Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 7 of 10
Found at i:2625577 original size:21 final size:21
Alignment explanation
Indices: 2625539--2625579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2625529 ATTAAATTTG
*
2625539 AATAACAAATAATACTTCAAA
1 AATAACAAAAAATACTTCAAA
2625560 AATAA-AAAAAATACCTTCAA
1 AATAACAAAAAATA-CTTCAA
2625580 GAACTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (21 bp):
AATAACAAAAAATACTTCAAA
Found at i:2639179 original size:19 final size:20
Alignment explanation
Indices: 2639143--2639180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2639133 TATACCCACT
*
2639143 TTGACTCTTCATATTCTGTC
1 TTGACTCTTCAAATTCTGTC
2639163 TTGACTCTT-AAATTCTGT
1 TTGACTCTTCAAATTCTGT
2639181 ATTCTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (20 bp):
TTGACTCTTCAAATTCTGTC
Found at i:2657010 original size:2 final size:2
Alignment explanation
Indices: 2657003--2657033 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2656993 TCTATATTTC
2657003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2657034 AAGTAGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2667815 original size:18 final size:18
Alignment explanation
Indices: 2667795--2667829 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2667785 TTTTTAAATT
*
2667795 TTTTAT-TATATATATAA
1 TTTTATATATAAATATAA
2667812 TTTTATATATAAATATAA
1 TTTTATATATAAATATAA
2667830 ATATATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTATATATAAATATAA
Found at i:2671027 original size:78 final size:78
Alignment explanation
Indices: 2670819--2671027 Score: 301
Period size: 78 Copynumber: 2.7 Consensus size: 78
2670809 AAAATGTTAA
* * * *
2670819 ATTTACATATTGGCACCATTATACCTTCATGTATAATAGGAATGTCACATGCCCACCTATCACAT
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGCTCACCTATCACAT
**
2670884 GGACCTTAATAGT
66 GGACCAAAATAGT
* * * *
2670897 ATTTACGTATTAGCATCATTATACCTTAATGCATAATAGGAATGCCACATGCTTACCTATCACAT
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGCTCACCTATCACAT
*
2670962 GGACCAAAATGGT
66 GGACCAAAATAGT
* *
2670975 ATTTACATAGTGGCATCATTATACCTTAATGTTTAATAGGAATGCCACATGCT
1 ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGCT
2671028 AATGCCTTGC
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 115 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (78 bp):
ATTTACATATTGGCATCATTATACCTTAATGTATAATAGGAATGCCACATGCTCACCTATCACAT
GGACCAAAATAGT
Found at i:2681433 original size:2 final size:2
Alignment explanation
Indices: 2681426--2681458 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2681416 TACTTTGTTT
*
2681426 TA TA TA TA TA TA TA TA TA TA TA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2681459 AAATCGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2684001 original size:2 final size:2
Alignment explanation
Indices: 2683994--2684029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2683984 CACTTCTAGC
2683994 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2684030 TTTTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2685252 original size:15 final size:15
Alignment explanation
Indices: 2685232--2685260 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2685222 AAAATTATAA
2685232 AGTCAATGCATGCTG
1 AGTCAATGCATGCTG
2685247 AGTCAATGCATGCT
1 AGTCAATGCATGCT
2685261 TTAACTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (15 bp):
AGTCAATGCATGCTG
Found at i:2691992 original size:62 final size:62
Alignment explanation
Indices: 2691922--2692052 Score: 154
Period size: 62 Copynumber: 2.1 Consensus size: 62
2691912 CCGTTAACTA
* ** * ** * * *
2691922 GTTAAAGCTTGAAGTGGTGGAAAATGGAAACTCTTTAATTGGTTCAGCAAGACTGTTAATTG
1 GTTAAAGCTTGAAATGACGAAAAATAAAAACTCTTTAATCGATTAAGCAAGACTGTTAATTG
* * *
2691984 GTTAAAGCTTGAAATGACGAAAAATAAAAACTCTTTAATCGATTAAGTAATATTGTTAATTG
1 GTTAAAGCTTGAAATGACGAAAAATAAAAACTCTTTAATCGATTAAGCAAGACTGTTAATTG
2692046 GTTAAAG
1 GTTAAAG
2692053 TTTTTACGAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (62 bp):
GTTAAAGCTTGAAATGACGAAAAATAAAAACTCTTTAATCGATTAAGCAAGACTGTTAATTG
Found at i:2694034 original size:21 final size:21
Alignment explanation
Indices: 2694010--2694049 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2694000 TCCAATATGT
2694010 AGAACATCAATCGATAGATGA
1 AGAACATCAATCGATAGATGA
* * *
2694031 AGAATATCTATGGATAGAT
1 AGAACATCAATCGATAGAT
2694050 AGGAGACAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (21 bp):
AGAACATCAATCGATAGATGA
Found at i:2694400 original size:21 final size:21
Alignment explanation
Indices: 2694302--2694402 Score: 89
Period size: 21 Copynumber: 4.8 Consensus size: 21
2694292 ACTTAGGATC
* *
2694302 TTCAAAACTTATTTAAACAAG
1 TTCAAAACTCATTCAAACAAG
* * *
2694323 TTTAAAA-TCTATTCAAATAGG
1 TTCAAAACTC-ATTCAAACAAG
*
2694344 TTCAAAAACTCATTCAAACAAC
1 TTC-AAAACTCATTCAAACAAG
*
2694366 TTCAAAACTAATTCAAACAAG
1 TTCAAAACTCATTCAAACAAG
*
2694387 TTTAAAGA-TCATTCAA
1 TTCAAA-ACTCATTCAA
2694403 GTAATATTCA
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.02
21 44 0.70
22 16 0.25
23 2 0.03
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (21 bp):
TTCAAAACTCATTCAAACAAG
Found at i:2694532 original size:21 final size:22
Alignment explanation
Indices: 2694482--2694532 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
2694472 TTAATAAATT
2694482 AAGTTCAAAAACATATTCAAAC
1 AAGTTCAAAAACATATTCAAAC
2694504 AA-TGTCAAAAATC-T-TTCAAAC
1 AAGT-TCAAAAA-CATATTCAAAC
2694525 AAGTTCAA
1 AAGTTCAA
2694533 GGACCACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 14 0.54
22 11 0.42
23 1 0.04
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.25
Consensus pattern (22 bp):
AAGTTCAAAAACATATTCAAAC
Found at i:2705325 original size:15 final size:16
Alignment explanation
Indices: 2705305--2705337 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2705295 ATAATAAGAA
2705305 ATGAAAAT-AAAATAT
1 ATGAAAATAAAAATAT
*
2705320 ATGAAATTAAAAATAT
1 ATGAAAATAAAAATAT
2705336 AT
1 AT
2705338 TTAAGTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (16 bp):
ATGAAAATAAAAATAT
Found at i:2705584 original size:19 final size:15
Alignment explanation
Indices: 2705539--2705586 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
2705529 ATTTTCTTTA
2705539 CAATCATATTGCTTG
1 CAATCATATTGCTTG
2705554 CAATCATATTGCTTG
1 CAATCATATTGCTTG
*
2705569 CAATCATATTACTTG
1 CAATCATATTGCTTG
2705584 CAA
1 CAA
2705587 GCACATTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (15 bp):
CAATCATATTGCTTG
Found at i:2708953 original size:22 final size:22
Alignment explanation
Indices: 2708897--2708989 Score: 118
Period size: 22 Copynumber: 4.3 Consensus size: 22
2708887 ATGTGACTGA
**
2708897 TTTTTAGGCATTATGTGATTAG
1 TTTTTAGGCATTGCGTGATTAG
* *
2708919 -TTATAAGCATTGCGTGATTAG
1 TTTTTAGGCATTGCGTGATTAG
2708940 TTTTTAGGCATTGCGTGATTAG
1 TTTTTAGGCATTGCGTGATTAG
*
2708962 TTTTTAGGCATTGCATGATT-G
1 TTTTTAGGCATTGCGTGATTAG
2708983 ATTTTTA
1 -TTTTTA
2708990 AGCAATGCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
21 18 0.29
22 44 0.71
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (22 bp):
TTTTTAGGCATTGCGTGATTAG
Found at i:2709027 original size:23 final size:23
Alignment explanation
Indices: 2709001--2709079 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
2708991 GCAATGCCTA
*
2709001 AGTCACACAATGCCTTACTAACT
1 AGTCACACAATGCCTTACAAACT
2709024 AGTCA-AGCAATGCCTTACAAACT
1 AGTCACA-CAATGCCTTACAAACT
* *
2709047 AGTCACGCAATGCC-TACCAACT
1 AGTCACACAATGCCTTACAAACT
*
2709069 AGTCACGCAAT
1 AGTCACACAAT
2709080 ACCTAAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (23 bp):
AGTCACACAATGCCTTACAAACT
Found at i:2709071 original size:22 final size:23
Alignment explanation
Indices: 2709001--2709104 Score: 115
Period size: 22 Copynumber: 4.6 Consensus size: 23
2708991 GCAATGCCTA
* *
2709001 AGTCACACAATGCCTTACTAACT
1 AGTCACGCAATGCCTTACAAACT
*
2709024 AGTCAAGCAATGCCTTACAAACT
1 AGTCACGCAATGCCTTACAAACT
*
2709047 AGTCACGCAATGCC-TACCAACT
1 AGTCACGCAATGCCTTACAAACT
* *
2709069 AGTCACGCAATACC-TA-AAAAT
1 AGTCACGCAATGCCTTACAAACT
*
2709090 AAGTCACGTAATGCC
1 -AGTCACGCAATGCC
2709105 CAAAGTCAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 3 0.04
22 34 0.49
23 33 0.47
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (23 bp):
AGTCACGCAATGCCTTACAAACT
Found at i:2709079 original size:45 final size:45
Alignment explanation
Indices: 2708999--2709104 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
2708989 AAGCAATGCC
* * * *
2708999 TAAGTCACACAATGCCTTACTAACTAGTCAAGCAATGCCTTACAAAC
1 TAAGTCACGCAATGCCTTACCAACTAGTCAAGCAATACC-TA-AAAA
*
2709046 T-AGTCACGCAATGCC-TACCAACTAGTCACGCAATACCTAAAAA
1 TAAGTCACGCAATGCCTTACCAACTAGTCAAGCAATACCTAAAAA
*
2709089 TAAGTCACGTAATGCC
1 TAAGTCACGCAATGCC
2709105 CAAAGTCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
43 4 0.08
44 15 0.29
45 19 0.37
46 13 0.25
47 1 0.02
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (45 bp):
TAAGTCACGCAATGCCTTACCAACTAGTCAAGCAATACCTAAAAA
Found at i:2709173 original size:22 final size:22
Alignment explanation
Indices: 2709133--2709174 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2709123 GTACAAAGTA
* **
2709133 AGTCATGCAATACTTAAAAATG
1 AGTCACGCAATACAAAAAAATG
2709155 AGTCACGCAATACAAAAAAA
1 AGTCACGCAATACAAAAAAA
2709175 CCACCAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (22 bp):
AGTCACGCAATACAAAAAAATG
Found at i:2717926 original size:27 final size:27
Alignment explanation
Indices: 2717891--2717942 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2717881 CTCAAAATGC
*
2717891 TAAACGTTAGGGATTTCAAATTTGTCT
1 TAAACGTTAAGGATTTCAAATTTGTCT
*
2717918 TAAATGTTAAGGATTTCAAATTTGT
1 TAAACGTTAAGGATTTCAAATTTGT
2717943 GTGAGTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (27 bp):
TAAACGTTAAGGATTTCAAATTTGTCT
Found at i:2717986 original size:359 final size:360
Alignment explanation
Indices: 2717321--2718006 Score: 1033
Period size: 359 Copynumber: 1.9 Consensus size: 360
2717311 TGTCAAATTT
* * *
2717321 GTGTGTGTTAAAGAATTTACTATAATTATTTTGTTTAAAGAGAAAAAATTTATTTGATTGCTTCA
1 GTGTGAGTTAAAGAATTTAATATAATTATTTTGTTTAAAAAGAAAAAATTTATTTGATTGCTTCA
* *
2717386 CAAGAAATGAGGGTTCAAAATGATAAAGGTTAGGGATTTCAAATTTGTGCGGGTTAAAGAGTTTA
66 CAAGAAATGAGGGTTCAAAATGATAAAGGTTAGGGATTTCAAATTTGTACGAGTTAAAGAGTTTA
* * * *
2717451 GTATAGTTATTTAGTTTAGAAAGAAAAAATTTGAAAGAAACTTTATTTGATTGATTCACAAAAAA
131 GTATAGTTATTTAGTTTAGAAAAAAAAAATTGGAAAAAAAATTTATTTGATTGATTCACAAAAAA
* *
2717516 AGAGAGCTCAAAATTCTAAATGTTAGGGATTTCAAAATTATCTTAAATGTTAAGGATTTCAAATT
196 AGAGAGCTCAAAATGCTAAACGTTAGGGATTTCAAAATTATCTTAAATGTTAAGGATTTCAAATT
* ** * **
