Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 17
Found at i:3708001 original size:21 final size:21
Alignment explanation
Indices: 3707954--3708003 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
3707944 CACCGAAGTG
*
3707954 CCACATATTTATCCCAAAGGA
1 CCACATAATTATCCCAAAGGA
** * *
3707975 AAACATAATTGTCCCAGAGGA
1 CCACATAATTATCCCAAAGGA
3707996 CCACATAA
1 CCACATAA
3708004 ACCCTTTACT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.20
Consensus pattern (21 bp):
CCACATAATTATCCCAAAGGA
Found at i:3713854 original size:23 final size:23
Alignment explanation
Indices: 3713828--3713893 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 23
3713818 TGCCATATAA
3713828 TTGTCCCAAAAG-ACCACATAGTT
1 TTGTCCC-AAAGTACCACATAGTT
* * *
3713851 TTGTACCGAAGTGCCACATAGTT
1 TTGTCCCAAAGTACCACATAGTT
* *
3713874 TT-TCCCTGAAGTGCCACATA
1 TTGTCCC-AAAGTACCACATA
3713894 TTTATTCTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.16
23 31 0.84
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (23 bp):
TTGTCCCAAAGTACCACATAGTT
Found at i:3713905 original size:21 final size:22
Alignment explanation
Indices: 3713858--3713919 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
3713848 GTTTTGTACC
3713858 GAAGTGCCACATAGTTT-TTCCCT
1 GAAGTGCCACATA-TTTATT-CCT
3713881 GAAGTGCCACATATTTATT-CT
1 GAAGTGCCACATATTTATTCCT
*
3713902 GAAG-GACCACATAATTAT
1 GAAGTG-CCACATATTTAT
3713920 CCCGGAGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 1 0.03
21 17 0.47
22 3 0.08
23 15 0.42
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (22 bp):
GAAGTGCCACATATTTATTCCT
Found at i:3719813 original size:44 final size:46
Alignment explanation
Indices: 3719760--3719875 Score: 130
Period size: 46 Copynumber: 2.6 Consensus size: 46
3719750 CAGCTCGTAA
*
3719760 TTTGCACCGAAGTGCAATATAATTGT-C-CCAAAAG-GCCACATAGT
1 TTTGCACCGAAGTGCAACATAATTGTGCACC-AAAGTGCCACATAGT
* * * * *
3719804 TTTGCACCGAAGTGCCACATAGTTTTGCACCGAAGTGGCACATAGT
1 TTTGCACCGAAGTGCAACATAATTGTGCACCAAAGTGCCACATAGT
* *
3719850 TTTGCACCGAAGTGCCACATATTTGT
1 TTTGCACCGAAGTGCAACATAATTGT
3719876 TCTGAAGGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 22 0.36
45 4 0.07
46 35 0.57
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (46 bp):
TTTGCACCGAAGTGCAACATAATTGTGCACCAAAGTGCCACATAGT
Found at i:3719824 original size:23 final size:23
Alignment explanation
Indices: 3719794--3719870 Score: 145
Period size: 23 Copynumber: 3.3 Consensus size: 23
3719784 GTCCCAAAAG
3719794 GCCACATAGTTTTGCACCGAAGT
1 GCCACATAGTTTTGCACCGAAGT
3719817 GCCACATAGTTTTGCACCGAAGT
1 GCCACATAGTTTTGCACCGAAGT
*
3719840 GGCACATAGTTTTGCACCGAAGT
1 GCCACATAGTTTTGCACCGAAGT
3719863 GCCACATA
1 GCCACATA
3719871 TTTGTTCTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (23 bp):
GCCACATAGTTTTGCACCGAAGT
Found at i:3726607 original size:22 final size:22
Alignment explanation
Indices: 3726582--3726663 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
3726572 CCACAGCTCG
*
3726582 TAATTTGCACCGAAGTGCCACA
1 TAATTTGCACCGAAGTACCACA
*
3726604 TAATTAT-C-CCAAAAG-ACCACA
1 TAATT-TGCACC-GAAGTACCACA
* *
3726625 TAGTTTTGCACCGAAGTACGACA
1 TA-ATTTGCACCGAAGTACCACA
* *
3726648 TAGTTTGCACTGAAGT
1 TAATTTGCACCGAAGT
3726664 GCTACATATT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
21 10 0.21
22 27 0.57
23 10 0.21
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (22 bp):
TAATTTGCACCGAAGTACCACA
Found at i:3732989 original size:37 final size:37
Alignment explanation
Indices: 3732948--3733348 Score: 369
Period size: 37 Copynumber: 10.7 Consensus size: 37
3732938 AAATATATAT
**
3732948 ATATATATAATATA-ATTTTTGAAAGTATTTTGAAAAC
1 ATATATATAATATATATTTTT-AAAACATTTTGAAAAC
** * *
3732985 ATATATATTTTATAT-TTTTTAAAACAATTTGGAAACAT
1 ATATATATAATATATATTTTTAAAAC-ATTTTGAAA-AC
3733023 ATATATATATATATATAGTTTTTTAAAACATTTTGAAAAC
1 ATATATATA-ATATATA--TTTTTAAAACATTTTGAAAAC
*
3733063 -T-TATATAATATATAGTTTTTAAAACATTTTGAAAAT
1 ATATATATAATATATA-TTTTTAAAACATTTTGAAAAC
* * * *
3733099 ATATATATAGTATATAGTTTTAAAATCATTTTGAATAT
1 ATATATATAATATATATTTTTAAAA-CATTTTGAAAAC
*
3733137 ATATATATATATAATATAGTTTTTAAAATATTTTGAAAAC
1 ATATATATA-AT-ATATA-TTTTTAAAACATTTTGAAAAC
3733177 -T-TATATAATATATAGTTTTTTAAAACATTTTGAAAAC
1 ATATATATAATATATA--TTTTTAAAACATTTTGAAAAC
3733214 -TA-ATATAATATATATTTTTTAAAACATTTTTGAAAAC
1 ATATATATAATATATA-TTTTTAAAACA-TTTTGAAAAC
* * *
3733251 ATAAATATAATATATAGTTTTTAAAAATATTTTTAAAA-
1 ATATATATAATATATA-TTTTT-AAAACATTTTGAAAAC
* *
3733289 A-ATATATAATATATAGTTTTGAAAAACATTTT--TAA-
1 ATATATATAATATATA-TTTT-TAAAACATTTTGAAAAC
* *
3733324 ATATATATAATATATAGTTTGAAAA
1 ATATATATAATATATATTTTTAAAA
3733349 TGTTTTTGAA
Statistics
Matches: 312, Mismatches: 31, Indels: 45
0.80 0.08 0.12
Matches are distributed among these distances:
34 4 0.01
35 6 0.02
36 54 0.17
37 113 0.36
38 56 0.18
39 33 0.11
40 20 0.06
41 16 0.05
42 10 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATATTTTTAAAACATTTTGAAAAC
Found at i:3733106 original size:114 final size:114
Alignment explanation
Indices: 3732951--3733339 Score: 458
Period size: 114 Copynumber: 3.4 Consensus size: 114
3732941 TATATATATA
** * *
3732951 TATATAATATA-A-TTTTTGAAAGTATTTTGAAAACATATATATTTTATATTTTTTAAAACAATT
1 TATATAATATATAGTTTTT-AAAACATTTTGAAAATATATATATTATATATTTTTTAAAACAATT
*
3733014 TGGAAACATATATATATATATATATAGTTTTTTAAAACATTTTGAAAACT
65 TGGAAACATATATATATATATATATAGTTTTTTAAAATATTTTGAAAACT
*
3733064 TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATA-TAGTATATAGTTTTAAAATC-A
1 TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATTA-TATAT-TTTTTAAAA-CAA
* *
3733127 TTTTG-AATATATATATATATATAATATAG-TTTTTAAAATATTTTGAAAACT
63 TTTGGAAACATATATATATATAT-ATATAGTTTTTTAAAATATTTTGAAAACT
* *
3733178 TATATAATATATAGTTTTTTAAAACATTTTGAAAACTA-ATATAATATATATTTTTTAAAACATT
1 TATATAATATATAG-TTTTTAAAACATTTTGAAAA-TATATATATTATATATTTTTTAAAACA-A
* * * **
3733242 TTTGAAAACATA-A-ATATA-ATATATAGTTTTTAAAAATATTTTTAAAAAA
63 TTTGGAAACATATATATATATATATATAGTTTTTTAAAATATTTTGAAAACT
* * *
3733291 TATATAATATATAGTTTTGAAAAACATTTT-TAAATATATATAATATATA
1 TATATAATATATAGTTTT-TAAAACATTTTGAAAATATATATATTATATA
3733340 GTTTGAAAAT
Statistics
Matches: 242, Mismatches: 19, Indels: 31
0.83 0.07 0.11
Matches are distributed among these distances:
111 2 0.01
112 25 0.10
113 57 0.24
114 90 0.37
115 58 0.24
116 10 0.04
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (114 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAATATATATATTATATATTTTTTAAAACAATTT
GGAAACATATATATATATATATATAGTTTTTTAAAATATTTTGAAAACT
Found at i:3733432 original size:13 final size:13
Alignment explanation
Indices: 3733399--3733441 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3733389 ACATATTTGT
*
3733399 TTTTATTTTTTTA
1 TTTTATTTTTTTC
**
3733412 TTCAATTTTTTTC
1 TTTTATTTTTTTC
3733425 TTTTATTTTTTTC
1 TTTTATTTTTTTC
