Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 139 of 204
Found at i:42088411 original size:13 final size:14
Alignment explanation
Indices: 42088393--42088421 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
42088383 AAGATTCCTT
42088393 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
42088406 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
42088420 AA
1 AA
42088422 GCCACTAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:42090753 original size:12 final size:12
Alignment explanation
Indices: 42090726--42090779 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
42090716 AGTTTTATAA
42090726 TTTTTATTTT-T
1 TTTTTATTTTGT
42090737 ATTTTTATTTTGT
1 -TTTTTATTTTGT
**
42090750 TTTTGGTTTTGGT
1 TTTTTATTTT-GT
42090763 TTTTT-TTTTGT
1 TTTTTATTTTGT
42090774 TTTTTA
1 TTTTTA
42090780 ATTATGCACT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 7 0.19
12 22 0.61
13 7 0.19
ACGTcount: A:0.07, C:0.00, G:0.11, T:0.81
Consensus pattern (12 bp):
TTTTTATTTTGT
Found at i:42094134 original size:20 final size:20
Alignment explanation
Indices: 42094109--42094150 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
42094099 CGTGCTCATA
*
42094109 AACAATTGGGTCCATGACCT
1 AACAATTGAGTCCATGACCT
42094129 AACAATTGAGTCCATGACCT
1 AACAATTGAGTCCATGACCT
42094149 AA
1 AA
42094151 AAATGAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
AACAATTGAGTCCATGACCT
Found at i:42094181 original size:29 final size:29
Alignment explanation
Indices: 42094148--42094205 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
42094138 GTCCATGACC
* *
42094148 TAAAAATGAACAACATACCTGCGTGCTCA
1 TAAAAATGAACAACATACCTACATGCTCA
42094177 TAAAAATGAACAACATACCTACATGCTCA
1 TAAAAATGAACAACATACCTACATGCTCA
42094206 ACAGTCGCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (29 bp):
TAAAAATGAACAACATACCTACATGCTCA
Found at i:42095742 original size:27 final size:27
Alignment explanation
Indices: 42095704--42096061 Score: 446
Period size: 27 Copynumber: 13.3 Consensus size: 27
42095694 CAGAAAGGTT
*
42095704 GTAAAATGACCGAAATACCCTTGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* *
42095731 GTAAAATTACCGAAATACCTTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* * * *
42095758 ATAAAATGATCAAAATACCATCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* * *
42095785 GTAAAATTACTGAAATACCTTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* *
42095812 GTAAAATTATCGAAATACCCTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* * *
42095839 GTAAAATTACCGAAATATCCTCAAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* ** *
42095866 GTAAAATTATTGAAATACCCTTGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* *
42095893 GTAAAATAACTGAAATACCCTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
*
42095920 GTAAAATGACTGAAATACCCTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* *
42095947 GTAAAATGACCTAAATACCCTCGAAAG
1 GTAAAATGACCGAAATACCCTCGAAGG
*
42095974 GTAAAATGACTGAAATACCCTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
*
42096001 GTAAAATGACCTAAATACCCTCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
* * *
42096028 GTAAAATTATCGAAATACCCCCGAAGG
1 GTAAAATGACCGAAATACCCTCGAAGG
*
42096055 TTAAAAT
1 GTAAAAT
42096062 AACTGTTATA
Statistics
Matches: 289, Mismatches: 42, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 289 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCTCGAAGG
Found at i:42102810 original size:24 final size:24
Alignment explanation
Indices: 42102778--42102825 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
42102768 CCCCTCAATG
42102778 GCTTCAATGAACTTGGTAAAGGCC
1 GCTTCAATGAACTTGGTAAAGGCC
42102802 GCTTCAATGAACTTGGTAAAGGCC
1 GCTTCAATGAACTTGGTAAAGGCC
42102826 ACTTAACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (24 bp):
GCTTCAATGAACTTGGTAAAGGCC
Found at i:42105431 original size:35 final size:35
Alignment explanation
Indices: 42105385--42105455 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
42105375 TGGTTGATAA
42105385 GTATACCTTTCATTGTCATCAATAACTGTTATCTG
1 GTATACCTTTCATTGTCATCAATAACTGTTATCTG
42105420 GTATACCTTTCATTGTCATCAATAACTGTTATCTG
1 GTATACCTTTCATTGTCATCAATAACTGTTATCTG
42105455 G
1 G
42105456 ACTGGCTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (35 bp):
GTATACCTTTCATTGTCATCAATAACTGTTATCTG
Found at i:42106715 original size:11 final size:11
Alignment explanation
Indices: 42106699--42106723 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
42106689 AACACTGAAC
42106699 TTTTTGGGTAA
1 TTTTTGGGTAA
42106710 TTTTTGGGTAA
1 TTTTTGGGTAA
42106721 TTT
1 TTT
42106724 GGTTAATTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (11 bp):
TTTTTGGGTAA
Found at i:42114097 original size:176 final size:177
Alignment explanation
Indices: 42113850--42114211 Score: 412
Period size: 176 Copynumber: 2.1 Consensus size: 177
42113840 ACCTGCTCTG
* * * *
42113850 AAAAAAAAACTTTAGGTATCTAAATGGAAAAAGTTGCATAATTTAAGTACCTAAAATGGTAATAG
1 AAAAAAAAACGTTAGGTATCTAAATGGAAAAAGTTACATAATTTAAGTACCTAAAATGGTAACAA
** * * ***
42113915 ATTAAAAATTTCACGTGTCAGAATTTGATTGGTTTTAATTCTGTTTTTAA-AGAAAGTTAACAAT
66 ATTAAAAACGTCACGTATCAGAATTTGATTGGTTTGAAAAATGTTTTTAACA-AAAGTTAACAAT
*
42113979 TGGTACCTAAAGTAATAACAGAATAAAA-TTTCA-AGTACCTACTTTAAT
130 TGATACCTAAAGTAATAACAGAATAAAACTTT-AGA-TACCTACTTTAAT
* *
42114027 AAAAAAAAA-GTTAGGTA-CTTAAATAGG-AAAAGTTACATAGTTTAAGTACCTAAAGTGGTAAC
1 AAAAAAAAACGTTAGGTATC-TAAAT-GGAAAAAGTTACATAATTTAAGTACCTAAAATGGTAAC
* * * * * * *
42114089 AAATTAAAACCGTCATGTATCATAATTTGATTGGTTTGAAAAATTTTTTTAACAAGAGTTAATAG
64 AAATTAAAAACGTCACGTATCAGAATTTGATTGGTTTGAAAAATGTTTTTAACAAAAGTTAACAA
* * * *
42114154 TTTATACCTAAAGTGATAATAGAATAAAACTTTAGATACCTACTTTGAT
129 TTGATACCTAAAGTAATAACAGAATAAAACTTTAGATACCTACTTTAAT
42114203 AAAAAAAAA
1 AAAAAAAAA
42114212 AAACTTTCAG
Statistics
Matches: 155, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
175 1 0.01
176 138 0.89
177 16 0.10
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (177 bp):
AAAAAAAAACGTTAGGTATCTAAATGGAAAAAGTTACATAATTTAAGTACCTAAAATGGTAACAA
ATTAAAAACGTCACGTATCAGAATTTGATTGGTTTGAAAAATGTTTTTAACAAAAGTTAACAATT
GATACCTAAAGTAATAACAGAATAAAACTTTAGATACCTACTTTAAT
Found at i:42116190 original size:22 final size:23
Alignment explanation
Indices: 42116127--42116203 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 23
42116117 GCACTAATGA
*
42116127 ACAGAGAGCACTAAAGTGCT-AT
1 ACAGAGAGCACAAAAGTGCTAAT
*
42116149 ACATAGAGCACAAATA-TGCTAAT
1 ACAGAGAGCACAAA-AGTGCTAAT
* *
42116172 -CAGAGAGCACCAACGTGCTAAT
1 ACAGAGAGCACAAAAGTGCTAAT
42116194 AATCAGAGAG
1 -A-CAGAGAG
42116204 AGCGCTAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
22 34 0.77
23 3 0.07
25 7 0.16
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (23 bp):
ACAGAGAGCACAAAAGTGCTAAT
Found at i:42117867 original size:13 final size:13
Alignment explanation
Indices: 42117849--42117914 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
42117839 AGTTCTTCAT
42117849 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42117862 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
42117875 TACTGTGGAAAAG
1 TGCTTTTGAAAAG
*
42117888 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
42117901 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
42117914 T
1 T
42117915 TTGGTTTAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:42121640 original size:7 final size:7
Alignment explanation
Indices: 42121628--42121652 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42121618 ACATTAGTAA
42121628 TTTATTC
1 TTTATTC
42121635 TTTATTC
1 TTTATTC
42121642 TTTATTC
1 TTTATTC
42121649 TTTA
1 TTTA
42121653 CGTGTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTC
Found at i:42123388 original size:43 final size:43
Alignment explanation
Indices: 42123250--42123388 Score: 149
Period size: 43 Copynumber: 3.3 Consensus size: 43
42123240 ATATCCCGGT
* * * * **
42123250 ATGGTCTTACATGTTATCACATATCGATGCCTCTGTCCCAGAC
1 ATGGTCTTACACGTAATCTCATATTGATGCCAATGTCCCAGAC
* * *
42123293 AGGGTCTTACAC--AA-ATCATATATGGTGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATCTCATAT-TGATGCCAATGTCCCAGAC
**
42123334 ATGGTCTTACACGTAATCTCATATTGATGCCAATGTCTTAGAC
1 ATGGTCTTACACGTAATCTCATATTGATGCCAATGTCCCAGAC
42123377 ATGGTCTTACAC
1 ATGGTCTTACAC
42123389 AAAATCACAA
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
40 5 0.06
41 27 0.35
43 40 0.51
44 6 0.08
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACACGTAATCTCATATTGATGCCAATGTCCCAGAC
Found at i:42123812 original size:68 final size:68
Alignment explanation
Indices: 42123750--42123884 Score: 209
Period size: 68 Copynumber: 2.0 Consensus size: 68
42123740 ATTCGGATAG
* * *
42123750 CTACATTTATTAAATAAAACAACATAAATGCTAGTGCATTGAAT-AGTGAATTTAACACATTCGA
1 CTACATTTACTAAATAAAACAACATAAATGATAGTGCATTG-ATCAGTGAATCTAACACATTCGA
42123814 ACAA
65 ACAA
* *
42123818 CTACATTTACTAAATAAAACAACATAAATGATGGTGCTTTGATCAGTGAATCTAACACATTCGAA
1 CTACATTTACTAAATAAAACAACATAAATGATAGTGCATTGATCAGTGAATCTAACACATTCGAA
42123883 CA
66 CA
42123885 GCTTAATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 2 0.03
68 59 0.97
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (68 bp):
CTACATTTACTAAATAAAACAACATAAATGATAGTGCATTGATCAGTGAATCTAACACATTCGAA
CAA
Found at i:42133121 original size:75 final size:75
Alignment explanation
Indices: 42132998--42133149 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
42132988 TACTTTTAAG