2717581 TGTGTGAGTTCAGCGATTTAATATAGTTATTTAGTTTGAAAAG-AAAAAATTTATCTGATTAATT
261 TGTGTGAGTTAAAAGATTTAATATAATTATTTAGTTCAAAAAGAAAAAAATTTATCTGATTAATT
2717645 CATGAAAAAAGAGAATAGGAAAAAGCGTGAAAGCC
326 CATGAAAAAAGAGAATAGGAAAAAGCGTGAAAGCC
* * *
2717680 GTGTGAGTTAAAGAATTTAATATAGTTA-TTT-TTTAAAAAGAAAAAATTTATTTGATTGGTTTA
1 GTGTGAGTTAAAGAATTTAATATAATTATTTTGTTTAAAAAGAAAAAATTTATTTGATTGCTTCA
* * * *
2717743 CGAA-AAATGAGGGCTT-AAAGTGCTAATGGTTAGGGATTTCAAATTTGTATGAGTTAAAGAGTT
66 C-AAGAAATGAGGG-TTCAAAATGATAAAGGTTAGGGATTTCAAATTTGTACGAGTTAAAGAGTT
*
2717806 TAGTATAGTTATTTAGTTTA-AAGAAAAAAAATTGGAGAGAAAAAATTTATTTGATTGATTCACG
129 TAGTATAGTTATTTAGTTTAGAA-AAAAAAAATTGGA-A-AAAAAATTTATTTGATTGATTCACA
* *
2717870 AAAAAAGAGAGCTCAAAATGCTAAACGTTAGGGATTTCAAATTTGTCTTAAATGTTAAGGATTTC
191 AAAAAAGAGAGCTCAAAATGCTAAACGTTAGGGATTTCAAAATTATCTTAAATGTTAAGGATTTC
*
2717935 AAATTTGTGTGAGTTAAAAGATTTAATATAATTATTTAGTTCAAAAAGAAAAAAATTTATTTGAT
256 AAATTTGTGTGAGTTAAAAGATTTAATATAATTATTTAGTTCAAAAAGAAAAAAATTTATCTGAT
2718000 TAATTCA
321 TAATTCA
2718007 CTAAAGAGAA
Statistics
Matches: 293, Mismatches: 28, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
356 2 0.01
357 111 0.38
358 8 0.03
359 150 0.51
360 22 0.08
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.36
Consensus pattern (360 bp):
GTGTGAGTTAAAGAATTTAATATAATTATTTTGTTTAAAAAGAAAAAATTTATTTGATTGCTTCA
CAAGAAATGAGGGTTCAAAATGATAAAGGTTAGGGATTTCAAATTTGTACGAGTTAAAGAGTTTA
GTATAGTTATTTAGTTTAGAAAAAAAAAATTGGAAAAAAAATTTATTTGATTGATTCACAAAAAA
AGAGAGCTCAAAATGCTAAACGTTAGGGATTTCAAAATTATCTTAAATGTTAAGGATTTCAAATT
TGTGTGAGTTAAAAGATTTAATATAATTATTTAGTTCAAAAAGAAAAAAATTTATCTGATTAATT
CATGAAAAAAGAGAATAGGAAAAAGCGTGAAAGCC
Found at i:2718441 original size:22 final size:23
Alignment explanation
Indices: 2718411--2718472 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
2718401 TGATTGACAG
2718411 TGTATAAAAGTTATACACT-ATTA
1 TGTATAAAAGTTATACACTCA-TA
** * *
2718434 T-TATAAAAAATATAAATTCATA
1 TGTATAAAAGTTATACACTCATA
2718456 TGTATAAAAGTTATACA
1 TGTATAAAAGTTATACA
2718473 TTATCAGTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.37
Consensus pattern (23 bp):
TGTATAAAAGTTATACACTCATA
Found at i:2723662 original size:78 final size:76
Alignment explanation
Indices: 2723528--2723704 Score: 232
Period size: 78 Copynumber: 2.3 Consensus size: 76
2723518 AATACTATCT
* * * *
2723528 ATTTTAATTTTGAGTAATTCACAAAGAATAGGAAATTGTTTCCTACTTAAAGTGAATTCCTAAAA
1 ATTTTAATTTTGGGTGATTCATAAAGAATAGGAAATTGTTTCCTACCTAAAGTGAATTCCTAAAA
2723593 TTATGGTTATAAC
66 TTATGG-T-TAAC
* * *
2723606 ATTTTAATTTTGGGTGTTTCATAAAGAAT-GAGAAATTGTTTCCTACCTAAATTGAATTTCTAAA
1 ATTTTAATTTTGGGTGATTCATAAAGAATAG-GAAATTGTTTCCTACCTAAAGTGAATTCCTAAA
*
2723670 ATTATGGTTAGC
65 ATTATGGTTAAC
*
2723682 ATTTTAA-TTTGGGAGATTCATAA
1 ATTTTAATTTTGGGTGATTCATAA
2723705 GAAATCATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
75 14 0.16
76 10 0.11
77 2 0.02
78 62 0.70
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.41
Consensus pattern (76 bp):
ATTTTAATTTTGGGTGATTCATAAAGAATAGGAAATTGTTTCCTACCTAAAGTGAATTCCTAAAA
TTATGGTTAAC
Found at i:2724608 original size:2 final size:2
Alignment explanation
Indices: 2724601--2724630 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2724591 TATTTTTCGG
2724601 TA TA TA TA TA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
2724631 GTGAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2741850 original size:40 final size:40
Alignment explanation
Indices: 2741795--2741876 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
2741785 AGTCTTTTTC
2741795 ATTTCTTTTCTTTTTCAAACTTACTTGACATTGTTTAGGG
1 ATTTCTTTTCTTTTTCAAACTTACTTGACATTGTTTAGGG
*
2741835 ATTTCTTTTCTTTTTCAAACTTACTTGACATTGTTTGGGG
1 ATTTCTTTTCTTTTTCAAACTTACTTGACATTGTTTAGGG
2741875 AT
1 AT
2741877 GTGAAAGCTT
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:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (40 bp):
ATTTCTTTTCTTTTTCAAACTTACTTGACATTGTTTAGGG
Found at i:2750174 original size:14 final size:15
Alignment explanation
Indices: 2750146--2750174 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2750136 TGGTCTATGG
2750146 AATTGATTATAAATT
1 AATTGATTATAAATT
2750161 AATTGATT-TAAATT
1 AATTGATTATAAATT
2750175 TATATTAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AATTGATTATAAATT
Found at i:2767221 original size:21 final size:21
Alignment explanation
Indices: 2767195--2767251 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
2767185 TCTAGATTGT
*
2767195 ATGTATCGATACTTTTTGGGA
1 ATGTATCGATACTTTTTGAGA
* *
2767216 ATGTATCAATCCTTTTTGAGA
1 ATGTATCGATACTTTTTGAGA
*
2767237 AAGTATCGATACTTT
1 ATGTATCGATACTTT
2767252 CTACACAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACTTTTTGAGA
Found at i:2768233 original size:20 final size:20
Alignment explanation
Indices: 2768185--2768233 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2768175 CCAATTAAGC
* *
2768185 TTTCTTTGACTTGCAAACTG
1 TTTCTTTGTCTTGCAAACTA
2768205 TTTCTTTGTCTTGCAAACTA
1 TTTCTTTGTCTTGCAAACTA
2768225 TTTCTTTGT
1 TTTCTTTGT
2768234 GTTAACTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTCTTTGTCTTGCAAACTA
Found at i:2784109 original size:24 final size:24
Alignment explanation
Indices: 2784080--2784130 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
2784070 ATCATGAGTC
2784080 ATACATAGTCACATTCATTTCGTA
1 ATACATAGTCACATTCATTTCGTA
2784104 ATACATAGTCACATTCATTTCGTA
1 ATACATAGTCACATTCATTTCGTA
2784128 ATA
1 ATA
2784131 ACTCACTTAT
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:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (24 bp):
ATACATAGTCACATTCATTTCGTA
Found at i:2790920 original size:30 final size:28
Alignment explanation
Indices: 2790880--2790962 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
2790870 ACCACTTTTT
* *
2790880 CTTTTGAAGGATCAAACATAACTTCTTTG-
1 CTTTTTAAGGATCAAACATAAC--CTTAGC
*
2790909 CTTTTTCAAGGATTAAACATAACCTTAGC
1 CTTTTT-AAGGATCAAACATAACCTTAGC
* *
2790938 CTTTTTAAGGATCAAATAAAACCTT
1 CTTTTTAAGGATCAAACATAACCTT
2790963 TCCAACACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 20 0.43
29 11 0.24
30 15 0.33
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (28 bp):
CTTTTTAAGGATCAAACATAACCTTAGC
Found at i:2797440 original size:17 final size:17
Alignment explanation
Indices: 2797415--2797456 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
2797405 GAAAGGCAAA
*
2797415 ACAATTAAGAGTGAGAC
1 ACAAATAAGAGTGAGAC
*
2797432 ACAAATAAGAGTGAGAT
1 ACAAATAAGAGTGAGAC
2797449 ACAAATAA
1 ACAAATAA
2797457 CAAGTTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.10, G:0.19, T:0.17
Consensus pattern (17 bp):
ACAAATAAGAGTGAGAC
Found at i:2810100 original size:21 final size:19
Alignment explanation
Indices: 2810075--2810116 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2810065 TACTTTAAAA
2810075 TAAAATAACATAAAATTTAAC
1 TAAAATAAC-TAAAA-TTAAC
*
2810096 TAAAATAACTTAAATTAAC
1 TAAAATAACTAAAATTAAC
2810115 TA
1 TA
2810117 CTCAACGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 4 0.20
21 9 0.45
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATAACTAAAATTAAC
Found at i:2811779 original size:20 final size:20
Alignment explanation
Indices: 2811754--2811797 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2811744 CAAATTTCTT
2811754 GTTTAAGTAATCCTTGAATA
1 GTTTAAGTAATCCTTGAATA
* * *
2811774 GTTTAAGTGATCTTTGAATG
1 GTTTAAGTAATCCTTGAATA
2811794 GTTT
1 GTTT
2811798 TGATGTGCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.45
Consensus pattern (20 bp):
GTTTAAGTAATCCTTGAATA
Found at i:2812321 original size:63 final size:63
Alignment explanation
Indices: 2812212--2812332 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
2812202 TGATTCCTAG
* * ** * *
2812212 AAAATAGAAAGCTCTAAAGACATAAAGAATTGCTTTCGTAGGAATGCATTAATCGATTACATT
1 AAAACAGAAAGCTCTAAAGACACAAAGAATAACTTTCGTAGAAATGCACTAATCGATTACATT
* *
2812275 AAAACAGAAAGCTCTACAGACACAAAGAATCAAC-TTCTTAGAAATGCACTAATCGATT
1 AAAACAGAAAGCTCTAAAGACACAAAGAAT-AACTTTCGTAGAAATGCACTAATCGATT
2812333 CTTTCAAGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 48 0.98
64 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (63 bp):
AAAACAGAAAGCTCTAAAGACACAAAGAATAACTTTCGTAGAAATGCACTAATCGATTACATT
Found at i:2812349 original size:63 final size:63
Alignment explanation
Indices: 2812219--2812350 Score: 142
Period size: 63 Copynumber: 2.1 Consensus size: 63
2812209 TAGAAAATAG
* ** * * *
2812219 AAAGCTCTAAAGACATAAAGAATTGCTTTCGTAGGAATGCATTAATCGATTACATTAAAACAG
1 AAAGCTCTAAAGACACAAAGAATAACTTTCGTAGAAATGCACTAATCGATTACATTAAAACAA
* * * *
2812282 AAAGCTCTACAGACACAAAGAATCAAC-TTCTTAGAAATGCACTAATCGATT-CTTTCAAGACAA
1 AAAGCTCTAAAGACACAAAGAAT-AACTTTCGTAGAAATGCACTAATCGATTACATT-AAAACAA
2812345 AAAGCT
1 AAAGCT
2812351 TCATACCTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
62 3 0.05
63 53 0.93
64 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (63 bp):
AAAGCTCTAAAGACACAAAGAATAACTTTCGTAGAAATGCACTAATCGATTACATTAAAACAA
Found at i:2812904 original size:30 final size:30
Alignment explanation
Indices: 2812823--2812910 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
2812813 AATGTTGTAA
* *
2812823 AAGTTTTGTCTAATCCTTGAAAAGGC---T
1 AAGTTATGTCTAATCCTTGAAAAGGCAAAG
* *
2812850 AAGTTATGTCTGAT-CTTTAGAAAGGCAAAG
1 AAGTTATGTCTAATCCTTGA-AAAGGCAAAG
*
2812880 AAGTTATGTCTAATCCTTGAAAAGGAAAAG
1 AAGTTATGTCTAATCCTTGAAAAGGCAAAG
2812910 A
1 A
2812911 GCTTTTGCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
26 4 0.08
27 18 0.37
30 23 0.47
31 4 0.08
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (30 bp):
AAGTTATGTCTAATCCTTGAAAAGGCAAAG
Found at i:2812955 original size:28 final size:30
Alignment explanation
Indices: 2812916--2812982 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 30
2812906 AAAGAGCTTT
*
2812916 TGCTTGATCCTTGGAAAG-GT-TGAGGTTA
1 TGCTTGATCCTTGAAAAGAGTGTGAGGTTA
2812944 TGCTTGATCCTTGAAAAGACAGTGTGAGGTTA
1 TGCTTGATCCTTGAAAAG--AGTGTGAGGTTA
2812976 TGCTTGA
1 TGCTTGA
2812983 AGCTCTTGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
28 17 0.50
31 2 0.06
32 15 0.44
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (30 bp):
TGCTTGATCCTTGAAAAGAGTGTGAGGTTA
Found at i:2812977 original size:32 final size:28
Alignment explanation
Indices: 2812916--2812996 Score: 90
Period size: 28 Copynumber: 2.7 Consensus size: 28
2812906 AAAGAGCTTT
*
2812916 TGCTTGATCCTTGGAAAGGTTGAGGTTA
1 TGCTTGATCCTTGAAAAGGTTGAGGTTA
2812944 TGCTTGATCCTTGAAAAGACAGTGTGAGGTTA
1 TGCTTGATCCTTGAAAAG---GT-TGAGGTTA
*
2812976 TGCTTGAAGCTCTTGAAAAGG
1 TGCTTG-ATC-CTTGAAAAGG
2812997 CAATGTGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 17 0.38
