Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold40
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: 1915636
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 67970 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:983480 original size:20 final size:21
Alignment explanation
Indices: 983439--983481 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
983429 AGTGGAATAC
*
983439 ATTAAAGCTCAAGTGGAGCGA
1 ATTAAAGCTCAAGTGCAGCGA
*
983460 ATTAAAGCTGAAG-GCAGCGA
1 ATTAAAGCTCAAGTGCAGCGA
983480 AT
1 AT
983482 CCTATTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.19
Consensus pattern (21 bp):
ATTAAAGCTCAAGTGCAGCGA
Found at i:983533 original size:51 final size:51
Alignment explanation
Indices: 983460--983601 Score: 194
Period size: 51 Copynumber: 2.8 Consensus size: 51
983450 AGTGGAGCGA
* * *
983460 ATTAAAGCTGAAGGCAGCGAATCCTATTTCCTTGGCATTACAGTGGAACAG
1 ATTAAAGCTGAAGGTAGCGAATCTTATTTCCTTGGCATTACAGCGGAACAG
* * * * *
983511 ATTAAAGCTAAAGGTAGTGAATCTTGTTTCCTTGGCATTGCAGCGGAATAG
1 ATTAAAGCTGAAGGTAGCGAATCTTATTTCCTTGGCATTACAGCGGAACAG
* *
983562 ATTAAAGCTGAAGGTAGCGAATCTTATCTCCTTGACATTA
1 ATTAAAGCTGAAGGTAGCGAATCTTATTTCCTTGGCATTA
983602 AAGACTGAAG
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (51 bp):
ATTAAAGCTGAAGGTAGCGAATCTTATTTCCTTGGCATTACAGCGGAACAG
Found at i:983742 original size:44 final size:44
Alignment explanation
Indices: 983645--983816 Score: 168
Period size: 44 Copynumber: 3.9 Consensus size: 44
983635 AAGACAGGCT
*
983645 ACAAATCTTATCT-CCTGAAGTTGTAGTGGAGCAGATTAAAGCC
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAC
* * * * * * *
983688 ACAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAC
* * *
983732 ACCAATCTTATCTCCCTGAAGTTGTAGTGGAGCATATGAAAG-C
1 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAC
** * * * *
983775 TATTAATCCTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAA
1 -ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAA
983817 ACGATGAATC
Statistics
Matches: 101, Mismatches: 26, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
43 12 0.12
44 89 0.88
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGAC
Found at i:983798 original size:88 final size:87
Alignment explanation
Indices: 983648--983807 Score: 234
Period size: 88 Copynumber: 1.8 Consensus size: 87
983638 ACAGGCTACA
*
983648 AATCTTATCTCCTGAAGTTGTAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCCTAAAGTTGC
1 AATCTTATCTCCTGAAGTTGTAGTGGAGCAGATGAAAGCCACAAACCTTATCTCCCTAAAGTTGC
983713 AGTGGAGTAGGTTGAAGATACC
66 AGTGGAGTAGGTTGAAGATACC
* * * *
983735 AATCTTATCTCCCTGAAGTTGTAGTGGAGCATATGAAAGCTATTAATCC-TATCTCCC-AGAAGT
1 AATCTTATCT-CCTGAAGTTGTAGTGGAGCAGATGAAAGCCA-CAAACCTTATCTCCCTA-AAGT
983798 TGCAGTGGAG
63 TGCAGTGGAG
983808 CGGATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
87 11 0.17
88 50 0.77
89 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (87 bp):
AATCTTATCTCCTGAAGTTGTAGTGGAGCAGATGAAAGCCACAAACCTTATCTCCCTAAAGTTGC
AGTGGAGTAGGTTGAAGATACC
Found at i:983827 original size:44 final size:44
Alignment explanation
Indices: 983735--983830 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
983725 TGAAGATACC
* * * * * * *
983735 AATCTTATCTCCCTGAAGTTGTAGTGGAGCATATGAAAGCTATT
1 AATCCTATCTCCCAGAAGTTGCAGTGGAGCAGATGAAAACGATG
* *
983779 AATCCTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAACGATG
1 AATCCTATCTCCCAGAAGTTGCAGTGGAGCAGATGAAAACGATG
983823 AATCCTAT
1 AATCCTAT
983831 ACCTCTGATG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCCTATCTCCCAGAAGTTGCAGTGGAGCAGATGAAAACGATG
Found at i:983986 original size:44 final size:44
Alignment explanation
Indices: 983936--984049 Score: 176
Period size: 44 Copynumber: 2.6 Consensus size: 44
983926 CACATCAAAC
983936 CTTATCTCCCTGAAGTTGTAGTGGAG-AAGATTGAAGATACCAAT
1 CTTATCTCCCTGAAGTTGTAGTGGAGTAA-ATTGAAGATACCAAT
* **
983980 CTTATCTCCCTGAAGTTGTAGTGGAGTAAATTGAAGCTATTAAT
1 CTTATCTCCCTGAAGTTGTAGTGGAGTAAATTGAAGATACCAAT
*
984024 CCTATCTCCCTGAAGTTGTAGTGGAG
1 CTTATCTCCCTGAAGTTGTAGTGGAG
984050 CGGATTAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
44 63 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGTAGTGGAGTAAATTGAAGATACCAAT
Found at i:984114 original size:242 final size:242
Alignment explanation
Indices: 983689--984290 Score: 841
Period size: 242 Copynumber: 2.5 Consensus size: 242
983679 ATTAAAGCCA
* * *
983689 CAAACCTTATCTCCCTAAAGTTGCAGTGGAGTAGGTTGAAGATACCAATCTTATCTCCCTGAAGT
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAATCTTATCTCCCTGAAGT
* * * *
983754 TGTAGTGGAGCATA-TGAAAGCTATTAATCCTATCTCCCAGAAGTTGCAGTGGAGCGGATTAAAA
66 TGTAGTGGAGTAAATTG-AAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAA
* * * *
983818 CGATGAATCCTATACCTCTGATGTTGTAGTAGATCAGATTAAGTCTATCATAACAAGTCTTATCT
130 AGATGAATCCTATACCTCTGACGTTGCAGTAGATCAGATTAAGTCTACCATAACAAGTCTTATCT
* *
983883 CCCTAAATTTGTAGTAGAGTAGACTGCAGATAGTGAATCTTATCACAT
195 CCCTAAAGTTGTAGTAGAGCAGACTGCAGATAGTGAATCTTATCACAT
*
983931 CAAACCTTATCTCCCTGAAGTTGTAGTGGAGAAGATTGAAGATACCAATCTTATCTCCCTGAAGT
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAATCTTATCTCCCTGAAGT
983996 TGTAGTGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAAA
66 TGTAGTGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAAA
* *
984061 GATGAATCCTATACCTCTGACGTTGCAGTAG-GCTGGATTAAGTCTACCATAACAAGTCTTATCT
131 GATGAATCCTATACCTCTGACGTTGCAGTAGATC-AGATTAAGTCTACCATAACAAGTCTTATCT
* * * *
984125 CCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATAT
195 CCCTAAAGTTGTAGTAGAGCAGACTGCAGATAGTGAATCTTATCACAT
* * * * *
984173 CAAACCTTATCTCCCTGAAATTGCAGTGGA-ACAGACTGAGGATAACAAACCTTATCTCCCTGAA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGA-AGATTGAAGAT-ACCAATCTTATCTCCCTGAA
* * * ** ** * *
984237 GTCGCAGTGGAGTAAGTTGAATATACCAATCTTATCTCCCTAAAGTTGTAGTGG
64 GTTGTAGTGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGG
984291 TGCAGATTGA
Statistics
Matches: 321, Mismatches: 35, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
241 2 0.01
242 254 0.79
243 65 0.20
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (242 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTGAAGATACCAATCTTATCTCCCTGAAGT
TGTAGTGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAAA
GATGAATCCTATACCTCTGACGTTGCAGTAGATCAGATTAAGTCTACCATAACAAGTCTTATCTC
CCTAAAGTTGTAGTAGAGCAGACTGCAGATAGTGAATCTTATCACAT
Found at i:984302 original size:287 final size:288
Alignment explanation
Indices: 983931--985051 Score: 1729
Period size: 287 Copynumber: 3.9 Consensus size: 288
983921 CTTATCACAT
*
983931 CAAACCTTATCTCCCTGAAGTTGTAGTGGAG-AAGATTGAAGATACCAATCTTATCTCCCTGAAG
1 CAAACCTTATCTCCCTGAAGTCGTAGTGGAGTAAGATTGAAGATACCAATCTTATCTCCCTGAAG
* * * *
983995 TTGTAGTGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAA
66 TTGTAGTGGAGCAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
* *
984060 AGATGAATCCTATACCTCTGACGTTGCAGTAGG-CTGGATTAAGTCTACCATAACAAGTCTTATC
131 TGATGAATCCTATACCTCTGACGTTGCAGTAGGTCT-GATTAAGTCTATCATAACAAGTCTTATC
984124 TCCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCT
195 TCCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCT
*
984189 GAAATTGCAGTGGAACAGACTGAGGATAA
260 GAAATTGCAGTGGAACAGACTGAAGATAA
* * *
984218 CAAACCTTATCTCCCTGAAGTCGCAGTGGAGTAAG-TTGAATATACCAATCTTATCTCCCTAAAG
1 CAAACCTTATCTCCCTGAAGTCGTAGTGGAGTAAGATTGAAGATACCAATCTTATCTCCCTGAAG
* * * *
984282 TTGTAGTGGTGCAGATTGAAGCTATTAATCCTATCTCCATGAAGTTGCAGTGGAGTGGATTAAAA
66 TTGTAGTGGAGCAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
*
984347 TGATGAATCCTATACCTCTGATGTTGCAGTAGGTCTGATTAAGTCTATCATAACAAGTCTTATCT
131 TGATGAATCCTATACCTCTGACGTTGCAGTAGGTCTGATTAAGTCTATCATAACAAGTCTTATCT
*
984412 CCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACGTTATCTCCCT-
196 CCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTG
**
984476 AAAGTTGCAGTGGAGA-AGGTTGAAGAT-A
261 AAA-TTGCAGTGGA-ACAGACTGAAGATAA
* * * * * ** *
984504 CCAATCTTATCTCCCTGAAGTTGTAGTGGAGT-AGATTAAAGCTATTAATCCTATCTCCCTGAAG
1 CAAACCTTATCTCCCTGAAGTCGTAGTGGAGTAAGATTGAAGATACCAATCTTATCTCCCTGAAG
*
984568 TTGTAGTGGAGTAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
66 TTGTAGTGGAGCAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
* * * * *
984633 CGATGAATCTTATACCTCTGACGTTACAGTAGGCCAGATTAAGTCTATCATAACAAGTCTTATCT
131 TGATGAATCCTATACCTCTGACGTTGCAGTAGGTCTGATTAAGTCTATCATAACAAGTCTTATCT
* * *
984698 TCCTAAAGTTGTAGTGGAGCATACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCTCTG
196 CCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTG
984763 AAATTGCAGTGGAACAGACTGAAGATAA
261 AAATTGCAGTGGAACAGACTGAAGATAA
* *
984791 CAAACCTTATCTCCCTGAAGTCATAGTGGAGCAAG-TTGAAGATACCAATCTTATCTCCCTGAAG
1 CAAACCTTATCTCCCTGAAGTCGTAGTGGAGTAAGATTGAAGATACCAATCTTATCTCCCTGAAG
* *
984855 TTGTAGTGGTA-CAGATTAAAGTTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
66 TTGTAGTGG-AGCAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
* * * *
984919 ATGATGAATCCTATATCTCTAACGTTGAAGTAGGTCTGATTAAGTATATCATAACAAGTCTTATC
130 ATGATGAATCCTATACCTCTGACGTTGCAGTAGGTCTGATTAAGTCTATCATAACAAGTCTTATC
* *
984984 TCCCTAAAGTTATAGTGGAGCAGACTGTAGATAGCGGATCTTATCATATCAAACCTTATCTCCCT
195 TCCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCT
985049 GAA
260 GAA
985052 GTCGTAGTGG
Statistics
Matches: 752, Mismatches: 72, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
285 3 0.00
286 252 0.34
287 488 0.65
288 9 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (288 bp):
CAAACCTTATCTCCCTGAAGTCGTAGTGGAGTAAGATTGAAGATACCAATCTTATCTCCCTGAAG
TTGTAGTGGAGCAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
TGATGAATCCTATACCTCTGACGTTGCAGTAGGTCTGATTAAGTCTATCATAACAAGTCTTATCT
CCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTG
AAATTGCAGTGGAACAGACTGAAGATAA
Found at i:984515 original size:44 final size:44
Alignment explanation
Indices: 984467--984631 Score: 222
Period size: 44 Copynumber: 3.8 Consensus size: 44
984457 TATCAAACGT
* * * * * ** *
984467 TATCTCCCTAAAGTTGCAGTGGAGAAGGTTGAAGATACCAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATTAATCC
*
984511 TATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGCTATTAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATTAATCC
*
984555 TATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGCTATTAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATTAATCC
**
984599 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
1 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAA
984632 ACGATGAATC
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 109 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTATTAATCC
Found at i:984746 original size:573 final size:573
Alignment explanation
Indices: 983936--985103 Score: 1917
Period size: 573 Copynumber: 2.0 Consensus size: 573
983926 CACATCAAAC
* *
983936 CTTATCTCCCTGAAGTTGTAGTGGAGAAGATTGAAGATACCAATCTTATCTCCCTGAAGTTGTAG
1 CTTATCTCCCTGAAGTTGTAGTGGAGAAGATTAAAGATACCAATCCTATCTCCCTGAAGTTGTAG
* *
984001 TGGAGTAAATTGAAGCTATTAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAAAGATGA
66 TGGAGTAAATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAAGATGA
* **
984066 ATCCTATACCTCTGACGTTGCAGTAGGCTGGATTAAGTCTACCATAACAAGTCTTATCTCCCTAA
131 ATCCTATACCTCTGACGTTACAGTAGGCCAGATTAAGTCTACCATAACAAGTCTTATCTCCCTAA
984131 AGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTGAAATTG
196 AGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTGAAATTG
* * * *
984196 CAGTGGAACAGACTGAGGATAACAAACCTTATCTCCCTGAAGTCGCAGTGGAGTAAGTTGAATAT
261 CAGTGGAACAGACTGAAGATAACAAACCTTATCTCCCTGAAGTCACAGTGGAGCAAGTTGAAGAT