42132998 GCACCGTTAGGAATGACTCCTTATCGGTTAGTTTTTGGAAAGGTATGTCATTTGCCACTTGAATT
1 GCACCGTTAGGAATGACTCCTTATCGGTTAGTTTTTGGAAAGGTATGTCATTTGCCACTTGAATT
42133063 GGAAAATAAA
66 GGAAAATAAA
42133073 GCACCGTTAGGAATGACTCCTTATCGGTTAGTTTTTGGAAAGGTATGTCATTTGCCACTTGAATT
1 GCACCGTTAGGAATGACTCCTTATCGGTTAGTTTTTGGAAAGGTATGTCATTTGCCACTTGAATT
42133138 GGAAAATAAA
66 GGAAAATAAA
42133148 GC
1 GC
42133150 TCATTAGGCC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (75 bp):
GCACCGTTAGGAATGACTCCTTATCGGTTAGTTTTTGGAAAGGTATGTCATTTGCCACTTGAATT
GGAAAATAAA
Found at i:42134330 original size:27 final size:27
Alignment explanation
Indices: 42134251--42134446 Score: 191
Period size: 27 Copynumber: 7.2 Consensus size: 27
42134241 CCTAGCTGTC
* *
42134251 ATTTTACCCTAACGGGGGTATTACGGTA
1 ATTTTACCCT-TCGGGGGTATTTCGGTA
42134279 ATTTTACCCTTCGGGGGGTATTTCGGTA
1 ATTTTACCCTTC-GGGGGTATTTCGGTA
*
42134307 ATTTTACCCTTCGGGGGTATTTCGATA
1 ATTTTACCCTTCGGGGGTATTTCGGTA
* * *
42134334 ATTTTACCCATCGAGGGTATTTCAGTA
1 ATTTTACCCTTCGGGGGTATTTCGGTA
* * * ** *
42134361 AATTTA-CCTATTGAGGGTATTTCAATG
1 ATTTTACCCT-TCGGGGGTATTTCGGTA
* **
42134388 ACTTTACCCTTCGGGGGTATTTCTATA
1 ATTTTACCCTTCGGGGGTATTTCGGTA
*
42134415 ATTTTA-CCTATCGAGGGTATTTCGGT-
1 ATTTTACCCT-TCGGGGGTATTTCGGTA
42134441 ATTTTA
1 ATTTTA
42134447 GGCTTATTAC
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
26 11 0.08
27 93 0.65
28 39 0.27
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.40
Consensus pattern (27 bp):
ATTTTACCCTTCGGGGGTATTTCGGTA
Found at i:42135494 original size:25 final size:24
Alignment explanation
Indices: 42135443--42135517 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
42135433 CTACTCAAAT
*
42135443 TCCTCAATTCTCTCCTAAAATCAC
1 TCCTCAATCCTCTCCTAAAATCAC
*
42135467 TCCTCCAATCCTCTCCTTGAAATC-C
1 TCCT-CAATCCTCTCC-TAAAATCAC
* * *
42135492 TCCAT-GATCCACTCCTTAAATCAC
1 TCC-TCAATCCTCTCCTAAAATCAC
42135516 TC
1 TC
42135518 ATTTGACCCA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
23 6 0.14
24 15 0.36
25 14 0.33
26 7 0.17
ACGTcount: A:0.25, C:0.40, G:0.03, T:0.32
Consensus pattern (24 bp):
TCCTCAATCCTCTCCTAAAATCAC
Found at i:42135666 original size:25 final size:25
Alignment explanation
Indices: 42135629--42135682 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
42135619 TGAACCTCTA
*
42135629 ACCTCCTTACCACACCTGTGACGCC
1 ACCTCCTTACCACACCTGTGACCCC
* *
42135654 ACCTCCTTGCCACACCTGTGTCCCC
1 ACCTCCTTACCACACCTGTGACCCC
42135679 ACCT
1 ACCT
42135683 TGCCACTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.17, C:0.50, G:0.11, T:0.22
Consensus pattern (25 bp):
ACCTCCTTACCACACCTGTGACCCC
Found at i:42139673 original size:23 final size:23
Alignment explanation
Indices: 42139643--42139690 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
42139633 GTCTGAATCG
42139643 ACCCATCAAACCTGGCCTTCTTA
1 ACCCATCAAACCTGGCCTTCTTA
42139666 ACCCATCAAACCTGGCCTTCTTA
1 ACCCATCAAACCTGGCCTTCTTA
42139689 AC
1 AC
42139691 ACGCCTCTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.40, G:0.08, T:0.25
Consensus pattern (23 bp):
ACCCATCAAACCTGGCCTTCTTA
Found at i:42141714 original size:27 final size:27
Alignment explanation
Indices: 42141670--42141732 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
42141660 CAATAGAGCT
42141670 ACCAGT-ACAGTATATGTGGCAAAGCC
1 ACCAGTAACAGTATATGTGGCAAAGCC
* *
42141696 ACCAGTAACAGTGAT-TGTGGTAGAGCC
1 ACCAGTAACAGT-ATATGTGGCAAAGCC
*
42141723 ACCAGAAACA
1 ACCAGTAACA
42141733 ATACTTCCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 6 0.19
27 24 0.75
28 2 0.06
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (27 bp):
ACCAGTAACAGTATATGTGGCAAAGCC
Found at i:42141914 original size:27 final size:27
Alignment explanation
Indices: 42141869--42142035 Score: 158
Period size: 27 Copynumber: 6.1 Consensus size: 27
42141859 TACCCTAACG
** * *
42141869 GGGTATTACGATAATTTTTCCCTTCAA
1 GGGTATTTTGATAATTTTACCCATCAA
* *
42141896 GGGGTATTTTGGTAATTTTACCCATCGA
1 -GGGTATTTTGATAATTTTACCCATCAA
*
42141924 GGGTATTTAGATAATTTTACCCATCGAA
1 GGGTATTTTGATAATTTTACCCATC-AA
**
42141952 -GGTATTTT-ATTAATTTTACCCATCGG
1 GGGTATTTTGA-TAATTTTACCCATCAA
* * *
42141978 GGGTACTTCGATAATTTTACCCTTCAA
1 GGGTATTTTGATAATTTTACCCATCAA
* * *
42142005 GAGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTTGATAATTTTACCCATCAA
42142032 GGGT
1 GGGT
42142036 GTTTCGGTAT
Statistics
Matches: 111, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.01
27 87 0.78
28 23 0.21
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTACCCATCAA
Found at i:42142044 original size:27 final size:27
Alignment explanation
Indices: 42141897--42142050 Score: 173
Period size: 27 Copynumber: 5.7 Consensus size: 27
42141887 TCCCTTCAAG
42141897 GGGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* *
42141924 GGGTATTTAGATAATTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* ** *
42141951 AGGTATTTTATTAATTTTACCCATCGG
1 GGGTATTTTGGTAATTTTACCCATCGA
* * * * *
42141978 GGGTACTTCGATAATTTTACCCTTCAA
1 GGGTATTTTGGTAATTTTACCCATCGA
*
42142005 GAGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTTGGTAATTTTACCCATCGA
* * *
42142032 GGGTGTTTCGGTATTTTTA
1 GGGTATTTTGGTAATTTTA
42142051 GGCCCATTAC
Statistics
Matches: 102, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACCCATCGA
Found at i:42142050 original size:54 final size:53
Alignment explanation
Indices: 42141855--42142050 Score: 232
Period size: 54 Copynumber: 3.6 Consensus size: 53
42141845 CCTAGCATTC
* * *
42141855 ATTTTACCCTAACG-GGGTATTACGATAATTTTTCCCTTCAAGGGGTATTTTGGTA
1 ATTTTACCC-ATCGAGGGTATTTCGATAATTTTACCCTTCAA--GGTATTTTGGTA
* * **
42141910 ATTTTACCCATCGAGGGTATTTAGATAATTTTACCCATCGAAGGTATTTTATTA
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTC-AAGGTATTTTGGTA
* *
42141964 ATTTTACCCATCGGGGGTACTTCGATAATTTTACCCTTCAAGAGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAG-GTATTTTGGTA
* * *
42142018 ATTTTACCCATCGAGGGTGTTTCGGTATTTTTA
1 ATTTTACCCATCGAGGGTATTTCGATAATTTTA
42142051 GGCCCATTAC
Statistics
Matches: 120, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
53 3 0.03
54 85 0.71
55 30 0.25
56 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.41
Consensus pattern (53 bp):
ATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGTATTTTGGTA
Found at i:42142845 original size:35 final size:35
Alignment explanation
Indices: 42142800--42142872 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
42142790 GAAGAAAAAG
42142800 AAAGAAAAAGGGAAAATTCGGCTATTCAGAGAGGA
1 AAAGAAAAAGGGAAAATTCGGCTATTCAGAGAGGA
42142835 AAAGAAAAAGGGAAAATTCGGCTATTCAGAGAGGA
1 AAAGAAAAAGGGAAAATTCGGCTATTCAGAGAGGA
42142870 AAA
1 AAA
42142873 AGGGAAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.51, C:0.08, G:0.27, T:0.14
Consensus pattern (35 bp):
AAAGAAAAAGGGAAAATTCGGCTATTCAGAGAGGA
Found at i:42143331 original size:25 final size:25
Alignment explanation
Indices: 42143293--42143346 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
42143283 TGAACCTCTG
*
42143293 ACCTCCTTATCACACCTGTGACGCC
1 ACCTCCTTAGCACACCTGTGACGCC
* *
42143318 ACCTCCTTGGCACACCTGTGTCGCC
1 ACCTCCTTAGCACACCTGTGACGCC
42143343 ACCT
1 ACCT
42143347 TGCCACTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.17, C:0.44, G:0.15, T:0.24
Consensus pattern (25 bp):
ACCTCCTTAGCACACCTGTGACGCC
Found at i:42147736 original size:15 final size:15
Alignment explanation
Indices: 42147718--42147750 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
42147708 AATTAATTAA
*
42147718 TTTATTATTATTATT
1 TTTAGTATTATTATT
42147733 TTTAGTATTATTATT
1 TTTAGTATTATTATT
42147748 TTT
1 TTT
42147751 CCTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTAGTATTATTATT
Found at i:42147758 original size:15 final size:15
Alignment explanation
Indices: 42147718--42147775 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
42147708 AATTAATTAA
*
42147718 TTTATTATTATTATT
1 TTTACTATTATTATT
*
42147733 TTTAGTATTATTATT
1 TTTACTATTATTATT
* * *
42147748 TTTCCTTTTATT-TA
1 TTTACTATTATTATT
42147762 TTTACTTATTATTA
1 TTTAC-TATTATTA
42147776 CTATATTATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 5 0.15
15 29 0.85
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (15 bp):
TTTACTATTATTATT
Found at i:42147907 original size:3 final size:3
Alignment explanation
Indices: 42147899--42147969 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
42147889 AAACTTTAGG
* *
42147899 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
42147947 TCA TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
42147970 CTTAAATTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:42152681 original size:27 final size:26
Alignment explanation
Indices: 42152589--42152686 Score: 115
Period size: 28 Copynumber: 3.6 Consensus size: 26
42152579 GTCAGAAAAG
* *
42152589 GGAAAGCCTTTGTGTCAAATCTCGAA
1 GGAAAGCCTTTGTGGCAAATCTTGAA
* *
42152615 TGGAAAAGCCTTTGTGGAAAATCTTAAAA
1 -GG-AAAGCCTTTGTGGCAAATCTT-GAA
42152644 GGAATAGCCTTTGTGGCAAATCTTGAA
1 GGAA-AGCCTTTGTGGCAAATCTTGAA
*
42152671 GGAAAGCCCTTGTGGC
1 GGAAAGCCTTTGTGGC
42152687 TACCATCTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
26 11 0.18
27 10 0.16
28 38 0.62
29 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.27
Consensus pattern (26 bp):
GGAAAGCCTTTGTGGCAAATCTTGAA
Found at i:42158605 original size:29 final size:28
Alignment explanation
Indices: 42158561--42158635 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
