Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 44 of 325
Found at i:16105930 original size:46 final size:44
Alignment explanation
Indices: 16105829--16105932 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
16105819 TGTCTTTGAC
* * * *
16105829 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGATCAATCCTGTCTCCAAAGCCATATATAAT
* * *
16105873 ATGGACTTACATGGCTCAATCCTGTCTCTAAAGCCATATTTCTAAT
1 ATGGACTTACATGGATCAATCCTGTCTCCAAAGCCATA--TATAAT
16105919 ATGGACTTACATGG
1 ATGGACTTACATGG
16105933 TTCATTTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 32 0.63
46 19 0.37
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (44 bp):
ATGGACTTACATGGATCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:16107799 original size:21 final size:21
Alignment explanation
Indices: 16107775--16107818 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16107765 TCGGAGTAAT
16107775 CACAATCCCCGCAGAAGCAAC
1 CACAATCCCCGCAGAAGCAAC
* * *
16107796 CACAATCCTCGCCGGAGCAAC
1 CACAATCCCCGCAGAAGCAAC
16107817 CA
1 CA
16107819 ATGAGGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.43, G:0.16, T:0.07
Consensus pattern (21 bp):
CACAATCCCCGCAGAAGCAAC
Found at i:16108007 original size:21 final size:21
Alignment explanation
Indices: 16107981--16108032 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
16107971 TAATTTTATA
16107981 TTTTGAATAAAATATAAGTTC
1 TTTTGAATAAAATATAAGTTC
16108002 TTTTGAATAAAATATAAGTTC
1 TTTTGAATAAAATATAAGTTC
16108023 TTTTGAATAA
1 TTTTGAATAA
16108033 GGCTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTTGAATAAAATATAAGTTC
Found at i:16109482 original size:126 final size:126
Alignment explanation
Indices: 16109207--16109708 Score: 609
Period size: 126 Copynumber: 4.0 Consensus size: 126
16109197 GGCCAATCAT
* ** *** *
16109207 GAACTACTGTAGAAAAAGACCGTCCACG-TAGGAACTTTTTTCACAAATTTTGCTGACATTGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTTA-GAGTTTTTTTCTGTAATTTTGCTGACAGTGCAT
* * *
16109271 CCTGTTTGAAGCGTTTTTGACACTATTTGTT-AAAAATATCTTCTCAAAATTATTTTTTCAG
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
16109332 GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
* * * * * *
16109397 TTGCTTGAAGCGTTTTTTACATTATTTGTTCAGAAACGTCTTCTAAAAATTATTTTTTCAT
66 CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * * *
16109458 AAATTACTGTAGAAAAAGAGCGTCCACGTGGTA-ACTTTTTTCCT-TAATTTTACTGACTGTGCA
1 GAACTACTGTAGAAAAAGAGCGTCCACGT--TAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCA
* * * * * *
16109521 TCCTACTTGAAGCGTTTTTTACAGTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTTAG
64 TCCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
* * * * * *
16109584 GAACTACTGTAGAAAATGAGCGTTCACGTGAGAGCTTTTTTT-TGTATTTTTGCTAACAATGCAT
1 GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAG-TTTTTTTCTGTAATTTTGCTGACAGTGCAT
* *
16109648 CCTGCTTGAAGTGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCA
65 CCTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCA
16109709 ATGTACAAAA
Statistics
Matches: 322, Mismatches: 48, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
124 1 0.00
125 83 0.26
126 227 0.70
127 9 0.03
128 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTTTCAG
Found at i:16109701 original size:252 final size:251
Alignment explanation
Indices: 16109211--16109708 Score: 698
Period size: 252 Copynumber: 2.0 Consensus size: 251
16109201 AATCATGAAC
* **
16109211 TACTGTAGAAAAAGACCGTCCACGTAGGAACTTTTTTCACAAATTTTGCTGACATTGCATCCTGT
1 TACTGTAGAAAAAGACCGTCCACGTAGGAACTTTTTTCACAAATTTTACTGACATTGCATCCTAC
*
16109276 TTGAAGCGTTTTTGACACTATTTGTTAAAAATATCTTCTCAAAATTATTTTTTCAGGAACTACTG
66 TTGAAGCGTTTTTGACACTATTTGTTAAAAACATCTTCTCAAAATTATTTTTTCAGGAACTACTG
* * * *
16109341 TAGAAAAAGAGCGTCCACGTTAGAGTTTTTTTCTGTAATTTTGCTGACAGTGCATCTTGCTTGAA
131 TAGAAAAAGAGCGTCCACGTGAGAGTTTTTTTCTGTAATTTTGCTAACAATGCATCCTGCTTGAA
* * *
16109406 GCGTTTTTTACATTATTTGTTCAGAAACGTCTTCTAAAAATTATTTTTTCATAAAT
196 GCGTTTTTGACACTATTTGTTCAGAAACATCTTCTAAAAATTATTTTTTCATAAAT
* *
16109462 TACTGTAGAAAAAGAGCGTCCACGT-GGTAACTTTTTTC-CTTAATTTTACTGAC-TGTGCATCC
1 TACTGTAGAAAAAGACCGTCCACGTAGG-AACTTTTTTCAC-AAATTTTACTGACAT-TGCATCC
* * * * * *
16109524 TACTTGAAGCGTTTTTTACAGTATTTGTTCAGAAACGTCTTCTTAAAATTATTTTTTTAGGAACT
63 TACTTGAAGCGTTTTTGACACTATTTGTT-AAAAACATCTTCTCAAAATTATTTTTTCAGGAACT
* * *
16109589 ACTGTAGAAAATGAGCGTTCACGTGAGAGCTTTTTTT-TGTATTTTTGCTAACAATGCATCCTGC
127 ACTGTAGAAAAAGAGCGTCCACGTGAGAG-TTTTTTTCTGTAATTTTGCTAACAATGCATCCTGC
* * *
16109653 TTGAAGTGTTTTTGACACTATTTGTTTAGAAACATCTTCTCAAAATTATTTTTTCA
191 TTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTAAAAATTATTTTTTCA
16109709 ATGTACAAAA
Statistics
Matches: 217, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
250 4 0.02
251 77 0.35
252 129 0.59
253 7 0.03
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (251 bp):
TACTGTAGAAAAAGACCGTCCACGTAGGAACTTTTTTCACAAATTTTACTGACATTGCATCCTAC
TTGAAGCGTTTTTGACACTATTTGTTAAAAACATCTTCTCAAAATTATTTTTTCAGGAACTACTG
TAGAAAAAGAGCGTCCACGTGAGAGTTTTTTTCTGTAATTTTGCTAACAATGCATCCTGCTTGAA
GCGTTTTTGACACTATTTGTTCAGAAACATCTTCTAAAAATTATTTTTTCATAAAT
Found at i:16115054 original size:211 final size:211
Alignment explanation
Indices: 16114690--16115115 Score: 843
Period size: 211 Copynumber: 2.0 Consensus size: 211
16114680 GGAAAGCTTC
*
16114690 ACATTTCATTCACTTCATAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
1 ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
16114755 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
66 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
16114820 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
131 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
16114885 TCTTCTTAGTCAAACA
196 TCTTCTTAGTCAAACA
16114901 ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
1 ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
16114966 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
66 CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
16115031 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
131 AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
16115096 TCTTCTTAGTCAAACA
196 TCTTCTTAGTCAAACA
16115112 ACAT
1 ACAT
16115116 GATCTAACAT
Statistics
Matches: 214, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 214 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (211 bp):
ACATTTCATTCACTTCACAATATGTGAAACAACCATAGCCCCGTGACTAAGTAAAGCAATGAATG
CCAAAAATTTAAATACTGAACAGTGGAGTTTTCTTACACGAAAAAATAATTAAATAAATTGTAAT
AAAAATGTCACAAGTTTCCTATCAGACCTCCCTCAATTTGATCAAAGGTACTATGCCAATTCTTA
TCTTCTTAGTCAAACA
Found at i:16129691 original size:18 final size:19
Alignment explanation
Indices: 16129668--16129704 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16129658 AAATAAATAT
*
16129668 AATAAAA-CAAGATTTTAA
1 AATAAAATCAACATTTTAA
16129686 AATAAAATCAACATTTTAA
1 AATAAAATCAACATTTTAA
16129705 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.30
Consensus pattern (19 bp):
AATAAAATCAACATTTTAA
Found at i:16139384 original size:7 final size:7
Alignment explanation
Indices: 16139366--16139400 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
16139356 GAGTTACTAT
*
16139366 TTTAAGG
1 TTTATGG
16139373 TTTATGG
1 TTTATGG
*
16139380 ATTATGG
1 TTTATGG
16139387 TTTATGG
1 TTTATGG
16139394 TTTATGG
1 TTTATGG
16139401 GTTAACGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (7 bp):
TTTATGG
Found at i:16139459 original size:7 final size:7
Alignment explanation
Indices: 16139449--16139481 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
16139439 TAAGGTTTGT
16139449 GGGTTAA
1 GGGTTAA
16139456 GGGTTAA
1 GGGTTAA
16139463 GGGTTAA
1 GGGTTAA
*
16139470 GTGTTAA
1 GGGTTAA
16139477 GGGTT
1 GGGTT
16139482 TATGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.33
Consensus pattern (7 bp):
GGGTTAA
Found at i:16143663 original size:2 final size:2
Alignment explanation
Indices: 16143656--16143680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16143646 AGAAAGGAGC
16143656 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
16143681 AGGCAGGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16144733 original size:15 final size:16
Alignment explanation
