Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 28 of 34
Found at i:4344928 original size:163 final size:162
Alignment explanation
Indices: 4344697--4345007 Score: 376
Period size: 162 Copynumber: 1.9 Consensus size: 162
4344687 GTTTGCAAAA
* * **
4344697 ATTCATTCATTTTCATGAGTTTTTTATTTTTCCTCAAAATTTCTCTTTTTTCGAAATACATTGTT
1 ATTCATTCATTTTCATCAGTTTTTTATTTTTCCTCAAAATTTCTCTTTTTTCAAAATACAGAGTT
* *
4344762 TTCTACTTCGTAATTTTGGGGGGGGAATTTTCTCGA-TTTTTAATTTTTAAAATTTATCAAATAT
66 TTCTACTTCGTAATTTT-GAGGGGGAATTTTCT-GAGTTTTTAATTTTTAAAATTCATCAAATAT
* *
4344826 CATCGTTTATTTCATATTAAATTAATTTTTAGAG
129 CATCATTTAATTCATATTAAATTAATTTTTAGAG
* ** * *
4344860 ATTCATTCATTTTCATTCA-TTTTTTATTTTTTCTTGAAA-TTCTCTTATTTTTAAAATATAGAG
1 ATTCATTCATTTTCA-TCAGTTTTTTATTTTTCCTCAAAATTTCTCTT-TTTTCAAAATACAGAG
* * * * * *
4344923 TTTTCTATTTCGTCATTTTTAGGGGGATTTTTCTTAGTTTTTATTTTTTAAAATTCATCAAATAT
64 TTTTCTACTTCGTAATTTTGAGGGGGAATTTTCTGAGTTTTTAATTTTTAAAATTCATCAAATAT
* *
4344988 TATTATTTAATTCATATTAA
129 CATCATTTAATTCATATTAA
4345008 TTCAGTTTTG
Statistics
Matches: 124, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
161 1 0.01
162 61 0.49
163 60 0.48
164 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.54
Consensus pattern (162 bp):
ATTCATTCATTTTCATCAGTTTTTTATTTTTCCTCAAAATTTCTCTTTTTTCAAAATACAGAGTT
TTCTACTTCGTAATTTTGAGGGGGAATTTTCTGAGTTTTTAATTTTTAAAATTCATCAAATATCA
TCATTTAATTCATATTAAATTAATTTTTAGAG
Found at i:4345053 original size:162 final size:161
Alignment explanation
Indices: 4344647--4345056 Score: 391
Period size: 163 Copynumber: 2.5 Consensus size: 161
4344637 TTCAAACATC
* * * *
4344647 AAAATTCCTTAAATATTATTGTTTAA-TCACCATTAAATCAG-TTTGCAAAAATTCATTCATTTT
1 AAAATTCATCAAATATTATTGTTTAATTCA-TATTAATTCAGTTTTG---AAATTCATTCATTTT
* * * **
4344710 CATGAGTTTTTTATTTTTCCTCAAAATTTCTCTTTTTTCGAAATACATTGTTTTCTACTTCGTAA
62 CATGAGTTTTTTATTTTTTCTTAAAATTTCTCTTTTTTCAAAATACAGAGTTTTCTACTTCGTAA
* *
4344775 TTTTGGGGGGGGAATTTTCTCGATTTTTAATTTTT
127 TTTTGGAGGGGGAATTTTCTAGATTTTTAATTTTT
* * * * * * *
4344810 AAAATTTATCAAATATCATCGTTTATTTCATATTAAATTAATTTTTAGAGATTCATTCATTTTCA
1 AAAATTCATCAAATATTATTGTTTAATTCATATT-AATTCAGTTTT-GAAATTCATTCATTTTCA
* * * * * *
4344875 TTCA-TTTTTTATTTTTTCTTGAAA-TTCTCTTATTTTTAAAATATAGAGTTTTCTATTTCGTCA
64 -TGAGTTTTTTATTTTTTCTTAAAATTTCTCTT-TTTTCAAAATACAGAGTTTTCTACTTCGTAA
* * *
4344938 TTTT-TAGGGGGATTTTTCTTAG-TTTTTATTTTTT
127 TTTTGGAGGGGGAATTTTC-TAGATTTTTAATTTTT
* * *
4344972 AAAATTCATCAAATATTATTATTTAATTCATATTAATTCAGTTTTGAAATTTTAATTTATTTTCA
1 AAAATTCATCAAATATTATTGTTTAATTCATATTAATTCAGTTTTGAAA--TTCATTCATTTTCA
* *
4345037 TGAGTTTCTGATTTTTTCTT
64 TGAGTTTTTTATTTTTTCTT
4345057 TCTTTGAAAT
Statistics
Matches: 197, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
160 3 0.02
161 11 0.06
162 84 0.43
163 86 0.44
164 9 0.05
165 3 0.02
166 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.53
Consensus pattern (161 bp):
AAAATTCATCAAATATTATTGTTTAATTCATATTAATTCAGTTTTGAAATTCATTCATTTTCATG
AGTTTTTTATTTTTTCTTAAAATTTCTCTTTTTTCAAAATACAGAGTTTTCTACTTCGTAATTTT
GGAGGGGGAATTTTCTAGATTTTTAATTTTT
Found at i:4347742 original size:155 final size:155
Alignment explanation
Indices: 4347514--4347839 Score: 379
Period size: 155 Copynumber: 2.1 Consensus size: 155
4347504 TCCCTAAACG
* ** * ** *
4347514 GCATTTTCGTAATTTTTTTGAACAAACTCCTAGGTTGTCACCGGGTCTGCTATTATGCCGAAGAT
1 GCATTTTAGTAATTTTTTAAAACAAACTCCTAGGTTGTCACCGAGTCCCCTATTATGCCAAAGAT
* * * * *
4347579 AGATATTTAGGATAGGTTCATGCT-TTTTAAAATCCTTTTTAAGTCCTTTAGGGATATCAAGCAC
66 AGATATTTAGGATAGGTTCA-CCTCATCTAAAATCCTTTTTAAGTCCTTTAGGGACAGCAAGCAC
* *
4347643 TTCTACATCGAAGATATCTCTTAGGA
130 TTCTACATCCAAGATATCTCCTAGGA
** *
4347669 GCATTTTAGTAATTTTTTAAAATCAAA-TCCTAGGTTGTCATTGAGTCCCCTATTATGCCAAAGG
1 GCATTTTAGTAATTTTTTAAAA-CAAACTCCTAGGTTGTCACCGAGTCCCCTATTATGCCAAAGA
** * ** *
4347733 TAGATATTTAGGATAGGTTCACCTCATCTATTATCCTTTTTAAGTCCTTTAGGGGCAGCGGGTAC
65 TAGATATTTAGGATAGGTTCACCTCATCTAAAATCCTTTTTAAGTCCTTTAGGGACAGCAAGCAC
* *
4347798 TTTTACATCCAAGGTATCTCCTAGGA
130 TTCTACATCCAAGATATCTCCTAGGA
4347824 GCATTTTCA-TAATTTT
1 GCATTTT-AGTAATTTT
4347840 CCTACAAAAT
Statistics
Matches: 143, Mismatches: 25, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
154 2 0.01
155 136 0.95
156 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (155 bp):
GCATTTTAGTAATTTTTTAAAACAAACTCCTAGGTTGTCACCGAGTCCCCTATTATGCCAAAGAT
AGATATTTAGGATAGGTTCACCTCATCTAAAATCCTTTTTAAGTCCTTTAGGGACAGCAAGCACT
TCTACATCCAAGATATCTCCTAGGA
Found at i:4349366 original size:80 final size:79
Alignment explanation
Indices: 4349117--4349796 Score: 532
Period size: 80 Copynumber: 8.5 Consensus size: 79
4349107 CCTAGCCTCA
*
4349117 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGTCATATCTTCTTCACTAAAGCCCA
1 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGTCAAATCTTCTTC-CTAAAGCCCA
*
4349182 ATGTCGTTGGCCTTG
65 ATGTCGCTGGCCTTG
* * * * *** * ** *
4349197 AATCAACATATTGGCACTTTGCCTAGGTCATGCGGCA-TCTGTTTAAATCTTCTTCC-CGAGGCC
1 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACT-TG-TCAAATCTTCTTCCTAAAGCCC
*
4349260 AATATCGCTGGCCTTG
64 AATGTCGCTGGCCTTG
* * * *
4349276 AATTAGCACATTGGCACCATGCTTATGTCAAAAGGCACTTGTCAAATCTTTTTCACTAAAGCCCA
1 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGTCAAATCTTCTTC-CTAAAGCCCA
* *
4349341 ACGTCGTTGGCCTTG
65 ATGTCGCTGGCCTTG
* * *** *
4349356 AATCAACACATTGGCACCTTGCCCTAGGTCATGCGGCATTTGTCTAAATCTTCTTCCT-AAGCCC
1 AATCAGCACATTGGCACCTTG-CCTATGTCAAAAGGCACTTGTC-AAATCTTCTTCCTAAAGCCC
* **
4349420 AATATCATTGGCCTTG
64 AATGTCGCTGGCCTTG
** * ** *** * * * *
4349436 AATCAGCACATTAACACCTTACCCTAACTCATGCGACATTTGTCAAAACCTTCTTCCTTAAGCCC
1 AATCAGCACATTGGCACCTT-GCCTATGTCAAAAGGCACTTGTC-AAATCTTCTTCCTAAAGCCC
** **
4349501 AATGTCGCTAACCTCA
64 AATGTCGCTGGCCTTG
* **
4349517 AATCAGCACATTGGCACCCTATCTATGTCAAAAGGCACTTGTCAAATCTTCTTCACTAAAGCCCA
1 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGTCAAATCTTCTTC-CTAAAGCCCA
* * *
4349582 ATGTCACTAGCCTTT
65 ATGTCGCTGGCCTTG
* * *** * *
4349597 AAACAGCACATTGGCACCTTGCCCTAAGTCATGCGGCA-TCTGTCTAAATCTTCTTTCT-AAGCT
1 AATCAGCACATTGGCACCTTG-CCTATGTCAAAAGGCACT-TGTC-AAATCTTCTTCCTAAAGCC
*
4349660 TAATGTCGCTGGCCTTG
63 CAATGTCGCTGGCCTTG
* * * ** *
4349677 AATCAGCACATTGGCACCCTACCTATGTCAAAAGGCACTGGTCGTATAGTTCTAGT-CT-AAGCC
1 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGTCAAAT-CTTCT--TCCTAAAGCC
** *
4349740 CAATGTCATTTGCCTTG
63 CAATGTCGCTGGCCTTG
* *
4349757 AATCAGCACATTGGCACC--CCCTATGCCAAAAGGCACTTGT
1 AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGT
4349797 TGTGTAATTC
Statistics
Matches: 471, Mismatches: 112, Indels: 36
0.76 0.18 0.06
Matches are distributed among these distances:
78 32 0.07
79 78 0.17
80 262 0.56
81 79 0.17
82 20 0.04
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (79 bp):
AATCAGCACATTGGCACCTTGCCTATGTCAAAAGGCACTTGTCAAATCTTCTTCCTAAAGCCCAA
TGTCGCTGGCCTTG
Found at i:4349556 original size:241 final size:239
Alignment explanation
Indices: 4349108--4349688 Score: 666
Period size: 241 Copynumber: 2.4 Consensus size: 239
4349098 ACCAATATCC
** * *** * *
4349108 CTAGCCTCAAATCAGCACATTGGCACCTTG-CCTATGTCAAAAGGCACTTGTC-ATATCTTCTTC
1 CTAGCCTTGAATCAGCACATTGGCACCTTGCCCTAAGTCATGCGGCATTTGTCTAAATCTTCTTC
* * ** ** ** *
4349171 ACTAAAGCCCAATGTCGTTGGCCTTGAATCAACATATTGGCACTTTGCCTAGGTCATGCGGCATC
66 -CT-AAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAACACTTACCCTAACTCATGCGACATC
** * * * ** ** *
4349236 TGTTTAAATCTTCTTCCCGAGGCCAATATCGCTGGCCTTGAATTAGCACATTGGCACCATGCTTA
129 TGTCAAAACCTTCTTCCCAAGCCCAATATCGCTAACCTCAAATCAGCACATTGGCACCATGCTTA
* *
4349301 TGTCAAAAGGCACTTGTCAAATCTTTTTCACTAAAGCCCAACGTCG
194 TGTCAAAAGGCACTTGTCAAATCTTCTTCACTAAAGCCCAACGTCA
* * * *
4349347 TTGGCCTTGAATCAACACATTGGCACCTTGCCCTAGGTCATGCGGCATTTGTCTAAATCTTCTTC
1 CTAGCCTTGAATCAGCACATTGGCACCTTGCCCTAAGTCATGCGGCATTTGTCTAAATCTTCTTC
* * *
4349412 CTAAGCCCAATATCATTGGCCTTGAATCAGCACATTAACACCTTACCCTAACTCATGCGACATTT
66 CTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAACA-CTTACCCTAACTCATGCGACATCT
* *
4349477 GTCAAAACCTTCTTCCTTAAGCCCAATGTCGCTAACCTCAAATCAGCACATTGGCACCCTAT-C-
130 GTCAAAACCTTCTTCC-CAAGCCCAATATCGCTAACCTCAAATCAGCACATTGGCA-CC-ATGCT
*
4349540 TATGTCAAAAGGCACTTGTCAAATCTTCTTCACTAAAGCCCAATGTCA
192 TATGTCAAAAGGCACTTGTCAAATCTTCTTCACTAAAGCCCAACGTCA
* * * *
4349588 CTAGCCTTTAAACAGCACATTGGCACCTTGCCCTAAGTCATGCGGCATCTGTCTAAATCTTCTTT
1 CTAGCCTTGAATCAGCACATTGGCACCTTGCCCTAAGTCATGCGGCATTTGTCTAAATCTTCTTC
** *
4349653 CTAAGCTTAATGTCGCTGGCCTTGAATCAGCACATT
66 CTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATT
4349689 GGCACCCTAC
Statistics
Matches: 285, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
239 57 0.20
240 50 0.18
241 173 0.61
242 3 0.01
243 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (239 bp):
CTAGCCTTGAATCAGCACATTGGCACCTTGCCCTAAGTCATGCGGCATTTGTCTAAATCTTCTTC
CTAAGCCCAATGTCGTTGGCCTTGAATCAGCACATTAACACTTACCCTAACTCATGCGACATCTG
TCAAAACCTTCTTCCCAAGCCCAATATCGCTAACCTCAAATCAGCACATTGGCACCATGCTTATG
TCAAAAGGCACTTGTCAAATCTTCTTCACTAAAGCCCAACGTCA
Found at i:4349833 original size:78 final size:79
Alignment explanation
Indices: 4349655--4349850 Score: 250
Period size: 78 Copynumber: 2.5 Consensus size: 79
4349645 TCTTCTTTCT
* *
4349655 AAGCTTAATGTCGCTGGCCTTGAATCAGCACATTGGCACCCTACCTATGTCAAAAGGCACTGGTC
1 AAGCTTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCC-ACCTATGCCAAAAGGCACTGGTC
* *
4349720 GTATAGTTCTAGTCT
65 GTATAATTCTAGTCA
** ** * * *
4349735 AAGCCCAATGTCATTTGCCTTGAATCAGCACATTGGCACCC-CCTATGCCAAAAGGCACTTGTTG
1 AAGCTTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCACCTATGCCAAAAGGCACTGGTCG
*
4349799 TGTAATTCTAGTCA
66 TATAATTCTAGTCA
* *
4349813 AAGCTTAATATTGCTAGCCTTGAATCAGCACATTGGCA
1 AAGCTTAATGTCGCTAGCCTTGAATCAGCACATTGGCA
4349851 TCCTATCACT
Statistics
Matches: 98, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 62 0.63
80 36 0.37
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (79 bp):
AAGCTTAATGTCGCTAGCCTTGAATCAGCACATTGGCACCCACCTATGCCAAAAGGCACTGGTCG
TATAATTCTAGTCA
Found at i:4358675 original size:12 final size:12
Alignment explanation
Indices: 4358653--4358686 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4358643 TTCTTTTCCC
4358653 AACACAAAAAAAA
1 AACA-AAAAAAAA
*
4358666 AAGAAAAAAAAA
1 AACAAAAAAAAA
4358678 AACAAAAAA
1 AACAAAAAA
4358687 TTTCGGTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (12 bp):
AACAAAAAAAAA
Found at i:4359746 original size:33 final size:33
Alignment explanation
Indices: 4359701--4360198 Score: 276
Period size: 33 Copynumber: 15.8 Consensus size: 33
4359691 CACCCTTCCA
** * *
4359701 AAGTCCATGACTCAGTGGCATCCTTTTCCTTTA
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
* * **
4359734 AAGTCCACGACTC-GATGGCATCCTTTTTCTTCC
1 AAGTCCACAACTCTG-TGGCATCCTTTTCCTTTT
*** * *
4359767 AAGTCCATGGCTCAGTGGCAT--TTTT-C-TCT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
*
4359796 AAGTCCACAACTCCT-TGGCA-CTTTTTCCCTTTT
1 AAGTCCACAACT-CTGTGGCATCCTTTT-CCTTTT
* * * *
4359829 AAGTCAACAACTTTGTGGC-GCCTTTTTCTTTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
** * *
4359861 CAAAG-CCTACAGGTCTGTGGCCTTTCTTTTTCCTTTT
1 --AAGTCC-ACAACTCTGTGG-C-ATCCTTTTCCTTTT
**
4359898 AAGTCCACAACTCCATGGCA-CCTTTT-CTTTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
*