42158551 CGGAAAGTAT
* **
42158561 TTTTAATAATTTTTATCAGTTTAATTGA
1 TTTTAATAATTTTTATAAGTTTAATAAA
*
42158589 TTTTAATAATTTATTATAATTTTAATAAA
1 TTTTAATAATTT-TTATAAGTTTAATAAA
*
42158618 TTTTAAATATTTTTTATA
1 TTTT-AATAATTTTTATA
42158636 TTTGTAATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 12 0.30
29 21 0.52
30 7 0.17
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTAATAATTTTTATAAGTTTAATAAA
Found at i:42158616 original size:9 final size:9
Alignment explanation
Indices: 42158561--42158647 Score: 59
Period size: 10 Copynumber: 9.2 Consensus size: 9
42158551 CGGAAAGTAT
42158561 TTTTAATAA
1 TTTTAATAA
* *
42158570 TTTTTATCA
1 TTTTAATAA
* *
42158579 GTTTAATTGA
1 TTTTAA-TAA
42158589 TTTTAATAA
1 TTTTAATAA
*
42158598 TTTATTATAA
1 TTT-TAATAA
42158608 TTTTAATAAA
1 TTTTAAT-AA
*
42158618 TTTTAAATAT
1 TTTT-AATAA
*
42158628 TTTTTAT-A
1 TTTTAATAA
42158636 TTTGTAATAA
1 TTT-TAATAA
42158646 TT
1 TT
42158648 ATTTGAAAAA
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
8 3 0.05
9 24 0.41
10 29 0.49
11 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTAATAA
Found at i:42158629 original size:19 final size:19
Alignment explanation
Indices: 42158588--42158630 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42158578 AGTTTAATTG
* *
42158588 ATTTTAATAATTTATTATA
1 ATTTTAATAAATTATTAAA
42158607 ATTTTAATAAATT-TTAAA
1 ATTTTAATAAATTATTAAA
42158625 TATTTT
1 -ATTTT
42158631 TTATATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTAATAAATTATTAAA
Found at i:42158643 original size:29 final size:29
Alignment explanation
Indices: 42158561--42158645 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
42158551 CGGAAAGTAT
* * **
42158561 TTTTAATAATTT-TTATCAGTTTAATTGA
1 TTTTAATAATTTATTATAATTTTAATAAA
42158589 TTTTAATAATTTATTATAATTTTAATAAA
1 TTTTAATAATTTATTATAATTTTAATAAA
*
42158618 TTTTAA-ATATTTTTTAT-ATTTGTAATAA
1 TTTTAATA-ATTTATTATAATTT-TAATAA
42158646 TTATTTGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
28 17 0.35
29 32 0.65
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.58
Consensus pattern (29 bp):
TTTTAATAATTTATTATAATTTTAATAAA
Found at i:42169968 original size:20 final size:20
Alignment explanation
Indices: 42169932--42169969 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42169922 ATTTATGATT
*
42169932 CCTTATTTCTATGTCATTAG
1 CCTTATTTCAATGTCATTAG
*
42169952 CCTTATTTCAATTTCATT
1 CCTTATTTCAATGTCATT
42169970 TCATATTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (20 bp):
CCTTATTTCAATGTCATTAG
Found at i:42170302 original size:34 final size:35
Alignment explanation
Indices: 42170231--42170303 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
42170221 TATTCTAATA
* *
42170231 TATAATAGTATTAGAACTTATTTCTATATTTTATT
1 TATAATAGTATTAGAAATTATTTCAATATTTTATT
42170266 TATAATA-TATTAGAATATTATATT-AATATTTT-TT
1 TATAATAGTATTAGAA-ATTAT-TTCAATATTTTATT
42170300 TATA
1 TATA
42170304 TTATTTACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
34 14 0.41
35 18 0.53
36 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (35 bp):
TATAATAGTATTAGAAATTATTTCAATATTTTATT
Found at i:42172173 original size:16 final size:15
Alignment explanation
Indices: 42172143--42172177 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
42172133 TTCTATTATC
42172143 TATATTTTTTATAGA
1 TATATTTTTTATAGA
*
42172158 TATATTTTTATCTAGA
1 TATATTTTT-TATAGA
42172174 TATA
1 TATA
42172178 CAAGATCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TATATTTTTTATAGA
Found at i:42172514 original size:20 final size:21
Alignment explanation
Indices: 42172489--42172531 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
42172479 TTACACGAGG
42172489 AAATTGCTATTTCTAATT-AA
1 AAATTGCTATTTCTAATTCAA
*
42172509 AAATTGGTATTTCTAATTCAA
1 AAATTGCTATTTCTAATTCAA
42172530 AA
1 AA
42172532 GAAAATAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (21 bp):
AAATTGCTATTTCTAATTCAA
Found at i:42178384 original size:26 final size:26
Alignment explanation
Indices: 42178340--42178391 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
42178330 CATATTTTGC
* *
42178340 ATATTTTTAGGATAGTGATCTAAATT
1 ATATTTTTAGCATAATGATCTAAATT
* *
42178366 ATATTTTTATCATAATGATTTAAATT
1 ATATTTTTAGCATAATGATCTAAATT
42178392 TTATACCACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (26 bp):
ATATTTTTAGCATAATGATCTAAATT
Found at i:42180465 original size:7 final size:8
Alignment explanation
Indices: 42180445--42180469 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42180435 ATCATTAAAT
42180445 ATTTTTAA
1 ATTTTTAA
42180453 ATTTTTAA
1 ATTTTTAA
42180461 ATTTTTAA
1 ATTTTTAA
42180469 A
1 A
42180470 AATTATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTTAA
Found at i:42181773 original size:24 final size:24
Alignment explanation
Indices: 42181722--42181773 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
42181712 CACATGGCTG
* * *
42181722 TGTGGTAGGCCGTGTGCCATGCCG
1 TGTGGTAGGCCGTGTGCAAGGCCC
* *
42181746 TGTGGTAGGCTGTGTGTAAGGCCC
1 TGTGGTAGGCCGTGTGCAAGGCCC
42181770 TGTG
1 TGTG
42181774 TGACACACGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.10, C:0.19, G:0.42, T:0.29
Consensus pattern (24 bp):
TGTGGTAGGCCGTGTGCAAGGCCC
Found at i:42191116 original size:23 final size:22
Alignment explanation
Indices: 42191045--42191117 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 22
42191035 CAATTCATGG
42191045 TAATTTTATAAATTCTTACCCCC
1 TAATTTTATAAATTC-TACCCCC
* * *
42191068 TAATTTT-TGGAGTT-TTCTCCCC
1 TAATTTTAT-AAATTCTAC-CCCC
42191090 TAATTTTATAAATTCTAACCCCC
1 TAATTTTATAAATTCT-ACCCCC
42191113 TAATT
1 TAATT
42191118 AATGGTCATT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
21 2 0.05
22 15 0.38
23 21 0.54
24 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.45
Consensus pattern (22 bp):
TAATTTTATAAATTCTACCCCC
Found at i:42198421 original size:22 final size:22
Alignment explanation
Indices: 42198352--42198423 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
42198342 CGTCCTTGAT
42198352 ATGTTTC-CAGTACTAAGCTCTC
1 ATGTTTCAC-GTACTAAGCTCTC
** *
42198374 ATGGCTAACGTACTAAGCTCTC
1 ATGTTTCACGTACTAAGCTCTC
42198396 ATGTTTCACGTACTAAGCTCTC
1 ATGTTTCACGTACTAAGCTCTC
42198418 ATGTTT
1 ATGTTT
42198424 GAACAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (22 bp):
ATGTTTCACGTACTAAGCTCTC
Found at i:42204042 original size:39 final size:38
Alignment explanation
Indices: 42203991--42204338 Score: 336
Period size: 39 Copynumber: 8.9 Consensus size: 38
42203981 TGCAAATCAC
* * * *
42203991 GGGTACCAAAGTACAATAGGGGCATGTCTGTGCAGTTAG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCA-TTAG
* * *
42204030 GGGTATCGAAGTACAATAGGGGCACGTAGGTGCATTCAG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCATT-AG
* * * * *
42204069 GGGTACCAAAGTACAAAATGGGAACGTATGTGTATTTAG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCA-TTAG
* * *
42204108 GGGTATCGAAGTACAATAGGGGCACATATGTGCATTTAG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCA-TTAG
* * ** *
42204147 GGGTACCGAAGTATAACAGGGGCATGTGGGTGCATTCCG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCATT-AG
* * *
42204186 GGGTACCAAAGTACAACAGGGGCACGTATCTACATCTAG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCAT-TAG
* * * *
42204225 AGGTATCGAAGTACAACAGGGGCACATATGTGCATTCAA
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCATT-AG
* *
42204264 GGGTACCAAAGTACAACAGGGGCACGTATATGCATTTAG
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCA-TTAG
* * *
42204303 GGGTACCGAAGTACAATAGGGGAAAGTATGTGCATT
1 GGGTACCGAAGTACAACAGGGGCACGTATGTGCATT
42204339 CAGTTTTAAT
Statistics
Matches: 250, Mismatches: 53, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
38 7 0.03
39 238 0.95
40 5 0.02
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.22
Consensus pattern (38 bp):
GGGTACCGAAGTACAACAGGGGCACGTATGTGCATTAG
Found at i:42204179 original size:117 final size:117
Alignment explanation
Indices: 42203999--42204337 Score: 426
Period size: 117 Copynumber: 2.9 Consensus size: 117
42203989 ACGGGTACCA
** * * * *
42203999 AAGTACAATAGGGGCATGTCTGTGCAGTTAGGGGTATCGAAGTACAATAGGGGCACGTAGGTGCA
1 AAGTACAATAGGGGCACATATGTGCATTTAGGGGTACCGAAGTACAACAGGGGCACGTAGGTGCA
* * * *
42204064 TTCAGGGGTACCAAAGTACAAAATGGGAACGTATGTGTATTTAGGGGTATCG
66 TTCAGGGGTACCAAAGTACAAAAGGGGAACGTATGTGCATCTAGAGGTATCG
* * *
42204116 AAGTACAATAGGGGCACATATGTGCATTTAGGGGTACCGAAGTATAACAGGGGCATGTGGGTGCA
1 AAGTACAATAGGGGCACATATGTGCATTTAGGGGTACCGAAGTACAACAGGGGCACGTAGGTGCA
* * * * *
42204181 TTCCGGGGTACCAAAGTACAACAGGGGCACGTATCTACATCTAGAGGTATCG
66 TTCAGGGGTACCAAAGTACAAAAGGGGAACGTATGTGCATCTAGAGGTATCG
* * * * **
42204233 AAGTACAACAGGGGCACATATGTGCATTCAAGGGTACCAAAGTACAACAGGGGCACGTATATGCA
1 AAGTACAATAGGGGCACATATGTGCATTTAGGGGTACCGAAGTACAACAGGGGCACGTAGGTGCA
* * * *
42204298 TTTAGGGGTACCGAAGTACAATAGGGGAAAGTATGTGCAT
66 TTCAGGGGTACCAAAGTACAAAAGGGGAACGTATGTGCAT
42204338 TCAGTTTTAA
Statistics
Matches: 187, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
117 187 1.00
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.22
Consensus pattern (117 bp):
AAGTACAATAGGGGCACATATGTGCATTTAGGGGTACCGAAGTACAACAGGGGCACGTAGGTGCA
TTCAGGGGTACCAAAGTACAAAAGGGGAACGTATGTGCATCTAGAGGTATCG
Found at i:42216932 original size:18 final size:18
Alignment explanation
Indices: 42216906--42216941 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42216896 TGACATAATG
*
42216906 AAATGAGAAATGAGAAAT
1 AAATAAGAAATGAGAAAT