31 3 0.07
32 14 0.31
33 2 0.04
34 9 0.20
ACGTcount: A:0.26, C:0.12, G:0.30, T:0.32
Consensus pattern (28 bp):
TGCTTGATCCTTGAAAAGGTTGAGGTTA
Found at i:2815942 original size:15 final size:15
Alignment explanation
Indices: 2815908--2815947 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2815898 ATATATATAT
* *
2815908 ATATATATACTTTTA
1 ATATATAAACTTTAA
*
2815923 GTATATAAACTTTAA
1 ATATATAAACTTTAA
2815938 ATATATAAAC
1 ATATATAAAC
2815948 ATATTCACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (15 bp):
ATATATAAACTTTAA
Found at i:2824537 original size:19 final size:19
Alignment explanation
Indices: 2824495--2824537 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2824485 TGTTTTTTTC
*
2824495 TTTTAAATTTCATCTTAAA
1 TTTTGAATTTCATCTTAAA
* *
2824514 ATTTGAATTTCATCTTAGA
1 TTTTGAATTTCATCTTAAA
2824533 TTTTG
1 TTTTG
2824538 TTCTTGATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.53
Consensus pattern (19 bp):
TTTTGAATTTCATCTTAAA
Found at i:2828763 original size:21 final size:19
Alignment explanation
Indices: 2828727--2828767 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2828717 ACATGTTGAG
2828727 TAGTTAATTTAAGTTATTT
1 TAGTTAATTTAAGTTATTT
*
2828746 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTAAGTTATTT
2828767 T
1 T
2828768 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (19 bp):
TAGTTAATTTAAGTTATTT
Found at i:2832817 original size:70 final size:71
Alignment explanation
Indices: 2832657--2832823 Score: 189
Period size: 71 Copynumber: 2.4 Consensus size: 71
2832647 TGGCTTTAAG
* * *
2832657 AGAGCAACTTCAAATGTATCAAGACCTACTTGAAATGTATGGAGACATCATCTCCAGACTTCAAT
1 AGAGCAACTTCAAATGTATCGAGACCTACTTAAAATGTATGAAGACATCATCTCCAGACTTCAAT
2832722 TTCCAA
66 TTCCAA
* * * * * * *
2832728 ATAGCAACTTCCAATGTATCGAGACTTGGC-TAAAATGTATTAAGACATCA-CTTTCA-ACCTTG
1 AGAGCAACTTCAAATGTATCGAGACCT-ACTTAAAATGTATGAAGACATCATC-TCCAGA-CTTC
2832790 AA-TTCCAA
63 AATTTCCAA
2832798 AGAGCAACTTCAAATGTATCGAGACC
1 AGAGCAACTTCAAATGTATCGAGACC
2832824 CAGAAGAAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
70 31 0.39
71 48 0.60
72 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (71 bp):
AGAGCAACTTCAAATGTATCGAGACCTACTTAAAATGTATGAAGACATCATCTCCAGACTTCAAT
TTCCAA
Found at i:2832834 original size:70 final size:71
Alignment explanation
Indices: 2832657--2832846 Score: 199
Period size: 70 Copynumber: 2.7 Consensus size: 71
2832647 TGGCTTTAAG
* * * *
2832657 AGAGCAACTTCAAATGTATCAAGACCTACTTGAAATGTATGGAGACATCATCTCCAGACTTCAAT
1 AGAGCAACTTCAAATGTATCGAGACCTAGTAGAAATGTATCGAGACATCATCTCCAGACTTCAAT
2832722 TTCCAA
66 TTCCAA
* * * * ** * *
2832728 ATAGCAACTTCCAATGTATCGAGACTTGGCTA-AAATGTATTAAGACATCA-CTTTCA-ACCTTG
1 AGAGCAACTTCAAATGTATCGAGACCTAG-TAGAAATGTATCGAGACATCATC-TCCAGA-CTTC
2832790 AA-TTCCAA
63 AATTTCCAA
* *
2832798 AGAGCAACTTCAAATGTATCGAGACCCAGAAGAAATGTATCGAGACATC
1 AGAGCAACTTCAAATGTATCGAGACCTAGTAGAAATGTATCGAGACATC
2832847 CTTCATTTTG
Statistics
Matches: 96, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
69 1 0.01
70 47 0.49
71 47 0.49
72 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (71 bp):
AGAGCAACTTCAAATGTATCGAGACCTAGTAGAAATGTATCGAGACATCATCTCCAGACTTCAAT
TTCCAA
Found at i:2838555 original size:131 final size:135
Alignment explanation
Indices: 2838301--2838557 Score: 333
Period size: 137 Copynumber: 1.9 Consensus size: 135
2838291 ATAAGAAATC
* *
2838301 CAATGTAAAAATAAAAATGACCATAGTCTAAGAGAAAAGGGATTAATTCCAAATGTTTTCCTATT
1 CAATGCAAAAATAAAAATGACCACAGTCTAAGAGAAAAGGGATTAATTCCAAATGTTTTCCTATT
* * **
2838366 GCAAAATGGCCTTTACCATACCAAGACAAGCAAGTTCTGTAATTTAATGACCTGAATAATCTCAG
66 GC--AATGGCCTTGACCATACCAAGACAAGCAAGTTCTGTAATCTAATGACCCAAATAATCTCAG
2838431 AGAAAGG
129 AGAAAGG
* * * * * *
2838438 CAATGCAAAAATATAAGTGACTACAGTTTAAGAGAAAAGTGATTAATTCTAAATGTTTTCC-A-T
1 CAATGCAAAAATAAAAATGACCACAGTCTAAGAGAAAAGGGATTAATTCCAAATGTTTTCCTATT
* * *
2838501 -C-ATGGCCTTGACCATACCAAGGCAAGCAAGTTTTTTAATCTAATGACCCAAATAATC
66 GCAATGGCCTTGACCATACCAAGACAAGCAAGTTCTGTAATCTAATGACCCAAATAATC
2838558 ATGGAGATTC
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
131 49 0.47
134 1 0.01
135 1 0.01
136 1 0.01
137 53 0.50
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (135 bp):
CAATGCAAAAATAAAAATGACCACAGTCTAAGAGAAAAGGGATTAATTCCAAATGTTTTCCTATT
GCAATGGCCTTGACCATACCAAGACAAGCAAGTTCTGTAATCTAATGACCCAAATAATCTCAGAG
AAAGG
Found at i:2841498 original size:20 final size:18
Alignment explanation
Indices: 2841450--2841509 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 18
2841440 GGACCGTTAT
* *
2841450 TTTTATATTTTTATTATTA
1 TTTTATAATTTTA-TATAA
*
2841469 TATATATAATTTAATATATAA
1 T-TTTATAATTT--TATATAA
2841490 TTTTATAATTTTATATAA
1 TTTTATAATTTTATATAA
2841508 TT
1 TT
2841510 ATTTTGAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 9 0.26
19 1 0.03
20 17 0.50
21 5 0.15
22 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTTATAATTTTATATAA
Found at i:2845772 original size:19 final size:19
Alignment explanation
Indices: 2845748--2845789 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
2845738 TAATTAAATA
2845748 TGTTTTTATTTTTTCATTG
1 TGTTTTTATTTTTTCATTG
2845767 TGTTTTTATTTTTTCATTG
1 TGTTTTTATTTTTTCATTG
2845786 TGTT
1 TGTT
2845790 ATATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.74
Consensus pattern (19 bp):
TGTTTTTATTTTTTCATTG
Found at i:2845797 original size:19 final size:19
Alignment explanation
Indices: 2845748--2845797 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2845738 TAATTAAATA
*
2845748 TGTTTTTATTTTTTCATTG
1 TGTTTATATTTTTTCATTG
*
2845767 TGTTTTTATTTTTTCATTG
1 TGTTTATATTTTTTCATTG
2845786 TG-TTATATTTTT
1 TGTTTATATTTTT
2845798 AATTTCTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.12, C:0.04, G:0.10, T:0.74
Consensus pattern (19 bp):
TGTTTATATTTTTTCATTG
Found at i:2846972 original size:19 final size:19
Alignment explanation
Indices: 2846948--2846985 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2846938 ATCATAGGCA
2846948 TGGCAATTACAAGGGTTGT
1 TGGCAATTACAAGGGTTGT
2846967 TGGCAATTACAAGGGTTGT
1 TGGCAATTACAAGGGTTGT
2846986 CCCACCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (19 bp):
TGGCAATTACAAGGGTTGT
Found at i:2854038 original size:15 final size:15
Alignment explanation
Indices: 2854018--2854048 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2854008 TAATAATAAA
2854018 AAATATTAATTAATT
1 AAATATTAATTAATT
*
2854033 AAATATTTATTAATT
1 AAATATTAATTAATT
2854048 A
1 A
2854049 TTTATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATTAATTAATT
Found at i:2854523 original size:15 final size:15
Alignment explanation
Indices: 2854463--2854523 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
2854453 TTTTAATTTT
*
2854463 TAAATTTTATCTTTA
1 TAAATATTATCTTTA
** *
2854478 TAAATATTAAATTTT
1 TAAATATTATCTTTA
*
2854493 TAATATGAGTAT-TTTA
1 TAA-AT-ATTATCTTTA
2854509 TAAATATTATCTTTA
1 TAAATATTATCTTTA
2854524 CTTATAAACA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
14 4 0.11
15 20 0.57
16 8 0.23
17 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (15 bp):
TAAATATTATCTTTA
Found at i:2855377 original size:2 final size:2
Alignment explanation
Indices: 2855370--2855401 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2855360 GTTGCTGGTG
*
2855370 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2855402 TTTGGTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2865052 original size:2 final size:2
Alignment explanation
Indices: 2865045--2865075 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2865035 AACTCACTTT
2865045 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2865076 CACAATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2865325 original size:35 final size:35
Alignment explanation
Indices: 2865285--2865380 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
2865275 ACAATGTGGG
* * *
2865285 TATTCTTATCCCCATATCTAGTTATATTTATATGA
1 TATTCTTACCCCCACATCTAGTTATATTCATATGA
* * * *
2865320 TATTCTTAGCCCCGCATCTAGTTATATTCATGTGG
1 TATTCTTACCCCCACATCTAGTTATATTCATATGA
* *
2865355 TATTCTTACCCCCACATATGGTTATA
1 TATTCTTACCCCCACATCTAGTTATA
2865381 CAAAATTCAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (35 bp):
TATTCTTACCCCCACATCTAGTTATATTCATATGA
Found at i:2869832 original size:22 final size:20
Alignment explanation
Indices: 2869801--2869863 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
2869791 TCCAACTTTT
2869801 AATAAAATATTAATAATTTA
1 AATAAAATATTAATAATTTA
*
2869821 ACATATTAATATT-A-AATTATA
1 A-ATA-AAATATTAATAATT-TA
2869842 AATAAAATATTAATAATTTA
1 AATAAAATATTAATAATTTA
2869862 AA
1 AA
2869864 ATAATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
19 6 0.17
20 13 0.36
21 11 0.31
22 6 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAATATTAATAATTTA
Found at i:2869865 original size:16 final size:15
Alignment explanation
Indices: 2869803--2869866 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 15
2869793 CAACTTTTAA
2869803 TAAAATATTAATAATT
1 TAAAATATTAATAA-T
*
2869819 TAACATATTAAT-AT
1 TAAAATATTAATAAT
*
2869833 T--AA-ATT-ATAAA
1 TAAAATATTAATAAT
2869844 TAAAATATTAATAATT
1 TAAAATATTAATAA-T
2869860 TAAAATA
1 TAAAATA
2869867 ATAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
10 2 0.05
11 5 0.13
12 1 0.03
13 2 0.05
14 5 0.13
15 5 0.13
16 18 0.47
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATATTAATAAT
Found at i:2869867 original size:25 final size:23
Alignment explanation
Indices: 2869823--2869898 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 23
2869813 ATAATTTAAC
2869823 ATATTAATATTAAATTATAAATAAA
1 ATATTAATATTAAA-TAT-AATAAA
2869848 ATATTAATAATTTAAA-ATAATAAA
1 ATATTAAT-A-TTAAATATAATAAA
* * *
2869872 AAATAAAT-TATAAATAAAAT-AA
1 ATATTAATAT-TAAATATAATAAA
2869894 ATATT
1 ATATT
2869899 TAAATTATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
21 1 0.02
22 9 0.21
23 4 0.10
24 12 0.29
25 10 0.24
26 1 0.02
27 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATTAATATTAAATATAATAAA
Found at i:2869892 original size:42 final size:41
Alignment explanation
Indices: 2869801--2869908 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
2869791 TCCAACTTTT
* * * *
2869801 AATAAAATATTAATAATTTAACATATTAATATTAAATTATA
1 AATAAAATATTAATAATTTAAAATATAAAAAATAAATTATA
2869842 AATAAAATATTAATAATTTAAAATAATAAAAAATAAATTATA
1 AATAAAATATTAATAATTTAAAAT-ATAAAAAATAAATTATA
*
2869884 AATAAAATA--AAT-ATTTAAATTATAA
1 AATAAAATATTAATAATTTAAAATATAA
2869909 GTTTATAATA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
38 4 0.07
39 8 0.13
40 3 0.05
41 23 0.38
42 23 0.38
