Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold393
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1263635
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 115792 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:665956 original size:17 final size:17
Alignment explanation
Indices: 665934--665982 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
665924 CCAAGGTTTT
665934 ACTTCGAGAGATCAAGA
1 ACTTCGAGAGATCAAGA
*
665951 ACTTCGAGAGATC--GG
1 ACTTCGAGAGATCAAGA
*
665966 AGTTCGAGAGATCAAGA
1 ACTTCGAGAGATCAAGA
665983 GTAAATTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.48
17 14 0.52
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (17 bp):
ACTTCGAGAGATCAAGA
Found at i:666067 original size:15 final size:16
Alignment explanation
Indices: 666030--666069 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
666020 CCGTGAGTTC
666030 ACTTCGAGAGATCAAGA
1 ACTTCGAGAGATC-AGA
666047 ACTTCGAGAGATC-GA
1 ACTTCGAGAGATCAGA
*
666062 AGTTCGAG
1 ACTTCGAG
666070 CCATCGAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (16 bp):
ACTTCGAGAGATCAGA
Found at i:674799 original size:11 final size:11
Alignment explanation
Indices: 674782--674815 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
674772 CTACTACACC
674782 ACACGCTCGCT
1 ACACGCTCGCT
*
674793 GCACGCTCGCT
1 ACACGCTCGCT
*
674804 ACCCGCTCGCT
1 ACACGCTCGCT
674815 A
1 A
674816 AACGGTTCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.15, C:0.47, G:0.21, T:0.18
Consensus pattern (11 bp):
ACACGCTCGCT
Found at i:674840 original size:21 final size:21
Alignment explanation
Indices: 674811--674917 Score: 142
Period size: 21 Copynumber: 5.1 Consensus size: 21
674801 GCTACCCGCT
* *
674811 CGCTAAACGGTTCACACGAAA
1 CGCTGAACGGTTTACACGAAA
674832 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
* * * *
674853 CGCTGCACGCTTTGCCCGAAA
1 CGCTGAACGGTTTACACGAAA
* *
674874 CGCTAAACGATTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
674895 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
674916 CG
1 CG
674918 ATTCTCGCAC
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:675443 original size:16 final size:16
Alignment explanation
Indices: 675419--675453 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
675409 ACTTGCATGC
675419 AACAAAGTTCATGTAA
1 AACAAAGTTCATGTAA
*
675435 AACACAGTTCATGTAA
1 AACAAAGTTCATGTAA
675451 AAC
1 AAC
675454 TGACTCAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (16 bp):
AACAAAGTTCATGTAA
Found at i:684367 original size:11 final size:11
Alignment explanation
Indices: 684353--684402 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
684343 CGGGTTTACT
684353 AGAGTGAACCC
1 AGAGTGAACCC
*
684364 AGAGTTAACCC
1 AGAGTGAACCC
*
684375 AGAGTAAACCC
1 AGAGTGAACCC
* *
684386 AAAGTTAACCC
1 AGAGTGAACCC
*
684397 TGAGTG
1 AGAGTG
684403 GATACAGAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 32 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (11 bp):
AGAGTGAACCC
Found at i:684384 original size:22 final size:22
Alignment explanation
Indices: 684353--684401 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
684343 CGGGTTTACT
* *
684353 AGAGTGAACCCAGAGTTAACCC
1 AGAGTAAACCCAAAGTTAACCC
684375 AGAGTAAACCCAAAGTTAACCC
1 AGAGTAAACCCAAAGTTAACCC
*
684397 TGAGT
1 AGAGT
684402 GGATACAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.16
Consensus pattern (22 bp):
AGAGTAAACCCAAAGTTAACCC
Found at i:685364 original size:21 final size:21
Alignment explanation
Indices: 685340--685379 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
685330 TGCAATTAAA
*
685340 TTTACACTATGTAACATTATG
1 TTTACACTATGTAAAATTATG
*
685361 TTTACATTATGTAAAATTA
1 TTTACACTATGTAAAATTA
685380 AAATACATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (21 bp):
TTTACACTATGTAAAATTATG
Found at i:685996 original size:37 final size:37
Alignment explanation
Indices: 685905--686182 Score: 439
Period size: 37 Copynumber: 7.4 Consensus size: 37
685895 ATCGGTATTG
* * *
685905 TACTGTTACCAAATATTGTTACAGTAGGTAAGTTTCATT
1 TACTGTTACCAAATGTTGTTACAGCAGGT--GTTACATT
* *
685944 CACTGTTACCAAATGTTTTTACAGCAGGTGTTACATT
1 TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
*
685981 TGCTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
1 TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
*
686018 TGCTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
1 TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
*
686055 TACTGTTACCAAATGTTGTTACATCAGGTGTTACATT
1 TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
*
686092 TGCTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
1 TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
*
686129 CACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
1 TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
686166 TACCTGTTACCAAATGT
1 TA-CTGTTACCAAATGT
686183 CGTCACTGTC
Statistics
Matches: 223, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
37 184 0.83
38 14 0.06
39 25 0.11
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (37 bp):
TACTGTTACCAAATGTTGTTACAGCAGGTGTTACATT
Found at i:693026 original size:21 final size:21
Alignment explanation
Indices: 692964--693028 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
692954 TTGTTTTCTC
692964 TGTCAGATAATTATGTTAA-T
1 TGTCAGATAATTATGTTAACT
* * **
692984 TGTCAGAT-CTTAACGTCGACT
1 TGTCAGATAATT-ATGTTAACT
693005 TGTCAGATAATTATGTTAACT
1 TGTCAGATAATTATGTTAACT
693026 TGT
1 TGT
693029 TAAATATATA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
19 2 0.06
20 12 0.35
21 18 0.53
22 2 0.06
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTCAGATAATTATGTTAACT
Found at i:694303 original size:1 final size:1
Alignment explanation
Indices: 694297--694341 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
694287 ATATTCAAAG
* * * *
694297 TTTTTTTTTGTTTTTTTTTTTGTTGTTATTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
694342 GGGGGGGGGG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.02, C:0.00, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:694480 original size:21 final size:21
Alignment explanation
Indices: 694454--694542 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
694444 AACAGGGGCT
* **
694454 TGACAAGTTGACATGCTTATC
1 TGACAAGTCGACATAATTATC
*
694475 TGACAAGTCGACATAATTATG
1 TGACAAGTCGACATAATTATC
* * *
694496 TGACAAGTCGATATCAA-GACC
1 TGACAAGTCGACAT-AATTATC
* **
694517 TTACAAGTTAACATAATTATC
1 TGACAAGTCGACATAATTATC
694538 TGACA
1 TGACA
694543 CAAACAAAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
20 2 0.04
21 47 0.92
22 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (21 bp):
TGACAAGTCGACATAATTATC
Found at i:699929 original size:21 final size:21
Alignment explanation
Indices: 699897--699962 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
699887 AATAAGTGAA
* **
699897 AAGTCGATATAAAGATCTGAC
1 AAGTCGACATAATTATCTGAC
699918 AAGTC-ATCATAATTATCTGAC
1 AAGTCGA-CATAATTATCTGAC
*
699939 ATGTCGACATAATTATCTGAC
1 AAGTCGACATAATTATCTGAC
699960 AAG
1 AAG
699963 CAGTGGCAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (21 bp):
AAGTCGACATAATTATCTGAC
Found at i:720606 original size:16 final size:16
Alignment explanation
Indices: 720579--720622 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
720569 GAAGTGGTAA
*
720579 AGACAGATGGACGGAC
1 AGACAGACGGACGGAC
*
720595 AGACGGACGGACGGAC
1 AGACAGACGGACGGAC
720611 AGACAGACGGAC
1 AGACAGACGGAC
720623 TGACTGAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.39, T:0.02
Consensus pattern (16 bp):
AGACAGACGGACGGAC
Found at i:721294 original size:13 final size:13
Alignment explanation
Indices: 721276--721301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
721266 AATTTCTAAA
721276 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
721289 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
721302 GGTGAAAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:726340 original size:146 final size:146
Alignment explanation
Indices: 726055--726562 Score: 702
Period size: 146 Copynumber: 3.5 Consensus size: 146
726045 TGCAATTGTT
* *
726055 TCCGGTCCA-TATCTTTCTTTTGGAGAAACATTGGAA-GTTCTTACTTCACACAAAGATTGCTTA
1 TCCGGT-CATTATCTTTCTTATGGAGAAGCATT-GAATGTTCTTACTTCACACAAAGATTGCTTA
* * *
726118 TGACCTAAGGGTGTGTCATGACCTTCACCCAAGGTCATTCGGGCAAGGTCAAGGTCACTGGCAGA
64 TGACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGA
* *
726183 AAAAATACAAAATTCGTG
129 AAAAGTGCAAAATTCGTG
* *
726201 TCCAGTCCA-TATCTTTCTTATGGAG-AGTTATTGGAA-GTTCTTACTTCACACAAAGATTGCTT
1 TCCGGT-CATTATCTTTCTTATGGAGAAG-CATT-GAATGTTCTTACTTCACACAAAGATTGCTT
* ** * *
726263 ATGACCAAAGGATGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCGTTGGGAT
63 ATGACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAG
* *
726328 AAATAGTGCAAAATTCGTT
128 AAAAAGTGCAAAATTCGTG
* * *
726347 TCCGGTCATTATCTTTCTTATGGAGAAGCATTGAATGTTCTAACTTCACACAAATATTGCTTAGG
1 TCCGGTCATTATCTTTCTTATGGAGAAGCATTGAATGTTCTTACTTCACACAAAGATTGCTTATG
* * *
726412 ACCAAAGGGTGTGTCATGACTTTGACCCAAGGTCATTTGGGCATGGTCAAGATCACTGGCAGAAA
66 ACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
**
726477 AAGTGCAAAATTTATG
131 AAGTGCAAAATTCGTG
* *
726493 TCCGGTCATTGTCTTTCTTATGGAGAAGCATTGAATGTTCTTACTTCACACAAATATTGCTTATG
1 TCCGGTCATTATCTTTCTTATGGAGAAGCATTGAATGTTCTTACTTCACACAAAGATTGCTTATG
726558 ACCAA
66 ACCAA
726563 CAGTTTTAAA
Statistics
Matches: 322, Mismatches: 36, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
145 6 0.02
146 314 0.98
147 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (146 bp):
TCCGGTCATTATCTTTCTTATGGAGAAGCATTGAATGTTCTTACTTCACACAAAGATTGCTTATG
ACCAAAGGGTGTGTCATGACCTTGACCCAAGGTCATTTGGGCAAGGTCAAGGTCACTGGCAGAAA
AAGTGCAAAATTCGTG
Found at i:729082 original size:2 final size:2
Alignment explanation
Indices: 729075--729119 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
729065 GCTTAACAAG
729075 CT CT CT CT 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 CT CT CT CT
729117 CT C
1 CT C
729120 NATAAATGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:743090 original size:21 final size:21
Alignment explanation
Indices: 743064--743108 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
743054 TTTTAGCTTC
743064 GCACGAGCTCTCGCATACGTT
1 GCACGAGCTCTCGCATACGTT
* *
743085 GCACGAGTTCTCGCATTCGTT
1 GCACGAGCTCTCGCATACGTT
743106 GCA
1 GCA
743109 TACGTTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (21 bp):
GCACGAGCTCTCGCATACGTT
Found at i:745285 original size:171 final size:165
Alignment explanation
Indices: 744945--745514 Score: 496
Period size: 171 Copynumber: 3.4 Consensus size: 165
744935 CCTCTCATGT
* * *
744945 CCTGAACCCCTGACCCAGAGGCCATCAATT-TCACAATTTAGGTAGAGGAG-TT-AGTGGACATC
1 CCTGAACCCCTGACCCAGGGGTCAT-AATTCTCAC--TTTAGGTAGAGG-GCTTCA-TGGACATT
*** * * * * * * * *
745007 ATAACCATTTATTCAGTTTTTTGCCCATATGTGTGGGA-TAGAGAAGAAGATTTTTTAAGATTTA
61 ATAACCAGGCATTTAGTTTTAT-ACAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGGTTTA
* ** * **
745071 A-ATCATATTTT-CAATATGGTTATATTGGCCCCACCCCAGAG
125 ATA-CAT-TTTTACTATATGGCCATATTTGCCCCACCTTAGAG
* * ** *
745112 CCTGAACCTCTTACATAGGGGTCATGAATTCTCACTTTAGGCAGAGGGCTTCATGGACATTATAA
1 CCTGAACCCCTGACCCAGGGGTCAT-AATTCTCACTTTAGGTAGAGGGCTTCATGGACATTATAA
*
745177 CCAGGCATTTAGTTTTAAACATATATATATATATGGGAGTAGAGAAGAAGATTTTCTAAGGTTTA