42216924 AAATAAGAAATGAGAAAT
1 AAATAAGAAATGAGAAAT
42216942 GAAAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (18 bp):
AAATAAGAAATGAGAAAT
Found at i:42222288 original size:22 final size:24
Alignment explanation
Indices: 42222260--42222303 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
42222250 TTTCCACAAG
42222260 ATCTTGC-ACCA-TATCCCCATCC
1 ATCTTGCTACCATTATCCCCATCC
*
42222282 ATCTTGCTACCATTTTCCCCAT
1 ATCTTGCTACCATTATCCCCAT
42222304 AAATTTACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.20, C:0.41, G:0.05, T:0.34
Consensus pattern (24 bp):
ATCTTGCTACCATTATCCCCATCC
Found at i:42223520 original size:18 final size:18
Alignment explanation
Indices: 42223486--42223524 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
42223476 AAAGTGGTCC
42223486 AATTGAACTGAACCAAGTA
1 AATTGAACTGAACCAAG-A
42223505 AATTGAACTG-ACCAAGA
1 AATTGAACTGAACCAAGA
42223522 AAT
1 AAT
42223525 GAAAAGCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.20
18 6 0.30
19 10 0.50
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (18 bp):
AATTGAACTGAACCAAGA
Found at i:42231087 original size:21 final size:22
Alignment explanation
Indices: 42231050--42231094 Score: 83
Period size: 21 Copynumber: 2.1 Consensus size: 22
42231040 TGAACATTGG
42231050 TTCTCTAGAGTTTTTGCTAAGC
1 TTCTCTAGAGTTTTTGCTAAGC
42231072 TTCTCTAGAG-TTTTGCTAAGC
1 TTCTCTAGAGTTTTTGCTAAGC
42231093 TT
1 TT
42231095 TTAGACATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (22 bp):
TTCTCTAGAGTTTTTGCTAAGC
Found at i:42234493 original size:26 final size:26
Alignment explanation
Indices: 42234455--42234516 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
42234445 CTCGTAAGTG
*
42234455 TTCTGAAATTGATACATGCTATGATA
1 TTCTGAAACTGATACATGCTATGATA
* *
42234481 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTGATACATGCTATGATA
42234507 TTCTGAAACT
1 TTCTGAAACT
42234517 ACTGTGGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (26 bp):
TTCTGAAACTGATACATGCTATGATA
Found at i:42238588 original size:17 final size:17
Alignment explanation
Indices: 42238566--42238602 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
42238556 AGCATTGAGG
42238566 AAGCCATGTGGGAGCCT
1 AAGCCATGTGGGAGCCT
42238583 AAGCCATGTGGGAGCCT
1 AAGCCATGTGGGAGCCT
42238600 AAG
1 AAG
42238603 GATGCGAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.22, G:0.35, T:0.16
Consensus pattern (17 bp):
AAGCCATGTGGGAGCCT
Found at i:42240914 original size:40 final size:40
Alignment explanation
Indices: 42240852--42240942 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
42240842 TATTGTGACA
* *
42240852 GGCTAAGGCCCTACTGCATTTTTGACACTGCACTAAGATG
1 GGCTAAAGCCCTACTGCATTTTTAACACTGCACTAAGATG
* * * *
42240892 GGTTAAAGCCCTATTGCATTTTTAACACTGTACTGAGATG
1 GGCTAAAGCCCTACTGCATTTTTAACACTGCACTAAGATG
*
42240932 GGCTAAGGCCC
1 GGCTAAAGCCC
42240943 AAACTGTCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (40 bp):
GGCTAAAGCCCTACTGCATTTTTAACACTGCACTAAGATG
Found at i:42243278 original size:339 final size:334
Alignment explanation
Indices: 42242769--42243403 Score: 922
Period size: 339 Copynumber: 1.9 Consensus size: 334
42242759 AGCAGCCCAG
* ** *
42242769 TAAGTTATCGTAGTTTTAAAAATTAATTAAAACATTTGTTTATTTTTTAAGGAAGTTTAGTCTAT
1 TAAGTTATCGAAGTTTTAAAAATTAATTAAAACATTTGTTTATTTTAGAAGAAAGTTTAGTCTAT
* * * *
42242834 TTTTTAGAAAAATATAGGAGTTTAAAAAAAGATTAAGTTTAACATCTTCATTATAATAGTGTTTA
66 TTTTGAGAAAAACACAGGAGTTTAAAAAAAGATTAAGTTTAACATCTTCATTATAATAGTATTTA
*
42242899 CTATTGAAAACTTAGTTGAAAATCCAAATTACTCTTTTAACAATACATATTTACAATTTAGCAAT
131 CTATTGAAAACTTAGTTGAAAATCCAAATTACTCTTTTAACAATACACATTTACAATTTAG-AA-
** * *
42242964 G-A-AAAAGTGATATTAATGTAACTTTAATAAAAACCATATTTCATGCATAATTAAATAAAAATT
194 GCAGAAAAGTGATATTAACATAAATTTAATAAAAAACATATTTCATGCATAATTAAATAAAAATT
*
42243027 CATATTCTAATAGCCTAAATGAATTAAGTGTCATGTATACCTAAGGATAAATCGTAAACTAGCTC
259 CATATTCTAATAGCCTAAATGAATTAAATGTCATGTATACCTAAGGATAAATCGTAAACTAGCTC
42243092 CCATGCCACGA
324 CCATGCCACGA
* * *
42243103 TAAGTTATCGAAGTTTTACAAATAGTTAATTAACATATTTGTTTATTTTAGACGAAAGTTTAGTC
1 TAAGTTATCGAAGTTTTA-AAA-A-TTAATTAAAACATTTGTTTATTTTAGAAGAAAGTTTAGTC
* *
42243168 T-TTTTTGAGAAAAAACACAGGAGTTTTTAAAAAACGATTAA-TTGTAACATCTTCATTATAATG
63 TATTTTTGAG-AAAAACACAGGAG--TTTAAAAAAAGATTAAGTT-TAACATCTTCATTATAATA
42243231 GTATTTACTATTGAAAACTTAGTTGAAAAT-CAGAATTAC-CTTTTTAACAATACACATTTACAA
124 GTATTTACTATTGAAAACTTAGTTGAAAATCCA-AATTACTC-TTTTAACAATACACATTTACAA
* * *
42243294 TTTAGTAGCAGAAAAGTGATATTAACATAAATTTAATAAAAAACATGTTTCATTCATAATTAAAT
187 TTTAGAAGCAGAAAAGTGATATTAACATAAATTTAATAAAAAACATATTTCATGCATAATTAAAT
*
42243359 AAAAATTCATATTCTAATAGCCTAAATGATTTAAATGTCATGTAT
252 AAAAATTCATATTCTAATAGCCTAAATGAATTAAATGTCATGTAT
42243404 GTGAAAGTAA
Statistics
Matches: 267, Mismatches: 23, Indels: 17
0.87 0.07 0.06
Matches are distributed among these distances:
334 17 0.06
335 3 0.01
336 8 0.03
337 47 0.18
338 7 0.03
339 185 0.69
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (334 bp):
TAAGTTATCGAAGTTTTAAAAATTAATTAAAACATTTGTTTATTTTAGAAGAAAGTTTAGTCTAT
TTTTGAGAAAAACACAGGAGTTTAAAAAAAGATTAAGTTTAACATCTTCATTATAATAGTATTTA
CTATTGAAAACTTAGTTGAAAATCCAAATTACTCTTTTAACAATACACATTTACAATTTAGAAGC
AGAAAAGTGATATTAACATAAATTTAATAAAAAACATATTTCATGCATAATTAAATAAAAATTCA
TATTCTAATAGCCTAAATGAATTAAATGTCATGTATACCTAAGGATAAATCGTAAACTAGCTCCC
ATGCCACGA
Found at i:42246870 original size:34 final size:28
Alignment explanation
Indices: 42246785--42246900 Score: 178
Period size: 28 Copynumber: 4.1 Consensus size: 28
42246775 TAACAGTATG
*
42246785 GTGTGGGCCTTAGCCCATTACAGTAATA
1 GTGTGGGCCTTAGCCCATTACAGTAACA
42246813 GTGTGGGCCTTAGCCCATTACAGTAACA
1 GTGTGGGCCTTAGCCCATTACAGTAACA
*
42246841 GTGTGGGCCTTAGCCCAATACAGTAACA
1 GTGTGGGCCTTAGCCCATTACAGTAACA
* * *
42246869 GTGTGGGCCTTAACCGAATACAGTAACCA
1 GTGTGGGCCTTAGCCCATTACAGTAA-CA
42246898 GTG
1 GTG
42246901 CAGTGCAGTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
28 78 0.94
29 5 0.06
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (28 bp):
GTGTGGGCCTTAGCCCATTACAGTAACA
Found at i:42247253 original size:27 final size:27
Alignment explanation
Indices: 42247234--42247430 Score: 285
Period size: 27 Copynumber: 7.3 Consensus size: 27
42247224 GGTATAATAG
42247234 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
42247261 TCATTTTACCCTTCGAGGGTATTTCGA
1 TCATTTTACCCTTCGAGGGTATTTCGA
* *
42247288 TCATTTTACGCATT-GGGGGTATTTCGA
1 TCATTTTAC-CCTTCGAGGGTATTTCGA
42247315 TCATTTTACCCTTC-AGGGGTATTTC-A
1 TCATTTTACCCTTCGA-GGGTATTTCGA
*
42247341 GTCATTTTACCCTTCGAGGGTATTTCAA
1 -TCATTTTACCCTTCGAGGGTATTTCGA
*
42247369 TCATTTTACCCTTCGAGGGTATTTCGT
1 TCATTTTACCCTTCGAGGGTATTTCGA
*
42247396 TCATTTTACCCTTC-AGGGGTATTTCGG
1 TCATTTTACCCTTCGA-GGGTATTTCGA
42247423 TCATTTTA
1 TCATTTTA
42247431 GGCCCATTAT
Statistics
Matches: 156, Mismatches: 7, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.03
27 146 0.94
28 5 0.03
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCGA
Found at i:42248022 original size:19 final size:19
Alignment explanation
Indices: 42247998--42248046 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
42247988 TGAGAGTTTC
*
42247998 TTTTATATTTCTTCTTCTG
1 TTTTATATTTCCTCTTCTG
*
42248017 TTTTATTAGTTCCTCTTCTG
1 TTTTA-TATTTCCTCTTCTG
*
42248037 TTTAATATTT
1 TTTTATATTT
42248047 TGAAGCTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.14, C:0.14, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTATATTTCCTCTTCTG
Found at i:42251319 original size:18 final size:18
Alignment explanation
Indices: 42251295--42251342 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
42251285 AGAATATGAG
*
42251295 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
*
42251313 GAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
42251331 AAATGATGTTCA
1 AAATGATGTTCA
42251343 AATTGATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:42253190 original size:13 final size:13
Alignment explanation
Indices: 42253172--42253204 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
42253162 CTCAAATTTG
42253172 TCAAAAGCACTTC
1 TCAAAAGCACTTC
42253185 TCAAAAGCACTTC
1 TCAAAAGCACTTC
42253198 TCAAAAG
1 TCAAAAG
42253205 TAATAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.27, G:0.09, T:0.21
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:42255159 original size:28 final size:28
Alignment explanation
Indices: 42255127--42255228 Score: 150
Period size: 28 Copynumber: 3.6 Consensus size: 28
42255117 AGTACAACAA
** *
42255127 GGGCCTTAGCCCAATTTAGTAGCAGTGT
1 GGGCCTTAGCCCAATACAGTATCAGTGT
**
42255155 GGGCCTTAGCCCAATACAGTATCAACGT
1 GGGCCTTAGCCCAATACAGTATCAGTGT
42255183 GGGCCTTAGCCCAATACAGTATCAGTGT
1 GGGCCTTAGCCCAATACAGTATCAGTGT
*
42255211 GGGCCTTAGCTCAATACA
1 GGGCCTTAGCCCAATACA
42255229 ATGACATTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (28 bp):
GGGCCTTAGCCCAATACAGTATCAGTGT
Found at i:42255622 original size:27 final size:27
Alignment explanation
Indices: 42255604--42255902 Score: 370
Period size: 27 Copynumber: 11.1 Consensus size: 27
42255594 GGTATAAAAA
*
42255604 TCATTTTACCCTATGGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCGG
42255631 TCATTTTACCCT-TCGGGGGTATTTCGG
1 TCATTTTACCCTAT-GGGGGTATTTCGG
* * *
42255658 TCATTTTACCCTATGGGGGAATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
42255685 TCATTTTACCATAT-GGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
42255711 TCATTTTAGCTTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