Indices: 16144713--16144745 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
16144703 TCCAACATGA
16144713 GGCAAATTGTGAG-GG
1 GGCAAATTGTGAGAGG
16144728 GGCAAATTGTGAGAGG
1 GGCAAATTGTGAGAGG
16144744 GG
1 GG
16144746 AGCCCATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.27, C:0.06, G:0.48, T:0.18
Consensus pattern (16 bp):
GGCAAATTGTGAGAGG
Found at i:16154485 original size:10 final size:10
Alignment explanation
Indices: 16154470--16154525 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
16154460 TCCCCCTATC
16154470 CAAATTCTCT
1 CAAATTCTCT
16154480 CAAATTCT-T
1 CAAATTCTCT
*
16154489 CCAAAAATTCCCT
1 -C--AAATTCTCT
*
16154502 CATATTCTCT
1 CAAATTCTCT
*
16154512 CAAATTTTCT
1 CAAATTCTCT
16154522 CAAA
1 CAAA
16154526 GCTCTCTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 1 0.03
10 28 0.76
12 7 0.19
13 1 0.03
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.38
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:16155731 original size:7 final size:7
Alignment explanation
Indices: 16155719--16155758 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
16155709 TACTCGTTTC
16155719 GTATTTA
1 GTATTTA
16155726 GTATTTA
1 GTATTTA
*
16155733 ATATTTA
1 GTATTTA
16155740 GTATTTA
1 GTATTTA
16155747 GTATTTA
1 GTATTTA
*
16155754 ATATT
1 GTATT
16155759 ATGTATACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:16155764 original size:21 final size:21
Alignment explanation
Indices: 16155719--16155758 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16155709 TACTCGTTTC
16155719 GTATTTAGTATTTAATATTTA
1 GTATTTAGTATTTAATATTTA
16155740 GTATTTAGTATTTAATATT
1 GTATTTAGTATTTAATATT
16155759 ATGTATACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
GTATTTAGTATTTAATATTTA
Found at i:16156871 original size:56 final size:56
Alignment explanation
Indices: 16156810--16156947 Score: 240
Period size: 56 Copynumber: 2.5 Consensus size: 56
16156800 TTCTTTCATT
*
16156810 TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCGTATTTG
1 TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCATATTTG
* *
16156866 TAATAAAATAAAAGTTGTTTTTAGTATTTTAATTATAATTTACTCTTTTATATTTG
1 TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCATATTTG
*
16156922 TAATAAAATAAAAGTTGTTTTGAATA
1 TAATAAAATAAAAGTTGTTTTTAATA
16156948 AGGAAATATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 77 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (56 bp):
TAATAAAATAAAAGTTGTTTTTAATATTTTAATTATAATTTACTCTTTCATATTTG
Found at i:16160053 original size:52 final size:49
Alignment explanation
Indices: 16159968--16160334 Score: 440
Period size: 46 Copynumber: 7.6 Consensus size: 49
16159958 TTTGAGTACT
* **
16159968 TCTGATCAAGTG---ATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
* *
16160014 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
16160066 TCTGATCAAGTG---ATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
16160112 TCTGATCAAGTGAC---AAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
16160158 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
16160210 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAA-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTA
* **
16160262 TCTGATCAAGAGAC---AAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
*
16160308 TCTGATCAAGAGAC---AAAGTGATAAGTG
1 TCTGATCAAGTGACAATAAAGTGATAAGTG
16160335 GCTACACTTA
Statistics
Matches: 292, Mismatches: 15, Indels: 28
0.87 0.04 0.08
Matches are distributed among these distances:
46 155 0.53
48 1 0.00
49 2 0.01
50 1 0.00
52 133 0.46
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (49 bp):
TCTGATCAAGTGACAATAAAGTGATAAGTGATAGCTTCGGCTACACTTA
Found at i:16160088 original size:98 final size:97
Alignment explanation
Indices: 16159968--16160334 Score: 501
Period size: 98 Copynumber: 3.7 Consensus size: 97
16159958 TTTGAGTACT
* *
16159968 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-
*
16160033 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
* *
16160066 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
16160126 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
*
16160158 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGA
16160223 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTATACTTA
* * * *
16160262 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGT
16160327 GATAAGTG
65 GA-AAGTG
16160335 GCTACACTTA
Statistics
Matches: 240, Mismatches: 15, Indels: 27
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.17
95 1 0.00
96 1 0.00
98 145 0.60
99 10 0.04
101 1 0.00
104 41 0.17
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCGGCTATACTTA
Found at i:16160316 original size:196 final size:196
Alignment explanation
Indices: 16159982--16160334 Score: 607
Period size: 196 Copynumber: 1.8 Consensus size: 196
16159972 ATCAAGTGAT
* * *
16159982 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
* * * *
16160047 ATAGCTTCGGCTATACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
16160112 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
16160177 G
196 G
* *
16160178 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
*
16160243 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
16160308 TCTGATCAAGAGACAAAGTGATAAGTG
131 TCTGATCAAGAGACAAAGTGATAAGTG
16160335 GCTACACTTA
Statistics
Matches: 146, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
196 146 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (196 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGTA
ATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
G
Found at i:16160342 original size:37 final size:37
Alignment explanation
Indices: 16160298--16160443 Score: 233
Period size: 37 Copynumber: 4.0 Consensus size: 37
16160288 GATAGCTTTA
*
16160298 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
16160335 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
* *
16160372 GCTACACTTATGTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
16160409 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
16160444 ATCATACGTA
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 87 0.85
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:16160371 original size:150 final size:149
Alignment explanation
Indices: 16159968--16160323 Score: 467
Period size: 150 Copynumber: 2.4 Consensus size: 149
16159958 TTTGAGTACT
* * * * *
16159968 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * *
16160033 GAAAGTGATAAGTAATAGCTTC-G---GCTATACTTATC---TGATCAAGTGATAAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGCAAACTAAACTGATCAAGTGA-CAAGTGATAAAGTGATAAG
16160091 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
* *
16160112 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
* * * * *
16160177 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA-AAAGTGATAAG
66 GAAAGTGATAACT-ATAGCTTCAGC-AAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAG
16160241 TGATAGCTTCGGCTATACTTA
129 TGATAGCTTCGGCTATACTTA
*
16160262 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAA
16160324 AGTGATAAGT
Statistics
Matches: 192, Mismatches: 12, Indels: 10
0.90 0.06 0.05
Matches are distributed among these distances:
144 83 0.43
145 1 0.01
149 7 0.04
150 91 0.47
151 7 0.04
152 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (149 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAGTG
GAAAGTGATAACTATAGCTTCAGCAAACTAAACTGATCAAGTGACAAGTGATAAAGTGATAAGTG
ATAGCTTCGGCTATACTTA
Found at i:16160387 original size:150 final size:143
Alignment explanation
Indices: 16159968--16160339 Score: 382
Period size: 144 Copynumber: 2.6 Consensus size: 143
16159958 TTTGAGTACT
* * * * *
16159968 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----
* * * * * * *
16160033 GAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T--AAAGTGATAAGT
61 GAAAGTGATAAGT--GAGCTACGACTACACTGATCAGAACAAGTGACAAGTGAAAAGTGATAAGT
16160092 GATAGCTTCGGCTATACTTA
124 GATAGCTTCGGCTATACTTA
* *
16160112 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC-----
* * * * *
16160177 GAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTGATAAGT
61 GAAAGTGATAAGTG--AGCTACGACTACACTGATCAGAACAAGTGACAAGTGAAAAGTGATAAGT
16160242 GATAGCTTCGGCTATACTTA
124 GATAGCTTCGGCTATACTTA
*