65 CCAGGCATTTAGTTTT----ATACA-ATATATATGGGAGTAGAGAAGAAGATTTTCTAAGGTTTA
*
745242 ATACATTTTTACTATTTGGCCATATTTGCCCCACCTTAGAG
125 ATACATTTTTACTATATGGCCATATTTGCCCCACCTTAGAG
* ** * *
745283 CCTGAACCCCTGACCCAGGGGTTATAGATATCAAAATTTAGGTAGAGGGCTTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATA-AT-TCTCACTTTAGGTAGAGGGCTTCATGGACATTATA
* * * *
745348 ATCATGCATTTAGTTTTTTACAATATATATGGCAGT--AG-AGAAGATTTTCTAAGGTTTAATAC
64 ACCAGGCATTTAGTTTTATACAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGGTTTAATAC
* * *
745410 ATTTTTACTATATGACCTTA-TTGGCCCACCTTAGAG
129 ATTTTTACTATATGGCCATATTTGCCCCACCTTAGAG
* * * * *
745446 CCAGAACCCCTGACCCAGGGGCCATAAATT-TCACAATTTTGGTAGAGGGTTTCATGGATATTAT
1 CCTGAACCCCTGACCCAGGGGTCAT-AATTCTCAC--TTTAGGTAGAGGGCTTCATGGACATTAT
745510 AACCA
63 AACCA
745515 TGCAACAAGT
Statistics
Matches: 329, Mismatches: 58, Indels: 36
0.78 0.14 0.09
Matches are distributed among these distances:
161 1 0.00
162 1 0.00
163 67 0.20
164 42 0.13
165 3 0.01
166 36 0.11
167 37 0.11
168 7 0.02
170 16 0.05
171 73 0.22
172 46 0.14
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (165 bp):
CCTGAACCCCTGACCCAGGGGTCATAATTCTCACTTTAGGTAGAGGGCTTCATGGACATTATAAC
CAGGCATTTAGTTTTATACAATATATATGGGAGTAGAGAAGAAGATTTTCTAAGGTTTAATACAT
TTTTACTATATGGCCATATTTGCCCCACCTTAGAG
Found at i:745492 original size:163 final size:164
Alignment explanation
Indices: 744945--745518 Score: 545
Period size: 163 Copynumber: 3.4 Consensus size: 164
744935 CCTCTCATGT
* *
744945 CCTGAACCCCTGACCCAGAGGCCATCAATTTCACAATTTAGGTAGAGGAG-TT-AGTGGACATCA
1 CCTGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTAGGTAGAGG-GCTTCA-TGGACATCA
** * * * * * * *
745008 TAACCATTTATTCAGTTTTTTGCCCATATGTGTGGGA-TAGAGAAGAAGATTTTTTAAGATTTAA
64 TAACCATGCATTTAGTTTTTT-ACAATATATATGGGAGTA-AGAAGAAGATTTTCTAAGGTTTAA
* ** **
745072 -ATCATATTTT-CAATATGGTTATATTGGCCCCACCCCAGAG
127 TA-CAT-TTTTACTATATGCCT-TATTGG-CCCACCTTAGAG
* * ** * * * *
745112 CCTGAACCTCTTACATAGGGGTCATGAATTCTCAC--TTTAGGCAGAGGGCTTCATGGACATTAT
1 CCTGAACCCCTGACCCAGGGGCCATAAATT-TCACAATTTAGGTAGAGGGCTTCATGGACATCAT
* * *
745175 AACCAGGCATTTAGTTTTAAACATATATATATATATGGGAGTAGAGAAGAAGATTTTCTAAGGTT
65 AACCATGCATTTAGTTTT----TTACA-ATATATATGGGAGTA-AGAAGAAGATTTTCTAAGGTT
* * *
745240 TAATACATTTTTACTATTTGGCCATATTTGCCCCACCTTAGAG
124 TAATACATTTTTACTATAT-GCCTTA-TTGGCCCACCTTAGAG
** * * *
745283 CCTGAACCCCTGACCCAGGGGTTATAGATATCAAAATTTAGGTAGAGGGCTTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATA
* *
745348 ATCATGCATTTAGTTTTTTACAATATATATGGCAGT-AG-AGAAGATTTTCTAAGGTTTAATACA
66 ACCATGCATTTAGTTTTTTACAATATATATGGGAGTAAGAAGAAGATTTTCTAAGGTTTAATACA
745411 TTTTTACTATATGACCTTATTGGCCCACCTTAGAG
131 TTTTTACTATATG-CCTTATTGGCCCACCTTAGAG
* * * * *
745446 CCAGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTTGGTAGAGGGTTTCATGGATATTATA
1 CCTGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATA
745511 ACCATGCA
66 ACCATGCA
745519 ACAAGTTTTT
Statistics
Matches: 332, Mismatches: 59, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
163 78 0.23
164 40 0.12
165 3 0.01
166 36 0.11
167 37 0.11
168 7 0.02
170 18 0.05
171 66 0.20
172 47 0.14
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (164 bp):
CCTGAACCCCTGACCCAGGGGCCATAAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATA
ACCATGCATTTAGTTTTTTACAATATATATGGGAGTAAGAAGAAGATTTTCTAAGGTTTAATACA
TTTTTACTATATGCCTTATTGGCCCACCTTAGAG
Found at i:756157 original size:31 final size:31
Alignment explanation
Indices: 756119--756184 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
756109 ACTGAAAGTT
756119 TGGGTTTCTACAGGTGACCGTTGTTTTCTGG
1 TGGGTTTCTACAGGTGACCGTTGTTTTCTGG
756150 TGGGTTTCTACAGGTGACCGTTGTTTTCTGG
1 TGGGTTTCTACAGGTGACCGTTGTTTTCTGG
756181 TGGG
1 TGGG
756185 GAATGGAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (31 bp):
TGGGTTTCTACAGGTGACCGTTGTTTTCTGG
Found at i:756790 original size:144 final size:145
Alignment explanation
Indices: 756463--756847 Score: 655
Period size: 144 Copynumber: 2.7 Consensus size: 145
756453 NNNNNNNNNN
756463 GTCCATATCTTTTTAATGGACAAATATTGGAAGTTCTTAATGCACATCAAGATTGCTTATGACAT
1 GTCCATATCTTTTTAATGGACAAATATTGGAAGTTCTTAATGCACATCAAGATTGCTTATGACAT
* *
756528 GAGGGTGTGACATGACCTTGACCCAAGGTCATTTGGGCAAGGCCAAGGTCATTGGCAGATAAGTG
66 GAGGGTGTGACATGACCTTGACCCAAGGTCATTTGGGCAAGGCCAAGGTCACTGACAGATAAGTG
756593 CAAAATTCATGTCCA
131 CAAAATTCATGTCCA
756608 GTCCATATCTTTTTAATGGACAAATATTGGAAGTTCTTAATGCACATCAAGATTGCTTATGACAT
1 GTCCATATCTTTTTAATGGACAAATATTGGAAGTTCTTAATGCACATCAAGATTGCTTATGACAT
* *
756673 GAGGGTGTGACATGACCTTGA-CCAAGGTCATTTGGGCAAGGCCAAGGTTACTGACAGATAATTG
66 GAGGGTGTGACATGACCTTGACCCAAGGTCATTTGGGCAAGGCCAAGGTCACTGACAGATAAGTG
756737 CAAAATTCATGTCCA
131 CAAAATTCATGTCCA
* * * * * *
756752 GTCCATATCTTTCTAATGGATAAATATTGGAAGTTCTTAATTCACACCAAGATTGCTTATAACCT
1 GTCCATATCTTTTTAATGGACAAATATTGGAAGTTCTTAATGCACATCAAGATTGCTTATGACAT
* *
756817 GAGGATGTGTCATGACCTTGACCCAAGGTCA
66 GAGGGTGTGACATGACCTTGACCCAAGGTCA
756848 ATTGAGGAGT
Statistics
Matches: 227, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
144 132 0.58
145 95 0.42
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (145 bp):
GTCCATATCTTTTTAATGGACAAATATTGGAAGTTCTTAATGCACATCAAGATTGCTTATGACAT
GAGGGTGTGACATGACCTTGACCCAAGGTCATTTGGGCAAGGCCAAGGTCACTGACAGATAAGTG
CAAAATTCATGTCCA
Found at i:759124 original size:34 final size:33
Alignment explanation
Indices: 759028--759158 Score: 99
Period size: 34 Copynumber: 3.9 Consensus size: 33
759018 ATTGATTTAC
* *
759028 GAAAAATATTATTCACGCACTGGGAATCTGTAA
1 GAAAACTATGATTCACGCACTGGGAATCTGTAA
* * **
759061 -AATGAACTTTTGATTCAGGCACTTCGAATCCTG-AA
1 GAA--AAC-TATGATTCACGCACTGGGAAT-CTGTAA
759096 TGAAAACTATGATTCACGCACTGGGAATCTGTAA
1 -GAAAACTATGATTCACGCACTGGGAATCTGTAA
* *
759130 -AATAATTTTTGATTCACGCACT-GGAATCT
1 GAA-AA-CTATGATTCACGCACTGGGAATCT
759159 TGAATGAAAC
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
32 4 0.05
33 12 0.16
34 35 0.45
35 21 0.27
36 3 0.04
37 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (33 bp):
GAAAACTATGATTCACGCACTGGGAATCTGTAA
Found at i:759404 original size:18 final size:18
Alignment explanation
Indices: 759381--759418 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
759371 GTAGAAGATC
759381 TACTAAATGTTTGACGTA
1 TACTAAATGTTTGACGTA
759399 TACTAAATGTTTGACGTA
1 TACTAAATGTTTGACGTA
759417 TA
1 TA
759419 AAATAAAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (18 bp):
TACTAAATGTTTGACGTA
Found at i:767330 original size:12 final size:12
Alignment explanation
Indices: 767313--767338 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
767303 ATTATAATCT
767313 TTACCAGAATTG
1 TTACCAGAATTG
767325 TTACCAGAATTG
1 TTACCAGAATTG
767337 TT
1 TT
767339 GCATATATTT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (12 bp):
TTACCAGAATTG
Found at i:778968 original size:4 final size:4
Alignment explanation
Indices: 778954--778996 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
778944 AATTGGTGTA
*
778954 TATC CATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TAT
778997 ATATAAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (4 bp):
TATC
Found at i:788562 original size:46 final size:46
Alignment explanation
Indices: 788495--788582 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
788485 TAATATTACG
788495 TACATGTGAATAATCCGAAACTTTCAGATTGACAT-CGTTTGCAGGT
1 TACATGTGAATAATCCGAAACTTTCAGATTGA-ATCCGTTTGCAGGT
* * * *
788541 TACATGTGACTCATGCGAAACTTTCGGATTGAATCCGTTTGC
1 TACATGTGAATAATCCGAAACTTTCAGATTGAATCCGTTTGC
788583 CGGTAAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.05
46 35 0.95
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (46 bp):
TACATGTGAATAATCCGAAACTTTCAGATTGAATCCGTTTGCAGGT
Found at i:801653 original size:168 final size:167
Alignment explanation
Indices: 801303--802142 Score: 1083
Period size: 168 Copynumber: 5.0 Consensus size: 167
801293 GGAAAACATA
* * * * *
801303 ATCATGCATTTAGTTTTTAGCAAATACATATGGGAGTAGAGAAGGAGATTTTTTAAGATTTAATA
1 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTAATA
* * *
801368 CATTTTGACTATATAGCCATATTTGCCCACACCCTAGAGTCAGAACCCATGACACAGGGGTCATG
66 CATTTT-ACTATATGGCCATATTGGCCC-CACCCTAGAGCCAGAACCCATGACACAGGGGTCATG
*
801433 AATTTCAAAATTTTGGTAGAGGGCTTCATGGACATCATT
129 AATTTCAAAATTTTGATAGAGGGCTTCATGGACATCATT
* *
801472 ATCATGCATTTAGTTTTTAACAAATATATATGGAAGTAGAGAAGAAGACTTTCTAAGATTTTATA
1 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTAATA
* * *
801537 CATTTGTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCAAGACACAGGGTTAATGA
66 CATTT-TACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCATGACACAGGGGTCATGA
** * * *
801602 ATTTCATGATTTTGATAGAGGGTTTTATGGACATCATG
130 ATTTCAAAATTTTGATAGAGGGCTTCATGGACATCATT
* * * *
801640 ATCATGTATTTAGTTGTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTTAGATTTAATA
1 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTAATA
* ** ** *
801705 CAGTTTTACTATATGACCATATTGGCCCCACCCTAGAGCGTGAACCCCGGAC-CAAGGGGCCATG
66 CA-TTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCATGACAC-AGGGGTCATG
* * * * * *
801769 AATTTCATAATTTGGATTGAGGGCTTCAGGGAAATCATA
129 AATTTCAAAATTTTGATAGAGGGCTTCATGGACATCATT
* ** * *
801808 ATCACGCATTTAGTTTTTAACAAATACCTATGGGAGTAGAGAAGATGACTTTCTATGATTTAATA
1 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTAATA
* * *
801873 TATTTTTCCTAAACT-GCCATATTGGCCCCACCCTAGAGCCAGAACCCATGACACAGGGGTCATG
66 CA-TTTTACTATA-TGGCCATATTGGCCCCACCCTAGAGCCAGAACCCATGACACAGGGGTCATG
* *
801937 AATTTCAAAATTTTGGTAGAGGGCTTCATGGACATCTTT
129 AATTTCAAAATTTTGATAGAGGGCTTCATGGACATCATT
* *
801976 ATCATGCATTTAGTTTTTAACAAATGTATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTTATA
1 ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTAATA
* * *
802041 CATTTGTACTATATGGCCGTATTGGCCCCACCCTAGAGCCTGAACTCC-TGACCCAGGGGTCATG
66 CATTT-TACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAAC-CCATGACACAGGGGTCATG
* * * * *
802105 ACTTTCACAATTTTGGTAGAAGGCTTCGTGGACATCAT
129 AATTTCAAAATTTTGATAGAGGGCTTCATGGACATCAT
802143 AACCATTTAA
Statistics
Matches: 577, Mismatches: 86, Indels: 17
0.85 0.13 0.03
Matches are distributed among these distances:
167 5 0.01
168 482 0.84
169 89 0.15
170 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (167 bp):
ATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGACTTTCTAAGATTTAATA
CATTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCAGAACCCATGACACAGGGGTCATGAA
TTTCAAAATTTTGATAGAGGGCTTCATGGACATCATT
Found at i:813855 original size:34 final size:34
Alignment explanation
Indices: 813817--813893 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
813807 GAAACTGGAA
813817 AGCATTTATTTTGTTAAAAAATGACTTACTAAAG
1 AGCATTTATTTTGTTAAAAAATGACTTACTAAAG
813851 AGCATTTATTTTGTTAAAAAATGACTTACTAAAG
1 AGCATTTATTTTGTTAAAAAATGACTTACTAAAG
813885 AGCATTTAT
1 AGCATTTAT
813894 GACCAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (34 bp):
AGCATTTATTTTGTTAAAAAATGACTTACTAAAG
Found at i:818277 original size:24 final size:25
Alignment explanation
Indices: 818231--818279 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
818221 CAAAATAATA
*
818231 TACAGTACTGTACATGTATTATATT
1 TACAGTACTGTACATGTAATATATT
* *
818256 TACAGTA-TGTAGATTTAATATATT
1 TACAGTACTGTACATGTAATATATT
818280 ATGTGACGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (25 bp):
TACAGTACTGTACATGTAATATATT
Found at i:820177 original size:2 final size:2