42255738 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * *
42255765 TCATTTTACCCTATGGGGGAATTTTGA
1 TCATTTTACCCTATGGGGGTATTTCGG
* *
42255792 TCATTTTACCATAT-GGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
* * * *
42255818 TCATTTTAGCTTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGG
*
42255845 TCATTTTACCCTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCGG
**
42255872 TCATTTTACCCTATAAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCGG
42255899 TCAT
1 TCAT
42255903 AATAGTGTAA
Statistics
Matches: 233, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
26 45 0.19
27 187 0.80
28 1 0.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGG
Found at i:42255732 original size:80 final size:81
Alignment explanation
Indices: 42255603--42255902 Score: 399
Period size: 80 Copynumber: 3.7 Consensus size: 81
42255593 GGGTATAAAA
** * *
42255603 ATCATTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTT-CGGGGGTATTTCGGTCATTTTAC
1 ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTA-CCTTATGAGGGTATTTCGGTCATTTTAC
* *
42255667 CCTATGGGGGAATTTTG
65 CCTATGGGGGTATTTCG
* * *
42255684 ATCATTTTACCATAT-GGGGTATTTTGGTCATTTTAGCTTATGAGGGTATTTCGATCATTTTACC
1 ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATGAGGGTATTTCGGTCATTTTACC
42255748 CTATGGGGGTATTTCG
66 CTATGGGGGTATTTCG
* * * * * *
42255764 GTCATTTTACCCTATGGGGGAATTTTGATCATTTTACCATATG-GGGTATTTTGGTCATTTTAGC
1 ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATGAGGGTATTTCGGTCATTTTACC
* *
42255828 TTATGAGGGTATTTCG
66 CTATGGGGGTATTTCG
* *
42255844 ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTCGGTCAT
1 ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATGAGGGTATTTCGGTCAT
42255903 AATAGTGTAA
Statistics
Matches: 190, Mismatches: 26, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
79 3 0.02
80 136 0.72
81 51 0.27
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (81 bp):
ATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCTTATGAGGGTATTTCGGTCATTTTACC
CTATGGGGGTATTTCG
Found at i:42255778 original size:107 final size:107
Alignment explanation
Indices: 42255604--42255885 Score: 496
Period size: 107 Copynumber: 2.6 Consensus size: 107
42255594 GGTATAAAAA
* * *
42255604 TCATTTTACCCTATGGGGGTATTTC-AGTCATTTTACCCT-TCGGGGGTATTTCGGTCATTTTAC
1 TCATTTTAGCTTATGAGGGTATTTCGA-TCATTTTACCCTAT-GGGGGTATTTCGGTCATTTTAC
42255667 CCTATGGGGGAATTTTGATCATTTTACCATATGGGGTATTTTGG
64 CCTATGGGGGAATTTTGATCATTTTACCATATGGGGTATTTTGG
42255711 TCATTTTAGCTTATGAGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCC
1 TCATTTTAGCTTATGAGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCC
42255776 TATGGGGGAATTTTGATCATTTTACCATATGGGGTATTTTGG
66 TATGGGGGAATTTTGATCATTTTACCATATGGGGTATTTTGG
*
42255818 TCATTTTAGCTTATGAGGGTATTTCGATCATTTTACCCTATGGGGGTATTTTGGTCATTTTACCC
1 TCATTTTAGCTTATGAGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCC
42255883 TAT
66 TAT
42255886 AAGGGTATTT
Statistics
Matches: 169, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
107 167 0.99
108 2 0.01
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (107 bp):
TCATTTTAGCTTATGAGGGTATTTCGATCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCC
TATGGGGGAATTTTGATCATTTTACCATATGGGGTATTTTGG
Found at i:42258128 original size:16 final size:16
Alignment explanation
Indices: 42258107--42258138 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42258097 AATTAGAGGA
42258107 CTTTGAATTAATCTTT
1 CTTTGAATTAATCTTT
42258123 CTTTGAATTAATCTTT
1 CTTTGAATTAATCTTT
42258139 AAGATCATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (16 bp):
CTTTGAATTAATCTTT
Found at i:42259063 original size:27 final size:27
Alignment explanation
Indices: 42259033--42259091 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
42259023 GTTGGAAAAA
42259033 ATGTTAGAAAAATTTTTACCCAATGCC
1 ATGTTAGAAAAATTTTTACCCAATGCC
42259060 ATGTTAGAAAAATTTTTACCCAATGCC
1 ATGTTAGAAAAATTTTTACCCAATGCC
42259087 ATGTT
1 ATGTT
42259092 GAAGGCTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (27 bp):
ATGTTAGAAAAATTTTTACCCAATGCC
Found at i:42260376 original size:43 final size:43
Alignment explanation
Indices: 42260306--42260480 Score: 217
Period size: 43 Copynumber: 4.1 Consensus size: 43
42260296 TTATGAGAAA
* * * * *
42260306 AAACGCTGCTAAAGATCATGTTTTTTAGCGGTGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* *
42260349 AAACGCCGTTAAAGAACATGACCTTTAGCGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
* * * *
42260392 AAAAGCCGCTAAGGAACATGATCTTTAGCGACGCTTTTA-TCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGC-TTTACCCAC
* *
42260435 AAACGCAGCTAAAGAACATGATCTTTAGTGGCGCTTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
42260478 AAA
1 AAA
42260481 TATCGCTAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 4 0.04
43 103 0.93
44 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTACCCAC
Found at i:42262688 original size:31 final size:31
Alignment explanation
Indices: 42262652--42262727 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
42262642 GTTGATTTAA
*
42262652 CAGCAAAAATCAATAGAAGGTACCATCTTAG
1 CAGCAAAAACCAATAGAAGGTACCATCTTAG
42262683 CAGCAAAAACCAATAGAAGGTACCATCTTAG
1 CAGCAAAAACCAATAGAAGGTACCATCTTAG
*
42262714 CTGCAAAAACCAAT
1 CAGCAAAAACCAAT
42262728 TAAAATCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.46, C:0.22, G:0.14, T:0.17
Consensus pattern (31 bp):
CAGCAAAAACCAATAGAAGGTACCATCTTAG
Found at i:42264215 original size:21 final size:21
Alignment explanation
Indices: 42264191--42264231 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42264181 CCATGCATTG
* * *
42264191 TAAACCTTAAATCATTAACAC
1 TAAACCGTAAACCATAAACAC
42264212 TAAACCGTAAACCATAAACA
1 TAAACCGTAAACCATAAACA
42264232 TCAAGCCCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAACCGTAAACCATAAACAC
Found at i:42264328 original size:14 final size:14
Alignment explanation
Indices: 42264311--42264350 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42264301 CGTAAACGCT
42264311 AAACCTTAAACCCC
1 AAACCTTAAACCCC
**
42264325 AAACCCCAAACCCC
1 AAACCTTAAACCCC
*
42264339 AAGCCTTAAACC
1 AAACCTTAAACC
42264351 TACAGCACAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.45, G:0.03, T:0.10
Consensus pattern (14 bp):
AAACCTTAAACCCC
Found at i:42264638 original size:41 final size:43
Alignment explanation
Indices: 42264584--42264745 Score: 165
Period size: 41 Copynumber: 3.9 Consensus size: 43
42264574 AGCCCCACTA
* *
42264584 AAATCCCCTGAGCATTAGCGGCGCTTTC-TAAAAAACGCTGCT
1 AAATCCCCAGAGCATTAGCGGCGCTTTCTTCAAAAACGCTGCT
* * * *
42264626 AAAT-CCCAGAGCAATAGCGGTGCTTTCTTCAAAAACACCGCT
1 AAATCCCCAGAGCATTAGCGGCGCTTTCTTCAAAAACGCTGCT
* * *
42264668 -AATGCCCAGAGCATTAGCGGCGC-TTCTTCAAAAATGCTACT
1 AAATCCCCAGAGCATTAGCGGCGCTTTCTTCAAAAACGCTGCT
* * **
42264709 AAA-GCCCAGTGCATTAGCGATGC-TTCTTCAAAAACGC
1 AAATCCCCAGAGCATTAGCGGCGCTTTCTTCAAAAACGC
42264746 CACCCATGGT
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
41 67 0.66
42 34 0.34
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
AAATCCCCAGAGCATTAGCGGCGCTTTCTTCAAAAACGCTGCT
Found at i:42264954 original size:21 final size:21
Alignment explanation
Indices: 42264914--42264955 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42264904 GTATTGCAGT
*
42264914 TTATATATTATTTTTATAGTA
1 TTATATATTATATTTATAGTA
42264935 TTATATATTATGATTT-TAGTA
1 TTATATATTAT-ATTTATAGTA
42264956 AATTCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
TTATATATTATATTTATAGTA
Found at i:42265095 original size:58 final size:57
Alignment explanation
Indices: 42264987--42265097 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 57
42264977 AAGAACCTTA
*
42264987 TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGG
1 TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGG
* *
42265044 TTAAATTATTTATTATTTTTATTAAATTATTTTTAATAATAATCT-TATTAAAAT
1 TTAAATTATATATTA-TTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
42265098 TTCATAACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 14 0.29
58 34 0.69
59 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (57 bp):
TTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAAATATGG
Found at i:42265281 original size:46 final size:44
Alignment explanation
Indices: 42265189--42265282 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
42265179 ATTACAACAT
* *
42265189 CATTCTATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
*
42265233 CATTCCATTCAACCAAACA-ATTGAACTACTGATTACAACTT-TATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACT-ATTAC-ACTTCTATTC
42265279 CATT
1 CATT
42265283 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 4 0.09
46 14 0.33
47 3 0.07
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
Found at i:42265285 original size:16 final size:16
Alignment explanation
Indices: 42265264--42265318 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
42265254 TGAACTACTG
* *
42265264 ATTACAACTTTATTCC
1 ATTACAGCTCTATTCC
*
42265280 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
42265296 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
42265312 ATTACAG
1 ATTACAG
42265319 TGAACCAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:42265504 original size:19 final size:20
Alignment explanation
Indices: 42265480--42265517 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
42265470 CCTTTTTGTA
42265480 CAAAAC-ATAAAATTTAAGG
