Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 102 of 173
Found at i:31545794 original size:34 final size:35
Alignment explanation
Indices: 31545740--31545806 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
31545730 CAAACACCAG
*
31545740 AAAATATTTTCCAGTAAATCATTGTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTGTACAGAAAAGT
* * *
31545775 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTGTACAGAAAA
31545807 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTGTACAGAAAAGT
Found at i:31548174 original size:26 final size:26
Alignment explanation
Indices: 31548143--31548199 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
31548133 CCCTTTGGAG
*
31548143 AGAACCCGAAAAGTTAGAGTGGAGAA
1 AGAACCCGAAAAGTTAGAGCGGAGAA
*
31548169 AGAACCCGAAGAGTTAGAGCGGAGAA
1 AGAACCCGAAAAGTTAGAGCGGAGAA
31548195 AGAAC
1 AGAAC
31548200 AAGGATTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.14, G:0.32, T:0.09
Consensus pattern (26 bp):
AGAACCCGAAAAGTTAGAGCGGAGAA
Found at i:31554953 original size:17 final size:18
Alignment explanation
Indices: 31554918--31554953 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
31554908 CCATATGGTT
*
31554918 CACTCGTGTGGGTCCATA
1 CACTCGTGTGGGCCCATA
31554936 CACTCGTGT-GGCCCATA
1 CACTCGTGTGGGCCCATA
31554953 C
1 C
31554954 GGCCTAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (18 bp):
CACTCGTGTGGGCCCATA
Found at i:31557879 original size:28 final size:28
Alignment explanation
Indices: 31557839--31558032 Score: 187
Period size: 28 Copynumber: 7.0 Consensus size: 28
31557829 AGTCGTGTGT
* **
31557839 CCACTGTTTTTCAAAACTTACAATTTTG
1 CCACAGTTTTTCAAATTTTACAATTTTG
31557867 CCACAGTTTTTCAAATTTTACAATTTTG
1 CCACAGTTTTTCAAATTTTACAATTTTG
* *
31557895 CCACAATTTTTCAGATTTTACAATTTTG
1 CCACAGTTTTTCAAATTTTACAATTTTG
** * *
31557923 CCATTGCTTTTCAAATTTT-CAAATTTTA
1 CCACAGTTTTTCAAATTTTAC-AATTTTG
* * *
31557951 CCACTG-TTTTGAAATTTTACAGTTTTG
1 CCACAGTTTTTCAAATTTTACAATTTTG
* * * *
31557978 CCACAATTTTTTAGATTTTACAGTTTTG
1 CCACAGTTTTTCAAATTTTACAATTTTG
* *
31558006 CCAC-GATTTTTTAGATTTTACAATTTT
1 CCACAG-TTTTTCAAATTTTACAATTTT
31558033 CCTCTATTTT
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 21 0.15
28 120 0.85
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (28 bp):
CCACAGTTTTTCAAATTTTACAATTTTG
Found at i:31558024 original size:83 final size:82
Alignment explanation
Indices: 31557846--31558059 Score: 234
Period size: 83 Copynumber: 2.6 Consensus size: 82
31557836 TGTCCACTGT
** * *
31557846 TTTTCAAAACTTACAATTTTGCCACAGTTTTTCAAATTTTACAATTTTGCCACAATTTTTCAGAT
1 TTTTCAAATTTTACAATTTT-CCACTG-TTTTCAAATTTTACAGTTTTGCCACAATTTTTCAGAT
*
31557911 TTTACAATTTTGCCATTGC
64 TTTACAATTTTGCCATCGC
* *
31557930 TTTTCAAATTTT-CAAATTTTACCACTGTTTTGAAATTTTACAGTTTTGCCACAATTTTTTAGAT
1 TTTTCAAATTTTAC-AATTTT-CCACTGTTTTCAAATTTTACAGTTTTGCCACAATTTTTCAGAT
* *
31557994 TTTACAGTTTTGCCA-CGAT
64 TTTACAATTTTGCCATCG-C
* * * * *
31558013 TTTTTAGATTTTACAATTTTCCTCTATTTTACAAATTTTATAGTTTT
1 TTTTCAAATTTTACAATTTTCCACTGTTTT-CAAATTTTACAGTTTT
31558060 TACCTAAGAT
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
82 9 0.08
83 79 0.72
84 22 0.20
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.50
Consensus pattern (82 bp):
TTTTCAAATTTTACAATTTTCCACTGTTTTCAAATTTTACAGTTTTGCCACAATTTTTCAGATTT
TACAATTTTGCCATCGC
Found at i:31558042 original size:55 final size:53
Alignment explanation
Indices: 31557856--31558052 Score: 159
Period size: 56 Copynumber: 3.5 Consensus size: 53
31557846 TTTTCAAAAC
*
31557856 TTACAATTTTGCCACAGTTTTTCAAATTTTACAATTTTGCCACAATTTTTCAGATT
1 TTACAATTTT-CC-CATTTTTTCAAATTTTACAATTTTGCCAC-ATTTTTCAGATT
* * * *
31557912 TTACAATTTTGCCATTGCTTTTCAAATTTT-CAAATTTTACCAC-TGTTTTGAAATT
1 TTACAATTTTCCCATT--TTTTCAAATTTTAC-AATTTTGCCACAT-TTTTCAGATT
* * * *
31557967 TTACAGTTTTGCCACAATTTTTT-AGATTTTACAGTTTTGCCACGATTTTTTAGATT
1 TTACAATTTT-CC-C-ATTTTTTCAAATTTTACAATTTTGCCAC-ATTTTTCAGATT
*
31558023 TTACAATTTTCCTC-TATTTTACAAATTTTA
1 TTACAATTTTCC-CAT-TTTTTCAAATTTTA
31558053 TAGTTTTTAC
Statistics
Matches: 113, Mismatches: 16, Indels: 25
0.73 0.10 0.16
Matches are distributed among these distances:
53 1 0.01
54 8 0.07
55 44 0.39
56 55 0.49
57 2 0.02
58 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (53 bp):
TTACAATTTTCCCATTTTTTCAAATTTTACAATTTTGCCACATTTTTCAGATT
Found at i:31558468 original size:21 final size:21
Alignment explanation
Indices: 31558444--31558509 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
31558434 AGTTTATTTG
31558444 CATCGTTTAGTGGTTTATCCA
1 CATCGTTTAGTGGTTTATCCA
* ***
31558465 CATCATTTGAGCAATTTA-CCTA
1 CATCGTTT-AGTGGTTTATCC-A
* *
31558487 CACCGTTGAGTGGTTTATCCA
1 CATCGTTTAGTGGTTTATCCA
31558508 CA
1 CA
31558510 CCTTATTAGT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (21 bp):
CATCGTTTAGTGGTTTATCCA
Found at i:31565470 original size:26 final size:26
Alignment explanation
Indices: 31565435--31565485 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
31565425 ATGTGAAAAG
*
31565435 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
31565461 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
31565486 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:31565491 original size:104 final size:104
Alignment explanation
Indices: 31565356--31565622 Score: 439
Period size: 104 Copynumber: 2.6 Consensus size: 104
31565346 TTGTATATAA
** *
31565356 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
31565421 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATT-CCCCG
66 TGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
31565460 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCT
31565524 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
** *
31565564 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCA
31565623 ATAACGGTTA
Statistics
Matches: 152, Mismatches: 8, Indels: 6
0.92 0.05 0.04
Matches are distributed among these distances:
103 24 0.16
104 127 0.84
105 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:31573426 original size:12 final size:13
Alignment explanation
Indices: 31573402--31573430 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31573392 GAGTTATAAC
31573402 TATTGCATTTATT
1 TATTGCATTTATT
31573415 TATTGC-TTTATT
1 TATTGCATTTATT
31573427 TATT
1 TATT
31573431 CATATATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:31580013 original size:31 final size:30
Alignment explanation
Indices: 31579978--31580036 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
31579968 TTTAAAAAAA
*
31579978 ATACATGGAAATG-ATTTTACATGATATATAG
1 ATACAT-GAAATGAATGTTACATG-TATATAG
*
31580009 ATACATGATATGAATGTTACATGTATAT
1 ATACATGAAATGAATGTTACATGTATAT
31580037 GGAAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (30 bp):
ATACATGAAATGAATGTTACATGTATATAG
Found at i:31583734 original size:38 final size:38
Alignment explanation
Indices: 31583683--31583759 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
31583673 AAACGGATGG
31583683 ATTGATGAGATTGTGTATTGACAACCGTCAGCTCAACA
1 ATTGATGAGATTGTGTATTGACAACCGTCAGCTCAACA
31583721 ATTGATGAGATTGTGTATTGACAACCGTCAGCTCAACA
1 ATTGATGAGATTGTGTATTGACAACCGTCAGCTCAACA
31583759 A
1 A
31583760 GATTACAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (38 bp):
ATTGATGAGATTGTGTATTGACAACCGTCAGCTCAACA
Found at i:31584773 original size:3 final size:3
Alignment explanation
Indices: 31584765--31584828 Score: 53
Period size: 3 Copynumber: 21.3 Consensus size: 3
31584755 ATTTAGTCTT
* * *
31584765 TTA TTA TTA TTTA TTA TTA -AA TT- TTA TT- TTC TTG TTA TTAA GTTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA
31584810 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
31584829 ACATACGCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
2 5 0.10
3 39 0.76
4 5 0.10
5 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31584973 original size:17 final size:17
Alignment explanation
Indices: 31584942--31584985 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
31584932 CATAACTTTT
*
31584942 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
31584958 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
31584975 ATATACATTTT
1 ATATACATTTT
31584986 TATTTCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:31585158 original size:31 final size:30
Alignment explanation
Indices: 31585120--31585237 Score: 98
Period size: 31 Copynumber: 3.8 Consensus size: 30
31585110 ATTAATTTCA
*
31585120 ATATATGTAATTATTATTATTTGTTTTATAT
1 ATATATGTAATTATTATTATTT-TTATATAT
* *
31585151 ATATATGTAATTATCT-TT-TTTATAATCTAT
1 ATATATGTAATTAT-TATTATTT-TTATATAT
*
31585181 ATATATGTAGATAATTATTATTTTTATATAT
1 ATATATGTA-ATTATTATTATTTTTATATAT
* *
31585212 GTACATGT-ATATATTTATATATTTTT
1 ATATATGTAAT-TA-TTAT-TATTTTT
31585238 TCCTAATGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
29 2 0.03
30 19 0.27
31 38 0.54
32 11 0.16
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.58
Consensus pattern (30 bp):
ATATATGTAATTATTATTATTTTTATATAT
Found at i:31590183 original size:14 final size:15
Alignment explanation
Indices: 31590157--31590189 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
31590147 TTCCAAGCTG
31590157 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
31590172 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
31590186 GGAA
1 GGAA
31590190 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:31591684 original size:88 final size:88
Alignment explanation
Indices: 31591532--31592288 Score: 804
Period size: 88 Copynumber: 8.6 Consensus size: 88
31591522 AGAACAGATC
* * * ** *
31591532 ATTGAAGATAGCAGATCTTGTCTTCCTGTACCGGTAGCGAAGCAGATCAAAGACACCAGCCTTGC
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
* * *
31591597 CTCCCTGGGTTACAGCGGAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * *
31591620 GTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
31591685 CTCCCTAGGTTGCAGTGGAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * *
31591708 ACT-AAAAGTAGTAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGCCACCAGTCTTG
1 ATTGAAAA-TAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTG
* *
31591772 CCTCCCTAGGTTGCATTGGAGCAT
65 CCTCCCTAGGTTGCAGTGGAGCAG
* * * *
31591796 ACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATC-AAGGGCACCAGCCTTG
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACACCAGCCTTG
* *
31591860 CC-CCCTTGGGTTGCAGCGGAGCAG
65 CCTCCC-TAGGTTGCAGTGGAGCAG
* * * * *
31591884 GTTGAAAATAGCAGATCTTGCCTTCATATACTGACACCGAAGCAGATCGAAGACACCAGTCTTGC
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
*
31591949 CTCCCAAGGTTGCAGTGGAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * ** *
31591972 ACTGAAGATAGTAGATCTTGCCTTCCTGTACCGGTAGCGAAGCAGATCAAAGACACCAGCCTTGC
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
* *
31592037 CTCCCT-GGATTGCAGCGGAGTAG
66 CTCCCTAGG-TTGCAGTGGAGCAG
* * * * *** ** *