Alignment explanation
Indices: 820170--820214 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
820160 TTAACAATAA
820170 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
820212 TC T
1 TC T
820215 GCTTATTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:821088 original size:19 final size:19
Alignment explanation
Indices: 821066--821106 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
821056 CCCCCCCCCC
* *
821066 AAAAAAAAAATAAATAAAT
1 AAAAAAAAAAGAAAGAAAT
*
821085 AAAAAATAAAGAAAGAAAT
1 AAAAAAAAAAGAAAGAAAT
821104 AAA
1 AAA
821107 TATTGTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.05, T:0.12
Consensus pattern (19 bp):
AAAAAAAAAAGAAAGAAAT
Found at i:821090 original size:15 final size:15
Alignment explanation
Indices: 821070--821108 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
821060 CCCCCCAAAA
* *
821070 AAAAAATAAATAAAT
1 AAAAAATAAAGAAAG
821085 AAAAAATAAAGAAAG
1 AAAAAATAAAGAAAG
821100 AAATAAATA
1 AAA-AAATA
821109 TTGTGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (15 bp):
AAAAAATAAAGAAAG
Found at i:832146 original size:165 final size:164
Alignment explanation
Indices: 831895--832287 Score: 714
Period size: 165 Copynumber: 2.4 Consensus size: 164
831885 GGGGACGAAG
* *
831895 TTTTACATTGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAACTTATCAGCCAGGA
1 TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAGGA
*
831960 AAGCTGAAACTTGTCTGAAAGCATCCTCAGGTTGTGTAGATTCAAAATTGTGAAAATCATGATCC
66 AAGCTGAAACTTATCTGAAAGCATCCTCAGGTTGTGTAGATTCAAAATTGTGAAAATCATGATCC
*
832025 CCAGGGGTAGGATGGGGCCACAATGGGTGTCAAA
131 CCAGGGGTAGGATGGGGCCACAATGGGGGTCAAA
832059 TTTTAACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAGG
1 TTTT-ACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAGG
*
832124 AAAGCTGAAACTTATGTGAAAGCATCCTCAGGTTGTGTAGATTCAAAATTGTGAAAATCATGATC
65 AAAGCTGAAACTTATCTGAAAGCATCCTCAGGTTGTGTAGATTCAAAATTGTGAAAATCATGATC
832189 CCCAGGGGTAGGATGGGGCCACAATGGGGGTCAAA
130 CCCAGGGGTAGGATGGGGCCACAATGGGGGTCAAA
*
832224 TTTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAG
1 -TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAG
832288 ATGATTCTTT
Statistics
Matches: 221, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
164 4 0.02
165 213 0.96
166 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (164 bp):
TTTTACATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAAAAACTAATCAGCCAGGA
AAGCTGAAACTTATCTGAAAGCATCCTCAGGTTGTGTAGATTCAAAATTGTGAAAATCATGATCC
CCAGGGGTAGGATGGGGCCACAATGGGGGTCAAA
Found at i:843653 original size:24 final size:24
Alignment explanation
Indices: 843626--843676 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
843616 ACCCTGTTCC
843626 GTCCGTCCGTCCGTCCGTCTGTCT
1 GTCCGTCCGTCCGTCCGTCTGTCT
843650 GTCCGTCCGTCCGTCCGTCTGTCT
1 GTCCGTCCGTCCGTCCGTCTGTCT
843674 GTC
1 GTC
843677 ACGTTTTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.00, C:0.41, G:0.25, T:0.33
Consensus pattern (24 bp):
GTCCGTCCGTCCGTCCGTCTGTCT
Found at i:843655 original size:20 final size:20
Alignment explanation
Indices: 843623--843672 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
843613 GTTACCCTGT
*
843623 TCCGTCCGTCCGTCCGTCCG
1 TCCGTCTGTCCGTCCGTCCG
*
843643 TCTGTCTGTCCGTCCGTCCG
1 TCCGTCTGTCCGTCCGTCCG
843663 TCCGTCTGTC
1 TCCGTCTGTC
843673 TGTCACGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.00, C:0.44, G:0.24, T:0.32
Consensus pattern (20 bp):
TCCGTCTGTCCGTCCGTCCG
Found at i:843676 original size:4 final size:4
Alignment explanation
Indices: 843623--843668 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
843613 GTTACCCTGT
* *
843623 TCCG TCCG TCCG TCCG TCCG TCTG TCTG TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
843669 TGTCTGTCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.00, C:0.46, G:0.24, T:0.30
Consensus pattern (4 bp):
TCCG
Found at i:844403 original size:163 final size:163
Alignment explanation
Indices: 844197--844591 Score: 580
Period size: 163 Copynumber: 2.4 Consensus size: 163
844187 TGGAGTAGCT
* * * * *
844197 ACATCATCTCTTGGGATATAATTGGGGCTGTCCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
* *
844262 ATTTCATCCTGGGAGTC-AAATAGTAGCAGAAAATTGACGTTTATCACTAAAAAAACAAACATTG
66 ATTTCATCCAGGGAGTCAAAAT-GTAGCAGAAAATTGACGTTTATCACTAAAAAAA-AAACATAG
*
844326 ATCCAAGAGCTCCTCTTATGATTTAATGGATAGAC
129 ATCCAAGAACTCCTCTTATGATTTAATGGATAGAC
* *
844361 A-ATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTCAAAATTTAA
1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
*
844425 ATTTCATCCAGGGAGTCAAAATGTAGCAGAAAATTGACGTTTATCACTTAAAAAAAAACATAGAT
66 ATTTCATCCAGGGAGTCAAAATGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAAACATAGAT
* *
844490 CCTAGAACTCCTTTTATGATTTAATGGATAGAC
131 CCAAGAACTCCTCTTATGATTTAATGGATAGAC
* * * * *
844523 ACATCATATCTTGGGATATGAAAGGAACTGTTCCATAGATGTGCATTACGGTTTTGAAAAA-TTA
1 ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTA
844587 AATTT
65 AATTT
844592 AACCCTGAGG
Statistics
Matches: 209, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
162 40 0.19
163 160 0.77
164 9 0.04
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (163 bp):
ACATCATATCTTGGGATATGATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAA
ATTTCATCCAGGGAGTCAAAATGTAGCAGAAAATTGACGTTTATCACTAAAAAAAAAACATAGAT
CCAAGAACTCCTCTTATGATTTAATGGATAGAC
Found at i:844787 original size:135 final size:135
Alignment explanation
Indices: 844639--844937 Score: 392
Period size: 134 Copynumber: 2.2 Consensus size: 135
844629 GATGCCCTTT
* *
844639 AAGGATCAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTCG-AGATATT-CGTGCA
1 AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTT-GAAGATATTAAG-GCA
* * * * *
844702 CTTCCTGTTCAAGGGGGGTCATGACCACCCCCGGGGCCCATGACCTACATACCGTTTGATGCCCC
64 CTTCCTGTTCAA-GGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCC
844767 TTGACA-C
128 TTGACATC
* *
844774 AAGGAACAAGAATATATATGGTTTAA-GGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGAC
1 AAGGAACAAGAATATATATGG-TTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCAC
* **
844838 TTGCTGTTTGAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
65 TTCCTGTTCAAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTT
844903 GACATC
130 GACATC
* * *
844909 -AGAAACATGAATATATATGGTTTAGGGGT
1 AAGGAACAAGAATATATATGGTTAAGGGGT
844938 CATGATTATA
Statistics
Matches: 144, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
133 3 0.02
134 76 0.53
135 60 0.42
136 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.26
Consensus pattern (135 bp):
AAGGAACAAGAATATATATGGTTAAGGGGTGGGGATCTCAACCGTTTTGAAGATATTAAGGCACT
TCCTGTTCAAGGGGGTCAGGACCACCCACAGGGCCCATGACCTACATAACATTTGATGCCCCTTG
ACATC
Found at i:847886 original size:16 final size:16
Alignment explanation
Indices: 847865--847899 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
847855 AAAATACCCG
847865 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
847881 GTAATTTGTGAAACTA
1 GTAATTTGTGAAACTA
847897 GTA
1 GTA
847900 TTTTTAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (16 bp):
GTAATTTGTGAAACTA
Found at i:848537 original size:16 final size:17
Alignment explanation
Indices: 848516--848548 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
848506 AGATAAGATT
848516 TTCCGTTTTCC-TTCCG
1 TTCCGTTTTCCGTTCCG
848532 TTCCGTTTTCCGTTCCG
1 TTCCGTTTTCCGTTCCG
848549 CGTTTTAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.00, C:0.36, G:0.15, T:0.48
Consensus pattern (17 bp):
TTCCGTTTTCCGTTCCG
Found at i:857205 original size:2 final size:2
Alignment explanation
Indices: 857198--857262 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
857188 TGCAATTTAT
857198 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
857240 GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA G
857263 TATTGGGCAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:861074 original size:2 final size:2
Alignment explanation
Indices: 861067--861123 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
861057 AGTTTACCTC
861067 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
861109 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
861124 ATAAATCAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:876566 original size:2 final size:2
Alignment explanation
Indices: 876559--876614 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
876549 GTGTTTTAAC
*
876559 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA TA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
876601 GA TA GA GA GA GA GA
1 GA GA GA GA GA GA GA
876615 CAGACAGACA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.46, T:0.04
Consensus pattern (2 bp):
GA
Found at i:876619 original size:4 final size:4
Alignment explanation
Indices: 876612--876639 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
876602 ATAGAGAGAG
876612 AGAC AGAC AGAC AGAC AGAC AGAC AGAC
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC
876640 GGAAAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.25, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:880513 original size:20 final size:20
Alignment explanation
Indices: 880488--880525 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
880478 TTCGAATACA
880488 CAATTTAAAATAAATTGATT
1 CAATTTAAAATAAATTGATT
* *
880508 CAATTTCAAATTAATTGA
1 CAATTTAAAATAAATTGA
880526 ATGTTTAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (20 bp):
CAATTTAAAATAAATTGATT
Found at i:880630 original size:44 final size:44
Alignment explanation
Indices: 880579--880734 Score: 186
Period size: 44 Copynumber: 3.5 Consensus size: 44
880569 CGCGTGAATA
* * *
880579 TGTCAGGTTTGACTTTTTGAGTGTGTAATATTTAGGAATGACTT
1 TGTCAGGTTTGACTTTTTGAGTGTGTACTATTTAGGCATTACTT
* * * * * *
880623 TATCAGGTTTTACTATTTGAGTGTGTACTATTAAGTCATTACTA
1 TGTCAGGTTTGACTTTTTGAGTGTGTACTATTTAGGCATTACTT
*
880667 TGTCAGGTTTGACTTTTTGAGTATGTACTATTTAGGCATTACTAAT
1 TGTCAGGTTTGACTTTTTGAGTGTGTACTATTTAGGCATTACT--T
* *
880713 TGTCAGGTTTTACATTTTGAGT
1 TGTCAGGTTTGACTTTTTGAGT
880735 ATACACTGCA
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
44 72 0.78
46 20 0.22
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.46
Consensus pattern (44 bp):
TGTCAGGTTTGACTTTTTGAGTGTGTACTATTTAGGCATTACTT
Found at i:880936 original size:44 final size:44
Alignment explanation
Indices: 880886--880981 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
880876 TTTAACTTCT
* * *
880886 GTGCAATATCCTAGTATTGTTTGACACTACTACTTTGAACTACA
1 GTGCAATATCCTAGTATGGTTTGACACTACGACTGTGAACTACA
** *
880930 GTGCAATATCCTAGTATGGTTTGACTTTACGACTGTGAACTACT
1 GTGCAATATCCTAGTATGGTTTGACACTACGACTGTGAACTACA
880974 GTGCAATA
1 GTGCAATA
880982 GTTTTTTCTG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (44 bp):
GTGCAATATCCTAGTATGGTTTGACACTACGACTGTGAACTACA
Found at i:884154 original size:2 final size:2
Alignment explanation
Indices: 884149--884185 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
884139 TGTAAACACA
*
884149 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
884186 ATAGGCCTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:887287 original size:12 final size:12
Alignment explanation
Indices: 887270--887299 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
887260 AATCATAGAA
887270 TGTAAATAGATG
1 TGTAAATAGATG
887282 TGTAAATAGATG