3733438 TTTT
1 TTTT
3733442 CCAGGTCCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTATTTTTTTC
Found at i:3733467 original size:12 final size:12
Alignment explanation
Indices: 3733445--3733475 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3733435 TTCTTTTCCA
3733445 GGTCC-AGCAAG
1 GGTCCAAGCAAG
3733456 GGTCCAAGCAAG
1 GGTCCAAGCAAG
3733468 GGTCCAAG
1 GGTCCAAG
3733476 TCCAACATGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.29, C:0.26, G:0.35, T:0.10
Consensus pattern (12 bp):
GGTCCAAGCAAG
Found at i:3734524 original size:25 final size:25
Alignment explanation
Indices: 3734487--3734541 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3734477 GTTTCTCTTC
* * *
3734487 TTTTCATTTTATTTC-ATTTTTCTAT
1 TTTTAATTCTATTTCTATTTTTAT-T
3734512 TTTTAATTCTATTTCTATTTTTATT
1 TTTTAATTCTATTTCTATTTTTATT
3734537 TTTTA
1 TTTTA
3734542 CTGAATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTAATTCTATTTCTATTTTTATT
Found at i:3738450 original size:94 final size:97
Alignment explanation
Indices: 3738279--3738522 Score: 365
Period size: 94 Copynumber: 2.5 Consensus size: 97
3738269 AGATTATAAT
* *
3738279 ATTAT-AT-GTATACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTT
1 ATTATAATAGTATACAATAAAG-TTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTT
3738342 TATGGATAAGATTCAGCTAGCCTGATAAAGGTC
65 TATGGATAAGATTCAGCTAGCCTGATAAAGGTC
*
3738375 ATTAT-A-A-TATACAATAAAGTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTT
1 ATTATAATAGTATACAATAAAGTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTT
*
3738437 ATGGATAATATTCAGCTAGCCTGATAAAGGTC
66 ATGGATAAGATTCAGCTAGCCTGATAAAGGTC
* *
3738469 ATTATAATATGTATACAATGATA-TTGAGCTGTCCCTCTAGAGCAATTAGTTAAA
1 ATTATAATA-GTATACAAT-AAAGTTGAGCTGTCCCTCTAGAGCAATTGGTTAAA
3738523 AGTCCTAGCA
Statistics
Matches: 135, Mismatches: 7, Indels: 10
0.89 0.05 0.07
Matches are distributed among these distances:
94 76 0.56
95 13 0.10
96 7 0.05
98 37 0.27
99 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (97 bp):
ATTATAATAGTATACAATAAAGTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCTGGCTTT
ATGGATAAGATTCAGCTAGCCTGATAAAGGTC
Found at i:3739773 original size:85 final size:85
Alignment explanation
Indices: 3739668--3740249 Score: 707
Period size: 85 Copynumber: 6.8 Consensus size: 85
3739658 CTATTAGCAG
*
3739668 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
*
3739733 AAGGCATGTCAAATTTACAA
66 AAGGCATATCAAATTTACAA
* *
3739753 CATAACTCAAGGCGAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTTGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
* *
3739818 ATGGAATATCAAATTTACAA
66 AAGGCATATCAAATTTACAA
* * * * * * *
3739838 CATAGCTCAAGGCGATAAGGGCTATCTGTCAACCAAGACTTTCAAGTTTGATTAGATTCACCTCA
1 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
* * * *
3739903 AATGCATATTAAATTTATAG
66 AAGGCATATCAAATTTACAA
* * * * * *
3739923 CATAGCTCAAGGTGAGAAGGGCTATCTATCAACCAAGACCTTCGAGTTTGATTACATTTAGCTTA
1 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
*
3739988 AAGGCATATCAAAGTTACAA
66 AAGGCATATCAAATTTACAA
* * * * *
3740008 CATAACTCAAGGAGAGAAGGGTTAACTGTCAATAAAGACCTTCGAGTTCGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
* *
3740073 AAGGCACATCAAAATTACAA
66 AAGGCATATCAAATTTACAA
* * ** * *
3740093 CATAACTCAAGGCGAGAAAGGTTATCAT-TCAGTAAATACCTTTGAGTTTGATTACATTCAGCTC
1 CATAACTCAAGGCGAGAAGGGCTATC-TGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTC
* * *
3740157 AAAGGCACAACAAATTTACAG
65 AAAGGCATATCAAATTTACAA
* ** * * * * *
3740178 TATAGTTCAATGTGAGAAGGGCTATCTGTCAATAAATACCTTCGAGTTTGATTCCATTCAGCTCA
1 CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
*
3740243 AGGGCAT
66 AAGGCAT
3740250 GTCCGATCTA
Statistics
Matches: 426, Mismatches: 69, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
84 1 0.00
85 424 1.00
86 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (85 bp):
CATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGCTCA
AAGGCATATCAAATTTACAA
Found at i:3740310 original size:255 final size:252
Alignment explanation
Indices: 3739665--3740339 Score: 742
Period size: 255 Copynumber: 2.6 Consensus size: 252
3739655 GAACTATTAG
* * *
3739665 CAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGC
1 CAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGC
* *
3739730 TCAAAGGCATGTCAAATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGTCATCAAAGACCTT
66 TCAAAGGCATGTCAAA-TTACAACATAACTCAAGGAGAGAAGGGTTATCTGTCA--AAAAACCTT
* * * * * * * *
3739795 CGAGTTTGATTACATTCAGCTCAATGGAATATCAAATTTACAACATAGCTCAAGGCGATAAGGGC
128 CGAGTTCGATTACATTCAGCTCAAAGGCACATCAAAATTACAACATAACTCAAGGCGAGAAAGGC
* * * * **
3739860 TATCTGTCAACCAAGACTTTCAAGTTTGATTAGATTCACCTCAAATGCATATTAAATTTA
193 TATCTGTCAACAAAGACTTTCAAGTTTGATTACATTCACCTCAAAGGCACAACAAATTTA
* * * *
3739920 TAGCATAGCTCAAGGTGAGAAGGGCTATCTATCAACCAAGACCTTCGAGTTTGATTACATTTAGC
1 CAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGC
* * *
3739985 TTAAAGGCATATCAAAGTTACAACATAACTCAAGGAGAGAAGGGTTAACTGTCAATAAAGACCTT
66 TCAAAGGCATGTCAAA-TTACAACATAACTCAAGGAGAGAAGGGTTATCTGTCAA-AAA-ACCTT
*
3740050 CGAGTTCGATTACATTCAGCTCAAAGGCACATCAAAATTACAACATAACTCAAGGCGAGAAAGGT
128 CGAGTTCGATTACATTCAGCTCAAAGGCACATCAAAATTACAACATAACTCAAGGCGAGAAAGGC
** * * *
3740115 TATCAT-TCAGTAAATACCTTT-GAGTTTGATTACATTCAGCTCAAAGGCACAACAAATTTA
193 TATC-TGTCAACAAAGA-CTTTCAAGTTTGATTACATTCACCTCAAAGGCACAACAAATTTA
* * * * * *
3740175 CAGTATAGTTCAATGTGAGAAGGGCTATCTGTCAATAAATACCTTCGAGTTTGATTCCATTCAGC
1 CAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGC
* ** ** * * ** ** * **
3740240 TCAAGGGCATGTCCGATCTACATGATAGCTTAAGTTGAGAAAAGCTATCTGTCAAAACAAATTGT
66 TCAAAGGCATGTCAAAT-TACAACATAACTCAAGGAGAGAAGGGTTATCTGTCAAAA-AACCT-T
* * *
3740305 CGAGTTCGATTCCATTCAGCTCAACGACACATCAA
128 CGAGTTCGATTACATTCAGCTCAAAGGCACATCAA
3740340 CCACATGGTA
Statistics
Matches: 350, Mismatches: 63, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
253 1 0.00
254 7 0.02
255 337 0.96
256 5 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (252 bp):
CAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTTGATTACATTCAGC
TCAAAGGCATGTCAAATTACAACATAACTCAAGGAGAGAAGGGTTATCTGTCAAAAAACCTTCGA
GTTCGATTACATTCAGCTCAAAGGCACATCAAAATTACAACATAACTCAAGGCGAGAAAGGCTAT
CTGTCAACAAAGACTTTCAAGTTTGATTACATTCACCTCAAAGGCACAACAAATTTA
Found at i:3741133 original size:38 final size:36
Alignment explanation
Indices: 3741041--3741429 Score: 423
Period size: 37 Copynumber: 10.6 Consensus size: 36
3741031 TTATATATAT
* * *
3741041 AAATATATA-ATATATATAATTTTGGAAAGCATTTTGA
1 AAATATATATA-ATATATAGTTTT-TAAAACATTTTGA
* * *
3741078 AAACATATATATTATATAGTTTTTTAAAACAATTTGA
1 AAATATATATAATATATAG-TTTTTAAAACATTTTGA
3741115 AACATATATATAATATATAGTTTTTAAAACATTTTGA
1 AA-ATATATATAATATATAGTTTTTAAAACATTTTGA
3741152 AAACT-TATATAATATATAG-TTTTAAAACATTTTGA
1 AAA-TATATATAATATATAGTTTTTAAAACATTTTGA