31592060 GTTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGGTGCCATTCTTCC
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
* *
31592125 CTCTCTAGGTTGCAGTGTAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * * * * *
31592148 ACTGAAGATAGCAGATCTTTCCTTCCTGTACCGGCAGCGAAGCAGATCGAAAACTCCAGCCTTGT
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
** *
31592213 CTCCCT-GAGCAGCAGTGGAGTAG
66 CTCCCTAG-GTTGCAGTGGAGCAG
* * * ** * *
31592236 GTTAAAAATAGCAGATCTTGCCTTCCTATACTGGTAGTGAAGTAGATCGAAGA
1 ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGA
31592289 AATCAGTCTT
Statistics
Matches: 551, Mismatches: 109, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
87 12 0.02
88 529 0.96
89 10 0.02
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24
Consensus pattern (88 bp):
ATTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGCCTTGC
CTCCCTAGGTTGCAGTGGAGCAG
Found at i:31591838 original size:176 final size:175
Alignment explanation
Indices: 31591533--31592298 Score: 908
Period size: 176 Copynumber: 4.4 Consensus size: 175
31591523 GAACAGATCA
* * * * * *
31591533 TTGAAGATAGCAGATCTTGTCTTCCTGTACCGGTAGCGAAGCAGATCAAAGACACCAGCCTTGCC
1 TTGAAAATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACCAGTCTTGCC
* * * ** * *
31591598 TCCCTGGGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
66 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
* * * *
31591663 AGATCGAAGACACTAGTCTTGCCTCCCTAGGTTGCAGTGGAGCAGA
131 AGATCGAAGACACCAGCCTTGCCTCCCT-GGTTGCAGCGGAGCAGG
* * *
31591709 CT-AAAAGTAGTAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGCCACCAGTCTTGC
1 TTGAAAA-TAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACCAGTCTTGC
* *
31591773 CTCCCTAGGTTGCATTGGAGCATACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAG
65 CTCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAG
*
31591838 CAGATC-AAGGGCACCAGCCTTGCC-CCCTTGGGTTGCAGCGGAGCAGG
130 CAGATCGAA-GACACCAGCCTTGCCTCCC-T-GGTTGCAGCGGAGCAGG
* * * *
31591885 TTGAAAATAGCAGATCTTGCCTTCATATACTGACACCGAAGCAGATCGAAGACACCAGTCTTGCC
1 TTGAAAATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACCAGTCTTGCC
* * **
31591950 TCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTGCCTTCCTGTACCGGTAGCGAAGC
66 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
* *
31592015 AGATCAAAGACACCAGCCTTGCCTCCCTGGATTGCAGCGGAGTAGG
131 AGATCGAAGACACCAGCCTTGCCTCCCTGG-TTGCAGCGGAGCAGG
* * * * *** * *
31592061 TTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGGTGCCATTCTTCCC
1 TTGAAAATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACCAGTCTTGCC
* * * *
31592126 TCTCTAGGTTGCAGTGTAGCAGACTGAAGATAGCAGATCTTTCCTTCCTGTACCGGCAGCGAAGC
66 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
* * * ** * *
31592191 AGATCGAAAACTCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGG
131 AGATCGAAGACACCAGCCTTGCCTCCCTG-GTTGCAGCGGAGCAGG
* * * * * * *
31592237 TTAAAAATAGCAGATCTTGCCTTCCTATACTGGTAGTGAAGTAGATCGAAGAAATCAGTCTT
1 TTGAAAATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACCAGTCTT
31592299 ATTGCCTTGA
Statistics
Matches: 507, Mismatches: 75, Indels: 16
0.85 0.13 0.03
Matches are distributed among these distances:
175 10 0.02
176 487 0.96
177 10 0.02
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.24
Consensus pattern (175 bp):
TTGAAAATAGCAGATCTTGCCTTCCTGTACTGATAGCGAAGCAGATCGAAGACACCAGTCTTGCC
TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
AGATCGAAGACACCAGCCTTGCCTCCCTGGTTGCAGCGGAGCAGG
Found at i:31592012 original size:264 final size:262
Alignment explanation
Indices: 31591534--31592288 Score: 899
Period size: 264 Copynumber: 2.9 Consensus size: 262
31591524 AACAGATCAT
* ** * *
31591534 TGAAGATAGCAGATCTTGTCTTCCTGTACCGGTAGCGAAGCAGATCAAAGACACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGGCACCAGCCTTGCC-
*
31591599 CCC-TGGGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
65 CCCTTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGC
*
31591663 AGATCGAAGACACTAGTCTTGCCTCCCTAGGTTGCAGTGGAGCAGACTAAAAGTAGTAGATCTTG
130 AGATCGAAGACACCAGTCTTGCCTCCC-AGGTTGCAGTGGAGCAGACTAAAA-TAGTAGATCTTG
* * * **
31591728 CCTTCCTGTACTGATAGCGAAGCAGATCGAAGCCACCAGTCTTGCCTCCCTAGG-TTGCATTGGA
193 CCTTCCTGTACTGGTAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-GGATTGCAGCGGA
*
31591792 GCATAC
257 GCAGAC
31591798 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGGCACCAGCCTTGCCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGGCACCAGCCTTGCCC
* * *
31591863 CCTTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCATATACTGACACCGAAGCA
66 CCTTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCA
*
31591928 GATCGAAGACACCAGTCTTGCCTCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTGC
131 GATCGAAGACACCAGTCTTGCCTCCC-AGGTTGCAGTGGAGCAGACT-AAAATAGTAGATCTTGC
* * *
31591993 CTTCCTGTACCGGTAGCGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGATTGCAGCGGAGT
194 CTTCCTGTACTGGTAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATTGCAGCGGAGC
**
31592058 AGGT
259 AGAC
* * * * * **
31592062 TGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGTGAAGCAGATTGAAGGTG--CCATTCTT-C
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGA-TCAAGG-GCACCAGCCTTGC
* * * * ** * * * *
31592124 CCTCTCTAGGTTGCAGTGTAGCAGACTGAAGATAGCAGATCTTTCCTTCCTGTACCGGCAGCGAA
64 CCCCT-TGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAA
* * * * * ** * ** *
31592189 GCAGATCGAAAACTCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTAAAAATAGCAGATCT
128 GCAGATCGAAGACACCAGTCTTGCCTCCCAG-GTTGCAGTGGAGCAGACT-AAAATAGTAGATCT
* * *
31592254 TGCCTTCCTATACTGGTAGTGAAGTAGATCGAAGA
191 TGCCTTCCTGTACTGGTAGCGAAGCAGATCGAAGA
31592289 AATCAGTCTT
Statistics
Matches: 423, Mismatches: 61, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
263 11 0.03
264 403 0.95
265 8 0.02
266 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.23
Consensus pattern (262 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGGCACCAGCCTTGCCC
CCTTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCA
GATCGAAGACACCAGTCTTGCCTCCCAGGTTGCAGTGGAGCAGACTAAAATAGTAGATCTTGCCT
TCCTGTACTGGTAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGATTGCAGCGGAGCAG
AC
Found at i:31592547 original size:117 final size:117
Alignment explanation
Indices: 31592356--31592726 Score: 580
Period size: 117 Copynumber: 3.2 Consensus size: 117
31592346 CTTATTTCCC
* * *
31592356 TGGCATTGTAGCAGAGCAGATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTG
1 TGGCATTGCAGTAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTG
31592421 GATTAGCTGAAGTGGAGCGGATTAAAGCTGAGGGCAGCGAATCCTATCTCTT
66 GATTAGCTGAAGTGGAGCGGATTAAAGCTGAGGGCAGCGAATCCTATCTCTT
31592473 TGGCATTGCAGTAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTG
1 TGGCATTGCAGTAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTG
* * **
31592538 GATAAGCTGAAATGGAGTAGATTAAAGCTGAGGGCAGCGAATCCTATCTCTT
66 GATTAGCTGAAGTGGAGCGGATTAAAGCTGAGGGCAGCGAATCCTATCTCTT
* * *
31592590 TGGCATTGCAGTGGAGCAAATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAAGCTTG
1 TGGCATTGCAGTAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTG
* * **
31592655 GATTAGCTGAAGTGGGGCGAATTAAAGCTGAGGATAGCGAATCCTATCTCTT
66 GATTAGCTGAAGTGGAGCGGATTAAAGCTGAGGGCAGCGAATCCTATCTCTT
** * *
31592707 TTTCATTACAGTGGAGCAGA
1 TGGCATTGCAGTAGAGCAGA
31592727 CTGAGTAAGA
Statistics
Matches: 232, Mismatches: 22, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 232 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (117 bp):
TGGCATTGCAGTAGAGCAGATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTG
GATTAGCTGAAGTGGAGCGGATTAAAGCTGAGGGCAGCGAATCCTATCTCTT
Found at i:31592765 original size:44 final size:44
Alignment explanation
Indices: 31592715--31592810 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
31592705 TTTTTCATTA
* * *
31592715 CAGTGGAGCAGACTGAGT-AAGAAAGTCTTATCCCCCTAAAATTG
1 CAGTGGAGCAGACTGAATGAACAAA-TCCTATCCCCCTAAAATTG
* *
31592759 CAGTGGAGCAGACTGAATGAACAAATCCTATCTCCCTAAAGTTG
1 CAGTGGAGCAGACTGAATGAACAAATCCTATCCCCCTAAAATTG
*
31592803 TAGTGGAG
1 CAGTGGAG
31592811 TGGATTAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 40 0.89
45 5 0.11
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (44 bp):
CAGTGGAGCAGACTGAATGAACAAATCCTATCCCCCTAAAATTG
Found at i:31593293 original size:19 final size:20
Alignment explanation
Indices: 31593251--31593302 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
31593241 TTCAAGGATG
31593251 TGCAATCTTAGATATGATATA
1 TGCAATCTTAGATATGA-ATA
31593272 TGCAATCTTAGATATG-ATA
1 TGCAATCTTAGATATGAATA
31593291 TGCAATCTTAGA
1 TGCAATCTTAGA
31593303 AGATGTGATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (20 bp):
TGCAATCTTAGATATGAATA
Found at i:31593607 original size:3 final size:3
Alignment explanation
Indices: 31593594--31593673 Score: 58
Period size: 3 Copynumber: 26.3 Consensus size: 3
31593584 ATTTAGTCTT
* * * *
31593594 TTA TTA TTTA TTA TTTA TTA TTA TTA -AA TT- TGA TT- TTC TTG TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
31593638 TTAA GTTG TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31593674 ACATACGCAT
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
2 4 0.06
3 49 0.79
4 7 0.11
5 2 0.03
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:31593823 original size:17 final size:17
Alignment explanation
Indices: 31593784--31593827 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
31593774 CATAACTTTT
*
31593784 ATATACA-TATATATAC
1 ATATACATTTTATATAC
* *
31593800 ATTTACATTTTATGTAC
1 ATATACATTTTATATAC
31593817 ATATACATTTT
1 ATATACATTTT
31593828 TATTTCCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:31594040 original size:34 final size:32
Alignment explanation
Indices: 31593964--31594052 Score: 83
Period size: 31 Copynumber: 2.8 Consensus size: 32
31593954 ATTAATTTCA
* * *
31593964 ATATATGTAATTATTATTATTTGT--TTTATAT
1 ATATATGTAATTATCATT-TTTATAATCTATAT
*
31593995 ATATATGTAATTATCCTTTTTATAATCTATAT
1 ATATATGTAATTATCATTTTTATAATCTATAT
* *
31594027 ATATGTAGATAATTATTATTTTTATA
1 ATATAT-G-TAATTATCATTTTTATA
31594053 TATGTACATG
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.09
31 16 0.34
32 11 0.23
33 1 0.02
34 15 0.32
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (32 bp):
ATATATGTAATTATCATTTTTATAATCTATAT
Found at i:31598253 original size:25 final size:25
Alignment explanation
Indices: 31598225--31598296 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
31598215 CAGCTCGTAT
*
31598225 GAGCTTATCGATTTACAGCTC-ATGA
1 GAGCATATCGATTTACAGCTCGA-GA
*
31598250 GAGCATATCGATTTATAGCTCGAGA
1 GAGCATATCGATTTACAGCTCGAGA
* * *
31598275 GAGCATACCGATTCATAGCTCG
1 GAGCATATCGATTTACAGCTCG
31598297 TATAAGCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 41 0.98
26 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (25 bp):
GAGCATATCGATTTACAGCTCGAGA
Found at i:31598487 original size:31 final size:30