* *
984261 ACCAATCTTATCTCCCTAAAGTTGTAGTGGTGCAGATTGAAGCTATTAATCCTATCTCCATGAAG
326 ACCAATCTTATCTCCCTAAAGTTGTAGTGGTACAGATTAAAGCTATTAATCCTATCTCCATGAAG
** * * *
984326 TTGCAGTGGAGTGGATTAAAATGATGAATCCTATACCTCTGATGTTGCAGTAGGTCTGATTAAGT
391 TTGCAGTGGAGCAGATTAAAATGATGAATCCTATACCTCTAACGTTGAAGTAGGTCTGATTAAGT
* * *
984391 CTATCATAACAAGTCTTATCTCCCTAAAGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATC
456 ATATCATAACAAGTCTTATCTCCCTAAAGTTATAGTGGAGCAGACTGTAGATAGCGGATCTTATC
* *
984456 ATATCAAACGTTATCTCCCTAAAGTTGCAGTGGAGAAGGTTGAAG-ATACCAA-T
521 ATATCAAACCTTATCTCCCTAAAGTCGCAGTGGAGAAGGTTGAAGCA-A-CAAGT
* * **
984509 CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGTAG
1 CTTATCTCCCTGAAGTTGTAGTGGAGAAGATTAAAGATACCAATCCTATCTCCCTGAAGTTGTAG
* *
984574 TGGAGTAGATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACGATGA
66 TGGAGTAAATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAAGATGA
* * *
984639 ATCTTATACCTCTGACGTTACAGTAGGCCAGATTAAGTCTATCATAACAAGTCTTATCTTCCTAA
131 ATCCTATACCTCTGACGTTACAGTAGGCCAGATTAAGTCTACCATAACAAGTCTTATCTCCCTAA
* *
984704 AGTTGTAGTGGAGCATACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCTCTGAAATTG
196 AGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTGAAATTG
*
984769 CAGTGGAACAGACTGAAGATAACAAACCTTATCTCCCTGAAGTCATAGTGGAGCAAGTTGAAGAT
261 CAGTGGAACAGACTGAAGATAACAAACCTTATCTCCCTGAAGTCACAGTGGAGCAAGTTGAAGAT
* * *
984834 ACCAATCTTATCTCCCTGAAGTTGTAGTGGTACAGATTAAAGTTATTAATCCTATCTCCCTGAAG
326 ACCAATCTTATCTCCCTAAAGTTGTAGTGGTACAGATTAAAGCTATTAATCCTATCTCCATGAAG
*
984899 TTGCAGTGGAGCAGATTAAAATGATGAATCCTATATCTCTAACGTTGAAGTAGGTCTGATTAAGT
391 TTGCAGTGGAGCAGATTAAAATGATGAATCCTATACCTCTAACGTTGAAGTAGGTCTGATTAAGT
984964 ATATCATAACAAGTCTTATCTCCCTAAAGTTATAGTGGAGCAGACTGTAGATAGCGGATCTTATC
456 ATATCATAACAAGTCTTATCTCCCTAAAGTTATAGTGGAGCAGACTGTAGATAGCGGATCTTATC
* * *
985029 ATATCAAACCTTATCTCCCTGAAGTCGTAGTGGAGTAGGTTGAAGCAACAAGT
521 ATATCAAACCTTATCTCCCTAAAGTCGCAGTGGAGAAGGTTGAAGCAACAAGT
*
985082 CTTATCTCCCTGACGTTGTAGT
1 CTTATCTCCCTGAAGTTGTAGT
985104 AGAGCAGACT
Statistics
Matches: 550, Mismatches: 43, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
572 3 0.01
573 546 0.99
574 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (573 bp):
CTTATCTCCCTGAAGTTGTAGTGGAGAAGATTAAAGATACCAATCCTATCTCCCTGAAGTTGTAG
TGGAGTAAATTAAAGCTATTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAAAGATGA
ATCCTATACCTCTGACGTTACAGTAGGCCAGATTAAGTCTACCATAACAAGTCTTATCTCCCTAA
AGTTGTAGTGGAGCAGACTGTAGATAGTGGATCTTATCATATCAAACCTTATCTCCCTGAAATTG
CAGTGGAACAGACTGAAGATAACAAACCTTATCTCCCTGAAGTCACAGTGGAGCAAGTTGAAGAT
ACCAATCTTATCTCCCTAAAGTTGTAGTGGTACAGATTAAAGCTATTAATCCTATCTCCATGAAG
TTGCAGTGGAGCAGATTAAAATGATGAATCCTATACCTCTAACGTTGAAGTAGGTCTGATTAAGT
ATATCATAACAAGTCTTATCTCCCTAAAGTTATAGTGGAGCAGACTGTAGATAGCGGATCTTATC
ATATCAAACCTTATCTCCCTAAAGTCGCAGTGGAGAAGGTTGAAGCAACAAGT
Found at i:984862 original size:44 final size:44
Alignment explanation
Indices: 984746--984915 Score: 155
Period size: 44 Copynumber: 3.8 Consensus size: 44
984736 CTTATCATAT
* * * * *
984746 CAAACCTTATCTCTCTGAAATTGCAGTGGAACAGACTGAAGATAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-A
* ***
984791 CAAACCTTATCTCCCTGAAGTCATAGTGGAGCA-AGTTGAAGATA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGATA
* * * *
984835 CCAATCTTATCTCCCTGAAGTTGTAGTGGTA-CAGATTAAAGTTA
1 CAAATCTTATCTCCCTGAAGTTGCAGTGG-AGCAGATTGAAGATA
** *
984879 TTAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATT
1 CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT
984916 AAAATGATGA
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 67 0.64
45 36 0.35
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (44 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA
Found at i:984916 original size:44 final size:44
Alignment explanation
Indices: 984837--984932 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
984827 TGAAGATACC
* * * * *
984837 AATCTTATCTCCCTGAAGTTGTAGTGGTACAGATTAAAGTTATT
1 AATCCTATCTCCCTGAAGTTGCAGTGGTACAGATTAAAATGATG
984881 AATCCTATCTCCCTGAAGTTGCAGTGG-AGCAGATTAAAATGATG
1 AATCCTATCTCCCTGAAGTTGCAGTGGTA-CAGATTAAAATGATG
984925 AATCCTAT
1 AATCCTAT
984933 ATCTCTAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.02
44 45 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (44 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGTACAGATTAAAATGATG
Found at i:986523 original size:16 final size:16
Alignment explanation
Indices: 986502--986532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
986492 ATTTAATACT
986502 ATTATTATGATTATTA
1 ATTATTATGATTATTA
*
986518 ATTATTATTATTATT
1 ATTATTATGATTATT
986533 TACTTATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATTATTATGATTATTA
Found at i:994297 original size:18 final size:18
Alignment explanation
Indices: 994274--994309 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
994264 TGCACCTTCT
994274 ATGCAAGAATTGCCTGCA
1 ATGCAAGAATTGCCTGCA
994292 ATGCAAGAATTGCCTGCA
1 ATGCAAGAATTGCCTGCA
994310 TTTTTATCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
ATGCAAGAATTGCCTGCA
Found at i:998028 original size:42 final size:42
Alignment explanation
Indices: 997939--998029 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 42
997929 GTTCCAACCC
** * *
997939 GTGTAACTTTCGAAATGGGCTCACACGCCCGTGTGCTAGACT
1 GTGTAACACTCGAAATGGGCTCACACGCCCGTGTCCAAGACT
*
997981 GTGTAACACTCGAAAT-GGCATCACACGCTCGTGTACCAAG-CT
1 GTGTAACACTCGAAATGGGC-TCACACGCCCGTGT-CCAAGACT
*
998023 TTGTAAC
1 GTGTAAC
998030 TGTCTGACTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
41 3 0.07
42 35 0.85
43 3 0.07
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (42 bp):
GTGTAACACTCGAAATGGGCTCACACGCCCGTGTCCAAGACT
Found at i:998423 original size:26 final size:26
Alignment explanation
Indices: 998390--998443 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
998380 CTACTACACA
998390 AAATACATTTGAAGCATTCATACTCC
1 AAATACATTTGAAGCATTCATACTCC
998416 AAATACATTTGAAGCATTCATACTCC
1 AAATACATTTGAAGCATTCATACTCC
998442 AA
1 AA
998444 CACTTTGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (26 bp):
AAATACATTTGAAGCATTCATACTCC
Found at i:998679 original size:27 final size:27
Alignment explanation
Indices: 998641--998695 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
998631 AAATAGAGTA
998641 AGAACCAAAATGAGTACTAAGATGATG
1 AGAACCAAAATGAGTACTAAGATGATG
998668 AGAACCAAAATGAGTACTAAGATGATG
1 AGAACCAAAATGAGTACTAAGATGATG
998695 A
1 A
998696 TGATAGTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (27 bp):
AGAACCAAAATGAGTACTAAGATGATG
Found at i:998695 original size:15 final size:15
Alignment explanation
Indices: 998650--998695 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
998640 AAGAACCAAA
998650 ATGAGTACTAAGATG
1 ATGAGTACTAAGATG
* *
998665 ATGAGAACCAA-A--
1 ATGAGTACTAAGATG
998677 ATGAGTACTAAGATG
1 ATGAGTACTAAGATG
998692 ATGA
1 ATGA
998696 TGATAGTGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 1 0.04
15 13 0.54
ACGTcount: A:0.46, C:0.09, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGAGTACTAAGATG
Found at i:1002607 original size:11 final size:11
Alignment explanation
Indices: 1002591--1002632 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1002581 AAAAAATGAT
1002591 AAAGAAAAAGA
1 AAAGAAAAAGA
*
1002602 AAAGAAATCAGA
1 AAAGAAA-AAGA
*
1002614 AAA-AAAAACA
1 AAAGAAAAAGA
1002624 AAAGAAAAA
1 AAAGAAAAA
1002633 AATAATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 5 0.19
11 15 0.58
12 6 0.23
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:1002620 original size:22 final size:22
Alignment explanation
Indices: 1002578--1002630 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1002568 AGTGATCAAG
* * *
1002578 AGAAAA-AAATGATAAAGAAAA
1 AGAAAAGAAATCAGAAAAAAAA
1002599 AGAAAAGAAATCAGAAAAAAAA
1 AGAAAAGAAATCAGAAAAAAAA
*
1002621 ACAAAAGAAA
1 AGAAAAGAAA
1002631 AAAATAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (22 bp):
AGAAAAGAAATCAGAAAAAAAA
Found at i:1013746 original size:38 final size:38
Alignment explanation
Indices: 1013695--1013808 Score: 158
Period size: 38 Copynumber: 3.0 Consensus size: 38
1013685 TTTAATACAT
*
1013695 CGACACATAGCCTGCTAGGCACAAAGCCTGAATAACAC
1 CGACACAAAGCCTGCTAGGCACAAAGCCTGAATAACAC
* *
1013733 CGACACAGAGCCTGCTAGGCACAAAACCTGAAATAACAC
1 CGACACAAAGCCTGCTAGGCACAAAGCCTG-AATAACAC
* *
1013772 C-AGCATAAAACCTGCTAGGCACAAAGCCTGAATAACA
1 CGA-CACAAAGCCTGCTAGGCACAAAGCCTGAATAACA
1013809 ACATACTTCT
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
38 36 0.53
39 32 0.47
ACGTcount: A:0.40, C:0.30, G:0.18, T:0.12
Consensus pattern (38 bp):
CGACACAAAGCCTGCTAGGCACAAAGCCTGAATAACAC
Found at i:1026040 original size:3 final size:3
Alignment explanation
Indices: 1026034--1026067 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1026024 AGATTGTTAA
1026034 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1026068 GAGAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1026121 original size:3 final size:3
Alignment explanation
Indices: 1026115--1026148 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1026105 AGACTGTTAA
1026115 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1026149 GAGGATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1026128 original size:81 final size:74
Alignment explanation
Indices: 1026006--1026164 Score: 237
Period size: 81 Copynumber: 2.1 Consensus size: 74
1025996 AATATATATA
*
1026006 TAATTAGAACCTATAATAAGATTGTTAAAATAATAATAATAATAATAATAATAATAATAATAGAG
1 TAATTAGAACCTATAATAAGACTGTTAAAATAATAATAATAATAATAATAATAATAATAATAGAG
1026071 AATAAAAAT
66 AATAAAAAT
1026080 TAATNNNNNNNTAGAACCTATAATAAGACTGTTAAAATAATAATAATAATAATAATAATAATAAT
1 TAAT-------TAGAACCTATAATAAGACTGTTAAAATAATAATAATAATAATAATAATAATAAT
*
1026145 AATAGAGGATAAAAAT
59 AATAGAGAATAAAAAT
1026161 TAAT
1 TAAT
1026165 ATATATTTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
74 4 0.05
81 72 0.95
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.30
Consensus pattern (74 bp):
TAATTAGAACCTATAATAAGACTGTTAAAATAATAATAATAATAATAATAATAATAATAATAGAG
AATAAAAAT
Found at i:1040530 original size:14 final size:14
Alignment explanation
Indices: 1040512--1040545 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1040502 TTAAATTTTG
1040512 AAAAATAAAAAAATT
1 AAAAAT-AAAAAATT
*
1040527 AAAAATTAAAAATT
1 AAAAATAAAAAATT
1040541 AAAAA
1 AAAAA
1040546 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAATAAAAAATT
Found at i:1040547 original size:8 final size:7
Alignment explanation
Indices: 1040520--1040545 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1040510 TGAAAAATAA
1040520 AAAAATT
1 AAAAATT
1040527 AAAAATT
1 AAAAATT
1040534 AAAAATT
1 AAAAATT
1040541 AAAAA
1 AAAAA
1040546 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:1044581 original size:14 final size:16
Alignment explanation
Indices: 1044551--1044584 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1044541 CGAAAAGAAA
1044551 AAAATATAATATTTTT
1 AAAATATAATATTTTT
1044567 AAAATAT-AT-TTTTT
1 AAAATATAATATTTTT
1044581 AAAA
1 AAAA
1044585 GTGAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 2 0.11
16 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATATAATATTTTT
Found at i:1044772 original size:84 final size:86
Alignment explanation
Indices: 1044579--1044786 Score: 264
Period size: 85 Copynumber: 2.4 Consensus size: 86
1044569 AATATATTTT
* * *
1044579 TTAAAAGTGAATAAAATATGTTTCGAGATTTATTCCTACCGTTCAACGGATGTTATTTCAATTTG
1 TTAAAATTAAATAAAATATGTTTCGAGATTTATTCCCACCGTTCAACGGATGTTATTTCAATTTG
1044644 ATTTTATTTCCAAAATGAGTA