*
3741187 AAATATATAAATAGTATATAGTTTTTAAAACATTTTGAAA
1 AAATATAT--ATAATATATAGTTTTTAAAACATTTTG--A
* *
3741227 AAATATGTATAATATATAGTTTTTAAAATATTTTGA
1 AAATATATATAATATATAGTTTTTAAAACATTTTGA
3741263 AAACT-TATATAATATATAGTTTTTTAAAACATTTT-A
1 AAA-TATATATAATATATAG-TTTTTAAAACATTTTGA
*
3741299 AACT-TATATAATATATAGTTTTTAAAACATTTTGAA
1 AAATATATATAATATATAGTTTTTAAAACATTTTG-A
* * *
3741335 AACATATATATAATATGTAGTTTTTAAAAATATTTTTA
1 AA-ATATATATAATATATAGTTTTT-AAAACATTTTGA
* * *** **
3741373 AAAAATATATAATATATAG-TTTTGAATTGTTTTTT
1 AAATATATATAATATATAGTTTTTAAAACATTTTGA
3741408 AAATATATATAATATATAGTTT
1 AAATATATATAATATATAGTTT
3741430 GAAAATATTT
Statistics
Matches: 307, Mismatches: 27, Indels: 37
0.83 0.07 0.10
Matches are distributed among these distances:
34 16 0.05
35 63 0.21
36 44 0.14
37 86 0.28
38 81 0.26
39 9 0.03
40 8 0.03
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
AAATATATATAATATATAGTTTTTAAAACATTTTGA
Found at i:3741238 original size:111 final size:109
Alignment explanation
Indices: 3741052--3741429 Score: 483
Period size: 111 Copynumber: 3.4 Consensus size: 109
3741042 AATATATAAT
* * * * *
3741052 ATATATAATTTTGGAAAGCATTTTGAAAACATATATATTATATAGTTTTTTAAAACAATTTG-AA
1 ATATATAGTTTT--AAAACATTTTGAAAATATATATAATATATAG-TTTTTAAAACATTTTGAAA
*
3741116 ACATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATA
63 ACATATATATAATATATAGTTTTTAAAATATTTTGAAAACTTATATA
*
3741163 ATATATAGTTTTAAAACATTTTGAAAATATATAAATAGTATATAGTTTTTAAAACATTTTGAAAA
1 ATATATAGTTTTAAAACATTTTGAAAATATAT--ATAATATATAGTTTTTAAAACATTTTGAAAA
* *
3741228 AATATGTATAATATATAGTTTTTAAAATATTTTGAAAACTTATATA
64 CATATATATAATATATAGTTTTTAAAATATTTTGAAAACTTATATA
*
3741274 ATATATAGTTTTTTAAAACATTTT-AAACT-TATATAATATATAGTTTTTAAAACATTTTGAAAA
1 ATATATAG--TTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAA
* * **
3741337 CATATATATAATATGTAGTTTTTAAAAATATTTTTAAAAAATATATA
64 CATATATATAATATATAGTTTTT-AAAATATTTTGAAAACTTATATA
* *** **
3741384 ATATATAGTTTTGAATTGTTTTTTAAATATATATAATATATAGTTT
1 ATATATAGTTTTAAAACATTTTGAAAATATATATAATATATAGTTT
3741430 GAAAATATTT
Statistics
Matches: 237, Mismatches: 22, Indels: 17
0.86 0.08 0.06
Matches are distributed among these distances:
108 10 0.04
109 71 0.30
110 60 0.25
111 78 0.33
112 4 0.02
113 14 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (109 bp):
ATATATAGTTTTAAAACATTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACA
TATATATAATATATAGTTTTTAAAATATTTTGAAAACTTATATA
Found at i:3741507 original size:18 final size:18
Alignment explanation
Indices: 3741484--3741545 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
3741474 TATATATTTG
3741484 TTTTTTATTTTATTTTTA
1 TTTTTTATTTTATTTTTA
**
3741502 TTTTTTATTCGA-TTTTA
1 TTTTTTATTTTATTTTTA
*
3741519 TATATTTATTTTATTCTTTTA
1 T-TTTTTATTTTA-T-TTTTA
3741540 TTTTTT
1 TTTTTT
3741546 TCTTTTCCTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 6 0.18
18 18 0.53
20 4 0.12
21 6 0.18
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTATTTTATTTTTA
Found at i:3741530 original size:31 final size:30
Alignment explanation
Indices: 3741484--3741541 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
3741474 TATATATTTG
*
3741484 TTTTTTATTTTATTTTTATT-TTTTATTCGA
1 TTTTATATTTTA-TTTTATTCTTTTATTCGA
3741514 TTTTATATATTTATTTTATTCTTTTATT
1 TTTTATAT-TTTATTTTATTCTTTTATT
3741542 TTTTTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (30 bp):
TTTTATATTTTATTTTATTCTTTTATTCGA
Found at i:3741548 original size:13 final size:13
Alignment explanation
Indices: 3741486--3741551 Score: 50
Period size: 13 Copynumber: 5.3 Consensus size: 13
3741476 TATATTTGTT
3741486 TTTTATTTTA-T-
1 TTTTATTTTATTC
*
3741497 TTTTATTTT-TTA
1 TTTTATTTTATTC
**
3741509 TTCGATTTTATAT-
1 TTTTATTTTAT-TC
*
3741522 ATTTATTTTATTC
1 TTTTATTTTATTC
*
3741535 TTTTATTTTTTTC
1 TTTTATTTTATTC
3741548 TTTT
1 TTTT
3741552 CCTAGTCCAG
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 10 0.23
12 8 0.19
13 24 0.56
14 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTATTTTATTC
Found at i:3745724 original size:34 final size:34
Alignment explanation
Indices: 3745685--3745764 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
3745675 CCATGGTAAG
*
3745685 GGTATCGATACCAAGCAATATTGAACCTAAAATT
1 GGTATCGATACCAAGCAACATTGAACCTAAAATT
3745719 GGTATCGATACCAAGCAACATTGAACCTAAAATT
1 GGTATCGATACCAAGCAACATTGAACCTAAAATT
3745753 GGTATCGATACC
1 GGTATCGATACC
3745765 GGAAGGGGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (34 bp):
GGTATCGATACCAAGCAACATTGAACCTAAAATT
Found at i:3745819 original size:20 final size:21
Alignment explanation
Indices: 3745770--3745823 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
3745760 ATACCGGAAG
*
3745770 GGGTATCGATACCATAGTATA
1 GGGTATCGATACCATAATATA
*
3745791 GTAGTATCGATACCATAATA-A
1 G-GGTATCGATACCATAATATA
3745812 GGGTATCGATAC
1 GGGTATCGATAC
3745824 TAGGAAGCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 3 0.10
22 16 0.55
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (21 bp):
GGGTATCGATACCATAATATA
Found at i:3745928 original size:95 final size:94
Alignment explanation
Indices: 3745742--3745920 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 94
3745732 AGCAACATTG
* *
3745742 AACCTAAAATTGGTATCGATACCGGAAGGGGTATCGATACCATAGTATAGTAGTATCGATACCAT
1 AACCTAAAATTGGTATCGATACCGGAAGGGGTATCGATACCATAGTATAGAAGTATCGATACCAG
*
3745807 AATAAGGGTATCGATACTAGGAAGCTTCA
66 AATAAGAGTATCGATACTAGGAAGCTTCA
* * * *
3745836 AACCTAAAATTGGTATCGATACTGTAAGGGGGTATCGGTACCATAGTATAGAAGTATCGGTACCA
1 AACCTAAAATTGGTATCGATACCGGAA-GGGGTATCGATACCATAGTATAGAAGTATCGATACCA
**
3745901 GGGT-AGTAGTATCGATACTA
65 GAATAAG-AGTATCGATACTA
3745921 TTGAGCTTGG
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
94 27 0.36
95 47 0.64
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (94 bp):
AACCTAAAATTGGTATCGATACCGGAAGGGGTATCGATACCATAGTATAGAAGTATCGATACCAG
AATAAGAGTATCGATACTAGGAAGCTTCA
Found at i:3746288 original size:59 final size:59
Alignment explanation
Indices: 3746220--3746426 Score: 272
Period size: 59 Copynumber: 3.5 Consensus size: 59
3746210 GTGTGAAAAA
* *
3746220 TTAAAAAATTCATACTAAGTGTACGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
* * * * *
3746279 TTAAGAAATTCATACTAAGTGTATGAATTTCCACAAAGGCCACTTCATGTGCTAAAATA
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
* * * *
3746338 TTAAGAAAATCATACTAAGTGCATGAATTTCCGTATTGGGCACCTT-GTGTGCTAAAATG
1 TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCA-CTTCGTGTGCTAAAATG
* * *
3746397 ATAAGAAATTCATATTAAGTGTAAGAATTT
1 TTAAGAAATTCATACTAAGTGTATGAATTT
3746427 TTGTATGGGA
Statistics
Matches: 126, Mismatches: 21, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
59 123 0.98
60 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (59 bp):
TTAAGAAATTCATACTAAGTGTATGAATTTCCATATAGGGCACTTCGTGTGCTAAAATG