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (41 bp):
AATAAAATATTAATAATTTAAAATATAAAAAATAAATTATA
Found at i:2869893 original size:47 final size:47
Alignment explanation
Indices: 2869841--2869933 Score: 118
Period size: 47 Copynumber: 2.0 Consensus size: 47
2869831 ATTAAATTAT
2869841 AAATAAAATATTAATAATT-TAAAATAATAA-AAAATAAATTATAAATA
1 AAAT-AAATATTAA-AATTATAAAATAATAATAAAATAAATTATAAATA
* ** *
2869888 AAATAAATATTTAAATTATAAGTTTATAATAAAATAAATTATAAAT
1 AAATAAATATTAAAATTATAAAATAATAATAAAATAAATTATAAAT
2869934 TATTCCTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
45 4 0.10
46 16 0.40
47 20 0.50
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (47 bp):
AAATAAATATTAAAATTATAAAATAATAATAAAATAAATTATAAATA
Found at i:2869933 original size:11 final size:11
Alignment explanation
Indices: 2869833--2869889 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
2869823 ATATTAATAT
2869833 TAAATTATAAA
1 TAAATTATAAA
* *
2869844 TAAAATATTAA
1 TAAATTATAAA
*
2869855 TAATTTA-AAA
1 TAAATTATAAA
* *
2869865 T-AATAAAAAA
1 TAAATTATAAA
2869875 TAAATTATAAA
1 TAAATTATAAA
2869886 TAAA
1 TAAA
2869890 ATAAATATTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 3 0.09
10 7 0.20
11 25 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATTATAAA
Found at i:2870033 original size:27 final size:28
Alignment explanation
Indices: 2869993--2870063 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
2869983 TTATATATAA
* *
2869993 AATATTAATAAATAAATAATCAATTATT
1 AATATTTATAAATAAATAACCAATTATT
*
2870021 AATATTT-TAAATAAATTACCAATTATT
1 AATATTTATAAATAAATAACCAATTATT
*
2870048 AATATTTAAAAATAAA
1 AATATTTATAAATAAA
2870064 ATAAAAAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 25 0.66
28 13 0.34
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.39
Consensus pattern (28 bp):
AATATTTATAAATAAATAACCAATTATT
Found at i:2870161 original size:31 final size:28
Alignment explanation
Indices: 2870112--2870196 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
2870102 ATTTAAATTA
* *
2870112 AATAAAGTATTGATATTTTAAAATATTAAT
1 AATAAATTATTAATATTTTAAAATA--AAT
*
2870142 GATTAAATTATTAATATTTT-AAATAAAT
1 -AATAAATTATTAATATTTTAAAATAAAT
* *
2870170 AATCAATTATTAATATTTAAAAATAAA
1 AATAAATTATTAATATTTTAAAATAAA
2870197 ATAAAATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
27 16 0.34
28 10 0.21
30 5 0.11
31 16 0.34
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (28 bp):
AATAAATTATTAATATTTTAAAATAAAT
Found at i:2870165 original size:16 final size:16
Alignment explanation
Indices: 2870114--2870165 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2870104 TTAAATTAAA
* *
2870114 TAAAGTATTGATATTT
1 TAAATTATTAATATTT
*
2870130 TAAAATATTAATGA--T
1 TAAATTATTAAT-ATTT
2870145 TAAATTATTAATATTT
1 TAAATTATTAATATTT
2870161 TAAAT
1 TAAAT
2870166 AAATAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
16 16 0.53
17 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
TAAATTATTAATATTT
Found at i:2871469 original size:119 final size:119
Alignment explanation
Indices: 2871258--2871489 Score: 401
Period size: 119 Copynumber: 1.9 Consensus size: 119
2871248 TTCAGAGAAA
* *
2871258 GAAGACTTTAATAAGTTCAAAACTCATCTTATCTCTTATTGATATGAAATCCTTGACATTTGTAC
1 GAAGACTTTAATAAGTTCAAAACTCATCTTATCTCTTACTGATATGAAATCCTTGACATTTATAC
* *
2871323 ATGTATGTATCATGCACACCAAATTTTGATAATTACTAATAGAAACATAGGAAT
66 ATGTATGTATCACGCACACCAAATTTTGATAATTACTAATAAAAACATAGGAAT
*
2871377 GAAGATTTTAATAAGTTCAAAACTCATCTTATCTCTTACTGATATGAAATCCTTGACATTTATAC
1 GAAGACTTTAATAAGTTCAAAACTCATCTTATCTCTTACTGATATGAAATCCTTGACATTTATAC
* *
2871442 ATGTATGTATCACGCACATCAAATTTTGATAATTATTAATAAAAACAT
66 ATGTATGTATCACGCACACCAAATTTTGATAATTACTAATAAAAACAT
2871490 GTTATTATTA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
119 106 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (119 bp):
GAAGACTTTAATAAGTTCAAAACTCATCTTATCTCTTACTGATATGAAATCCTTGACATTTATAC
ATGTATGTATCACGCACACCAAATTTTGATAATTACTAATAAAAACATAGGAAT
Found at i:2874109 original size:586 final size:584
Alignment explanation
Indices: 2873190--2876681 Score: 3814
Period size: 585 Copynumber: 6.0 Consensus size: 584
2873180 ATTGAACTCA
* * *
2873190 AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCAT-AGAAGCAAGTAAAAATTTAA
1 AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGA-AAGCATGTAAAAATCTAA
* * * *
2873254 TTTTATGTTAAA-TAATATATTTAAATTTTTACCG-TCAAAATTGATGA-TTAAGAGTAATACGA
65 TTTTATGATAAACTAATATATTCAAGTTTTTA-CGATCAAAATTGATGAGTT-AGAGTAATATGA
* * * *
2873316 AAATCAAATCATATT-ATCTTAAAATGAGTTATTTTATGTTTTGTGTTCATATTTTTATGTTTTA
128 AAATCAAATCATATTCA-CTTAAAATAAGTTATGTTAAGTTTTGTGTTCATATTTTTATATTTTA
* * * * * *
2873380 TCTTCTACCTATGTAATGAATGTCATACTAGTGACTATTATTATGGTATTATCTTTTTTTTATAA
192 TCTTCCACC-ATCTAATGAATGTCATAC-CGTGACTATTATTATGATATTATCATTTTTTGATAA
* * * * ** * *
2873445 ATGCTATAATTATGGTATTATCTCTATTATATATTTGTAACGCCTTATTATTTGGTATACACGTG
255 ATGTTATTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTG
* *
2873510 TTTTTAATAGTTTTTTCTTTTGA-CTTTTTTATATATTAGTTTG-ATTATATATACACGTGTTTG
320 TTTTTAGTAGTTTTTTCTTTTGACCATTTTTATATATTAG-TTGAATTATATATACACGTGTTTG
* * * *
2873573 TGCATGTATGTATCACACT-TATCAAATTTTAATAATTACTAACAAAAACATATTATTGTTATCT
384 TACATGTATGTATCACACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCT
** *
2873637 TATACATTGGTAATGAAAAAATTAGAAGAATTTTTAACTTATTATGTGTTTCTTTATTTAAAAAA
449 TATACATTAATAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTGTTT-TTTATTTAAAAAA
* * * *
2873702 GGTTAACAATAAATACAATAATCAAATAAAAATTTAAAATATAATTTTGACTGTGCATTTGCCCT
513 -GTTAACAATAATTACAATAATCAAATAAAAATTTAAAATCTAATTTTGATTGTGCATTTGCCAT
2873767 TAACAATT
577 TAACAATT
* * *
2873775 AAACTCAAAAGTAAATCACCATCACTACAAAAATAAATTTTTGTGAAAGCATGTGAAAATCTAAT
1 AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTAAT
* * * *
2873840 TTTATGATAAACTAATATCTTCAAATTTTTACGATCAAAATGGATAAGTTAGAGTAATATGAAAA
66 TTTATGATAAACTAATATATTCAAGTTTTTACGATCAAAATTGATGAGTTAGAGTAATATGAAAA
* * * * * * * *
2873905 TCAAATTACACTCACTTAAACTAAGTTACGTTAAGTTGTTGTGATCATATTTGTATGTTTTATCT
131 TCAAATCATATTCACTTAAAATAAGTTATGTTAAGTT-TTGTGTTCATATTTTTATATTTTATCT
* * * * * *
2873970 TCTACTCATCTAACGAATGTTATACCGATTACTATTATTATGATATTATTATTTTTT-ATAAATA
195 TCCAC-CATCTAATGAATGTCATACCG-TGACTATTATTATGATATTATCATTTTTTGATAAATG
* * **** ** *
2874034 TTACTATTATGGTATTATCTCTATCATGGACTTGTAATATTTTATTATTTAATGTACATGTGTTT
258 TTATTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTGTTT
* * * * * * *
2874099 CTAGTAGTTTTTTTTTGTTTTTATCATTTTTATATATTAGTTGAATTATATATATAAGCGTTTGT
323 TTAGTAG---TTTTTTCTTTTGACCATTTTTATATATTAGTTGAATTATATATACACGTGTTTGT
* * * * * *
2874164 CCATGTATATATCGCA-TACATTAAGTTTTAATAATTACTAATAAAAACACATTATTGTTATATT
385 ACATGTATGTATCACACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCTT
* * *
2874228 ATACATTGATAAAGAAAAAAATTAGAAGAATATTTGACTTATTATGT-TTTTTTATTTAAAAAAA
450 ATACATTAATAAAG-AAAAAATTAGAAGAATTTTTAACTTATTATGTGTTTTTTATTT--AAAAA
* * * * *
2874292 AGTTAACACTAATTCCAATAATGAAATAAAGATTTAAAATCTAATTTTGATTGTACATTTGCCAT
512 AGTTAACAATAATTACAATAATCAAATAAAAATTTAAAATCTAATTTTGATTGTGCATTTGCCAT
2874357 TAACAATAAAACT
577 TAACAAT-----T
* *
2874370 CAAAACTCAAAAGTAAATGACCATCACTACAAAAATAAATTTTCGTGAAAGCATGTAAAAATCTA
1 --AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTA
* * * * *
2874435 ATTTT-TAATAAACTAATATATTCAAGTTTTTACCATCAAAATTGATGAGCTAAAGTAATAAG-A
64 ATTTTATGATAAACTAATATATTCAAGTTTTTACGATCAAAATTGATGAGTTAGAGTAATATGAA
* *
2874498 AATCAAATCATATTCACTTAAAATGAGTTATGTTAAGTTTTTGTGTTCATATTTCTATATTTTAT
129 AATCAAATCATATTCACTTAAAATAAGTTATGTTAAG-TTTTGTGTTCATATTTTTATATTTTAT
*
2874563 CTTCCACCCA-CGTAATGAATGTCATACCTGTGACTATTATTATGATATTATCATTTTTTGGTAA
193 CTTCCA-CCATC-TAATGAATGTCATACC-GTGACTATTATTATGATATTATCATTTTTTGATAA
** * * * * * *
2874627 ATACTATTATTATGATATTATCACTTTCATGGACGTGTAACACCATATTATTTGGTGTACACGTG
255 ATGTTATTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTG
* * * *
2874692 TTTTTAGTAGTTTTTTCATTTGACCATTTTTATATATTA-TT--A-CATAT-T-CACATGTTTGC
320 TTTTTAGTAGTTTTTTCTTTTGACCATTTTTATATATTAGTTGAATTATATATACACGTGTTTGT
* *** * * * *
2874751 GCGCATATGTATTATA-TACATCAAATTTTAATAATTATTAATAAAAATACATTATTGTTATCTT
385 ACATGTATGTATCACACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCTT
* * * *
2874815 ATGCATTAATAAAGAAAAAATTAAAAGAATTTTTAAATTACTATGTGTTTTTTTATTTAAAAAAG
450 ATACATTAATAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTG-TTTTTTATTTAAAAAAG
* * * * *
2874880 TTAACAATAATTATAATAATCAAATAAAGATTT-GAATCTAATTTTAATTATGCATTTGCCATTA
514 TTAACAATAATTACAATAATCAAATAAAAATTTAAAATCTAATTTTGATTGTGCATTTGCCATTA
*
2874944 ACGATT
579 ACAATT
* * *
2874950 ATACTCAAAAGTAAATCACCGTCACTACAAAAATAAATTTTCGTGAAAGCATGTAAAAATCTAAT
1 AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTAAT
* * * * *
2875015 TTTATGATAAATTAATATATTCAAGTTTTTGCTATCAAACTTGATGAGTTAGAATAATATGAAAA
66 TTTATGATAAACTAATATATTCAAGTTTTTACGATCAAAATTGATGAGTTAGAGTAATATGAAAA
* * *
2875080 TCAAA-CAATATTCACTT---A-AA---A--CT---TTTTGAGTTCATATTTTTATATTTTATTT
131 TCAAATC-ATATTCACTTAAAATAAGTTATGTTAAGTTTTGTGTTCATATTTTTATATTTTATCT
* * ** *
2875132 TCCACCTATGTAATGAATGACATATATGTGGCTATTATTATGATATTATCATTTTTTGATAAATG
195 TCCACC-ATCTAATGAATGTCATA-CCGTGACTATTATTATGATATTATCATTTTTTGATAAATG
* * * ** * *
2875197 TTATTATTATGGTATTATATCTGTCGTGGACCTGTAACGTTTTATTATTTAGTGTACACGTGTGT
258 TTATTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTGTTT
* * ** * *
2875262 TTAGTTGTTTTTTCTTATGATTATTTTTATATATTAGTTGAATTATATATACACGTGTTTATACG
323 TTAGTAGTTTTTTCTTTTGACCATTTTTATATATTAGTTGAATTATATATACACGTGTTTGTACA
2875327 TGTATGTATCACAC-ACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCTTATA
388 TGTATGTATCACACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCTTATA
*
2875391 CATTACT-AA-AAAAAATTAGAAGAATTTTTAACTTATTATGTGTTTTTTAATTTAAACAAAGTT
453 CATTAATAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTGTTTTTT-ATTTAAA-AAAGTT
* *
2875454 AACATTAATTACAATAATCAAA-AAAAGATTTGAAAA-CTAATTTTGATTGTGTATTTGCCATGT
516 AACAATAATTACAATAATCAAATAAAA-ATTT-AAAATCTAATTTTGATTGTGCATTTG-C----
2875517 ACGATTAAACTCAAAATT
574 -C-ATT-AA--C--AATT
* * * * **
2875535 AAAAACTTAAAAGTAAATCACCATCACTAAAAAAACAAATTTTAGTGAAAGCATATGGAAATCTA
1 --AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTA
* * *
2875600 ATTTTTTGATAAACTAATATATTTAAGTTTTTATC-ATCAAAATTCATGAGTTAGAGTAATATGA
64 ATTTTATGATAAACTAATATATTCAAGTTTTTA-CGATCAAAATTGATGAGTTAGAGTAATATGA
* *
2875664 AAATCAAATTATATTCACTTAAAATGAGTTATGTTAAGTTATTGTGTTCATATTTTTATATTTTA
128 AAATCAAATCATATTCACTTAAAATAAGTTATGTTAAGTT-TTGTGTTCATATTTTTATATTTTA
* * *
2875729 TCTTCCACCCATATAATGAATGTCATACCTGTGACTATTATTATGATATTATTATTTTTTAATAA
