TCTTTCTTTTTT-TGTGTTTTTTATATATCTTT-TCTTTTT
1 TTTCTTTTTTCTCTTTCTTTTTTCTGT-TTTTTT-TATATCTTTCTCTTTTT
346028 CTCTCTATGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
49 3 0.07
50 25 0.57
51 16 0.36
ACGTcount: A:0.03, C:0.13, G:0.05, T:0.79
Consensus pattern (51 bp):
TTTCTTTTTTCTCTTTCTTTTTTCTGTTTTTTTTATATCTTTCTCTTTTTT
Found at i:347419 original size:21 final size:23
Alignment explanation
Indices: 347378--347428 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
347368 ATGCACATGC
347378 AAATG-AAAAGATACAAAAATGG
1 AAATGCAAAAGATACAAAAATGG
* *
347400 GAATGCAAAA-ATAC-AAAATGT
1 AAATGCAAAAGATACAAAAATGG
347421 AAATGCAA
1 AAATGCAA
347429 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (23 bp):
AAATGCAAAAGATACAAAAATGG
Found at i:352082 original size:13 final size:13
Alignment explanation
Indices: 352064--352094 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
352054 TTATTGATAA
352064 AAATATTTTTTTT
1 AAATATTTTTTTT
352077 AAATATTTTTTTT
1 AAATATTTTTTTT
352090 AAATA
1 AAATA
352095 ATCGTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AAATATTTTTTTT
Done.