Found at i:3746763 original size:68 final size:68
Alignment explanation
Indices: 3746648--3747047 Score: 568
Period size: 68 Copynumber: 5.9 Consensus size: 68
3746638 AAAAGTTTTA
* *
3746648 AGGCCTAACTGTGCATATGACATAAAGGTGTCATTTATGCCAATTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
3746713 TTG
66 TTG
* * * *
3746716 AGGCCTAACTGTGCATATGCCAGAAAGGTGTCATTTATACCGGTTAGATAAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
3746781 TTG
66 TTG
* * *
3746784 ACGCCTAACTGTGCATATGAGATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
3746849 TTG
66 TTG
* * * * * *
3746852 AGGCCTAACTGTGCATATGAAAGAAAGGTGTCAATTATGCCATTTAGACGAAAGGTTAGGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
3746917 TTA
66 TTG
* *
3746920 AGGCCTAACTGTGCATATGACAGAAATGTATCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
*
3746985 TAG
66 TTG
* * * * * *
3746988 AGGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGT
1 AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGT
3747048 ACTGTTGAGT
Statistics
Matches: 292, Mismatches: 40, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
67 19 0.07
68 273 0.93
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (68 bp):
AGGCCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:3747142 original size:81 final size:81
Alignment explanation
Indices: 3746989--3747387 Score: 611
Period size: 81 Copynumber: 4.9 Consensus size: 81
3746979 GTGCCTTAGA
*
3746989 GGCCTAGCTATGCATTTGACAGAAAGGTGTCAATTATG-CAGTTAGATGAACGGTTAAGTACTGT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
3747053 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * *
3747069 GGCCTAACTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACGGT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
3747134 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
3747150 GACCTAGCTGTGCATTTGATAGAAAGATGTAAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
3747215 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * ** **
3747231 AGCCTAGCTGTACATTTGACAGAAAGGTGTCAATTATGCTAGTTAGATGAACAATTAAGTACCAT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
*
3747296 TGAGTAAAAGAATACT
66 TGAGTAAAAGAATAAT
* ** *
3747312 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTCAGATGAACGGTTAAACATTGT
1 GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
3747377 TGAGTAAAAGA
66 TGAGTAAAAGA
3747388 TGAATAGTAA
Statistics
Matches: 284, Mismatches: 34, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
80 35 0.12
81 249 0.88
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (81 bp):
GGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACTGT
TGAGTAAAAGAATAAT
Found at i:3749424 original size:11 final size:10
Alignment explanation
Indices: 3749403--3749429 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3749393 TATTCATGCA
3749403 TTTTTTCTTT
1 TTTTTTCTTT
3749413 TTTTTTCTTT
1 TTTTTTCTTT
3749423 TTTTTTC
1 TTTTTTC
3749430 GAACAACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:3752359 original size:1 final size:1
Alignment explanation
Indices: 3752349--3752540 Score: 114
Period size: 1 Copynumber: 192.0 Consensus size: 1
3752339 CAGTTGAAAT
* * * * * * * * * *
3752349 AAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * * * *
3752414 TAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAAAAAATAAAAATAAAAATAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
3752479 AAAAATAAAAAAAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAATAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3752541 TGAAAATAAA
Statistics
Matches: 131, Mismatches: 60, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 131 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (1 bp):
A
Found at i:3752619 original size:6 final size:6
Alignment explanation
Indices: 3752345--3752618 Score: 389
Period size: 6 Copynumber: 46.7 Consensus size: 6
3752335 TGCTCAGTTG
3752345 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
3752393 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
3752441 AAATAA AAAT-A AAA-AA AAATAA AAATAA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
*
3752487 AAAAAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-A AAAT-A
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * * * *
3752533 AAAT-A AAATGA AAAT-A AAATGA AAATGA AAATGA AAATGA AAATGA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
* * * * * *
3752579 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT
3752619 GTAACGGAAT
Statistics
Matches: 262, Mismatches: 2, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
5 28 0.11
6 234 0.89
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:3758778 original size:29 final size:30
Alignment explanation
Indices: 3758717--3758772 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
3758707 AGCATATTTA
3758717 AAAACAAAGCTTGAAAATAAAAGAAAAATG
1 AAAACAAAGCTTGAAAATAAAAGAAAAATG
*
3758747 AAAA-AAA-CTTGAAAAGTAAAATAAAA
1 AAAACAAAGCTTGAAAA-TAAAAGAAAA
3758773 GAGAAAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 12 0.50
30 4 0.17
ACGTcount: A:0.70, C:0.05, G:0.11, T:0.14
Consensus pattern (30 bp):
AAAACAAAGCTTGAAAATAAAAGAAAAATG
Found at i:3763773 original size:21 final size:21
Alignment explanation
Indices: 3763710--3763817 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
3763700 GCAAGAAAGT
** * *
3763710 GATCGATCCTTTAGGGGAAGT
1 GATCGATCCTTTTCGTGAAGG
* *
3763731 GATCGATCCTTTCCATCG-AGG
1 GATCGATCCTTTTCGT-GAAGG
*
3763752 GATCGATCCTTTTGGTGAAGG
1 GATCGATCCTTTTCGTGAAGG
* * * *
3763773 GATTGATCTTTTTCCTCAAGG
1 GATCGATCCTTTTCGTGAAGG
3763794 GATC-ATTCCTTTT-GTGAAGG
1 GATCGA-TCCTTTTCGTGAAGG
3763814 GATC
1 GATC
3763818 AATCTAAAAC
Statistics
Matches: 67, Mismatches: 17, Indels: 7
0.74 0.19 0.08
Matches are distributed among these distances:
20 11 0.16
21 55 0.82
22 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
GATCGATCCTTTTCGTGAAGG
Found at i:3763795 original size:42 final size:42
Alignment explanation
Indices: 3763710--3763817 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
3763700 GCAAGAAAGT
* * * *
3763710 GATCGATCCTTTAGGGGAAGTGATCGATCCTTTCCATCGAGG
1 GATCGATCCTTTTGGTGAAGGGATCGATCCTTTCCATCAAGG
* *
3763752 GATCGATCCTTTTGGTGAAGGGATTGATCTTTTTCC-TCAAGG
1 GATCGATCCTTTTGGTGAAGGGATCGATC-CTTTCCATCAAGG
3763794 GATC-ATTCCTTTT-GTGAAGGGATC
1 GATCGA-TCCTTTTGGTGAAGGGATC
3763818 AATCTAAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
41 11 0.19
42 41 0.72
43 5 0.09
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (42 bp):
GATCGATCCTTTTGGTGAAGGGATCGATCCTTTCCATCAAGG
Found at i:3763865 original size:20 final size:21
Alignment explanation
Indices: 3763840--3763892 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
3763830 ACTGGAATCT
3763840 AAGGGATTGATC-TTTTCTCA
1 AAGGGATTGATCTTTTTCTCA
*