66 ATTTTATTTCCAAAATGAGTA
* * * * *
1044665 TTTAAATTAAAATAAAATCTGTTT-G-GGTTTATTCCCACCGTTCAACGGATTTTATTAT-TATT
1 TTAAAATT-AAATAAAATATGTTTCGAGATTTATTCCCACCGTTCAACGGATGTTATT-TCAATT
1044727 T-ATTTTATTTCCAAAATGA-TAAA
64 TGATTTTATTTCCAAAATGAGT--A
*
1044750 TTAAAATTAAATAAAATTTGTTTCGAGATTTATTCCC
1 TTAAAATTAAATAAAATATGTTTCGAGATTTATTCCC
1044787 GTCGATAACA
Statistics
Matches: 105, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
83 1 0.01
84 32 0.30
85 41 0.39
86 18 0.17
87 13 0.12
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (86 bp):
TTAAAATTAAATAAAATATGTTTCGAGATTTATTCCCACCGTTCAACGGATGTTATTTCAATTTG
ATTTTATTTCCAAAATGAGTA
Found at i:1044961 original size:83 final size:86
Alignment explanation
Indices: 1044712--1044973 Score: 231
Period size: 84 Copynumber: 3.1 Consensus size: 86
1044702 CCGTTCAACG
* * * * * * *
1044712 GATTTTATT-ATTATTTATTTTATTTCCAAAATGATAAATTAAAATTAAATAAAATT-TGTTTCG
1 GATTTTATTCAATATTAATTTTGTTTCC-AAATCAGAAA-T-AAATCAAATTAAATTATGTTTCG
* *
1044775 AGATTTATTCCCGTCG-ATAACAA
63 GGATTTATTCCCGTCGTTTAACAA
* * * * *
1044798 GATTTTATTCGATTTTAATTTTGTTTTCAAATTAGAAATAAATTAAATTAAATCTAT-TTT-GGG
1 GATTTTATTCAATATTAATTTTGTTTCCAAATCAGAAATAAATCAAATTAAAT-TATGTTTCGGG
*
1044861 ATTTATTCCCGTTGTTTAACAA
65 ATTTATTCCCGTCGTTTAACAA
*
1044883 GATTTTATTCAATATTAATTTT-TTTCCAAA-CA-AAGACTTAATCAAA-T-AATTATGTTTCGG
1 GATTTTATTCAATATTAATTTTGTTTCCAAATCAGAA-A-TAAATCAAATTAAATTATGTTTCGG
*
1044943 GATTTATTCCCGCCGTTTAAC-A
64 GATTTATTCCCGTCGTTTAACAA
*
1044965 GAATTTATT
1 GATTTTATT
1044974 TTTATTTAAT
Statistics
Matches: 147, Mismatches: 21, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
81 3 0.02
82 17 0.12
83 24 0.16
84 42 0.29
85 31 0.21
86 18 0.12
87 12 0.08
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.45
Consensus pattern (86 bp):
GATTTTATTCAATATTAATTTTGTTTCCAAATCAGAAATAAATCAAATTAAATTATGTTTCGGGA
TTTATTCCCGTCGTTTAACAA
Found at i:1052751 original size:20 final size:20
Alignment explanation
Indices: 1052728--1052773 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1052718 ATAATTTGCC
*
1052728 ATTTTTATATA-TTTTTAATA
1 ATTTTTAAATATTTTTTAA-A
1052748 ATTTTTAAATATTTTTTAAA
1 ATTTTTAAATATTTTTTAAA
1052768 ATTTTT
1 ATTTTT
1052774 TGAATTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTAAATATTTTTTAAA
Found at i:1055119 original size:139 final size:140
Alignment explanation
Indices: 1054858--1055137 Score: 553
Period size: 139 Copynumber: 2.0 Consensus size: 140
1054848 CGTTAGAGCT
1054858 TGCTACAGAGTTAGTTGAGCTTTCGGTTTTTCAACAAAAGCATAAAGTGGTGAGTGTATGGAATT
1 TGCTACAGAGTTAGTTGAGCTTTCGGTTTTTCAACAAAAGCATAAAGTGGTGAGTGTATGGAATT
1054923 GCTACTCGTAAACATGAGTCATGTGTTATTTAGGAATTTAGATGTAGCCTCAACCCCTACTCTAA
66 GCTACTCGTAAACATGAGTCATGTGTTATTTAGGAATTTAGATGTAGCCTCAACCCCTACTCTAA
1054988 GTTCCAGGTG
131 GTTCCAGGTG
1054998 TGCTACAGAG-TAGTTGAGCTTTCGGTTTTTCAACAAAAGCATAAAGTGGTGAGTGTATGGAATT
1 TGCTACAGAGTTAGTTGAGCTTTCGGTTTTTCAACAAAAGCATAAAGTGGTGAGTGTATGGAATT
1055062 GCTACTCGTAAACATGAGTCATGTGTTATTTAGGAATTTAGATGTAGCCTCAACCCCTACTCTAA
66 GCTACTCGTAAACATGAGTCATGTGTTATTTAGGAATTTAGATGTAGCCTCAACCCCTACTCTAA
1055127 GTTCCAGGTG
131 GTTCCAGGTG
1055137 T
1 T
1055138 AAGCTTTTTT
Statistics
Matches: 140, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 130 0.93
140 10 0.07
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (140 bp):
TGCTACAGAGTTAGTTGAGCTTTCGGTTTTTCAACAAAAGCATAAAGTGGTGAGTGTATGGAATT
GCTACTCGTAAACATGAGTCATGTGTTATTTAGGAATTTAGATGTAGCCTCAACCCCTACTCTAA
GTTCCAGGTG
Found at i:1066272 original size:21 final size:24
Alignment explanation
Indices: 1066230--1066272 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
1066220 GTACCAAAAA
*
1066230 TATTATTACAAATAAAGTAAATGG
1 TATTATTACAAATAAAGAAAATGG
1066254 TATTA-TA-AAATAAA-AAAAT
1 TATTATTACAAATAAAGAAAAT
1066273 AATTGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 2 0.11
24 5 0.28
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (24 bp):
TATTATTACAAATAAAGAAAATGG
Found at i:1075448 original size:31 final size:31
Alignment explanation
Indices: 1075413--1075475 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1075403 TCAATTCTAA
1075413 TCCCTATACTTTTTTACTTTTGAATTTTCAG
1 TCCCTATACTTTTTTACTTTTGAATTTTCAG
1075444 TCCCTATACTTTTTTACTTTTGAATTTTCAG
1 TCCCTATACTTTTTTACTTTTGAATTTTCAG
1075475 T
1 T
1075476 TTTTGAGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (31 bp):
TCCCTATACTTTTTTACTTTTGAATTTTCAG
Found at i:1078443 original size:9 final size:9
Alignment explanation
Indices: 1078429--1078597 Score: 82
Period size: 9 Copynumber: 18.4 Consensus size: 9
1078419 AATTGATGAT
1078429 TTTTTATAA
1 TTTTTATAA
*
1078438 TTTTTAAAA
1 TTTTTATAA
** **
1078447 TTGTCAATGG
1 TT-TTTATAA
*
1078457 TTTTTTTA-
1 TTTTTATAA
1078465 TTT-TATAA
1 TTTTTATAA
* *
1078473 TTTTAATTA
1 TTTTTATAA
1078482 -TTTTATAA
1 TTTTTATAA
1078490 TTCTTTATAAA
1 TT-TTTAT-AA
1078501 TTTTTAATGAA
1 TTTTT-AT-AA
1078512 -TTTTATAA
1 TTTTTATAA
1078520 TTTTTATAAA
1 TTTTTAT-AA
* *
1078530 TCTTGATAA
1 TTTTTATAA
**
1078539 TAAGTTATAAA
1 T-TTTTAT-AA
1078550 TTTTTTAATAA
1 -TTTTT-ATAA
1078561 TTTTTATAA
1 TTTTTATAA
1078570 TTTTT-T-A
1 TTTTTATAA
1078577 TTTTT-TAA
1 TTTTTATAA
*
1078585 TTTTTAGAA
1 TTTTTATAA
1078594 TTTT
1 TTTT
1078598 AGAATGATTC
Statistics
Matches: 121, Mismatches: 24, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
7 10 0.08
8 21 0.17
9 42 0.35
10 31 0.26
11 14 0.12
12 3 0.02
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1078498 original size:10 final size:9
Alignment explanation
Indices: 1078465--1078597 Score: 87
Period size: 9 Copynumber: 14.3 Consensus size: 9
1078455 GGTTTTTTTA
1078465 TTTTATAAT
1 TTTTATAAT
* *
1078474 TTTAATTA-
1 TTTTATAAT
1078482 TTTTATAAT
1 TTTTATAAT
1078491 TCTTTATAAAT
1 T-TTTAT-AAT
1078502 TTTTAATGAA-
1 TTTT-AT-AAT
1078512 TTTTATAAT
1 TTTTATAAT
1078521 TTTTATAAAT
1 TTTTAT-AAT
* *
1078531 CTTGATAAT
1 TTTTATAAT
**
1078540 AAGTTATAAATT
1 -TTTTAT-AA-T
1078552 TTTTAATAAT
1 TTTT-ATAAT
1078562 TTTTATAAT
1 TTTTATAAT
1078571 TTTT-T-AT
1 TTTTATAAT
1078578 TTTT-TAAT
1 TTTTATAAT
*
1078586 TTTTAGAAT
1 TTTTATAAT
1078595 TTT
1 TTT
1078598 AGAATGATTC
Statistics
Matches: 99, Mismatches: 13, Indels: 24
0.73 0.10 0.18
Matches are distributed among these distances:
7 7 0.07
8 15 0.15
9 33 0.33
10 27 0.27
11 14 0.14
12 3 0.03
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:1078503 original size:19 final size:18
Alignment explanation
Indices: 1078465--1078597 Score: 69
Period size: 19 Copynumber: 7.2 Consensus size: 18
1078455 GGTTTTTTTA
*
1078465 TTTTAT-AATTTTA-ATT
1 TTTTATAAATTTTATAAT
*
1078481 ATTTTATAATTCTTTATAAAT
1 -TTTTATAAAT-TTTAT-AAT
*
1078502 TTTTAATGAATTTTATAAT
1 TTTT-ATAAATTTTATAAT
*
1078521 TTTTATAAATCTTGATAAT
1 TTTTATAAAT-TTTATAAT
**
1078540 AAGTTATAAATTTTTTAATAAT
1 -TTTTATAAA--TTTT-ATAAT
*
1078562 TTTTAT-AATTTT-TTAT
1 TTTTATAAATTTTATAAT
* *
1078578 TTTT-TAATTTTTAGAAT
1 TTTTATAAATTTTATAAT
1078595 TTT
1 TTT
1078598 AGAATGATTC
Statistics
Matches: 89, Mismatches: 15, Indels: 24
0.70 0.12 0.19
Matches are distributed among these distances:
15 1 0.01
16 12 0.13
17 11 0.12
18 11 0.12
19 18 0.20
20 18 0.20
21 12 0.13
22 6 0.07
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAAATTTTATAAT
Found at i:1078585 original size:15 final size:16
Alignment explanation
Indices: 1078560--1078589 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1078550 TTTTTTAATA
1078560 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
1078576 ATTTTT-TAATTTTT
1 ATTTTTATAATTTTT
1078590 AGAATTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTTATAATTTTTT
Found at i:1079106 original size:16 final size:16
Alignment explanation
Indices: 1079087--1079119 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1079077 AATAAAAAAT
1079087 ATTTA-AAATTTTATAA
1 ATTTATAAA-TTTATAA
1079103 ATTTATAAATTTATAA
1 ATTTATAAATTTATAA
1079119 A
1 A
1079120 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTATAAATTTATAA
Found at i:1081559 original size:18 final size:16
Alignment explanation
Indices: 1081524--1081562 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
1081514 TTCTCACCCT
1081524 AATTTTACCCCAGTAA
1 AATTTTACCCCAGTAA
*
1081540 AATTTTAACCCCTGGTAA
1 AATTTT-ACCCC-AGTAA
1081558 AATTT
1 AATTT
1081563 CGAGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.36, C:0.21, G:0.08, T:0.36
Consensus pattern (16 bp):
AATTTTACCCCAGTAA
Found at i:1081713 original size:18 final size:18
Alignment explanation
Indices: 1081690--1081726 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1081680 AGGATTACAA
1081690 GTTTCCATTTCCAATTTT
1 GTTTCCATTTCCAATTTT
*
1081708 GTTTCCATTTCCATTTTT
1 GTTTCCATTTCCAATTTT
1081726 G
1 G
1081727 GAAATCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.22, G:0.08, T:0.57
Consensus pattern (18 bp):
GTTTCCATTTCCAATTTT
Found at i:1084051 original size:50 final size:50
Alignment explanation
Indices: 1083905--1084140 Score: 254
Period size: 50 Copynumber: 4.8 Consensus size: 50
1083895 GATAATAACA
* ** * *
1083905 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATATAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
1083954 TGCCAATGCCAT-ACCC---CA-GATATTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
1083999 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
1084049 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
1084099 TGCCAACGCCATGTCCCAGACATGGTCTTACATAGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1084141 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
43 1 0.01
44 19 0.12
45 13 0.08
46 3 0.02
48 3 0.02
49 14 0.09
50 106 0.66
51 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:1086342 original size:18 final size:19
Alignment explanation
Indices: 1086319--1086355 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1086309 AATATTTTTT
1086319 ATTTATTT-TGAATATTAG
1 ATTTATTTCTGAATATTAG
*
1086337 ATTTATTTCTGATTATTAG
1 ATTTATTTCTGAATATTAG
1086356 GAATTAGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.57
Consensus pattern (19 bp):
ATTTATTTCTGAATATTAG
Found at i:1087881 original size:21 final size:19
Alignment explanation
Indices: 1087857--1087908 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1087847 CAAGGGCAAA
*
1087857 GTATCGATACTTATACAAAAG
1 GTATCTATACTTAT--AAAAG
1087878 GTATCTATACCTTATAAAAG
1 GTATCTATA-CTTATAAAAG
1087898 GTATCTATACT
1 GTATCTATACT
1087909 ATTGCACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 14 0.48
21 8 0.28
22 5 0.17
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (19 bp):
GTATCTATACTTATAAAAG
Found at i:1088838 original size:28 final size:27
Alignment explanation
Indices: 1088780--1088855 Score: 88
Period size: 28 Copynumber: 2.9 Consensus size: 27
1088770 TGCATATCAT
*
1088780 ATATCACTAAGCA-CAAAGT---AAAA
1 ATATCAATAAGCACCAAAGTGCAAAAA
*
1088803 ATAACAATAAGCACCAAAGTGCAAAATA
1 ATATCAATAAGCACCAAAGTGCAAAA-A
*
1088831 ATATCAATAAGCACCGAAGTGCAAA
1 ATATCAATAAGCACCAAAGTGCAAA
1088856 TTTTACAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
23 11 0.25
24 6 0.14
27 3 0.07
28 24 0.55
ACGTcount: A:0.54, C:0.18, G:0.12, T:0.16
Consensus pattern (27 bp):
ATATCAATAAGCACCAAAGTGCAAAAA
Found at i:1093958 original size:27 final size:27
Alignment explanation
Indices: 1093899--1094057 Score: 128
Period size: 27 Copynumber: 5.9 Consensus size: 27
1093889 CGGAAAGGTT
* ** *
1093899 GTAAGATGACCGT-ATACCCCCATAAG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
1093925 GTTAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