192 TCTTCCA-CCATCTAATGAATGTCATACC-GTGACTATTATTATGATATTATCATTTTTTGATAA
* * * * ** *
2875794 ATGTTATTGTTATGGTATTTTCTCTGTCATGGAGTTGTAATGCCTTATTATTTGGTGTTTATGTG
255 ATGTTATTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTG
* * * *
2875859 TTTTTAGTAGTTTTTTCTTTTGATCATATTTATATATTAGTTAAATTATATATACACCTGTTTGT
320 TTTTTAGTAGTTTTTTCTTTTGACCATTTTTATATATTAGTTGAATTATATATACACGTGTTTGT
*
2875924 ACATGTATGTATCAC-CTACATCAAATTTTAATAATTACTAATAAAAACATATTATTGTTATCTT
385 ACATGTATGTATCACACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCTT
* *
2875988 ATACATTGACAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTGTTTTTTTATTTAAAAAAG
450 ATACATTAATAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTG-TTTTTTATTTAAAAAAG
* * * * *
2876053 TTAACAATAATTATAATAATCAAA-AAAAGAATTGAAATCTAATTTTGATTGTGCATTAGCTATT
514 TTAACAATAATTACAATAATCAAATAAAA-ATTTAAAATCTAATTTTGATTGTGCATTTGCCATT
**
2876117 AATGATT
578 AACAATT
* ** *
2876124 -AACTCAAAAGTAAATCACAATCTTTATAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTAAT
1 AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTAAT
* * * * * *
2876188 GTTATGATAAATTAACATATTCAAGTTTTTACTATTAAAATTGATGAGTTAAAGTAATAT-AAAA
66 TTTATGATAAACTAATATATTCAAGTTTTTACGATCAAAATTGATGAGTTAGAGTAATATGAAAA
* *
2876252 TCAAATCATATTCACTTAAAACAAGTTATGTTAAGTTTTTGTGTTCATATTTTTATGTTTTATCT
131 TCAAATCATATTCACTTAAAATAAGTTATGTTAAG-TTTTGTGTTCATATTTTTATATTTTATCT
* * * ** *
2876317 TTCACTCATGC-AATGAATGTCATACCAATGACCATTATTATGATATTATCCGTTTTTGGTAAAT
195 TCCAC-CAT-CTAATGAATGTCATACC-GTGACTATTATTATGATATTATCATTTTTTGATAAAT
* * *
2876381 GTTGTTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGTTGTACACGTATT
257 GTTATTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTGTT
* * * * * *
2876446 TTTAGT-GATTTTTTCTTTTGACCATTATTATATATTAATTGAATTATTTATACACGCGCTTGCA
322 TTTAGTAG-TTTTTTCTTTTGACCATTTTTATATATTAGTTGAATTATATATACACGTGTTTGTA
* * * * * * * * * *
2876510 TATGTATGTACCACGCAC-ATATTAAAATTTGATAATTATTAAT-AAAA-ATA-TATTATTATTT
386 CATGTATGTATCA--CACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCT
* * * * * * *
2876571 TATACATTAAGAAATAAAAAATTATAAAAACTTTTAATTTATTATGTGTATTTTTATTTATAAAA
449 TATACATTAATAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTGT-TTTTTATTTAAAAAA
* * * *
2876636 -TTAATATTAATTATAATAATCTAAATAAAAA-TTAGAGATCTAATTT
513 GTTAACAATAATTACAATAATC-AAATAAAAATTTA-AAATCTAATTT
2876682 CACTTTGATT
Statistics
Matches: 2453, Mismatches: 357, Indels: 195
0.82 0.12 0.06
Matches are distributed among these distances:
566 2 0.00
567 162 0.07
568 2 0.00
570 7 0.00
571 45 0.02
572 33 0.01
573 91 0.04
574 3 0.00
576 1 0.00
577 1 0.00
578 65 0.03
579 50 0.02
580 22 0.01
581 2 0.00
583 23 0.01
584 80 0.03
585 342 0.14
586 306 0.12
587 290 0.12
588 14 0.01
589 29 0.01
590 165 0.07
591 37 0.02
592 2 0.00
593 27 0.01
594 5 0.00
595 103 0.04
596 117 0.05
597 65 0.03
599 3 0.00
600 256 0.10
601 57 0.02
602 40 0.02
603 6 0.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (584 bp):
AAACTCAAAAGTAAATCACCATCACTACAAAAACAAATTTTCGTGAAAGCATGTAAAAATCTAAT
TTTATGATAAACTAATATATTCAAGTTTTTACGATCAAAATTGATGAGTTAGAGTAATATGAAAA
TCAAATCATATTCACTTAAAATAAGTTATGTTAAGTTTTGTGTTCATATTTTTATATTTTATCTT
CCACCATCTAATGAATGTCATACCGTGACTATTATTATGATATTATCATTTTTTGATAAATGTTA
TTATTATGGTATTATCTCTGTCATGGACTTGTAACGCCTTATTATTTGGTGTACACGTGTTTTTA
GTAGTTTTTTCTTTTGACCATTTTTATATATTAGTTGAATTATATATACACGTGTTTGTACATGT
ATGTATCACACTACATCAAATTTTAATAATTACTAATAAAAACACATTATTGTTATCTTATACAT
TAATAAAGAAAAAATTAGAAGAATTTTTAACTTATTATGTGTTTTTTATTTAAAAAAGTTAACAA
TAATTACAATAATCAAATAAAAATTTAAAATCTAATTTTGATTGTGCATTTGCCATTAACAATT
Found at i:2882732 original size:11 final size:11
Alignment explanation
Indices: 2882718--2882751 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
2882708 CATATCAAAG
2882718 GAATGTAAAAT
1 GAATGTAAAAT
2882729 GAATGTAAAAT
1 GAATGTAAAAT
2882740 GAATGTAAAAT
1 GAATGTAAAAT
2882751 G
1 G
2882752 TGTTATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (11 bp):
GAATGTAAAAT
Found at i:2887423 original size:11 final size:12
Alignment explanation
Indices: 2887407--2887436 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2887397 GAAATGAAAA
2887407 AAAATTAATT-T
1 AAAATTAATTAT
2887418 AAAATTAATTAT
1 AAAATTAATTAT
2887430 AAAATTA
1 AAAATTA
2887437 TAAACTCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTAATTAT
Found at i:2888410 original size:17 final size:17
Alignment explanation
Indices: 2888388--2888455 Score: 50
Period size: 17 Copynumber: 3.9 Consensus size: 17
2888378 TTTTTAAATA
2888388 ATTATTTTTAATTTATT
1 ATTATTTTTAATTTATT
**
2888405 ATTATTACT-A-TTATT
1 ATTATTTTTAATTTATT
**
2888420 ATAATATTTTTAAATTTAAA
1 AT--TATTTTT-AATTTATT
*
2888440 ATTATTTTTTATTTAT
1 ATTATTTTTAATTTAT
2888456 AATATAATTA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
15 7 0.18
16 1 0.03
17 17 0.45
18 7 0.18
19 1 0.03
20 5 0.13
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTATTTTTAATTTATT
Found at i:2888456 original size:34 final size:34
Alignment explanation
Indices: 2888418--2888482 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2888408 ATTACTATTA
**
2888418 TTATAATATTTTTAAATTTAAAATTATTTTTTAT
1 TTATAATATAATTAAATTTAAAATTATTTTTTAT
2888452 TTATAATATAATTAAATTTAAAATTATTTTT
1 TTATAATATAATTAAATTTAAAATTATTTTT
2888483 AATAAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (34 bp):
TTATAATATAATTAAATTTAAAATTATTTTTTAT
Found at i:2890885 original size:2 final size:2
Alignment explanation
Indices: 2890878--2890925 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2890868 ATAAAAGGAT
2890878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2890920 TA TA TA
1 TA TA TA
2890926 CGCATTCTCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2892483 original size:33 final size:33
Alignment explanation
Indices: 2892422--2892485 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
2892412 TCATATTATC
*
2892422 ATTAATTATGATATATTAGTGTATCACATTACT
1 ATTAATTATGATATATTAGTATATCACATTACT
2892455 ATTAATTATGATATATTAGTATGA-CACATTA
1 ATTAATTATGATATATTAGTAT-ATCACATTA
2892486 ACGTCATGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.44
Consensus pattern (33 bp):
ATTAATTATGATATATTAGTATATCACATTACT
Found at i:2911552 original size:2 final size:2
Alignment explanation
Indices: 2911545--2911598 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
2911535 GTCCAATCTC
* *
2911545 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT A- AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2911586 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
2911599 GATGATTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2913450 original size:3 final size:3
Alignment explanation
Indices: 2913442--2913467 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2913432 ATGTTCTCTT
2913442 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2913468 TAAATGTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2913874 original size:15 final size:14
Alignment explanation
Indices: 2913854--2913906 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
2913844 ACAGGTAATA
2913854 TTTAAAAGAAATATT
1 TTTAAAA-AAATATT
2913869 TTTAAAAATAATA-T
1 TTTAAAAA-AATATT
*
2913883 TTAAAATTAAAATATT
1 TTTAAA--AAAATATT
2913899 TTTAAAAA
1 TTTAAAAA
2913907 TAACTCTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.28
15 15 0.47
16 8 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
TTTAAAAAAATATT
Found at i:2913888 original size:28 final size:29
Alignment explanation
Indices: 2913849--2913909 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
2913839 ATTTAACAGG
*
2913849 TAATATTTAAAA-GAAATATTTTTAAAAA
1 TAATATTTAAAATAAAATATTTTTAAAAA
2913877 TAATATTTAAAATTAAAATATTTTTAAAAA
1 TAATATTTAAAA-TAAAATATTTTTAAAAA
2913907 TAA
1 TAA
2913910 CTCTCTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 12 0.40
30 18 0.60
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
TAATATTTAAAATAAAATATTTTTAAAAA
Found at i:2914021 original size:21 final size:21
Alignment explanation
Indices: 2913995--2914049 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
2913985 TACAGAAACA
*
2913995 TGTTACATGTCATAATT-AGAT
1 TGTTACACGTCATAATTAAG-T
2914016 TGTTACACGTCATAATTAAGT
1 TGTTACACGTCATAATTAAGT
*
2914037 TGTTACACATCAT
1 TGTTACACGTCAT
2914050 GTTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (21 bp):
TGTTACACGTCATAATTAAGT
Found at i:2919188 original size:27 final size:29
Alignment explanation
Indices: 2919156--2919217 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
2919146 AAGCATTAAA
*
2919156 GTGTAACAA-AAT-GTTTTTGAATATGAT
1 GTGTAACAATAATAGTTTTTCAATATGAT
* *
2919183 GTGTAACAATAATATTTTTTCAATATGGT
1 GTGTAACAATAATAGTTTTTCAATATGAT
2919212 GTGTAA
1 GTGTAA
2919218 TAACAGTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 9 0.30
28 3 0.10
29 18 0.60
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (29 bp):
GTGTAACAATAATAGTTTTTCAATATGAT
Found at i:2919214 original size:29 final size:28
Alignment explanation
Indices: 2919156--2919231 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 28
2919146 AAGCATTAAA
* *
2919156 GTGTAACAAAAT-GTTTTTGAATATGAT
1 GTGTAACAAAATATTTTTTCAATATGAT
*
2919183 GTGTAACAATAATATTTTTTCAATATGGT
1 GTGTAACAA-AATATTTTTTCAATATGAT
* *
2919212 GTGTAATAACAGTATTTTTT
1 GTGTAACAA-AATATTTTTT
2919232 TTGCAACATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 9 0.22
28 3 0.07
29 29 0.71
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (28 bp):
GTGTAACAAAATATTTTTTCAATATGAT
Found at i:2919518 original size:142 final size:142
Alignment explanation
Indices: 2919296--2919565 Score: 328
Period size: 142 Copynumber: 1.9 Consensus size: 142
2919286 GTATATGGTG
2919296 TGTAACAATAGTATTTTTTTTTTAACATAACGTATAACAACCTAACCATGGCATGTAACATAATT
1 TGTAACAATAGTATTTTTTTTTTAACATAACGTATAACAACCTAACCATGGCATGTAACATAATT
* * * * * * *
2919361 TGTAAATGACGTGTAAAAACCTAATCATGGTGTGTTACATGTTTTTATACATGGCGTGTAACAAC
66 TGTAAATGACGTGTAAAAACCTAACCATGGCGTGTAACATATTTCTATACATGACGTATAACAAC
2919426 CTAACCATGTTA
131 CTAACCATGTTA
* * * * * * **
2919438 TGTAACGATAGTATTTTTTTTTTAACATGACGTGTAACAACCT-ACCATGGCGTGTCATATGTTT
1 TGTAACAATAGTATTTTTTTTTTAACATAACGTATAACAACCTAACCATGGCATGTAACAT-AAT
* * * * *
2919502 TTGTATATG-GGATGTAATAACTTAACCATGGCGTGTAACATATTTCTGTACATGACGTATAACA
65 TTGTAAATGACG-TGTAAAAACCTAACCATGGCGTGTAACATATTTCTATACATGACGTATAACA
2919566 TGTTTCTGTA
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
141 15 0.14
142 91 0.86
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (142 bp):
TGTAACAATAGTATTTTTTTTTTAACATAACGTATAACAACCTAACCATGGCATGTAACATAATT
TGTAAATGACGTGTAAAAACCTAACCATGGCGTGTAACATATTTCTATACATGACGTATAACAAC