Alignment explanation
Indices: 31598452--31598512 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
31598442 TATTTAAATG
*
31598452 AGATACATGGAAAT-GATTTTACATGATATAT
1 AGATACAT-GAAATGGATGTTACATG-TATAT
*
31598483 AGATACATGATATGGATGTTACATGTATAT
1 AGATACATGAAATGGATGTTACATGTATAT
31598513 GGAAATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (30 bp):
AGATACATGAAATGGATGTTACATGTATAT
Found at i:31603621 original size:18 final size:17
Alignment explanation
Indices: 31603588--31603626 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
31603578 TTTTATAAAT
31603588 TGTGAATTATATTTGACA
1 TGTGAATTATATTTGA-A
31603606 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
31603623 TGTG
1 TGTG
31603627 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:31603880 original size:23 final size:22
Alignment explanation
Indices: 31603854--31603972 Score: 112
Period size: 23 Copynumber: 5.2 Consensus size: 22
31603844 GTTATTGATT
*
31603854 AGTGGTAGCTTCAGCTACATTTC
1 AGTGGTAGCTTC-GCTACATATC
* * *
31603877 AGTGATAGCTACGACTACCTATC
1 AGTGGTAGCTTCG-CTACATATC
*
31603900 AGTGGTAGCTTCGACTACATTTC
1 AGTGGTAGCTTCG-CTACATATC
* *
31603923 AGTGGTAGCTATGGCTACGTATC
1 AGTGGTAGCT-TCGCTACATATC
* *
31603946 AGTGGTAGTTTCGGCTACATATT
1 AGTGGTAGCTTC-GCTACATATC
31603969 AGTG
1 AGTG
31603973 TGGCACTTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
22 2 0.03
23 74 0.95
24 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (22 bp):
AGTGGTAGCTTCGCTACATATC
Found at i:31603906 original size:46 final size:45
Alignment explanation
Indices: 31603854--31603965 Score: 152
Period size: 46 Copynumber: 2.4 Consensus size: 45
31603844 GTTATTGATT
31603854 AGTGGTAGCTTCAGCTACATTTCAGTGATAGCTACGACTACCTATC
1 AGTGGTAGCTTC-GCTACATTTCAGTGATAGCTACGACTACCTATC
* * * *
31603900 AGTGGTAGCTTCGACTACATTTCAGTGGTAGCTATGGCTACGTATC
1 AGTGGTAGCTTCG-CTACATTTCAGTGATAGCTACGACTACCTATC
*
31603946 AGTGGTAGTTTCGGCTACAT
1 AGTGGTAGCTTC-GCTACAT
31603966 ATTAGTGTGG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 1 0.02
46 57 0.97
47 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (45 bp):
AGTGGTAGCTTCGCTACATTTCAGTGATAGCTACGACTACCTATC
Found at i:31605241 original size:49 final size:49
Alignment explanation
Indices: 31605142--31605241 Score: 137
Period size: 49 Copynumber: 2.0 Consensus size: 49
31605132 ATGAACCATG
* **
31605142 TCAATACGTGATATGTAATTCCGTGTAAGACCATAGTTGGGTTATAGCA
1 TCAATACGTGATATGTAATTACGTGTAAGACCATAGTTGGACTATAGCA
* * * *
31605191 TCAATATGTGTTATGTGATTACGTGTAAGACCATAGTTGGACTATGGCA
1 TCAATACGTGATATGTAATTACGTGTAAGACCATAGTTGGACTATAGCA
31605240 TC
1 TC
31605242 GAGAAAATAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (49 bp):
TCAATACGTGATATGTAATTACGTGTAAGACCATAGTTGGACTATAGCA
Found at i:31619554 original size:18 final size:16
Alignment explanation
Indices: 31619533--31619566 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
31619523 GTTTTGAAAT
31619533 TGAATAATTATTTGTAAA
1 TGAATAA-TATTT-TAAA
31619551 TGAATAATATTTTAAA
1 TGAATAATATTTTAAA
31619567 AACGAACGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (16 bp):
TGAATAATATTTTAAA
Found at i:31633772 original size:13 final size:13
Alignment explanation
Indices: 31633754--31633778 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31633744 ACGTCTAAGT
31633754 TTAGCTAGCTGAG
1 TTAGCTAGCTGAG
31633767 TTAGCTAGCTGA
1 TTAGCTAGCTGA
31633779 TTTCGAATTC
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:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (13 bp):
TTAGCTAGCTGAG
Found at i:31637015 original size:17 final size:16
Alignment explanation
Indices: 31636993--31637032 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
31636983 TTTGCACACT
*
31636993 TTTTTTATATTCGAAAC
1 TTTTTTATACTCG-AAC
*
31637010 TTTTTTTTACTCGAAC
1 TTTTTTATACTCGAAC
31637026 TTTTTTA
1 TTTTTTA
31637033 CTTCTTTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (16 bp):
TTTTTTATACTCGAAC
Found at i:31637026 original size:16 final size:18
Alignment explanation
Indices: 31636990--31637031 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
31636980 TATTTTGCAC
*
31636990 ACTTTTTTTATATTCGAA
1 ACTTTTTTTATACTCGAA
31637008 ACTTTTTTT-TACTCG-A
1 ACTTTTTTTATACTCGAA
31637024 ACTTTTTT
1 ACTTTTTT
31637032 ACTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 5 0.22
18 9 0.39
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.60
Consensus pattern (18 bp):
ACTTTTTTTATACTCGAA
Found at i:31640399 original size:20 final size:19
Alignment explanation
Indices: 31640376--31640443 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 19
31640366 TAAATTTTAA
*
31640376 AATTAATTTTTATAAAATT
1 AATTAATTTTTAAAAAATT
*
31640395 GAATTAAATTTTAAAAAATT
1 -AATTAATTTTTAAAAAATT
31640415 AACTTAATTTTTAAAAAATT
1 AA-TTAATTTTTAAAAAATT
31640435 AAATTAATT
1 -AATTAATT
31640444 AGAAGTATCC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.91
21 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
AATTAATTTTTAAAAAATT
Found at i:31640788 original size:7 final size:7
Alignment explanation
Indices: 31640752--31640803 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
31640742 ATTATTTCAT
*
31640752 TAAAAAG
1 TAAAAGG
*
31640759 TAAAAGA
1 TAAAAGG
*
31640766 AAAAAGAG
1 TAAAAG-G
31640774 -AAAA-G
1 TAAAAGG
31640779 TAAAAGG
1 TAAAAGG
31640786 TAAAAGG
1 TAAAAGG
31640793 TAAAAGG
1 TAAAAGG
31640800 TAAA
1 TAAA
31640804 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 1 0.03
6 4 0.11
7 33 0.87
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (7 bp):
TAAAAGG
Found at i:31650570 original size:23 final size:24
Alignment explanation
Indices: 31650534--31650584 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
31650524 AAAATGTTGG
**
31650534 AAATTGTTTTATTG-GATTTTATT
1 AAATTGTTCAATTGAGATTTTATT
*
31650557 AAATTGTTCAATTGATGATTTTGTT
1 AAATTGTTCAATTGA-GATTTTATT
31650582 AAA
1 AAA
31650585 AGAAATTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 12 0.52
25 11 0.48
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (24 bp):
AAATTGTTCAATTGAGATTTTATT
Found at i:31657278 original size:17 final size:17
Alignment explanation
Indices: 31657256--31657288 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31657246 CCAAAATCGC
31657256 TATCTGGTCATCTCAAT
1 TATCTGGTCATCTCAAT
31657273 TATCTGGTCATCTCAA
1 TATCTGGTCATCTCAA
31657289 AGGTTGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (17 bp):
TATCTGGTCATCTCAAT
Found at i:31658958 original size:11 final size:11
Alignment explanation
Indices: 31658942--31658970 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
31658932 TAGTTTCTCG
31658942 AAAAAAATTCA
1 AAAAAAATTCA
31658953 AAAAAAATTCA
1 AAAAAAATTCA
31658964 AAAAAAA
1 AAAAAAA
31658971 AATTTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:31658968 original size:13 final size:13
Alignment explanation
Indices: 31658942--31658985 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
31658932 TAGTTTCTCG
31658942 AAAAAAATTC--A
1 AAAAAAATTCAAA
31658953 AAAAAAATTCAAA
1 AAAAAAATTCAAA
*
31658966 AAAAAAATTTGAAA
1 AAAAAAA-TTCAAA
31658980 AAAAAA
1 AAAAAA
31658986 CTAGTTTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 10 0.34
13 8 0.28
14 11 0.38
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:31659045 original size:14 final size:14
Alignment explanation
Indices: 31659026--31659077 Score: 79
Period size: 14 Copynumber: 3.8 Consensus size: 14
31659016 TATCAAGTTG
31659026 TGAAAAAAAAATTT
1 TGAAAAAAAAATTT
*
31659040 TGAAAAAAAAATTG
1 TGAAAAAAAAATTT
*
31659054 T-AAAAAAAAAATT
1 TGAAAAAAAAATTT
31659067 TGAAAAAAAAA
1 TGAAAAAAAAA
31659078 GAGAGCTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
13 11 0.32
14 23 0.68
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (14 bp):
TGAAAAAAAAATTT
Found at i:31659054 original size:28 final size:27
Alignment explanation
Indices: 31659023--31659077 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
31659013 GGATATCAAG
*
31659023 TTGTGAAAAAAAAATTTTGAAAAAAAAA
1 TTGT-AAAAAAAAAATTTGAAAAAAAAA
31659051 TTGTAAAAAAAAAATTTGAAAAAAAAA
1 TTGTAAAAAAAAAATTTGAAAAAAAAA
31659078 GAGAGCTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (27 bp):
TTGTAAAAAAAAAATTTGAAAAAAAAA
Found at i:31660060 original size:21 final size:19
Alignment explanation
Indices: 31660020--31660062 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
31660010 AAAAATTGAA
* *
31660020 AAAGATAAAAAGATTGGAG
1 AAAGAAAAAAAGAGTGGAG
31660039 AAAGAAAAGAAAGAGTGCGAG
1 AAAGAAAA-AAAGAGTG-GAG
31660060 AAA
1 AAA
31660063 CAAGTGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.28, T:0.09
Consensus pattern (19 bp):
AAAGAAAAAAAGAGTGGAG
Found at i:31665619 original size:11 final size:11
Alignment explanation
Indices: 31665605--31665629 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31665595 ATTTTTCAAA
31665605 TTTTTAGAATT
1 TTTTTAGAATT
31665616 TTTTTAGAATT
1 TTTTTAGAATT
31665627 TTT
1 TTT
31665630 AAATAATTGT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTAGAATT
Found at i:31669178 original size:25 final size:26
Alignment explanation
Indices: 31669125--31669180 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
31669115 AAATTGGGAA
*
31669125 ATGGGTTGGGGTAGAAGGGGGGTGGG
1 ATGGGTTGGGGTAGAAGGAGGGTGGG
31669151 ATGGGTTGGGGTAGAA-GAGGGTGGG
1 ATGGGTTGGGGTAGAAGGAGGGTGGG
31669176 ATGGG
1 ATGGG
31669181 ATAGAAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.18, C:0.00, G:0.62, T:0.20
Consensus pattern (26 bp):
ATGGGTTGGGGTAGAAGGAGGGTGGG
Found at i:31669244 original size:30 final size:30
Alignment explanation
Indices: 31669186--31669244 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
31669176 ATGGGATAGA
*
31669186 AGTAAAAGTTTTGAGGGGAAAGTGAGAGGG
1 AGTAAAAGTTTTGAGGGGAAAGTAAGAGGG
31669216 AGTAAAAGTTTT-AGGGGAAAGTAAAGAGG
1 AGTAAAAGTTTTGAGGGGAAAGT-AAGAGG
31669245 TTTGGGAGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (30 bp):
AGTAAAAGTTTTGAGGGGAAAGTAAGAGGG
Found at i:31670894 original size:129 final size:129
Alignment explanation
Indices: 31670664--31670924 Score: 513
Period size: 129 Copynumber: 2.0 Consensus size: 129
31670654 CCTAAGACAC
31670664 TAAGGAGGATAGAGTGATGTTTGACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
1 TAAGGAGGATAGAGTGATGTTTGACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
*
31670729 TTATTTCTTATACTAACTTCCTAATTGTTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
66 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
31670793 TAAGGAGGATAGAGTGATGTTTGACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
1 TAAGGAGGATAGAGTGATGTTTGACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
31670858 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
66 TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
31670922 TAA
1 TAA
31670925 AACTTGGTTC