1 TGTAAATAGATG
887294 TGTAAA
1 TGTAAA
887300 AGGTTGCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (12 bp):
TGTAAATAGATG
Found at i:889557 original size:366 final size:365
Alignment explanation
Indices: 888886--889614 Score: 1054
Period size: 366 Copynumber: 2.0 Consensus size: 365
888876 CAGGCAACAC
* *
888886 TATATAAATAGTGCCTGTTTGGGAGGGAAACAGTTAAATTGACACCCGAGGAAACCATTGTCAAC
1 TATATAAATAGTGCCTGTTTGGGAGGGAAACAGTTAAATTGACACCCGAGAAAACCATTATCAAC
* * * ** *
888951 CGACGCGAAGCGGAGGTTGACAGTGGTTATCGAAGGGTGTCAATTTCAACTGTTATCCTCCCAAA
66 CGACGCGAAGCGGAGATTGACAATGGTTATCGAAGGGGGTCAATTTCAACACTTACCCTCCCAAA
* * ** *
889016 CAGGCACTATTTATTTTATTATACTGAATGTCTTAATCTTAGAGAATTTTTTACTGCTTTTAAAT
131 CAGGCACTATTTATTTTATTATACTAAATGTCTTAATCTTAAAGAATAATTTACAGCTTTTAAAT
** *
889081 AGAAAAAACGTGAATTCTATCGCGAACTGTACGCGCATGATTTACACGCATGTAACAATTTGTTG
196 AGAAAAAACGTGAATTCTATCGCGAACCATACGCGCATGATTTACACGCATGTAACAATTCGTTG
* **
889146 TGTTACCCGTTGCTAAGTGTGTTGCTAACGCTGAGGGTAATAGAACGGATTATTAACTGCGTCTA
261 TGTTACCCGTTGCTAAGTGTGTTGCTAACGCTGAAGGTAATAGAACGGATTACCAACTGCGTCTA
*
889211 AACCAATCAGATTTCAGTA-TTTAGCATGAAAGTATAATGA
326 AACCAATCAGATATCAGTATTTTA-CATGAAAGTATAATGA
* *
889251 TATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTGACACCCCGATAAAACCATTATCA
1 TATATAAATAGTGCCTGTTTGGGAGGGAAACAGTT-AAATTGACA-CCCGAGAAAACCATTATCA
* *
889316 ACCGACGCGAAGCGGAGATTGACAATGGTTTTCGAGGGGGGTCAATTTCAACACTTACCCTCCCA
64 ACCGACGCGAAGCGGAGATTGACAATGGTTATCGAAGGGGGTCAATTTCAACACTTACCCTCCCA
* * * *
889381 AACAGGCACTATTTATTTTATTATACTAAATGTTTTATTTTTAAAGAA-AATTTACAGCTTTTAT
129 AACAGGCACTATTTATTTTATTATACTAAATGTCTTAATCTTAAAGAATAATTTACAGCTTTTAA
*** * * * *
889445 ATAGAAGTGATGTGAATTTTA-CGGCTAACCATACGCGCAT-ACTTTACGCGCATGTAACAATTC
194 ATAGAAAAAACGTGAATTCTATC-GCGAACCATACGCGCATGA-TTTACACGCATGTAACAATTC
889508 GTTGTGTTACCCGTTG-TCAAGTGTGTTGCTAACGCTGAAGGTAATAGAACGGATTACCAACTGC
257 GTTGTGTTACCCGTTGCT-AAGTGTGTTGCTAACGCTGAAGGTAATAGAACGGATTACCAACTGC
889572 GTCTAAACCAATCAGATATCAGTATTTTACATGAAAGTATAAT
321 GTCTAAACCAATCAGATATCAGTATTTTACATGAAAGTATAAT
889615 TAAACGAATT
Statistics
Matches: 323, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
365 37 0.11
366 166 0.51
367 120 0.37
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (365 bp):
TATATAAATAGTGCCTGTTTGGGAGGGAAACAGTTAAATTGACACCCGAGAAAACCATTATCAAC
CGACGCGAAGCGGAGATTGACAATGGTTATCGAAGGGGGTCAATTTCAACACTTACCCTCCCAAA
CAGGCACTATTTATTTTATTATACTAAATGTCTTAATCTTAAAGAATAATTTACAGCTTTTAAAT
AGAAAAAACGTGAATTCTATCGCGAACCATACGCGCATGATTTACACGCATGTAACAATTCGTTG
TGTTACCCGTTGCTAAGTGTGTTGCTAACGCTGAAGGTAATAGAACGGATTACCAACTGCGTCTA
AACCAATCAGATATCAGTATTTTACATGAAAGTATAATGA
Found at i:893073 original size:2 final size:2
Alignment explanation
Indices: 893066--893128 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
893056 GAATTATACG
893066 TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
893107 TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC
893129 ATAAGAACAT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 59 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:893709 original size:52 final size:52
Alignment explanation
Indices: 893234--893695 Score: 692
Period size: 52 Copynumber: 8.9 Consensus size: 52
893224 GAATTACTAT
* * *
893234 AAATAAGACTAACTGTGTGACATCAGTAGAG-TCTCCTGACATGGTGTAGTAG
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCT-CTGACATGGTGTAGTAA
* * *
893286 AAATAAGACTAACTTTGTGACATCAGGAGAGAGCTCAGACATGGTGTAGTAT
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
* * * * *
893338 AAATAAGATTAACTTTGTGACATCAGCAGAGTGTTCTGACATGGTGTAGTAA
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
* * *
893390 AAATAAGACTAACTGTGTGACTTCAGTAGGGAGCTCTGACATGGTGTAGTAA
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
* * *
893442 AAATAAGACTAACTGTGTGACTTCAGTAGGGAGCTCTGACATGGTGTAGTAA
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
* * *
893494 AAATAAGACTAACTGTGTGACTTCAGTAGGGAGCTCTGACATGGTGTAGTAA
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
*
893546 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAT
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
* *
893598 AAATAAGACTAACTGTGTGACATCAGGAGAGAACTCTGACATGGTGTAGTAT
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
*
893650 AAATAAGACTAACTTTGTGACATCAGGAGAGAGCTCTGACATGGTG
1 AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTG
893696 ATGGTGTAGT
Statistics
Matches: 384, Mismatches: 25, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
52 382 0.99
53 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (52 bp):
AAATAAGACTAACTGTGTGACATCAGGAGAGAGCTCTGACATGGTGTAGTAA
Found at i:899254 original size:2 final size:2
Alignment explanation
Indices: 899247--899297 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
899237 AGATTAAAAG
*
899247 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT AT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
899289 CT CT CT CT C
1 CT CT CT CT C
899298 ATGCTATTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:900524 original size:2 final size:2
Alignment explanation
Indices: 900517--900575 Score: 57
Period size: 2 Copynumber: 29.5 Consensus size: 2
900507 TAAGCGGTCT
* * *
900517 GA GA GA GA GA GA TA GA GA GA -A CGA GA AA GA GA CA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA
* *
900559 GA CA GA GA GA GG GA GA G
1 GA GA GA GA GA GA GA GA G
900576 GGAGGGCAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
1 1 0.02
2 43 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.44, T:0.02
Consensus pattern (2 bp):
GA
Found at i:900535 original size:12 final size:12
Alignment explanation
Indices: 900517--900569 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
900507 TAAGCGGTCT
*
900517 GAGAGAGAGAGA
1 GAGAGAGAGACA
*
900529 TAGAGAGA-AC-
1 GAGAGAGAGACA
*
900539 GAGAAAGAGACA
1 GAGAGAGAGACA
900551 GAGAGAGAGACA
1 GAGAGAGAGACA
900563 GAGAGAG
1 GAGAGAG
900570 GGAGAGGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
12 25 0.74
ACGTcount: A:0.51, C:0.06, G:0.42, T:0.02
Consensus pattern (12 bp):
GAGAGAGAGACA
Found at i:900685 original size:2 final size:2
Alignment explanation
Indices: 900678--900718 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
900668 AAGCGGTCCC
900678 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
900719 TAAGGTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:902574 original size:2 final size:2
Alignment explanation
Indices: 902567--902600 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
902557 GGGGTATGTG
*
902567 GA GA GA GA GA TA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
902601 ATAAATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:907910 original size:8 final size:8
Alignment explanation
Indices: 907893--907926 Score: 50
Period size: 9 Copynumber: 4.0 Consensus size: 8
907883 TAGGCAGAAA
907893 AAAAACAAC
1 AAAAA-AAC
907902 AAAAAAAC
1 AAAAAAAC
907910 AAAAAACAC
1 AAAAAA-AC
907919 AAAAAAAC
1 AAAAAAAC
907927 CAACCTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.46
9 13 0.54
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:907920 original size:17 final size:18
Alignment explanation
Indices: 907892--907926 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
907882 GTAGGCAGAA
907892 AAAAAACAACAAAAAAAC
1 AAAAAACAACAAAAAAAC
907910 AAAAAAC-ACAAAAAAAC
1 AAAAAACAACAAAAAAAC
907927 CAACCTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAACAACAAAAAAAC
Found at i:914864 original size:4 final size:4
Alignment explanation
Indices: 914853--914891 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
914843 CTGTCGTTCC
* * *
914853 GTCG GTCT GTCT GTCG GTCG GTCG GTCG GTCT GTCG GTC
1 GTCG GTCG GTCG GTCG GTCG GTCG GTCG GTCG GTCG GTC
914892 CACCATCAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.00, C:0.26, G:0.41, T:0.33
Consensus pattern (4 bp):
GTCG
Found at i:914864 original size:20 final size:20
Alignment explanation
Indices: 914839--914892 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
914829 TGCTTTGCTG
*
914839 CTGTCTGTCGTTCCGTCGGT
1 CTGTCTGTCGGTCCGTCGGT
*
914859 CTGTCTGTCGGTCGGTCGGT
1 CTGTCTGTCGGTCCGTCGGT
*
914879 CGGTCTGTCGGTCC
1 CTGTCTGTCGGTCC
914893 ACCATCAGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.00, C:0.30, G:0.35, T:0.35
Consensus pattern (20 bp):
CTGTCTGTCGGTCCGTCGGT
Found at i:914870 original size:12 final size:12
Alignment explanation
Indices: 914853--914891 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
914843 CTGTCGTTCC
*
914853 GTCGGTCTGTCT
1 GTCGGTCTGTCG
*
914865 GTCGGTCGGTCG
1 GTCGGTCTGTCG
914877 GTCGGTCTGTCG
1 GTCGGTCTGTCG
914889 GTC
1 GTC
914892 CACCATCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.26, G:0.41, T:0.33
Consensus pattern (12 bp):
GTCGGTCTGTCG
Found at i:915488 original size:15 final size:16
Alignment explanation
Indices: 915441--915489 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 16
915431 TCATTGATTA
915441 ATATAATAGTATAGTCT
1 ATATAATAGTATAGT-T
915458 ATA-AGTATAGTATAGTT
1 ATATA--ATAGTATAGTT
915475 ATATAATA-TATAGTT
1 ATATAATAGTATAGTT
915490 TCTGTTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 7 0.24
16 4 0.14
17 7 0.24
18 11 0.38
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (16 bp):
ATATAATAGTATAGTT
Found at i:919564 original size:2 final size:2
Alignment explanation
Indices: 919545--919582 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
919535 ATAGTTTGCG
* *
919545 CA CA CG CA CA CG CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
919583 ATTGGCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00
Consensus pattern (2 bp):
CA
Found at i:923062 original size:20 final size:20
Alignment explanation
Indices: 923037--923079 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
923027 ACAGAGTTTG
923037 AAATTCTTTGTTTTATAAAC
1 AAATTCTTTGTTTTATAAAC
*
923057 AAATTCTTTGTTTTGTAAAC
1 AAATTCTTTGTTTTATAAAC
923077 AAA
1 AAA
923080 GTTAGAGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (20 bp):
AAATTCTTTGTTTTATAAAC
Found at i:929494 original size:2 final size:2
Alignment explanation
Indices: 929487--929527 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
929477 AATCTGAGCT
929487 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
929528 TTACACACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:930828 original size:21 final size:21
Alignment explanation
Indices: 930742--930917 Score: 127
Period size: 21 Copynumber: 8.3 Consensus size: 21
930732 ATGCACACTT
* * *
930742 TAAAATTTACACTTAAATATA
1 TAAAATTTACACTTTAATCTG
* *
930763 TAAATTTTACATTTTAATCTG
1 TAAAATTTACACTTTAATCTG
*** *
930784 TAAAATTTACACTTTTGCCAG
1 TAAAATTTACACTTTAATCTG
* *
930805 TAAAAGTCACACTTTAATCTG
1 TAAAATTTACACTTTAATCTG
* *
930826 TAAATTTTACACCTTAATCTG
1 TAAAATTTACACTTTAATCTG
* * * *
930847 TAAATTTTACACCTAAATCCG
1 TAAAATTTACACTTTAATCTG
* **
930868 TAAACTTTACACTTTAAAGTG
1 TAAAATTTACACTTTAATCTG
* * * *
930889 TGATATTTACCCCTTTAATTTG
1 TAAAATTTA-CACTTTAATCTG
930911 TAAAATT
1 TAAAATT
930918 CGCATTTAAA
Statistics
Matches: 117, Mismatches: 37, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
21 103 0.88
22 14 0.12
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (21 bp):
TAAAATTTACACTTTAATCTG
Found at i:930880 original size:63 final size:63
Alignment explanation