3763860 AAGGGATCGATCTTTTTCTCA
1 AAGGGATTGATCTTTTTCTCA
*
3763881 AACGGATTGATC
1 AAGGGATTGATC
3763893 CTTTAAGCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (21 bp):
AAGGGATTGATCTTTTTCTCA
Found at i:3776948 original size:22 final size:23
Alignment explanation
Indices: 3776893--3776948 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
3776883 GTATATTTAT
3776893 ATGAAACTTGGACCAAGTTAAGG
1 ATGAAACTTGGACCAAGTTAAGG
3776916 ATGAAACTTGGACCAAGTTAAGG
1 ATGAAACTTGGACCAAGTTAAGG
3776939 ATG-AACTTGG
1 ATGAAACTTGG
3776949 GCTTGTGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.21
23 26 0.79
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (23 bp):
ATGAAACTTGGACCAAGTTAAGG
Found at i:3779112 original size:12 final size:12
Alignment explanation
Indices: 3779095--3779119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3779085 AAAGATCTTC
3779095 TGAAATATTTTT
1 TGAAATATTTTT
3779107 TGAAATATTTTT
1 TGAAATATTTTT
3779119 T
1 T
3779120 TTGCTAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TGAAATATTTTT
Found at i:3781017 original size:24 final size:27
Alignment explanation
Indices: 3780975--3781024 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 27
3780965 TAATTTTTTT
*
3780975 AATATTATATTATATTTTATATAAATA
1 AATATTATATTATATTTTATAAAAATA
3781002 AATA-TATATT-TA-TTTATAAAAAT
1 AATATTATATTATATTTTATAAAAAT
3781025 TATTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 2 0.09
26 6 0.27
27 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
AATATTATATTATATTTTATAAAAATA
Found at i:3782205 original size:60 final size:60
Alignment explanation
Indices: 3782137--3782255 Score: 238
Period size: 60 Copynumber: 2.0 Consensus size: 60
3782127 TAGGTTGGTT
3782137 CAACCAAAAATATTAAAAAATTAACATTTTAATTTACATTTAACCGAAATGTTATGATTC
1 CAACCAAAAATATTAAAAAATTAACATTTTAATTTACATTTAACCGAAATGTTATGATTC
3782197 CAACCAAAAATATTAAAAAATTAACATTTTAATTTACATTTAACCGAAATGTTATGATT
1 CAACCAAAAATATTAAAAAATTAACATTTTAATTTACATTTAACCGAAATGTTATGATT
3782256 TTTTATAATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (60 bp):
CAACCAAAAATATTAAAAAATTAACATTTTAATTTACATTTAACCGAAATGTTATGATTC
Found at i:3788574 original size:42 final size:42
Alignment explanation
Indices: 3788492--3788599 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
3788482 GCAAGAAAGT
* * *
3788492 GATCGATCCTTTAGGGGAAGAGATCGATCCTTTCCATCGAGG
1 GATCGATCCTTTTGGTGAAGGGATCGATCCTTTCCATCGAGG
* *
3788534 GATCGATCCTTTTGGTGAAGGGATTGATCTTTTTCC-TCGAGG
1 GATCGATCCTTTTGGTGAAGGGATCGATC-CTTTCCATCGAGG
*
3788576 GATCGTTCCTTTT-GTGAAGGGATC
1 GATCGATCCTTTTGGTGAAGGGATC
3788600 AATCTAAAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
41 10 0.17
42 43 0.74
43 5 0.09
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (42 bp):
GATCGATCCTTTTGGTGAAGGGATCGATCCTTTCCATCGAGG
Found at i:3788598 original size:20 final size:21
Alignment explanation
Indices: 3788492--3788599 Score: 78
Period size: 21 Copynumber: 5.2 Consensus size: 21
3788482 GCAAGAAAGT
** * *
3788492 GATCGATCCTTTAGGGGAAGA
1 GATCGATCCTTTTCGTGAAGG
* *
3788513 GATCGATCCTTTCCATCG-AGG
1 GATCGATCCTTTTCGT-GAAGG
*
3788534 GATCGATCCTTTTGGTGAAGG
1 GATCGATCCTTTTCGTGAAGG
* * *
3788555 GATTGATCTTTTTCCTCG-AGG
1 GATCGATCCTTTTCGT-GAAGG
*
3788576 GATCGTTCCTTTT-GTGAAGG
1 GATCGATCCTTTTCGTGAAGG
3788596 GATC
1 GATC
3788600 AATCTAAAAC
Statistics
Matches: 67, Mismatches: 16, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
19 1 0.01
20 9 0.13
21 55 0.82
22 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (21 bp):
GATCGATCCTTTTCGTGAAGG
Found at i:3788647 original size:20 final size:21
Alignment explanation
Indices: 3788622--3788678 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
3788612 ACTGGAATCT
3788622 AAGGGATCGATCCTTT-CTCA
1 AAGGGATCGATCCTTTGCTCA
*
3788642 AAGGGATCGATCTTTTGCTCA
1 AAGGGATCGATCCTTTGCTCA
*
3788663 AAGGGATTGATCCTTT
1 AAGGGATCGATCCTTT
3788679 TAGCCAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (21 bp):
AAGGGATCGATCCTTTGCTCA
Found at i:3788686 original size:22 final size:21
Alignment explanation
Indices: 3788622--3788679 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
3788612 ACTGGAATCT
*
3788622 AAGGGATCGATCCTTT-CTCA
1 AAGGGATCGATCTTTTGCTCA
3788642 AAGGGATCGATCTTTTGCTCA
1 AAGGGATCGATCTTTTGCTCA
*
3788663 AAGGGATTGATCCTTTT
1 AAGGGATCGAT-CTTTT
3788680 AGCCAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 15 0.44
21 14 0.41
22 5 0.15
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (21 bp):
AAGGGATCGATCTTTTGCTCA
Found at i:3804086 original size:24 final size:24
Alignment explanation
Indices: 3804054--3804100 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
3804044 CATGGAGATC
3804054 CTTCCGCACGTTAATCTTGATATT
1 CTTCCGCACGTTAATCTTGATATT
3804078 CTTCCGCACGTTAATCTTGATAT
1 CTTCCGCACGTTAATCTTGATAT
3804101 CCCACTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.26, G:0.13, T:0.40
Consensus pattern (24 bp):
CTTCCGCACGTTAATCTTGATATT
Found at i:3805393 original size:24 final size:24
Alignment explanation
Indices: 3805363--3805408 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3805353 CTTCCTGATT
3805363 ATGTATAAAACATCTATGTACATG
1 ATGTATAAAACATCTATGTACATG
3805387 ATGTATAAAACATCTATGTACA
1 ATGTATAAAACATCTATGTACA
3805409 ATGTCATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (24 bp):
ATGTATAAAACATCTATGTACATG
Found at i:3806622 original size:55 final size:55
Alignment explanation
Indices: 3806527--3806867 Score: 368
Period size: 55 Copynumber: 6.2 Consensus size: 55
3806517 ATTAAGCTAA
* * * * * * *
3806527 ACACGTAGTTCCTATACGG-TAGTTCATCAAATTATAATGAATTTCGTGGGTTTGC
1 ACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTTCGTGGATTTGC
* *
3806582 ACAGATAGTGCCTATACGGTTATTCATCAACTCATGATGAA-TTCTGTGGATTTGC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTC-GTGGATTTGC
** * * * *
3806637 ACACATAGTTTCTGTATGGTTATTCATCAACTCATGATGAATTAT-ATCGATTTAC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGATTTGC
* * * *
3806692 ACACATAGTGCTTGTACGGTTATTC--CAACTCATGATGAATTCCATGCATTTGC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGC
* * * * * * *
3806745 ACACATAGTTCATGTACAGTTATTAATCAACTTATGATGAATTTCGTGAATTTTC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGC
* *
3806800 ACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCGTGGATTTGC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGC
3806855 ACACATAGTGCCT
1 ACACATAGTGCCT
3806868 TTAGTACACA
Statistics
Matches: 240, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
53 44 0.18
54 3 0.01
55 189 0.79
56 3 0.01
57 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (55 bp):
ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGC
Found at i:3806767 original size:108 final size:108
Alignment explanation
Indices: 3806563--3806863 Score: 374
Period size: 108 Copynumber: 2.8 Consensus size: 108