1 CAAAACTATAAAATTTAAGG
42265499 CAAAACTATAAAATTTAAG
1 CAAAACTATAAAATTTAAG
42265518 AAGTAAGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.24
Consensus pattern (20 bp):
CAAAACTATAAAATTTAAGG
Found at i:42266931 original size:18 final size:18
Alignment explanation
Indices: 42266908--42266942 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42266898 TTATCTAATG
42266908 TTTATCATTCATTCATAA
1 TTTATCATTCATTCATAA
*
42266926 TTTATCATTCTTTCATA
1 TTTATCATTCATTCATA
42266943 TTATCCAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTATCATTCATTCATAA
Found at i:42270447 original size:52 final size:52
Alignment explanation
Indices: 42270369--42270469 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
42270359 CATGCACATA
* *
42270369 TTTGAGCTTCAACCGAGCTATAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
*
42270421 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGTTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTA
42270470 CTTTTCCTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCCATTATTG
Found at i:42277301 original size:73 final size:73
Alignment explanation
Indices: 42277216--42277426 Score: 395
Period size: 73 Copynumber: 2.9 Consensus size: 73
42277206 TGGCCTAACA
* *
42277216 TGGGTAATGAGATATTGAGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGCAAAAA
1 TGGGTAACGAGATATTGGGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGCAAAAA
42277281 TGTTTGTT
66 TGTTTGTT
42277289 TGGGTAACGAGATATTGGGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGCAAAAA
1 TGGGTAACGAGATATTGGGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGCAAAAA
42277354 TGTTTGTT
66 TGTTTGTT
*
42277362 TGGGTAACGAGATATTGGGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGAAAAAA
1 TGGGTAACGAGATATTGGGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGCAAAAA
42277427 AGGTCTGTTT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
73 135 1.00
ACGTcount: A:0.38, C:0.05, G:0.31, T:0.26
Consensus pattern (73 bp):
TGGGTAACGAGATATTGGGAATTGGAGGGAAATAGAAAGATTACTACTAAATGGGTGGGCAAAAA
TGTTTGTT
Found at i:42287038 original size:26 final size:26
Alignment explanation
Indices: 42287009--42287058 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
42286999 TATTTTGCAA
* *
42287009 ATTTTTATGATAGTGATTTAAATTAT
1 ATTTTTATCATAATGATTTAAATTAT
*
42287035 ATTTTTCTCATAATGATTTAAATT
1 ATTTTTATCATAATGATTTAAATT
42287059 TTATAGAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (26 bp):
ATTTTTATCATAATGATTTAAATTAT
Found at i:42290909 original size:10 final size:10
Alignment explanation
Indices: 42290894--42290984 Score: 93
Period size: 10 Copynumber: 9.3 Consensus size: 10
42290884 AACAGACATT
42290894 ATTTTTAATA
1 ATTTTTAATA
*
42290904 ATTTTT-ATT
1 ATTTTTAATA
42290913 ATTTTTAAATA
1 ATTTTT-AATA
42290924 A-TTTTAATA
1 ATTTTTAATA
42290933 ATTTATT-ATA
1 ATTT-TTAATA
*
42290943 ATTTTTAACA
1 ATTTTTAATA
42290953 ATTTTTAA-A
1 ATTTTTAATA
*
42290962 TATTTTTTAT-
1 -ATTTTTAATA
42290972 ATTTTTAATA
1 ATTTTTAATA
42290982 ATT
1 ATT
42290985 ATTCGAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
9 24 0.35
10 39 0.57
11 5 0.07
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:42290913 original size:19 final size:19
Alignment explanation
Indices: 42290891--42290984 Score: 93
Period size: 19 Copynumber: 4.8 Consensus size: 19
42290881 CATAACAGAC
42290891 ATTATTTTTAATAATTTTT
1 ATTATTTTTAATAATTTTT
*
42290910 ATTATTTTTAAATAATTTTA
1 ATTATTTTT-AATAATTTTT
*
42290930 ATAATTTATT-ATAATTTTT
1 ATTATTT-TTAATAATTTTT
** *
42290949 AACAATTTTTAAATATTTTTT
1 -ATTATTTTT-AATAATTTTT
42290970 A-TATTTTTAATAATT
1 ATTATTTTTAATAATT
42290985 ATTCGAAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
18 6 0.10
19 25 0.40
20 22 0.35
21 10 0.16
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTTTTAATAATTTTT
Found at i:42290947 original size:29 final size:28
Alignment explanation
Indices: 42290896--42290984 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 28
42290886 CAGACATTAT
*
42290896 TTTTAATAATTTTTATTATTTTTAAATAA
1 TTTTAATAATTTTTATAATTTTT-AATAA
*
42290925 TTTTAATAATTTATTATAATTTTTAACAA
1 TTTTAATAATTT-TTATAATTTTTAATAA
*
42290954 TTTTTAAATATTTTTTAT-ATTTTTAATAA
1 -TTTT-AATAATTTTTATAATTTTTAATAA
42290983 TT
1 TT
42290985 ATTCGAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 2 0.04
29 26 0.49
30 18 0.34
31 7 0.13
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTAATAATTTTTATAATTTTTAATAA
Found at i:42291092 original size:10 final size:9
Alignment explanation
Indices: 42291077--42291115 Score: 69
Period size: 9 Copynumber: 4.2 Consensus size: 9
42291067 GATTTTATTT
42291077 ATTTTTTAA
1 ATTTTTTAA
42291086 ATATTTTTAA
1 AT-TTTTTAA
42291096 ATTTTTTAA
1 ATTTTTTAA
42291105 ATTTTTTAA
1 ATTTTTTAA
42291114 AT
1 AT
42291116 ATTGCAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:42291101 original size:19 final size:18
Alignment explanation
Indices: 42291077--42291115 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
42291067 GATTTTATTT
42291077 ATTTTTTAAATATTTTTAA
1 ATTTTTTAAAT-TTTTTAA
42291096 ATTTTTTAAATTTTTTAA
1 ATTTTTTAAATTTTTTAA
42291114 AT
1 AT
42291116 ATTGCAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTTAAATTTTTTAA
Found at i:42295120 original size:63 final size:64
Alignment explanation
Indices: 42295021--42295147 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 64
42295011 ATAAATGAAA
* * *
42295021 AAAATGGAGAACTGAGAAATCATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATC
1 AAAATGGAGAAAT-AGAAATCATCTAGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATC
* * *
42295086 AAAATGGAGAAAT-GAAATCATCTAGAAATTATTATGGTTTTCTCTAAACTGAAAATGAAAAT
1 AAAATGGAGAAATAGAAATCATCTAGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAAT
42295148 GGAAAACGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 44 0.79
65 12 0.21
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.29
Consensus pattern (64 bp):
AAAATGGAGAAATAGAAATCATCTAGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATC
Found at i:42310836 original size:48 final size:49
Alignment explanation
Indices: 42310776--42310881 Score: 153
Period size: 48 Copynumber: 2.2 Consensus size: 49
42310766 TAATAGTTTT
* *
42310776 AATATTTAATTTAAT-TTAATACTTATCTTGAT-AATATTCTATTAATTC
1 AATATTAAATTTAATCTT-ATACTTATCTTGATAAATATTATATTAATTC
* *
42310824 AATATTAAATTTAATCTTATATTTATCTTGATAAATATTATATTAATTT
1 AATATTAAATTTAATCTTATACTTATCTTGATAAATATTATATTAATTC
42310873 AATATTAAA
1 AATATTAAA
42310882 GTAATTAAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
48 27 0.52
49 25 0.48
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (49 bp):
AATATTAAATTTAATCTTATACTTATCTTGATAAATATTATATTAATTC
Found at i:42314251 original size:25 final size:24
Alignment explanation
Indices: 42314216--42314263 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
42314206 AAATAGTGCA
42314216 GTTAAGCCGCCAAATAACAGTATACG
1 GTTAAGCCGCCAAA-AACA-TATACG
42314242 GTTAA-CCGCCAAAAACATATAC
1 GTTAAGCCGCCAAAAACATATAC
42314264 TCATGGCTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.23
24 4 0.18
25 8 0.36
26 5 0.23
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (24 bp):
GTTAAGCCGCCAAAAACATATACG
Found at i:42315256 original size:16 final size:17
Alignment explanation
Indices: 42315224--42315271 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
42315214 TAAATAAGTA
* *
42315224 AAAAGACAAAA-AGAAC
1 AAAAGAGAAAAGAAAAC
42315240 AAAAG-GAAAAGAAAAC
1 AAAAGAGAAAAGAAAAC
42315256 AAAAGAAGAAAAGAAA
1 AAAAG-AGAAAAGAAA
42315272 GAAAACCCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.15
16 14 0.52
18 9 0.33
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAAC
Found at i:42315267 original size:24 final size:22
Alignment explanation
Indices: 42315232--42315277 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
42315222 TAAAAAGACA
42315232 AAAAGAACAAAAGGAAAAGAAAAC
1 AAAAGAACAAAA-G-AAAGAAAAC
*
42315256 AAAAGAAGAAAAGAAAGAAAAC
1 AAAAGAACAAAAGAAAGAAAAC
42315278 CCCAAAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 1 0.05
24 11 0.52
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAGAACAAAAGAAAGAAAAC
Found at i:42315268 original size:18 final size:16
Alignment explanation
Indices: 42315237--42315271 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
42315227 AGACAAAAAG
42315237 AACAAAAGGAAAAGAA
1 AACAAAAGGAAAAGAA
42315253 AACAAAAGAAGAAAAGAA
1 AACAAAAG--GAAAAGAA
42315271 A
1 A
42315272 GAAAACCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
18 9 0.53
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (16 bp):
AACAAAAGGAAAAGAA
Found at i:42320469 original size:37 final size:38
Alignment explanation
Indices: 42320326--42320486 Score: 182
Period size: 38 Copynumber: 4.3 Consensus size: 38
42320316 TAGAAACGTG
* * *
42320326 GTGATATTCGGGCTCCATGCATAACAGGTTTTGTGTC-
1 GTGATATTCGGGCTCCATGCCTAACAGGCTTTGTGCCA
* * * *
42320363 GATGATATTCGGGCTTCATACCTAACAGGCTTTATGCTA
1 G-TGATATTCGGGCTCCATGCCTAACAGGCTTTGTGCCA
* * *
42320402 GTGATATTTGGGCTCCGTGCCTATCAGGCTTTGTGCCA
1 GTGATATTCGGGCTCCATGCCTAACAGGCTTTGTGCCA
* * *
42320440 GTGATATTCGAGC-CCATGCCTAATAGGCTTTGTGCCG
1 GTGATATTCGGGCTCCATGCCTAACAGGCTTTGTGCCA
42320477 GTGATATTCG
1 GTGATATTCG
42320487 AGTTTTGTGC
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
37 31 0.30
38 70 0.69
39 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (38 bp):
GTGATATTCGGGCTCCATGCCTAACAGGCTTTGTGCCA