Indices: 930742--930884 Score: 155
Period size: 63 Copynumber: 2.3 Consensus size: 63
930732 ATGCACACTT
* ** **
930742 TAAAATTTACACTTAAATATATAAATTTTACATTTTAATCTGTAAAATTTACACTTTTGCCAG
1 TAAAATTTACACTTTAATATATAAATTTTACACCTTAATCTGTAAAATTTACACTAATGCCAG
* * * * *
930805 TAAAAGTCACACTTTAATCTGTAAATTTTACACCTTAATCTGTAAATTTTACACCTAAAT-CC-G
1 TAAAATTTACACTTTAATATATAAATTTTACACCTTAATCTGTAAAATTTACA-CT-AATGCCAG
*
930868 TAAACTTTACACTTTAA
1 TAAAATTTACACTTTAA
930885 AGTGTGATAT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
63 60 0.92
64 4 0.06
65 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (63 bp):
TAAAATTTACACTTTAATATATAAATTTTACACCTTAATCTGTAAAATTTACACTAATGCCAG
Found at i:931213 original size:21 final size:22
Alignment explanation
Indices: 931166--931214 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
931156 AAATTTATTG
* *
931166 TAAATTTCACACTTTTATCAGT
1 TAAATTTCACACTTTCATCACT
* *
931188 AAAATTT-ACACTTTCATCTCT
1 TAAATTTCACACTTTCATCACT
931209 TAAATT
1 TAAATT
931215 CATACTTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (22 bp):
TAAATTTCACACTTTCATCACT
Found at i:931292 original size:21 final size:21
Alignment explanation
Indices: 931268--931308 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
931258 ACAGTTTAGG
*
931268 CTGTAAAATTCACATTTTAAA
1 CTGTAAAATTCACACTTTAAA
*
931289 CTGTAAAATTCTCACTTTAA
1 CTGTAAAATTCACACTTTAA
931309 TCTCTACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (21 bp):
CTGTAAAATTCACACTTTAAA
Found at i:932292 original size:20 final size:21
Alignment explanation
Indices: 932257--932332 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
932247 TCTAACGTCC
*
932257 TTAATTTCTAAAATTTACACT
1 TTAATCTCTAAAATTTACACT
*
932278 TTAATCTCT-AAATTTACTCAT
1 TTAATCTCTAAAATTTACAC-T
* * *
932299 TT-ATCTGTAAAAATTACACA
1 TTAATCTCTAAAATTTACACT
*
932319 TTAATCTGTAAAAT
1 TTAATCTCTAAAAT
932333 ATTGTGTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.43
Consensus pattern (21 bp):
TTAATCTCTAAAATTTACACT
Found at i:933073 original size:14 final size:14
Alignment explanation
Indices: 933054--933080 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
933044 AAGACATTTG
933054 TATCCTTATGATAT
1 TATCCTTATGATAT
933068 TATCCTTATGATA
1 TATCCTTATGATA
933081 AGAAACGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (14 bp):
TATCCTTATGATAT
Found at i:935059 original size:21 final size:21
Alignment explanation
Indices: 934925--935516 Score: 162
Period size: 21 Copynumber: 28.1 Consensus size: 21
934915 ACATTTTGAA
* *
934925 GTGAATTTTACCGATTGAAGT
1 GTGAATTTTACAGATTAAAGT
* *
934946 -TTAATTTCACAGATTAAAGT
1 GTGAATTTTACAGATTAAAGT
* *
934966 GTGAATATCACAGATTTAAA-T
1 GTGAATTTTACAGA-TTAAAGT
* **
934987 GTTAATTTTAC-TTTGTAAAGT
1 GTGAATTTTACAGAT-TAAAGT
* * * *
935008 GTAAATTTTACATATTATAGA
1 GTGAATTTTACAGATTAAAGT
* *
935029 GTAAAATTTACAGATTAAAGT
1 GTGAATTTTACAGATTAAAGT
* **
935050 TTGAATTTTACAGATTGCAGT
1 GTGAATTTTACAGATTAAAGT
* ** * ** *
935071 GTAAATGCTACA-CTTTTATT
1 GTGAATTTTACAGATTAAAGT
* * * * *
935091 GTAAACTTTATAGATAAAAAT
1 GTGAATTTTACAGATTAAAGT
* * ** *
935112 -TAACAATAAACAGATTTAAGT
1 GTGA-ATTTTACAGATTAAAGT
*
935133 GTAAATTTTACAGATTAAAGT
1 GTGAATTTTACAGATTAAAGT
*
935154 GT-AAGTTTTACAGATTATAGT
1 GTGAA-TTTTACAGATTAAAGT
935175 GTGAATGTTT-CAG-TTGAAAGT
1 GTGAAT-TTTACAGATT-AAAGT
* * * *
935196 GT-AGTATT-C-GTATAAAAAT
1 GTGAATTTTACAG-ATTAAAGT
* *
935215 GTAAAATTTACAGATTAAAGT
1 GTGAATTTTACAGATTAAAGT
* * * *
935236 GTGAATTGTACAAATGAAAAT
1 GTGAATTTTACAGATTAAAGT
*
935257 TTGAATTTTACAGATTAAAGT
1 GTGAATTTTACAGATTAAAGT
* * * ** * *
935278 ATGAATTGTCCACTTTTAATT
1 GTGAATTTTACAGATTAAAGT
* * *
935299 GTAAATTTTACATATTAAAAT
1 GTGAATTTTACAGATTAAAGT
* *
935320 GTAAATTTAACAGATTACTGTAAAGT
1 GTGAATTTTACAG---A-T-TAAAGT
* * *
935346 GTGAATTTAACAGTTTCAAGT
1 GTGAATTTTACAGATTAAAGT
* * *
935367 GT-AAGATATACAG-TTTAAGT
1 GTGAA-TTTTACAGATTAAAGT
* *
935387 GTGAATTTTAAAGATTTGAA-T
1 GTGAATTTTACAGA-TTAAAGT
*
935408 TTGAATTTTACAGATGTAAGACTGAGT
1 GTGAATTTTACAGAT-T-A-A---AGT
*
935435 GTGAA-TTT-C--ATTAATGT
1 GTGAATTTTACAGATTAAAGT
* *
935452 GTAAATTTTACAGATTGAAGT
1 GTGAATTTTACAGATTAAAGT
* * *
935473 GT-ACAATTTACCGACTAAAGT
1 GTGA-ATTTTACAGATTAAAGT
*
935494 GTTAATTTTACA-AGTTAAAGT
1 GTGAATTTTACAGA-TTAAAGT
935515 GT
1 GT
935517 TTTTAAAATT
Statistics
Matches: 413, Mismatches: 118, Indels: 80
0.68 0.19 0.13
Matches are distributed among these distances:
17 6 0.01
18 4 0.01
19 11 0.03
20 64 0.15
21 273 0.66
22 23 0.06
23 3 0.01
24 1 0.00
25 2 0.00
26 21 0.05
27 5 0.01
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.39
Consensus pattern (21 bp):
GTGAATTTTACAGATTAAAGT
Found at i:935910 original size:11 final size:11
Alignment explanation
Indices: 935894--935923 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
935884 GATAAACAAT
935894 CTTTAAGCCAC
1 CTTTAAGCCAC
*
935905 CTTTAAGTCAC
1 CTTTAAGCCAC
935916 CTTTAAGC
1 CTTTAAGC
935924 TGAGCTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:935970 original size:11 final size:11
Alignment explanation
Indices: 935954--935988 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
935944 GTCCAAACTT
*
935954 CTTTAAGTCAC
1 CTTTAAGCCAC
*
935965 CTTTAAGCCAT
1 CTTTAAGCCAC
935976 CTTTAAGCCAC
1 CTTTAAGCCAC
935987 CT
1 CT
935989 AAATGCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:935981 original size:22 final size:21
Alignment explanation
Indices: 935953--936004 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
935943 TGTCCAAACT
*
935953 TCTTTAAGTCACCTTTAA-GCCA
1 TCTTTAAGTCACC-TAAATG-CA
*
935975 TCTTTAAGCCACCTAAATGCA
1 TCTTTAAGTCACCTAAATGCA
935996 TCTTTAAGT
1 TCTTTAAGT
936005 GGCATTTACG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.37
Consensus pattern (21 bp):
TCTTTAAGTCACCTAAATGCA
Found at i:936396 original size:2 final size:2
Alignment explanation
Indices: 936389--936422 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
936379 AATAAATAAA
* *
936389 TC TC TC TC TC TC TC TC TC TC TC TA TC TA TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
936423 AGTTCATCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.06, C:0.44, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:936853 original size:112 final size:112
Alignment explanation
Indices: 936640--936866 Score: 373
Period size: 112 Copynumber: 2.0 Consensus size: 112
936630 TAGTTTTGTT
* * * * *
936640 CGTTTGTGTTTATCTAATTAGAGTCTATTGTTTGTCCAACTTAAGAAAACCCATGGAACTAACAC
1 CGTTCGTGTATATCAAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCATGGAACTAACAA
* *
936705 AGAATATACAAGATATACACAACAGTTGTGTTGTGTGCCCAGGTGCA
66 AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
*
936752 CGTTCGTGTATATCAAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCCTGGAACTAACAA
1 CGTTCGTGTATATCAAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCATGGAACTAACAA
*
936817 AGAATATACAAGATATACACAACGGGTGTGTCGTGTGCCCAGGTGCA
66 AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
936864 CGT
1 CGT
936867 CAGGGTTTCT
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (112 bp):
CGTTCGTGTATATCAAATTAAAGTCTATTGTTTGTCCAACTTAAGAAAACCCATGGAACTAACAA
AGAATATACAAGATATACACAACAGGTGTGTCGTGTGCCCAGGTGCA
Found at i:939993 original size:52 final size:53
Alignment explanation
Indices: 939863--940025 Score: 260
Period size: 52 Copynumber: 3.1 Consensus size: 53
939853 TAAATATTAA
*
939863 TTATTAGGGGTTTTCGACTTTCGGTCGAAAAGACCTATTGTTTTCGTTCTGTT
1 TTATTAGGGCTTTTCGACTTTCGGTCGAAAAGACCTATTGTTTTCGTTCTGTT
*
939916 TTATTAGGGCTTTTCGACTTTCGGTCGAAGAGACCTATTGTTATTC-TTCTG-T
1 TTATTAGGGCTTTTCGACTTTCGGTCGAAAAGACCTATTGTT-TTCGTTCTGTT
* *
939968 TTATTAGGGCTTTTCGACTTTCGGTCGAAAAGACCTTTTGTTTTCG-TCTTTT
1 TTATTAGGGCTTTTCGACTTTCGGTCGAAAAGACCTATTGTTTTCGTTCTGTT
940020 TTATTA
1 TTATTA
940026 ATATTCTCGA
Statistics
Matches: 102, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
51 6 0.06
52 48 0.47
53 45 0.44
54 3 0.03
ACGTcount: A:0.17, C:0.16, G:0.20, T:0.47
Consensus pattern (53 bp):
TTATTAGGGCTTTTCGACTTTCGGTCGAAAAGACCTATTGTTTTCGTTCTGTT
Found at i:954165 original size:16 final size:17
Alignment explanation
Indices: 954144--954175 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
954134 GCATTACTTT
954144 GTAGGACT-GTATAATA
1 GTAGGACTGGTATAATA
954160 GTAGGACTGGTATAAT
1 GTAGGACTGGTATAAT
954176 CTTTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (17 bp):
GTAGGACTGGTATAATA
Found at i:957043 original size:16 final size:17
Alignment explanation
Indices: 957022--957053 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
957012 GCATTACTTT
957022 GTAGGACT-GTATAATA
1 GTAGGACTGGTATAATA
957038 GTAGGACTGGTATAAT
1 GTAGGACTGGTATAAT
957054 CTTTTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (17 bp):
GTAGGACTGGTATAATA
Found at i:959405 original size:31 final size:30
Alignment explanation
Indices: 959365--959429 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
959355 AAAGATGATA
* *
959365 AAAATCGAATTATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAAGTACGACTTAAC
*
959395 AAAATACGAATGATTTTAAGTACGACTTAAC
1 AAAAT-CGAATGATTCTAAGTACGACTTAAC
959426 AAAA
1 AAAA
959430 ACCTTTCCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAATCGAATGATTCTAAGTACGACTTAAC
Found at i:960228 original size:108 final size:108
Alignment explanation
Indices: 960039--960260 Score: 399
Period size: 108 Copynumber: 2.1 Consensus size: 108
960029 AAAATAATAA
* *
960039 TAACTAGAGCAAAGCTCGTTGCAAAGCAACGAGTGGGTCTTCCGTAAATGTCGGAAGTAAAGCTG
1 TAACTAGAGCAAAGCTCGTTGCAAAGCAACGAGAGAGTCTTCCGTAAATGTCGGAAGTAAAGCTG
*
960104 GAAGTTCCTGTAAGAAGCAGAGCTCTTAAACCAACAACAAGAG
66 GAAGTTCCTGTAAGAAGAAGAGCTCTTAAACCAACAACAAGAG
*
960147 TAACTAGAGCAAAGCTCGTTGCAAAGCAACGAGAGAGTCTTCCGTTAATGTCGGAAGTAAAGCTG
1 TAACTAGAGCAAAGCTCGTTGCAAAGCAACGAGAGAGTCTTCCGTAAATGTCGGAAGTAAAGCTG
*
960212 GAAGTTCCTGTAAGAAGAAGAGCTCTTAAACCAATAACAAGAG
66 GAAGTTCCTGTAAGAAGAAGAGCTCTTAAACCAACAACAAGAG
960255 TAACTA
1 TAACTA
960261 AAATAAAAAG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.20
Consensus pattern (108 bp):
TAACTAGAGCAAAGCTCGTTGCAAAGCAACGAGAGAGTCTTCCGTAAATGTCGGAAGTAAAGCTG
GAAGTTCCTGTAAGAAGAAGAGCTCTTAAACCAACAACAAGAG
Found at i:962129 original size:31 final size:30
Alignment explanation
Indices: 962089--962153 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
962079 TAAGATGAAA
* *
962089 AAAATCGAATTATTCCT-GGTACGACTTAAC
1 AAAATCGAATGATT-CTAAGTACGACTTAAC
*
962119 AAAATACGAATGATTTTAAGTACGACTTAAC
1 AAAAT-CGAATGATTCTAAGTACGACTTAAC
962150 AAAA
1 AAAA
962154 ACTTTTTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.20
31 24 0.80
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAATCGAATGATTCTAAGTACGACTTAAC
Found at i:967216 original size:13 final size:13
Alignment explanation
Indices: 967198--967222 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
967188 CAGGGATGGG
967198 GTAATGGTAATTT
1 GTAATGGTAATTT
967211 GTAATGGTAATT
1 GTAATGGTAATT
967223 AAGTGTAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (13 bp):
GTAATGGTAATTT
Found at i:968892 original size:39 final size:39
Alignment explanation
Indices: 968818--968900 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
968808 GCTAGTAGCT
* *
968818 CTACATGTATGAATTAATGATGTTAGTTATTTAATAGTG
1 CTACATGTATGAATTAATAATGTTAGTTATCTAATAGTG
* * * *
968857 CTACATGTATGAATTGATAATTTTATTTGTCTAATAGTG
1 CTACATGTATGAATTAATAATGTTAGTTATCTAATAGTG