4359929 CAAGTCCACAACTCCGTGGCA-CCTTTTTTCCTTTT
1 -AAGTCCACAACTCTGTGGCATCC--TTTTCCTTTT
* *
4359964 AAGTCCATAACTCTGTGGCA-CTTTTTCCTTTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
* *
4359996 AAGTCCAAAACTCTGTGGCAT-CTCTTCCTTTTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCC-TTTT
4360029 AAGTCCACAACTCTGTGGCA--C----CCTTTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
* * *
4360056 AAGTCTACAACTCCGTGGCA-CCTTTTTCCTTTC
1 AAGTCCACAACTCTGTGGCATCC-TTTTCCTTTT
*
4360089 AAGTCCACAACTCCGTGGCA--C----CCTTTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
* * *
4360116 AAGTACACAACTTTGTGGCA-CCTTTTCCTTTC
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
* *
4360148 AAAT-CATAACTCTGTGGCA-CC----CC-TTT
1 AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
*
4360174 AAGTCCATAACTCTGTGGCA-CCTTT
1 AAGTCCACAACTCTGTGGCATCCTTT
4360199 AACCTTCTTT
Statistics
Matches: 376, Mismatches: 51, Indels: 79
0.74 0.10 0.16
Matches are distributed among these distances:
26 5 0.01
27 63 0.17
28 4 0.01
29 16 0.04
30 6 0.02
31 24 0.06
32 78 0.21
33 114 0.30
34 37 0.10
35 17 0.05
36 2 0.01
37 10 0.03
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.37
Consensus pattern (33 bp):
AAGTCCACAACTCTGTGGCATCCTTTTCCTTTT
Found at i:4359976 original size:66 final size:65
Alignment explanation
Indices: 4359701--4360198 Score: 319
Period size: 66 Copynumber: 7.9 Consensus size: 65
4359691 CACCCTTCCA
** * * *
4359701 AAGTCCATGACTCAGTGGCATCCTTTTCCTTTAAAGTCCACGACT-CGATGGCATCC-TTTTT-C
1 AAGTCCACAACTCTGTGGCA-CCTTTT-CTTTTAAGTCCACAACTCCG-TGGCA-CCTTTTTTCC
**
4359763 TTCC
62 TTTT
*** * * * * *
4359767 AAGTCCATGGCTCAGTGGCA-TTTTTC-TCTAAGTCCACAACTCCTTGGCA-CTTTTTCCCTTTT
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCCTTTT
* * * ** * *
4359829 AAGTCAACAACTTTGTGGCGCCTTTTTCTTTTCAAAG-CCTACAGGTCTGTGGC-CTTTCTTTTT
1 AAGTCCACAACTCTGTGGCACC-TTTTCTTTT--AAGTCC-ACAACTCCGTGGCAC-CT-TTTTT
4359892 CCTTTT
60 CCTTTT
**
4359898 AAGTCCACAACTCCATGGCACCTTTTCTTTTCAAGTCCACAACTCCGTGGCACCTTTTTTCCTTT
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTT-AAGTCCACAACTCCGTGGCACCTTTTTTCCTTT
4359963 T
65 T
* * * * * *
4359964 AAGTCCATAACTCTGTGGCACTTTTTCCTTTTAAGTCCAAAACTCTGTGGCA--TCTCTTCCTTT
1 AAGTCCACAACTCTGTGGCACCTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCC-TT
4360027 TT
64 TT
* *
4360029 AAGTCCACAACTCTGTGGCACC----CTTTTAAGTCTACAACTCCGTGGCACC-TTTTTCCTTTC
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCCTTTT
* * ** *
4360089 AAGTCCACAACTCCGTGGCACC----CTTTTAAGTACACAACTTTGTGGCACC--TTTTCCTTTC
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCCTTTT
* * * * *
4360148 AAAT-CATAACTCTGTGGCACC----CCTTTAAGTCCATAACTCTGTGGCACCTTT
1 AAGTCCACAACTCTGTGGCACCTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTT
4360199 AACCTTCTTT
Statistics
Matches: 350, Mismatches: 62, Indels: 46
0.76 0.14 0.10
Matches are distributed among these distances:
58 38 0.11
59 13 0.04
60 71 0.20
61 9 0.03
62 33 0.09
63 2 0.01
64 15 0.04
65 26 0.07
66 72 0.21
67 31 0.09
68 13 0.04
69 27 0.08
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.37
Consensus pattern (65 bp):
AAGTCCACAACTCTGTGGCACCTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCCTTTT
Found at i:4360065 original size:27 final size:27
Alignment explanation
Indices: 4359958--4360195 Score: 154
Period size: 27 Copynumber: 8.0 Consensus size: 27
4359948 CACCTTTTTT
*
4359958 CCTTTTAAGTCCATAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCTGTGGCAC
*
4359985 TTTTTCCTTTTAAGTCCAAAACTCTGTGGCATCTC
1 -----CCTTTTAAGTCCACAACTCTGTGGCA---C
4360020 TTCCTTTTTAAGTCCACAACTCTGTGGCAC
1 --CC-TTTTAAGTCCACAACTCTGTGGCAC
* *
4360050 CCTTTTAAGTCTACAACTCCGTGGCACC
1 CCTTTTAAGTCCACAACTCTGTGGCA-C
* *
4360078 TTTTTCCTTTCAAGTCCACAACTCCGTGGCAC
1 -----CCTTTTAAGTCCACAACTCTGTGGCAC
* *
4360110 CCTTTTAAGTACACAACTTTGTGGCACC
1 CCTTTTAAGTCCACAACTCTGTGGCA-C
* * *
4360138 TTTTCCTTTCAAAT-CATAACTCTGTGGCAC
1 ----CCTTTTAAGTCCACAACTCTGTGGCAC
* *
4360168 CCCTTTAAGTCCATAACTCTGTGGCAC
1 CCTTTTAAGTCCACAACTCTGTGGCAC
4360195 C
1 C
4360196 TTTAACCTTC
Statistics
Matches: 173, Mismatches: 17, Indels: 37
0.76 0.07 0.16
Matches are distributed among these distances:
26 7 0.04
27 61 0.35
28 4 0.02
30 2 0.01
31 13 0.08
32 38 0.22
33 47 0.27
35 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCTGTGGCAC
Found at i:4360093 original size:60 final size:60
Alignment explanation
Indices: 4359886--4360198 Score: 335
Period size: 60 Copynumber: 5.1 Consensus size: 60
4359876 TGTGGCCTTT
** *
4359886 CTTTTTCCTTTTAAGTCCACAACTCCATGGCACCTTTTCTTTTCAAGTCCACAACTCCGTGGCAC
1 CTTTTTCCTTTTAAGTCCACAACTCTGTGGCACC----CTTTT-AAGTCCACAACTCTGTGGCAC
* *
4359951 CTTTTTTCCTTTTAAGTCCATAACTCTGTGGCACTTTTTCCTTTTAAGTCCAAAACTCTGTGGCA
1 C-TTTTTCCTTTTAAGTCCACAACTCTGTGGCAC-----CCTTTTAAGTCCACAACTCTGTGGCA
*
4360016 T
60 C
* * *
4360017 C-TCTTCCTTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCTACAACTCCGTGGCAC
1 CTTTTTCC-TTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCAC
* * * *
4360077 CTTTTTCCTTTCAAGTCCACAACTCCGTGGCACCCTTTTAAGTACACAACTTTGTGGCAC
1 CTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCAC
* * * * *
4360137 C-TTTTCCTTTCAAAT-CATAACTCTGTGGCACCCCTTTAAGTCCATAACTCTGTGGCAC
1 CTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCAC
4360195 CTTT
1 CTTT
4360199 AACCTTCTTT
Statistics
Matches: 213, Mismatches: 26, Indels: 24
0.81 0.10 0.09
Matches are distributed among these distances:
58 38 0.18
59 15 0.07
60 71 0.33
61 5 0.02
64 5 0.02
65 25 0.12
66 48 0.23
67 5 0.02
71 1 0.00
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (60 bp):
CTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCAC
Found at i:4360249 original size:32 final size:32
Alignment explanation
Indices: 4360208--4360279 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
4360198 TAACCTTCTT
4360208 TAAAGCCCACACAAGTTGGTGGCAAC-CCTTTC
1 TAAAGCCCACACAAGTTGGTGGCAACTCC-TTC
*
4360240 TAAAGCCCACACAAGTTGGTGGCATCTCCTTC
1 TAAAGCCCACACAAGTTGGTGGCAACTCCTTC
4360272 T-AAGCCCA
1 TAAAGCCCA
4360280 ATGGCATTGG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 7 0.18
32 29 0.76
33 2 0.05
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (32 bp):
TAAAGCCCACACAAGTTGGTGGCAACTCCTTC
Found at i:4360454 original size:52 final size:52
Alignment explanation
Indices: 4360331--4360683 Score: 257
Period size: 52 Copynumber: 6.9 Consensus size: 52
4360321 CATCTCTTTC
* * * **
4360331 TAAGTCCAATGTCGTTGGCCTTG-A--AGCACATTAGCA-CTTT-TTTTC-T
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTT
* *
4360377 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTT
* * *
4360429 TAAGTCCAATGTCACTGGCCTTGAATCAGCACATTGGCACC--T-CCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTT
* * * *
4360478 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTGA-CAT-TCC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-ATCATCT-T
* ** * * *
4360530 TAAGCCCAACGTCGTTGGCCTTGAATCAGCACATTGGCA-TTCTTCTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCT-TTATCATCTT
* ** * * * * *
4360582 CAAGTTTAATGTCGCTGGCCGTGAATCAACACATTTG-ACATTCT-TCGCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT-TAT--CATCTT
* * * * *
4360635 TAAGCCCAATATCGTTGGCCTTGAATCAGCATATTAGCATCTTTATCAT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCAT
4360684 TCTTCTCATC
Statistics
Matches: 238, Mismatches: 49, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
46 20 0.08
47 1 0.00
49 52 0.22
50 5 0.02
51 9 0.04
52 112 0.47
53 35 0.15
54 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCATCTT
Found at i:4360492 original size:101 final size:103
Alignment explanation
Indices: 4360376--4360609 Score: 296
Period size: 101 Copynumber: 2.3 Consensus size: 103
4360366 ACTTTTTTTC
* * *
4360376 TTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-ATCA-TCTTTAAGTCCAAT
1 TTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGA-CATTC-CTAAGCCCAAC
4360439 GTCACTGGCCTTGAATCAGCACATTGGCA-CCTC-CATCT
64 GTCACTGGCCTTGAATCAGCACATTGGCATCCTCTCATCT
* * *
4360477 TTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTGACATTCCTAAGCCCAACGT
1 TTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGACATTCCTAAGCCCAACGT
** *
4360542 CGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCT
66 CACTGGCCTTGAATCAGCACATTGGCA-TCCTCTCATCT
* * * *
4360581 TCAAGTTTAATGTCGCTGGCCGTGAATCA
1 TTAAGTCTAATATCGCTGGCCTTGAATCA
4360610 ACACATTTGA
Statistics
Matches: 113, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
101 79 0.70
102 3 0.03
103 3 0.03
104 28 0.25
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.32
Consensus pattern (103 bp):
TTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGACATTCCTAAGCCCAACGT
CACTGGCCTTGAATCAGCACATTGGCATCCTCTCATCT
Found at i:4360580 original size:153 final size:156
Alignment explanation
Indices: 4360392--4360678 Score: 393
Period size: 153 Copynumber: 1.9 Consensus size: 156
4360382 CTAATATCGC
* * *
4360392 TGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGTCCAATGTCACTGGCCTTGAATCA
1 TGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTCAAGTCCAATGTCACTGGCCGTGAATCA
* * * *
4360457 GCACA-TTGGCA-CCTC-CATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATC
66 ACACATTTGACATCCTCGCATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTAGCATC
4360519 TTTGACATTCCTAAGCCCAACGTCGT
131 TTTGACATTCCTAAGCCCAACGTCGT
* * ** *
4360545 TGGCCTTGAATCAGCACATTGGCA-TTCTTCTCATCTTCAAGTTTAATGTCGCTGGCCGTGAATC
1 TGGCCTTGAATCAGCACATTGGCACCT-TTATCATCTTCAAGTCCAATGTCACTGGCCGTGAATC
* * *
4360609 AACACATTTGACATTCTTCGCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTAGCA
65 AACACATTTGACA-TCCTCGCATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTAGCA
4360674 TCTTT
129 TCTTT
4360679 ATCATTCTTC
Statistics
Matches: 114, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
152 1 0.01
153 59 0.52
154 5 0.04
156 3 0.03
157 46 0.40
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.33
Consensus pattern (156 bp):
TGGCCTTGAATCAGCACATTGGCACCTTTATCATCTTCAAGTCCAATGTCACTGGCCGTGAATCA
ACACATTTGACATCCTCGCATCTTTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTAGCATC
TTTGACATTCCTAAGCCCAACGTCGT
Found at i:4360660 original size:105 final size:102
Alignment explanation
Indices: 4360374--4360675 Score: 272
Period size: 101 Copynumber: 3.0 Consensus size: 102
4360364 GCACTTTTTT
* * * * * * * * *
4360374 TCTT-AAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-TATCATCTTTAAGTCCA
1 TCTTCAAGTCCAATATCGCTAGCCGTGAATCAACACATTGACATCTTCGA-CATCTTTAAGCCCA
**
4360437 ATGTCACTGGCCTTGAATCAGCACATTGGCA-CCTCCA
65 ATGTCGTTGGCCTTGAATCAGCACATTGGCATCCTCCA
* * * * * * *
4360474 TCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCATCTTTGACAT-TCCTAAGCCCA
1 TCTTCAAGTCCAATATCGCTAGCCGTGAATCAACACATTGACATCTTCGACATCT-TTAAGCCCA
* *
4360538 ACGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCA
65 ATGTCGTTGGCCTTGAATCAGCACATTGGCA-TCCTC-CA
** * *
4360578 TCTTCAAGTTTAATGTCGCTGGCCGTGAATCAACACATTTGACATTCTTCG-CATCTTTAAGCCC
1 TCTTCAAGTCCAATATCGCTAGCCGTGAATCAACACA-TTGACA-TCTTCGACATCTTTAAGCCC
* * *
4360642 AATATCGTTGGCCTTGAATCAGCATATTAGCATC
64 AATGTCGTTGGCCTTGAATCAGCACATTGGCATC
4360676 TTTATCATTC
Statistics