CTAACCATGTTA
Found at i:2919588 original size:24 final size:23
Alignment explanation
Indices: 2919532--2919590 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
2919522 CTTAACCATG
2919532 GCGTGTAACATATTTCTGTACAT
1 GCGTGTAACATATTTCTGTACAT
* *
2919555 GACGTATAACATGTTTCTGTACATT
1 G-CGTGTAACATATTTCTGTACA-T
2919580 GCGTGTAACAT
1 GCGTGTAACAT
2919591 TATAGCGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 28 0.90
25 2 0.06
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (23 bp):
GCGTGTAACATATTTCTGTACAT
Found at i:2929759 original size:2 final size:2
Alignment explanation
Indices: 2929742--2929776 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2929732 TACTGACTAC
* *
2929742 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2929777 GTCAATATTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2936297 original size:1 final size:1
Alignment explanation
Indices: 2936293--2936650 Score: 563
Period size: 1 Copynumber: 358.0 Consensus size: 1
2936283 AATTTTTGCT
2936293 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* * * * * *
2936358 CCCCCCCCCCCCCCCCACCTCCCTCCCCCCTCCCCCCCCCCTCCCCCTCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* * * * * *
2936423 CCACCCCCCCCCCCCCCCTCCCCCCCCCCCGCCACCCCCCCCCCCCCCCCCCCCCGCCCTCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* *
2936488 CCCCCCCCCCCCCCCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCACC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
* *
2936553 TCCCCCCCCCCCCCCCCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
*
2936618 CCCCCACCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2936651 TCTCATCTCT
Statistics
Matches: 323, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 323 1.00
ACGTcount: A:0.02, C:0.95, G:0.01, T:0.02
Consensus pattern (1 bp):
C
Found at i:2964233 original size:18 final size:18
Alignment explanation
Indices: 2964210--2964244 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2964200 AATATTTAAA
*
2964210 TTAAAATCATACATTTAG
1 TTAAAATCATAAATTTAG
2964228 TTAAAATCATAAATTTA
1 TTAAAATCATAAATTTA
2964245 TTATCTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAAAATCATAAATTTAG
Found at i:2967681 original size:18 final size:18
Alignment explanation
Indices: 2967655--2967696 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2967645 ATGCCTTTTT
*
2967655 TGTGATGAACAATGGTTG
1 TGTGGTGAACAATGGTTG
*
2967673 TGTGGTGAATAATGGTTG
1 TGTGGTGAACAATGGTTG
2967691 TGTGGT
1 TGTGGT
2967697 TTATATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.38
Consensus pattern (18 bp):
TGTGGTGAACAATGGTTG
Found at i:2970042 original size:21 final size:19
Alignment explanation
Indices: 2970016--2970056 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
2970006 AATTTAAAAC
2970016 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
2970037 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
2970056 A
1 A
2970057 TTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:2974537 original size:39 final size:39
Alignment explanation
Indices: 2974494--2974612 Score: 238
Period size: 39 Copynumber: 3.1 Consensus size: 39
2974484 CTCAAATATC
2974494 TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
1 TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
2974533 TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
1 TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
2974572 TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
1 TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
2974611 TA
1 TA
2974613 TAATAAAGTT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.34
Consensus pattern (39 bp):
TAACTATTTAAGCCTCCAAAATGTGTCAAAATAACTTTA
Found at i:2978676 original size:2 final size:2
Alignment explanation
Indices: 2978669--2978712 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2978659 AACATGCATT
* *
2978669 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2978711 TA
1 TA
2978713 AAACCTTACA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2979428 original size:48 final size:48
Alignment explanation
Indices: 2979372--2979510 Score: 251
Period size: 48 Copynumber: 2.9 Consensus size: 48
2979362 TTGTCGACTG
**
2979372 TTTTTGCTTTTCTTCTTTTGTCAGTTGTTTTCGGCTGCTTTGATGCTA
1 TTTTTGCTTTTCTTCTTTTGTCAGTTACTTTCGGCTGCTTTGATGCTA
*
2979420 TTTTTGCTTTTCTTCTTTTGTCAGTTACTTTCGGCTGCTTTGATGCTG
1 TTTTTGCTTTTCTTCTTTTGTCAGTTACTTTCGGCTGCTTTGATGCTA
2979468 TTTTTGCTTTTCTTCTTTTGTCAGTTACTTTCGGCTGCTTTGA
1 TTTTTGCTTTTCTTCTTTTGTCAGTTACTTTCGGCTGCTTTGA
2979511 CGTCTTTACT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.06, C:0.18, G:0.18, T:0.58
Consensus pattern (48 bp):
TTTTTGCTTTTCTTCTTTTGTCAGTTACTTTCGGCTGCTTTGATGCTA
Found at i:2985077 original size:26 final size:27
Alignment explanation
Indices: 2985029--2985083 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
2985019 TTATTTTTAT
* *
2985029 TTTATTTTATTTTTTAAATATTAATAA
1 TTTATTTTATTTTATAAAAATTAATAA
2985056 TTTATTTT-TTTTATAAAAATTAATAA
1 TTTATTTTATTTTATAAAAATTAATAA
2985082 TT
1 TT
2985084 GATAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTATTTTATTTTATAAAAATTAATAA
Found at i:2985289 original size:139 final size:141
Alignment explanation
Indices: 2985137--2985429 Score: 326
Period size: 139 Copynumber: 2.1 Consensus size: 141
2985127 ATTAAAAACT
* * * * * * *
2985137 ATTAAGATATTATTTATAATTTAACTTTTATTAGGATTATTTGCTTTCAT-TTATTTCA-TTTTT
1 ATTAATATTTTATTTATAATTTAAATATTAGTAGGATTATTT-ATTTCATGTCATTTCAGTTTTT
* * *
2985200 AAATATTAATAATTTATAAATTATTCAAAATA-TCAATAACTAACAATTTAAATATTAATA-TT-
65 -AATATTAATAATATATAAATTATTCAAAAAACT-AAAAACTAACAATTTAAATATTAATATTTA
* *
2985262 TTTATATTTTAGTC
128 TTTATAATTTAATC
* * *
2985276 ATTAATATTTTATTTATAATTTAAATATTAGTATGATTATTTATTTTATGTCATTTTAGTTTTTA
1 ATTAATATTTTATTTATAATTTAAATATTAGTAGGATTATTTATTTCATGTCATTTCAGTTTTTA
* * * * **
2985341 ATATTAATAATATATAATTTATTTAAAAAACTAAAAATTGATTATTTAAATATTAATATTTTATT
66 ATATTAATAATATATAAATTATTCAAAAAACTAAAAACTAACAATTTAAATATTAATA-TTTATT
2985406 TATAATTTAATC
130 TATAATTTAATC
2985418 ATTAATATTTTA
1 ATTAATATTTTA
2985430 AATTATTAAT
Statistics
Matches: 127, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
138 5 0.04
139 90 0.71
140 6 0.05
141 2 0.02
142 24 0.19
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (141 bp):
ATTAATATTTTATTTATAATTTAAATATTAGTAGGATTATTTATTTCATGTCATTTCAGTTTTTA
ATATTAATAATATATAAATTATTCAAAAAACTAAAAACTAACAATTTAAATATTAATATTTATTT
ATAATTTAATC
Found at i:2989682 original size:26 final size:26
Alignment explanation
Indices: 2989649--2989702 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2989639 TTATGAATTG
2989649 ATAATTTAAATAGTAGTAT-TTTATTT
1 ATAATTTAAA-AGTAGTATGTTTATTT
* *
2989675 ATAATTTAAAATTATTATGTTTATTT
1 ATAATTTAAAAGTAGTATGTTTATTT
2989701 AT
1 AT
2989703 TTTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (26 bp):
ATAATTTAAAAGTAGTATGTTTATTT
Found at i:2989717 original size:110 final size:110
Alignment explanation
Indices: 2989589--2989793 Score: 288
Period size: 110 Copynumber: 1.9 Consensus size: 110
2989579 ATATATATGA
* * **
2989589 TTATTTATTTTTATTTTTAAATATTAAT-ATTATATAATTTATTTAAAAAATTATGAATTGATAA
1 TTATTTATTTTTATTTTTAAATATTAATAATT-TATAATCTATCTAAAAAATTAACAATTGATAA
* **
2989653 TTTAAATAGTAGTATTTTATTTATAATTTAAAATTATTATGTTTAT
65 TTTAAATAGTAATATTTTAAATATAATTTAAAATTATTATGTTTAT
* *
2989699 TTATTT-TTTTTATTTTTTAAGTATTAATAATTTATAATCTATCTAAAATATTAACAATTGATAA
1 TTATTTATTTTTA-TTTTTAAATATTAATAATTTATAATCTATCTAAAAAATTAACAATTGATAA
*
2989763 TTTAAATATTAATATTTTAAATATAATTTAA
65 TTTAAATAGTAATATTTTAAATATAATTTAA
2989794 TCATTAATAT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
109 6 0.07
110 74 0.89
111 3 0.04
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.54
Consensus pattern (110 bp):
TTATTTATTTTTATTTTTAAATATTAATAATTTATAATCTATCTAAAAAATTAACAATTGATAAT
TTAAATAGTAATATTTTAAATATAATTTAAAATTATTATGTTTAT
Found at i:2989790 original size:26 final size:26
Alignment explanation
Indices: 2989759--2989809 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2989749 TTAACAATTG
2989759 ATAATTTAAAT-ATTAATATTTTAAAT
1 ATAATTT-AATCATTAATATTTTAAAT
2989785 ATAATTTAATCATTAATATTTTAAA
1 ATAATTTAATCATTAATATTTTAAA
2989810 ATATTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.12
26 21 0.88
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (26 bp):
ATAATTTAATCATTAATATTTTAAAT
Found at i:2990915 original size:15 final size:15
Alignment explanation
Indices: 2990895--2990954 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 15
2990885 TAATGTTATA
2990895 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
2990910 ATTAAAATAAAATATAT
1 ATTAAAATAAAA-A-AT
2990927 AATATAAGAAT-AAAAA-
1 -AT-TAA-AATAAAAAAT
2990943 ATTAAAATAAAA
1 ATTAAAATAAAA
2990955 TAAAATATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 3 0.08
14 6 0.15
15 14 0.36
16 1 0.03
17 3 0.08
18 3 0.08
19 6 0.15
20 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:2990947 original size:33 final size:34
Alignment explanation
Indices: 2990891--2990966 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 34
2990881 TTTATAATGT
2990891 TATAAT-TAAAATAAAAAATATTAAAATAAAATA
1 TATAATATAAAATAAAAAATATTAAAATAAAATA
2990924 TATAATATAAGAAT-AAAAA-ATTAAAATAAAATA
1 TATAATATAA-AATAAAAAATATTAAAATAAAATA
2990957 -A-AATATAAAA
1 TATAATATAAAA
2990967 AATTAACATT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
30 2 0.05
31 7 0.17
32 1 0.02
33 20 0.49
34 8 0.20
35 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (34 bp):
TATAATATAAAATAAAAAATATTAAAATAAAATA
Found at i:2990957 original size:24 final size:25
Alignment explanation
Indices: 2990897--2991026 Score: 75
Period size: 25 Copynumber: 4.8 Consensus size: 25
2990887 ATGTTATAAT
* *
2990897 TAAAATAAAAAATATTAAAA-TAAAA
1 TAAAATAAAATATA-AAAAATTAAAA
2990922 TATATAATATAAGA-ATAAAAAATTAAAA
1 TA-A-AATA-AA-ATATAAAAAATTAAAA
*
2990950 TAAAATAAAATATAAAAAATTAACAT
1 TAAAATAAAATATAAAAAATTAA-AA
* * * *
2990976 TTATATAATATAGGTAAAACAAATTGAAA
1 TAAAATAAAATA--T-AAA-AAATTAAAA
2991005 TAAAATATATAATATAAAAAAT
1 TAAAATA-A-AATATAAAAAAT
2991027 ATATTAAAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
24 1 0.01
25 16 0.20
26 15 0.18
27 13 0.16
28 16 0.20
29 11 0.13
30 7 0.09
31 3 0.04
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (25 bp):
TAAAATAAAATATAAAAAATTAAAA
Found at i:2991052 original size:33 final size:33
Alignment explanation
Indices: 2991001--2991086 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
2990991 AAAACAAATT
*
2991001 GAAAT-AAAATATATAATATAAAAAA-TATATTAAA