3806553 TCAAATTATA
* ** * * * *
3806563 ATGAATTTCGTGGGTTTGCACAGATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCTG
1 ATGAATTTCATGAATTTACACACATAGTGCCTGTACGGTTATTCA-CAACTCATGATGAATTCCG
** *
3806628 TGGATTTGCACACATAGTTTCTGTATGGTTATTCATCAACTCATG
65 TGGATTTGCACACATAG-TTCTGTACAGTTATTAATCAACTCATG
*
3806673 ATGAATTAT-ATCG-ATTTACACACATAGTGCTTGTACGGTTATTC-CAACTCATGATGAATTCC
1 ATGAATT-TCAT-GAATTTACACACATAGTGCCTGTACGGTTATTCACAACTCATGATGAATTCC
* * *
3806735 ATGCATTTGCACACATAGTTCATGTACAGTTATTAATCAACTTATG
64 GTGGATTTGCACACATAGTTC-TGTACAGTTATTAATCAACTCATG
* * *
3806781 ATGAATTTCGTGAATTTTCACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCCG
1 ATGAATTTCATGAATTTACACACATAGTGCCTGTACGGTTATTCA-CAACTCATGATGAATTCCG
3806846 TGGATTTGCACACATAGT
65 TGGATTTGCACACATAGT
3806864 GCCTTTAGTA
Statistics
Matches: 165, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
107 5 0.03
108 89 0.54
110 69 0.42
111 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (108 bp):
ATGAATTTCATGAATTTACACACATAGTGCCTGTACGGTTATTCACAACTCATGATGAATTCCGT
GGATTTGCACACATAGTTCTGTACAGTTATTAATCAACTCATG
Found at i:3807259 original size:19 final size:21
Alignment explanation
Indices: 3807208--3807261 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 21
3807198 TACCCATACC
3807208 ATGGTATCGATACTACTATAAT
1 ATGGTATCGATACTACTAT-AT
* *
3807230 ATTGTACCGATACT-CTAT-T
1 ATGGTATCGATACTACTATAT
3807249 ATGGTATCGATAC
1 ATGGTATCGATAC
3807262 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
ATGGTATCGATACTACTATAT
Found at i:3813972 original size:54 final size:54
Alignment explanation
Indices: 3813889--3814173 Score: 360
Period size: 55 Copynumber: 5.2 Consensus size: 54
3813879 CATTAAGCTT
* * * * *
3813889 CACACGTAGTGCCTATACGG-TAGTTCATCAAATTATGATGAATTTCGTTGG-TTTG
1 CACACATAGTGCATGTACGGTTA-TTCATCAACTCATGATGAA-TTC-TTGGATTTG
* * *
3813944 CACACATAGTG-TTGTACGGTTATTCATCAACTCATAATGAATTCTGTGGATTTA
1 CACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-TGGATTTG
* * *
3813998 CACACATAGTGCATGTATGATTATTCATCAACTCATGATGAATTCATGGATTTG
1 CACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTTGGATTTG
* *
3814052 CACACATAGTGCCTGTACAGTTATTCATCAACTCATGATGAATTCTGTGGATTTG
1 CACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCT-TGGATTTG
* *
3814107 CACACATAGTGCGTGTACGGTTATTCATCAACTCATGATGAATTCCATGGATTTG
1 CACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATT-CTTGGATTTG
3814162 CACACATAGTGC
1 CACACATAGTGC
3814174 CTATAGTACA
Statistics
Matches: 203, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.00
53 6 0.03
54 84 0.41
55 111 0.55
56 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (54 bp):
CACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCTTGGATTTG
Found at i:3814080 original size:109 final size:109
Alignment explanation
Indices: 3813912--3814175 Score: 397
Period size: 109 Copynumber: 2.4 Consensus size: 109
3813902 TATACGGTAG
* * * * *
3813912 TTCATCAAATTATGATGAATTTCGTTGG-TTTGCACACATAGTG-TTGTACGGTTATTCATCAAC
1 TTCATCAACTCATGATGAA-TTC-ATGGATTTGCACACATAGTGCCTGTACAGTTATTCATCAAC
*
3813975 TCATAATGAATTCTGTGGATTTACACACATAGTGCATGTATGATTA
64 TCATAATGAATTCTGTGGATTTACACACATAGTGCATGTACGATTA
3814021 TTCATCAACTCATGATGAATTCATGGATTTGCACACATAGTGCCTGTACAGTTATTCATCAACTC
1 TTCATCAACTCATGATGAATTCATGGATTTGCACACATAGTGCCTGTACAGTTATTCATCAACTC
* * * *
3814086 ATGATGAATTCTGTGGATTTGCACACATAGTGCGTGTACGGTTA
66 ATAATGAATTCTGTGGATTTACACACATAGTGCATGTACGATTA
3814130 TTCATCAACTCATGATGAATTCCATGGATTTGCACACATAGTGCCT
1 TTCATCAACTCATGATGAATT-CATGGATTTGCACACATAGTGCCT
3814176 ATAGTACACA
Statistics
Matches: 142, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
107 3 0.02
108 18 0.13
109 97 0.68
110 24 0.17
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (109 bp):
TTCATCAACTCATGATGAATTCATGGATTTGCACACATAGTGCCTGTACAGTTATTCATCAACTC
ATAATGAATTCTGTGGATTTACACACATAGTGCATGTACGATTA
Found at i:3815555 original size:23 final size:23
Alignment explanation
Indices: 3815492--3815558 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
3815482 GTTCTTTTGT
* * *
3815492 ATTAGTGTATTCGTGTACTCCTGT
1 ATTAGTGCATTCGTGCACT-CTGA
* *
3815516 ATCAGTGCAATT-TTGCACTCTGA
1 ATTAGTGC-ATTCGTGCACTCTGA
3815539 ATTAGTGCATTCGTGCACTC
1 ATTAGTGCATTCGTGCACTC
3815559 ATGATTCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
22 3 0.09
23 17 0.50
24 11 0.32
25 3 0.09
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (23 bp):
ATTAGTGCATTCGTGCACTCTGA
Found at i:3819402 original size:72 final size:71
Alignment explanation
Indices: 3819269--3819402 Score: 155
Period size: 72 Copynumber: 1.9 Consensus size: 71
3819259 ATCCGATGTT
* * *
3819269 AGTGCAACATGCACTCCTATATTAATGCAAATATGTACTTCTGTATCAGTGCCTTCGTGCACTCC
1 AGTGCAACATGCACTCCTATATTAATGCAAATATGTACTGCTGTATCAGTGCATTCATGCACTCC
3819334 GGAATC
66 GGAATC
* * * * *
3819340 AGTGCAATTATGCACTCCTGTATTATTGTAAATACT-TACTGCTGTATTAGTGCAATT-ATGCAC
1 AGTGCAA-CATGCACTCCTATATTAATGCAAATA-TGTACTGCTGTATCAGTGC-ATTCATGCAC
3819403 ACCCGTATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
71 7 0.13
72 42 0.81
73 3 0.06
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (71 bp):
AGTGCAACATGCACTCCTATATTAATGCAAATATGTACTGCTGTATCAGTGCATTCATGCACTCC
GGAATC
Found at i:3819525 original size:30 final size:30
Alignment explanation
Indices: 3819491--3819551 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3819481 ATCAGTGCAT
*
3819491 TCGTGCACT-CTTGATTCTAGTACATTTGTG
1 TCGTGCACTCCTT-ATTCTACTACATTTGTG
*
3819521 TCGTGGACTCCTTATTCTACTACATTTGTG
1 TCGTGCACTCCTTATTCTACTACATTTGTG
3819551 T
1 T
3819552 ACTCCTGGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (30 bp):
TCGTGCACTCCTTATTCTACTACATTTGTG
Found at i:3823973 original size:47 final size:47
Alignment explanation
Indices: 3823916--3824008 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
3823906 GTTAATTTCA
* *
3823916 TTAATGGCATCCATTCATGCATTTTTAGTTATGGCATCCTTTTATGCC
1 TTAATGGCATCCATTCATGCA-TTTCAGTTATGGCATCCTTTCATGCC
* * *
3823964 TTAAT-GCATCCTTTCATGCATTTCATTTATGGTATCCTTTCATGC
1 TTAATGGCATCCATTCATGCATTTCAGTTATGGCATCCTTTCATGC
3824009 ATTTTAGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 21 0.52
47 14 0.35
48 5 0.12
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (47 bp):
TTAATGGCATCCATTCATGCATTTCAGTTATGGCATCCTTTCATGCC
Found at i:3824029 original size:72 final size:73
Alignment explanation
Indices: 3823910--3824080 Score: 281
Period size: 72 Copynumber: 2.4 Consensus size: 73
3823900 TTATTCGTTA
* * *
3823910 ATTTCATTAATGGCATCCATTCATGCATTTTTAGTTATGGCATCCTTTTATGCCTTAATGCATCC
1 ATTTCATTAATGGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCC
3823975 TTTCATGC
66 TTTCATGC
* *
3823983 ATTTCATTTATGGTATCCTTTCATGCA-TTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCC
1 ATTTCATTAATGGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCC
3824047 TTTCATGC
66 TTTCATGC
*
3824055 ATTTCATTAATGGCATCATTTCATGC
1 ATTTCATTAATGGCATCCTTTCATGC
3824081 CTTAATGCAT
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 66 0.73
73 24 0.27
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.44
Consensus pattern (73 bp):
ATTTCATTAATGGCATCCTTTCATGCATTTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCC
TTTCATGC
Found at i:3824047 original size:46 final size:46
Alignment explanation
Indices: 3823997--3824482 Score: 525
Period size: 46 Copynumber: 10.5 Consensus size: 46
3823987 CATTTATGGT
* *
3823997 ATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGA
1 ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
*
3824043 ATCCTTTCATGCATTTCA-TTAATGGCATCATTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTCAGTT-ATGGCATCCTTTCATGCCTTAATGC
* *
3824089 ATCTTTTCATGCATTTCAATTATGGCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* * * * *
3824135 AACCTTTCATGCATTTCATTTATTGTATCCTTTCATGCCTTAATGT
1 ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* * * * *
3824181 AT--TGTTCATGCATTTTTTAGTTATGACATCTTTTCATTCCTTAATTC
1 ATCCT-TTCATGCA--TTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* *
3824228 AT-CTGTTCATGCATTTCATTTAT-GCAATCATTTCATGCCTTAATGC
1 ATCCT-TTCATGCATTTCAGTTATGGC-ATCCTTTCATGCCTTAATGC
* * *
3824274 A-CCATTTCTTGCATTTCAGTTATGGTATCTTTTCATGCCTTAATGC
1 ATCC-TTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* * ** * *
3824320 ATCCTTTCATGCAGTTCATTTATTACATCTTTTCATTCCTTAATGC
1 ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* ** * * *
3824366 ATCATTTCATGTTTTTCCGTTATTGAATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* * *
3824412 ATCATTTCATGCATTTCAGTTACGTCATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
* *
3824458 ATCCGTTCATGCATTTTTAGTTATG
1 ATCCTTTCATGCA-TTTCAGTTATG
3824483 AATTCAGTTT
Statistics
Matches: 369, Mismatches: 59, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
44 1 0.00
45 11 0.03
46 306 0.83
47 41 0.11
48 10 0.03
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (46 bp):
ATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATGC
Found at i:3824048 original size:20 final size:20
Alignment explanation
Indices: 3824021--3824146 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
3824011 TTTAGTTATG
3824021 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
3824041 GAATCCTTTCATGCATTTCATTAAT
1 GCATCCTTTCATGC----C-TTAAT
*
3824066 GGCATCATTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
3824087 GCATCTTTTCATGCATTTCAATTAT
1 GCATCCTTTCATGC-CTT--A--AT
3824112 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
3824133 GCAACCTTTCATGC
1 GCATCCTTTCATGC
3824147 ATTTCATTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
20 39 0.45
21 9 0.10
22 1 0.01
23 2 0.02
24 1 0.01
25 9 0.10
26 25 0.29
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.40
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:3824329 original size:20 final size:20
Alignment explanation
Indices: 3824304--3824469 Score: 71
Period size: 20 Copynumber: 7.4 Consensus size: 20
3824294 TATGGTATCT
3824304 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
* * *
3824324 TTTCATGCAGTTCATTTATTACATCT
1 TTTCATGC----C--TTAATGCATCC
* *
3824350 TTTCATTCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCC
* *
3824370 TTTCATGTTTTTCCGTTATTGAATCC
1 TTTCATG-----CC-TTAATGCATCC
*
3824396 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGCATCC
* *
3824416 TTTCATGCATTTCAGTTACGTCATCC
1 TTTCATGC-CTT-A---ATG-CATCC
3824442 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGCATCC
*
3824462 GTTCATGC
1 TTTCATGC
3824470 ATTTTTAGTT
Statistics
Matches: 108, Mismatches: 20, Indels: 36
0.66 0.12 0.22
Matches are distributed among these distances:
20 50 0.46
21 6 0.06
22 2 0.02
24 2 0.02
25 6 0.06
26 42 0.39
ACGTcount: A:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCATGCCTTAATGCATCC
Found at i:3824482 original size:185 final size:181
Alignment explanation
Indices: 3824002--3824482 Score: 569
Period size: 185 Copynumber: 2.6 Consensus size: 181
3823992 ATGGTATCCT
* *
3824002 TTCATGCA-TTTT-AGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTCATTAA
1 TTCATG-ATTTTTCAGTTATGACATCCTTTCATGCCTTAATGCAT-CTTTCATGCATTTCATT-A
* *
3824065 TGGCATCATTTCATGCCTTAATGCATCTTTTCATGCATTTCAATTATGGCATCCTTTCATGCCTT
63 T-GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTT
* ** *
3824130 AATGCAACCTTTCATGCATTTCATTTATTGTATCCTTTCATGCCTTAATGTATTG
127 AATGCAACCTTTCATGCAGTTCATTTATTACATCCTTTCATGCCTTAATGCATTG
* * * *
3824185 TTCATGCATTTTTTAGTTATGACATCTTTTCATTCCTTAATTCATCTGTTCATGCATTTCATTTA
1 TTCATG-ATTTTTCAGTTATGACATCCTTTCATGCCTTAATGCATCT-TTCATGCATTTCA-TTA
* * *
3824250 TGCAATCATTTCATGCCTTAATGCA-CCATTTCTTGCATTTCAGTTATGGTATCTTTTCATGCCT
63 TGC-ATCATTTCATGCCTTAATGCATCC-TTTCATGCATTTCAGTTATGGCATCCTTTCATGCCT
* * *
3824314 TAATGCATCCTTTCATGCAGTTCATTTATTACATCTTTTCATTCCTTAATGCATCAT-
126 TAATGCAACCTTTCATGCAGTTCATTTATTACATCCTTTCATGCCTTAATGCAT--TG
*
3824371 TTCATG-TTTTTCCGTTATTGA-ATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCAGTTA
1 TTCATGATTTTTCAGTTA-TGACATCCTTTCATGCCTTAATGCATC-TTTCATGCATTTCA-TTA
* * * *
3824434 CGTCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTTAGTTATG
63 TG-CATCATTTCATGCCTTAATGCATCCTTTCATGCA-TTTCAGTTATG
3824483 AATTCAGTTT
Statistics
Matches: 257, Mismatches: 28, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
183 8 0.03
184 82 0.32
185 158 0.61
186 8 0.03
187 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (181 bp):
TTCATGATTTTTCAGTTATGACATCCTTTCATGCCTTAATGCATCTTTCATGCATTTCATTATGC
ATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCTTTCATGCCTTAATG
CAACCTTTCATGCAGTTCATTTATTACATCCTTTCATGCCTTAATGCATTG
Found at i:3842425 original size:49 final size:49
Alignment explanation
Indices: 3842353--3842474 Score: 183
Period size: 49 Copynumber: 2.5 Consensus size: 49
3842343 GTCACAGTGT
* *
3842353 ATTTCGGCATAGAAGGTGCCACTAATGAAAGTTAAATGCATAA-TGGTGC
1 ATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAGT-ATGC
*
3842402 ATTTCGGCATAAAAGATGCCACTAATGAAAGTTAAATGCATAAGTATGC
1 ATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAGTATGC
*
3842451 ATTTTCGGTATAAAAGGTGCCACT
1 A-TTTCGGCATAAAAGGTGCCACT
3842475 CGTGGTATTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
49 45 0.68
50 21 0.32
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (49 bp):
ATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATGCATAAGTATGC
Found at i:3842599 original size:21 final size:20
Alignment explanation
Indices: 3842557--3842599 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
3842547 ACATACATTG
* *
3842557 GGAAAAATAAAAGATAATTA
1 GGAAAAATAAAAGAAAAATA
3842577 GGAAAAATATAAAGAAAAATA
1 GGAAAAATA-AAAGAAAAATA