Matches: 168, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
100 5 0.03
101 77 0.46
102 1 0.01
103 3 0.02
104 33 0.20
105 43 0.26
106 6 0.04
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (102 bp):
TCTTCAAGTCCAATATCGCTAGCCGTGAATCAACACATTGACATCTTCGACATCTTTAAGCCCAA
TGTCGTTGGCCTTGAATCAGCACATTGGCATCCTCCA
Found at i:4360721 original size:61 final size:61
Alignment explanation
Indices: 4360620--4360753 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 61
4360610 ACACATTTGA
* ** *
4360620 CATTCTTCGCATCTTTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTAGCATCTTTAT
1 CATTCTTCTCATCTTTAAGCCCAATATCACTGGCCTTGAATCAACATATTAGCATCTTTAT
* *
4360681 CATTCTTCTCATCTTTAAGCCCCATATCACTGG-CTCTGAATCAACATATTGGCATCTTTAT
1 CATTCTTCTCATCTTTAAGCCCAATATCACTGGCCT-TGAATCAACATATTAGCATCTTTAT
**
4360742 CACCCTTCTCAT
1 CATTCTTCTCAT
4360754 TTTCATCAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 2 0.03
61 62 0.97
ACGTcount: A:0.24, C:0.28, G:0.10, T:0.37
Consensus pattern (61 bp):
CATTCTTCTCATCTTTAAGCCCAATATCACTGGCCTTGAATCAACATATTAGCATCTTTAT
Found at i:4375357 original size:12 final size:11
Alignment explanation
Indices: 4375335--4375410 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
4375325 AGAGAAAGAA
*
4375335 GAGAGAGGAGG
1 GAGATAGGAGG
4375346 GATGATAGGAGG
1 GA-GATAGGAGG
*
4375358 AGAGACAGGA--
1 -GAGATAGGAGG
*
4375368 GAGATAGTA--
1 GAGATAGGAGG
4375377 GAGATAGGAGG
1 GAGATAGGAGG
4375388 GATGATAGGAGG
1 GA-GATAGGAGG
*
4375400 AGAGACAGGAG
1 -GAGATAGGAG
4375411 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:4375367 original size:24 final size:24
Alignment explanation
Indices: 4375334--4375419 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
4375324 AAGAGAAAGA
*
4375334 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
4375358 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
4375376 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
4375400 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
4375420 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:4375386 original size:42 final size:42
Alignment explanation
Indices: 4375325--4375443 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
4375315 TAGCCCTCAA
* *
4375325 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
4375367 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
4375409 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
4375444 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:4378203 original size:42 final size:42
Alignment explanation
Indices: 4378148--4378266 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
4378138 CAGCCCTCAA
* * *
4378148 AGAGAAAGAAGAGAGAGGATGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
4378190 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
4378232 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
4378267 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.43, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:4378233 original size:24 final size:24
Alignment explanation
Indices: 4378157--4378242 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
4378147 AAGAGAAAGA
* *
4378157 AGAGAGAGGATGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
4378181 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
4378199 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
4378223 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
4378243 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.44, T:0.12
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:4384167 original size:12 final size:11
Alignment explanation
Indices: 4384145--4384220 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
4384135 AGAGAAAGAA
*
4384145 GAGAGAGGAGG
1 GAGATAGGAGG
4384156 GATGATAGGAGG
1 GA-GATAGGAGG
*
4384168 AGAGACAGGA--
1 -GAGATAGGAGG
*
4384178 GAGATAGTA--
1 GAGATAGGAGG
4384187 GAGATAGGAGG
1 GAGATAGGAGG
4384198 GATGATAGGAGG
1 GA-GATAGGAGG
*
4384210 AGAGACAGGAG
1 -GAGATAGGAG
4384221 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:4384177 original size:24 final size:24
Alignment explanation
Indices: 4384144--4384229 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
4384134 AAGAGAAAGA
*
4384144 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
4384168 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
4384186 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
4384210 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
4384230 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:4384196 original size:42 final size:42
Alignment explanation
Indices: 4384135--4384253 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
4384125 TAGCCCTCAA
* *
4384135 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
4384177 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
4384219 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
4384254 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:4388479 original size:12 final size:11
Alignment explanation
Indices: 4388457--4388532 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
4388447 AGAGAAAGAA
*
4388457 GAGAGAGGAGG
1 GAGATAGGAGG
4388468 GATGATAGGAGG
1 GA-GATAGGAGG
*
4388480 AGAGACAGGA--
1 -GAGATAGGAGG
*
4388490 GAGATAGTA--
1 GAGATAGGAGG
4388499 GAGATAGGAGG
1 GAGATAGGAGG
4388510 GATGATAGGAGG
1 GA-GATAGGAGG
*
4388522 AGAGACAGGAG
1 -GAGATAGGAG
4388533 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:4388489 original size:24 final size:24
Alignment explanation
Indices: 4388456--4388541 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
4388446 AAGAGAAAGA
*
4388456 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
4388480 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
4388498 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
4388522 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
4388542 AGAGAGTAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:4388508 original size:42 final size:42
Alignment explanation
Indices: 4388447--4388565 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
4388437 TAGCCCTCAA
* *
4388447 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
4388489 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * * *
4388531 AGAGATAATAGAGAGAGTAGGGATGACAGAAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
4388566 GAGAGAAAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.44, C:0.03, G:0.45, T:0.09
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:4395970 original size:24 final size:24
Alignment explanation
Indices: 4395942--4395987 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4395932 ATTAACTATA
4395942 GGTTGAACATATTAAAATGCATAG
1 GGTTGAACATATTAAAATGCATAG
* *
4395966 GGTTGGACATGTTAAAATGCAT
1 GGTTGAACATATTAAAATGCAT
4395988 GGAACACAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (24 bp):
GGTTGAACATATTAAAATGCATAG
Found at i:4397023 original size:20 final size:22
Alignment explanation
Indices: 4396998--4397051 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 22
4396988 CATTGCAAGC
*
4396998 ATGTATTGATACATTCA-TT-T
1 ATGTATTGATACATTAACTTGT
*
4397018 ATGTATCGATACATTAACTTGT
1 ATGTATTGATACATTAACTTGT
4397040 -TGTATTGATACA
1 ATGTATTGATACA
4397052 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 15 0.52
21 13 0.45
22 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.44
Consensus pattern (22 bp):
ATGTATTGATACATTAACTTGT
Found at i:4407650 original size:51 final size:51
Alignment explanation
Indices: 4407589--4407835 Score: 320
Period size: 51 Copynumber: 4.9 Consensus size: 51
4407579 GCCTTTATCC
* *
4407589 TTATTAATTACTATTAGGACTGTGACTAGAATTGTCCTTGTTTAGTCAAGA
1 TTATTAATTACTATTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
* * *
4407640 TTATTGATTAC-AGTTAGGACTATGATTAGGATTGTCCTTGTTTAGT--TGA
1 TTATTAATTACTA-TTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
* * * **
4407689 TTATTGATTACCATTAGGATTGCAATTAGGATTGTCCTTGTTTAGTCAAGA
1 TTATTAATTACTATTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
*
4407740 TTATTAATTACTGTTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
1 TTATTAATTACTATTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
* * * * *
4407791 TTATTCATTACTATTAGGATTGTCATTAGGATTATCTTTGTTTAG
1 TTATTAATTACTATTAGGACTGTGATTAGGATTGTCCTTGTTTAG
4407836 CTAGGACTTT
Statistics
Matches: 170, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
49 42 0.25
50 2 0.01
51 126 0.74
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (51 bp):
TTATTAATTACTATTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
Found at i:4407766 original size:100 final size:101
Alignment explanation
Indices: 4407589--4407835 Score: 336
Period size: 100 Copynumber: 2.4 Consensus size: 101
4407579 GCCTTTATCC
* * * * * * *
4407589 TTATTAATTACTATTAGGACTGTGACTAGAATTGTCCTTGTTTAGTCAAGATTATTGATTACAGT
1 TTATTCATTACCATTAGGATTGTCATTAGGATTGTCCTTGTTTAGTCAAGATTATTAATTACAGT
*
4407654 TAGGACTATGATTAGGATTGTCCTTGTTTAGT-TGA
66 TAGGACTATGATTAGGATTGTCCTTGTTTAGTAAGA
* *
4407689 TTATTGATTACCATTAGGATTG-CAATTAGGATTGTCCTTGTTTAGTCAAGATTATTAATTACTG
1 TTATTCATTACCATTAGGATTGTC-ATTAGGATTGTCCTTGTTTAGTCAAGATTATTAATTACAG
*
4407753 TTAGGACTGTGATTAGGATTGTCCTTGTTTAGTCAAGA
65 TTAGGACTATGATTAGGATTGTCCTTGTTTAGT-AAGA
* * *
4407791 TTATTCATTACTATTAGGATTGTCATTAGGATTATCTTTGTTTAG
1 TTATTCATTACCATTAGGATTGTCATTAGGATTGTCCTTGTTTAG
4407836 CTAGGACTTT
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
100 87 0.67
102 41 0.32
103 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.44
Consensus pattern (101 bp):
TTATTCATTACCATTAGGATTGTCATTAGGATTGTCCTTGTTTAGTCAAGATTATTAATTACAGT
TAGGACTATGATTAGGATTGTCCTTGTTTAGTAAGA
Found at i:4414565 original size:22 final size:22
Alignment explanation
Indices: 4414540--4414581 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4414530 AAAAGATAAC
4414540 AAACAT-ATAAGGGGATGGCACA
1 AAACATGA-AAGGGGATGGCACA
*
4414562 AAACATGAATGGGGATGGCA
1 AAACATGAAAGGGGATGGCA
4414582 ACTTTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.43, C:0.12, G:0.31, T:0.14
Consensus pattern (22 bp):
AAACATGAAAGGGGATGGCACA
Found at i:4416452 original size:31 final size:32
Alignment explanation
Indices: 4416388--4416453 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
4416378 GGGCTTTAAC
* * *
4416388 TTGAATTAGGTGGCCACCAGCTTATATGGGCT
1 TTGAATTAGGTGGCCACCAACTTATACGAGCT
* *
4416420 TTGACTTAGGT-GCCACCAACTTATGCGAGCT
1 TTGAATTAGGTGGCCACCAACTTATACGAGCT
4416451 TTG
1 TTG
4416454 GTGTCTAGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (32 bp):
TTGAATTAGGTGGCCACCAACTTATACGAGCT
Found at i:4416559 original size:28 final size:28
Alignment explanation
Indices: 4416540--4416599 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
4416530 TGCCATGAAT
4416540 TTGTGGGCCTAAAAAGGGTGCCACTGAC
1 TTGTGGGCCTAAAAAGGGTGCCACTGAC
* *
4416568 TTGTGGGCCTAAAAAGAGTACCACTGAC
1 TTGTGGGCCTAAAAAGGGTGCCACTGAC
4416596 TTGT
1 TTGT
4416600 AGGCTTAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (28 bp):
TTGTGGGCCTAAAAAGGGTGCCACTGAC
Found at i:4416647 original size:29 final size:28
Alignment explanation
Indices: 4416615--4416669 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
4416605 TAGGAGACAA
4416615 TGCCACTAACTTATGGACTTTTGAAAGAG