** * *
1093952 GTAAAATGACTATAAT-GCCCTTTAAGG
1 GTAAAATGACCGTAATACCCCTGT-AGG
* *
1093979 GTAAAATGACCGTAATA-CCCTCATAAG
1 GTAAAATGACCGTAATACCCCT-GTAGG
* * *
1094006 GTTAAATGACCATAATACCCTTGTAGG
1 GTAAAATGACCGTAATACCCCTGTAGG
*
1094033 GTAAAATGATCGTAA-AGCCCCTGTA
1 GTAAAATGACCGTAATA-CCCCTGTA
1094058 TGATCGATTT
Statistics
Matches: 104, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
26 17 0.16
27 83 0.80
28 4 0.04
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTGTAGG
Found at i:1093991 original size:54 final size:54
Alignment explanation
Indices: 1093928--1094057 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 54
1093918 CCATAAGGTT
* * *
1093928 AAATGACCGTAATACCCCTGTAGGGTAAAATGACTATAATGCCCTT-TAAGGGTA
1 AAATGACCGTAATACCCCTGTAAGGTAAAATGACCATAATACCCTTGT-AGGGTA
* *
1093982 AAATGACCGTAATA-CCCTCATAAGGTTAAATGACCATAATACCCTTGTAGGGTA
1 AAATGACCGTAATACCCCT-GTAAGGTAAAATGACCATAATACCCTTGTAGGGTA
*
1094036 AAATGATCGTAA-AGCCCCTGTA
1 AAATGACCGTAATA-CCCCTGTA
1094058 TGATCGATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
53 5 0.08
54 55 0.85
55 5 0.08
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (54 bp):
AAATGACCGTAATACCCCTGTAAGGTAAAATGACCATAATACCCTTGTAGGGTA
Found at i:1098775 original size:28 final size:28
Alignment explanation
Indices: 1098707--1098776 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1098697 AGACTTTCGA
* *
1098707 CACTAAGTGTGCAAGTTTAATGGTAAAG
1 CACTAAGTGTGCGAGTTTAATGATAAAG
* * *
1098735 CACTAAGTGTGCGAGTTTGATTATTAAG
1 CACTAAGTGTGCGAGTTTAATGATAAAG
1098763 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
1098777 ACTTATTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATGATAAAG
Found at i:1099613 original size:23 final size:23
Alignment explanation
Indices: 1099514--1099783 Score: 200
Period size: 23 Copynumber: 11.5 Consensus size: 23
1099504 TGATGCTTAA
* *
1099514 ATGCTGCCCAATTTCTTGTACAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
1099537 ATACTGCTCAATTTGTTGCATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
1099560 ATGCTGTCCAATTTTTATGCT-TAA
1 ATGCTGCCCAATTTGT-TG-TATAT
*
1099584 ATGCTGCCCAATTTGTTGTATTT
1 ATGCTGCCCAATTTGTTGTATAT
* *
1099607 ATGCTGCCCAAATTATTGTATATAT
1 ATGCTGCCCAATTTGTTG--TATAT
* * * *
1099632 ATGCTGTCCAATTTTGATGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* *
1099656 ATGCTGCTCAATTTGCTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
*
1099679 TTGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * * * * *
1099702 AAGTTGTCCAATTTTTGGTGTAAAA
1 ATGCTGCCCAA--TTTGTTGTATAT
* *
1099727 ATGCTACTCAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* *
1099750 TTGCTGCCTAATTTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* *
1099773 AAGCTGTCCAA
1 ATGCTGCCCAA
1099784 ATTTTGGTGT
Statistics
Matches: 184, Mismatches: 55, Indels: 16
0.72 0.22 0.06
Matches are distributed among these distances:
22 1 0.01
23 120 0.65
24 30 0.16
25 29 0.16
26 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTGTATAT
Found at i:1099747 original size:71 final size:71
Alignment explanation
Indices: 1099512--1099800 Score: 334
Period size: 71 Copynumber: 4.1 Consensus size: 71
1099502 TTTGATGCTT
* * * * * * *
1099512 AAATGCTGCCCAATTTCTTGTACATATACTGCTCAATTTGTTGCATATATGCTGTCCAATTTTT-
1 AAATGCTGCCCAATTTGTTGTATATTTGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTTG
*
1099576 ATGCT-T
66 ATG-TAA
* *
1099582 AAATGCTGCCCAATTTGTTGTAT-TTATGCTGCCCAAATTATTGTATATATATGCTGTCCAA-TT
1 AAATGCTGCCCAATTTGTTGTATATT-TGCTGCCCAATTTGTTGTATATA-A-GCTGTCCAATTT
1099645 TTGATGTAA
63 TTGATGTAA
* * *
1099654 AAATGCTGCTCAATTTGCTGTATATTTGCTGCCCAATTTGTTGTATATAAGTTGTCCAATTTTTG
1 AAATGCTGCCCAATTTGTTGTATATTTGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTTG
*
1099719 GTGTAA
66 ATGTAA
* * * *
1099725 AAATGCTACTCAATTTGTTGTATATTTGCTGCCTAATTTGTTGTATATAAGCTGTCCAAATTTTG
1 AAATGCTGCCCAATTTGTTGTATATTTGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTTG
* *
1099790 GTGTGA
66 ATGTAA
1099796 AAATG
1 AAATG
1099801 TTGTCTAGTT
Statistics
Matches: 190, Mismatches: 22, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
69 1 0.01
70 47 0.25
71 86 0.45
72 54 0.28
73 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (71 bp):
AAATGCTGCCCAATTTGTTGTATATTTGCTGCCCAATTTGTTGTATATAAGCTGTCCAATTTTTG
ATGTAA
Found at i:1099841 original size:71 final size:71
Alignment explanation
Indices: 1099512--1099856 Score: 270
Period size: 71 Copynumber: 4.9 Consensus size: 71
1099502 TTTGATGCTT
* * * * * * * *
1099512 AAATGCTGCCCAATTT-CTTGTACATATACTGCTCAATTTGTTGCATATATGCTGTCC-AATTTT
1 AAATGCTGCTCAATTTGC-TGTATATATGCTGCCCAAATTGATGTATATAAGCTGTCCAAATTTT
** *
1099575 TATGCT-T
65 GGTG-TAA
* * *
1099582 AAATGCTGCCCAATTTGTTGTATTTATGCTGCCCAAATT-ATTGTATATATATGCTGTCC-AATT
1 AAATGCTGCTCAATTTGCTGTATATATGCTGCCCAAATTGA-TGTATATA-A-GCTGTCCAAATT
*
1099645 TTGATGTAA
63 TTGGTGTAA
* * * * *
1099654 AAATGCTGCTCAATTTGCTGTATATTTGCTGCCCAATTTGTTGTATATAAGTTGTCCAATTTTTG
1 AAATGCTGCTCAATTTGCTGTATATATGCTGCCCAAATTGATGTATATAAGCTGTCCAAATTTTG
1099719 GTGTAA
66 GTGTAA
* * * * * *
1099725 AAATGCTACTCAATTTGTTGTATATTTGCTGCCTAATTTGTTGTATATAAGCTGTCCAAATTTTG
1 AAATGCTGCTCAATTTGCTGTATATATGCTGCCCAAATTGATGTATATAAGCTGTCCAAATTTTG
*
1099790 GTGTGA
66 GTGTAA
* * * * * * ***
1099796 AAATGTTG-TCTAGTTTGGTATATAAATGCTGTCCAAATTGATGTATAGGGGCTGTCCAAAT
1 AAATGCTGCTC-AATTTGCTGTATATATGCTGCCCAAATTGATGTATATAAGCTGTCCAAAT
1099857 AGGGTAGATT
Statistics
Matches: 227, Mismatches: 40, Indels: 15
0.80 0.14 0.05
Matches are distributed among these distances:
70 47 0.21
71 122 0.54
72 58 0.26
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (71 bp):
AAATGCTGCTCAATTTGCTGTATATATGCTGCCCAAATTGATGTATATAAGCTGTCCAAATTTTG
GTGTAA
Found at i:1106148 original size:30 final size:30
Alignment explanation
Indices: 1106114--1106237 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
1106104 GTACATATTT
* * *
1106114 TATACACTACCGAATTGATTTTTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
1106144 TATACATTGCTGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
1106174 TATACATTGCCGAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
1106204 TATACATTGCCGAATTGATTTGTATATGTA
1 TATACATTGCCGAATTGATTTGTATATGGA
1106234 TATA
1 TATA
1106238 TATATTTCCA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 86 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:1106252 original size:32 final size:32
Alignment explanation
Indices: 1106114--1106257 Score: 174
Period size: 30 Copynumber: 4.7 Consensus size: 32
1106104 GTACATATTT
* * *
1106114 TATACACTACCGAATTGATTTTTATATG--GA
1 TATACATTGCCGAATTGATTTGTATATGTAGA
*
1106144 TATACATTGCTGAATTGATTTGTATATG--GA
1 TATACATTGCCGAATTGATTTGTATATGTAGA
1106174 TATACATTGCCGAATTGATTTGTATA--TAGA
1 TATACATTGCCGAATTGATTTGTATATGTAGA
*
1106204 TATACATTGCCGAATTGATTTGTATATGTATA
1 TATACATTGCCGAATTGATTTGTATATGTAGA
* * *
1106236 TATATATTTCCAAATTGATTTG
1 TATACATTGCCGAATTGATTTG
1106258 AGCATTTGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
30 79 0.78
32 22 0.22
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (32 bp):
TATACATTGCCGAATTGATTTGTATATGTAGA
Found at i:1111648 original size:50 final size:50
Alignment explanation
Indices: 1111574--1112141 Score: 282
Period size: 50 Copynumber: 11.4 Consensus size: 50
1111564 CCATAGTTTC
* * *
1111574 CAAT-GAAAAGATTG-AGTCCACAACGGCAAATCTTACTTCCCAGGCAGTG
1 CAATGGAAAAGATTGAAG-CTACAACGGCGAATCTTACTTCCCAGACAGTG
* * * *
1111623 CAATGGAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCTC-GACATTG
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCC-CAGACAGTG
* ** * * * * *
1111673 AAATTTAAAAGATTGAGGCCACAACGGCAAATCTTACTTCCTAGGC-G-G
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAGTG
* ** * * * *
1111721 TACGGCGAAACAGATTGAAGCTACAACGGTGAATCTTGCTTCCCCCGACATTG
1 CAATG-GAAA-AGATTGAAGCTACAACGGCGAATCTTACTT-CCCAGACAGTG
* ** * ** *
1111774 TAATTTAAAAGATTGAAGCCACAATAGCGAATCTTACTTCCCTAGA-GGTG
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCC-AGACAGTG
* * * * * * *
1111824 CAGTGGAACATATTGAAGCTACAACGGTGAATCTTGCTTCCCCGACATTG
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAGTG
* * * * * * ** * *
1111874 TAAT-TAAAAGATCGATGCCATAACGATGAATCTTAC-TCCCTGGC-GTTG
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAG-TG
* * * *
1111922 CAGTGGAACAA-ATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTG
1 CAATGGAA-AAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAGTG
* * * * * *
1111972 CAAT-TAAAAGA-TCAAGGCCATAATGGCGAATCTTACTT-CCAGGC-GTTG
1 CAATGGAAAAGATTGAA-GCTACAACGGCGAATCTTACTTCCCAGACAG-TG
*** * * * * *
1112020 CAGCAGAATAGATTGAAGCTACAACAGCGAATCTTGCTTCCCTGACATTG
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAGTG
** * * * *
1112070 CAATTTAAAAGATTGAAGCCACAACTGCGAATCTTACTTCCCTGACGGTG
1 CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAGTG
* * * *
1112120 TAGTGGAATATATTGAAGCTAC
1 CAATGGAAAAGATTGAAGCTAC
1112142 GATGACAAAT
Statistics
Matches: 370, Mismatches: 126, Indels: 45
0.68 0.23 0.08
Matches are distributed among these distances:
48 25 0.07
49 96 0.26
50 209 0.56
51 34 0.09
52 3 0.01
53 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (50 bp):
CAATGGAAAAGATTGAAGCTACAACGGCGAATCTTACTTCCCAGACAGTG
Found at i:1111752 original size:100 final size:100
Alignment explanation
Indices: 1111579--1112141 Score: 652
Period size: 98 Copynumber: 5.7 Consensus size: 100
1111569 GTTTCCAATG
* * * * *
1111579 AAAAGATTGAGTCCACAACGGCAAATCTTACTTCCCAGGCAGTGCAATGGAACAGATTGAAGCTA
1 AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACAGATTGAAGCTA
* *
1111644 CAACGGTGAATCTTGCTTCCTCGACATTGAAATTT
66 CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
* * * * *
1111679 AAAAGATTGAGGCCACAACGGCAAATCTTACTTCCTAGGCGGTACGGCGAAACAGATTGAAGCTA
1 AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACAGATTGAAGCTA
*
1111744 CAACGGTGAATCTTGCTTCCCCCGACATTGTAATTT
66 CAACGGTGAATCTTGCTT-CCCCGACATTGCAATTT
* ** * *
1111780 AAAAGATTGAAGCCACAATAGCGAATCTTACTTCCCTA-GAGGTGCAGTGGAACATATTGAAGCT
1 AAAAGATTGAGGCCACAACGGCGAATCTTACTT-CCTAGGCGGTGCAGTGGAACAGATTGAAGCT
*
1111844 ACAACGGTGAATCTTGCTTCCCCGACATTGTAA-TT
65 ACAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
* * * ** * * *
1111879 AAAAGATCGATGCCATAACGATGAATCTTACTCCCT-GGCGTTGCAGTGGAACAAATTGAAGCTA
1 AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACAGATTGAAGCTA
*
1111943 CAACGGCGAATCTTGCTTCCCCGACATTGCAA-TT
66 CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
** * * * ** *
1111977 AAAAGATCAAGGCCATAATGGCGAATCTTACTTCC-AGGCGTTGCAGCAGAATAGATTGAAGCTA
1 AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACAGATTGAAGCTA
* * *
1112041 CAACAGCGAATCTTGCTTCCCTGACATTGCAATTT
66 CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
* * * * * *
1112076 AAAAGATTGAAGCCACAACTGCGAATCTTACTTCCCT-GACGGTGTAGTGGAATATATTGAAGCT
1 AAAAGATTGAGGCCACAACGGCGAATCTTACTT-CCTAGGCGGTGCAGTGGAACAGATTGAAGCT
1112140 AC
65 AC
1112142 GATGACAAAT
Statistics
Matches: 399, Mismatches: 57, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
98 142 0.36
99 56 0.14
100 114 0.29
101 83 0.21
102 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (100 bp):
AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCTAGGCGGTGCAGTGGAACAGATTGAAGCTA
CAACGGTGAATCTTGCTTCCCCGACATTGCAATTT
Found at i:1113630 original size:3 final size:3
Alignment explanation
Indices: 1113610--1113687 Score: 59
Period size: 3 Copynumber: 25.7 Consensus size: 3
1113600 CATTTTGTTC
* * * *
1113610 ATT ATT TTT ATT ATTT ATT ATT ATT ATCT -TT ACT ATT ACT ATT AGT