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
129 131 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (129 bp):
TAAGGAGGATAGAGTGATGTTTGACCATTAGGTTGCTACCCATTTCTTGGTCATTTTCTACCAAT
TTATTTCTTATACTAACTTCCTAATTGCTGAAAAATAAAAAGGAAAAATGCAAATAGGAGGGCT
Found at i:31671722 original size:43 final size:43
Alignment explanation
Indices: 31671674--31671760 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
31671664 ATCCCCCTAC
31671674 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
1 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
31671717 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
1 AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
31671760 A
1 A
31671761 GTCTCAGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (43 bp):
AACAGCATAACCTGAATTTATTTTGATTGAACCATTAAATCTT
Found at i:31682814 original size:103 final size:103
Alignment explanation
Indices: 31682631--31682834 Score: 354
Period size: 103 Copynumber: 2.0 Consensus size: 103
31682621 CTAATTTATG
* *
31682631 GAATGGAGGCAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGGGTGTTATCTAAACTCCAA
1 GAATGGAGGCAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGATATCTAAACTCCAA
*
31682696 TTGGATGAAGTTGAATGGGTCCAATCTCGATATGACTA
66 TTGGATGAAGCTGAATGGGTCCAATCTCGATATGACTA
* * *
31682734 GAATGGAGGCAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGATATCTGAACTCTAG
1 GAATGGAGGCAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGATATCTAAACTCCAA
31682799 TTGGATGAAGCTGAATGGGTCCAATCTCGATATGAC
66 TTGGATGAAGCTGAATGGGTCCAATCTCGATATGAC
31682835 CAGTTGAACC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (103 bp):
GAATGGAGGCAGTATTACCCATTGAAGTTGAGATCCCTTCTCTACGAGTGATATCTAAACTCCAA
TTGGATGAAGCTGAATGGGTCCAATCTCGATATGACTA
Found at i:31684659 original size:44 final size:44
Alignment explanation
Indices: 31684477--31684792 Score: 132
Period size: 44 Copynumber: 7.2 Consensus size: 44
31684467 AAATTACAGG
* * * * *
31684477 TCTTGTCTCCCTAAACAGTAGTGGAGAAGATCAAAGACGGCAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAA
* ** * *
31684521 TCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACCAAG
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGACGA-CAAA
* * * * * * * * *
31684565 CCTTGTCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGA-TAGCAGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGA-CAAA
* *
31684609 TATTATCTCCCTAAGCAGTAGTGCAGCAGATCGAAGACGACAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAA
* ** * *
31684653 TCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTTAAG-CCACTAAG
1 TCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATCGAAGACGAC-AAA
* * * * * * * *
31684697 CCTTGTCTCCCTGAA-CAGCAGTGGAGTAGGTTGAAGA-TAGCAGA
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGACGA-CAAA
* *
31684741 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGACAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAA
31684785 TCTTATCT
1 TCTTATCT
31684793 TTCCAAGATA
Statistics
Matches: 195, Mismatches: 56, Indels: 42
0.67 0.19 0.14
Matches are distributed among these distances:
42 8 0.04
43 18 0.09
44 145 0.74
45 17 0.09
46 7 0.04
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAA
Found at i:31684882 original size:132 final size:132
Alignment explanation
Indices: 31684477--31684884 Score: 647
Period size: 132 Copynumber: 3.1 Consensus size: 132
31684467 AAATTACAGG
* * * * *
31684477 TCTTGTCTCCCTAAACAGTAGTGGAGAAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAGTG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
* *
31684542 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTTCCTGAGCAGTAGTGGAGTAGGTTGAAGATAGCA
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
31684607 GA
131 GA
* *
31684609 TATTATCTCCCTAAGCAGTAGTGCAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
* *
31684674 GGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAGATAGCA
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
31684739 GA
131 GA
* *
31684741 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
* *
31684806 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAACAGCGGAGTAGGTTGAAGATTA-C
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGA-TAGC
*
31684870 AAA
130 AGA
*
31684873 TCCTATCTCCCT
1 TCTTATCTCCCT
31684885 GAAGTTGCAG
Statistics
Matches: 252, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
132 250 0.99
133 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (132 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTG
GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
GA
Found at i:31688033 original size:26 final size:26
Alignment explanation
Indices: 31687989--31688045 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
31687979 GCGACTCTCG
*
31687989 TTTCCTTTTTCAAAATCGATAT-CCAT
1 TTTCATTTTTCAAAATCGAT-TCCCAT
31688015 TTTCATTTTT-AAAAGTCGATTCCCAT
1 TTTCATTTTTCAAAA-TCGATTCCCAT
31688041 TTTCA
1 TTTCA
31688046 AACTTATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 5 0.18
26 23 0.82
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTCATTTTTCAAAATCGATTCCCAT
Found at i:31692380 original size:15 final size:16
Alignment explanation
Indices: 31692362--31692394 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31692352 TCTCATATTT
*
31692362 TTCTTTA-TTTTTTTA
1 TTCTTTACTCTTTTTA
31692377 TTCTTTACTCTTTTTA
1 TTCTTTACTCTTTTTA
31692393 TT
1 TT
31692395 TCTCTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTACTCTTTTTA
Found at i:31698493 original size:6 final size:6
Alignment explanation
Indices: 31698482--31698550 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
31698472 TATAAAAATA
31698482 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
31698530 TTATAT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTA
31698551 ATCAATAACC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:31703288 original size:15 final size:16
Alignment explanation
Indices: 31703258--31703289 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
31703248 CAAATAGGTT
31703258 TAGTGCATTATTTTTTA
1 TAGTGCATTA-TTTTTA
31703275 TAGTGCATTATTTTT
1 TAGTGCATTATTTTT
31703290 GAACGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (16 bp):
TAGTGCATTATTTTTA
Found at i:31709084 original size:19 final size:18
Alignment explanation
Indices: 31709060--31709105 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31709050 TAAAAAATCT
*
31709060 AAAAAAATTTAAAGAATAC
1 AAAAAAATTTAAA-AATAA
* *
31709079 ATAAAAACTTAAAAATAA
1 AAAAAAATTTAAAAATAA
31709097 AAAAAAATT
1 AAAAAAATT
31709106 GGAGACCTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAAAATTTAAAAATAA
Found at i:31709102 original size:18 final size:19
Alignment explanation
Indices: 31709060--31709103 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
31709050 TAAAAAATCT
* *
31709060 AAAAAAATTTAAAGAATAC
1 AAAAAAACTTAAAGAATAA
*
31709079 ATAAAAACTTAAA-AATAA
1 AAAAAAACTTAAAGAATAA
31709097 AAAAAAA
1 AAAAAAA
31709104 TTGGAGACCT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAAAACTTAAAGAATAA
Found at i:31717719 original size:20 final size:21
Alignment explanation
Indices: 31717694--31717741 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31717684 GTTTCATTCA
*
31717694 AACCCTAGGTT-AAACATGCG
1 AACCCTAGATTCAAACATGCG
*
31717714 AACCCTAGATTCAAATATGCG
1 AACCCTAGATTCAAACATGCG
31717735 AACCCTA
1 AACCCTA
31717742 TATATGTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (21 bp):
AACCCTAGATTCAAACATGCG
Found at i:31717789 original size:22 final size:22
Alignment explanation
Indices: 31717764--31717806 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31717754 GTGAATTCTA
* *
31717764 TATATGTGTTATATGCAAACCC
1 TATATATGATATATGCAAACCC
31717786 TATATATGATATATGCAAACC
1 TATATATGATATATGCAAACC
31717807 ATTGTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
TATATATGATATATGCAAACCC
Found at i:31732648 original size:14 final size:14
Alignment explanation
Indices: 31732628--31732660 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
31732618 CATCATTTCG
31732628 CTATTATATTGCTA
1 CTATTATATTGCTA
*
31732642 TTATTATATTGCTA
1 CTATTATATTGCTA
31732656 CTATT
1 CTATT
31732661 TTGTTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (14 bp):
CTATTATATTGCTA
Found at i:31733579 original size:15 final size:17
Alignment explanation
Indices: 31733561--31733592 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
31733551 TTAATTTATG
31733561 TTATC-TTATT-TATTT
1 TTATCATTATTCTATTT
31733576 TTATCATTATTCTATTT
1 TTATCATTATTCTATTT
31733593 ACGTTTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATCATTATTCTATTT
Found at i:31738389 original size:28 final size:28
Alignment explanation
Indices: 31738354--31738410 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
31738344 AATTTAAAAG
31738354 TAAAAAGAAATCTAAATAGGTAAATACA
1 TAAAAAGAAATCTAAATAGGTAAATACA
31738382 TAAAAAGAAATCTAAATAGGTAAATACA
1 TAAAAAGAAATCTAAATAGGTAAATACA
31738410 T
1 T
31738411 CTAATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.23
Consensus pattern (28 bp):
TAAAAAGAAATCTAAATAGGTAAATACA
Found at i:31738406 original size:14 final size:14
Alignment explanation
Indices: 31738361--31738406 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
31738351 AAGTAAAAAG
31738361 AAATCTAAATAGGT
1 AAATCTAAATAGGT
*
31738375 AAATACATAAA-AAG-
1 AAAT-C-TAAATAGGT
31738389 AAATCTAAATAGGT
1 AAATCTAAATAGGT
31738403 AAAT
1 AAAT
31738407 ACATCTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 4 0.15
13 3 0.12
14 12 0.46
15 3 0.12
16 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.24
Consensus pattern (14 bp):
AAATCTAAATAGGT
Found at i:31744210 original size:27 final size:27
Alignment explanation
Indices: 31744180--31744250 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
31744170 GAGTTCACTA
* *
31744180 GGACAGTAAAAACAAAATAGTTTGCCG
1 GGACAGTAAACACAAAATAGTTCGCCG
* * **
31744207 GGACAATAAACACAAGATAGTTCGTTG
1 GGACAGTAAACACAAAATAGTTCGCCG
31744234 GGACAGTAAACACAAAA
1 GGACAGTAAACACAAAA
31744251 ATGTCTGCCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (27 bp):
GGACAGTAAACACAAAATAGTTCGCCG
Found at i:31748427 original size:9 final size:9
Alignment explanation
Indices: 31748413--31748500 Score: 140
Period size: 9 Copynumber: 9.8 Consensus size: 9
31748403 TTTGGTTAAA
31748413 AATTACCCG
1 AATTACCCG
31748422 AATTACCCG
1 AATTACCCG
31748431 AATTACCCG
1 AATTACCCG
31748440 AATTACCCG
1 AATTACCCG
31748449 AATTACCCG
1 AATTACCCG
31748458 AATTACCCG
1 AATTACCCG
* *
31748467 AATTAACTG
1 AATTACCCG
*
31748476 AATTAACCG
1 AATTACCCG
*
31748485 AATTAACCG
1 AATTACCCG
31748494 AATTACC
1 AATTACC
31748501 GAAAAATACT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 75 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTACCCG
Found at i:31749837 original size:34 final size:34
Alignment explanation