1 TGCCACTAACTTATGGAC-TTTGAAAGAG
* *
4416644 TGCCACTGACTTATGGGCTTTGAAAG
1 TGCCACTAACTTATGGACTTTGAAAG
4416670 GATTCAACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (28 bp):
TGCCACTAACTTATGGACTTTGAAAGAG
Found at i:4416785 original size:28 final size:28
Alignment explanation
Indices: 4416752--4416941 Score: 175
Period size: 28 Copynumber: 6.5 Consensus size: 28
4416742 GCTACTGTGA
*
4416752 GCTTTAAAAAGGTGCCACAAACTCATGG
1 GCTTTAAAAAGGTGCCACCAACTCATGG
4416780 GCTTTAAAAAGGTGCCA-CAGACTCATGG
1 GCTTTAAAAAGGTGCCACCA-ACTCATGG
* ** *
4416808 GCTTTAAAAGGGTGCCACTGACTTATGG
1 GCTTTAAAAAGGTGCCACCAACTCATGG
* *
4416836 GCTTTGAAAAGGTTGCCACCAACTTATGTG
1 GCTTTAAAAAGG-TGCCACCAACTCATG-G
*
4416866 GACTTTGAAAAAGTTGCCACCAACTCATGTG
1 G-CTTT-AAAAAGGTGCCACCAACTCATG-G
** *
4416897 GACTTTGACTAGGGTGCCACCAACTCTTATGG
1 G-CTTT-AAAAAGGTGCCACCAACTC--ATGG
*
4416929 ACTTTAAAAAGGT
1 GCTTTAAAAAGGT
4416942 TTGGTTGCCT
Statistics
Matches: 134, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.01
28 58 0.43
29 13 0.10
30 7 0.05
31 46 0.34
32 6 0.04
33 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (28 bp):
GCTTTAAAAAGGTGCCACCAACTCATGG
Found at i:4416875 original size:31 final size:29
Alignment explanation
Indices: 4416752--4416942 Score: 167
Period size: 31 Copynumber: 6.5 Consensus size: 29
4416742 GCTACTGTGA
*
4416752 GCTTTAAAAAGG-TGCCACAAACTCATGG
1 GCTTTAAAAAGGTTGCCACCAACTCATGG
4416780 GCTTTAAAAAGG-TGCCA-CAGACTCATGG
1 GCTTTAAAAAGGTTGCCACCA-ACTCATGG
* ** *
4416808 GCTTT-AAAAGGGTGCCACTGACTTATGG
1 GCTTTAAAAAGGTTGCCACCAACTCATGG
* *
4416836 GCTTTGAAAAGGTTGCCACCAACTTATGTG
1 GCTTTAAAAAGGTTGCCACCAACTCATG-G
4416866 GACTTTGAAAAA-GTTGCCACCAACTCATGTG
1 G-CTTT-AAAAAGGTTGCCACCAACTCATG-G
* ** *
4416897 GACTTTGACTAGGGTGCCACCAACTCTTATGG
1 G-CTTTAAAAAGGTTGCCACCAACTC--ATGG
*
4416929 ACTTTAAAAAGGTT
1 GCTTTAAAAAGGTT
4416943 TGGTTGCCTC
Statistics
Matches: 135, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
27 7 0.05
28 47 0.35
29 19 0.14
30 4 0.03
31 50 0.37
32 5 0.04
33 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (29 bp):
GCTTTAAAAAGGTTGCCACCAACTCATGG
Found at i:4417061 original size:37 final size:37
Alignment explanation
Indices: 4416986--4417144 Score: 227
Period size: 37 Copynumber: 4.4 Consensus size: 37
4416976 GGTGTTACCA
* *
4416986 ACTTGTGTGGACTTTGTAAAA-G-TT-G-TGCCATCG
1 ACTTGTGTGGACTTTGAAAAAGGTTTGGTTGCCACCG
*
4417019 ACTTGTGTGGACTTTGGAAAAGGTTTGGTTGCCACCG
1 ACTTGTGTGGACTTTGAAAAAGGTTTGGTTGCCACCG
* *
4417056 ACTTGTGTGAACTTTGAAAAAGGTTTGGTTGCCACTG
1 ACTTGTGTGGACTTTGAAAAAGGTTTGGTTGCCACCG
* *
4417093 ACTTGTGTGAACTTTGAAAAAGGTTTGGTTGCCACCA
1 ACTTGTGTGGACTTTGAAAAAGGTTTGGTTGCCACCG
4417130 ACTTGTGTGGACTTT
1 ACTTGTGTGGACTTT
4417145 ATAAATGATT
Statistics
Matches: 114, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
33 20 0.18
34 1 0.01
35 2 0.02
36 1 0.01
37 90 0.79
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (37 bp):
ACTTGTGTGGACTTTGAAAAAGGTTTGGTTGCCACCG
Found at i:4418404 original size:33 final size:33
Alignment explanation
Indices: 4418362--4418493 Score: 219
Period size: 33 Copynumber: 4.0 Consensus size: 33
4418352 AAAGGGTGGC
* **
4418362 TTGACAAGAAAAGTGATATAATTTGATTTATTT
1 TTGACAAGAAATGTGATACGATTTGATTTATTT
4418395 TTGACAAGAAATGTGATACGATTTGATTTATTT
1 TTGACAAGAAATGTGATACGATTTGATTTATTT
4418428 TTGACAAGAAATGTGATACGATTTGATTTATTT
1 TTGACAAGAAATGTGATACGATTTGATTTATTT
* *
4418461 TTGACAAGAAAGGTGATACGATTTGGTTTATTT
1 TTGACAAGAAATGTGATACGATTTGATTTATTT
4418494 CCAACAAAAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 94 1.00
ACGTcount: A:0.34, C:0.05, G:0.19, T:0.42
Consensus pattern (33 bp):
TTGACAAGAAATGTGATACGATTTGATTTATTT
Found at i:4419774 original size:32 final size:32
Alignment explanation
Indices: 4419733--4419795 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
4419723 GAACCCTTAG
4419733 GATCATCTTCAAAGTTAAGCAAAAAGAACTTT
1 GATCATCTTCAAAGTTAAGCAAAAAGAACTTT
4419765 GATCATCTTCAAAGTTAAGCAAAAAGAACTT
1 GATCATCTTCAAAGTTAAGCAAAAAGAACTT
4419796 GACCCCAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (32 bp):
GATCATCTTCAAAGTTAAGCAAAAAGAACTTT
Found at i:4423990 original size:159 final size:160
Alignment explanation
Indices: 4423706--4424202 Score: 438
Period size: 159 Copynumber: 3.1 Consensus size: 160
4423696 TCATCTGTCT
* ** * * *
4423706 AATGAGACTAACATTTATTCTTATTATAATCTCCATTTTTTTCATGATT-GGGCACCATAAAGAC
1 AATGAGACAAACATAGATTCTTGTAATAATCTCCATTCTTTTCATGATTGGGGCACCATAAAGAC
* * ** **
4423770 ATTTTCCTCATTGGGATACAAAATATTAATGCTTTTCTTTTGCAAGAAAAGCTTCTCTTTCCATT
66 ATTCTCCTCATTGGGATACAAAATATTAATGCTTTACTTTCCCAAGAAAAGCTTCTCTTTCCACC
*
4423835 ATTTTCTTTA-AAGTCAAAGTTCATCCCTTA
131 ATTTTCCTTATAAG-CAAAGTTCATCCCTTA
* * * * * *
4423865 AATTAGATAAATATGGATTCTTGTAATAATCTACATTCTTTTCATGATTGGGGGA-CA-AAA-AC
1 AATGAGACAAACATAGATTCTTGTAATAATCTCCATTCTTTTCATGATTGGGGCACCATAAAGAC
** * *
4423927 AGGTTCTCCTCATTGGGAATACATGATATTAATGCTTTAGTTTCCCAAGAAAAGCTT-TTTTTCC
66 A--TTCTCCTCATTGGG-ATACAAAATATTAATGCTTTACTTTCCCAAGAAAAGCTTCTCTTTCC
* *
4423991 ACCATTTTCCTTATAAGCAAAGTTCATTCCTTG
128 ACCATTTTCCTTATAAGCAAAGTTCATCCCTTA
* * * * * *
4424024 AGTGAGACAAACATAGATTCTCGTAACAATCTCCACTCTTTT-ATTGATT-GGGTACCATAAAAA
1 AATGAGACAAACATAGATTCTTGTAATAATCTCCATTCTTTTCA-TGATTGGGGCACCATAAAGA
* ** * * * ** * *
4424087 AATTCTTGT-ACTTGGGATACACAATATTGATACTTTGGTTTCCCAAGAAAAGCTT-TTTTTTCA
65 CATTCTCCTCA-TTGGGATACAAAATATTAATGCTTTACTTTCCCAAGAAAAGCTTCTCTTTCCA
* * * * *
4424150 CCATTTTCCTTAGAATCAAAATTCAACCCTCA
129 CCATTTTCCTTATAAGCAAAGTTCATCCCTTA
* *
4424182 AATGATACAAACATGGATTCT
1 AATGAGACAAACATAGATTCT
4424203 CAAAATAATC
Statistics
Matches: 275, Mismatches: 53, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
157 3 0.01
158 93 0.34
159 134 0.49
160 43 0.16
161 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (160 bp):
AATGAGACAAACATAGATTCTTGTAATAATCTCCATTCTTTTCATGATTGGGGCACCATAAAGAC
ATTCTCCTCATTGGGATACAAAATATTAATGCTTTACTTTCCCAAGAAAAGCTTCTCTTTCCACC
ATTTTCCTTATAAGCAAAGTTCATCCCTTA
Found at i:4424213 original size:158 final size:155
Alignment explanation
Indices: 4423952--4424299 Score: 378
Period size: 158 Copynumber: 2.2 Consensus size: 155
4423942 GGAATACATG
* * * *
4423952 ATATTAATGCTTTAGTTTCCCAAGAAAAGCTTTTTTTCCACCATTTTCCTTATAAGCAAAGTTCA
1 ATATTGATGCTTTGGTTTCCCAAGAAAAGCTTTTTTTCCACCATTTTCCTTAGAAGCAAAATTCA
** ** * ** * * *
4424017 TTCCTTGAGTGAGACAAACATAGATTCTCGTAACAATCTCCACTCTTTTATTGATTGGGTACCAT
66 ACCCTCAAATGAGACAAACATAGATTCTCAAAACAATCTCCA-T-TTTT-GTGATTGGGAAAC-T
*
4424082 AAAA-AAATTCT-TGT-ACTTGGGATACACA
127 AAAATAAATTCTCT-TCA-TTAGGATACACA
* * *
4424110 ATATTGATACTTTGGTTTCCCAAGAAAAGCTTTTTTTTCACCATTTTCCTTAGAATCAAAATTCA
1 ATATTGATGCTTTGGTTTCCCAAGAAAAGCTTTTTTTCCACCATTTTCCTTAGAAGCAAAATTCA
* * * *
4424175 ACCCTCAAATGATACAAACATGGATTCTCAAAATAATCTCTATTTTTGTGATTGGGAAACTAAAA
66 ACCCTCAAATGAGACAAACATAGATTCTCAAAACAATCTCCATTTTTGTGATTGGGAAACTAAAA
* *
4424240 TAAGTTCTCTTCATTAGGATACATA
131 TAAATTCTCTTCATTAGGATACACA
* *
4424265 ATATTGAGTGCTTTGGATTCCTAAGAAAAGCTTTT
1 ATATTGA-TGCTTTGGTTTCCCAAGAAAAGCTTTT
4424300 CTTTGAAGGG
Statistics
Matches: 159, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
154 5 0.03
155 34 0.21
156 30 0.19
157 1 0.01
158 89 0.56
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.37
Consensus pattern (155 bp):
ATATTGATGCTTTGGTTTCCCAAGAAAAGCTTTTTTTCCACCATTTTCCTTAGAAGCAAAATTCA
ACCCTCAAATGAGACAAACATAGATTCTCAAAACAATCTCCATTTTTGTGATTGGGAAACTAAAA
TAAATTCTCTTCATTAGGATACACA
Found at i:4431277 original size:42 final size:42
Alignment explanation
Indices: 4431222--4431331 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
4431212 TTCTTCTCTC
* * *
4431222 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCACCTGTCT
*
4431264 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCACCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCACCTGTCT
4431306 CTCCTCCTATCATCCCTCCTCTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCT
4431332 TCTTTCTCTT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.10, C:0.47, G:0.03, T:0.40
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCACCTGTCT
Found at i:4431282 original size:24 final size:24
Alignment explanation
Indices: 4431246--4431331 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
4431236 CCTCCTCTCT
* *
4431246 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
4431270 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
*
4431291 CTATC-T--CACCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
4431312 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
4431332 TCTTTCTCTT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
18 3 0.06
20 5 0.11
21 14 0.30
22 5 0.11
24 20 0.43
ACGTcount: A:0.12, C:0.45, G:0.02, T:0.41
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:4435941 original size:18 final size:18
Alignment explanation
Indices: 4435910--4436005 Score: 106
Period size: 18 Copynumber: 5.4 Consensus size: 18
4435900 CCTAAATCGC
*
4435910 AGATTTT-T-GGAATCAC
1 AGATTTTCTAGGAATCAT
*
4435926 AGATTTTCTAGGAATCAA
1 AGATTTTCTAGGAATCAT
* * *
4435944 AGATTTACTAAGAATAATT
1 AGATTTTCTAGGAATCA-T
4435963 AGATTTTCTAGGAATCAT
1 AGATTTTCTAGGAATCAT
**
4435981 AGATTTTCTAAAAATCAT
1 AGATTTTCTAGGAATCAT
4435999 AGATTTT
1 AGATTTT
4436006 TGTAATCTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
16 7 0.10
17 1 0.01
18 45 0.67
19 14 0.21
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (18 bp):
AGATTTTCTAGGAATCAT
Found at i:4435968 original size:37 final size:36
Alignment explanation
Indices: 4435926--4436005 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 36
4435916 TTGGAATCAC
*
4435926 AGATTTTCTAGGAATCAAAGATTTACTAAGAATAATT
1 AGATTTTCTAGGAATCAAAGATTTACTAAAAATAA-T
* * *
4435963 AGATTTTCTAGGAATCATAGATTTTCTAAAAATCAT
1 AGATTTTCTAGGAATCAAAGATTTACTAAAAATAAT
4435999 AGATTTT
1 AGATTTT
4436006 TGTAATCTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 8 0.21
37 31 0.79
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (36 bp):
AGATTTTCTAGGAATCAAAGATTTACTAAAAATAAT
Found at i:4446298 original size:18 final size:19
Alignment explanation
Indices: 4446277--4446317 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
4446267 ATCTTCTTCT
4446277 CTCCTTCTC-CTATCATCC
1 CTCCTTCTCTCTATCATCC
* *
4446295 CTCC-TCTCTCTATTATCT
1 CTCCTTCTCTCTATCATCC
4446313 CTCCT
1 CTCCT
4446318 AACTCTCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.10, C:0.46, G:0.00, T:0.44
Consensus pattern (19 bp):
CTCCTTCTCTCTATCATCC
Found at i:4446337 original size:42 final size:41
Alignment explanation
Indices: 4446286--4446398 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 41
4446276 TCTCCTTCTC
* * *
4446286 CTATCATCCCTCCTCTCTCTATTATCTCTCCTAACTCTCCTT
1 CTATCATCCCTCCTATCTCTACTATCTCTCCTAACACTCC-T
* * *
4446328 CTATCATCCCTTCAATCTCTACTATCTCTCCTATCACTCCT
1 CTATCATCCCTCCTATCTCTACTATCTCTCCTAACACTCCT
* *
4446369 CATATCATCCCTCCTATCTCTTCTTTCTCT
1 C-TATCATCCCTCCTATCTCTACTATCTCT
4446399 TTGAGGGCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 2 0.03
42 58 0.97
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (41 bp):
CTATCATCCCTCCTATCTCTACTATCTCTCCTAACACTCCT
Found at i:4449034 original size:18 final size:18
Alignment explanation
Indices: 4449007--4449110 Score: 109