1 ATT ATT ATT ATT A-TT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * * *
1113656 ATT ATT ACT AAT ATT ATT ATT ACT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1113688 ATTTACACTT
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
2 1 0.02
3 52 0.91
4 4 0.07
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1113686 original size:15 final size:15
Alignment explanation
Indices: 1113624--1113687 Score: 67
Period size: 15 Copynumber: 4.3 Consensus size: 15
1113614 TTTTTATTAT
* *
1113624 TTATTATTATTATCT
1 TTATTATTACTATCA
* *
1113639 TTACTATTACTATTA
1 TTATTATTACTATCA
*
1113654 GTATTATTACTAAT-A
1 TTATTATTACT-ATCA
1113669 TTATTATTACTATCA
1 TTATTATTACTATCA
1113684 TTAT
1 TTAT
1113688 ATTTACACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 2 0.05
15 36 0.90
16 2 0.05
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATTATTACTATCA
Found at i:1116925 original size:118 final size:119
Alignment explanation
Indices: 1116702--1116914 Score: 330
Period size: 118 Copynumber: 1.8 Consensus size: 119
1116692 AAATAGTTGA
*
1116702 AAAAGATCAAAACTTTGTTTTAAAATTTTAAACTTCTTCTTTAAAATGACTGAAAAACAGATTTT
1 AAAAGATCAAAACTTTGTTTTAAAATTTTAAACTTCTTCTTTAAAATGACTAAAAAACAGATTTT
1116767 TATTTTTAAAAATCTAAACTTCCTCTTTTTTTAAAAAAAAATCACTTTTTTCTT
66 TATTTTTAAAAATCTAAACTTCCTCTTTTTTTAAAAAAAAATCACTTTTTTCTT
* *
1116821 AAAA-ATCAAAATTTTGTTTTCAAAA-TTTAAA-TGT-TTCCTTTAAAATGACTAAAAAATAGAT
1 AAAAGATCAAAACTTTGTTTT-AAAATTTTAAACT-TCTT-CTTTAAAATGACTAAAAAACAGAT
1116882 TTTTATTTTTAAAAATCTAAAC-T-CTCTTTTTTT
63 TTTTATTTTTAAAAATCTAAACTTCCTCTTTTTTT
1116915 TTTTTAAAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
116 10 0.11
117 4 0.05
118 66 0.75
119 8 0.09
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (119 bp):
AAAAGATCAAAACTTTGTTTTAAAATTTTAAACTTCTTCTTTAAAATGACTAAAAAACAGATTTT
TATTTTTAAAAATCTAAACTTCCTCTTTTTTTAAAAAAAAATCACTTTTTTCTT
Found at i:1117061 original size:17 final size:19
Alignment explanation
Indices: 1117041--1117084 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1117031 TTTTTAAAAA
*
1117041 AAAAATC-CT-TTTTTTTT
1 AAAAATCACTATTTTTCTT
1117058 AAAAATCACTATTTTTCTT
1 AAAAATCACTATTTTTCTT
1117077 AAAAATCA
1 AAAAATCA
1117085 AAGCTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 7 0.29
18 2 0.08
19 15 0.62
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAATCACTATTTTTCTT
Found at i:1119134 original size:39 final size:39
Alignment explanation
Indices: 1119091--1119173 Score: 148
Period size: 39 Copynumber: 2.1 Consensus size: 39
1119081 TTATTAAAAT
*
1119091 CTAAGACAATTTAGCAAATTAGTCCCTAGGTTAGCTAGA
1 CTAAGACAATTTAACAAATTAGTCCCTAGGTTAGCTAGA
*
1119130 CTAAGACAATTTAACAAGTTAGTCCCTAGGTTAGCTAGA
1 CTAAGACAATTTAACAAATTAGTCCCTAGGTTAGCTAGA
1119169 CTAAG
1 CTAAG
1119174 TTACAACGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (39 bp):
CTAAGACAATTTAACAAATTAGTCCCTAGGTTAGCTAGA
Found at i:1124946 original size:3 final size:3
Alignment explanation
Indices: 1124928--1125007 Score: 63
Period size: 3 Copynumber: 26.3 Consensus size: 3
1124918 AAGTGTAAAT
* * * * * * *
1124928 ATA ATG ATA GTA ATA ATA ATA TTA GTA ATA ATA CTA ATA GTA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
1124976 A-A GATA ATA ATA ATAA ATA ATA AAA ATA ATA A
1 ATA -ATA ATA ATA AT-A ATA ATA ATA ATA ATA A
1125008 ACAAAATGAT
Statistics
Matches: 59, Mismatches: 15, Indels: 6
0.74 0.19 0.08
Matches are distributed among these distances:
2 1 0.02
3 54 0.92
4 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1131681 original size:29 final size:30
Alignment explanation
Indices: 1131629--1131687 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1131619 CTACACTAAT
*
1131629 CAAAGTTTAAGTGTGAAACAAAAAA-AAAA
1 CAAAGTTTAAGTGAGAAACAAAAAATAAAA
*
1131658 CAAAGTTTAATTGAGAAA-AGAAAAATAAAA
1 CAAAGTTTAAGTGAGAAACA-AAAAATAAAA
1131688 AAATACGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.04
29 21 0.81
30 4 0.15
ACGTcount: A:0.63, C:0.05, G:0.14, T:0.19
Consensus pattern (30 bp):
CAAAGTTTAAGTGAGAAACAAAAAATAAAA
Found at i:1137280 original size:21 final size:21
Alignment explanation
Indices: 1137256--1137318 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
1137246 NNNNNNNNNN
1137256 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
1137277 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
1137296 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
1137317 AT
1 AT
1137319 CCTCGAAGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:1137301 original size:19 final size:19
Alignment explanation
Indices: 1137256--1137319 Score: 110
Period size: 19 Copynumber: 3.3 Consensus size: 19
1137246 NNNNNNNNNN
1137256 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
1137275 ATATATCATATCTAAGATTGC
1 --ATATCATATCTAAGATTGC
1137296 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
1137315 ATATC
1 ATATC
1137320 CTCGAAGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
19 24 0.56
21 19 0.44
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:1137329 original size:17 final size:18
Alignment explanation
Indices: 1137256--1137329 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 18
1137246 NNNNNNNNNN
*
1137256 ATATCATATCTAAGATTGC
1 ATATCA-ATCGAAGATTGC
*
1137275 ATATATCATATCTAAGATTGC
1 --ATATCA-ATCGAAGATTGC
*
1137296 ATATCATATCTAAGATTGC
1 ATATCA-ATCGAAGATTGC
*
1137315 ATATC-CTCGAAGATT
1 ATATCAATCGAAGATT
1137330 ATGTTTCCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.16
19 24 0.47
21 19 0.37
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (18 bp):
ATATCAATCGAAGATTGC
Found at i:1138183 original size:44 final size:44
Alignment explanation
Indices: 1138117--1138492 Score: 468
Period size: 44 Copynumber: 8.7 Consensus size: 44
1138107 GCTATTTTCT
* *
1138117 ACCTATTCCACTGCTG-CTCAGGGAGATAGGGTTCACGATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* *
1138161 ACCTATTCCACTGCTGACCAGGGAGATAAGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * * *
1138205 ATCTATTCCACTGC-AACCCAGGGAGATAGAATTCTCAATATTCA
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGATTCACAATCTTCA
*
1138249 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
1138293 ACCTATTCCACTGCT-ATCCAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTGA-CCAGGGAGATAGGATTCACAATCTTCA
* * *
1138331 ATCTATTCCACTGCTG-CCTAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACC-AGGGAGATAGGATTCACAATCTTCA
*
1138375 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
1138419 ACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
1138463 ACCTATTCCACTACTGATCAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
1138493 GTTGGGGTCA
Statistics
Matches: 290, Mismatches: 27, Indels: 30
0.84 0.08 0.09
Matches are distributed among these distances:
37 2 0.01
38 28 0.10
39 2 0.01
40 2 0.01
42 2 0.01
43 5 0.02
44 244 0.84
45 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:1138356 original size:170 final size:170
Alignment explanation
Indices: 1138117--1138492 Score: 501
Period size: 170 Copynumber: 2.2 Consensus size: 170
1138107 GCTATTTTCT
* * * *
1138117 ACCTATTCCACTGCTGCTCAGGGAGATAGGGTTCACGATCTTCAACCTATTCCACTGCTGACCAG
1 ACCTATTCCACTACTGATCAGGGAGATAGGATT--C--T-TT-AATCTATTCCACTGCTGACCAG
* *
1138182 GGAGATA-AGA-CCTACAATCTTCAATCTATTCCACTGC-AACCCAGGGAGATAGAATTCTCAAT
60 GGAGATAGA-ATCCT-CAATCTTCAACCTATTCCACTGCTAA-CCAGGGAGATAGAATTCACAAT
1138244 ATTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
122 ATTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
*
1138293 ACCTATTCCACTGCT-ATCCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTG-CCTAGGGAG
1 ACCTATTCCACTACTGAT-CAGGGAGATAGGATTCTTTAATCTATTCCACTGCTGACC-AGGGAG
* * * * *
1138356 ATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAAC
64 ATAGAATCCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAGAATTCACAATATTCAAC
*
1138421 CTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTA
129 CTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1138463 ACCTATTCCACTACTGATCAGGGAGATAGG
1 ACCTATTCCACTACTGATCAGGGAGATAGG
1138493 GTTGGGGTCA
Statistics
Matches: 182, Mismatches: 12, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
169 2 0.01
170 140 0.77
171 8 0.04
172 1 0.01
174 1 0.01
175 1 0.01
176 29 0.16
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (170 bp):
ACCTATTCCACTACTGATCAGGGAGATAGGATTCTTTAATCTATTCCACTGCTGACCAGGGAGAT
AGAATCCTCAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAGAATTCACAATATTCAACCT
ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
Found at i:1138396 original size:126 final size:126
Alignment explanation
Indices: 1138117--1138452 Score: 496
Period size: 126 Copynumber: 2.6 Consensus size: 126
1138107 GCTATTTTCT
* * *
1138117 ACCTATTCCACTGCTG-CTCAGGGAGATAGGGTTCACGATCTTCAACCTATTCCACTGCTGA-CC
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCT-ATCC
*
1138180 AGGGAGATAAGACCTACAATCTTCAATCTATTCCACTGCAACCCAGGGAGATAGAATTCTCAATA
64 AGGGAGATAGGA--T----TCTTCAATCTATTCCACTGCAACCCAGGGAGATAGAATTCTCAATA
1138245 TTCA
123 TTCA
1138249 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTATCCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTATCCAG
* ** * *
1138314 GGAGATAGGATTCTTTAATCTATTCCACTGCTGCCTAGGGAGATAGAATTCTCAATCTTCA
66 GGAGATAGGATTCTTCAATCTATTCCACTGCAACCCAGGGAGATAGAATTCTCAATATTCA
*
1138375 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTATCCAG
1138440 GGAGATAGGATTC
66 GGAGATAGGATTC
1138453 ACAATCTTTA
Statistics
Matches: 192, Mismatches: 10, Indels: 10
0.91 0.05 0.05
Matches are distributed among these distances:
126 122 0.64
130 1 0.01
131 1 0.01
132 67 0.35
133 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (126 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTATCCAG
GGAGATAGGATTCTTCAATCTATTCCACTGCAACCCAGGGAGATAGAATTCTCAATATTCA
Found at i:1138615 original size:88 final size:88
Alignment explanation
Indices: 1138506--1138776 Score: 425
Period size: 88 Copynumber: 3.1 Consensus size: 88
1138496 GGGGTCATCA
* * * ** *
1138506 ATCTGCTTCGCTGTCTGTGCAGGAAGGCAAGATCTACTATTTTTAATCTGCTCCGCTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCA
*
1138571 GGGAGGCAAGGCTGGTGTCTTCG
66 GGGAGGCAAGGCTGGTGACTTCG
*
1138594 ATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATTTGCTATTTTTAGCCTGCTCCACTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCA
1138659 GGGAGGCAAGGCTGGTGACTTCG
66 GGGAGGCAAGGCTGGTGACTTCG
* * *
1138682 ATCTGCTTCGTTGTTGGTGCAGGAAGGTAAGATCTGCTATTTTCAGCCTGCTCCACTGCAACCCA
1 ATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCA
* *
1138747 AGGAGGCAAGGCTGATGACTTCG
66 GGGAGGCAAGGCTGGTGACTTCG
1138770 ATCTGCT
1 ATCTGCT
1138777 ATTTTTAGCC
Statistics
Matches: 169, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 169 1.00
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (88 bp):
ATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCA
GGGAGGCAAGGCTGGTGACTTCG
Found at i:1138800 original size:57 final size:57
Alignment explanation
Indices: 1138712--1138833 Score: 165
Period size: 57 Copynumber: 2.1 Consensus size: 57
1138702 AGGAAGGTAA
1138712 GATCTGCTATTTTCAGCCTGCTCCACTGCAACCCAAGGAGGCAAGGCT-GATGACTTC
1 GATCTGCTATTTTCAGCCTGCTCCACTGCAACCCAAGGAGGCAAGGCTAG-TGACTTC
* ** * * *
1138769 GATCTGCTATTTTTAGCCTGCTCTGCTGCAACCGAGGGAGGCAAGGCTAGTGTCTTC
1 GATCTGCTATTTTCAGCCTGCTCCACTGCAACCCAAGGAGGCAAGGCTAGTGACTTC
*
1138826 GATTTGCT
1 GATCTGCT
1138834 TCGCTGTCGG
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
57 56 0.98
58 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (57 bp):