Indices: 31749784--31749871 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
31749774 TAGGTACCAT
* * * * * *
31749784 AGCACATCCCTCCAACACAATCAGACTGCACATC
1 AGCATATCCATCCCACACAACCAAACTGCACATA
** *
31749818 AGTGTATCCATCCCACACAACCAAATTGCACATA
1 AGCATATCCATCCCACACAACCAAACTGCACATA
31749852 AGCATATCCATCCCACACAA
1 AGCATATCCATCCCACACAA
31749872 GTAGATAGCA
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.17
Consensus pattern (34 bp):
AGCATATCCATCCCACACAACCAAACTGCACATA
Found at i:31762061 original size:28 final size:28
Alignment explanation
Indices: 31762030--31762094 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 28
31762020 ACACAAAAAA
31762030 GCCCTTTTTTAAAAAATTACCGAAATGG
1 GCCCTTTTTTAAAAAATTACCGAAATGG
* * * * *
31762058 GCCCGTTATTTAAATATTTACTGGAATGG
1 GCCC-TTTTTTAAAAAATTACCGAAATGG
*
31762087 GCCATTTT
1 GCCCTTTT
31762095 CGGTAAATCA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (28 bp):
GCCCTTTTTTAAAAAATTACCGAAATGG
Found at i:31762447 original size:125 final size:126
Alignment explanation
Indices: 31762218--31762582 Score: 522
Period size: 125 Copynumber: 2.9 Consensus size: 126
31762208 GTCTTGGAAG
* *
31762218 AATTAATTTTGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTTTAGCAGGATGCTTTAT
1 AATT-ATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCTTTAT
* * * *
31762282 GAGAAGAATTTGTTAAATCGCGTCCACATGGTCGCGCTTTTGCTACAGTAGGTCCT-GAAAA
65 GAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAA
* * *
31762343 AATTATTTCGAGTTGACGTTTCTAAGCAAATAGTATAAAAAACGCTTCAAGCAGGATGCTATT-T
1 AATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCT-TTAT
* * * * * *
31762407 GAGAAGAATTTGTGAAATCGAGCCCTCGTGGACGCACTTTTGCTACATTTGGTCCTGGAAGA
65 GAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAA
* * *
31762469 AATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATA-GCTTCTACCAGGATGCTTTATG
1 AATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCTTTATG
31762533 AGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
66 AGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAG
31762583 CATGTTTGGG
Statistics
Matches: 210, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
124 32 0.15
125 134 0.64
126 44 0.21
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (126 bp):
AATTATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCTAGCAGGATGCTTTATG
AGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTAGGTCCTGGAAAA
Found at i:31766904 original size:7 final size:7
Alignment explanation
Indices: 31766894--31766926 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31766884 TTATATACAT
31766894 AATACTA
1 AATACTA
31766901 AATACTA
1 AATACTA
31766908 AATACTA
1 AATACTA
31766915 AATACTA
1 AATACTA
31766922 AATAC
1 AATAC
31766927 CAATCGACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:31767133 original size:20 final size:20
Alignment explanation
Indices: 31767096--31767133 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31767086 TTTATTTTTA
*
31767096 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
31767116 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
31767134 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:31768173 original size:11 final size:11
Alignment explanation
Indices: 31768159--31768235 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
31768149 TTAAATATGG
31768159 ATTTGAGAGAA
1 ATTTGAGAGAA
*
31768170 ATTTG-GAAGGA
1 ATTTGAG-AGAA
31768181 ATTTGAGAGCAA
1 ATTTGAGAG-AA
31768193 A-TTGAGAGAAA
1 ATTTGAGAG-AA
31768204 ATTT-AGAGGAA
1 ATTTGAGA-GAA
31768215 A-TTGAGAGGAA
1 ATTTGAGA-GAA
31768226 ATTTGAGAGA
1 ATTTGAGAGA
31768236 GGATTAGTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.05
11 41 0.73
12 12 0.21
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:31768203 original size:33 final size:33
Alignment explanation
Indices: 31768159--31768235 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
31768149 TTAAATATGG
* *
31768159 ATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAG-AGGAAATTGAGAGCAA
*
31768193 A-TTGAGAGAAAATTTAGAGGAAATTGAGAGGAA
1 ATTTGAGAG-AAATTTAGAGGAAATTGAGAGCAA
31768226 ATTTGAGAGA
1 ATTTGAGAGA
31768236 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAGGAAATTGAGAGCAA
Found at i:31768216 original size:22 final size:23
Alignment explanation
Indices: 31768180--31768234 Score: 85
Period size: 22 Copynumber: 2.4 Consensus size: 23
31768170 ATTTGGAAGG
31768180 AATTTGAGAGCAAATTGAGAGAA
1 AATTTGAGAGCAAATTGAGAGAA
* *
31768203 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGAA
31768225 AATTTGAGAG
1 AATTTGAGAG
31768235 AGGATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
23 9 0.31
ACGTcount: A:0.45, C:0.02, G:0.29, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGAA
Found at i:31771328 original size:73 final size:73
Alignment explanation
Indices: 31771201--31771363 Score: 258
Period size: 73 Copynumber: 2.2 Consensus size: 73
31771191 TACAAAAGAT
* * * *
31771201 TGGCATTAGCGGCCCTTCTGTTAAACGCCGCAAAAAATTAAATCCAAACGCATCGTTTTGATTTG
1 TGGCATTAGCGGCGCTTCTGTAAAACGCCGCAAAAAATTAAATCAAAACACATCGTTTTGATTTG
31771266 AGATGTAG
66 AGATGTAG
31771274 TGGCATTAGCGGCGCTTCTGTAAAAGCGCCGCAAAAAGA-T-AATCAAAACACATCGTTTTGATT
1 TGGCATTAGCGGCGCTTCTGTAAAA-CGCCGCAAAAA-ATTAAATCAAAACACATCGTTTTGATT
31771337 TGAGATGTAG
64 TGAGATGTAG
31771347 TGGCATTAGCGGCGCTT
1 TGGCATTAGCGGCGCTT
31771364 TTTCGTAAAA
Statistics
Matches: 84, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
73 71 0.85
74 12 0.14
75 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (73 bp):
TGGCATTAGCGGCGCTTCTGTAAAACGCCGCAAAAAATTAAATCAAAACACATCGTTTTGATTTG
AGATGTAG
Found at i:31771940 original size:21 final size:22
Alignment explanation
Indices: 31771910--31771957 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
31771900 GGTGTTTGTG
31771910 GTTTACGGGTTTA-ATGTTTACA
1 GTTTACGGGTTTACA-GTTTACA
*
31771932 GTTTA-GGGTTTACAGTTTATA
1 GTTTACGGGTTTACAGTTTACA
31771953 GTTTA
1 GTTTA
31771958 TGATTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (22 bp):
GTTTACGGGTTTACAGTTTACA
Found at i:31771964 original size:21 final size:21
Alignment explanation
Indices: 31771925--31771964 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
31771915 CGGGTTTAAT
*
31771925 GTTTACAGTTTAGGGTTTACA
1 GTTTACAGTTTAGGATTTACA
* *
31771946 GTTTATAGTTTATGATTTA
1 GTTTACAGTTTAGGATTTA
31771965 GGGTTTAAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (21 bp):
GTTTACAGTTTAGGATTTACA
Found at i:31772481 original size:147 final size:145
Alignment explanation
Indices: 31772275--31772681 Score: 401
Period size: 147 Copynumber: 2.8 Consensus size: 145
31772265 TTCAAAATTT
* * * * *
31772275 CCATGTTCTTAGTGGCGTTTTATGCAAAAACGCCACAAAATTGTCCTAATTATCG-GGGAAACGA
1 CCATATTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTGTCCTAATTGT-GTGGGAAACGA
*
31772339 CAGCGTTTCACGGTTATTTAGTGGCGCATACGTATAAACGCCACAAACGGGTTAATTTAATCCCA
65 C-GCGTTTCACGGTTATTTAGTGGCGCATACGTATAAACGCCGCAAACGGGTTAATTTAAT--CA
31772404 -AAAAACGACATCGTATTA
127 TAAAAACGACATCGTATTA
* * *
31772422 CTATATTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATT-TACATAATTGTGTGGGAAATGA
1 CCATATTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTGT-CCTAATTGTGTGGGAAACGA
* * * * * *
31772486 CGTCGTTTCTGCGGTTATTTAGTGGCGCA-A-GATTATAAACGTCGCGAATGGGTTCATTTAGTC
65 CG-CGTTTC-ACGGTTATTTAGTGGCGCATACG--TATAAACGCCGCAAACGGGTTAATTTAATC
* * * * * *
31772549 ATGAATACGTCGTCGTTTTT
126 ATAAAAACGACATCGTATTA
* * * * *
31772569 CCATGTTCTTAGTGGCGTTTTATACCAAAATGCCAGAATGTTGTCCTAATTGTTTGGGAAACGAC
1 CCATATTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTGTCCTAATTGTGTGGGAAACGAC
* * * *
31772634 TTCGTTTCCATGGTTAATTTAGTGGCGCTTACGTGTAAACGCCGCAAA
66 -GCGTTT-CACGGTT-ATTTAGTGGCGCATACGTATAAACGCCGCAAA
31772682 GTTCTTCGTT
Statistics
Matches: 211, Mismatches: 36, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
146 6 0.03
147 136 0.64
148 67 0.32
149 1 0.00
150 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (145 bp):
CCATATTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTGTCCTAATTGTGTGGGAAACGAC
GCGTTTCACGGTTATTTAGTGGCGCATACGTATAAACGCCGCAAACGGGTTAATTTAATCATAAA
AACGACATCGTATTA
Found at i:31773033 original size:292 final size:295
Alignment explanation
Indices: 31772519--31773049 Score: 721
Period size: 292 Copynumber: 1.8 Consensus size: 295
31772509 GGCGCAAGAT
* * ** * * **
31772519 TATAAACGTCGCGAATGGGTTCATTTAGTCATGAATACGTCGTCGTTTTTCCATGTTCTTAGTGG
1 TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
* * * * *
31772584 CGTTTTATACCAAAATGCCAGAATGTTGTCCTAATTGTTTGGGAAACGACTTCGTTTCCATGGTT
66 CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTT
* * *
31772649 AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTCGTTTAGTCATGGAAAATGTCGTCAT
131 AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCAT
* * * * * *
31772714 TTTTCCATGTTGTGATTGGCATTTTATGCCTAAATGCCACAATTTTGACTAACTGGCTGTTAAAA
196 TTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTTTGACTAACTGGCTGTTAAAA
31772779 GACAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
261 GACAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
* *
31772814 TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTTGTTTTACTA-GTTAGTAGTGG
1 TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
* **
31772878 CGTTTTATACCAAAACGCCAGAAAT-TTGTCGTAAGTGTTT-GGAAACGACATCATTTCTGGGGT
66 CGTTTTATACCAAAACGCCAG-AATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGT
* * *
31772941 T-ATTTAGTGGCGCTTATGTAG-AAACGCCGCAAATTTGTTAGTTTAGTCAAGGAAAACGTCGTC
130 TAATTTAGTGGCGCTTACGT-GTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTC
* *
31773004 GTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATT
194 ATTTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATT
31773050 AAGACTGTCT
Statistics
Matches: 202, Mismatches: 32, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
292 92 0.46
293 20 0.10
294 42 0.21
295 48 0.24
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.36
Consensus pattern (295 bp):
TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTT
AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCAT
TTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTTTGACTAACTGGCTGTTAAAA
GACAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
Found at i:31773097 original size:292 final size:294
Alignment explanation
Indices: 31772519--31773117 Score: 690
Period size: 292 Copynumber: 2.0 Consensus size: 294
31772509 GGCGCAAGAT
* * ** * * **
31772519 TATAAACGTCGCGAATGGGTTCATTTAGTCATGAATACGTCGTCGTTTTTCCATGTTCTTAGTGG
1 TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
* * * * *
31772584 CGTTTTATACCAAAATGCCAGAATGTTGTCCTAATTGTTTGGGAAACGACTTCGTTTCCATGGTT
66 CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTT
* * *
31772649 AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTCGTTTAGTCATGGAAAATGTCGTCAT