Period size: 18 Copynumber: 5.7 Consensus size: 18
4448997 GATTAGCCTA
* *
4449007 AATCACAGATTTTTTAGG
1 AATCATAGATTTTCTAGG
*
4449025 AATCTTAGATTTTCTAGG
1 AATCATAGATTTTCTAGG
* **
4449043 AATCACAGATTTTCTAAA
1 AATCATAGATTTTCTAGG
*
4449061 AATCATTAGATTTTTTAGG
1 AATCA-TAGATTTTCTAGG
* **
4449080 AATCACAGATTTTCTAAA
1 AATCATAGATTTTCTAGG
4449098 AATCATAGATTTT
1 AATCATAGATTTT
4449111 TGTAATCTTA
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
18 55 0.80
19 14 0.20
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AATCATAGATTTTCTAGG
Found at i:4449080 original size:37 final size:37
Alignment explanation
Indices: 4449007--4449111 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
4448997 GATTAGCCTA
* ** *
4449007 AATCACAGATTTTTTAGGAATC-TTAGATTTTCTAGG
1 AATCACAGATTTTCTAAAAATCATTAGATTTTTTAGG
4449043 AATCACAGATTTTCTAAAAATCATTAGATTTTTTAGG
1 AATCACAGATTTTCTAAAAATCATTAGATTTTTTAGG
4449080 AATCACAGATTTTCTAAAAATCA-TAGATTTTT
1 AATCACAGATTTTCTAAAAATCATTAGATTTTT
4449112 GTAATCTTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 28 0.44
37 36 0.56
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (37 bp):
AATCACAGATTTTCTAAAAATCATTAGATTTTTTAGG
Found at i:4452146 original size:12 final size:11
Alignment explanation
Indices: 4452124--4452199 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
4452114 AGAGAAAGAA
*
4452124 GAGAGAGGAGG
1 GAGATAGGAGG
4452135 GATGATAGGAGG
1 GA-GATAGGAGG
*
4452147 AGAGAAAGGA--
1 -GAGATAGGAGG
*
4452157 GAGATAGTA--
1 GAGATAGGAGG
4452166 GAGATAGGAGG
1 GAGATAGGAGG
4452177 GATGATAGGAGG
1 GA-GATAGGAGG
*
4452189 AGAGACAGGAG
1 -GAGATAGGAG
4452200 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:4452156 original size:24 final size:24
Alignment explanation
Indices: 4452123--4452208 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
4452113 AAGAGAAAGA
*
4452123 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGAAAGGAGGGATGATAGGAGG
*
4452147 AGAGAAAGGA--GA-GAT---AGT
1 AGAGAAAGGAGGGATGATAGGAGG
*
4452165 AGAGATAGGAGGGATGATAGGAGG
1 AGAGAAAGGAGGGATGATAGGAGG
* * *
4452189 AGAGACAGGAGAGATAATAG
1 AGAGAAAGGAGGGATGATAG
4452209 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.43, C:0.01, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGAAAGGAGGGATGATAGGAGG
Found at i:4452175 original size:42 final size:42
Alignment explanation
Indices: 4452114--4452232 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
4452104 TAGCCCTCAA
* *
4452114 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGAAAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGAAAGG
* *
4452156 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGAAAGG
* *
4452198 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
4452233 GAGAGAAGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.44, C:0.02, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGAAAGG
Found at i:4458449 original size:19 final size:18
Alignment explanation
Indices: 4458412--4458525 Score: 120
Period size: 18 Copynumber: 6.2 Consensus size: 18
4458402 GGATCTTAGT
* * *
4458412 TTTTCTAGGAATTACAGA
1 TTTTCTAAGAATCATAGA
*
4458430 TTTTATAAGAATCATTAGA
1 TTTTCTAAGAATCA-TAGA
*
4458449 TTTTCTAAGAATTATAGA
1 TTTTCTAAGAATCATAGA
4458467 TTTTCTAAGAATCATTAGA
1 TTTTCTAAGAATCA-TAGA
* * *
4458486 TTTTTTAGGAATCACAGA
1 TTTTCTAAGAATCATAGA
* *
4458504 TTTTCTAAAAATAATAGA
1 TTTTCTAAGAATCATAGA
4458522 TTTT
1 TTTT
4458526 TGTAATCAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
18 48 0.61
19 31 0.39
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTTCTAAGAATCATAGA
Found at i:4458461 original size:37 final size:37
Alignment explanation
Indices: 4458407--4458525 Score: 159
Period size: 37 Copynumber: 3.2 Consensus size: 37
4458397 TTTTGGGATC
* *
4458407 TTAGTTTTTCTAGGAATTACAGATTTTATAAGAATCA
1 TTAGATTTTCTAGGAATTACAGATTTTCTAAGAATCA
* *
4458444 TTAGATTTTCTAAGAATTATAGATTTTCTAAGAATCA
1 TTAGATTTTCTAGGAATTACAGATTTTCTAAGAATCA
* * *
4458481 TTAGATTTTTTAGGAATCACAGATTTTCTAAAAAT-A
1 TTAGATTTTCTAGGAATTACAGATTTTCTAAGAATCA
*
4458517 ATAGATTTT
1 TTAGATTTT
4458526 TGTAATCAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 9 0.12
37 63 0.88
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.44
Consensus pattern (37 bp):
TTAGATTTTCTAGGAATTACAGATTTTCTAAGAATCA
Found at i:4467070 original size:18 final size:18
Alignment explanation
Indices: 4467049--4467083 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4467039 CCTCCTCCTG
*
4467049 TTATCCCTCCTCTCTCTA
1 TTATCCCTCCTATCTCTA
*
4467067 TTATCTCTCCTATCTCT
1 TTATCCCTCCTATCTCT
4467084 CCTCCTAGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.40, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATCCCTCCTATCTCTA
Found at i:4467088 original size:12 final size:12
Alignment explanation
Indices: 4467073--4467137 Score: 54
Period size: 12 Copynumber: 5.9 Consensus size: 12
4467063 TCTATTATCT
4467073 CTCCTATCTCTC
1 CTCCTATCTCTC
*
4467085 CTCCTAGCATC-C
1 CTCCTATC-TCTC
4467097 CTCCTA--TC-C
1 CTCCTATCTCTC
*
4467106 CTACTATCTCT-
1 CTCCTATCTCTC
4467117 CT--TATCTCTC
1 CTCCTATCTCTC
4467127 CTCCTATCTCT
1 CTCCTATCTCT
4467138 TCTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
9 15 0.34
10 2 0.05
11 4 0.09
12 21 0.48
13 2 0.05
ACGTcount: A:0.12, C:0.46, G:0.02, T:0.40
Consensus pattern (12 bp):
CTCCTATCTCTC
Found at i:4467097 original size:42 final size:42
Alignment explanation
Indices: 4467051--4467132 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
4467041 TCCTCCTGTT
* * *
4467051 ATCCCTCCTCTCTCTATTATCTCTCCTATCTCTCCTCCTAGC
1 ATCCCTCCTATCCCTACTATCTCTCCTATCTCTCCTCCTAGC
*
4467093 ATCCCTCCTATCCCTACTATCTCTCTTATCTCTCCTCCTA
1 ATCCCTCCTATCCCTACTATCTCTCCTATCTCTCCTCCTA
4467133 TCTCTTCTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.13, C:0.45, G:0.01, T:0.40
Consensus pattern (42 bp):
ATCCCTCCTATCCCTACTATCTCTCCTATCTCTCCTCCTAGC
Found at i:4471080 original size:49 final size:48
Alignment explanation
Indices: 4471009--4471107 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 48
4470999 ATCACCATTA
* *
4471009 CTTTGGCTCCTAGGACTTAGGAAGACTATTTAGAAGCTTCTTTACCAT
1 CTTTGGCTCCCAAGACTTAGGAAGACTATTTAGAAGCTTCTTTACCAT
4471057 CTTTGGCTCCCCAAGACTTAGGAAGACTATTTAGAAGCTTCTTTACCAT
1 CTTTGGCT-CCCAAGACTTAGGAAGACTATTTAGAAGCTTCTTTACCAT
4471106 CT
1 CT
4471108 CTTTGTTTGA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 8 0.17
49 40 0.83
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.34
Consensus pattern (48 bp):
CTTTGGCTCCCAAGACTTAGGAAGACTATTTAGAAGCTTCTTTACCAT
Found at i:4472093 original size:23 final size:23
Alignment explanation
Indices: 4472050--4472093 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
4472040 CCTCTCAGTC
*
4472050 TCTTCAAGAATTATACCCCAAAT
1 TCTTCAAGAATTATACACCAAAT
*
4472073 TCTT-AAGAGATTTTACACCAA
1 TCTTCAAGA-ATTATACACCAA
4472094 GGTTGAATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (23 bp):
TCTTCAAGAATTATACACCAAAT
Found at i:4472483 original size:20 final size:20
Alignment explanation
Indices: 4472458--4472512 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
4472448 GTTGGGCTCA
* *
4472458 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATCCACC
**
4472478 ATGTATCGATACAATCCTTC
1 ATGTATCGATACAATCCACC
4472498 ATGTATCGATACAAT
1 ATGTATCGATACAAT
4472513 ACAATGTGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATCCACC
Found at i:4475455 original size:110 final size:109
Alignment explanation
Indices: 4475279--4475493 Score: 333
Period size: 110 Copynumber: 2.0 Consensus size: 109
4475269 GAGGCTAATC
*
4475279 AAGACAAGAACAACTTGATAAAAGAAATAACATATATCAGCTTGATCTGAGCCAAAGCTCTAATA
1 AAGACAAGAACAACTTGATAAAAGAAATAACATAGATCAGCTTGATCTGAGCCAAAGCTCTAATA
** *
4475344 CCAAATGATGTGGAAACCCCAAGAATGATGTCTTAAAACCGCCG
66 CCAAATGATGCAGAAACCCCAAGAACGATGTCTTAAAACCGCCG
* * * *
4475388 AAGACACGAACAACTTGAT-AAAGAAATAAAAGATAGATTAGCTTGATCTGAGCCAAAGCTCTGA
1 AAGACAAGAACAACTTGATAAAAGAAAT--AACATAGATCAGCTTGATCTGAGCCAAAGCTCTAA
4475452 TACCAAATGATGCAGAAACCCCAAGAACGATGTCTTAAAACC
64 TACCAAATGATGCAGAAACCCCAAGAACGATGTCTTAAAACC
4475494 CAAAAAAAGA
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 8 0.08
109 18 0.19
110 70 0.73
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (109 bp):
AAGACAAGAACAACTTGATAAAAGAAATAACATAGATCAGCTTGATCTGAGCCAAAGCTCTAATA
CCAAATGATGCAGAAACCCCAAGAACGATGTCTTAAAACCGCCG
Found at i:4478013 original size:12 final size:12
Alignment explanation
Indices: 4477980--4478056 Score: 62
Period size: 12 Copynumber: 6.9 Consensus size: 12
4477970 AAGAGAAAGA
4477980 AGAGATAGGAGG
1 AGAGATAGGAGG
*
4477992 -GATGAAAGGAGG
1 AGA-GATAGGAGG
4478004 AGAGAT---AGG
1 AGAGATAGGAGG
*
4478013 AGAGAT---AGT
1 AGAGATAGGAGG
4478022 AGAGATAGGAGG
1 AGAGATAGGAGG
4478034 -GATGATAGGAGG
1 AGA-GATAGGAGG
4478046 AGAGATAGGAG
1 AGAGATAGGAG
4478057 AGATAATAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
9 17 0.31
11 4 0.07
12 29 0.54
13 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.47, T:0.12
Consensus pattern (12 bp):
AGAGATAGGAGG
Found at i:4478026 original size:11 final size:9
Alignment explanation
Indices: 4478001--4478061 Score: 65
Period size: 9 Copynumber: 7.1 Consensus size: 9
4477991 GGATGAAAGG
4478001 AGGAGAGAT
1 AGGAGAGAT
4478010 AGGAGAGAT
1 AGGAGAGAT
*
4478019 AGTAGAGAT
1 AGGAGAGAT
*
4478028 AGGAGGGAT
1 AGGAGAGAT
* *
4478037 --GATAG-G
1 AGGAGAGAT
4478043 AGGAGAGAT
1 AGGAGAGAT
4478052 AGGAGAGAT
1 AGGAGAGAT
4478061 A
1 A
4478062 ATAAAGAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
7 3 0.07
8 4 0.10
9 34 0.83
ACGTcount: A:0.43, C:0.00, G:0.44, T:0.13
Consensus pattern (9 bp):
AGGAGAGAT
Found at i:4478030 original size:42 final size:42
Alignment explanation
Indices: 4477971--4478086 Score: 160
Period size: 42 Copynumber: 2.7 Consensus size: 42
4477961 TAGCCTTCAA
* *
4477971 AGAGAAAGAAGAGATAGGAGGGATGAAAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGAAAGGAGGAGAGATAGG
*
4478013 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGATAGG
1 AGAGATAGTAGAGATAGGAGGGATGAAAGGAGGAGAGATAGG
* * * *
4478055 AGAGATAATAAAGAGAGGAGGGAATGACAGGA
1 AGAGATAGTAGAGATAGGAGGG-ATGAAAGGA
4478087 AGAGGAGAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
42 58 0.88
43 8 0.12
ACGTcount: A:0.46, C:0.01, G:0.43, T:0.10
Consensus pattern (42 bp):
AGAGATAGTAGAGATAGGAGGGATGAAAGGAGGAGAGATAGG
Found at i:4483155 original size:69 final size:69
Alignment explanation
Indices: 4483044--4483204 Score: 304
Period size: 69 Copynumber: 2.3 Consensus size: 69
4483034 TCATCTAATC
4483044 ACCCTTATGTGTATGACCCATTAGGCCCCCATCATATTGGCAATAATTATAAATTATCCAATTAA
1 ACCCTTATGTGTATGACCCATTAGGCCCCCATCATATTGGCAATAATTATAAATTATCCAATTAA
4483109 GAAT
66 GAAT
* *
4483113 ACCCTTATGTGTATGACTCTTTAGGCCCCCATCATATTGGCAATAATTATAAATTATCCAATTAA
1 ACCCTTATGTGTATGACCCATTAGGCCCCCATCATATTGGCAATAATTATAAATTATCCAATTAA
4483178 GAAT
66 GAAT
4483182 ACCCTTATGTGTATGACCCATTA
1 ACCCTTATGTGTATGACCCATTA
4483205 TGATGAGAAC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 88 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34
Consensus pattern (69 bp):
ACCCTTATGTGTATGACCCATTAGGCCCCCATCATATTGGCAATAATTATAAATTATCCAATTAA
GAAT
Found at i:4495542 original size:52 final size:52
Alignment explanation