1 GAAATGAAAATA-A-AATATAAAAAATTATAAT-AA
* *
2991035 GAAATGAAAATAAAATATATAAGATTATAATAA
1 GAAATGAAAATAAAATATAAAAAATTATAATAA
*
2991068 TAAATGAAAATAAAATATA
1 GAAATGAAAATAAAATATA
2991087 TGATATTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
33 29 0.63
34 11 0.24
35 6 0.13
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (33 bp):
GAAATGAAAATAAAATATAAAAAATTATAATAA
Found at i:2991112 original size:27 final size:25
Alignment explanation
Indices: 2991080--2991216 Score: 78
Period size: 27 Copynumber: 4.9 Consensus size: 25
2991070 AATGAAAATA
*
2991080 AAATATATGATATTAAAAATATATTT
1 AAATATAT-ATATTAAAAATATATAT
2991106 AAGATATGATATTATATAAAAATTAATAATAT
1 AA-ATAT-ATA-TAT-TAAAAA-T-AT-ATAT
*
2991138 AAATATAAATATATTAAAAATAAAATAT
1 AAATAT--ATATATTAAAAAT-ATATAT
* * *
2991166 AAA-ATATTATAATAATAAATAAAAAT
1 AAATATA-TATATTAA-AAATATATAT
*
2991192 AAAATATATGACATTAAAAATATAT
1 -AAATATAT-ATATTAAAAATATAT
2991217 TTAAGAAATT
Statistics
Matches: 89, Mismatches: 9, Indels: 25
0.72 0.07 0.20
Matches are distributed among these distances:
25 1 0.01
26 14 0.16
27 21 0.24
28 20 0.22
29 9 0.10
30 7 0.08
31 9 0.10
32 8 0.09
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (25 bp):
AAATATATATATTAAAAATATATAT
Found at i:2991143 original size:21 final size:22
Alignment explanation
Indices: 2991119--2991192 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
2991109 ATATGATATT
2991119 ATATAAAA-ATTAATAATATAA
1 ATATAAAATATTAATAATATAA
*
2991140 ATATAAATATATTAAAAATA-AA
1 ATATAAA-ATATTAATAATATAA
2991162 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAAT-ATAA
2991184 ATA-AAAATA
1 ATATAAAATA
2991193 AAATATATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.09
21 19 0.40
22 15 0.32
23 9 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATATAA
Found at i:2991144 original size:6 final size:6
Alignment explanation
Indices: 2991133--2991199 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
2991123 AAAAATTAAT
* *
2991133 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
2991183 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
2991200 TGACATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:2991165 original size:16 final size:16
Alignment explanation
Indices: 2991138--2991269 Score: 53
Period size: 16 Copynumber: 8.1 Consensus size: 16
2991128 TTAATAATAT
2991138 AAATATAAATATATTAA
1 AAATA-AAATATATTAA
2991155 AAATAAAATATA--AA
1 AAATAAAATATATTAA
*
2991169 ATATTATAATAATA-AATAA
1 A-A--ATAA-AATATATTAA
*
2991188 AAATAAAATATA-TGA
1 AAATAAAATATATTAA
* *
2991203 CATTAAAAATATATTTAA
1 AAAT-AAAATATA-TTAA
* *
2991221 GAAATTATAT-TATATAA
1 -AAATAAAATATAT-TAA
* *
2991238 AAAT-TAATA-ATAAA
1 AAATAAAATATATTAA
2991252 AAATATAAATATATTAA
1 AAATA-AAATATATTAA
2991269 A
1 A
2991270 CTTGTATTTT
Statistics
Matches: 86, Mismatches: 13, Indels: 32
0.66 0.10 0.24
Matches are distributed among these distances:
14 9 0.10
15 13 0.15
16 29 0.34
17 20 0.23
18 10 0.12
19 5 0.06
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATAAAATATATTAA
Found at i:2991191 original size:113 final size:114
Alignment explanation
Indices: 2991041--2991269 Score: 388
Period size: 113 Copynumber: 2.0 Consensus size: 114
2991031 TAAAGAAATG
* * *
2991041 AAAATAAAATATATAAGATTATAATAATAAATGAAAATAAAATATATGATATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
* *
2991106 AAGATATGATATTATATAAAAATTAATAAT-ATAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
*
2991154 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
2991219 AAGAAATTATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
2991268 AA
1 AA
2991270 CTTGTATTTT
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 89 0.82
114 19 0.18
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (114 bp):
AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
Found at i:2991456 original size:15 final size:15
Alignment explanation
Indices: 2991414--2991457 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2991404 TGTTATTTTC
2991414 CCTGCAATCACATTA
1 CCTGCAATCACATTA
*
2991429 CTTGCAATCACATTA
1 CCTGCAATCACATTA
* *
2991444 CCTGTAATTACATT
1 CCTGCAATCACATT
2991458 GCATTGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:3013286 original size:36 final size:36
Alignment explanation
Indices: 3013209--3013310 Score: 100
Period size: 36 Copynumber: 2.9 Consensus size: 36
3013199 CAACGGTCTT
* * **
3013209 ACTTTTTAACAGGATCAAGTGATAA-TCCTTATATTA
1 ACTTTTTAACAAGATCAAATGATAACT-CTTATAACA
*
3013245 GCTTTTTAACAAGATCAAATGATAACTCTTATAACA
1 ACTTTTTAACAAGATCAAATGATAACTCTTATAACA
* ** *
3013281 ACTTTTTTATGAGATC-AATAATAACTCTTA
1 ACTTTTTAACAAGATCAAATGATAACTCTTA
3013311 CACTTACTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
35 13 0.24
36 41 0.75
37 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (36 bp):
ACTTTTTAACAAGATCAAATGATAACTCTTATAACA
Found at i:3013333 original size:35 final size:35
Alignment explanation
Indices: 3013246--3013360 Score: 83
Period size: 36 Copynumber: 3.2 Consensus size: 35
3013236 CTTATATTAG
*
3013246 CTTTTTAAC-AAGATCAAATGATAACTCTTATAACAA
1 CTTTTTAACGAA-ATC-AATAATAACTCTTATAACAA
* * * * *
3013282 CTTTTTTATGAGATCAATAATAACTCTTA-CACTTA
1 CTTTTTAACGAAATCAATAATAACTCTTATAAC-AA
* **
3013317 CTTTTTAACGAAATCAAGCAATAACTCACAT-ACTAA
1 CTTTTTAACGAAATCAA-TAATAACTCTTATAAC-AA
3013353 CTTTTTAA
1 CTTTTTAA
3013361 AATTAAGTTA
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
34 2 0.03
35 28 0.45
36 31 0.50
37 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (35 bp):
CTTTTTAACGAAATCAATAATAACTCTTATAACAA
Found at i:3014388 original size:13 final size:12
Alignment explanation
Indices: 3014349--3014394 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
3014339 AATTTTTATT
3014349 TTAAA-AAAAAC
1 TTAAAGAAAAAC
*
3014360 -TAAAAAAATAAC
1 TTAAAGAAA-AAC
3014372 TTAAAGAAAAAC
1 TTAAAGAAAAAC
3014384 TTTAAAGAAAA
1 -TTAAAGAAAA
3014395 TTTTTCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
10 4 0.13
11 3 0.10
12 6 0.20
13 17 0.57
ACGTcount: A:0.70, C:0.07, G:0.04, T:0.20
Consensus pattern (12 bp):
TTAAAGAAAAAC
Found at i:3014545 original size:21 final size:22
Alignment explanation
Indices: 3014489--3014536 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3014479 TATATTGTAT
*
3014489 AAAACTATTTTTTATATTTCAA
1 AAAAATATTTTTTATATTTCAA
3014511 AAAAATATTTTTTATATTTCAA
1 AAAAATATTTTTTATATTTCAA
3014533 AAAA
1 AAAA
3014537 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAAATATTTTTTATATTTCAA
Found at i:3028710 original size:21 final size:19
Alignment explanation
Indices: 3028677--3028717 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
3028667 ATATGTTGAG
3028677 TAGTTAATTTATGTTATTT
1 TAGTTAATTTATGTTATTT
3028696 TAGTTAAATTTTATGTTATTT
1 TAGTT-AA-TTTATGTTATTT
3028717 T
1 T
3028718 GTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (19 bp):
TAGTTAATTTATGTTATTT
Found at i:3033054 original size:38 final size:38
Alignment explanation
Indices: 3032984--3033138 Score: 112
Period size: 38 Copynumber: 3.9 Consensus size: 38
3032974 AGAGTTTATT
** * * *
3032984 TCTTTTTAAAGTTATGTAGTCTTATTCCAAATGAGTAG
1 TCTTTTTAAAGTTACATAGCCTCATTTCAAATGAGTAG
* *
3033022 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATT
1 TCTTTTTAAAGTTACATAGCCTCATTTCAAAT---GAG--TA-G
* * * * * *
3033066 TCTTTTTAAATTTGCGTAACGTCATTTCAAATGAGGAG
1 TCTTTTTAAAGTTACATAGCCTCATTTCAAATGAGTAG
* * *
3033104 TCCTTTTAAAGTTACATAGCCTTATTTTAAATGAG
1 TCTTTTTAAAGTTACATAGCCTCATTTCAAATGAG
3033139 AATCTTATTC
Statistics
Matches: 88, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
38 53 0.60
39 1 0.01
41 6 0.07
43 2 0.02
44 26 0.30
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (38 bp):
TCTTTTTAAAGTTACATAGCCTCATTTCAAATGAGTAG
Found at i:3033097 original size:82 final size:81
Alignment explanation
Indices: 3032940--3033319 Score: 275
Period size: 82 Copynumber: 4.6 Consensus size: 81
3032930 TGTTTAAAAA
* * ** * * * * *
3032940 TCTTTTTAAAGTTACGTAGCTTCATTCCAGATGAAGAGTTTATTTCTTTTTAAAGTTATGTAGTC
1 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTACGTAGTC
*
3033005 TTATTCCAAATGAGTAG
66 -TATTCCAAATGAGGAG
*
3033022 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTGCGTAACG
1 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTACGT-A-G
*
3033087 TC-ATTTCAAATGAGGAG
64 TCTATTCCAAATGAGGAG
* * * * *
3033104 TCCTTTTAAAGTTACATAGCCTTATTTTAAATGAGAATCTTA-TTCCTTTTAAA-TTACGTAGTC
1 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTACGTAGTC
* *
3033167 TCATTCCAAATGAAAAGTTATAT
66 T-ATTCCAAATG---AG---GAG
* * ** * * * * *
3033190 TCTTTTT-AAGTTACATAACTTCATTCCAAATAAAGAGTTTATTT-ATTTTAAAGTTACGTAGCT
1 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTACGTAG-T
* **
3033253 TTATTCCAAATGAAAAG
65 CTATTCCAAATGAGGAG
* * * * * ** *
3033270 TCTTTTTAAAATCACATAACCTCATTCTAGATGAAAAGCTTATTCCTTTT
1 TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTT
3033320 AAAGTTATAT
Statistics
Matches: 236, Mismatches: 47, Indels: 30
0.75 0.15 0.10
Matches are distributed among these distances:
78 3 0.01
79 1 0.00
80 22 0.09
81 38 0.16
82 105 0.44
83 4 0.02
84 3 0.01
85 31 0.13
86 27 0.11
87 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (81 bp):
TCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTACGTAGTC
TATTCCAAATGAGGAG
Found at i:3033191 original size:43 final size:42
Alignment explanation
Indices: 3033143--3033431 Score: 151
Period size: 43 Copynumber: 6.9 Consensus size: 42
3033133 AATGAGAATC
*
3033143 TTATTCCTTTTAAATTACGTAG-TCTCATTCCAAATGAAAAGT
1 TTATTCATTTTAAATTACGTAGCT-TCATTCCAAATGAAAAGT
* * * *
3033185 TATATTCTTTTTAAGTTACATAACTTCATTCCAAAT-AAAGAGT
1 T-TATTCATTTTAAATTACGTAGCTTCATTCCAAATGAAA-AGT
* *
3033228 TTATTTATTTTAAAGTTACGTAGCTTTATTCCAAATGAAAAG-
1 TTATTCATTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGT
* * * * * * * * *
3033270 -TCTT--TTTAAAATCACATAACCTCATTCTAGATGAAAAGC
1 TTATTCATTTTAAATTACGTAGCTTCATTCCAAATGAAAAGT
* ** * * * ** *
3033309 TTATTCCTTTTAAAGTTATATGGCTTCATTCTAGATGAGGAGC
1 TTATTCATTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGT
* * * * **
3033352 TTATTCCTTTTAAAGTTACATAGCATCATTCCAGATGAGGAG-
1 TTATTCATTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGT
* * * *
3033394 TTATTCATTTTAAAGCTACGTAACCTCAATCCAAATGA
1 TTATTCATTTTAAA-TTACGTAGCTTCATTCCAAATGA
3033432 CGAGCTTATT
Statistics
Matches: 198, Mismatches: 39, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
38 20 0.10
39 6 0.03
40 3 0.02
41 3 0.02
42 51 0.26
43 111 0.56
44 4 0.02
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (42 bp):
TTATTCATTTTAAATTACGTAGCTTCATTCCAAATGAAAAGT