GATCTGCTATTTTCAGCCTGCTCCACTGCAACCCAAGGAGGCAAGGCTAGTGACTTC
Found at i:1138949 original size:232 final size:233
Alignment explanation
Indices: 1138536--1139008 Score: 716
Period size: 232 Copynumber: 2.0 Consensus size: 233
1138526 AGGAAGGCAA
* * *
1138536 GATCTACTATTTTTAATCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
1 GATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
*
1138601 TCGCTGTCGGTGCAGGAAGGTAAGATTTGCTATTTTTAGCCTGCTCCACTGCAACCCAGGGAGGC
66 TCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCAGGGAGGC
* * * *
1138666 AAGGCTGGTGACTTCGATCTGCTTCGTTGTTGGTGCAGGAAGGTAAGATCTGCTA-TTTTCAGCC
131 AAAGCTGGTGACTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTACTTTT-AGCC
*
1138730 TGCTCCACTGCAACCCAAGGAGGCAAGGCTGATGACTTC
195 TGCTCCACTACAACCCAAGGAGGCAAGGCTGATGACTTC
* * * *
1138769 GATCTGCTATTTTTAGCCTGCTCTGCTGCAACCGAGGGAGGCAAGGCTAGTGTCTTCGATTTGCT
1 GATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
* *
1138834 TCGCTGTCGGTGCAGGAAGG-AAGGTCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGC
66 TCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCAGGGAGGC
* * *
1138898 AAAGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGTTACTTTTAGCCT
131 AAAGCTGGTGACTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTACTTTTAGCCT
** * * *
1138963 GCTCTGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTC
196 GCTCCACTACAACCCAAGGAGGCAAGGCTGATGACTTC
1139001 GATCTGCT
1 GATCTGCT
1139009 TCGCTGTCGG
Statistics
Matches: 216, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
232 134 0.62
233 82 0.38
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (233 bp):
GATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCT
TCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAGCCTGCTCCACTGCAACCCAGGGAGGC
AAAGCTGGTGACTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTACTTTTAGCCT
GCTCCACTACAACCCAAGGAGGCAAGGCTGATGACTTC
Found at i:1138993 original size:88 final size:88
Alignment explanation
Indices: 1138769--1139301 Score: 762
Period size: 88 Copynumber: 6.1 Consensus size: 88
1138759 TGATGACTTC
* * * *
1138769 GATCTGCTATTTTTAGCCTGCTCTGCTGCAACCGAGGGAGGCAAGGCTAGTGTCTTCGATTTGCT
1 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
1138834 TCGCTGTCGGTGCAGGAAGG-AA
66 TCGCTGTCGGTGCAGGAAGGCAA
* *
1138856 GGTCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAAGCTGGTGTCTTCGATCTGCT
1 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
*
1138921 TTGCTGTCGGTGCAGGAAGGCAA
66 TCGCTGTCGGTGCAGGAAGGCAA
* * * *
1138944 GATCTGTTACTTTTAGCCTGCTCTGCTACAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
1 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
1139009 TCGCTGTCGGTGCAGGAAGGCAA
66 TCGCTGTCGGTGCAGGAAGGCAA
* * *
1139032 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGAGAGGCAAGGCTGGTGACTTCAATCTGCT
1 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
* * *
1139097 TCACTGTCAGTGCAGGAAGGTAA
66 TCGCTGTCGGTGCAGGAAGGCAA
* ** * * *
1139120 GATCTGTTATTTTTAGCCTATTCCGCTGCAACCCAGGGAGGCAAGACTGGTGACTTCGATCTACT
1 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
* *
1139185 TCGCTGTCGGTGTAGGAAAGCAA
66 TCGCTGTCGGTGCAGGAAGGCAA
* * * * *
1139208 GATATGCTATTTTTAACCTGCTCCGCTGCAACCCCGAGAGGCAAGGCTGGTGTCTTTGATCTGCT
1 GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
* * *
1139273 TCGCTGCCAGTACAGGAAGGCAA
66 TCGCTGTCGGTGCAGGAAGGCAA
1139296 GATCTG
1 GATCTG
1139302 TTATCTTCAC
Statistics
Matches: 392, Mismatches: 53, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
87 78 0.20
88 314 0.80
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.27
Consensus pattern (88 bp):
GATCTGCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCT
TCGCTGTCGGTGCAGGAAGGCAA
Found at i:1139030 original size:44 final size:44
Alignment explanation
Indices: 1138807--1139032 Score: 124
Period size: 44 Copynumber: 5.2 Consensus size: 44
1138797 CAACCGAGGG
* *
1138807 AGGCAAGGCTAGTGTCTTCGATTTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* * ** * * **** *
1138851 AGG-AAGGTCTGCTAT-TTTTAGCCTGCTCCGCTG-CAACCCAGGG
1 AGGCAAGG-CTGGTGTCTTCGA-TCTGCTTCGCTGTCGGTGCAGGA
* *
1138894 AGGCAAAGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
* ** * * **** *
1138938 AGGCAAGATCT-GT-TACTTTTAGCCTGC-TCTGCT-ACAACCCAGGG
1 AGGCAAG-GCTGGTGT-CTTCGA-TCTGCTTC-GCTGTCGGTGCAGGA
1138982 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
1139026 AGGCAAG
1 AGGCAAG
1139033 ATCTGCTATT
Statistics
Matches: 121, Mismatches: 48, Indels: 26
0.62 0.25 0.13
Matches are distributed among these distances:
43 39 0.32
44 72 0.60
45 10 0.08
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.27
Consensus pattern (44 bp):
AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGA
Found at i:1146296 original size:23 final size:22
Alignment explanation
Indices: 1146253--1146310 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
1146243 AAAGGGTATC
* *
1146253 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1146274 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
1146297 TACATATCATATCT
1 TACAAATCATATCT
1146311 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1146313 original size:19 final size:19
Alignment explanation
Indices: 1146266--1146344 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 19
1146256 AAATTAAATC
*
1146266 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
1146286 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
1146308 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
1146329 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
1146345 CTCGAAGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.28
21 18 0.36
22 7 0.14
23 11 0.22
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:1146326 original size:21 final size:21
Alignment explanation
Indices: 1146300--1146343 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1146290 CTAAGATTAC
1146300 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
1146321 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
1146342 AT
1 AT
1146344 CCTCGAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:1148188 original size:3 final size:3
Alignment explanation
Indices: 1148169--1148217 Score: 82
Period size: 3 Copynumber: 16.3 Consensus size: 3
1148159 CCTTAATTTG
1148169 TTA TTA -TA TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1148214 TTA T
1 TTA T
1148218 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1148560 original size:18 final size:18
Alignment explanation
Indices: 1148539--1148578 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1148529 ATATATGTTC
1148539 ATAATTTATTAATATATT
1 ATAATTTATTAATATATT
* * *
1148557 ATAATTTTTTTATATTTT
1 ATAATTTATTAATATATT
1148575 ATAA
1 ATAA
1148579 ATACATGTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATAATTTATTAATATATT
Found at i:1149894 original size:16 final size:16
Alignment explanation
Indices: 1149873--1149907 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1149863 ACTTGTTGTG
1149873 TTTTGACTGCATGGCA
1 TTTTGACTGCATGGCA
* *
1149889 TTTTGATTGCATTGCA
1 TTTTGACTGCATGGCA
1149905 TTT
1 TTT
1149908 GCATCTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (16 bp):
TTTTGACTGCATGGCA
Found at i:1152531 original size:1 final size:1
Alignment explanation
Indices: 1152527--1152601 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
1152517 TAAAAAAGGG
* * * * * * * * * *
1152527 AAAAAAAAAGAAAACAATAAAAAAAGAAGAACAAAAAAGAACAAAAAAACAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1152592 CAAAAAAAAA
1 AAAAAAAAAA
1152602 CTTTACGGGG
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.01
Consensus pattern (1 bp):
A
Found at i:1152550 original size:16 final size:15
Alignment explanation
Indices: 1152527--1152601 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 15
1152517 TAAAAAAGGG
*
1152527 AAAAAAAAAGAAAAC
1 AAAAAAAAAAAAAAC
*
1152542 AATAAAAAAAGAAGAAC
1 AA-AAAAAAA-AAAAAC
1152559 AAAAAAGAACAAAAAAAC
1 -AAAAA-AA-AAAAAAAC
1152577 AAAAACAAAAAAAAAC
1 AAAAA-AAAAAAAAAC
1152593 AAAAAAAAA
1 AAAAAAAAA
1152602 CTTTACGGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
15 6 0.12
16 20 0.39
17 14 0.27
18 9 0.18
19 2 0.04
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:1152572 original size:24 final size:24
Alignment explanation
Indices: 1152527--1152599 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
1152517 TAAAAAAGGG
* *
1152527 AAAAA-AAAAGAAAACAATAAAAAA
1 AAAAACAAAAAAAAACAA-AAAAAC
*
1152551 AGAAGAACAAAAAAGAACAAAAAAAC
1 A-AA-AACAAAAAAAAACAAAAAAAC
1152577 AAAAACAAAAAAAAACAAAAAAA
1 AAAAACAAAAAAAAACAAAAAAA
1152600 AACTTTACGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 20 0.48
25 4 0.10
26 8 0.19
27 10 0.24
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.01
Consensus pattern (24 bp):
AAAAACAAAAAAAAACAAAAAAAC
Found at i:1152602 original size:10 final size:10
Alignment explanation
Indices: 1152527--1152602 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
1152517 TAAAAAAGGG
1152527 AAAAA-AAAA
1 AAAAACAAAA
*
1152536 GAAAACAATAA
1 AAAAACAA-AA
*
1152547 AAAAAGAAGAA
1 AAAAACAA-AA
*
1152558 CAAAAA-AGAA
1 -AAAAACAAAA
* *
1152568 CAAAA-AAAC
1 AAAAACAAAA
1152577 AAAAACAAAA
1 AAAAACAAAA
1152587 AAAAACAAAA
1 AAAAACAAAA
1152597 AAAAAC
1 AAAAAC
1152603 TTTACGGGGG
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
9 14 0.26
10 23 0.43
11 11 0.21
12 5 0.09
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.01
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:1153133 original size:15 final size:16
Alignment explanation
Indices: 1153091--1153144 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
1153081 GATGATGTAA
1153091 AAAAATGTGAAAAAATG
1 AAAAATG-GAAAAAATG
*
1153108 -AAAAT-G-TAAAATG
1 AAAAATGGAAAAAATG
1153121 AAAAATGGAAAAAAT-
1 AAAAATGGAAAAAATG
1153136 AAAAATGGA
1 AAAAATGGA
1153145 GAGGCTAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 6 0.19
14 6 0.19
15 10 0.31
16 10 0.31
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AAAAATGGAAAAAATG
Found at i:1155145 original size:50 final size:49
Alignment explanation
Indices: 1154511--1155136 Score: 365
Period size: 50 Copynumber: 12.5 Consensus size: 49
1154501 TCTCGACATA
*** * * * *
1154511 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGT
1 GCAATT-AAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * ** * * * *
1154561 GCAGTGGAGCAGATTGAAGTCACAACGGCGGATTTGGTTTTCCTGACAGC
1 GCAAT-TAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* *** * * * *
1154611 GCAATTAAAAAGATTGAAGCCACAACGGCGGGTCTTACTTCCCTGGCGGT
1 GCAATT-AAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * ** * * *
1154661 GCAGTGGAGCAGATTGAAGTCACAACAGTGGATCTGGTTTCCCCGACAGC
1 GCAAT-TAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* ** * * * *
1154711 GCAATTAAAAAGATTGAAGCCTCAACGGCGGATCTTATTTCCCTGGCGGT
1 GCAATT-AAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * ** * * *
1154761 GCAGTGGAGCAGATTGAAGTCACAACGGCAGG-TCTAGTTTTCCCGACAGC
1 GCAAT-TAAAAGATTGAAGCCACAACGGC-GGATCTGGTTTCCCCGACAGC
* ** * * * *
1154811 GCAATTAAAAAGATTGAAGCCTCAACGGCGGATCTTATTTCCCTGGCGGT
1 GCAATT-AAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * ** *
1154861 GCAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
1 GCAAT-TAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * * *** * *
1154911 GTAATTAAAAAGATTGAAGCCACAACAGCGGGTCTTACTTCCCCGACGGT
1 GCAATT-AAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * * ** *
1154961 GTAGTGGAGCAGATTGAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