16160262 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC-AAAG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAG
16160326 TGATAAGTG-GCTAC
66 TGATAAGTGAGCTAC
16160340 ACTTATCTGA
Statistics
Matches: 211, Mismatches: 9, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
141 4 0.02
144 116 0.55
147 1 0.00
148 1 0.00
150 89 0.42
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (143 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACGAAAG
TGATAAGTGAGCTACGACTACACTGATCAGAACAAGTGACAAGTGAAAAGTGATAAGTGATAGCT
TCGGCTATACTTA
Found at i:16163346 original size:126 final size:125
Alignment explanation
Indices: 16163062--16163451 Score: 403
Period size: 125 Copynumber: 3.1 Consensus size: 125
16163052 AATAGGAACT
** * * * * *
16163062 ACTGTAGAAAAAGAGCGTTCACGTGAGAGCTTTTTTCAGTAATTTTGCTGAAAATGCATAC--CA
1 ACTGTAGAAAAA-AAAGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCT
* * ** *
16163125 TGAAGCGTTTTTGACTCTATTTGTTT-AGAAAGGTAATCTCACAATTATTTTTTCAGATACC
65 TGAAGCGTTTTTGACACTATTT-TTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGATACC
* * ** *
16163186 ACTGTATCAAAAGAGCGTCCACGTGAGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCTGCT
1 ACTGTA-GAAAAAAAAGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCT
* * *
16163251 TAAAGCATTTTTTACACTATTTTTTCAGAAACGTCTTCTCAAAATTATTTTCTT-AGATACC
65 TGAAGCGTTTTTGACACTATTTTTTCAGAAACGTCTTCTCAAAATTATTTT-TTCAGATACC
* * * * *
16163312 ACTGTAGAAAAAAAAGTCTACGTGGGAGCATTTTTCAGTAATTTTACTAACAGTGCATCCTGCTT
1 ACTGTAGAAAAAAAAGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTT
* * * * * * *
16163377 GAAGTGTTTTGGATACTATTTCTTCAGAAACTTCTTCTTAAAATT-TTTTTTCCAGATACT
66 GAAGCGTTTTTGACACTATTTTTTCAGAAACGTCTTCTCAAAATTATTTTTT-CAGATACC
*
16163437 ACTGAAGAAAAAAAA
1 ACTGTAGAAAAAAAA
16163452 CCAAAAATTT
Statistics
Matches: 222, Mismatches: 37, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
123 2 0.01
124 53 0.24
125 112 0.50
126 53 0.24
127 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.37
Consensus pattern (125 bp):
ACTGTAGAAAAAAAAGTCCACGTGAGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATCCTGCTT
GAAGCGTTTTTGACACTATTTTTTCAGAAACGTCTTCTCAAAATTATTTTTTCAGATACC
Found at i:16163569 original size:12 final size:12
Alignment explanation
Indices: 16163551--16163593 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
16163541 CTAAACTCGA
16163551 ATTTAATTAATT
1 ATTTAATTAATT
*
16163563 TTTTAATTAA-T
1 ATTTAATTAATT
16163574 ATTTAATTTAATT
1 ATTTAA-TTAATT
*
16163587 AATTAAT
1 ATTTAAT
16163594 CTTAGACCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 6 0.23
12 14 0.54
13 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTAATTAATT
Found at i:16166337 original size:6 final size:6
Alignment explanation
Indices: 16166314--16166353 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
16166304 CTCTGATTTT
16166314 TCTTT- TCTTTC T-TCTTC TCTTTC TCTTTC TCTTTC TCTTT
1 TCTTTC TCTTTC TCT-TTC TCTTTC TCTTTC TCTTTC TCTTT
16166354 ATCCTTGTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 6 0.19
6 25 0.78
7 1 0.03
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (6 bp):
TCTTTC
Found at i:16171228 original size:34 final size:35
Alignment explanation
Indices: 16171157--16171228 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 35
16171147 ATTACTCTAT
*
16171157 TAAATATATTTAAAATATATTTGTAATTATAAATTA
1 TAAATATATCTAAAATATATTTGTAA-TATAAATTA
* *
16171193 TAAATATATCTCAAATATATTTTTAA-ATAAATTA
1 TAAATATATCTAAAATATATTTGTAATATAAATTA
16171227 TA
1 TA
16171229 GTTTAATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 10 0.30
36 23 0.70
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (35 bp):
TAAATATATCTAAAATATATTTGTAATATAAATTA
Found at i:16181638 original size:6 final size:6
Alignment explanation
Indices: 16181627--16181655 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
16181617 GAACTTTGTT
16181627 GGTGAG GGTGAG GGTGAG GGTGAG GGTGA
1 GGTGAG GGTGAG GGTGAG GGTGAG GGTGA
16181656 TTGACGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
GGTGAG
Found at i:16188470 original size:21 final size:21
Alignment explanation
Indices: 16188440--16188480 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16188430 CTATAATATT
*
16188440 TTTTATTTTTACCC-TAAATTC
1 TTTTACTTTT-CCCTTAAATTC
16188461 TTTTACTTTTCCCTTAAATT
1 TTTTACTTTTCCCTTAAATT
16188481 ATTTGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTACTTTTCCCTTAAATTC
Found at i:16191322 original size:18 final size:18
Alignment explanation
Indices: 16191279--16191432 Score: 166
Period size: 18 Copynumber: 8.6 Consensus size: 18
16191269 TATCAATATA
*
16191279 ATTCAGTAAC-GATCAATT
1 ATTCAGTAACAG-TCAGTT
* *
16191297 GTTTAGTAACAGTCAGTT
1 ATTCAGTAACAGTCAGTT
*
16191315 ATTCAGTAACAGTCATTT
1 ATTCAGTAACAGTCAGTT
* *
16191333 ATTTAGTAACAGTCAATT
1 ATTCAGTAACAGTCAGTT
* * *
16191351 ATTCAATAATAATCAGTT
1 ATTCAGTAACAGTCAGTT
16191369 ATTCAGTAACAGTCAGTT
1 ATTCAGTAACAGTCAGTT
* *
16191387 ATTCAGTAACAGTTAATT
1 ATTCAGTAACAGTCAGTT
* *
16191405 ATTCAATAGCAGTCAGTT
1 ATTCAGTAACAGTCAGTT
*
16191423 ATTTAGTAAC
1 ATTCAGTAAC
16191433 TTTATTTACC
Statistics
Matches: 110, Mismatches: 25, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
18 109 0.99
19 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (18 bp):
ATTCAGTAACAGTCAGTT
Found at i:16191342 original size:54 final size:54
Alignment explanation
Indices: 16191279--16191432 Score: 202
Period size: 54 Copynumber: 2.9 Consensus size: 54
16191269 TATCAATATA
* * * *
16191279 ATTCAGTAAC-GATCAATTGTTTAGTAACAGTCAGTTATTCAGTAACAGTCATTT
1 ATTCAGTAACAG-TCAATTATTCAATAACAGTCAGTTATTCAGTAACAGTCAGTT
* * *
16191333 ATTTAGTAACAGTCAATTATTCAATAATAATCAGTTATTCAGTAACAGTCAGTT
1 ATTCAGTAACAGTCAATTATTCAATAACAGTCAGTTATTCAGTAACAGTCAGTT
* * *
16191387 ATTCAGTAACAGTTAATTATTCAATAGCAGTCAGTTATTTAGTAAC
1 ATTCAGTAACAGTCAATTATTCAATAACAGTCAGTTATTCAGTAAC
16191433 TTTATTTACC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 85 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (54 bp):
ATTCAGTAACAGTCAATTATTCAATAACAGTCAGTTATTCAGTAACAGTCAGTT
Found at i:16191670 original size:44 final size:44
Alignment explanation
Indices: 16191583--16191674 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
16191573 CTAAAGTAAC
*
16191583 AGTAACAGTACGACACACGAAGTGCCTCATCGACACAAAGTCGA
1 AGTAACAGTACGACACACGAAGTGCCTCATCAACACAAAGTCGA
** * **
16191627 AGTAACAGTACGACACTA-TTAGTGCCTCATCAACCCATGGTCGA
1 AGTAACAGTACGACAC-ACGAAGTGCCTCATCAACACAAAGTCGA
16191671 AGTA
1 AGTA
16191675 TCCCTGTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (44 bp):
AGTAACAGTACGACACACGAAGTGCCTCATCAACACAAAGTCGA
Found at i:16193261 original size:4 final size:4
Alignment explanation
Indices: 16193247--16193280 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
16193237 CACATTTGTC
16193247 TTTA TTTTA TTTA TTTA TTTA TTTA CTTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA -TTTA TTTA
16193281 ATTAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 20 0.71
5 8 0.29
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:16193269 original size:17 final size:17
Alignment explanation
Indices: 16193247--16193280 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16193237 CACATTTGTC
16193247 TTTATTTTA-TTTATTTA
1 TTTA-TTTACTTTATTTA
16193264 TTTATTTACTTTATTTA
1 TTTATTTACTTTATTTA
16193281 ATTAATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTACTTTATTTA
Found at i:16193280 original size:13 final size:13
Alignment explanation
Indices: 16193246--16193280 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
16193236 ACACATTTGT
16193246 CTTTATTTTATTTA
1 CTTTA-TTTATTTA
16193260 -TTTATTTATTTA
1 CTTTATTTATTTA
16193272 CTTTATTTA
1 CTTTATTTA
16193281 ATTAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
CTTTATTTATTTA
Found at i:16215550 original size:14 final size:15
Alignment explanation
Indices: 16215511--16215552 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
16215501 GATAATTGAT
16215511 TTTTA-ATTATTCTA
1 TTTTATATTATTCTA
16215525 TTTTAATAATTATT-TA
1 TTTT-AT-ATTATTCTA
16215541 TTTTATATTATT
1 TTTTATATTATT
16215553 AGGGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 6 0.24
17 6 0.24
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATATTATTCTA
Found at i:16215553 original size:17 final size:17
Alignment explanation
Indices: 16215514--16215545 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16215504 AATTGATTTT
16215514 TAATTATTCTATTTTAA
1 TAATTATTCTATTTTAA
16215531 TAATTATT-TATTTTA
1 TAATTATTCTATTTTA
16215546 TATTATTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTATTCTATTTTAA
Found at i:16215626 original size:12 final size:12
Alignment explanation
Indices: 16215611--16215635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16215601 AAAAATACCT
16215611 GAAAAAAAAAAA
1 GAAAAAAAAAAA
16215623 GAAAAAAAAAAA
1 GAAAAAAAAAAA
16215635 G
1 G
16215636 CTAGAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:16220640 original size:21 final size:22
Alignment explanation
Indices: 16220616--16220656 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16220606 CCTGTTACAA
*
16220616 TTTATCTATTT-TATTTTTATT
1 TTTATCTATTTCAATTTTTATT
*
16220637 TTTATTTATTTCAATTTTTA
1 TTTATCTATTTCAATTTTTA
16220657 ATTACAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTATCTATTTCAATTTTTATT
Found at i:16222497 original size:13 final size:13
Alignment explanation
Indices: 16222481--16222515 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
16222471 TGTTGTGGAA
16222481 AAGTACTTTTGAG
1 AAGTACTTTTGAG
16222494 AAGTACTTTTGAG
1 AAGTACTTTTGAG
*
16222507 AAGTGCTTT
1 AAGTACTTT
16222516 AGAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:16224868 original size:4 final size:4
Alignment explanation
Indices: 16224859--16224884 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
16224849 GAGATGGGGC
16224859 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
16224885 TGAGGAGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:16229876 original size:50 final size:50
Alignment explanation
Indices: 16229801--16229900 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
16229791 TAAGACAGAA
16229801 TGTAAGAACTATACACTTATATGGGCAATACATGGTCATGGACTCTATTT
1 TGTAAGAACTATACACTTATATGGGCAATACATGGTCATGGACTCTATTT
16229851 TGTAAGAACTATACACTTATATGGGCAATACATGGTCATGGACTCTATTT
1 TGTAAGAACTATACACTTATATGGGCAATACATGGTCATGGACTCTATTT
16229901 GTTGTAACAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (50 bp):
TGTAAGAACTATACACTTATATGGGCAATACATGGTCATGGACTCTATTT
Found at i:16242647 original size:14 final size:14
Alignment explanation
Indices: 16242628--16242668 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
16242618 TTGTTTTACT
* *
16242628 GAAAATAATTTTTA
1 GAAAATGATTTATA
*
16242642 GAAAATGATTTATG
1 GAAAATGATTTATA
16242656 GAAAATGATTTAT
1 GAAAATGATTTAT
16242669 TTTTGTGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (14 bp):
GAAAATGATTTATA
Found at i:16243149 original size:15 final size:15
Alignment explanation
Indices: 16243129--16243180 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
16243119 ACTACAAAAC
16243129 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
16243144 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
16243163 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
16243178 ATT
1 ATT
16243181 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:16243299 original size:22 final size:22
Alignment explanation
Indices: 16243274--16243315 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16243264 TATTAAATAA
16243274 TTATTAAAATAATAAATTATAT
1 TTATTAAAATAATAAATTATAT
* * *
16243296 TTATTATATTAATAATTTAT
1 TTATTAAAATAATAAATTAT
16243316 TATATGACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATTAAAATAATAAATTATAT
Found at i:16247217 original size:14 final size:15
Alignment explanation
Indices: 16247193--16247221 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16247183 GACCGTCCCA
16247193 TATTAATTTTTATAT
1 TATTAATTTTTATAT
16247208 TATT-ATTTTTATAT
1 TATTAATTTTTATAT
16247222 AATTTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTAATTTTTATAT
Found at i:16247732 original size:7 final size:7
Alignment explanation
Indices: 16247720--16247744 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16247710 CATAAATATA
16247720 AATTGAT
1 AATTGAT
16247727 AATTGAT
1 AATTGAT
16247734 AATTGAT
1 AATTGAT
16247741 AATT
1 AATT
16247745 TGGATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTGAT
Found at i:16248137 original size:31 final size:30
Alignment explanation
Indices: 16248066--16248138 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
16248056 ATATATATAT
* *
16248066 AAATTTTAATTTGATATAATTATAAACTTA
1 AAATTTTAATTTGATTTAAATATAAACTTA
* * *
16248096 AAACTCTAATTGTGATTTAAATA-AATATTTA
1 AAATTTTAATT-TGATTTAAATATAA-ACTTA
16248127 AAATTTTAATTT
1 AAATTTTAATTT
16248139 TAATTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (30 bp):
AAATTTTAATTTGATTTAAATATAAACTTA
Found at i:16250005 original size:15 final size:15
Alignment explanation
Indices: 16249985--16250033 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
16249975 TCCAATACAG
16249985 GATCTGAATGAAGAT
1 GATCTGAATGAAGAT
16250000 GATCTGAATGAAGAT
1 GATCTGAATGAAGAT
16250015 GTTTATCTGAATGAAGAT
1 G---ATCTGAATGAAGAT
16250033 G
1 G
16250034 TTTGTTGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.52
18 15 0.48
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (15 bp):
GATCTGAATGAAGAT
Found at i:16250024 original size:18 final size:18
Alignment explanation
Indices: 16249986--16250036 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
16249976 CCAATACAGG
16249986 ATCTGAATGAAGATG---
1 ATCTGAATGAAGATGTTT
16250001 ATCTGAATGAAGATGTTT
1 ATCTGAATGAAGATGTTT
16250019 ATCTGAATGAAGATGTTT
1 ATCTGAATGAAGATGTTT
16250037 GTTGTTCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.45
18 18 0.55
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (18 bp):
ATCTGAATGAAGATGTTT
Found at i:16260374 original size:2 final size:2
Alignment explanation
Indices: 16260367--16260398 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
16260357 AAAGAAAGAC
16260367 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
16260399 TGTAGTAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16260381 original size:968 final size:968
Alignment explanation
Indices: 16258456--16260375 Score: 3625
Period size: 968 Copynumber: 2.0 Consensus size: 968
16258446 TTTCACATAG
16258456 ATCCTGACAACTCATTAATGGGATGTTTATCAGTAAATTCGGAGACACCATCTAACAAGAAATCA
1 ATCCTGACAACTCATTAATGGGATGTTTATCAGTAAATTCGGAGACACCATCTAACAAGAAATCA
* *
16258521 AGTAATAAAAGCAACAGAGAACCAGAATCATACAAACCACTATGGATATTAATGAGCAAGCTTAA
66 AGTAATAAAAGCAACAGAGAACCAGAATCATACAAACCACTATGGACATTAATGAACAAGCTTAA
16258586 ATGGCTTTTTATTTTATCATTGATTTTACCTTACTTCTAGCTGAATAAGATCCTCTAGCAAACAT
131 ATGGCTTTTTATTTTATCATTGATTTTACCTTACTTCTAGCTGAATAAGATCCTCTAGCAAACAT
16258651 TCCAGATGGAGTTGTTTCTTCACAAATTTCATGTGTGTAAGGCTCTGCCTGGGGACTGAAGGTTC
196 TCCAGATGGAGTTGTTTCTTCACAAATTTCATGTGTGTAAGGCTCTGCCTGGGGACTGAAGGTTC
16258716 CGATCATCTCTTTCGTGCTATCAACTGGTACAAGAGTTCATGGTGAAGAATATCAAATCCAATGG
261 CGATCATCTCTTTCGTGCTATCAACTGGTACAAGAGTTCATGGTGAAGAATATCAAATCCAATGG
16258781 TTAACATGAGAGGGTACAATTCTTCCATATGAACAACAGAGAAAGGGAAAGAGGAATTACCCTTG
326 TTAACATGAGAGGGTACAATTCTTCCATATGAACAACAGAGAAAGGGAAAGAGGAATTACCCTTG
16258846 ACACCAGTTTTCCAAACCATATTAGTGTACTTGAGGCCGGATACAATGTTGTTGCTCACTTGGAA
391 ACACCAGTTTTCCAAACCATATTAGTGTACTTGAGGCCGGATACAATGTTGTTGCTCACTTGGAA
16258911 AGTGAATTGCAGGCTGTATTTGCTTCCTTCTTTTAGGGTAAACCACAAGCCTTTAGGCTTTCCGT
456 AGTGAATTGCAGGCTGTATTTGCTTCCTTCTTTTAGGGTAAACCACAAGCCTTTAGGCTTTCCGT
16258976 TCTCCGGAATTGGAAGTACCATATCAGGTCTACCATGTGATTTGATCGCAAGGCTCAATATCTTC
521 TCTCCGGAATTGGAAGTACCATATCAGGTCTACCATGTGATTTGATCGCAAGGCTCAATATCTTC
16259041 ACTTCAGGTTCTAGCTTTTATAACATCATAAACAATAGAAGAAAATGTCAGGATACAAAGAAAGG
586 ACTTCAGGTTCTAGCTTTTATAACATCATAAACAATAGAAGAAAATGTCAGGATACAAAGAAAGG
16259106 ACACGTTACAGAGCATGGAAACTATTGATGAAATCATAGACAAAAAGAAGGTATGAAGCTATACT
651 ACACGTTACAGAGCATGGAAACTATTGATGAAATCATAGACAAAAAGAAGGTATGAAGCTATACT
16259171 CTACGCCTACAATGTTAAGATAAACTGTCCACCAACAAAAAGTTACATTAAAAGAAGCTGAAATT
716 CTACGCCTACAATGTTAAGATAAACTGTCCACCAACAAAAAGTTACATTAAAAGAAGCTGAAATT
16259236 CAATATGCAAACAAATTGATCTTGCATCCCATTCTTACCTTTTTAATAATGGTCTACCAAGTATT
781 CAATATGCAAACAAATTGATCTTGCATCCCATTCTTACCTTTTTAATAATGGTCTACCAAGTATT