131 AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCAT
* * * * * * ** *
31772714 TTTTCCATGTTGTGATTGGCATTTTATGCCTAAATGCCACAATTTTGACTAACTGGCTGTTAAAA
196 TTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTAAGACTAACTGGCTCTTAAAA
** *
31772779 GACAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
261 GACAGCGTTTC-ACTGATAGTTTGTGGCACTTGTG
* *
31772814 TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTTGTTTTACTA-GTTAGTAGTGG
1 TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
* **
31772878 CGTTTTATACCAAAACGCCAGAAAT-TTGTCGTAAGTGTTT-GGAAACGACATCATTTCTGGGGT
66 CGTTTTATACCAAAACGCCAG-AATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGT
* * *
31772941 T-ATTTAGTGGCGCTTATGTAG-AAACGCCGCAAATTTGTTAGTTTAGTCAAGGAAAACGTCGTC
130 TAATTTAGTGGCGCTTACGT-GTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTC
* * **
31773004 GTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATTAAGACTGTCT-GCTACTTA
194 ATTTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTAAGACTAACTGGCT-CTTA
* ** * *
31773068 AATGACTTCGTTTC-CGTGGATATTTTGTGGCACTTGTT
258 AAAGACAGCGTTTCAC-T-GATAGTTTGTGGCACTTGTG
31773106 TATAAACGCCGC
1 TATAAACGCCGC
31773118 TACCAGTGGG
Statistics
Matches: 254, Mismatches: 45, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
290 1 0.00
291 4 0.02
292 139 0.55
293 20 0.08
294 42 0.17
295 48 0.19
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (294 bp):
TATAAACGCCGCAAATGGGTAAATTTAGTCAGGAATACGTCGTCGTTTTACCATGTTAGTAGTGG
CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCATTTCCAGGGTT
AATTTAGTGGCGCTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCAAGGAAAACGTCGTCAT
TTTTCAATGTTATGAGTGGCATTTTATGCCAAAACGCCAAAATTAAGACTAACTGGCTCTTAAAA
GACAGCGTTTCACTGATAGTTTGTGGCACTTGTG
Found at i:31773098 original size:147 final size:145
Alignment explanation
Indices: 31772635--31773117 Score: 347
Period size: 147 Copynumber: 3.3 Consensus size: 145
31772625 GGAAACGACT
* * * * * *
31772635 TCGTTTCCATGGTTAATTTAGTGGCGCTTACGT-GTAAACGCCGCAAAGTTCTTCGTTTAGTCAT
1 TCGTTTCCGTGGTT-ATTTAGTGGCGCTTATGTAG-AAACGCCGCAAATTTGTTAGTTTAGTCAA
* * * * * * * * *
31772699 GGAAAATGTCGTCATTTTTCCATGTTGTGATTGGCATTTTATGCCTAAATGCCACAATTTTGACT
64 GGAAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCA-AAATTTGACT
** *
31772764 AACTGGCTGTTAAAAGACA
128 GTCT-GCTCTTAAAAGACA
* * * * ** * *
31772783 GCGTTTCTAC-T-TTTAGTTT-GTGGCGCTTGTGTATAAACGCCGCAAATGGGTAAATTTAGTC-
1 TCGTTTC--CGTGGTTA-TTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCA
* * * * * *
31772844 AGGAATACGTCGTTGTTTTACTA-GTTA-GTAGTGGCGTTTTATACCAAAACGCCAGAAATTTGT
63 AGGAAAACGTCGTCGTTTTTCAATGTTATG-AGTGGCGTTTTATGCCAAAACGCCA-AAATTTGA
* *
31772907 C-GTAAGTG-T-TTGGAAACGACA
126 CTGT--CTGCTCTT--AAAAGACA
* * *
31772928 TCATTTCTGGGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCAAGG
1 TCGTTTCCGTGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCAAGG
*
31772993 AAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATTAAGACTGT
66 AAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATT-TGACTGT
* *
31773058 CTGCTACTTAAATGACT
130 CTGCT-CTTAAAAGACA
* * * * * *
31773075 TCGTTTCCGTGGATATTTTGTGGCACTTGTTTATAAACGCCGC
1 TCGTTTCCGTGGTTATTTAGTGGCGCTTATGTAGAAACGCCGC
31773118 TACCAGTGGG
Statistics
Matches: 253, Mismatches: 62, Indels: 41
0.71 0.17 0.12
Matches are distributed among these distances:
143 2 0.01
144 5 0.02
145 82 0.32
146 43 0.17
147 103 0.41
148 14 0.06
149 3 0.01
150 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (145 bp):
TCGTTTCCGTGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTTAGTTTAGTCAAGG
AAAACGTCGTCGTTTTTCAATGTTATGAGTGGCGTTTTATGCCAAAACGCCAAAATTTGACTGTC
TGCTCTTAAAAGACA
Found at i:31773586 original size:14 final size:14
Alignment explanation
Indices: 31773567--31773596 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31773557 TGTGGAATAT
*
31773567 TTCAGATTTTTTTA
1 TTCAGATTTTGTTA
31773581 TTCAGATTTTGTTA
1 TTCAGATTTTGTTA
31773595 TT
1 TT
31773597 TGGGTTTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (14 bp):
TTCAGATTTTGTTA
Found at i:31773612 original size:11 final size:11
Alignment explanation
Indices: 31773596--31773620 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31773586 ATTTTGTTAT
31773596 TTGGGTTTCTG
1 TTGGGTTTCTG
31773607 TTGGGTTTCTG
1 TTGGGTTTCTG
31773618 TTG
1 TTG
31773621 AATTTTGACT
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:0.00, C:0.08, G:0.36, T:0.56
Consensus pattern (11 bp):
TTGGGTTTCTG
Found at i:31774760 original size:69 final size:69
Alignment explanation
Indices: 31774687--31774828 Score: 230
Period size: 69 Copynumber: 2.1 Consensus size: 69
31774677 AAATTTTATT
* * * *
31774687 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTTTAAATATTAAAACCTATAT
1 AATAATAAATTGTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
31774752 TTTC
66 TTTC
*
31774756 AATAATAAATTGTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAACACCTATAT
1 AATAATAAATTGTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
*
31774821 TTTT
66 TTTC
31774825 AATA
1 AATA
31774829 TATCACCCCA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (69 bp):
AATAATAAATTGTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
TTTC
Found at i:31774949 original size:9 final size:9
Alignment explanation
Indices: 31774935--31775184 Score: 135
Period size: 9 Copynumber: 27.2 Consensus size: 9
31774925 ACTTACGTAA
31774935 TACATAACT
1 TACATAACT
31774944 TACATAATAACT
1 TAC---ATAACT
31774956 TACATAACT
1 TACATAACT
*
31774965 TATATAGAAACTT
1 TACAT---AAC-T
*
31774978 ATATATAAACT
1 -TACAT-AACT
*
31774989 TGCATAACT
1 TACATAACT
31774998 TACATAA--
1 TACATAACT
* * *
31775005 TATATAGCC
1 TACATAACT
*
31775014 TACATAAAT
1 TACATAACT
*
31775023 TGCATAACT
1 TACATAACT
*
31775032 CACATAA--
1 TACATAACT
*
31775039 TACACAACT
1 TACATAACT
31775048 TACATAACT
1 TACATAACT
*
31775057 TAAATAACT
1 TACATAACT
31775066 TACATAA--
1 TACATAACT
31775073 TACATAACT
1 TACATAACT
*
31775082 TACATTAATAT
1 TACA-TAA-CT
31775093 TAGACATAACT
1 T--ACATAACT
31775104 TACATAACT
1 TACATAACT
31775113 TAC--AACT
1 TACATAACT
31775120 TACATAACT
1 TACATAACT
*
31775129 TA-ATTACAT
1 TACATAAC-T
*
31775138 TATATACAACT
1 TACAT--AACT
*
31775149 TACATAACA
1 TACATAACT
31775158 TACATAA--
1 TACATAACT
*
31775165 TATATAACT
1 TACATAACT
31775174 TACATAACT
1 TACATAACT
31775183 TA
1 TA
31775185 TATATAAACT
Statistics
Matches: 188, Mismatches: 27, Indels: 52
0.70 0.10 0.19
Matches are distributed among these distances:
7 30 0.16
8 4 0.02
9 106 0.56
10 8 0.04
11 10 0.05
12 21 0.11
13 4 0.02
14 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:31775030 original size:34 final size:34
Alignment explanation
Indices: 31774924--31775126 Score: 148
Period size: 34 Copynumber: 5.8 Consensus size: 34
31774914 CTTATATATA
* *
31774924 AACTTACGTAATACATAACTTACATAATAACTTACAT
1 AACTTACATAATACATAACTTACAT-A-AA-TTGCAT
* *
31774961 AACTT--AT-ATAGA-AACTTATATATAAACTTGCAT
1 AACTTACATAATACATAAC-T-TACATAAA-TTGCAT
* * *
31774994 AACTTACATAATATATAGCCTACATAAATTGCAT
1 AACTTACATAATACATAACTTACATAAATTGCAT
* * * **
31775028 AACTCACATAATACACAACTTACATAACTTAAAT
1 AACTTACATAATACATAACTTACATAAATTGCAT
31775062 AACTTACATAATACATAACTTACATTAATATTAGACAT
1 AACTTACATAATACATAACTTACA-TAA-ATT-G-CAT
31775100 AACTTACATAACTTAC--AACTTACATAA
1 AACTTACATAA--TACATAACTTACATAA
31775127 CTTAATTACA
Statistics
Matches: 133, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
33 16 0.12
34 60 0.45
35 17 0.13
36 6 0.05
37 10 0.08
38 21 0.16
40 3 0.02
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (34 bp):
AACTTACATAATACATAACTTACATAAATTGCAT
Found at i:31775130 original size:25 final size:25
Alignment explanation
Indices: 31774985--31775130 Score: 53
Period size: 25 Copynumber: 6.0 Consensus size: 25
31774975 CTTATATATA
* *
31774985 AACTTGCATAACTTACATAA-TATAT
1 AACTTACATAACTTACATAACT-TAC
* * * * *
31775010 AGCCTACATAAATTGCATAACTCAC
1 AACTTACATAACTTACATAACTTAC
* * *
31775035 ATA-ATACACAACTTACATAACTTAAAT
1 A-ACTTACATAACTTACATAACTT--AC
31775062 AACTTACATAA--TACATAACTTAC
1 AACTTACATAACTTACATAACTTAC
31775085 -A-TTA-AT-A-TTAGACATAACTTAC
1 AACTTACATAACTT--ACATAACTTAC
31775107 ATAACTTAC--AACTTACATAACTTA
1 --AACTTACATAACTTACATAACTTA
31775131 ATTACATTAT
Statistics
Matches: 89, Mismatches: 17, Indels: 30
0.65 0.12 0.22
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 3 0.03
22 12 0.13
23 1 0.01
25 53 0.60
26 6 0.07
27 10 0.11
ACGTcount: A:0.46, C:0.20, G:0.03, T:0.32
Consensus pattern (25 bp):
AACTTACATAACTTACATAACTTAC
Found at i:31775161 original size:25 final size:25
Alignment explanation
Indices: 31775096--31775201 Score: 96
Period size: 25 Copynumber: 4.2 Consensus size: 25
31775086 TTAATATTAG
*
31775096 ACATAACTTACATAACT-TACAACTT
1 ACATAACATACATAA-TATACAACTT
*
31775121 ACATAACTTAATTACATTATATACAACTT
1 ACATAAC---A-TACATAATATACAACTT
*
31775150 ACATAACATACATAATATATAACTT
1 ACATAACATACATAATATACAACTT
*
31775175 ACATAAC-T-TAT-ATATA-AACTT
1 ACATAACATACATAATATACAACTT
31775196 ACATAA
1 ACATAA
31775202 TTTACTTAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
21 11 0.15
22 5 0.07
23 2 0.03
24 1 0.01
25 29 0.41
26 1 0.01
28 1 0.01
29 21 0.30
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (25 bp):
ACATAACATACATAATATACAACTT
Found at i:31775186 original size:16 final size:17
Alignment explanation
Indices: 31775044--31775184 Score: 94
Period size: 16 Copynumber: 7.9 Consensus size: 17
31775034 CATAATACAC
31775044 AACTTACATAACTTAAAT
1 AACTTACATAACTT-AAT
31775062 AACTTACATAA--TACAT
1 AACTTACATAACTTA-AT
*
31775078 AACTTACATTAATATTAGACAT
1 AACTTACA-TAA-CTT--A-AT
*
31775100 AACTTACATAACTT-AC
1 AACTTACATAACTTAAT
31775116 AACTTACATAACTTAAT
1 AACTTACATAACTTAAT
* *
31775133 TACATTATATACAACTTACAT
1 AAC-TTACAT--AACTTA-AT
*
31775154 AACATACATAA--TATAT
1 AACTTACATAACTTA-AT
31775170 AACTTACATAACTTA
1 AACTTACATAACTTA
31775185 TATATAAACT
Statistics
Matches: 99, Mismatches: 10, Indels: 28
0.72 0.07 0.20
Matches are distributed among these distances:
15 1 0.01
16 40 0.40
17 6 0.06
18 20 0.20
20 13 0.13
21 7 0.07
22 12 0.12
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (17 bp):
AACTTACATAACTTAAT
Found at i:31780738 original size:21 final size:21
Alignment explanation
Indices: 31780712--31780760 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31780702 ACAACTTAAG
*
31780712 GCAGAGGCGGCAGCGAGGGAA
1 GCAGAGGCGGCAGCGAGAGAA
* *
31780733 GCAGAGGCTGCAGTGAGAGAA
1 GCAGAGGCGGCAGCGAGAGAA
*
31780754 GTAGAGG
1 GCAGAGG
31780761 TTCAAGCTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.14, G:0.49, T:0.06
Consensus pattern (21 bp):
GCAGAGGCGGCAGCGAGAGAA
Found at i:31780999 original size:26 final size:26
Alignment explanation
Indices: 31780978--31781035 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
31780968 GAATTACATC
*
31780978 TTATTTATTT-ATATTTATATTATATA