Found at i:42320513 original size:38 final size:41
Alignment explanation
Indices: 42320456--42320609 Score: 125
Period size: 41 Copynumber: 3.8 Consensus size: 41
42320446 TTCGAGCCCA
* * * **
42320456 TGCCTAATAGGCTTTGTGCCGGTG-A-TAT-TCGAGTTTTG
1 TGCCTAGTAGGCTTCGTGCCGGTGTATTATATCAAGCCTTG
* *
42320494 TGCTTAGTAGGCTTCGTGCCAGTGTATTATATCAAGCCTTG
1 TGCCTAGTAGGCTTCGTGCCGGTGTATTATATCAAGCCTTG
* * * * *
42320535 TGCCTAGCAGGCTTCGTGCTGGTGTGTTATATCAGGCTTTG
1 TGCCTAGTAGGCTTCGTGCCGGTGTATTATATCAAGCCTTG
* * * ** *
42320576 AGCCTAGCAGTCTTCGTGCCAATGTATTGTATCA
1 TGCCTAGTAGGCTTCGTGCCGGTGTATTATATCA
42320610 GGTAAGTTGT
Statistics
Matches: 92, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
38 20 0.22
39 1 0.01
40 3 0.03
41 68 0.74
ACGTcount: A:0.18, C:0.19, G:0.27, T:0.36
Consensus pattern (41 bp):
TGCCTAGTAGGCTTCGTGCCGGTGTATTATATCAAGCCTTG
Found at i:42320610 original size:41 final size:41
Alignment explanation
Indices: 42320502--42320611 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 41
42320492 TGTGCTTAGT
* *
42320502 AGGCTTCGTGCCAGTGTATTATATCAAGCCTTGTGCCTAGC
1 AGGCTTCGTGCCAGTGTATTATATCAGGCCTTGAGCCTAGC
** * *
42320543 AGGCTTCGTGCTGGTGTGTTATATCAGGCTTTGAGCCTAGC
1 AGGCTTCGTGCCAGTGTATTATATCAGGCCTTGAGCCTAGC
* * *
42320584 AGTCTTCGTGCCAATGTATTGTATCAGG
1 AGGCTTCGTGCCAGTGTATTATATCAGG
42320612 TAAGTTGTAC
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (41 bp):
AGGCTTCGTGCCAGTGTATTATATCAGGCCTTGAGCCTAGC
Found at i:42330960 original size:11 final size:11
Alignment explanation
Indices: 42330944--42330969 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42330934 CGATGGATAC
42330944 TCAATGTATAA
1 TCAATGTATAA
42330955 TCAATGTATAA
1 TCAATGTATAA
42330966 TCAA
1 TCAA
42330970 ATTACAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (11 bp):
TCAATGTATAA
Found at i:42333715 original size:22 final size:21
Alignment explanation
Indices: 42333690--42333733 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
42333680 TGATAAACTT
42333690 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
42333712 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
42333733 T
1 T
42333734 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:42334357 original size:13 final size:13
Alignment explanation
Indices: 42334339--42334365 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42334329 AATTTTTATC
42334339 CTTTGAAACCCAA
1 CTTTGAAACCCAA
42334352 CTTTGAAACCCAA
1 CTTTGAAACCCAA
42334365 C
1 C
42334366 CATGATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.33, G:0.07, T:0.22
Consensus pattern (13 bp):
CTTTGAAACCCAA
Found at i:42339974 original size:129 final size:129
Alignment explanation
Indices: 42339754--42340692 Score: 1583
Period size: 129 Copynumber: 7.3 Consensus size: 129
42339744 AGGATTCGCT
* * * * *
42339754 GTCTTCTATCTGCTCCACTAAC-ACTTAGGGAGATAAGATATGTAATTTCCCAACCTATTCCACT
1 GTCTTCGATCTGCTCCGCT-ACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACT
* * *
42339818 GCTAACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAAATTCGTC
65 GCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
* *
42339883 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTATAATTACCCAACCTATTCCACTG
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
* *
42339948 CTGACCAGGGATATAGGACTTTTGGCTTAAATCTGCTTCCTTACTCTTGATGATAAGATTTGTC
66 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
**
42340012 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCTGACCTATTCCACTG
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
42340077 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
66 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
* * *
42340141 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAACATCTGTAATTTCCCAACCTATTCCACTG
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
* *
42340206 CTGACCAGGGATATAGGACTTTTGGCTTAAATCTGCTTCCTTACTCTTGATGATAAGATTTGTC
66 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
42340270 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
*
42340335 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGATGATAAGATTTGTC
66 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
** *
42340399 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCTGACCTATTCCACTA
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
* * * *
42340464 CTAACCAGGGATATAGGACTTCTGGCTTAAATTTGCTTCCTTACTTTTGAAGATAAGATTTGTC
66 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
* *
42340528 GTCTTCGATCTGCTTCGCTACTGCTTAGGGGGACAAGATCTGTAATTTCCCAACCTATTCCACTG
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
*
42340593 CTGGCCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
66 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
*
42340657 ATCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAA
1 GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAA
42340693 ATATTCATTA
Statistics
Matches: 759, Mismatches: 50, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
128 2 0.00
129 757 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (129 bp):
GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTG
CTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTC
Found at i:42341964 original size:7 final size:7
Alignment explanation
Indices: 42341946--42341988 Score: 54
Period size: 6 Copynumber: 6.1 Consensus size: 7
42341936 AGCCTCTCCA
42341946 TCATTTT
1 TCATTTT
42341953 T-ATTTT
1 TCATTTT
42341959 TCA-TTT
1 TCATTTT
42341965 TCACTTTT
1 TCA-TTTT
42341973 TCATTTT
1 TCATTTT
42341980 TCATCTTT
1 TCAT-TTT
42341988 T
1 T
42341989 TTTTGACTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
6 12 0.38
7 10 0.31
8 10 0.31
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (7 bp):
TCATTTT
Found at i:42341974 original size:14 final size:14
Alignment explanation
Indices: 42341946--42341989 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
42341936 AGCCTCTCCA
*
42341946 TCATTTTTA-TTTT
1 TCATTTTCACTTTT
42341959 TCATTTTCACTTTT
1 TCATTTTCACTTTT
42341973 TCATTTTTCATCTTTT
1 TCA-TTTTCA-CTTTT
42341989 T
1 T
42341990 TTTGACTCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.30
14 7 0.26
15 6 0.22
16 6 0.22
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (14 bp):
TCATTTTCACTTTT
Found at i:42342893 original size:6 final size:6
Alignment explanation
Indices: 42342865--42342910 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
42342855 TCTTCTCTCT
* * * *
42342865 TTTTCA TTTTCA TTTTTA CTTTGA TTTTGA TTTTGA TTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTT
42342911 TCTTCTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.15, C:0.07, G:0.09, T:0.70
Consensus pattern (6 bp):
TTTTGA
Found at i:42348982 original size:23 final size:23
Alignment explanation
Indices: 42348949--42349011 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
42348939 AGCGGTGTGA
*
42348949 CGTGGCGCGTACGGAGGCGCAGG
1 CGTGGCGCGTACGGAGGCGAAGG
* *
42348972 CGTGGCACGTACGGAGGTGAAGG
1 CGTGGCGCGTACGGAGGCGAAGG
*
42348995 CGT-GCGCGCACGGAGGC
1 CGTGGCGCGTACGGAGGC
42349012 TCGTCACATG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.16, C:0.25, G:0.49, T:0.10
Consensus pattern (23 bp):
CGTGGCGCGTACGGAGGCGAAGG
Found at i:42352781 original size:30 final size:30
Alignment explanation
Indices: 42352717--42352781 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
42352707 ATTCCCTAAT
*
42352717 TTTAAAAAAATATTAATTAGACCTTCAAAC
1 TTTAAAAAAATATTAATTAGACCTCCAAAC
*
42352747 TTTAAAAAAA-ATTAATTAAGCCCTCCATAA-
1 TTTAAAAAAATATTAATT-AGACCTCCA-AAC
42352777 TTTAA
1 TTTAA
42352782 TGTCACATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 7 0.23
30 22 0.71
31 2 0.06
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (30 bp):
TTTAAAAAAATATTAATTAGACCTCCAAAC
Found at i:42354296 original size:9 final size:9
Alignment explanation
Indices: 42354282--42354312 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42354272 GTTAAACGAA
42354282 TCGAGTTAT
1 TCGAGTTAT
*
42354291 TCGAGTTAA
1 TCGAGTTAT
42354300 TCGAGTTAT
1 TCGAGTTAT
42354309 TCGA
1 TCGA
42354313 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42354382 original size:9 final size:9
Alignment explanation
Indices: 42354365--42354401 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42354355 TGAGTTTTCG
42354365 AATTCGAAT
1 AATTCGAAT
*
42354374 AACTCGAAT
1 AATTCGAAT
42354383 AATTCGAAT
1 AATTCGAAT
42354392 AATTCGAAT
1 AATTCGAAT
42354401 A
1 A
42354402 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42354478 original size:21 final size:21
Alignment explanation
Indices: 42354437--42354479 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42354427 ACCCCAAACT
* *
42354437 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTATTCC
42354458 CTCAAAAC-TTTTACTCATTCC
1 CTCAAAACTTTTTACT-ATTCC
42354479 C
1 C
42354480 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.23, C:0.35, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTATTCC
Found at i:42354647 original size:19 final size:20
Alignment explanation
Indices: 42354607--42354647 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
42354597 CAAAAACCCT
*
42354607 CAAAATCTTTTATTTTCCCC
1 CAAAATCTTTTATCTTCCCC
42354627 CAAAAT-TTTTA-CTTCCTCC
1 CAAAATCTTTTATCTTCC-CC
42354646 CA
1 CA
42354648 CTTTTCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (20 bp):
CAAAATCTTTTATCTTCCCC
Found at i:42354845 original size:17 final size:15