16259301 GCAACATTTGAGATCAAGGGATTATATTCCAGATATTTTACACACAATATAAATTCATCAACAGT
846 GCAACATTTGAGATCAAGGGATTATATTCCAGATATTTTACACACAATATAAATTCATCAACAGT
16259366 GAAAGAAATCCTCAAGTTTGAAAGAATGAAATGAAAGACGAGAGAGAGCCTGTTTCAC
911 GAAAGAAATCCTCAAGTTTGAAAGAATGAAATGAAAGACGAGAGAGAGCCTGTTTCAC
16259424 ATCCTGACAACTCATTAATGGGATGTTTATCAGTAAAATTCGGAGACA-CATCTAACAAGAAATC
1 ATCCTGACAACTCATTAATGGGATGTTTATCAGT-AAATTCGGAGACACCATCTAACAAGAAATC
16259488 AAGTAATAAAAGCAACAGAGAACCAGAATCATACAAACCACTATGGACATTAATGAACAAGCTTA
65 AAGTAATAAAAGCAACAGAGAACCAGAATCATACAAACCACTATGGACATTAATGAACAAGCTTA
*
16259553 AATGGTTTTTTATTTTATCATTGATTTTACCTTACTTCTAGCTGAATAAGATCCTCTAGCAAACA
130 AATGGCTTTTTATTTTATCATTGATTTTACCTTACTTCTAGCTGAATAAGATCCTCTAGCAAACA
16259618 TTCCAGATGGAGTTGTTTCTTCACAAATTTCATGTGTGTAAGGCTCTGCCTGGGGACTGAAGGTT
195 TTCCAGATGGAGTTGTTTCTTCACAAATTTCATGTGTGTAAGGCTCTGCCTGGGGACTGAAGGTT
16259683 CC-ATCATCTCTTTCGTGCTATCAACTGGTACAAGAGTTCATGGTGAAGAATATCAAATCCAATG
260 CCGATCATCTCTTTCGTGCTATCAACTGGTACAAGAGTTCATGGTGAAGAATATCAAATCCAATG
16259747 GTTAACATGAGAGGGTACAATTCTTCCATATGAACAACAGAGAAAGGGAAAGAGGAATTACCCTT
325 GTTAACATGAGAGGGTACAATTCTTCCATATGAACAACAGAGAAAGGGAAAGAGGAATTACCCTT
16259812 GACA-CAGTTTTTCCAAACCATA-TAGTGTACTTGAGGCCGGA-ACAATGTTGTTGCTCACTTGG
390 GACACCAG-TTTTCCAAACCATATTAGTGTACTTGAGGCCGGATACAATGTTGTTGCTCACTTGG
16259874 AAAGTGAATTGCAGGCTGTA-TTGCTTCCTTCTTTTAGGGT-AACCACAAGCCTTTAGGCTTTCC
454 AAAGTGAATTGCAGGCTGTATTTGCTTCCTTCTTTTAGGGTAAACCACAAGCCTTTAGGCTTTCC
*
16259937 GTTCTCCGGAATTGGAAGTA-CATATCAGGTCTACCATGTGATTTGATCGCAAGGCTCAGTATCT
519 GTTCTCCGGAATTGGAAGTACCATATCAGGTCTACCATGTGATTTGATCGCAAGGCTCAATATCT
*
16260001 TCACTTCAGGTTCTAGCTTTTCTATACATCATAAACAATAGAAGAAAATGTCAGGATACAAAGAA
584 TCACTTCAGGTTCTAGCTTTTATA-ACATCATAAACAATAGAAGAAAATGTCAGGATACAAAGAA
16260066 AGGACACGTTACAGAGCATGGAAACTATTGATGAAATCATAGACAAAAAGAAGGTATGAAGCT-T
648 AGGACACGTTACAGAGCATGGAAACTATTGATGAAATCATAGACAAAAAGAAGGTATGAAGCTAT
16260130 ACTCTACGCCTACAATGTTAAGATAAACTGTCCACCAACAAAAAAGTTACATTAAAA-AAGCTGA
713 ACTCTACGCCTACAATGTTAAGATAAACTGTCCACCAAC-AAAAAGTTACATTAAAAGAAGCTGA
16260194 AATTCAATATGCAAAC-AATTGATTCTTGCATCCCATCTCTTACC-TTTTAATAATGGTCTACCA
777 AATTCAATATGCAAACAAATTGA-TCTTGCATCCCAT-TCTTACCTTTTTAATAATGGTCTACCA
16260257 AGTATTGCAACATTTGAGATCAAGGGATTATATTCCAGATATTTTACACACAATATAAATTTCAT
840 AGTATTGCAACATTTGAGATCAAGGGATTATATTCCAGATATTTTACACACAATATAAA-TTCAT
16260322 CAACAGTGAAAGAAATCCTCAAGTTT-AAAGAATAGAAA-GAAAGACGAGAGAGAG
904 CAACAGTGAAAGAAATCCTCAAGTTTGAAAGAAT-GAAATGAAAGACGAGAGAGAG
16260376 AGAGAGAGAG
Statistics
Matches: 939, Mismatches: 5, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
961 6 0.01
962 243 0.26
963 205 0.22
964 20 0.02
965 41 0.04
966 22 0.02
967 145 0.15
968 244 0.26
969 13 0.01
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (968 bp):
ATCCTGACAACTCATTAATGGGATGTTTATCAGTAAATTCGGAGACACCATCTAACAAGAAATCA
AGTAATAAAAGCAACAGAGAACCAGAATCATACAAACCACTATGGACATTAATGAACAAGCTTAA
ATGGCTTTTTATTTTATCATTGATTTTACCTTACTTCTAGCTGAATAAGATCCTCTAGCAAACAT
TCCAGATGGAGTTGTTTCTTCACAAATTTCATGTGTGTAAGGCTCTGCCTGGGGACTGAAGGTTC
CGATCATCTCTTTCGTGCTATCAACTGGTACAAGAGTTCATGGTGAAGAATATCAAATCCAATGG
TTAACATGAGAGGGTACAATTCTTCCATATGAACAACAGAGAAAGGGAAAGAGGAATTACCCTTG
ACACCAGTTTTCCAAACCATATTAGTGTACTTGAGGCCGGATACAATGTTGTTGCTCACTTGGAA
AGTGAATTGCAGGCTGTATTTGCTTCCTTCTTTTAGGGTAAACCACAAGCCTTTAGGCTTTCCGT
TCTCCGGAATTGGAAGTACCATATCAGGTCTACCATGTGATTTGATCGCAAGGCTCAATATCTTC
ACTTCAGGTTCTAGCTTTTATAACATCATAAACAATAGAAGAAAATGTCAGGATACAAAGAAAGG
ACACGTTACAGAGCATGGAAACTATTGATGAAATCATAGACAAAAAGAAGGTATGAAGCTATACT
CTACGCCTACAATGTTAAGATAAACTGTCCACCAACAAAAAGTTACATTAAAAGAAGCTGAAATT
CAATATGCAAACAAATTGATCTTGCATCCCATTCTTACCTTTTTAATAATGGTCTACCAAGTATT
GCAACATTTGAGATCAAGGGATTATATTCCAGATATTTTACACACAATATAAATTCATCAACAGT
GAAAGAAATCCTCAAGTTTGAAAGAATGAAATGAAAGACGAGAGAGAGCCTGTTTCAC
Found at i:16264018 original size:16 final size:15
Alignment explanation
Indices: 16263993--16264022 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
16263983 TTTAATGTGA
16263993 CATAATTATATTTAG
1 CATAATTATATTTAG
16264008 CATATATTATATTTA
1 CATA-ATTATATTTA
16264023 AAAAGTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (15 bp):
CATAATTATATTTAG
Found at i:16269633 original size:56 final size:56
Alignment explanation
Indices: 16269547--16269660 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
16269537 CTCACCGCCC
*
16269547 TTTCTATTGTTCCTGTTCCTCAACTCAAAACTCAAGCTACTAATGGGCTATTGTCT
1 TTTCTATTGTTCCTCTTCCTCAACTCAAAACTCAAGCTACTAATGGGCTATTGTCT
* *
16269603 TTTCTATTGTTCCTCTTTCTCAACTCAAAACTCAAGCTACTAATTGGCTATTGTCT
1 TTTCTATTGTTCCTCTTCCTCAACTCAAAACTCAAGCTACTAATGGGCTATTGTCT
16269659 TT
1 TT
16269661 GTTTCATAGC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.42
Consensus pattern (56 bp):
TTTCTATTGTTCCTCTTCCTCAACTCAAAACTCAAGCTACTAATGGGCTATTGTCT
Found at i:16272798 original size:149 final size:149
Alignment explanation
Indices: 16272640--16272941 Score: 387
Period size: 149 Copynumber: 2.0 Consensus size: 149
16272630 TCATGAAAAT
* *
16272640 TACATTAATT-TAATTTAAAAAATTATTAAAATAT-TTTTATACATAAAAT-A-ATATATATTAT
1 TACATTAATTCT--TTTAAAAAATTACTAAAATATCTTTTATACATAAAATGAGAGATATATTAT
* * * *
16272701 TATGAGGGTGTTTTTATCTTTTTTACATTTTTATTTAAATTTTATACTAATATTAAATCCTAAAC
64 CATAAGGGTGTTTTTATC-TTTTTACATTTTTATATAAA-TCTATACTAATATTAAATCCTAAAC
*
16272766 TATGTTGGTATCACGAGTTAACA
127 TATGTTGGTATCACAAGTTAACA
* * *
16272789 TACATTAATTCTTTTGAAAAATTACTAAAATATCTTTTATATATAAATTGAGAGATATATTATCA
1 TACATTAATTCTTTTAAAAAATTACTAAAATATCTTTTATACATAAAATGAGAGATATATTATCA
* * * * * *
16272854 TAAGGGTGTTTTTATCTTTTTGCATTTTTATATAAATCTATATTTATATTAAGTCTTAAACTGTG
66 TAAGGGTGTTTTTATCTTTTTACATTTTTATATAAATCTATACTAATATTAAATCCTAAACTATG
*
16272919 TTGGTATCACAAGTTAATA
131 TTGGTATCACAAGTTAACA
16272938 TACA
1 TACA
16272942 CCAATGCAAG
Statistics
Matches: 132, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
148 19 0.14
149 67 0.51
150 20 0.15
151 26 0.20
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (149 bp):
TACATTAATTCTTTTAAAAAATTACTAAAATATCTTTTATACATAAAATGAGAGATATATTATCA
TAAGGGTGTTTTTATCTTTTTACATTTTTATATAAATCTATACTAATATTAAATCCTAAACTATG
TTGGTATCACAAGTTAACA
Found at i:16273118 original size:28 final size:29
Alignment explanation
Indices: 16273086--16273142 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
16273076 ATTCTTTTTT
16273086 TTTAATAGTAAAAA-ATTAAATTAATTTA
1 TTTAATAGTAAAAATATTAAATTAATTTA
*
16273114 TTTAATAGTAAAAATATTAATTTAATTTA
1 TTTAATAGTAAAAATATTAAATTAATTTA
16273143 ATCGATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.46
Consensus pattern (29 bp):
TTTAATAGTAAAAATATTAAATTAATTTA
Found at i:16273523 original size:11 final size:11
Alignment explanation
Indices: 16273509--16273577 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
16273499 ATATCTAAAC
16273509 AATAACAATAA-
1 AATAA-AATAAT
16273520 AATAATAATAAT
1 AATAA-AATAAT
*
16273532 AATATAATAAT
1 AATAAAATAAT
16273543 AA-AAATATAAT
1 AATAAA-ATAAT
* *
16273554 AATAAAATGAC
1 AATAAAATAAT
*
16273565 AATAAAACAAT
1 AATAAAATAAT
16273576 AA
1 AA
16273578 CATTAAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
10 2 0.04
11 38 0.81
12 7 0.15
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:16273528 original size:3 final size:3
Alignment explanation
Indices: 16273509--16273558 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
16273499 ATATCTAAAC
* *
16273509 AAT AAC AAT AA- AAT AAT AAT AAT AAT -AT AAT AAT AAA AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16273554 AAT AA
1 AAT AA
16273559 AATGACAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.15
3 34 0.85
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:16273532 original size:14 final size:14
Alignment explanation
Indices: 16273509--16273561 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
16273499 ATATCTAAAC
*
16273509 AATAACAATAAAAT
1 AATAATAATAAAAT
*
16273523 AATAATAATAATAT
1 AATAATAATAAAAT
16273537 AATAAT-A-AAAAT
1 AATAATAATAAAAT
16273549 -ATAATAATAAAAT
1 AATAATAATAAAAT
16273562 GACAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 5 0.15
12 5 0.15
13 6 0.18
14 18 0.53
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATAATAAAAT
Found at i:16273538 original size:25 final size:24
Alignment explanation