Indices: 4495395--4495522 Score: 204
Period size: 52 Copynumber: 2.5 Consensus size: 52
4495385 GAAATATGAA
*
4495395 AAATT-GCCTGCATGTATCGATACATTTCATAGTGTATCGATACATTTGGGC
1 AAATTGGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
4495446 AAATTGGCCTGTATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTGGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
4495498 AAATTTGTCTGCATGTATCGATACA
1 AAATTGGCCTGCATGTATCGATACA
4495523 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
51 5 0.07
52 65 0.93
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (52 bp):
AAATTGGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:4495549 original size:13 final size:13
Alignment explanation
Indices: 4495531--4495555 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4495521 CAAAGATCAG
4495531 TGTATCGATACAA
1 TGTATCGATACAA
4495544 TGTATCGATACA
1 TGTATCGATACA
4495556 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4495632 original size:19 final size:18
Alignment explanation
Indices: 4495608--4495670 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
4495598 AGCAATACAT
4495608 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
4495627 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
4495640 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
4495659 TGTATCGATACA
1 TGTATCGATACA
4495671 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:4495643 original size:32 final size:32
Alignment explanation
Indices: 4495602--4495685 Score: 159
Period size: 32 Copynumber: 2.6 Consensus size: 32
4495592 CTTTGTAGCA
4495602 ATACATTGTATCGATACAAAACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
*
4495634 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
4495666 ATACATTGTATCGATACAAA
1 ATACATTGTATCGATACAAA
4495686 TCGTTGAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATGTATCG
Found at i:4495645 original size:13 final size:13
Alignment explanation
Indices: 4495627--4495683 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
4495617 ACAAAACTTA
4495627 TGTATCGATACAT
1 TGTATCGATACAT
4495640 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
4495658 ATGTATCGATACAT
1 -TGTATCGATACAT
4495672 TGTATCGATACA
1 TGTATCGATACA
4495684 AATCGTTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4508424 original size:21 final size:21
Alignment explanation
Indices: 4508400--4508476 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
4508390 AATTTATCCA
4508400 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
4508421 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
4508442 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
4508463 AATGTATCGATACA
1 AATGTATCGATACA
4508477 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:4508536 original size:19 final size:18
Alignment explanation
Indices: 4508512--4508579 Score: 56
Period size: 19 Copynumber: 3.9 Consensus size: 18
4508502 AATTCAACAA
4508512 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
4508530 TTTTGTATTGATAC--AA-
1 -TTTGTATCGATACATAAG
*
4508546 --TGTATCAATACATAAG
1 TTTGTATCGATACATAAG
*
4508562 CATTGTATCGATACATAA
1 -TTTGTATCGATACATAA
4508580 TTAGCTACTG
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
13 9 0.23
15 2 0.05
17 2 0.05
19 26 0.67
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:4508557 original size:32 final size:32
Alignment explanation
Indices: 4508514--4508576 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
4508504 TTCAACAATT
* ** *
4508514 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCAATACATAAGCATTGTATCGATACAA
4508546 TGTATCAATACATAAGCATTGTATCGATACA
1 TGTATCAATACATAAGCATTGTATCGATACA
4508577 TAATTAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGCATTGTATCGATACAA
Found at i:4508637 original size:13 final size:13
Alignment explanation
Indices: 4508619--4508644 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4508609 CATTTTTCTG
4508619 TGTATCGATACAT
1 TGTATCGATACAT
4508632 TGTATCGATACAT
1 TGTATCGATACAT
4508645 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4508641 original size:33 final size:33
Alignment explanation
Indices: 4508599--4508665 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4508589 GCCAAGGAAA
***
4508599 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
4508632 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
4508665 T
1 T
4508666 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:4511153 original size:27 final size:28
Alignment explanation
Indices: 4511123--4511193 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
4511113 CTTCACAATG
**
4511123 GGGGATACTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATATCAGA
* *
4511150 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATATCAGA
4511178 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
4511194 TGGTTTTATC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.24, C:0.34, G:0.21, T:0.21
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATATCAGA
Found at i:4511245 original size:52 final size:50
Alignment explanation
Indices: 4511178--4511348 Score: 166
Period size: 52 Copynumber: 3.3 Consensus size: 50
4511168 TTATTTCCGA
*
4511178 GGGGATACTCCAACCCTGGTTTTATCACTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCC-GGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** * **
4511230 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAA-CCCGGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
4511282 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAAC-CCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
*
4511334 GAGGATACTCCAACC
1 GGGGATACTCCAACC
4511349 TCGTAATTTC
Statistics
Matches: 97, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
51 9 0.09
52 71 0.73
53 12 0.12
54 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:4511331 original size:104 final size:104
Alignment explanation
Indices: 4511011--4511348 Score: 296
Period size: 104 Copynumber: 3.2 Consensus size: 104
4511001 CTCAATTCTC
* ** * * *
4511011 CACAATCGGGGATATTCCAAATCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGAT
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
*
4511075 ACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
66 ACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TT
* * ** * * * ** * *
4511116 CACAATGGGGGATACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTCCG
1 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTTCCTTTA-AT-C-
* * *
4511177 AGGGGATACTCCAAC-CCTGGTTTTA--TCACTAAAACACTAATTTTT
60 -GGGGATACTCCAACTCC-GATTTTATTTC-CAAAAACACCAATTTTT
*
4511222 CCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGA
1 -CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGA
*
4511287 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
65 TACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
*
4511327 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
4511349 TCGTAATTTC
Statistics
Matches: 178, Mismatches: 37, Indels: 37
0.71 0.15 0.15
Matches are distributed among these distances:
103 6 0.03
104 41 0.23
105 39 0.22
106 19 0.11
107 39 0.22
108 9 0.05
109 25 0.14
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (104 bp):
CACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGAT
ACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
Found at i:4511376 original size:212 final size:212
Alignment explanation
Indices: 4511006--4511458 Score: 612
Period size: 212 Copynumber: 2.1 Consensus size: 212
4510996 AGTTTCTCAA
* ** *
4511006 TTCTCCACAATCGGGGATATTCCAAATCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
* * *
4511071 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATGGGGGATACTCCAA
66 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* * *
4511136 CCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTTCCGAGGGGATACTCCAACCCTGGTTT
131 CCCCGTTAATCATCGAGGATACTCCAACCCCGTTACTTT-CGAGGGGATACTCCAACCCCGGCTT
*
4511200 TA-TCACTAAAACACTAAT
195 TATTC-CCAAAACACTAAT
* * * *
4511218 TTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCG
*
4511283 GGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCA
65 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCA
* *
4511346 ACCTCG-TAATTTCATCGAGGATACTCCAACCTCGTTACTTTCGAGGGGATACTCCAACCCCGGC
130 ACCCCGTTAA--TCATCGAGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGC
* * *
4511410 TTTATTCCCAAAATATTGAT
193 TTTATTCCCAAAACACTAAT
* *
4511430 TTCT-CATAATTGGGGATACTCCAACCCCG
1 TTCTCCACAATCGGGGATACTCCAACCCCG
4511459 TTATTTTCGA
Statistics
Matches: 212, Mismatches: 24, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
210 3 0.01
211 47 0.22
212 122 0.58
213 40 0.19
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGG
GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
CCCCGTTAATCATCGAGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACCCCGGCTTT
ATTCCCAAAACACTAAT
Found at i:4511395 original size:28 final size:27
Alignment explanation
Indices: 4511333--4511404 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 27
4511323 TTTTCACAAT
4511333 CGAGGATACTCCAACCTCGTAATTTCA
1 CGAGGATACTCCAACCTCGTAATTTCA
*
4511360 TCGAGGATACTCCAACCTCGTTACTTTCGA
1 -CGAGGATACTCCAACCTCG-TAATTTC-A
*
4511390 -GGGGATACTCCAACC
1 CGAGGATACTCCAACC
4511405 CCGGCTTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 33 0.82
29 6 0.15
30 1 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (27 bp):
CGAGGATACTCCAACCTCGTAATTTCA
Found at i:4511477 original size:107 final size:107
Alignment explanation
Indices: 4511069--4511481 Score: 278
Period size: 107 Copynumber: 3.9 Consensus size: 107
4511059 TTCTATAATC
* * * * * *
4511069 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATGGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTCC-AAAAATACCAATTTC-TCACAATCGAGGATACTCC
* * *
4511134 AACCCCGTTAA-TCATCGGGGATACTCCAACCCCGTTA-TTTCCGA
64 AACCCCG-TAATTTATCGAGGATACTCCAACCTCGTTACTTT-CGA
* * * * * * * *
4511178 GGGGATACTCCAACCCTG-GTTT-TATCACTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTCC
* * * * * *
4511241 AACCCCGGTTTTATTT-TC-A--AAACGCCAA--T-TTTCCTTT-AA
64 AACCCC-G--TAATTTATCGAGGATACTCCAACCTCGTTACTTTCGA
* * *
4511280 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCC
1 --GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCC
*
4511345 AACCTCGTAATTTCATCGAGGATACTCCAACCTCGTTACTTTCGA
64 AACCCCGTAATTT-ATCGAGGATACTCCAACCTCGTTACTTTCGA
* * *** * * *
4511390 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
4511454 CCCCGTTATTT-TCGAGGGGATACTCCAA
66 CCCCGTAATTTATCGA--GGATACTCCAA
4511482 TCCCGATTTT
Statistics
Matches: 237, Mismatches: 46, Indels: 44
0.72 0.14 0.13
Matches are distributed among these distances:
101 5 0.02
102 1 0.00
103 5 0.02
104 42 0.18
105 21 0.09
106 18 0.08
107 90 0.38
108 27 0.11
109 26 0.11
110 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTAATTTATCGAGGATACTCCAACCTCGTTACTTTCGA
Found at i:4520591 original size:19 final size:19
Alignment explanation
Indices: 4520567--4520634 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
4520557 AATTCAACGA
4520567 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4520586 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4520601 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