968896 CTACA
1 CTACA
968901 AGAAGGAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (39 bp):
CTACATGTATGAATTAATAATGTTAGTTATCTAATAGTG
Found at i:969694 original size:39 final size:39
Alignment explanation
Indices: 969650--969861 Score: 161
Period size: 39 Copynumber: 5.5 Consensus size: 39
969640 TCTTATACGG
*
969650 CTACATGTATAAATTAATGATTTTATTTGACTAATAGCA
1 CTACATGTATAAATTGATGATTTTATTTGACTAATAGCA
* * * * *
969689 CTACATGTATGAATTGATG-TTGTTATTTGGCCAAAAGTGA
1 CTACATGTATAAATTGATGATT-TTATTTGACTAATAG-CA
* * * * ** *
969729 -TACATGTATTAATTGATAATAGTT-GTCCACT-ATTG--
1 CTACATGTATAAATTGATGAT-TTTATTTGACTAATAGCA
*
969764 CTACATGTATAAATTGATGATTTTACTTGACTAATAGCA
1 CTACATGTATAAATTGATGATTTTATTTGACTAATAGCA
* * * *
969803 CTACATGTAT-TATTGATGATGTTATTTGGCTAATAGGGA
1 CTACATGTATAAATTGATGATTTTATTTGACTAATA-GCA
*
969842 -TACATGTATTAATTGATGAT
1 CTACATGTATAAATTGATGAT
969862 GATAACTTTC
Statistics
Matches: 133, Mismatches: 29, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
35 2 0.02
36 22 0.17
37 3 0.02
38 34 0.26
39 68 0.51
40 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.41
Consensus pattern (39 bp):
CTACATGTATAAATTGATGATTTTATTTGACTAATAGCA
Found at i:969750 original size:114 final size:113
Alignment explanation
Indices: 969618--969858 Score: 340
Period size: 114 Copynumber: 2.1 Consensus size: 113
969608 ACAGTGTTAA
* * * *
969618 ATGTATGAATTGAAAATAGATGTCTTA-TACGGCTACATGTATAAATTAATGATTTTATTTGACT
1 ATGTATTAATTGATAATAGATGTC-CACTACGGCTACATGTATAAATTAATGATTTTACTTGACT
* *
969682 AATAGCACTACATGTATGAATTGATGTTGTTATTTGGCCAAAAGTGATAC
65 AATAGCACTACATGTAT-AATTGATGATGTTATTTGGCCAAAAGGGATAC
* ** *
969732 ATGTATTAATTGATAATAGTTGTCCACTATTGCTACATGTATAAATTGATGATTTTACTTGACTA
1 ATGTATTAATTGATAATAGATGTCCACTACGGCTACATGTATAAATTAATGATTTTACTTGACTA
* * *
969797 ATAGCACTACATGTATTATTGATGATGTTATTTGGCTAATAGGGATAC
66 ATAGCACTACATGTATAATTGATGATGTTATTTGGCCAAAAGGGATAC
969845 ATGTATTAATTGAT
1 ATGTATTAATTGAT
969859 GATGATAACT
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
113 42 0.37
114 71 0.63
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (113 bp):
ATGTATTAATTGATAATAGATGTCCACTACGGCTACATGTATAAATTAATGATTTTACTTGACTA
ATAGCACTACATGTATAATTGATGATGTTATTTGGCCAAAAGGGATAC
Found at i:988022 original size:31 final size:30
Alignment explanation
Indices: 987963--988027 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
987953 TTGGAAAGGT
* ** *
987963 TTTTGTTAATTCGTACTTGAAATCATTCGGA
1 TTTTGTTAAGTCGTACCAGAAATAATTC-GA
*
987994 TTTTGTTAAGTCGTACCAGGAATAATTCGA
1 TTTTGTTAAGTCGTACCAGAAATAATTCGA
988024 TTTT
1 TTTT
988028 TTCATCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 6 0.21
31 23 0.79
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (30 bp):
TTTTGTTAAGTCGTACCAGAAATAATTCGA
Found at i:997434 original size:49 final size:48
Alignment explanation
Indices: 997379--997550 Score: 227
Period size: 49 Copynumber: 3.5 Consensus size: 48
997369 AATAATTAAG
*
997379 GAATTTCCACCTAGTAATCGGAGAAATGTTCACCTAGTGATCGGAAGAC
1 GAATTTCCACCTAGTAATCGGAGAAAT-TTCACCTAGTGATCGGAAGAA
*
997428 GAATTTCCACCTAGTAATCGGAGAAATTTTCACCTAGTGATCGGAACAA
1 GAATTTCCACCTAGTAATCGGAGAAA-TTTCACCTAGTGATCGGAAGAA
* * * **
997477 GAATTTCTACCTAGTGATCGGAAGAAGGATTTCCACCTAGTAATCCCAAGAA
1 GAATTTCCACCTAGTAATCGG-AGAA--ATTT-CACCTAGTGATCGGAAGAA
997529 GAATTTCCACCTAGTAATCGGA
1 GAATTTCCACCTAGTAATCGGA
997551 AAAAGAATTT
Statistics
Matches: 108, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
49 64 0.59
50 5 0.05
51 4 0.04
52 35 0.32
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (48 bp):
GAATTTCCACCTAGTAATCGGAGAAATTTCACCTAGTGATCGGAAGAA
Found at i:997440 original size:26 final size:26
Alignment explanation
Indices: 997379--997572 Score: 224
Period size: 26 Copynumber: 7.7 Consensus size: 26
997369 AATAATTAAG
997379 GAATTTCCACCTAGTAATCGG-AG-A
1 GAATTTCCACCTAGTAATCGGAAGAA
* *
997403 -AATGTT-CACCTAGTGATCGGAAGAC
1 GAAT-TTCCACCTAGTAATCGGAAGAA
997428 GAATTTCCACCTAGTAATCGG-AG-A
1 GAATTTCCACCTAGTAATCGGAAGAA
* * *
997452 -AATTTTCACCTAGTGATCGGAACAA
1 GAATTTCCACCTAGTAATCGGAAGAA
* *
997477 GAATTTCTACCTAGTGATCGGAAGAA
1 GAATTTCCACCTAGTAATCGGAAGAA
* **
997503 GGATTTCCACCTAGTAATCCCAAGAA
1 GAATTTCCACCTAGTAATCGGAAGAA
*
997529 GAATTTCCACCTAGTAATCGGAAAAA
1 GAATTTCCACCTAGTAATCGGAAGAA
997555 GAATTTCC-CCTAGTAATC
1 GAATTTCCACCTAGTAATC
997573 ATATACCTTT
Statistics
Matches: 143, Mismatches: 19, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
23 34 0.24
24 5 0.03
25 15 0.10
26 89 0.62
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (26 bp):
GAATTTCCACCTAGTAATCGGAAGAA
Found at i:997541 original size:52 final size:49
Alignment explanation
Indices: 997379--997572 Score: 221
Period size: 49 Copynumber: 3.9 Consensus size: 49
997369 AATAATTAAG
* *
997379 GAATTTCCACCTAGTAATCGGAGAAATGTT-CACCTAGTGATCGGAAGAC
1 GAATTTCCACCTAGTAATCGGAGAAAT-TTCCACCTAGTAATCGGAAGAA
* * *
997428 GAATTTCCACCTAGTAATCGGAGAAATTTTCACCTAGTGATCGGAACAA
1 GAATTTCCACCTAGTAATCGGAGAAATTTCCACCTAGTAATCGGAAGAA
* * **
997477 GAATTTCTACCTAGTGATCGGAAGAAGGATTTCCACCTAGTAATCCCAAGAA
1 GAATTTCCACCTAGTAATCGG-AGAA--ATTTCCACCTAGTAATCGGAAGAA
*
997529 GAATTTCCACCTAGTAATCGGAAAAAGAATTTCC-CCTAGTAATC
1 GAATTTCCACCTAGTAATCGG--AGA-AATTTCCACCTAGTAATC
997573 ATATACCTTT
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
48 2 0.02
49 63 0.50
50 4 0.03
51 10 0.08
52 44 0.35
53 3 0.02
54 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (49 bp):
GAATTTCCACCTAGTAATCGGAGAAATTTCCACCTAGTAATCGGAAGAA
Found at i:1000332 original size:10 final size:10
Alignment explanation
Indices: 1000317--1000350 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1000307 TTCAGAATTT
1000317 AAAAACATAA
1 AAAAACATAA
*
1000327 AAAAACAT-C
1 AAAAACATAA
1000336 AAAAACATAA
1 AAAAACATAA
1000346 AAAAA
1 AAAAA
1000351 AAATACCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAACATAA
Found at i:1005217 original size:17 final size:18
Alignment explanation
Indices: 1005192--1005231 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1005182 GTAAGAAGTC
*
1005192 TTTACATTTTCAA-ATAT
1 TTTACATTTTAAACATAT
*
1005209 TTTAGATTTTAAACATAT
1 TTTACATTTTAAACATAT
1005227 TTTAC
1 TTTAC
1005232 GTCATCTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTACATTTTAAACATAT
Found at i:1007057 original size:2 final size:2
Alignment explanation
Indices: 1007050--1007109 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1007040 CATTTCATAT
1007050 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1007092 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
1007110 AAAATCATCG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1009441 original size:214 final size:213
Alignment explanation
Indices: 1009072--1009499 Score: 847
Period size: 214 Copynumber: 2.0 Consensus size: 213
1009062 GATAAAGTGA
1009072 AAATCACAGTTTCAAGGATATGTAAATTCGTGGCCAATGACCCCATGAATACAAAATGTTAATAG
1 AAATCACAGTTTCAAGGATATGTAAATTCGTGGCCAATGACCCCATGAATACAAAATGTTAATAG
1009137 AAATTGCATTTCAATGAACATTTAATTTCATGGATCCACTTAAAAACGAAATCCACGAAAATTGG
66 AAATTGCATTTCAATGAACATTTAATTTCATGGATCCACTTAAAAACGAAATCCACGAAAATTGG
1009202 TATTCAACGAATAATGATGAAACCACAGTAGTGTGTTGTACTGGAAATGTTCCTGTTACTTTTCG
131 TATTCAACGAATAATGATGAAACCACAGTAGTGTGTTGTACTGGAAATGTTCCTGTTACTTTTCG
1009267 TTTTATATATATATATAT
196 TTTTATATATATATATAT
1009285 NAAATCACAGTTTCAAGGATATGTAAATTCGTGGCCAATGACCCCATGAATACAAAATGTTAATA
1 -AAATCACAGTTTCAAGGATATGTAAATTCGTGGCCAATGACCCCATGAATACAAAATGTTAATA
1009350 GAAATTGCATTTCAATGAACATTTAATTTCATGGATCCACTTAAAAACGAAATCCACGAAAATTG
65 GAAATTGCATTTCAATGAACATTTAATTTCATGGATCCACTTAAAAACGAAATCCACGAAAATTG
1009415 GTATTCAACGAATAATGATGAAACCACAGTAGTGTGTTGTACTGGAAATGTTCCTGTTACTTTTC
130 GTATTCAACGAATAATGATGAAACCACAGTAGTGTGTTGTACTGGAAATGTTCCTGTTACTTTTC
1009480 GTTTTATATATATATATAT
195 GTTTTATATATATATATAT
1009499 A
1 A
1009500 TATANNNNNN
Statistics
Matches: 214, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
213 1 0.00
214 213 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (213 bp):
AAATCACAGTTTCAAGGATATGTAAATTCGTGGCCAATGACCCCATGAATACAAAATGTTAATAG
AAATTGCATTTCAATGAACATTTAATTTCATGGATCCACTTAAAAACGAAATCCACGAAAATTGG
TATTCAACGAATAATGATGAAACCACAGTAGTGTGTTGTACTGGAAATGTTCCTGTTACTTTTCG
TTTTATATATATATATAT
Found at i:1010958 original size:21 final size:21
Alignment explanation
Indices: 1010932--1010995 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
1010922 ATTGTATACA
*
1010932 ATTTTAATGATATGCTATGAT
1 ATTTTAATGATATGCTATGAG
*
1010953 ATTTTAAATCA-ATGCTATGAG
1 ATTTT-AATGATATGCTATGAG
*
1010974 ATTTGT-ATGCTATGCTATGAG
1 ATTT-TAATGATATGCTATGAG
1010995 A
1 A
1010996 AATTGAAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 2 0.06
21 29 0.81
22 5 0.14
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (21 bp):
ATTTTAATGATATGCTATGAG
Found at i:1011277 original size:21 final size:21
Alignment explanation
Indices: 1011251--1011316 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
1011241 ATTGTATGTA
1011251 ATGGTAAGAGATTCCAATGCT
1 ATGGTAAGAGATTCCAATGCT
* *
1011272 ATGGTATGAGATTTCAATGCT
1 ATGGTAAGAGATTCCAATGCT
* *
1011293 ATGCTATA-AGATTGCAATGCT
1 ATGGTA-AGAGATTCCAATGCT
1011314 ATG
1 ATG
1011317 CTATGGTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (21 bp):
ATGGTAAGAGATTCCAATGCT
Found at i:1011317 original size:21 final size:21
Alignment explanation
Indices: 1011259--1011320 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
1011249 TAATGGTAAG
* *
1011259 AGATTCCAATGCTATGGTATG
1 AGATTCCAATGCTATGCTATA
*
1011280 AGATTTCAATGCTATGCTATA
1 AGATTCCAATGCTATGCTATA
*
1011301 AGATTGCAATGCTATGCTAT
1 AGATTCCAATGCTATGCTAT
1011321 GGTGTATGTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (21 bp):
AGATTCCAATGCTATGCTATA
Found at i:1011590 original size:21 final size:21
Alignment explanation
Indices: 1011564--1011817 Score: 393
Period size: 21 Copynumber: 12.1 Consensus size: 21
1011554 AAAATATTTT
*
1011564 TTTCGCAAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
*
1011585 TTTCGCGAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
1011606 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
*
1011627 TTTCGCGAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
*
1011648 TTTCGCGAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
1011669 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
* ** *
1011690 GTTCGCGAATAAACGCGTTAG
1 TTTCGCGAATAAACGCGAAAC
1011711 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
1011732 TTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
*
1011753 GTTCGCGAATAAACGCGAAAC
1 TTTCGCGAATAAACGCGAAAC
*
1011774 TTTCGCGAATAAACGCGTAAC
1 TTTCGCGAATAAACGCGAAAC
*
1011795 TTTCGCG-ATATAACTCGAAAC
1 TTTCGCGAATA-AACGCGAAAC
1011816 TT
1 TT
1011818 AAATATAAAT
Statistics
Matches: 214, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
20 3 0.01
21 211 0.99
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (21 bp):
TTTCGCGAATAAACGCGAAAC
Found at i:1012607 original size:21 final size:21
Alignment explanation
Indices: 1012581--1012786 Score: 267
Period size: 21 Copynumber: 9.8 Consensus size: 21
1012571 TTTATGGTTT
* *
1012581 CGCGTTTATTCGCGAAACTAA
1 CGCGTTTATTCGCGAAAGTTA
1012602 CGCGTTTATTCGCGAAAGTTA
1 CGCGTTTATTCGCGAAAGTTA
*
1012623 CGCG-TTATATCGCGAAAGTTT
1 CGCGTTTAT-TCGCGAAAGTTA
* *
1012644 CGCGTTTATTCGCGAAACTAA
1 CGCGTTTATTCGCGAAAGTTA