Indices: 16273509--16273577 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
16273499 ATATCTAAAC
16273509 AATAACAATAAAATAATAATAATAA
1 AATAACAATAAAA-AATAATAATAA
* *
16273534 TATAATAATAAAAATATAATAATAA
1 AATAACAATAAAAA-ATAATAATAA
*
16273559 AATGACAATAAAACAATAA
1 AATAACAATAAAA-AATAA
16273578 CATTAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 1 0.03
25 35 0.95
26 1 0.03
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (24 bp):
AATAACAATAAAAAATAATAATAA
Found at i:16296481 original size:3 final size:3
Alignment explanation
Indices: 16296475--16296501 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16296465 ACTCTCTTCT
16296475 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
16296502 CTCATAATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16302071 original size:3 final size:3
Alignment explanation
Indices: 16302063--16302090 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16302053 ATTATATCTT
16302063 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16302091 ACTTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16303629 original size:3 final size:3
Alignment explanation
Indices: 16303621--16303649 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16303611 TAATGATCTG
16303621 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
16303650 CCGCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:16317016 original size:3 final size:3
Alignment explanation
Indices: 16317008--16317034 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16316998 TTAACCTTAT
16317008 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
16317035 ACATTAACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16319128 original size:16 final size:16
Alignment explanation
Indices: 16319095--16319128 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16319085 ATGAACTGTT
* *
16319095 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16319111 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16319127 AA
1 AA
16319129 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16321958 original size:21 final size:21
Alignment explanation
Indices: 16321932--16321972 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16321922 AGACGAGCAA
* *
16321932 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
16321953 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
16321973 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:16323912 original size:16 final size:16
Alignment explanation
Indices: 16323879--16323912 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16323869 GGAGATTGTT
* *
16323879 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
16323895 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
16323911 AA
1 AA
16323913 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:16326824 original size:235 final size:234
Alignment explanation
Indices: 16326413--16326881 Score: 911
Period size: 235 Copynumber: 2.0 Consensus size: 234
16326403 TGGCTCTTTC
16326413 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
1 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
*
16326478 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTTAAATAGTTTTTTTCTTCGATCTTC
66 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
16326543 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
131 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
*
16326608 TCACTTAGAGTTCACTGATAGAAATTTTTTTTAGAAAAAA
196 TCACTTAGAGTTCACAGATAG-AATTTTTTTTAGAAAAAA
16326648 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
1 TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
16326713 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
66 TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
16326778 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
131 AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
16326843 TCACTTAGAGTTCACAGATAGAATTTTTTTTAGAAAAAA
196 TCACTTAGAGTTCACAGATAGAATTTTTTTTAGAAAAAA
16326882 CTTAACAAGT
Statistics
Matches: 232, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
234 18 0.08
235 214 0.92
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (234 bp):
TATTTGTACTGTTTGTAACAATCGAAAGTTCTCTTTCCCTTTTTCTTCTACAGTAGTTTTTTTCA
TGAAATAACTTTGGACATCATGAATCAGCGAACCAAAATTCAAATAGTTTTTTTCTTCGATCTTC
AACATTGATCGTTTAGATCGGCTAGGATCTAAAGTATGTTTTTCTACTTGTCAAATTTCAAATTG
TCACTTAGAGTTCACAGATAGAATTTTTTTTAGAAAAAA
Found at i:16326961 original size:31 final size:31
Alignment explanation
Indices: 16326899--16326961 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
16326889 AGTCAGTGAA
* * * *
16326899 TTAAATAAAAACTTTCGAATAATTTACTAAC
1 TTAAACAAAAACTTTCAAATAATTCAATAAC
*
16326930 TTAAACAAAAATTTTCAAATAATTCAATAAC
1 TTAAACAAAAACTTTCAAATAATTCAATAAC
16326961 T
1 T
16326962 AAATTATACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.35
Consensus pattern (31 bp):
TTAAACAAAAACTTTCAAATAATTCAATAAC
Found at i:16335656 original size:19 final size:19
Alignment explanation
Indices: 16335629--16335665 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16335619 CAAAATTTAT
* *
16335629 ATTTTTAAAAAATTATAAA
1 ATTTCTAAAAAAATATAAA
16335648 ATTTCTAAAAAAATATAA
1 ATTTCTAAAAAAATATAA
16335666 GAAATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTCTAAAAAAATATAAA
Found at i:16339599 original size:33 final size:33
Alignment explanation
Indices: 16339557--16339621 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
16339547 ATACATAAAT
16339557 AAGAGAACATGAATAATTATGGGGCATTTGAAG
1 AAGAGAACATGAATAATTATGGGGCATTTGAAG
16339590 AAGAGAACATGAATAATTATGGGGCATTTGAA
1 AAGAGAACATGAATAATTATGGGGCATTTGAA
16339622 AAACAAGTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.26, T:0.25
Consensus pattern (33 bp):
AAGAGAACATGAATAATTATGGGGCATTTGAAG
Found at i:16344693 original size:35 final size:34
Alignment explanation
Indices: 16344670--16344862 Score: 210
Period size: 35 Copynumber: 5.6 Consensus size: 34
16344660 GGCAAAGTGC
16344670 AAAATATAGGTATGGTATTATCCATACCGAGTTG
1 AAAATATAGGTATGGTATTATCCATACCGAGTTG
* * *
16344704 TGAAATGTAGGTATGGTATCATCCATACCGAGTTG
1 -AAAATATAGGTATGGTATTATCCATACCGAGTTG
* *
16344739 AGAAATATAGGTATGGTATTATCCATACTGAGTTA
1 A-AAATATAGGTATGGTATTATCCATACCGAGTTG
* *
16344774 AGAAATGTAGGTATGGCATT-TCCCATACCGAGTTG
1 A-AAATATAGGTATGGTATTAT-CCATACCGAGTTG
* ** *
16344809 TGAAACGTAGGTATGGTATTTTCCATACCGAGTAT-
1 -AAAATATAGGTATGGTATTATCCATACCGAGT-TG
*
16344844 AAAATGTAGGTATGGTATT
1 AAAATATAGGTATGGTATT
16344863 TCAATGAGGA
Statistics
Matches: 136, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
34 18 0.13
35 116 0.85
36 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (34 bp):
AAAATATAGGTATGGTATTATCCATACCGAGTTG
Found at i:16344772 original size:70 final size:70
Alignment explanation
Indices: 16344671--16344861 Score: 269
Period size: 70 Copynumber: 2.7 Consensus size: 70
16344661 GCAAAGTGCA
*
16344671 AAATATAGGTATGGTATTATCCATACCGAGTTGTGAAATGTAGGTATGGTATCAT-CCATACCGA
1 AAATATAGGTATGGTATTATCCATACCGAGTTATGAAATGTAGGTATGGTAT-ATCCCATACCGA
16344735 GTTGAG
65 GTTGAG
* * * *
16344741 AAATATAGGTATGGTATTATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCCCATACCGAG
1 AAATATAGGTATGGTATTATCCATACCGAGTTATGAAATGTAGGTATGGTATATCCCATACCGAG
*
16344806 TTGTG
66 TTGAG
** * *
16344811 AAACGTAGGTATGGTATTTTCCATACCGAG-TATAAAATGTAGGTATGGTAT
1 AAATATAGGTATGGTATTATCCATACCGAGTTATGAAATGTAGGTATGGTAT
16344862 TTCAATGAGG
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
69 19 0.18
70 88 0.82
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (70 bp):
AAATATAGGTATGGTATTATCCATACCGAGTTATGAAATGTAGGTATGGTATATCCCATACCGAG
TTGAG
Found at i:16344836 original size:105 final size:104
Alignment explanation
Indices: 16344671--16344862 Score: 289
Period size: 105 Copynumber: 1.8 Consensus size: 104
16344661 GCAAAGTGCA
* *
16344671 AAATATAGGTATGGTATTATCCATACCGAGTTGTGAAATGTAGGTATGGTATCATCCATACCGAG
1 AAATATAGGTATGGCATTATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAG
16344736 T-TGAGAAATATAGGTATGGTATTATCCATACTGAGTTAAG
66 TAT-A-AAATATAGGTATGGTATTATCCATACTGAGTTAAG
* **
16344776 AAATGTAGGTATGGCATT-TCCCATACCGAGTTGTGAAACGTAGGTATGGTATTTTCCATACCGA
1 AAATATAGGTATGGCATTAT-CCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGA
*
16344840 GTATAAAATGTAGGTATGGTATT
65 GTATAAAATATAGGTATGGTATT
16344863 TCAATGAGGA
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
104 18 0.23
105 60 0.76
106 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (104 bp):
AAATATAGGTATGGCATTATCCATACCGAGTTGTGAAACGTAGGTATGGTATCATCCATACCGAG
TATAAAATATAGGTATGGTATTATCCATACTGAGTTAAG
Found at i:16346512 original size:24 final size:24
Alignment explanation
Indices: 16346480--16346538 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
16346470 ACCGGTGTTT
16346480 CTGGTGGTTTCCG-GAGTAAAGTAG
1 CTGGTGGTTTCCGCG-GTAAAGTAG
*
16346504 CTGGTGGTTTCTGCGGTAAAGTAG
1 CTGGTGGTTTCCGCGGTAAAGTAG
16346528 CTGGTGGTTTC
1 CTGGTGGTTTC
16346539 GGCAGTGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 32 0.97
25 1 0.03
ACGTcount: A:0.15, C:0.14, G:0.37, T:0.34
Consensus pattern (24 bp):
CTGGTGGTTTCCGCGGTAAAGTAG
Found at i:16349597 original size:24 final size:24
Alignment explanation
Indices: 16349570--16349618 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
16349560 ATATAGTAAA
16349570 TGTTAATGTGAAATGATTGTAAGG
1 TGTTAATGTGAAATGATTGTAAGG
16349594 TGTTAATGTGAAATGATTGTAAGG
1 TGTTAATGTGAAATGATTGTAAGG
16349618 T
1 T
16349619 CAGCCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.39
Consensus pattern (24 bp):
TGTTAATGTGAAATGATTGTAAGG
Found at i:16349686 original size:23 final size:23
Alignment explanation
Indices: 16349660--16349704 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
16349650 TTGGTATGTG
*
16349660 ATGAGGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
16349683 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
16349705 TTGAATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:16353168 original size:9 final size:9
Alignment explanation
Indices: 16353114--16353224 Score: 52
Period size: 10 Copynumber: 12.2 Consensus size: 9
16353104 TAAATTTTCA
16353114 AAAAATTAT
1 AAAAATTAT
*
16353123 AAACATTATT
1 AAAAATTA-T
*
16353133 AAAAA-TAA
1 AAAAATTAT
*
16353141 AAAAAATAT
1 AAAAATTAT
16353150 GAAAATATTAT
1 -AAAA-ATTAT
16353161 AAAAATTA-
1 AAAAATTAT
* * *
16353169 AATATTTAA
1 AAAAATTAT
*
16353178 AAAAACTA-
1 AAAAATTAT
16353186 AAAAA-TA-
1 AAAAATTAT
**
16353193 AAATTTTATT
1 AAAAATTA-T
16353203 AATAAATTAT
1 AA-AAATTAT
16353213 AAAAAATTAT
1 -AAAAATTAT
16353223 AA
1 AA
16353225 TTTATAAGTT
Statistics
Matches: 78, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
7 5 0.06
8 18 0.23
9 22 0.28
10 23 0.29
11 10 0.13
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:16362007 original size:21 final size:22
Alignment explanation
Indices: 16361966--16362016 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
16361956 AGAGATTCTT
*
16361966 TTAAAATAAACTCAGTAATTTTA-
1 TTAAAA-AAACTCAATAA-TTTAC
16361989 TTAAAAAAACT-AATAATTTAC
1 TTAAAAAAACTCAATAATTTAC
16362010 TTAAAAA
1 TTAAAAA
16362017 CATTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 11 0.42
22 5 0.19
23 6 0.23
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (22 bp):
TTAAAAAAACTCAATAATTTAC
Found at i:16364820 original size:15 final size:15
Alignment explanation
Indices: 16364802--16364836 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16364792 GGAAAACAAG
16364802 GAAGAAGAGAAGAAA
1 GAAGAAGAGAAGAAA
*
16364817 GAAGCAGAGAAGAAA
1 GAAGAAGAGAAGAAA
*
16364832 CAAGA
1 GAAGA
16364837 TGACGGAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.31, T:0.00
Consensus pattern (15 bp):
GAAGAAGAGAAGAAA
Found at i:16376640 original size:18 final size:19
Alignment explanation
Indices: 16376608--16376648 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
16376598 ATGTATCTAA
16376608 AATAAGAACAAAATTA-AC
1 AATAAGAACAAAATTATAC
16376626 AATAA-AACAAGAATTATAC
1 AATAAGAACAA-AATTATAC
16376645 AATA
1 AATA
16376649 TTCAAATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.05, T:0.20
Consensus pattern (19 bp):
AATAAGAACAAAATTATAC
Found at i:16379701 original size:13 final size:13
Alignment explanation
Indices: 16379682--16379732 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
16379672 TAAATCAAAT
16379682 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
16379695 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
* *
16379708 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
*
16379721 TTTTTAAAAGCA
1 TTTTCAAAAGCA
16379733 TTGTCAAACT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:16385130 original size:29 final size:29
Alignment explanation
Indices: 16385097--16385156 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
16385087 GGTGAAAGTT
16385097 AGAAAGCTCACATCATTTGTTTTAATGAA
1 AGAAAGCTCACATCATTTGTTTTAATGAA
16385126 AGAAAGCTCACATCATTTGTTTTAATGAA
1 AGAAAGCTCACATCATTTGTTTTAATGAA
16385155 AG
1 AG
16385157 TCTTACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (29 bp):
AGAAAGCTCACATCATTTGTTTTAATGAA
Found at i:16562521 original size:13 final size:13
Alignment explanation
Indices: 16562503--16562543 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
16562493 CTGAACATAT
16562503 AATAAACAAAGCC
1 AATAAACAAAGCC
* *
16562516 AATAAACATA--T
1 AATAAACAAAGCC
16562527 AATAAACAAAGCC
1 AATAAACAAAGCC
16562540 AATA
1 AATA
16562544 CAAGTAGGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.63, C:0.17, G:0.05, T:0.15
Consensus pattern (13 bp):
AATAAACAAAGCC
Found at i:16562528 original size:24 final size:24
Alignment explanation
Indices: 16562496--16562543 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16562486 CATGCCTCTG
16562496 AACATATAATAAACAAAGCCAATA
1 AACATATAATAAACAAAGCCAATA
16562520 AACATATAATAAACAAAGCCAATA
1 AACATATAATAAACAAAGCCAATA
16562544 CAAGTAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.04, T:0.17
Consensus pattern (24 bp):
AACATATAATAAACAAAGCCAATA
Found at i:16562708 original size:9 final size:9
Alignment explanation
Indices: 16562679--16562715 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
16562669 TGAATTTTCG
16562679 AATTCGAAT
1 AATTCGAAT
*
16562688 AACTCGAAT
1 AATTCGAAT
16562697 AATTCGAAT
1 AATTCGAAT
*
16562706 AATTCAAAT
1 AATTCGAAT
16562715 A
1 A
16562716 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16562800 original size:29 final size:30
Alignment explanation
Indices: 16562758--16562817 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
16562748 ACTCCCAAAT
* *
16562758 CTTTTTACTTTTCCCTCAAAACTTTTACTC
1 CTTTCTACTTTTCCCCCAAAACTTTTACTC
16562788 CTTTCTAC-TTTCCCCCAAAACTTTTACTC
1 CTTTCTACTTTTCCCCCAAAACTTTTACTC
16562817 C
1 C
16562818 CCTTCTATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (30 bp):
CTTTCTACTTTTCCCCCAAAACTTTTACTC
Found at i:16562824 original size:30 final size:29
Alignment explanation
Indices: 16562767--16562824 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
16562757 TCTTTTTACT
* *
16562767 TTTCCCTCAAAACTTTTACTCCTTTCTAC
1 TTTCCCCCAAAACTTTTACTCCCTTCTAC
16562796 TTTCCCCCAAAACTTTTACTCCCCTTCTA
1 TTTCCCCCAAAACTTTTACT-CCCTTCTA
16562825 TCCCAACCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTCCCCCAAAACTTTTACTCCCTTCTAC
Found at i:16563974 original size:24 final size:24
Alignment explanation
Indices: 16563942--16563989 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
16563932 GAAGTAAGAG
16563942 ACGACAAAGACAATATTATTACAA
1 ACGACAAAGACAATATTATTACAA
16563966 ACGACAAAGACAATATTATTACAA
1 ACGACAAAGACAATATTATTACAA
16563990 GCTTGTTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.08, T:0.21
Consensus pattern (24 bp):
ACGACAAAGACAATATTATTACAA
Found at i:16569521 original size:21 final size:22
Alignment explanation
Indices: 16569469--16569511 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 22
16569459 AGTACTTGAT
16569469 TAAATTAAATTTTATATTATTAGA
1 TAAATT-AA-TTTATATTATTAGA
16569493 TAAATTAATTTA-ATTATTA
1 TAAATTAATTTATATTATTA
16569512 TATTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 2 0.11
24 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAATTAATTTATATTATTAGA
Found at i:16586238 original size:18 final size:18
Alignment explanation
Indices: 16586212--16586249 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
16586202 ACGTGCATTA
*
16586212 TTATTAATTATATAAT-TT
1 TTATAAATTAT-TAATGTT
16586230 TTATAAATTATTAATGTT
1 TTATAAATTATTAATGTT