1 GCAAT-TAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* *** * * *
1155011 ACAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGT
1 GCAATT-AAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
* * ** *
1155061 GCAGTGGAGCAGATTGAA-CTCACAACGACGGATCTGGTTTCCCCGACAGC
1 GCAAT-TAAAAGATTGAAGC-CACAACGGCGGATCTGGTTTCCCCGACAGC
1155111 GCAATTAAAAGGATTGAAGCCACAAC
1 GCAATTAAAA-GATTGAAGCCACAAC
1155137 AACAGATCTT
Statistics
Matches: 412, Mismatches: 148, Indels: 32
0.70 0.25 0.05
Matches are distributed among these distances:
49 5 0.01
50 404 0.98
51 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (49 bp):
GCAATTAAAAGATTGAAGCCACAACGGCGGATCTGGTTTCCCCGACAGC
Found at i:1155208 original size:100 final size:100
Alignment explanation
Indices: 1154511--1155179 Score: 1043
Period size: 100 Copynumber: 6.7 Consensus size: 100
1154501 TCTCGACATA
1154511 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* * *
1154576 GAAGTCACAACGGCGGATTTGGTTTTCCTGACAGC
66 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
*
1154611 GCAATTAAAAAGATTGAAGCCACAACGGCGGGTCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
1154676 GAAGTCACAACAGTGGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
* *
1154711 GCAATTAAAAAGATTGAAGCCTCAACGGCGGATCTTATTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
1154776 GAAGTCACAACGGCAGG-TCTAGTTTTCCCGACAGC
66 GAAGTCACAACGGC-GGATCTGGTTTCCCCGACAGC
* *
1154811 GCAATTAAAAAGATTGAAGCCTCAACGGCGGATCTTATTTCCCTGGCGGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1154876 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
* * * * * *
1154911 GTAATTAAAAAGATTGAAGCCACAACAGCGGGTCTTACTTCCCCGACGGTGTAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1154976 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
* *
1155011 ACAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCAGTGCAGTGGAGCAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
* *
1155076 GAACTCACAACGACGGATCTGGTTTCCCCGACAGC
66 GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
* ** * * * * * *
1155111 GCAATTAAAAGGATTGAAGCCACAACAACAGATCTTACCTCCTTAGCGGTGCAGTTGAACAGATT
1 GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
1155176 GAAG
66 GAAG
1155180 CTACGACGGT
Statistics
Matches: 522, Mismatches: 45, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
99 2 0.00
100 518 0.99
101 2 0.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.22
Consensus pattern (100 bp):
GCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGGCGGTGCAGTGGAGCAGATT
GAAGTCACAACGGCGGATCTGGTTTCCCCGACAGC
Found at i:1156646 original size:3 final size:3
Alignment explanation
Indices: 1156627--1156731 Score: 119
Period size: 3 Copynumber: 35.7 Consensus size: 3
1156617 CCTTAATTTG
1156627 TTA TTA -TA TTA TATA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1156671 TTA TTA TTA TTA TTA TATA TTG TTA TAA GTA TTG TTA TT- TCA -TA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1156715 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
1156732 TTTTATTGAT
Statistics
Matches: 86, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
2 6 0.07
3 74 0.86
4 6 0.07
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1181781 original size:10 final size:10
Alignment explanation
Indices: 1181754--1181787 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1181744 TGGCAAAAAC
*
1181754 TTTTAATATA
1 TTTTAAAATA
1181764 TATTTAAAATA
1 T-TTTAAAATA
1181775 TTTTAAAATA
1 TTTTAAAATA
1181785 TTT
1 TTT
1181788 ATGTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:1184088 original size:16 final size:16
Alignment explanation
Indices: 1184067--1184100 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1184057 TACCTTAGCA
1184067 AAATAATTATATAATT
1 AAATAATTATATAATT
* *
1184083 AAATAATTTTGTAATT
1 AAATAATTATATAATT
1184099 AA
1 AA
1184101 TAGACGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATAATTATATAATT
Found at i:1187407 original size:24 final size:25
Alignment explanation
Indices: 1187380--1187436 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1187370 GGCTGTCCGA
* *
1187380 AGCTTCTTGA-ATATGGA-TCTTTTG
1 AGCTTCTTGATATAT-GACTCATATG
*
1187404 AGCTTCCTGATATATGACTCATATG
1 AGCTTCTTGATATATGACTCATATG
1187429 AGCTTCTT
1 AGCTTCTT
1187437 ATTATATAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.42
Consensus pattern (25 bp):
AGCTTCTTGATATATGACTCATATG
Found at i:1194574 original size:26 final size:26
Alignment explanation
Indices: 1194540--1194606 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
1194530 AAGCTCTTAT
* * *
1194540 GAGCGTCCCGATATATA-GCTCTTTGG
1 GAGCTTCCCGAT-TAAAGGCTCTTTCG
*
1194566 GAGCTTCCCGATTAAAGGCTCTTTCT
1 GAGCTTCCCGATTAAAGGCTCTTTCG
*
1194592 GAGCTTCCTGATTAA
1 GAGCTTCCCGATTAA
1194607 TGCCTTTCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 3 0.09
26 32 0.91
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (26 bp):
GAGCTTCCCGATTAAAGGCTCTTTCG
Found at i:1194625 original size:25 final size:26
Alignment explanation
Indices: 1194557--1194628 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
1194547 CCGATATATA
** *
1194557 GCTCTTTGGGAGCTTCCCGATTAAAG
1 GCTCTTTCAGAGCTTCCTGATTAAAG
* *
1194583 GCTCTTTCTGAGCTTCCTGATT-AAT
1 GCTCTTTCAGAGCTTCCTGATTAAAG
1194608 GC-CTTTCCAGAGCTTCCTGAT
1 GCTCTTT-CAGAGCTTCCTGAT
1194629 ATGGCTCGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 4 0.10
25 17 0.43
26 19 0.47
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (26 bp):
GCTCTTTCAGAGCTTCCTGATTAAAG
Found at i:1202016 original size:19 final size:19
Alignment explanation
Indices: 1201992--1202030 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1201982 TAGTGGAAAA
*
1201992 ATTAGATAATTCTACTAAC
1 ATTAGATAATTCCACTAAC
1202011 ATTAGATAATTCCACTAAC
1 ATTAGATAATTCCACTAAC
1202030 A
1 A
1202031 CCCTTGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTAGATAATTCCACTAAC
Found at i:1213021 original size:16 final size:16
Alignment explanation
Indices: 1213002--1213037 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1212992 CGTAATAACG
1213002 AAAAAAATTAATTCGA
1 AAAAAAATTAATTCGA
*
1213018 AAAAAAATTAATTTGA
1 AAAAAAATTAATTCGA
1213034 AAAA
1 AAAA
1213038 CTCCGATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAAAAATTAATTCGA
Found at i:1213099 original size:18 final size:18
Alignment explanation
Indices: 1213076--1213113 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1213066 GGATTACCTC
*
1213076 GTAAATATAGGTAGGGGT
1 GTAAATATAGATAGGGGT
1213094 GTAAATATAGATAGGGGT
1 GTAAATATAGATAGGGGT
1213112 GT
1 GT
1213114 TACAATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (18 bp):
GTAAATATAGATAGGGGT
Found at i:1216402 original size:318 final size:318
Alignment explanation
Indices: 1215825--1216460 Score: 1272
Period size: 318 Copynumber: 2.0 Consensus size: 318
1215815 ATGGGGGTAT
1215825 TTTTATAATTTTGTTTATTTTTAGTTTTCAAATATATAAAAATTTTAATAAATTTGTTAATCTCA
1 TTTTATAATTTTGTTTATTTTTAGTTTTCAAATATATAAAAATTTTAATAAATTTGTTAATCTCA
1215890 ACTAAAATTGAGTTTATCTTTAATTAGAAGTTAAAATTGAAAGGATATTTAATAAAAAAATTCTA
66 ACTAAAATTGAGTTTATCTTTAATTAGAAGTTAAAATTGAAAGGATATTTAATAAAAAAATTCTA
1215955 TAAAATAATTTAGGGTAAACAATTAAAATAGTCACTTTTGTTTATCTCAATTCATTTTAGTCACT
131 TAAAATAATTTAGGGTAAACAATTAAAATAGTCACTTTTGTTTATCTCAATTCATTTTAGTCACT
1216020 TATGTTTGAAATGTTATATTTTAGTCACTTATGTTATCGTGTTGTAACATTTTAATCACTAAGCC
196 TATGTTTGAAATGTTATATTTTAGTCACTTATGTTATCGTGTTGTAACATTTTAATCACTAAGCC
1216085 ATTAATTGTCGTTAATGGTGTAACAGTAAGTTGGCGTGGCACGTTAAATAATCATTTC
261 ATTAATTGTCGTTAATGGTGTAACAGTAAGTTGGCGTGGCACGTTAAATAATCATTTC
1216143 TTTTATAATTTTGTTTATTTTTAGTTTTCAAATATATAAAAATTTTAATAAATTTGTTAATCTCA
1 TTTTATAATTTTGTTTATTTTTAGTTTTCAAATATATAAAAATTTTAATAAATTTGTTAATCTCA
1216208 ACTAAAATTGAGTTTATCTTTAATTAGAAGTTAAAATTGAAAGGATATTTAATAAAAAAATTCTA
66 ACTAAAATTGAGTTTATCTTTAATTAGAAGTTAAAATTGAAAGGATATTTAATAAAAAAATTCTA
1216273 TAAAATAATTTAGGGTAAACAATTAAAATAGTCACTTTTGTTTATCTCAATTCATTTTAGTCACT
131 TAAAATAATTTAGGGTAAACAATTAAAATAGTCACTTTTGTTTATCTCAATTCATTTTAGTCACT
1216338 TATGTTTGAAATGTTATATTTTAGTCACTTATGTTATCGTGTTGTAACATTTTAATCACTAAGCC
196 TATGTTTGAAATGTTATATTTTAGTCACTTATGTTATCGTGTTGTAACATTTTAATCACTAAGCC
1216403 ATTAATTGTCGTTAATGGTGTAACAGTAAGTTGGCGTGGCACGTTAAATAATCATTTC
261 ATTAATTGTCGTTAATGGTGTAACAGTAAGTTGGCGTGGCACGTTAAATAATCATTTC
1216461 AAACAAAAAT
Statistics
Matches: 318, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
318 318 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (318 bp):
TTTTATAATTTTGTTTATTTTTAGTTTTCAAATATATAAAAATTTTAATAAATTTGTTAATCTCA
ACTAAAATTGAGTTTATCTTTAATTAGAAGTTAAAATTGAAAGGATATTTAATAAAAAAATTCTA
TAAAATAATTTAGGGTAAACAATTAAAATAGTCACTTTTGTTTATCTCAATTCATTTTAGTCACT
TATGTTTGAAATGTTATATTTTAGTCACTTATGTTATCGTGTTGTAACATTTTAATCACTAAGCC
ATTAATTGTCGTTAATGGTGTAACAGTAAGTTGGCGTGGCACGTTAAATAATCATTTC
Found at i:1216562 original size:10 final size:10
Alignment explanation
Indices: 1216523--1216573 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
1216513 AGTAATTTAA
1216523 TTTTTTTTTC
1 TTTTTTTTTC
* *
1216533 TTTTATGTTC
1 TTTTTTTTTC
1216543 TTTTAATTTTTC
1 TTTT--TTTTTC
1216555 -TTTTTTTTC
1 TTTTTTTTTC
*
1216564 TTTATTTTTC
1 TTTTTTTTTC
1216574 ATTCTCTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 6 0.18
10 20 0.61
11 3 0.09
12 4 0.12
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1216839 original size:21 final size:22
Alignment explanation
Indices: 1216815--1216859 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1216805 AATAGAAAAT
* *
1216815 AAAGAA-AAAAAAGGAAAGTTA
1 AAAGAACAAAAAAGAAAAATTA
*
1216836 AAAGAACATAAAAGAAAAATTA
1 AAAGAACAAAAAAGAAAAATTA
1216858 AA
1 AA
1216860 TTGCTCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.11
Consensus pattern (22 bp):
AAAGAACAAAAAAGAAAAATTA
Found at i:1219513 original size:100 final size:100
Alignment explanation
Indices: 1219251--1220024 Score: 1071
Period size: 100 Copynumber: 7.7 Consensus size: 100
1219241 AAGAATTGAT
* ** * * *
1219251 GCTTCAATCTTTTTAATTGCGCTGTCGAAGAAATCAGATCCGCCGTTATGACTTCAATCTGCTCT
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
* * **
1219316 ACTACACCGCCAGGTAAGTAAGATCTGCTATTGTG
66 ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
** * * *
1219351 GCTTCAAAAAAAGAATTTTAAATTACACTGTCAGGGAAACCAGATCCGCCGTTGTGACTTCAATC
1 GCTTC-----AA-TCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATC
* * *
1219416 TGCTCCACTGCACTGCCAGGGAAGTAAGATATGCTGTTGTG
60 TGCTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
* * *
1219457 GCTTCAAACTTTTAAATTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
* *
1219522 ACTGTACCGCCAGGGAAGTAAGATCCGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
* * *
1219557 GCTTCAATCTTTTTAATTGCATTGTCGAGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCT
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
** *
1219622 ACTGCACCGCCAGGGAAGTAAGATCCACCGTTGTA
66 ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
* * *
1219657 GCTTCAACCTTTTTAGTTGCACTGTCGGGAAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
**
1219722 ACTGCACCGCTGGGGAAGTAAGATCTGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
* * * *
1219757 GCTTCAATCTTTTTAATTGCCCTGTTGAGGAAACCAGATCCGCAGTTGTGACTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
*
1219822 ACTGCATCGCCAGGGAAGTAAGATCTGCCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
* * *
1219857 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACCAGATTCGCCGTTGTAACTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
* **