1 TTATTCATTTAAT-TTTATATTATATA
*
31781004 TTATTCGTTTAATTTTATATTATATA
1 TTATTCATTTAATTTTATATTATATA
31781030 TTATTC
1 TTATTC
31781036 GGTTAGTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.93
27 2 0.07
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (26 bp):
TTATTCATTTAATTTTATATTATATA
Found at i:31781204 original size:43 final size:43
Alignment explanation
Indices: 31781157--31781426 Score: 353
Period size: 43 Copynumber: 6.3 Consensus size: 43
31781147 GTTAAAAGTT
* * *
31781157 ATGGCCTATAGCGGCGTTTGTGGGAAAACCGCTGCTAAAGGTC
1 ATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC
*
31781200 ATGGCCTATAGCGGCGTTTGTGGGAGAAA-CGCCGCTAAAGGTC
1 ATGGCCTATAGCGGCGTTTGTGGGA-AAAGCGCCGCTAAAGATC
* *
31781243 ATGGCCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTC
1 ATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC
* *
31781286 ATGGCCTATAACGGCATTTGTGGGAAAAGCGCCGCTAAAGATC
1 ATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC
* *
31781329 ATGGTCTATAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGATC
1 ATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC
* * * * * * *
31781372 ATAGTCTATAGCGGTGTTTGTAGGAGAAGCACTGCTAAAGATC
1 ATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC
**
31781415 ATGTTCTATAGC
1 ATGGCCTATAGC
31781427 AGTGTTTATT
Statistics
Matches: 206, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
42 3 0.01
43 200 0.97
44 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (43 bp):
ATGGCCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATC
Found at i:31788064 original size:19 final size:20
Alignment explanation
Indices: 31787989--31788085 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 20
31787979 TCATTATATA
*
31787989 TTATTTAGAATTTTTAAAAT
1 TTATTTTGAATTTTTAAAAT
*
31788009 TT-TTAT-AATTTTTTTAAAAAT
1 TTATTTTGAA--TTTTT-AAAAT
* *
31788030 ATAAGTTTTGGAATTTTTATAA-
1 -TTA-TTTT-GAATTTTTAAAAT
31788052 TTATTTTGAA-TTTTAAAAT
1 TTATTTTGAATTTTTAAAAT
31788071 TTATTTTGAATTTTT
1 TTATTTTGAATTTTT
31788086 TTGTAATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
18 9 0.15
19 15 0.25
20 15 0.25
21 7 0.12
22 1 0.02
23 3 0.05
24 8 0.13
26 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
TTATTTTGAATTTTTAAAAT
Found at i:31790987 original size:51 final size:50
Alignment explanation
Indices: 31790905--31791182 Score: 287
Period size: 51 Copynumber: 5.5 Consensus size: 50
31790895 GATGAACACG
31790905 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA-AAACT-ATGGTCACA
* * * *
31790956 TGTGTAGTACTAAT-TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
1 TGTGTAGTACT-ATGTGAAGGCTACTACGTGTATCGAAAA-CTATGGTCACA
* * * *
31791007 TGTGTAGTACTGTGTGAAGGTTACTACGTGAATCGGTAAA-TGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GAAAACT-ATGGTCACA
* * * *
31791058 TGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CTGAAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GAAAA-CTATGGTCACA
* * * *
31791109 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACT-TGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-AAAACTATGGTCACA
*
31791159 TATGTAGTACTATGTGAAGGCTAC
1 TGTGTAGTACTATGTGAAGGCTAC
31791183 ACTACACCAA
Statistics
Matches: 191, Mismatches: 26, Indels: 21
0.80 0.11 0.09
Matches are distributed among these distances:
50 40 0.21
51 138 0.72
52 13 0.07
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAACTATGGTCACA
Found at i:31791081 original size:102 final size:102
Alignment explanation
Indices: 31790905--31791183 Score: 400
Period size: 102 Copynumber: 2.7 Consensus size: 102
31790895 GATGAACACG
* * *
31790905 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTACTAAG
31790970 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
66 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
* * *
31791007 TGTGTAGTACTGTGTGAAGGTTACTACGTGAATCGGTAAATGATGGTCACATGTGTAGTACTAAG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTACTAAG
* * *
31791072 TGAAGGCTACTATGTGTACTGAAAAGCTTTGGTCACG
66 TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
* * * * * *
31791109 TGTGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAA-ACTTGATCACGTATGTAGTACTAT
1 TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATA-ATGGTCACATGTGTAGTACTAA
31791172 GTGAAGGCTACA
65 GTGAAGGCTACA
31791184 CTACACCAAA
Statistics
Matches: 157, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
101 34 0.22
102 123 0.78
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTACTAAG
TGAAGGCTACAATGTGTACCGAAAAGCTTTGGTCACA
Found at i:31791432 original size:41 final size:41
Alignment explanation
Indices: 31791375--31791599 Score: 360
Period size: 41 Copynumber: 5.5 Consensus size: 41
31791365 TGAACTTTCG
31791375 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
*
31791416 GGGCTTTAGCAGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
* *
31791457 GGGATTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
* *
31791498 GGGCTTTAGCAGCGTTTTTGAAGAAGTGCCGCTAATGCTTA
1 GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
* * * *
31791539 GGGATTTAGCGGTGTTTTTTGGAGAAGCGCCGCTAATGCTTG
1 GGGCTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTTA
31791581 GGGCTTTAGCGGCGTTTTT
1 GGGCTTTAGCGGCGTTTTT
31791600 AGGGAAGCGT
Statistics
Matches: 167, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
41 131 0.78
42 36 0.22
ACGTcount: A:0.19, C:0.18, G:0.32, T:0.31
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTTA
Found at i:31792017 original size:14 final size:15
Alignment explanation
Indices: 31791984--31792017 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
31791974 TAAGGTTTAT
31791984 AGATTATGGAATTAG
1 AGATTATGGAATTAG
31791999 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
31792013 GGATT
1 AGATT
31792018 CTAGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:31792061 original size:21 final size:21
Alignment explanation
Indices: 31792027--31792068 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31792017 TCTAGTTTAA
* * *
31792027 GGGTTGTGATTTAGGGGTTAG
1 GGGTTATGAGTTAGAGGTTAG
31792048 GGGTTATGAGTTAGAGGTTAG
1 GGGTTATGAGTTAGAGGTTAG
31792069 AGATTAAGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.36
Consensus pattern (21 bp):
GGGTTATGAGTTAGAGGTTAG
Found at i:31792079 original size:21 final size:21
Alignment explanation
Indices: 31792037--31792081 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31792027 GGGTTGTGAT
* * * *
31792037 TTAGGGGTTAGGGGTTATGAG
1 TTAGAGGTTAGAGATTAAGAG
31792058 TTAGAGGTTAGAGATTAAGAG
1 TTAGAGGTTAGAGATTAAGAG
31792079 TTA
1 TTA
31792082 TAGATTTGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (21 bp):
TTAGAGGTTAGAGATTAAGAG
Found at i:31792219 original size:67 final size:68
Alignment explanation
Indices: 31792090--31792232 Score: 200
Period size: 67 Copynumber: 2.1 Consensus size: 68
31792080 TATAGATTTG
* * * *
31792090 GGGTTTAGATTAATTAGTGTGTTTTAATTTATATTAAATAAGGTTTAGGGCTTAGGGCTTA-GGG
1 GGGTTTAGATTAATCAGTGTGTTTTAAGTTATATTAAATAAGATTTAGGGCTTAGAGCTTAGGGG
31792154 TTA
66 TTA
* *
31792157 GGGTTTAGATTAATCAGTGTTTTTTAAGTTATATTAAATAAGATTTAGGGCTTTGTAG-TTAGGG
1 GGGTTTAGATTAATCAGTGTGTTTTAAGTTATATTAAATAAGATTTAGGGCTTAG-AGCTTAGGG
31792221 GTTA
65 GTTA
*
31792225 GGGGTTAG
1 GGGTTTAG
31792233 GGGTTAAGGG
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
67 53 0.79
68 14 0.21
ACGTcount: A:0.27, C:0.03, G:0.28, T:0.43
Consensus pattern (68 bp):
GGGTTTAGATTAATCAGTGTGTTTTAAGTTATATTAAATAAGATTTAGGGCTTAGAGCTTAGGGG
TTA
Found at i:31792246 original size:7 final size:7
Alignment explanation
Indices: 31792214--31792245 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31792204 GGGCTTTGTA
31792214 GTTAGGG
1 GTTAGGG
31792221 GTTAGGG
1 GTTAGGG
31792228 GTTAGGG
1 GTTAGGG
*
31792235 GTTAAGG
1 GTTAGGG
31792242 GTTA
1 GTTA
31792246 AAGGTTCAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.50, T:0.31
Consensus pattern (7 bp):
GTTAGGG
Found at i:31796806 original size:20 final size:19
Alignment explanation
Indices: 31796762--31796808 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
31796752 ATTTAAAAAA
31796762 TAAAATAAAATATTTATCAT
1 TAAAAT-AAATATTTATCAT
*
31796782 AAAAATAAATA-TTATTCGAT
1 TAAAATAAATATTTA-TC-AT
31796802 TAAAATA
1 TAAAATA
31796809 TATTATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 7 0.30
20 13 0.57
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAATAAATATTTATCAT
Found at i:31796927 original size:43 final size:42
Alignment explanation
Indices: 31796866--31796960 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 42
31796856 ATAAAATTGC
* * *
31796866 CGCTAAAGATTATGGTCTTTAACGGCGTTTGTGGGAAAAGTGT
1 CGCTAAAGGTTATGGTCTTTAACGGCGTTAGTGGG-AAAGCGT
*
31796909 CGCTAAAGGTTATGGTCTTTAGCGGCGTTAGTGGGAAAGCGT
1 CGCTAAAGGTTATGGTCTTTAACGGCGTTAGTGGGAAAGCGT
31796951 CGCTAAAGGT
1 CGCTAAAGGT
31796961 CATAATCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
42 16 0.33
43 32 0.67
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (42 bp):
CGCTAAAGGTTATGGTCTTTAACGGCGTTAGTGGGAAAGCGT
Found at i:31796970 original size:42 final size:43
Alignment explanation
Indices: 31796881--31796972 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 43
31796871 AAGATTATGG
* * * **
31796881 TCTTTAACGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTATGG
1 TCTTTAACGGCGTTAGTGGGAAAAGCGTCGCTAAAGGTCATAA
*
31796924 TCTTTAGCGGCGTTAGTGGG-AAAGCGTCGCTAAAGGTCATAA
1 TCTTTAACGGCGTTAGTGGGAAAAGCGTCGCTAAAGGTCATAA
31796966 TCTTTAA
1 TCTTTAA
31796973 AGGTCATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 24 0.57
43 18 0.43
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (43 bp):
TCTTTAACGGCGTTAGTGGGAAAAGCGTCGCTAAAGGTCATAA
Found at i:31796975 original size:16 final size:16
Alignment explanation
Indices: 31796954--31796987 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
31796944 AAAGCGTCGC
31796954 TAAAGGTCATAATCTT
1 TAAAGGTCATAATCTT
31796970 TAAAGGTCATAATCTT
1 TAAAGGTCATAATCTT
31796986 TA
1 TA
31796988 GCGGCGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (16 bp):
TAAAGGTCATAATCTT
Found at i:31797030 original size:43 final size:43
Alignment explanation
Indices: 31796969--31797160 Score: 204
Period size: 43 Copynumber: 4.7 Consensus size: 43
31796959 GTCATAATCT
* *
31796969 TTAAAGGTCATAATCTTTAGCGGCGTTTGTGGAAAAAGTGCCG
1 TTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAAAGCGCCG
* * *
31797012 TTAAAGGTCATGGTCTTTAGCAGC-------G-AAAAGCACCG
1 TTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAAAGCGCCG
* *
31797047 TTAAAGTTCATGTTCTTTAGCGGCGTTTGTGGGAAAAA-CGCCG
1 TTAAAGGTCATGATCTTTAGCGGCGTTTGT-GGAAAAAGCGCCG
* * *
31797090 TTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGCCA
1 TTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAAAGCGCCG
* *
31797133 CTAAAGGTTATGATCTTTAGCGGCGTTT
1 TTAAAGGTCATGATCTTTAGCGGCGTTT
31797161 TTTCTTGCGC
Statistics