Found at i:3033195 original size:42 final size:41
Alignment explanation
Indices: 3032943--3033449 Score: 141
Period size: 43 Copynumber: 12.2 Consensus size: 41
3032933 TTAAAAATCT
* *
3032943 TTTTAAAGTTACGTAGCTTCATTCCAGATGAAGAGTTTATTTC
1 TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTA-TTC
* *
3032986 TTTTTAAAGTTATGTAGTCTT-ATTCCAAATG---AG--TAGTC
1 -TTTTAAA-TTACGTAG-CTTCATTCCAAATGAAAAGTTTATTC
* * ** ** *
3033024 TTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTC
1 -TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTA-TTC
* * * * ** *
3033068 TTTTTAAATTTGCGTAACGTCATTTCAAATGAGGAG----TCC
1 -TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTATTC
* ** *
3033107 TTTTAAAGTTACATAGCCTT-ATTTTAAATGAGAA-TCTTATTCC
1 TTTTAAA-TTACGTAG-CTTCATTCCAAATGAAAAGT-TTATT-C
3033150 TTTTAAATTACGTAG-TCTCATTCCAAATGAAAAGTTATATTC
1 TTTTAAATTACGTAGCT-TCATTCCAAATGAAAAGTT-TATTC
* * * *
3033192 TTTTTAAGTTACATAACTTCATTCCAAAT-AAAGAGTTTATTTA
1 -TTTTAAATTACGTAGCTTCATTCCAAATGAAA-AGTTTA-TTC
* *
3033235 TTTTAAAGTTACGTAGCTTTATTCCAAATGAAAAG--TCTT-
1 TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTATTC
* * * * * * * *
3033274 TTTAAAATCACATAACCTCATTCTAGATGAAAAGCTTATTCC
1 TTTTAAATTACGTAGCTTCATTCCAAATGAAAAGTTTATT-C
** * * * ** *
3033316 TTTTAAAGTTATATGGCTTCATTCTAGATGAGGAGCTTATTCC
1 TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTATT-C
* * * **
3033359 TTTTAAAGTTACATAGCATCATTCCAGATGAGGAG-TTATTC
1 TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTATTC
* * * * ** *
3033400 ATTTTAAAGCTACGTAACCTCAATCCAAATGACGAGCTTATTC
1 -TTTTAAA-TTACGTAGCTTCATTCCAAATGAAAAGTTTATTC
*
3033443 CTTTAAA
1 TTTTAAA
3033450 GCTATATAGC
Statistics
Matches: 365, Mismatches: 66, Indels: 66
0.73 0.13 0.13
Matches are distributed among these distances:
37 2 0.01
38 69 0.19
39 12 0.03
40 6 0.02
41 7 0.02
42 77 0.21
43 129 0.35
44 60 0.16
45 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (41 bp):
TTTTAAATTACGTAGCTTCATTCCAAATGAAAAGTTTATTC
Found at i:3033294 original size:124 final size:125
Alignment explanation
Indices: 3032940--3033390 Score: 373
Period size: 124 Copynumber: 3.6 Consensus size: 125
3032930 TGTTTAAAAA
* * * * **
3032940 TCTTTTTAAAGTTACGTAGCTTCATTCCAGATGAAGAGTTTATTTCTTTTTAAAGTTATGTAG-T
1 TCTTTTTAAAGTTACATAACTTCATTCCAAATGAAGAGTTTA-TTCCTTTTAAAGTTACATAGCT
* * * **
3033004 CTTATTCCAAATGAGTAGTCTTTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATT
65 -TTATTCCAAATGAGAAGTCTTTTTAAAATTACATAGCCTCATTCTAAATGAAAAGCTTATT
* * * * * * *
3033066 TCTTTTTAAATTTGCGTAACGTCATTTCAAATG-AG-G---AGTCCTTTTAAAGTTACATAGCCT
1 TCTTTTTAAAGTTACATAACTTCATTCCAAATGAAGAGTTTATTCCTTTTAAAGTTACATAGCTT
** * * * *
3033126 TATTTTAAATGAGAA-TCTTATTCCTTTTAAATTACGTAGTCTCATTCCAAATGAAAAG-TTATA
66 TATTCCAAATGAGAAGTC---TT--TTTAAAATTACATAGCCTCATTCTAAATGAAAAGCTTAT-
3033189 T
125 T
* ** *
3033190 TCTTTTT-AAGTTACATAACTTCATTCCAAATAAAGAGTTTATTTATTTTAAAGTTACGTAGCTT
1 TCTTTTTAAAGTTACATAACTTCATTCCAAATGAAGAGTTTATTCCTTTTAAAGTTACATAGCTT
* * * *
3033254 TATTCCAAATGAAAAGTCTTTTTAAAATCACATAACCTCATTCTAGATGAAAAGCTTA-T
66 TATTCCAAATGAGAAGTCTTTTTAAAATTACATAGCCTCATTCTAAATGAAAAGCTTATT
* * ** * * * * *
3033313 TCCTTTTAAAGTTATATGGCTTCATTCTAGATGAGGAGCTTATTCCTTTTAAAGTTACATAGCAT
1 TCTTTTTAAAGTTACATAACTTCATTCCAAATGAAGAGTTTATTCCTTTTAAAGTTACATAGCTT
* *
3033378 CATTCCAGATGAG
66 TATTCCAAATGAG
3033391 GAGTTATTCA
Statistics
Matches: 251, Mismatches: 59, Indels: 32
0.73 0.17 0.09
Matches are distributed among these distances:
119 2 0.01
120 29 0.12
121 1 0.00
122 2 0.01
123 30 0.12
124 119 0.47
125 6 0.02
126 29 0.12
128 31 0.12
129 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (125 bp):
TCTTTTTAAAGTTACATAACTTCATTCCAAATGAAGAGTTTATTCCTTTTAAAGTTACATAGCTT
TATTCCAAATGAGAAGTCTTTTTAAAATTACATAGCCTCATTCTAAATGAAAAGCTTATT
Found at i:3033406 original size:166 final size:165
Alignment explanation
Indices: 3033025--3033431 Score: 397
Period size: 166 Copynumber: 2.4 Consensus size: 165
3033015 TGAGTAGTCT
* ** * * *
3033025 TTTTAAAGTTACATAGCCTCATTTTAAATGAGGAGCTTATTTCTTTTTAAATTTGCGTAACGTCA
1 TTTTAAAGTTACATAGCATCATTCCAAATGAGGAGCTTA-TTCATTTTAAAGTTACGTAACGTCA
* ** * * * * * * *
3033090 TTTCAAATGAGGAGTCCTTTTAAAGTTACATAGCCTTATTTTAAATGAGAATCTTATTCCTTTTA
65 TTCCAAATGAAAAGTCCTTTTAAAATCACATAACCTCATTCTAAATGAAAAGCTTATTCCTTTTA
* *
3033155 AATTACGTAGTCTCATTCCAAATGAAAAGTTATATTC
130 AATTAC-TAGGCTCATTCCAAATGAAAAGTTATATCC
* * * * * * * * * *
3033192 TTTTTAAGTTACATAACTTCATTCCAAATAAAGAGTTTATTTATTTTAAAGTTACGTAGCTTTAT
1 TTTTAAAGTTACATAGCATCATTCCAAATGAGGAGCTTATTCATTTTAAAGTTACGTAACGTCAT
* *
3033257 TCCAAATGAAAAGTCTTTTTAAAATCACATAACCTCATTCTAGATGAAAAGCTTATTCCTTTTAA
66 TCCAAATGAAAAGTCCTTTTAAAATCACATAACCTCATTCTAAATGAAAAGCTTATTCCTTTTAA
* * **
3033322 AGTTA-TATGGCTTCATTCTAGATGAGGAGCTTAT-TCC
131 A-TTACTA-GGC-TCATTCCAAATGAAAAG-TTATATCC
* * * *
3033359 TTTTAAAGTTACATAGCATCATTCCAGATGAGGAG-TTATTCATTTTAAAGCTACGTAACCTCAA
1 TTTTAAAGTTACATAGCATCATTCCAAATGAGGAGCTTATTCATTTTAAAGTTACGTAACGTCAT
3033423 TCCAAATGA
66 TCCAAATGA
3033432 CGAGCTTATT
Statistics
Matches: 191, Mismatches: 45, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
165 2 0.01
166 107 0.56
167 78 0.41
168 4 0.02
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (165 bp):
TTTTAAAGTTACATAGCATCATTCCAAATGAGGAGCTTATTCATTTTAAAGTTACGTAACGTCAT
TCCAAATGAAAAGTCCTTTTAAAATCACATAACCTCATTCTAAATGAAAAGCTTATTCCTTTTAA
ATTACTAGGCTCATTCCAAATGAAAAGTTATATCC
Found at i:3033479 original size:42 final size:42
Alignment explanation
Indices: 3033291--3033487 Score: 198
Period size: 42 Copynumber: 4.6 Consensus size: 42
3033281 TCACATAACC
** * * *
3033291 TCATTCTAGATGAAAAGCTTATTCCTTTTAAAGTTATATGGCT
1 TCATTCTAGATGAGGAGCTTATTCC-TTTAAAGCTACATAGCT
* *
3033334 TCATTCTAGATGAGGAGCTTATTCCTTTTAAAGTTACATAGCA
1 TCATTCTAGATGAGGAGCTTATTCC-TTTAAAGCTACATAGCT
* * * * *
3033377 TCATTCCAGATGAGGAG-TTATTCATTTTAAAGCTACGTAACC
1 TCATTCTAGATGAGGAGCTTATTC-CTTTAAAGCTACATAGCT
* * * * *
3033419 TCAATCCAAATGACGAGCTTATTCCTTTAAAGCTATATAGCT
1 TCATTCTAGATGAGGAGCTTATTCCTTTAAAGCTACATAGCT
*
3033461 TCATTCTAGATGAGGAGCTTCTTCCTT
1 TCATTCTAGATGAGGAGCTTATTCCTT
3033488 CTTTAAAATT
Statistics
Matches: 128, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 68 0.53
43 60 0.47
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (42 bp):
TCATTCTAGATGAGGAGCTTATTCCTTTAAAGCTACATAGCT
Found at i:3036587 original size:33 final size:34
Alignment explanation
Indices: 3036545--3036630 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
3036535 TGCTTTAGAT
* * *
3036545 AAAAGGCATTGTAA-GGTTTCGCTTGCT-CTTGTG
1 AAAAAGCATTGTAAGGGTTCCGCTTGCTCCCT-TG
3036578 AAAAAGCATTGTAAGGGTTCCGCTTGCTCCCTTG
1 AAAAAGCATTGTAAGGGTTCCGCTTGCTCCCTTG
*
3036612 AAAAAGCATTGTGAGGGTT
1 AAAAAGCATTGTAAGGGTT
3036631 TAATGTTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
33 13 0.28
34 32 0.68
35 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (34 bp):
AAAAAGCATTGTAAGGGTTCCGCTTGCTCCCTTG
Found at i:3037169 original size:44 final size:44
Alignment explanation
Indices: 3037119--3037206 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
3037109 AAGGAGCTAT
* *
3037119 TTATAATAGATAACTAAACCTAAACCTACTTGGTGTGTAAGTAA
1 TTATAATAGACAACTAAACCTAAACCTACTTGGTGTGCAAGTAA
* * *
3037163 TTATAATAGCCAACTAAACCTAATCCTATTTGGTGTGCAAGTAA
1 TTATAATAGACAACTAAACCTAAACCTACTTGGTGTGCAAGTAA
3037207 AGAAAATGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (44 bp):
TTATAATAGACAACTAAACCTAAACCTACTTGGTGTGCAAGTAA
Found at i:3052520 original size:4 final size:4
Alignment explanation
Indices: 3052513--3052552 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
3052503 TGTGTGTGTA
* *
3052513 TATG TATG TATG TATG TATG TATG CAAG TATG TAT- TATG T
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T
3052553 GGGCGCATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:3055384 original size:27 final size:26
Alignment explanation
Indices: 3055354--3055415 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
3055344 TATGAAAATT
3055354 ATTTTTTTAGTATTTTA-TTAGCTTAG-G
1 ATTTTTTT--TATTTTATTTAG-TTAGAG
*
3055381 ATTTTATTTTATTTTATTTAGTTTGAG
1 ATTTT-TTTTATTTTATTTAGTTAGAG
3055408 ATTTTTTT
1 ATTTTTTT
3055416 GCTTTTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 13 0.42
27 15 0.48
28 3 0.10
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (26 bp):
ATTTTTTTTATTTTATTTAGTTAGAG
Found at i:3064767 original size:27 final size:26
Alignment explanation
Indices: 3064737--3064819 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 26
3064727 TATTTTACCC
*
3064737 AAAATAATATTGTTACATGCCATATTT
1 AAAA-AATATTATTACATGCCATATTT
* * * * *
3064764 AAAAAAAAATATTACATACCATGTTAA
1 AAAAAATATTATTACATGCCATATT-T
* *
3064791 AAAAAATATTATTACACGTCATATTT
1 AAAAAATATTATTACATGCCATATTT
3064817 AAA
1 AAA
3064820 GTGTTTAACT
Statistics
Matches: 42, Mismatches: 13, Indels: 3
0.72 0.22 0.05
Matches are distributed among these distances:
26 19 0.45
27 23 0.55
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.34
Consensus pattern (26 bp):
AAAAAATATTATTACATGCCATATTT
Found at i:3064945 original size:127 final size:124
Alignment explanation
Indices: 3064748--3065126 Score: 360
Period size: 128 Copynumber: 3.1 Consensus size: 124
3064738 AAATAATATT
* * * * * *
3064748 GTTACATGCCATATTTAAAAAAAAA-TATTACATACCATGTTAAAAAAAATATTATTACACGTCA
1 GTTACAAGCCATGTTGAAAAAAAAATTGTTACATATCATGTTAAAAAAAA-ATTATTACATGTCA
* *
3064812 TATTTAAAGTGTTTAACTTCAA-AAGTTTATGTCTTAGTAAAATATAAAGATAAAAACTAA
65 TATTTAAAGTGTTTAACTTCAACAA-TTTATGTCTTAGTAAAATACAAAGATAAAAACCAA
* * *
3064872 ATTACAAGCCATGTT-AAACTAAAAAATTGTTACATATTATGTTAGAAAAAAAAGTTATAACATG
1 GTTACAAGCCATGTTGAAA--AAAAAATTGTTACATATCATGTTA-AAAAAAAA-TTATTACATG
* * * * * * * * * *
3064936 TCATGTTTAAGGTATTTTAATTTGAAGAATTTATGTCTTAATTAAATACAGAGATAAAGACCAA
62 TCATATTTAAAGT-GTTTAACTTCAACAATTTATGTCTTAGTAAAATACAAAGATAAAAACCAA
* ** * ** *
3065000 GTTACATGTTATGTTGAAAAAAAAATTGTTATACGTCATGTT----AAAAATTATTACATGCCAT
1 GTTACAAGCCATGTTGAAAAAAAAATTGTTACATATCATGTTAAAAAAAAATTATTACATGTCAT
* *
3065061 ATTT-AAGATGTTTAACTCCAACAATTTATGTCTTAGTAAAATACAAAGATAGAAACCAA
66 ATTTAAAG-TGTTTAACTTCAACAATTTATGTCTTAGTAAAATACAAAGATAAAAACCAA
3065120 GTTACAA
1 GTTACAA
3065127 AAAAAAAATT
Statistics
Matches: 204, Mismatches: 42, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
120 48 0.24
121 16 0.08
122 5 0.02
123 3 0.01
124 12 0.06
125 6 0.03
126 15 0.07
127 45 0.22
128 49 0.24
129 5 0.02
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (124 bp):
GTTACAAGCCATGTTGAAAAAAAAATTGTTACATATCATGTTAAAAAAAAATTATTACATGTCAT
ATTTAAAGTGTTTAACTTCAACAATTTATGTCTTAGTAAAATACAAAGATAAAAACCAA
Done.