4520618 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
4520635 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4520605 original size:32 final size:32
Alignment explanation
Indices: 4520569--4520631 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4520559 TTCAACGATT
*
4520569 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
4520601 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
4520632 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:4520606 original size:13 final size:13
Alignment explanation
Indices: 4520588--4520612 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4520578 ACATAAGTTT
4520588 TGTATCGATACAA
1 TGTATCGATACAA
4520601 TGTATCGATACA
1 TGTATCGATACA
4520613 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4520692 original size:13 final size:13
Alignment explanation
Indices: 4520674--4520699 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4520664 CATTTTTCTG
4520674 TGTATCGATACAT
1 TGTATCGATACAT
4520687 TGTATCGATACAT
1 TGTATCGATACAT
4520700 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4520696 original size:33 final size:33
Alignment explanation
Indices: 4520654--4520720 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
4520644 GCCAAGGAAA
***
4520654 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
4520687 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
4520720 T
1 T
4520721 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:4520758 original size:15 final size:15
Alignment explanation
Indices: 4520738--4520766 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4520728 TTTACCCAGA
4520738 TGTATCGATACATTG
1 TGTATCGATACATTG
4520753 TGTATCGATACATT
1 TGTATCGATACATT
4520767 CAGGCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (15 bp):
TGTATCGATACATTG
Found at i:4523115 original size:51 final size:54
Alignment explanation
Indices: 4523051--4523181 Score: 171
Period size: 51 Copynumber: 2.5 Consensus size: 54
4523041 AGTTTCTCAA
* * * *
4523051 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAG-ACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAAT
* *
4523102 TT-TTCTATAATCGGCGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAAT
4523156 TTCTTCACAATCGGGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
4523182 CCTGTTATTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 33 0.49
52 3 0.04
53 6 0.09
54 20 0.30
55 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (54 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAGAACACCAAT
Found at i:4523197 original size:28 final size:28
Alignment explanation
Indices: 4523165--4523241 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
4523155 TTTCTTCACA
* *
4523165 ATCGGGGATACTCCAACCCTGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
4523193 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
4523221 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
4523242 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:4523345 original size:79 final size:79
Alignment explanation
Indices: 4523195--4523399 Score: 232
Period size: 79 Copynumber: 2.6 Consensus size: 79
4523185 GTTATTTCAT
* * *
4523195 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
** * *
4523260 TGATTTCTCATAAT
66 CAATTTCTCACAAC
* * * * ** *
4523274 TGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
4523338 TCAATTTCTCACAAC
65 TCAATTTCTCACAAC
* * * *
4523353 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
4523400 TTATTATCTC
Statistics
Matches: 105, Mismatches: 20, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 3 0.03
79 102 0.97
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CAATTTCTCACAAC
Found at i:4529356 original size:55 final size:54
Alignment explanation
Indices: 4529075--4529741 Score: 793
Period size: 55 Copynumber: 12.0 Consensus size: 54
4529065 GATGCCTTTT
* * * * *
4529075 CCTTTTAAAGCCCACACGAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCGGGACG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACA
* * *
4529130 CCTTTTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGAC-
1 CC---TTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
* * *
4529186 CCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTTAAAGAGCGGGACG
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
* * *
4529245 CCTTTTCTTTTAACGCCCACACAAGTTGGTGGTACCTTCAGTCCTCAAAGAGCAGGACA
1 CC-TTTC----AAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
* *
4529304 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACA
* *
4529359 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTTAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGCAGGACA
* *
4529414 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGTAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
* * *
4529469 CCTTTCAAAGCACACCCAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACA
*
4529524 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
*
4529579 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACA
* * *
4529634 CCTCTT-AAAGCCCACACCAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACG
1 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACA
* * * *
4529689 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGA
4529742 TACACTTTAT
Statistics
Matches: 547, Mismatches: 43, Indels: 44
0.86 0.07 0.07
Matches are distributed among these distances:
54 41 0.07
55 336 0.61
56 18 0.03
57 20 0.04
58 77 0.14
59 55 0.10
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACA
Found at i:4530471 original size:21 final size:21
Alignment explanation
Indices: 4530445--4530521 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
4530435 AAATTATCCA
4530445 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
4530466 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
4530487 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
4530508 AATGTATCGATACA
1 AATGTATCGATACA
4530522 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:4530581 original size:19 final size:19
Alignment explanation
Indices: 4530557--4530624 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
4530547 AATTCAACAA
4530557 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
4530576 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
4530591 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
* *
4530608 ATCGTATCGATACATAA
1 TTTGTATCGATACATAA
4530625 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:4530596 original size:13 final size:13
Alignment explanation
Indices: 4530578--4530602 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4530568 ACATAAGTTT
4530578 TGTATCGATACAA
1 TGTATCGATACAA
4530591 TGTATCGATACA
1 TGTATCGATACA
4530603 TAAGTATCGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4530600 original size:32 final size:32
Alignment explanation
Indices: 4530559--4530621 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
4530549 TTCAACAATT
* *
4530559 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATCGTATCGATACAA
4530591 TGTATCGATACATAAGTATCGTATCGATACA
1 TGTATCGATACATAAGTATCGTATCGATACA
4530622 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATCGTATCGATACAA
Found at i:4530662 original size:13 final size:13
Alignment explanation
Indices: 4530644--4530669 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4530634 GCCAAGAAAA
4530644 TGTATCGATACAT
1 TGTATCGATACAT
4530657 TGTATCGATACAT
1 TGTATCGATACAT
4530670 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4533098 original size:51 final size:53
Alignment explanation
Indices: 4533034--4533375 Score: 199
Period size: 52 Copynumber: 6.5 Consensus size: 53
4533024 AGTTTCTCAA
* * * *
4533034 TTCTCCACAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
4533085 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * * *
4533139 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGTGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAAT
** ** * * * *
4533192 CCCGTT-A-TTTCTGAGGGGATACTCCAACCCCGGTTTTA--TCACTAAAACACTAAT
1 TTC-TTCACAATC---GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * * *
4533246 TT-TTCCACAATCGGAGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-T
* * *
4533299 TTCCTT--TAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
4533351 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
4533376 CTCGTTATTT
Statistics
Matches: 220, Mismatches: 47, Indels: 47
0.70 0.15 0.15
Matches are distributed among these distances:
50 4 0.02
51 33 0.15
52 87 0.40
53 33 0.15
54 35 0.16
55 25 0.11
57 3 0.01
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.32
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:4533178 original size:27 final size:28
Alignment explanation
Indices: 4533148--4533232 Score: 102
Period size: 27 Copynumber: 3.0 Consensus size: 28
4533138 TTTCTTCACA
4533148 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
4533175 ATCGTGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
4533203 -TGAGGGGATACTCCAACCCCGGTTTTATC
1 AT-CGGGGATACTCCAACCCC-GTTATATC
4533232 A
1 A
4533233 CTAAAACACT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
27 24 0.50
28 18 0.38
29 6 0.12
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:4533258 original size:107 final size:103
Alignment explanation
Indices: 4533097--4533490 Score: 319
Period size: 107 Copynumber: 3.7 Consensus size: 103
4533087 TTCTATAATC
* * *
4533097 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGGTTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
4533162 AACCCCGTTAATCATCGTGGATACTCCAACCCCGTTATTTCTGA
63 AACCCCGTT-ATCATCGTGGATACTCCAACCCCGTTA-TTC-GA
* * *
4533206 GGGGATACTCCAACCCCGGTTTTA-TCACTAAAACACTAATTTTTCCACAATCGGAGATACTCCA
1 GGGGATACTCCAACCCCGGTTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
* ** ** * * ** * *
4533270 ACCCCGGTT-TTATTTTCAAAACACCAATTTTCCTTTAATC--
64 ACCCC-GTTATCATCGTGGATACTCCAA--CCCCGTTATTCGA
* * * * *
4533310 GGGGATACTCTAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
4533375 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA--TCATCGTGGATACTCCAACCCCGTTA-TT-CGA
* * * *** * * *
4533418 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
4533483 CCCGTTAT
66 CCCGTTAT
4533491 TTTCGAGGGG
Statistics
Matches: 220, Mismatches: 51, Indels: 32
0.73 0.17 0.11
Matches are distributed among these distances:
103 3 0.01
104 47 0.21
105 16 0.07
106 26 0.12
107 78 0.35
108 29 0.13
109 21 0.10
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (103 bp):
GGGGATACTCCAACCCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATCATCGTGGATACTCCAACCCCGTTATTCGA
Found at i:4533395 original size:28 final size:28
Alignment explanation
Indices: 4533359--4533435 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
4533349 ATTTTTCACA
* * *
4533359 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
4533387 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
4533415 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
4533436 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:4533404 original size:212 final size:212
Alignment explanation
Indices: 4533037--4533442 Score: 654
Period size: 212 Copynumber: 1.9 Consensus size: 212