1219922 ACTGCACCGCCGGGGAAGTAAGATCCACCGTTGTG
66 ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
* *
1219957 GCTTCAATCTTTTTAATTGCACTGTCAGGGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCC
1 GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
1220022 ACT
66 ACT
1220025 ACAACGCCCA
Statistics
Matches: 598, Mismatches: 70, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
100 512 0.86
101 2 0.00
105 2 0.00
106 82 0.14
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.29
Consensus pattern (100 bp):
GCTTCAATCTTTTTAATTGCACTGTCGGGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCC
ACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
Found at i:1224416 original size:15 final size:15
Alignment explanation
Indices: 1224396--1224442 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
1224386 CCTTAGCCTC
1224396 TCCATTTTTACTTTT
1 TCCATTTTTACTTTT
1224411 TCCATTTTT-CATTTT
1 TCCATTTTTAC-TTTT
*
1224426 TCCATTTTTATTTTT
1 TCCATTTTTACTTTT
1224441 TC
1 TC
1224443 ATATCTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.03
15 28 0.97
ACGTcount: A:0.13, C:0.19, G:0.00, T:0.68
Consensus pattern (15 bp):
TCCATTTTTACTTTT
Found at i:1224418 original size:8 final size:8
Alignment explanation
Indices: 1224396--1224434 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
1224386 CCTTAGCCTC
1224396 TCCATTTT
1 TCCATTTT
*
1224404 TAC-TTTT
1 TCCATTTT
1224411 TCCATTTT
1 TCCATTTT
1224419 T-CATTTT
1 TCCATTTT
1224426 TCCATTTT
1 TCCATTTT
1224434 T
1 T
1224435 ATTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.67
Consensus pattern (8 bp):
TCCATTTT
Found at i:1224982 original size:24 final size:24
Alignment explanation
Indices: 1224948--1224993 Score: 76
Period size: 23 Copynumber: 1.9 Consensus size: 24
1224938 GTAGAGGTTT
1224948 TTTTTGTTTCTTTTTTTGTTTTTAG
1 TTTTTGTTTC-TTTTTTGTTTTTAG
1224973 TTTTTG-TTCTTTTTTGTTTTT
1 TTTTTGTTTCTTTTTTGTTTTT
1224994 TTGTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 12 0.57
24 3 0.14
25 6 0.29
ACGTcount: A:0.02, C:0.04, G:0.11, T:0.83
Consensus pattern (24 bp):
TTTTTGTTTCTTTTTTGTTTTTAG
Found at i:1224992 original size:6 final size:6
Alignment explanation
Indices: 1224948--1225037 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
1224938 GTAGAGGTTT
*
1224948 TTTTTG TTTCTT- TTTTTG TTTTTAG TTTTTG -TTCT- TTTTTG TTTTT-
1 TTTTTG TTT-TTG TTTTTG TTTTT-G TTTTTG TTTTTG TTTTTG TTTTTG
* * * *
1224994 TTGTTG CTTTTTTG TTTTTG TTGTTG TTGTTG TTTTTT TTTTTG
1 TTTTTG --TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
1225038 GATTGAATTT
Statistics
Matches: 68, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
5 12 0.18
6 43 0.63
7 8 0.12
8 5 0.07
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.80
Consensus pattern (6 bp):
TTTTTG
Found at i:1224994 original size:24 final size:25
Alignment explanation
Indices: 1224948--1225037 Score: 82
Period size: 25 Copynumber: 3.7 Consensus size: 25
1224938 GTAGAGGTTT
1224948 TTTTTGTTTCTTTTTTTGTTTTTAG
1 TTTTTGTTTCTTTTTTTGTTTTTAG
1224973 TTTTTG-TTC-TTTTTTGTTTTT--
1 TTTTTGTTTCTTTTTTTGTTTTTAG
* * *
1224994 TTGTTGCTTTTTTGTTTTTGTTGTT-G
1 TTTTTG-TTTCTT-TTTTTGTTTTTAG
* *
1225020 TTGTTGTTTTTTTTTTTG
1 TTTTTGTTTCTTTTTTTG
1225038 GATTGAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
21 5 0.09
23 14 0.25
24 10 0.18
25 22 0.39
26 6 0.11
ACGTcount: A:0.01, C:0.03, G:0.16, T:0.80
Consensus pattern (25 bp):
TTTTTGTTTCTTTTTTTGTTTTTAG
Found at i:1230939 original size:18 final size:18
Alignment explanation
Indices: 1230916--1230998 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 18
1230906 ATAAAACATG
1230916 AAAATATAA-ATATCATAA
1 AAAATATAATATAT-ATAA
*
1230934 AAAATATGAATGTATATAA
1 AAAATAT-AATATATATAA
*
1230953 AAAATAT-ATAAACTAT-A
1 AAAATATAATATA-TATAA
*
1230970 AAAATAAAATAATATGATAA
1 AAAATATAAT-ATAT-ATAA
1230990 TAAAATATA
1 -AAAATATA
1230999 TACGTACTAC
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
17 10 0.20
18 13 0.25
19 17 0.33
20 4 0.08
21 7 0.14
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
AAAATATAATATATATAA
Found at i:1235722 original size:20 final size:20
Alignment explanation
Indices: 1235697--1235748 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1235687 ATATACACAT
1235697 TAAAAATATAAAAAAATTCA
1 TAAAAATATAAAAAAATTCA
* * *
1235717 TAAAAATAT-ATATAATTTA
1 TAAAAATATAAAAAAATTCA
1235736 TAAAACATATAAA
1 TAAAA-ATATAAA
1235749 TTATAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.46
20 13 0.50
21 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TAAAAATATAAAAAAATTCA
Found at i:1235747 original size:16 final size:16
Alignment explanation
Indices: 1235726--1235766 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1235716 ATAAAAATAT
*
1235726 ATATAATTTATAAAAC
1 ATATAAATTATAAAAC
1235742 ATATAAATTATAAAA-
1 ATATAAATTATAAAAC
*
1235757 ATAAAAATTA
1 ATATAAATTA
1235767 CAATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATTATAAAAC
Found at i:1237130 original size:15 final size:16
Alignment explanation
Indices: 1237110--1237143 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1237100 CCTTATCAAA
1237110 TTTCAATTAAT-TTAT
1 TTTCAATTAATCTTAT
*
1237125 TTTCAATTTATCTTAT
1 TTTCAATTAATCTTAT
1237141 TTT
1 TTT
1237144 TTAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTCAATTAATCTTAT
Found at i:1242792 original size:2 final size:2
Alignment explanation
Indices: 1242785--1242819 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1242775 AATATGAATC
1242785 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1242820 TCATATAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1252445 original size:39 final size:39
Alignment explanation
Indices: 1252402--1252476 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 39
1252392 TTATTTATGC
*
1252402 AGTTGTTACTATTTAGAGATAAACATGAGACATTCGGTA
1 AGTTGTTACTATTTAGAGACAAACATGAGACATTCGGTA
1252441 AGTTGTTACTATTTAGAGACAAACATGAGACATTCG
1 AGTTGTTACTATTTAGAGACAAACATGAGACATTCG
1252477 ATACTCCACA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (39 bp):
AGTTGTTACTATTTAGAGACAAACATGAGACATTCGGTA
Found at i:1253592 original size:12 final size:12
Alignment explanation
Indices: 1253575--1253608 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1253565 AAAATGTTAC
1253575 TATTTTTGGATA
1 TATTTTTGGATA
1253587 TATTTTTGGATA
1 TATTTTTGGATA
1253599 TATTTTTGGA
1 TATTTTTGGA
1253609 CAAAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (12 bp):
TATTTTTGGATA
Found at i:1258377 original size:26 final size:26
Alignment explanation
Indices: 1258346--1258398 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1258336 GTCGCATGAC
1258346 AAAGCTCATGATATAACGTCGCCAAA
1 AAAGCTCATGATATAACGTCGCCAAA
1258372 AAAGCTCATGATATAACGTCGCCAAA
1 AAAGCTCATGATATAACGTCGCCAAA
1258398 A
1 A
1258399 TCATTGAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (26 bp):
AAAGCTCATGATATAACGTCGCCAAA
Found at i:1261436 original size:2 final size:2
Alignment explanation
Indices: 1261431--1261464 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1261421 ATCAATTAAG
1261431 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1261465 GTGCACTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1263687 original size:22 final size:22
Alignment explanation
Indices: 1263647--1263688 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1263637 TTTTTTACAA
*
1263647 TTTTTTACTATTTTCTTGTTGT
1 TTTTTTACTATTATCTTGTTGT
*
1263669 TTTTTTACTATTATGTTGTT
1 TTTTTTACTATTATCTTGTT
1263689 ATTGTTTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.07, G:0.10, T:0.71
Consensus pattern (22 bp):
TTTTTTACTATTATCTTGTTGT
Found at i:1263934 original size:101 final size:102
Alignment explanation
Indices: 1263813--1264015 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 102
1263803 TTTAATTTAT
1263813 TTTTAATTTATTGAGAAACATTTATTTTAATATTTTTAGTATTTTGATGTATTATATATATTTAA
1 TTTTAATTTATTGAGAAACATTTATTTTAATATTTTTAGTATTTTGATGTATTATATATATTTAA
1263878 AAAATTACATAATGAATAATATAAAAAAATTAATACA
66 AAAATTACATAATGAATAATATAAAAAAATTAATACA
1263915 TTTTAATTTA-TGAGAAACATTTATTTTAATATTTTTAGTATTTTGATGTATTATATATATTTAA
1 TTTTAATTTATTGAGAAACATTTATTTTAATATTTTTAGTATTTTGATGTATTATATATATTTAA
1263979 AAAATTACATAATGAATAATATAAAAAAATTAATACA
66 AAAATTACATAATGAATAATATAAAAAAATTAATACA
1264016 GGCAGACTAG
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 91 0.90
102 10 0.10
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (102 bp):
TTTTAATTTATTGAGAAACATTTATTTTAATATTTTTAGTATTTTGATGTATTATATATATTTAA
AAAATTACATAATGAATAATATAAAAAAATTAATACA
Found at i:1264789 original size:21 final size:21
Alignment explanation
Indices: 1264763--1264807 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1264753 CTAATGAAAT
1264763 CCATTTTCTTCAGTTTTCTCA
1 CCATTTTCTTCAGTTTTCTCA
*
1264784 CCATTTTCTTTAGTTTTCTCA
1 CCATTTTCTTCAGTTTTCTCA
1264805 CCA
1 CCA
1264808 ATCAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.04, T:0.51
Consensus pattern (21 bp):
CCATTTTCTTCAGTTTTCTCA
Found at i:1272081 original size:21 final size:20
Alignment explanation
Indices: 1272033--1272108 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
1272023 GATTGTTTGA
*
1272033 TGTTTAAATCAATTCATTCT
1 TGTTTAAATCGATTCATTCT
* *
1272053 TATTTAAATTGATTCATTGCT
1 TGTTTAAATCGATTCATT-CT
*
1272074 AT-TTTAAATCAATTCATTCT
1 -TGTTTAAATCGATTCATTCT
1272094 TGTTTAAATCGATTC
1 TGTTTAAATCGATTC
1272109 TATATTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.02
20 29 0.62
21 16 0.34
22 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (20 bp):
TGTTTAAATCGATTCATTCT
Found at i:1276487 original size:54 final size:55
Alignment explanation
Indices: 1276368--1276491 Score: 144
Period size: 54 Copynumber: 2.3 Consensus size: 55
1276358 ATGTATTAAG
* * *
1276368 TCAGTGTGTTACACGGTCTAGCACACGGCCTACCGACAAGACCGTGTGTCGCAAG
1 TCAGTGAGTTACACGGTCTAGCACACGGCCTACCGACAAGACCGTGTGACGCAAC
** ** * *
1276423 TCAAAGAGTTACACGGTCTAGCACACGG-CTTGCGACACGACTGTGTGAC-CTAAC
1 TCAGTGAGTTACACGGTCTAGCACACGGCCTACCGACAAGACCGTGTGACGC-AAC
1276477 TCAGTGAGTTACACG
1 TCAGTGAGTTACACG
1276492 ATTTAAAACA
Statistics
Matches: 57, Mismatches: 11, Indels: 3
0.80 0.15 0.04
Matches are distributed among these distances:
53 1 0.02
54 31 0.54
55 25 0.44
ACGTcount: A:0.26, C:0.27, G:0.26, T:0.21
Consensus pattern (55 bp):
TCAGTGAGTTACACGGTCTAGCACACGGCCTACCGACAAGACCGTGTGACGCAAC
Found at i:1312861 original size:12 final size:12
Alignment explanation
Indices: 1312844--1312869 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1312834 CCATAGCAAA
1312844 AAAAAAAAAAAC
1 AAAAAAAAAAAC
1312856 AAAAAAAAAAAC
1 AAAAAAAAAAAC
1312868 AA
1 AA
1312870 CTTAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1316542 original size:17 final size:17
Alignment explanation
Indices: 1316494--1316541 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
1316484 ATACTCGAAT
1316494 AAAATAAAAAGAAAATG
1 AAAATAAAAAGAAAATG
* *
1316511 AAAATGAAATGAAAATG
1 AAAATAAAAAGAAAATG
*
1316528 ATAATAAAAA-AAAA
1 AAAATAAAAAGAAAA
1316542 ACAAATAGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (17 bp):
AAAATAAAAAGAAAATG
Found at i:1316798 original size:27 final size:27
Alignment explanation
Indices: 1316768--1316821 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1316758 AATGTTGTGG
1316768 AAAATGTTATCTTTGAGAAATTTGAGT
1 AAAATGTTATCTTTGAGAAATTTGAGT
1316795 AAAATGTTATCTTTGAGAAATTTGAGT
1 AAAATGTTATCTTTGAGAAATTTGAGT
1316822 TGTTGAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (27 bp):
AAAATGTTATCTTTGAGAAATTTGAGT
Done.