Alignment explanation
Indices: 42354804--42354851 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
42354794 NNNATTTACT
42354804 TTCCCTCAAACTTTTA
1 TTCCC-CAAACTTTTA
*
42354820 TTCCCCAAACTTTATT
1 TTCCCCAAACTTT-TA
42354836 TTCTCCCAAACTTTTA
1 TTC-CCCAAACTTTTA
42354852 CTTCTCACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 10 0.36
17 10 0.36
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (15 bp):
TTCCCCAAACTTTTA
Found at i:42354856 original size:17 final size:16
Alignment explanation
Indices: 42354810--42354857 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
42354800 TACTTTCCCT
42354810 CAAACTTTTATTC-CC
1 CAAACTTTTATTCTCC
*
42354825 CAAACTTTATTTTCTCC
1 CAAACTTT-TATTCTCC
42354842 CAAACTTTTACTTCTC
1 CAAACTTTTA-TTCTC
42354858 ACCCTTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 5 0.18
17 15 0.54
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (16 bp):
CAAACTTTTATTCTCC
Found at i:42354996 original size:17 final size:17
Alignment explanation
Indices: 42354974--42355020 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
42354964 CACATTTTAT
42354974 ATTGTTTATATTATTGA
1 ATTGTTTATATTATTGA
42354991 ATTGTTTAGTCA-TATTGA
1 ATTGTTTA-T-ATTATTGA
*
42355009 A-TATTTATATTA
1 ATTGTTTATATTA
42355021 AAATTGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.12
17 13 0.50
18 8 0.31
19 1 0.04
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (17 bp):
ATTGTTTATATTATTGA
Found at i:42355359 original size:5 final size:5
Alignment explanation
Indices: 42355349--42355374 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42355339 GAACAAATAT
42355349 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
42355375 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:42361356 original size:8 final size:8
Alignment explanation
Indices: 42361345--42361397 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
42361335 TATTTGCTTG
42361345 ATTCATTT
1 ATTCATTT
42361353 ATTCATTT
1 ATTCATTT
*
42361361 ACTCATTT
1 ATTCATTT
42361369 A--C--TT
1 ATTCATTT
42361373 ATTCATTT
1 ATTCATTT
*
42361381 ATCCATTAT
1 ATTCATT-T
42361390 ATTCATTT
1 ATTCATTT
42361398 TTACTCAGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
4 3 0.08
6 2 0.05
8 25 0.68
9 7 0.19
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTCATTT
Found at i:42375989 original size:27 final size:27
Alignment explanation
Indices: 42375950--42376141 Score: 246
Period size: 27 Copynumber: 7.2 Consensus size: 27
42375940 GGTTGGGCCA
* *
42375950 TAAAATTACCGAAATACCCTTGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
42375977 TAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
* *
42376004 TAAAATTATAGAAATACCCTC-AAAGG
1 TAAAATTATCGAAATACCCTCGAAGGG
42376030 TAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
* * *
42376057 TAAAATTACCAAAATACCCTCAAAGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
* *
42376084 TACAATTA-CTGAAATACCC-CAAAGGG
1 TAAAATTATC-GAAATACCCTCGAAGGG
* * *
42376110 TAAAATTATCAAAATACCCCCGATGGG
1 TAAAATTATCGAAATACCCTCGAAGGG
42376137 TAAAA
1 TAAAA
42376142 CGACCGTAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
26 47 0.32
27 99 0.68
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (27 bp):
TAAAATTATCGAAATACCCTCGAAGGG
Found at i:42376083 original size:80 final size:80
Alignment explanation
Indices: 42375950--42376141 Score: 271
Period size: 80 Copynumber: 2.4 Consensus size: 80
42375940 GGTTGGGCCA
* * * * *
42375950 TAAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTA-TA
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTAAAATTACT-
42376014 GAAATACCCTCAAA-GG
65 GAAATACCC-CAAAGGG
*
42376030 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTACAATTACTG
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTAAAATTACTG
42376095 AAATACCCCAAAGGG
66 AAATACCCCAAAGGG
* * *
42376110 TAAAATTATCAAAATACCCCCGATGGGTAAAA
1 TAAAATTATCGAAATACCCTCGAAGGGTAAAA
42376142 CGACCGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
79 4 0.04
80 96 0.95
81 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (80 bp):
TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTAAAATTACTG
AAATACCCCAAAGGG
Found at i:42376138 original size:53 final size:54
Alignment explanation
Indices: 42375950--42376141 Score: 248
Period size: 53 Copynumber: 3.6 Consensus size: 54
42375940 GGTTGGGCCA
* *
42375950 TAAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
* *
42376004 TAAAATTA-TAGAAATACCCTC-AAAGGTAAAATTATCGAAATACCCTCGAAGGG
1 TAAAATTACCA-AAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
* * *
42376057 TAAAATTACCAAAATACCCTCAAAGGGTACAATTA-CTGAAATACCC-CAAAGGG
1 TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATC-GAAATACCCTCGAAGGG
* * *
42376110 TAAAATTATCAAAATACCCCCGATGGGTAAAA
1 TAAAATTACCAAAATACCCTCGAAGGGTAAAA
42376142 CGACCGTAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
53 83 0.69
54 38 0.31
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.21
Consensus pattern (54 bp):
TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAATACCCTCGAAGGG
Found at i:42376164 original size:80 final size:80
Alignment explanation
Indices: 42375950--42376169 Score: 212
Period size: 80 Copynumber: 2.8 Consensus size: 80
42375940 GGTTGGGCCA
* * ** ** * * * *
42375950 TAAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTATAG
1 TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCAAAGGGTAAAATTATAG
42376015 AAATACCCTCAAAGG
66 AAATACCCTCAAAGG
* * ** * *
42376030 TAAAATTATCGAAATACCCTCGAAGGGTAAAATTACCAAAATACCCTCAAAGGGTACAATTACT-
1 TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCAAAGGGTAAAATTA-TA
42376094 GAAATACCC-CAAAGGG
65 GAAATACCCTCAAA-GG
* ** *
42376110 TAAAATTATCAAAATACCCCCGATGGGTAAAACGACCGTAATAACC-CATTAGGGTAAAAT
1 TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCA-AAGGGTAAAAT
42376170 AACCATGATG
Statistics
Matches: 121, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
79 6 0.05
80 114 0.94
81 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.15, T:0.21
Consensus pattern (80 bp):
TAAAATTATCAAAATACCCCCGAAGGGTAAAACGACCAAAATAACCTCAAAGGGTAAAATTATAG
AAATACCCTCAAAGG
Found at i:42376523 original size:16 final size:16
Alignment explanation
Indices: 42376502--42376532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42376492 AATCAAGATT
42376502 TCAAGAATCAAGAAAA
1 TCAAGAATCAAGAAAA
*
42376518 TCAAGAATCAGGAAA
1 TCAAGAATCAAGAAA
42376533 TCTTGGTCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (16 bp):
TCAAGAATCAAGAAAA
Found at i:42376534 original size:24 final size:24
Alignment explanation
Indices: 42376479--42376527 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
42376469 GATCTTGGTC
*
42376479 CAAGAATCAAGAAAATCAAGATTT
1 CAAGAATCAAGAAAATCAAGATAT
42376503 CAAGAATCAAGAAAATCAAGA-AT
1 CAAGAATCAAGAAAATCAAGATAT
42376526 CA
1 CA
42376528 GGAAATCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.16
Consensus pattern (24 bp):
CAAGAATCAAGAAAATCAAGATAT
Found at i:42379004 original size:18 final size:20
Alignment explanation
Indices: 42378983--42379032 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
42378973 AAAGGAAGAC
42378983 AGAAAAAGA-AAT-AAAAAA
1 AGAAAAAGAGAATGAAAAAA
*
42379001 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATGAAAAAA
42379021 AGCAAAAAGAGA
1 AG-AAAAAGAGA
42379033 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 3 0.11
20 7 0.25
21 9 0.32
ACGTcount: A:0.74, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATGAAAAAA
Found at i:42382100 original size:24 final size:24
Alignment explanation
Indices: 42382054--42382100 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42382044 CCCTCAGGGT
* *
42382054 TAAATGATTGATTTGTCCGTGATG
1 TAAATGACTGATTTGTCCATGATG
*
42382078 TAAATGACTGATTTGTCTATGAT
1 TAAATGACTGATTTGTCCATGAT
42382101 TTGTATGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (24 bp):
TAAATGACTGATTTGTCCATGATG
Found at i:42382259 original size:26 final size:26
Alignment explanation
Indices: 42382230--42382283 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
42382220 TTGGCCACAT
*
42382230 ATACTGTTAATGGCAGCTTTGTTGCG
1 ATACTGTTAATGGCAGCTTTGCTGCG
** *
42382256 ATACTGTTGCTGGTAGCTTTGCTGCG
1 ATACTGTTAATGGCAGCTTTGCTGCG
42382282 AT
1 AT
42382284 GCTATTGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (26 bp):
ATACTGTTAATGGCAGCTTTGCTGCG
Found at i:42382379 original size:32 final size:32
Alignment explanation
Indices: 42382289--42382379 Score: 119
Period size: 32 Copynumber: 2.8 Consensus size: 32
42382279 GCGATGCTAT
* * * * *
42382289 TGATGTCTTTGTGCCAGTCATATTACCATTAC
1 TGATGGCTCTGTGCCAATCATATTACTACTAC
* *
42382321 TGATGGTTGTGTGCCAATCATATTACTACTAC
1 TGATGGCTCTGTGCCAATCATATTACTACTAC
42382353 TGATGGCTCTGTGCCAATCATATTACT
1 TGATGGCTCTGTGCCAATCATATTACT
42382380 GTACTTATGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (32 bp):
TGATGGCTCTGTGCCAATCATATTACTACTAC
Found at i:42395753 original size:7 final size:6
Alignment explanation
Indices: 42395731--42395777 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
42395721 TTCATTTTGA
* *
42395731 TTTAAT TTTAAA TTTAAT CTTTATT TTTAAT TTT-AT TGTTAAT TTTA
1 TTTAAT TTTAAT TTTAAT -TTTAAT TTTAAT TTTAAT T-TTAAT TTTA
42395778 TTTATTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
5 3 0.09
6 23 0.68
7 8 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (6 bp):
TTTAAT
Done.