Matches: 123, Mismatches: 16, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
35 29 0.24
36 1 0.01
42 6 0.05
43 83 0.67
44 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (43 bp):
TTAAAGGTCATGATCTTTAGCGGCGTTTGTGGAAAAAGCGCCG
Found at i:31803962 original size:51 final size:51
Alignment explanation
Indices: 31803906--31804151 Score: 266
Period size: 50 Copynumber: 4.9 Consensus size: 51
31803896 CCGAGAAGCT
* **
31803906 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATG
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * * * *
31803957 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CCG-AAAAGC
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAA-C
* *
31804007 TTTGGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAAC
1 -TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * *
31804058 TTGATCACATATGTAGTATTATGTGAAGGCTACTACGTGAATC-GTAAAAC
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * * *
31804108 TTGATCATGTGTGTAGTGCTATATGAAGGCTACTACGTGTATCG
1 TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCG
31804152 AATGATAAAA
Statistics
Matches: 165, Mismatches: 25, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
49 3 0.02
50 83 0.50
51 75 0.45
52 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (51 bp):
TTGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
Found at i:31804017 original size:102 final size:102
Alignment explanation
Indices: 31803855--31804151 Score: 357
Period size: 102 Copynumber: 2.9 Consensus size: 102
31803845 TAAGGTATCG
* * * * *
31803855 ATGAACACTTGTGTAGTACTGTGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGT
* **
31803920 AGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATG
66 AGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * *
31803957 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTATGT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGT
*
31804022 AGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAAC
66 AGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
* * * * * * * *
31804058 TTGATCACATATGTAGTATTATGTGAAGGCTACTACGTGAATCGTAAAA-C-TTGATCATGTGTG
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGTCACGTGTG
* * *
31804121 TAGTGCTATATGAAGGCTACTACGTGTATCG
65 TAGTACTATGTGAAGGCTACTACGTGAATCG
31804152 AATGATAAAA
Statistics
Matches: 166, Mismatches: 27, Indels: 5
0.84 0.14 0.03
Matches are distributed among these distances:
100 35 0.21
101 44 0.27
102 87 0.52
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGTGT
AGTACTATGTGAAGGCTACTACGTGAATCGGTAAAAC
Found at i:31804081 original size:50 final size:50
Alignment explanation
Indices: 31803866--31804146 Score: 260
Period size: 51 Copynumber: 5.6 Consensus size: 50
31803856 TGAACACTTG
* * * * * * * *
31803866 TGTAGTACTGTGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCACGTG
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACATA
* * *** * *
31803917 TGTAGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATGATGGTCACATG
1 TGTAGTACTATGTGAAGGCTACTACGTGAA-CCGTAAAACTTGATCACATA
* * * * *
31803968 TGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGTCACGTA
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGATCACATA
31804019 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
* * ** *
31804069 TGTAGTATTATGTGAAGGCTACTACGTGAATCGTAAAACTTGATCATGTG
1 TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
* *
31804119 TGTAGTGCTATATGAAGGCTACTACGTG
1 TGTAGTACTATGTGAAGGCTACTACGTG
31804147 TATCGAATGA
Statistics
Matches: 194, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
49 3 0.02
50 81 0.42
51 101 0.52
52 8 0.04
53 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACATA
Found at i:31805558 original size:26 final size:25
Alignment explanation
Indices: 31805526--31805712 Score: 141
Period size: 25 Copynumber: 7.5 Consensus size: 25
31805516 TACAATATGA
* * * *
31805526 CACAAGGGTTTTTCGTAAGATTAGC
1 CACAAAGGCTTTTCATAAGAATAGC
31805551 CACAAAGGCTTTTCATAAGAATAGC
1 CACAAAGGCTTTTCATAAGAATAGC
* *
31805576 CACAAAAGC-TTTC-TAGACAATACGC
1 CACAAAGGCTTTTCATA-AGAATA-GC
* * *
31805601 CACAAAGGCTTTCCATAAGATTAGT
1 CACAAAGGCTTTTCATAAGAATAGC
* *
31805626 CACAAAGGCTTTCCA-GAGAATA-C
1 CACAAAGGCTTTTCATAAGAATAGC
* * *
31805649 ACTACAAAGACTTTCCA-AACAATACGC
1 -C-ACAAAGGCTTTTCATAAGAATA-GC
* *
31805676 CACAAAGTCTTTTCATAAGATTAGC
1 CACAAAGGCTTTTCATAAGAATAGC
*
31805701 CACAAAAGCTTT
1 CACAAAGGCTTT
31805713 CTAGATAATT
Statistics
Matches: 130, Mismatches: 23, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
23 2 0.02
24 15 0.12
25 97 0.75
26 13 0.10
27 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (25 bp):
CACAAAGGCTTTTCATAAGAATAGC
Found at i:31805632 original size:75 final size:75
Alignment explanation
Indices: 31805509--31805713 Score: 227
Period size: 75 Copynumber: 2.7 Consensus size: 75
31805499 ATCATACAGT
* * * * * * * *
31805509 CTTTCCATACAATATGACACAAGGGTTTTTCGTAAGATTAGCCACAAAGGCTTTTCATAAGAATA
1 CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTCCA-AAGAATA
31805574 GC-C-ACAAA-A
65 -CACTACAAAGA
* * * *
31805583 GCTTTCTAGACAATACGCCACAAAGGCTTTCCATAAGATTAGTCACAAAGGCTTTCCAGAGAATA
1 -CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTCCAAAGAATA
31805648 CACTACAAAGA
65 CACTACAAAGA
* * *
31805659 CTTTCCAAACAATACGCCACAAAGTCTTTTCATAAGATTAGCCACAAAAGCTTTC
1 CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTC
31805714 TAGATAATTC
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
73 1 0.01
74 7 0.06
75 101 0.92
76 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (75 bp):
CTTTCCAAACAATACGCCACAAAGGCTTTCCATAAGATTAGCCACAAAGGCTTTCCAAAGAATAC
ACTACAAAGA
Found at i:31805682 original size:50 final size:50
Alignment explanation
Indices: 31805550--31805687 Score: 161
Period size: 50 Copynumber: 2.8 Consensus size: 50
31805540 GTAAGATTAG
* * * *
31805550 CCACAAAGGCTTTTCATAAGAATAGCCACAAAAGCTTTCTAGACAATACG
1 CCACAAAGGCTTTCCATAAGAATAGCCACAAAGGCTTTCCAGACAATACA
* * *
31805600 CCACAAAGGCTTTCCATAAGATTAGTCACAAAGGCTTTCCAGAGAATACA
1 CCACAAAGGCTTTCCATAAGAATAGCCACAAAGGCTTTCCAGACAATACA
* * * *
31805650 CTACAAAGACTTTCCA-AACAATACGCCACAAAGTCTTT
1 CCACAAAGGCTTTCCATAAGAATA-GCCACAAAGGCTTT
31805688 TCATAAGATT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 5 0.07
50 69 0.93
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.22
Consensus pattern (50 bp):
CCACAAAGGCTTTCCATAAGAATAGCCACAAAGGCTTTCCAGACAATACA
Found at i:31809404 original size:69 final size:69
Alignment explanation
Indices: 31809293--31809427 Score: 261
Period size: 69 Copynumber: 2.0 Consensus size: 69
31809283 AAGCTTTGGT
31809293 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGATTTTTAGCAGCCTTTTTC
1 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGATTTTTAGCAGCCTTTTTC
31809358 TAGC
66 TAGC
*
31809362 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGGTTTTTAGCAGCCTTTTTC
1 TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGATTTTTAGCAGCCTTTTTC
31809427 T
66 T
31809428 GGCCCTATAG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (69 bp):
TTCTAGCTGTTCCAACTTAGTATTTAAACTCACTATAGCAAAACAGATTTTTAGCAGCCTTTTTC
TAGC
Found at i:31812174 original size:25 final size:25
Alignment explanation
Indices: 31812120--31812174 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
31812110 AGCACTCTCT
*
31812120 CGAGCCATATAACAGAATGCTCATG
1 CGAGCCATATAACAGAATGCTCATC
* *
31812145 TGAGCCATATAACAGGAA-GCTTATC
1 CGAGCCATATAACA-GAATGCTCATC
31812170 CGAGC
1 CGAGC
31812175 AATAATAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (25 bp):
CGAGCCATATAACAGAATGCTCATC
Found at i:31812322 original size:25 final size:24
Alignment explanation
Indices: 31812288--31812340 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
31812278 AAGTTCAAGT
31812288 GAGCCATATCAGGA-AGCTCACAAA
1 GAGCCATATCAGGACA-CTCACAAA
*
31812312 GAGCCTATATCAGGACACTCATAAA
1 GAGCC-ATATCAGGACACTCACAAA
31812337 GAGC
1 GAGC
31812341 TGCAGTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 20 0.77
26 1 0.04
ACGTcount: A:0.40, C:0.25, G:0.21, T:0.15
Consensus pattern (24 bp):
GAGCCATATCAGGACACTCACAAA
Found at i:31818684 original size:14 final size:14
Alignment explanation
Indices: 31818665--31818693 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
31818655 TCGAAAACTT
31818665 CTTTTGTAGGGATC
1 CTTTTGTAGGGATC
31818679 CTTTTGTAGGGATC
1 CTTTTGTAGGGATC
31818693 C
1 C
31818694 AATTCACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.41
Consensus pattern (14 bp):
CTTTTGTAGGGATC
Found at i:31819534 original size:26 final size:24
Alignment explanation
Indices: 31819505--31819559 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
31819495 AGCAGCAGAC
*
31819505 GGATGGGAAGGAAAAAACTAAGTTAG
1 GGATGGG--GGAAAAAACTAAGTTAA
*
31819531 GGATTTGGGGAAAAAACTAAGTTAA
1 GGA-TGGGGGAAAAAACTAAGTTAA
31819556 GGAT
1 GGAT
31819560 TTAGGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 1 0.04
25 19 0.73
26 3 0.12
27 3 0.12
ACGTcount: A:0.44, C:0.04, G:0.33, T:0.20
Consensus pattern (24 bp):
GGATGGGGGAAAAAACTAAGTTAA
Found at i:31819542 original size:25 final size:25
Alignment explanation
Indices: 31819514--31819569 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
31819504 CGGATGGGAA
* *
31819514 GGAAAAAACTAAGTTAGGGATTTGG
1 GGAAAAAACTAAGTTAAGGATTTAG
31819539 GGAAAAAACTAAGTTAAGGATTTAG
1 GGAAAAAACTAAGTTAAGGATTTAG
31819564 GGAAAA
1 GGAAAA
31819570 CGATTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (25 bp):
GGAAAAAACTAAGTTAAGGATTTAG
Found at i:31819777 original size:40 final size:41
Alignment explanation
Indices: 31819659--31819796 Score: 127
Period size: 41 Copynumber: 3.3 Consensus size: 41
31819649 TTTATAGGCG
* * *
31819659 AAACGCCGCTATTGCTTTACCTTTAGTGGCATTTGTGAGAA
1 AAACGCCGCTATTGCTTTACCTTTTGTGGCATTTATGACAA
** * *
31819700 AAACGCCGCTATCTTTTTTAACCTTTT-TCAGCGTTTATG-CAA
1 AAACGCCGCTAT-TGCTTT-ACCTTTTGT-GGCATTTATGACAA
* * **
31819742 AAATGCTGCTATTGCTTTACCTTTTGTGGCATTTATGGGAA
1 AAACGCCGCTATTGCTTTACCTTTTGTGGCATTTATGACAA
*
31819783 AAACACCGCTATTG
1 AAACGCCGCTATTG
31819797 TTGTTATACC
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
40 15 0.20
41 30 0.40
42 17 0.23
43 13 0.17
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (41 bp):
AAACGCCGCTATTGCTTTACCTTTTGTGGCATTTATGACAA
Found at i:31821250 original size:14 final size:15
Alignment explanation
Indices: 31821228--31821304 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
31821218 CAATCAAACA
31821228 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
31821242 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
31821257 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
31821277 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
31821291 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
31821305 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Done.