3842598 GG
1 GG
3842600 CATGTTGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (20 bp):
GGAAAAATAAAAGAAAAATA
Found at i:3843207 original size:23 final size:23
Alignment explanation
Indices: 3843181--3843260 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
3843171 GATCATTTGA
* **
3843181 TCCTATATTAGTGCAACATGTTC
1 TCCTATATTAATGCAACATGCAC
*
3843204 TCCTATATTAATACAACATGCAC
1 TCCTATATTAATGCAACATGCAC
*
3843227 TCCTATATTAATGCAAATATGCAC
1 TCCTATATTAATGC-AACATGCAC
* *
3843251 TTCTGTATTA
1 TCCTATATTA
3843261 GTGCCTTCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 32 0.67
24 16 0.33
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (23 bp):
TCCTATATTAATGCAACATGCAC
Found at i:3845330 original size:125 final size:125
Alignment explanation
Indices: 3845187--3845417 Score: 385
Period size: 125 Copynumber: 1.8 Consensus size: 125
3845177 GGCTTATGGT
** *
3845187 TATAGGGTTTTAGAAGTGGTAGGTTGTGATGGA-ATATAATAAAAAGTTAAAAAGTATG-AAAGA
1 TATAGGGTTTTAGAAGTGGTAGAATGTGATGGACAT-TAATAAAAAGTGAAAAAGTA-GAAAAGA
3845250 GAATCTAAAAAGTACAATAATTGTGGGGATAGGTTTGAAATTTTTAAAAAATAACTTACGGC
64 GAATCTAAAAAGTACAATAATTGTGGGGATAGGTTTGAAATTTTTAAAAAATAACTTACGGC
*
3845312 TATAGGGTTTTAGGAGTGGTAGAATGTGATGGACATTAATAAAAAGTGAAAAAGTAGAAAAGAGA
1 TATAGGGTTTTAGAAGTGGTAGAATGTGATGGACATTAATAAAAAGTGAAAAAGTAGAAAAGAGA
*
3845377 ATCTGAAAAGTACAATAATTGTGGGGATAGGTTTGAAATTT
66 ATCTAAAAAGTACAATAATTGTGGGGATAGGTTTGAAATTT
3845418 AAAATAACCC
Statistics
Matches: 99, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
124 1 0.01
125 96 0.97
126 2 0.02
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.29
Consensus pattern (125 bp):
TATAGGGTTTTAGAAGTGGTAGAATGTGATGGACATTAATAAAAAGTGAAAAAGTAGAAAAGAGA
ATCTAAAAAGTACAATAATTGTGGGGATAGGTTTGAAATTTTTAAAAAATAACTTACGGC
Found at i:3845794 original size:21 final size:21
Alignment explanation
Indices: 3845739--3845794 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
3845729 AAACTTTCAA
*
3845739 GCATTGTGAAGAAGCAAGGAT
1 GCATTGTCAAGAAGCAAGGAT
*
3845760 GCATTGTGAAGAAGCAAGGAT
1 GCATTGTCAAGAAGCAAGGAT
*
3845781 G-ATTTGTCACGAAG
1 GCA-TTGTCAAGAAG
3845795 AATTGGATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.36, C:0.11, G:0.32, T:0.21
Consensus pattern (21 bp):
GCATTGTCAAGAAGCAAGGAT
Found at i:3845796 original size:24 final size:21
Alignment explanation
Indices: 3845739--3845781 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3845729 AAACTTTCAA
3845739 GCATTGTGAAGAAGCAAGGAT
1 GCATTGTGAAGAAGCAAGGAT
3845760 GCATTGTGAAGAAGCAAGGAT
1 GCATTGTGAAGAAGCAAGGAT
3845781 G
1 G
3845782 ATTTGTCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (21 bp):
GCATTGTGAAGAAGCAAGGAT
Found at i:3865749 original size:15 final size:17
Alignment explanation
Indices: 3865729--3865761 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3865719 TTGTGCCTAG
3865729 CACGTA-CTT-TATTCT
1 CACGTACCTTGTATTCT
3865744 CACGTACCTTGTATTCT
1 CACGTACCTTGTATTCT
3865761 C
1 C
3865762 TTACATATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.18, C:0.30, G:0.09, T:0.42
Consensus pattern (17 bp):
CACGTACCTTGTATTCT
Found at i:3874105 original size:22 final size:22
Alignment explanation
Indices: 3874077--3874792 Score: 1073
Period size: 22 Copynumber: 32.5 Consensus size: 22
3874067 AGTAATAATC
*
3874077 TTTTAAAATAAATCATTCCATA
1 TTTTAAAATAAATCAATCCATA
3874099 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3874121 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
3874143 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
* ** *
3874165 ATTTAAAATAAAAT-TTTCCATG
1 TTTTAAAAT-AAATCAATCCATA
*
3874187 TTTTAAAATGAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
3874209 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
3874231 TTTTAAAATAAATCCATCCATA
1 TTTTAAAATAAATCAATCCATA
*
3874253 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
3874275 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3874297 TTTTAAAATAAAT-ATATCCATA
1 TTTTAAAATAAATCA-ATCCATA
* *
3874319 TTTTAAAATAAATCTATCTATA
1 TTTTAAAATAAATCAATCCATA
3874341 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3874363 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3874385 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
* ***
3874407 ATTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
3874429 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3874451 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
3874473 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
3874495 TTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATCCATA
3874517 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
3874539 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
3874561 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
3874583 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
3874605 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
3874627 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
3874649 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
3874671 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
3874693 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
*
3874715 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
3874737 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
3874759 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
3874781 TTTTAAAATAAA
1 TTTTAAAATAAA
3874793 ATTTTAAAAT
Statistics
Matches: 630, Mismatches: 56, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
21 12 0.02
22 606 0.96
23 12 0.02
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:3874838 original size:10 final size:10
Alignment explanation
Indices: 3874825--3874852 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
3874815 TTTTAATTTC
3874825 TTTGAAGACG
1 TTTGAAGACG
3874835 TTTGAAGACG
1 TTTGAAGACG
3874845 TTTGAAGA
1 TTTGAAGA
3874853 TATAAAACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (10 bp):
TTTGAAGACG
Found at i:3883210 original size:31 final size:31
Alignment explanation
Indices: 3883172--3883238 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
3883162 CTAGAGTATA
* * *
3883172 AGGCAGCTCTTTCCTGGTATAAGTTAGGTAG
1 AGGCAGCTCCTTCCTAGTATAAGTTAGGCAG
*
3883203 AGGCAGCTCCTTCCTAGTATGAGTTAGGCAG
1 AGGCAGCTCCTTCCTAGTATAAGTTAGGCAG
3883234 AGGCA
1 AGGCA
3883239 TCTCGACGCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (31 bp):
AGGCAGCTCCTTCCTAGTATAAGTTAGGCAG
Found at i:3885642 original size:18 final size:18
Alignment explanation
Indices: 3885601--3885643 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3885591 TTATAAGGTG
* *
3885601 AAAATATTATTATTGTAA
1 AAAATATAATTATTGAAA
3885619 AAAATATAATTATT-AAA
1 AAAATATAATTATTGAAA
3885636 AATAATAT
1 AA-AATAT
3885644 TTAATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATATAATTATTGAAA
Done.