*
1012665 CGCG-TTATATCGCGAAAGTTT
1 CGCGTTTAT-TCGCGAAAGTTA
1012686 CGCGTTTATTCGCGAAAGTTA
1 CGCGTTTATTCGCGAAAGTTA
*
1012707 CGCGTTTATTCGCGAAAGTTT
1 CGCGTTTATTCGCGAAAGTTA
*
1012728 CGCGTTTATTCGCGAAA-CTA
1 CGCGTTTATTCGCGAAAGTTA
*
1012748 CCGCG-TTATATCGCGAAAGTTT
1 -CGCGTTTAT-TCGCGAAAGTTA
1012770 CGCGTTTATTCGCGAAA
1 CGCGTTTATTCGCGAAA
1012787 CAAATATTTT
Statistics
Matches: 162, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.08
21 136 0.84
22 13 0.08
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.32
Consensus pattern (21 bp):
CGCGTTTATTCGCGAAAGTTA
Found at i:1012628 original size:42 final size:42
Alignment explanation
Indices: 1012602--1012786 Score: 311
Period size: 42 Copynumber: 4.4 Consensus size: 42
1012592 GCGAAACTAA
1012602 CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTT
1 CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTT
* *
1012644 CGCGTTTATTCGCGAAACTAACGCGTTATATCGCGAAAGTTT
1 CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTT
1012686 CGCGTTTATTCGCGAAAGTTACGCGTT-TATTCGCGAAAGTTT
1 CGCGTTTATTCGCGAAAGTTACGCGTTATA-TCGCGAAAGTTT
*
1012728 CGCGTTTATTCGCGAAA-CTACCGCGTTATATCGCGAAAGTTT
1 CGCGTTTATTCGCGAAAGTTA-CGCGTTATATCGCGAAAGTTT
1012770 CGCGTTTATTCGCGAAA
1 CGCGTTTATTCGCGAAA
1012787 CAAATATTTT
Statistics
Matches: 135, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
41 4 0.03
42 129 0.96
43 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (42 bp):
CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTT
Found at i:1012678 original size:63 final size:63
Alignment explanation
Indices: 1012577--1012787 Score: 320
Period size: 63 Copynumber: 3.3 Consensus size: 63
1012567 TTATTTTATG
1012577 GTTTCGCGTTTATTCGCGAAACTAACGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAA
1 GTTTCGCGTTTATTCGCGAAACTAACGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAA
*
1012640 GTTTCGCGTTTATTCGCGAAACTAACGCG-TTATATCGCGAAAGTTTCGCGTT-TATTCGCGAAA
1 GTTTCGCGTTTATTCGCGAAACTAACGCGTTTAT-TCGCGAAAGTTACGCGTTATA-TCGCGAAA
* * ** *
1012703 GTTACGCGTTTATTCGCGAAAGTTTCGCGTTTATTCGCGAAA-CTACCGCGTTATATCGCGAAA
1 GTTTCGCGTTTATTCGCGAAACTAACGCGTTTATTCGCGAAAGTTA-CGCGTTATATCGCGAAA
1012766 GTTTCGCGTTTATTCGCGAAAC
1 GTTTCGCGTTTATTCGCGAAAC
1012788 AAATATTTTT
Statistics
Matches: 134, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
62 7 0.05
63 121 0.90
64 6 0.04
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (63 bp):
GTTTCGCGTTTATTCGCGAAACTAACGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAA
Found at i:1012722 original size:84 final size:84
Alignment explanation
Indices: 1012602--1012786 Score: 345
Period size: 84 Copynumber: 2.2 Consensus size: 84
1012592 GCGAAACTAA
1012602 CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACG
1 CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACG
1012667 CGTTATATCGCGAAAGTTT
66 CGTTATATCGCGAAAGTTT
*
1012686 CGCGTTTATTCGCGAAAGTTACGCGTT-TATTCGCGAAAGTTTCGCGTTTATTCGCGAAACTACC
1 CGCGTTTATTCGCGAAAGTTACGCGTTATA-TCGCGAAAGTTTCGCGTTTATTCGCGAAACTAAC
1012750 GCGTTATATCGCGAAAGTTT
65 GCGTTATATCGCGAAAGTTT
1012770 CGCGTTTATTCGCGAAA
1 CGCGTTTATTCGCGAAA
1012787 CAAATATTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
83 2 0.02
84 97 0.98
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (84 bp):
CGCGTTTATTCGCGAAAGTTACGCGTTATATCGCGAAAGTTTCGCGTTTATTCGCGAAACTAACG
CGTTATATCGCGAAAGTTT
Found at i:1030199 original size:61 final size:61
Alignment explanation
Indices: 1030008--1030550 Score: 951
Period size: 61 Copynumber: 8.8 Consensus size: 61
1029998 GACACCCTGT
* * *
1030008 CTATATCCAAGTGGCGCTGGAATACCCAACTAATATATCTATATCTTACCAGATATAATTATG
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACC--ATATAATTATA
* * *
1030071 CTATATCCAAGTGACGTTGGAATAGCCAACTAATATATCTATATCTTACCATATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACC--ATATAATTATA
*
1030134 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCGATATCTTACCATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
1030195 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
*
1030256 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCGATATCTTACCATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
1030317 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
*
1030378 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCGATATCTTACCATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
1030439 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
* *
1030500 CTATATCCAAGTGGCGTTGGAATAGCCAACTTATATATCGATATCTTACCA
1 CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCA
1030551 AAGGCTATGA
Statistics
Matches: 464, Mismatches: 16, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
61 360 0.78
63 104 0.22
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (61 bp):
CTATATCCAAGTGGCGCTGGAATAGCCAACTTATATATCTATATCTTACCATATAATTATA
Found at i:1031582 original size:19 final size:18
Alignment explanation
Indices: 1031547--1031585 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
1031537 GGCTAAACAT
1031547 TAAACAAAATATTCAAAA
1 TAAACAAAATATTCAAAA
1031565 TAAAGCAAAA-ATTACAAAA
1 TAAA-CAAAATATT-CAAAA
1031584 TA
1 TA
1031586 GTTATAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.67, C:0.10, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAACAAAATATTCAAAA
Found at i:1045231 original size:32 final size:33
Alignment explanation
Indices: 1045171--1045235 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 33
1045161 ATATAATTAT
*
1045171 GCATGCAACTGCTTATCTAGAAGGTCATTTGTA
1 GCATGCAACTGCTTATCTAGAAGATCATTTGTA
*
1045204 GCATGCAACTGC-TATCTTGAAGATCATTTGTA
1 GCATGCAACTGCTTATCTAGAAGATCATTTGTA
1045236 AATTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (33 bp):
GCATGCAACTGCTTATCTAGAAGATCATTTGTA
Found at i:1045862 original size:40 final size:40
Alignment explanation
Indices: 1045818--1045899 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1045808 GGTCAACACG
*
1045818 AATATATTAATTAGATATTTCCTGATATGCATAAAGAAAA
1 AATATATTAATTAAATATTTCCTGATATGCATAAAGAAAA
1045858 AATATATTAATTAAATATTTCCTGATATGCATAAAGAAAA
1 AATATATTAATTAAATATTTCCTGATATGCATAAAGAAAA
1045898 AA
1 AA
1045900 AAAACAAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.34
Consensus pattern (40 bp):
AATATATTAATTAAATATTTCCTGATATGCATAAAGAAAA
Found at i:1047900 original size:15 final size:16
Alignment explanation
Indices: 1047880--1047920 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1047870 ATATTTTTGC
1047880 TGGTACA-AAATGACT
1 TGGTACACAAATGACT
1047895 TGGTACACCAAATGACT
1 TGGTACA-CAAATGACT
*
1047912 TGCTACACA
1 TGGTACACA
1047921 TATGTACCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 2 0.09
17 14 0.61
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (16 bp):
TGGTACACAAATGACT
Found at i:1049372 original size:15 final size:16
Alignment explanation
Indices: 1049352--1049392 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
1049342 ATATTTTTGC
1049352 TGGTACA-AAATGACT
1 TGGTACACAAATGACT
1049367 TGGTACACCAAATGACT
1 TGGTACA-CAAATGACT
*
1049384 TGCTACACA
1 TGGTACACA
1049393 TATGTTCCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 7 0.30
16 2 0.09
17 14 0.61
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (16 bp):
TGGTACACAAATGACT
Found at i:1050996 original size:177 final size:176
Alignment explanation
Indices: 1050807--1051488 Score: 796
Period size: 177 Copynumber: 3.8 Consensus size: 176
1050797 TGGAGCAGGA
* * * * * *
1050807 TAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGCTGGTCCTAACTTCACC
1 TAAAGTTTTTGTAGCAGGTGCCCTCTGAT-GTAATATCTTAGTTACTACTGGTCCAAACTTCACC
* * *
1050872 AAACTTGCATGGATGGTGTGTCTTATGATACTAATGCACCTGACAGGCTTGAGTGCTGAATCTGA
65 AAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGA
* *
1050937 GCTATAGGTTTCGGATGCTGGAGGTGGTTAAGGTTTTAAGAGCTGGT
130 GCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGT
* * * *
1050984 TAGAGTTTTTGTTGAAGGTGCCCTCTGGTGATAATATCTTAGTTTCTGTACTACTGGTCCAAACT
1 TAAAGTTTTTGTAGCAGGTGCCCTCTGATG-TAATATCTTAG----T-TACTACTGGTCCAAACT
* * *
1051049 TCACCAAACTGGTATGGTTGGTGCGTCTTATGTATACTGATGCACCTGACAGGCTTGAATGCTGA
60 TCACCAAACTTGCATGGATGGTGCGTCTTATG-ATACTGATGCACCTGACAGGCTTGAATGCTGA
** * ** *
1051114 ATCTGAGTAATAGGTTTCGGATGCTGGAGGAGGATAAGGTTTTTGGAGCTAGT
124 ATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGT
* * * * *
1051167 TAAAGTTTTT-TGAGCAGGTGCCCTCTAATGTTATATCTTAGCTACTCCTGGTCCAAACTTCATC
1 TAAAGTTTTTGT-AGCAGGTGCCCTCTGATGTAATATCTTAGTTACTACTGGTCCAAACTTCACC
** * * *
1051231 AAACTTGTGTGGATGGTGCGTCTTATTATACTGATGTACCTGA-ACGGCTTGAATTCT-ACATCT
65 AAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACA-GGCTTGAATGCTGA-ATCT
* *
1051294 GAGCCATAGGTTTTGGATGCTGGAGGAGGTTAAGGTTTTAAGAGTTGGT
128 GAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGT
* * * * * * *
1051343 TAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTCGTTATTACTTGTCCTAACTTCACC
1 TAAAGTTTTTGTAGCAGGTGCCCTCTGATG-TAATATCTTAGTTACTACTGGTCCAAACTTCACC
* * * *
1051408 AGACTT-CAATGGATGGCGCGTTTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAGTCTG
65 AAACTTGC-ATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTG
1051472 AGCCATAGGTTTCGGAT
129 AGCCATAGGTTTCGGAT
1051489 NNNNNNNNNN
Statistics
Matches: 425, Mismatches: 65, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
175 2 0.00
176 98 0.23
177 169 0.40
178 2 0.00
181 1 0.00
182 54 0.13
183 99 0.23
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.34
Consensus pattern (176 bp):
TAAAGTTTTTGTAGCAGGTGCCCTCTGATGTAATATCTTAGTTACTACTGGTCCAAACTTCACCA
AACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAG
CCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGT
Found at i:1051352 original size:359 final size:354
Alignment explanation
Indices: 1050791--1051488 Score: 886
Period size: 359 Copynumber: 2.0 Consensus size: 354
1050781 AGGAAGTTAT
* * * * *
1050791 GGTTTTTGGAGCAGGATAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAATATCTAAGTTACTGC
1 GGTTTTTGGAGCAGGATAAAGTTTTTGTAGCAGGTGCCCTCTAATAGCAATATCTAAGCTACTCC
* *
1050856 TGGTCCTAACTTCACCAAACTTGCATGGATGGTGTGTCTTATGATACTAATGCACCTGACAGGCT
66 TGGTCCAAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTAATGCACCTGACAGGCT
* * *
1050921 TGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGTGGTTAAGGTTTTAAGAGCTGGTTA
131 TGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTA
* ** * *
1050986 GAGTTTTTGTTGA-AGGTGCCCTCTGGTGATAATATCTTAGTTTCTGTACTACTGGTCCAAACTT
196 AAGTTTTTG-AAACAGGTGCCCTCTGATGATAATATCTTAG-TTAT-TACT--T-GTCCAAACTT
** * *
1051050 CACCAAACTGGTATGGTTGGTGCGTCTTATGTATACTGATGCACCTGACAGGCTTGAATGCTGAA
255 CACCAAACTGCAATGGATGGCGCGTCTTATG-ATACTGATGCACCTGACAGGCTTGAATGCTGAA
*
1051115 TCTGAGTAATAGGTTTCGGATGCTGGAGGAGGATAA
319 TCTGAGCAATAGGTTTCGGATGCTGGAGGAGGATAA
* ** *
1051151 GGTTTTTGGAGCTA-GTTAAAGTTTTT-TGAGCAGGTGCCCTCTAAT-GTTATATCTTAGCTACT
1 GGTTTTTGGAGC-AGGATAAAGTTTTTGT-AGCAGGTGCCCTCTAATAGCAATATCTAAGCTACT
* ** * * *
1051213 CCTGGTCCAAACTTCATCAAACTTGTGTGGATGGTGCGTCTTATTATACTGATGTACCTGA-ACG
64 CCTGGTCCAAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTAATGCACCTGACA-G
* * *
1051277 GCTTGAATTCT-ACATCTGAGCCATAGGTTTTGGATGCTGGAGGAGGTTAAGGTTTTAAGAGTTG
128 GCTTGAATGCTGA-ATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTG
* * *
1051341 GTTAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTCGTTATTACTTGTCCTAACTTCA