4533027 TTCTCAATTC
* * * *
4533037 TCCACAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
*
4533102 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * * *
4533167 CGTTAATCATCGTGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGGTTTTATC
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
4533232 ACTAAAACACTAATTTT
196 ACTAAAACACTAATTTT
* *
4533249 TCCACAATCGGAGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGG
1 TCCACAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGGG
*
4533314 ATACTCTAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCCAACC
65 ATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* *
4533377 TCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
130 CCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
4533442 T
194 T
4533443 TCCCAAAATA
Statistics
Matches: 178, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
211 28 0.16
212 114 0.64
213 36 0.20
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
ACTAAAACACTAATTTT
Found at i:4536369 original size:20 final size:20
Alignment explanation
Indices: 4536346--4536462 Score: 130
Period size: 20 Copynumber: 5.8 Consensus size: 20
4536336 AGGTACCCAG
4536346 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
4536366 ATGTATAGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
4536386 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
* * *
4536406 ATGTATAGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
4536426 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATTCTTCA
*
4536446 ATATATCGATACATTCT
1 ATGTATCGATACATTCT
4536463 ATCCTTTTAC
Statistics
Matches: 80, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 76 0.95
21 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:4536401 original size:40 final size:40
Alignment explanation
Indices: 4536346--4536459 Score: 201
Period size: 40 Copynumber: 2.9 Consensus size: 40
4536336 AGGTACCCAG
4536346 ATGTATCGATACATTCTTCAATGTATAGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATAGATACATGTATGA
4536386 ATGTATCGATACATTCTTCAATGTATAGATACATGTATGA
1 ATGTATCGATACATTCTTCAATGTATAGATACATGTATGA
* * *
4536426 ATGTATCGATACATTCTTTAATATATCGATACAT
1 ATGTATCGATACATTCTTCAATGTATAGATACAT
4536460 TCTATCCTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (40 bp):
ATGTATCGATACATTCTTCAATGTATAGATACATGTATGA
Found at i:4536502 original size:20 final size:20
Alignment explanation
Indices: 4536477--4536531 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
4536467 TTTTACCCAG
*
4536477 ATGTATCGAGACATTGAAGA
1 ATGTATCGATACATTGAAGA
*
4536497 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
4536517 ATGTATCGATACATT
1 ATGTATCGATACATT
4536532 ATGTCTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:4536571 original size:71 final size:71
Alignment explanation
Indices: 4536425--4536581 Score: 188
Period size: 71 Copynumber: 2.2 Consensus size: 71
4536415 TACATGTATG
**** * *
4536425 AATGTATCGATACATTCTTTAATATATCGATACATTCTATCCTTTTACCCAGATGTATCGAGACA
1 AATGTATCGATACATTGAAGAATGTATCGATACATTATATCCTTTTACCCAGATGTATCGAGACA
*
4536490 TTGAAG
66 TTGAAC
* * * *
4536496 AATGTATTGATACATTGAAGAATGTATCGATACATTATGTCTTTTTACCCAGATGTATCGATACA
1 AATGTATCGATACATTGAAGAATGTATCGATACATTATATCCTTTTACCCAGATGTATCGAGACA
***
4536561 TTTTTC
66 TTGAAC
4536567 AATGTATCGATACAT
1 AATGTATCGATACAT
4536582 CTAGTTAAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.38
Consensus pattern (71 bp):
AATGTATCGATACATTGAAGAATGTATCGATACATTATATCCTTTTACCCAGATGTATCGAGACA
TTGAAC
Found at i:4545664 original size:26 final size:28
Alignment explanation
Indices: 4545628--4545679 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4545618 ATTTTTTTTC
4545628 AAGAATAC-AAAAGA-AAAAAAAAAAGA
1 AAGAATACAAAAAGAGAAAAAAAAAAGA
*
4545654 AAGAATACAAAAAGAGAGAAAAAAAA
1 AAGAATACAAAAAGAGAAAAAAAAAA
4545680 CCAGTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 6 0.26
28 9 0.39
ACGTcount: A:0.79, C:0.04, G:0.13, T:0.04
Consensus pattern (28 bp):
AAGAATACAAAAAGAGAAAAAAAAAAGA
Found at i:4545667 original size:15 final size:15
Alignment explanation
Indices: 4545628--4545673 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
4545618 ATTTTTTTTC
4545628 AAGAATAC-AAAAGA
1 AAGAATACAAAAAGA
4545642 AA-AA-A-AAAAAGA
1 AAGAATACAAAAAGA
4545654 AAGAATACAAAAAGA
1 AAGAATACAAAAAGA
*
4545669 GAGAA
1 AAGAA
4545674 AAAAAACCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
12 9 0.33
13 4 0.15
14 3 0.11
15 11 0.41
ACGTcount: A:0.76, C:0.04, G:0.15, T:0.04
Consensus pattern (15 bp):
AAGAATACAAAAAGA
Found at i:4546448 original size:12 final size:11
Alignment explanation
Indices: 4546426--4546501 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
4546416 AGAGAAAGAA
*
4546426 GAGAGAGGAGG
1 GAGATAGGAGG
4546437 GATGATAGGAGG
1 GA-GATAGGAGG
*
4546449 AGAGACAGGA--
1 -GAGATAGGAGG
*
4546459 GAGATAGTA--
1 GAGATAGGAGG
4546468 GAGATAGGAGG
1 GAGATAGGAGG
4546479 GATGATAGGAGG
1 GA-GATAGGAGG
*
4546491 AGAGACAGGAG
1 -GAGATAGGAG
4546502 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:4546477 original size:42 final size:42
Alignment explanation
Indices: 4546416--4546538 Score: 201
Period size: 42 Copynumber: 2.9 Consensus size: 42
4546406 TAGCCCTCAA
* *
4546416 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
4546458 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
4546500 AGAGATAATAGAGAGAGGAGGGATGATAGGAGGATGAGA
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGA-GAGA
4546539 GAAGAAGATG
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 71 0.95
43 4 0.05
ACGTcount: A:0.43, C:0.02, G:0.46, T:0.10
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:4555284 original size:52 final size:52
Alignment explanation
Indices: 4555206--4555334 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
4555196 CAAAATATGA
* *
4555206 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* * *
4555258 AAATTTGCCTACATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
4555310 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
4555335 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:4555347 original size:52 final size:51
Alignment explanation
Indices: 4555206--4555354 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
4555196 CAAAATATGA
*
4555206 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * * *
4555258 AAATTTGCCTACATGTATCGATACATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
4555310 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
4555355 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:4555361 original size:13 final size:13
Alignment explanation
Indices: 4555343--4555367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4555333 CAAAGATCAG
4555343 TGTATCGATACAA
1 TGTATCGATACAA
4555356 TGTATCGATACA
1 TGTATCGATACA
4555368 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4555447 original size:13 final size:13
Alignment explanation
Indices: 4555429--4555453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4555419 ACAAAACTTA
4555429 TGTATCGATACAT
1 TGTATCGATACAT
4555442 TGTATCGATACA
1 TGTATCGATACA
4555454 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4555448 original size:32 final size:33
Alignment explanation
Indices: 4555408--4555473 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
4555398 AGTAGCTTAA
4555408 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
4555440 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
4555473 A
1 A
4555474 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:4556388 original size:67 final size:68
Alignment explanation
Indices: 4556262--4556388 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 68
4556252 ATTGGGTTTT
* * *
4556262 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGGAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCACGAATATTGGACTTAAAGATGAAGATG
4556327 AGA
66 AGA
* * * *
4556330 AAAG-TGATAAAGATGCTAATATGTTGATTCACGGCCAACG-ATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCC-ACGAATATTGGACTTAAAGATGA
4556389 GAAAAAGGAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
67 45 0.88
68 6 0.12
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCACGAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:4556506 original size:43 final size:43
Alignment explanation
Indices: 4556445--4556843 Score: 456
Period size: 43 Copynumber: 8.7 Consensus size: 43
4556435 TAAAGATGGA
* *
4556445 AAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
4556488 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
4556531 AAAGAAGAAGTTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTT
1 --A-AAG--G-TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
4556580 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
*
4556623 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
4556672 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
4556715 AAAGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* *
4556764 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
4556807 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGC
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGC
4556844 GATATTAGGA
Statistics
Matches: 306, Mismatches: 26, Indels: 42
0.82 0.07 0.11
Matches are distributed among these distances:
43 151 0.49
44 1 0.00
45 3 0.01
46 6 0.02
47 4 0.01
48 1 0.00
49 140 0.46
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:4556583 original size:92 final size:92
Alignment explanation
Indices: 4556392--4556849 Score: 774
Period size: 92 Copynumber: 4.9 Consensus size: 92
4556382 AAGATGAGAA
*
4556392 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATT-GAGCTTAAAGATGGAAAAGGTGCCAA
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA-CTTAAAGAT-G--AAGGTGCCAA
*
4556456 TATGCTGATTCAAGGCCAACTATATTGGACTT
61 TATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
4556488 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGTTGCCAATATGT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
4556553 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
4556580 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
4556645 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
4556672 AAAGGTGCCAATGTACTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
4556737 TAATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
*
4556764 AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
4556829 TGATTCAAGGCCAGCGATATT
66 TGATTCAAGGCCAGCTATATT
4556850 AGGATTAGAA
Statistics
Matches: 345, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
92 298 0.86
94 1 0.00
95 39 0.11
96 7 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:4556676 original size:22 final size:22
Alignment explanation
Indices: 4556651--4556718 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
4556641 ATGCTGATTC
4556651 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
4556673 AAGGTGCCA-ATGTACT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
4556694 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
4556716 AAG
1 AAG
4556719 ATGAAGGTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 9 0.28
23 5 0.16
24 4 0.12
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Done.