192 GTTAAAGTTTTTGAAACAGGTGCCCTCTGATGATAATATCTTAGTTATTACTTGTCCAAACTTCA
* * * *
1051406 CCAGACTTCAATGGATGGCGCGTTTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAGTCT
257 CCAAACTGCAATGGATGGCGCGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCT
*
1051471 GAGCCATAGGTTTCGGAT
322 GAGCAATAGGTTTCGGAT
1051489 NNNNNNNNNN
Statistics
Matches: 292, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
353 51 0.17
354 33 0.11
355 1 0.00
357 4 0.01
358 6 0.02
359 159 0.54
360 37 0.13
361 1 0.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (354 bp):
GGTTTTTGGAGCAGGATAAAGTTTTTGTAGCAGGTGCCCTCTAATAGCAATATCTAAGCTACTCC
TGGTCCAAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTAATGCACCTGACAGGCT
TGAATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTA
AAGTTTTTGAAACAGGTGCCCTCTGATGATAATATCTTAGTTATTACTTGTCCAAACTTCACCAA
ACTGCAATGGATGGCGCGTCTTATGATACTGATGCACCTGACAGGCTTGAATGCTGAATCTGAGC
AATAGGTTTCGGATGCTGGAGGAGGATAA
Found at i:1052455 original size:2 final size:2
Alignment explanation
Indices: 1052448--1052496 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1052438 NNNNNNNNNN
1052448 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
1052490 CG AG AG A
1 AG AG AG A
1052497 TTTCCAGTCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1052978 original size:15 final size:14
Alignment explanation
Indices: 1052944--1052981 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
1052934 ATATAATATT
1052944 ATATTGTATCTATA
1 ATATTGTATCTATA
1052958 ATATTGTATC-ATA
1 ATATTGTATCTATA
1052971 CGATATTGTAT
1 --ATATTGTAT
1052982 AATATGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 10 0.45
15 9 0.41
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (14 bp):
ATATTGTATCTATA
Found at i:1056246 original size:23 final size:23
Alignment explanation
Indices: 1056183--1056251 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1056173 AAAGCTGTCA
* *
1056183 TAAGATTTATCATAAGACATGTCT
1 TAAGA-TTATCATAAGATATGACT
* *
1056207 TAAGATTGTCATAAGATTTGACT
1 TAAGATTATCATAAGATATGACT
*
1056230 TATGATTATCATAAGATATGAC
1 TAAGATTATCATAAGATATGAC
1056252 ATAGCTGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (23 bp):
TAAGATTATCATAAGATATGACT
Found at i:1063877 original size:16 final size:16
Alignment explanation
Indices: 1063853--1063887 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1063843 ATAAACAATT
1063853 ATTTGATGACTACCTA
1 ATTTGATGACTACCTA
*
1063869 ATTTTATGACTACCTA
1 ATTTGATGACTACCTA
1063885 ATT
1 ATT
1063888 GAAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (16 bp):
ATTTGATGACTACCTA
Found at i:1066260 original size:18 final size:18
Alignment explanation
Indices: 1066016--1068312 Score: 818
Period size: 18 Copynumber: 126.8 Consensus size: 18
1066006 TTGGCATATA
1066016 ATATCTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
* * * *
1066034 ATACCAACATG-CATGGT
1 ATATCTACCTGTCATAGT
*
1066051 GA-ATCTATCTGTCATAGT
1 -ATATCTACCTGTCATAGT
* * *
1066069 ATACCTACCTGTTAAAGT
1 ATATCTACCTGTCATAGT
* *
1066087 ATACCTACCTATCATAGT
1 ATATCTACCTGTCATAGT
* *
1066105 AAATTTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
* * ** *
1066123 AAACCTATATGTCAT-GAA
1 ATATCTACCTGTCATAG-T
* * *
1066141 AAATCTACCTGTTAAAGT
1 ATATCTACCTGTCATAGT
* * *
1066159 TTATCAACCTGTCATAGC
1 ATATCTACCTGTCATAGT
*
1066177 ATATCTACCTGTCACAGT
1 ATATCTACCTGTCATAGT
*
1066195 ATATCTACCTGTCATAGA
1 ATATCTACCTGTCATAGT
* * * *
1066213 ATGTATAACTGTACTACTATT
1 ATATCTACCTGT-C-A-TAGT
* *
1066234 ATATTTACCCGTCATAGT
1 ATATCTACCTGTCATAGT
*
1066252 ATATCTACCTGTCATAGA
1 ATATCTACCTGTCATAGT
* * *
1066270 ATATCTATCTGTCACAAT
1 ATATCTACCTGTCATAGT
* *
1066288 AAATCTAACC-GTCATAAT
1 ATATCT-ACCTGTCATAGT
* *
1066306 AAATTTACC--T-AT--T
1 ATATCTACCTGTCATAGT
* * * *
1066319 A-AT-AATCTGTCACAAT
1 ATATCTACCTGTCATAGT
* *
1066335 AAATCTAACC-GTCATAAT
1 ATATCT-ACCTGTCATAGT
* * * * *
1066353 AAATTTACCTATTAATTGAATT
1 ATATCTACCT-GTCA-T--AGT
* * **
1066375 AAATCAACCTAACATAGT
1 ATATCTACCTGTCATAGT
* * ** *
1066393 AAACCTATATGTCATGGT
1 ATATCTACCTGTCATAGT
* * *
1066411 AAATCTACCTGTTAAAGT
1 ATATCTACCTGTCATAGT
* * *
1066429 AAATCAACCTGTCATAGC
1 ATATCTACCTGTCATAGT
* *
1066447 ATATTTACCTGTCACAGT
1 ATATCTACCTGTCATAGT
* ** *
1066465 ATATCTAACAATCACAGT
1 ATATCTACCTGTCATAGT
*
1066483 ATATCTACCTGTTATAGT
1 ATATCTACCTGTCATAGT
* *
1066501 ATATCTACCCGTCATAGA
1 ATATCTACCTGTCATAGT
*
1066519 ATATTTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
**
1066537 ATATCTACCTGTCATTTT
1 ATATCTACCTGTCATAGT
* *
1066555 CTATCTACCTATCATAGT
1 ATATCTACCTGTCATAGT
1066573 ATATCTACAC-GTCATAGT
1 ATATCTAC-CTGTCATAGT
* **
1066591 TTATCTATATGTCATAGT
1 ATATCTACCTGTCATAGT
* *
1066609 ATATCTACCTATCATAAT
1 ATATCTACCTGTCATAGT
1066627 ATATCTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
*
1066645 TTATCTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
* *
1066663 ATATCAACCCGTCA-AGGT
1 ATATCTACCTGTCATA-GT
* * *
1066681 ATATATTCTTGTCATAGT
1 ATATCTACCTGTCATAGT
1066699 ATATCTACCTG-C-----
1 ATATCTACCTGTCATAGT
* * *
1066711 -CATCTACATATCATAGT
1 ATATCTACCTGTCATAGT
* * * * *
1066728 ATCTATTCTTGTCATATT
1 ATATCTACCTGTCATAGT
* * *
1066746 ATATCTATCTGTCACAAT
1 ATATCTACCTGTCATAGT
* *
1066764 ATGTCTACCCGTCATAGT
1 ATATCTACCTGTCATAGT
* *
1066782 ATATCTGCCTGTCATAGA
1 ATATCTACCTGTCATAGT
* ** *
1066800 AAATCTACCAAAT-TTAGT
1 ATATCTACC-TGTCATAGT
* ** * *
1066818 -TAACCTATATGTTATGGT
1 AT-ATCTACCTGTCATAGT
* * *
1066836 AAATCTACCCTATATGTCATTGC
1 ATATCTA-CC----TGTCATAGT
* * * *
1066859 AAATCTACATGTTACAGT
1 ATATCTACCTGTCATAGT
* *
1066877 ATATCAACCTGTCATAGC
1 ATATCTACCTGTCATAGT
* *
1066895 ATATCAACCTGTCACAGT
1 ATATCTACCTGTCATAGT
* *
1066913 ATATCTACCAGTAATAGT
1 ATATCTACCTGTCATAGT
* * *
1066931 TTATCCACCTGTCAGAGT
1 ATATCTACCTGTCATAGT
* *
1066949 ATATCTACCCGTCAAAGT
1 ATATCTACCTGTCATAGT
* * *
1066967 A-AACTTCAATGTCAT-GTT
1 ATATCTAC-CTGTCATAG-T
* * * * *
1066985 AAATCTACCTATTACAGG
1 ATATCTACCTGTCATAGT
* * * *
1067003 ATATCAATCTGTCATTGC
1 ATATCTACCTGTCATAGT
* * *
1067021 ATATCTACATTTCATAGC
1 ATATCTACCTGTCATAGT
* *
1067039 ATATCTATCTGTCATAAT
1 ATATCTACCTGTCATAGT
*
1067057 ATATCAACCTGTCATAGT
1 ATATCTACCTGTCATAGT
* * * *
1067075 ATATATACCTTTAAATTAAACAT
1 ATATCTACCTGT-CA-T--A-GT
* ** *
1067098 ATAACTATATGTCAAAGT
1 ATATCTACCTGTCATAGT
* * * * *
1067116 ACATATTCTTGTCATAGA
1 ATATCTACCTGTCATAGT
* * *
1067134 ATCTCTAACTGTCATAAT
1 ATATCTACCTGTCATAGT
* ** *
1067152 ATTTCTATTTGTCATGGT
1 ATATCTACCTGTCATAGT
* **
1067170 ATATCTACTTGTCATAAC
1 ATATCTACCTGTCATAGT
*** *
1067188 ATATCTTTATGTCATGGT
1 ATATCTACCTGTCATAGT
* *
1067206 AAATCTATCTGTCATAGT
1 ATATCTACCTGTCATAGT
*
1067224 ATATCTA-C-GTCACAGT
1 ATATCTACCTGTCATAGT
* *
1067240 ATATCTACCTGTTAAAGT
1 ATATCTACCTGTCATAGT
*
1067258 ATATCTACCTGTCATAAT
1 ATATCTACCTGTCATAGT
* * *
1067276 TTAT-TATTCTTTCATAGT
1 ATATCTA-CCTGTCATAGT
* * * *
1067294 GTAT-AAACTCGTC-TAATT
1 ATATCTACCT-GTCAT-AGT
* * **
1067312 ATATATATCTGTCCCAGT
1 ATATCTACCTGTCATAGT
* *
1067330 ATATCTACCCGTCATTGT
1 ATATCTACCTGTCATAGT
* * *
1067348 ATATATTCTTGTCATAGT
1 ATATCTACCTGTCATAGT
* *
1067366 ATA--TA--TGTCACAAT
1 ATATCTACCTGTCATAGT
* *
1067380 ATATCTATCCT-TGAAAGT
1 ATATCTA-CCTGTCATAGT
*
1067398 ATATCTACCCGTCATAGT
1 ATATCTACCTGTCATAGT
* *
1067416 ATATCTTCCTGTCATCGT
1 ATATCTACCTGTCATAGT
* *
1067434 ATATCTACCTATCATAAT
1 ATATCTACCTGTCATAGT
1067452 ATATCTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
*
1067470 ATATCTACCCGTCATAGT
1 ATATCTACCTGTCATAGT
**
1067488 ATATCTACCTGTCATTTT
1 ATATCTACCTGTCATAGT
*
1067506 CA-ATCTACCTATCATAGT
1 -ATATCTACCTGTCATAGT
1067524 ATATCTACAC-GTCATAGT
1 ATATCTAC-CTGTCATAGT
* *
1067542 ATATCTTCCTATCATAGT
1 ATATCTACCTGTCATAGT
1067560 ATATCTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
*
1067578 ATATCTACCTCTCATTATGTAGT
1 ATATCTACCTGTC---A--TAGT
* * *
1067601 ATATTTACCCGTCAAAGT
1 ATATCTACCTGTCATAGT
* * * *
1067619 ATATATTCTTGTTATAGT
1 ATATCTACCTGTCATAGT
1067637 ATATCTACCTGTCATAGT
1 ATATCTACCTGTCATAGT
*
1067655 ATATTTTCTACCTGTCACAGT
1 ATA---TCTACCTGTCATAGT
* *
1067676 CTATCTAACC-ATCATAGT
1 ATATCT-ACCTGTCATAGT
* ** *
1067694 TTATCTACCCATCAAAGTAT
1 ATATCTACCTGTCATAG--T
*
1067714 ATATCATA-ATAGAACTGC-TAGT
1 ATATC-TACCT-G---T-CATAGT
* ** *
1067736 ATATTTCAAAATAT-ATA-T
1 ATA--TCTACCTGTCATAGT
* * * * *
1067754 ACATGTACCTGTAAGAAT
1 ATATCTACCTGTCATAGT
* * * * *
1067772 ACAACTACCAGACAAAGT
1 ATATCTACCTGTCATAGT
* *
1067790 ATATCTATCTGTTAT-GAT
1 ATATCTACCTGTCATAG-T
* *
1067808 ATATCTATCTGTCATAAT
1 ATATCTACCTGTCATAGT
* * *
1067826 ATATCAATCTGTCATAAT
1 ATATCTACCTGTCATAGT
* *
1067844 ATATCTACCTGTCAAAAT
1 ATATCTACCTGTCATAGT
*
1067862 ATATTTACCTGTCATTA-T
1 ATATCTACCTGTCA-TAGT
* *
1067880 ATATCTATCTGTCATAAT
1 ATATCTACCTGTCATAGT
* *
1067898 ATATCTACCTGTAATCGT
1 ATATCTACCTGTCATAGT
* *
1067916 ATATCTACATGTCCTAGT
1 ATATCTACCTGTCATAGT
* * **
1067934 ACATTTACCTGTTGTAGT
1 ATATCTACCTGTCATAGT
*
1067952 ATATACTAGTATACCCGTCATAGT
1 ATAT-C-----TACCTGTCATAGT
*
1067976 ATATCTACCTGTCACAGT
1 ATATCTACCTGTCATAGT
* *
1067994 ATATCTACATGTCACAGT
1 ATATCTACCTGTCATAGT
*
1068012 ATATCTACCTGTCATGGT
1 ATATCTACCTGTCATAGT
* * * * *
1068030 ATATCTGCATATCCTATT
1 ATATCTACCTGTCATAGT
* * * *
1068048 ACATTTACTTGTTGA-AGT
1 ATATCTACCTG-TCATAGT
* * * *
1068066 AT-T-TAACTCTCTTAAT
1 ATATCTACCTGTCATAGT
* ** *
1068082 ATATTTATATTTCATAGT
1 ATATCTACCTGTCATAGT
* *
1068100 ATATCTTCCTGTCATAGA
1 ATATCTACCTGTCATAGT
**
1068118 ATATCTACCTGTCATAAA
1 ATATCTACCTGTCATAGT
**
1068136 ATATCTACCTGTCATAAA
1 ATATCTACCTGTCATAGT
* *
1068154 ATATCTACCTGTTATAAT
1 ATATCTACCTGTCATAGT
** * *
1068172 ATATAAACCTGTCATGGG
1 ATATCTACCTGTCATAGT
* * * *
1068190 ATATCTACATGGCCTGGT
1 ATATCTACCTGTCATAGT
* * * **
1068208 ACATTTCCCTGTTGTAGT
1 ATATCTACCTGTCATAGT
* * * *
1068226 ATATCAACTTGTCTTAAT
1 ATATCTACCTGTCATAGT
* ** *
1068244 AAATCTATATTTCATAGT
1 ATATCTACCTGTCATAGT
* *
1068262 ATATCTTCCTGTCATAGA
1 ATATCTACCTGTCATAGT
* *
1068280 ATATCAACTTGTCATAGT
1 ATATCTACCTGTCATAGT
* * *
1068298 AAATATACGTGTCAT
1 ATATCTACCTGTCAT
1068313 GGTAAATCTT
Statistics
Matches: 1640, Mismatches: 533, Indels: 212
0.69 0.22 0.09
Matches are distributed among these distances:
11 9 0.01
12 3 0.00
13 3 0.00
14 11 0.01
15 3 0.00
16 31 0.02
17 49 0.03
18 1381 0.84
19 32 0.02
20 12 0.01
21 30 0.02
22 17 0.01
23 37 0.02
24 21 0.01
25 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (18 bp):
ATATCTACCTGTCATAGT
Found at i:1066345 original size:47 final size:47
Alignment explanation
Indices: 1066276--1066368 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
1066266 TAGAATATCT
1066276 ATCTGTCACAATAAATCTAACCGTCATAATAAATTTACCTATTAATA
1 ATCTGTCACAATAAATCTAACCGTCATAATAAATTTACCTATTAATA
1066323 ATCTGTCACAATAAATCTAACCGTCATAATAAATTTACCTATTAAT
1 ATCTGTCACAATAAATCTAACCGTCATAATAAATTTACCTATTAAT
1066369 TGAATTAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.34
Consensus pattern (47 bp):
ATCTGTCACAATAAATCTAACCGTCATAATAAATTTACCTATTAATA
Found at i:1066851 original size:23 final size:23
Alignment explanation
Indices: 1066821--1066866 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1066811 ATTTAGTTAA
* *
1066821 CCTATATGTTATGGTAAATCTAC
1 CCTATATGTCATGGCAAATCTAC
*
1066844 CCTATATGTCATTGCAAATCTAC
1 CCTATATGTCATGGCAAATCTAC
1066867 ATGTTACAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (23 bp):
CCTATATGTCATGGCAAATCTAC
Done.