16586248 TT
1 TT
16586250 TATATTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTATAAATTATTAATGTT
Found at i:16590956 original size:6 final size:6
Alignment explanation
Indices: 16590936--16590979 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
16590926 ACACTTCTTC
*
16590936 TCCCCTT TCCCCT TCCTCT TCCCCT TCCCCT TCCCCT TCCCCT T
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT T
16590980 TTGAAATCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
6 30 0.86
7 5 0.14
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
TCCCCT
Found at i:16592214 original size:17 final size:18
Alignment explanation
Indices: 16592181--16592217 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
16592171 TGTTTCCTTT
*
16592181 GAGGTCCATGATAATTGG
1 GAGGTCCAAGATAATTGG
16592199 GAGGTCCAAG-TAATTGG
1 GAGGTCCAAGATAATTGG
16592216 GA
1 GA
16592218 ATTCCATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.30, C:0.11, G:0.35, T:0.24
Consensus pattern (18 bp):
GAGGTCCAAGATAATTGG
Found at i:16594484 original size:18 final size:19
Alignment explanation
Indices: 16594444--16594486 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
16594434 CAAACACTAG
*
16594444 AAAAATAAATCATTTTCAG
1 AAAAATAAATCATTTTCAC
16594463 AAAAATAAATCATTTTC-C
1 AAAAATAAATCATTTTCAC
16594481 AAAAAT
1 AAAAAT
16594487 TATTTTTCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATAAATCATTTTCAC
Found at i:16594485 original size:19 final size:19
Alignment explanation
Indices: 16594442--16594479 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
16594432 TCCAAACACT
16594442 AGAAAAATAAATCATTTTC
1 AGAAAAATAAATCATTTTC
16594461 AGAAAAATAAATCATTTTC
1 AGAAAAATAAATCATTTTC
16594480 CAAAAATTAT
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:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
AGAAAAATAAATCATTTTC
Found at i:16599336 original size:3 final size:3
Alignment explanation
Indices: 16599328--16599365 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
16599318 TATACGAACA
*
16599328 AAG AAG AAG AAG AAG AAG AAG CAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
16599366 ACGAGGCGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16602498 original size:125 final size:126
Alignment explanation
Indices: 16602314--16602558 Score: 429
Period size: 125 Copynumber: 1.9 Consensus size: 126
16602304 AAAAGAAATT
16602314 AAAAGAACTTTAATCAAGCAGCCTTTTACACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCAC
1 AAAAGAACTTTAATCAAGCAGCC-TTTACACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCAC
*
16602379 CAAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGTCTAGTGCTAAGGAAAACTA
65 CAAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGGAAAACTA
* ** *
16602441 AAAAGAACTTTAATCAAGCAGCC-TTATACCTATTGCTTTACAAAAATGTGTGTCTAGGTGCACC
1 AAAAGAACTTTAATCAAGCAGCCTTTACACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCACC
16602505 AAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGG
66 AAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGG
16602559 GACAAGCACA
Statistics
Matches: 113, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
125 90 0.80
127 23 0.20
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (126 bp):
AAAAGAACTTTAATCAAGCAGCCTTTACACCTATTGCTTTACAAAAAACTGTGCCTAGGTGCACC
AAGAGTGCGCCTGATCAAATGAGTTTGAAGCACTTTTGTTGCCTAGTGCTAAGGAAAACTA
Found at i:16606035 original size:29 final size:29
Alignment explanation
Indices: 16605968--16606044 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 29
16605958 TTTTTTTAGA
*
16605968 TTCAA-AATTTAGT-TGTTATAGTTTTGTT
1 TTCAAGAATTTAGTCT-TTATAGTTTTATT
16605996 TTCAAGAATTTAGTCTTTATAGTTTTATGT
1 TTCAAGAATTTAGTCTTTATAGTTTTAT-T
16606026 TT-AATG-ATTTAGTCCTTTA
1 TTCAA-GAATTTAGT-CTTTA
16606045 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
28 5 0.12
29 28 0.65
30 10 0.23
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (29 bp):
TTCAAGAATTTAGTCTTTATAGTTTTATT
Found at i:16607865 original size:15 final size:16
Alignment explanation
Indices: 16607845--16607877 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16607835 ATATGTATTT
16607845 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
16607860 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
16607877 T
1 T
16607878 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:16607950 original size:21 final size:22
Alignment explanation
Indices: 16607924--16607982 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
16607914 GTTTTAAGAA
*
16607924 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
16607945 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
16607967 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
16607983 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:16607997 original size:26 final size:24
Alignment explanation
Indices: 16607953--16608002 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
16607943 ATTTGTTTTA
*
16607953 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
16607977 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
16608003 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:16613370 original size:5 final size:5
Alignment explanation
Indices: 16613362--16613390 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
16613352 TATAATATGG
16613362 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAA
16613391 ATAGTCATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TTAAT
Found at i:16616531 original size:17 final size:17
Alignment explanation
Indices: 16616498--16616531 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16616488 TTTATAGTAC
*
16616498 TTTATATTATGTTATTT
1 TTTATATTATGTAATTT
*
16616515 TTTATATTTTGTAATTT
1 TTTATATTATGTAATTT
16616532 ACAACACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATATTATGTAATTT
Found at i:16619565 original size:17 final size:18
Alignment explanation
Indices: 16619543--16619576 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16619533 TTAACTTAAC
16619543 TAAATTA-ATTTCTCAAA
1 TAAATTATATTTCTCAAA
*
16619560 TAAATTATTTTTCTCAA
1 TAAATTATATTTCTCAA
16619577 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATTATATTTCTCAAA
Found at i:16625217 original size:18 final size:19
Alignment explanation
Indices: 16625179--16625216 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
16625169 TCACGTCAAC
16625179 AAGTAATTTACAAATTTAA
1 AAGTAATTTACAAATTTAA
16625198 AAGT-ATTTA-AAATTTAA
1 AAGTAATTTACAAATTTAA
16625215 AA
1 AA
16625217 ACTATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (19 bp):
AAGTAATTTACAAATTTAA
Found at i:16629277 original size:19 final size:19
Alignment explanation
Indices: 16629255--16629294 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
16629245 GTCGCTCACG
16629255 ACTCTCGGCCCCGCTCTCC
1 ACTCTCGGCCCCGCTCTCC
16629274 ACTCTCGGCCCCGCTCTCC
1 ACTCTCGGCCCCGCTCTCC
16629293 AC
1 AC
16629295 CGTTTCTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.57, G:0.15, T:0.20
Consensus pattern (19 bp):
ACTCTCGGCCCCGCTCTCC
Found at i:16650326 original size:52 final size:52
Alignment explanation
Indices: 16650136--16650328 Score: 175
Period size: 52 Copynumber: 3.8 Consensus size: 52
16650126 ATGGATTTGA
* * * *
16650136 GCCATAGCCCTGCCATGGTCTTACAC-GGATCACATAT-A-AT---ACCGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACATCACACCGAT
* * * * *
16650182 GTCATATCCCAGATATGATCTTATAC-GGAATCACATTATCACATCACACCGAC
1 GCCATAGCCCAGCTATGGTCTTATACGGGAA-CACA-TATCACATCACACCGAT
* * * **
16650235 GCCATAGCCCAGCTATGGTCTTATATGCGAACACGTATCACATTGCACCGAT
1 GCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACATCACACCGAT
**
16650287 GCCATAGCCCAGCTATGGTCTTATACGGGCGCACATATCACA
1 GCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACA
16650329 ACTTTTATGT
Statistics
Matches: 115, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
46 22 0.19
47 4 0.03
48 3 0.03
49 1 0.01
50 2 0.02
52 51 0.44
53 29 0.25
54 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (52 bp):
GCCATAGCCCAGCTATGGTCTTATACGGGAACACATATCACATCACACCGAT
Found at i:16652972 original size:17 final size:18
Alignment explanation
Indices: 16652952--16652991 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
16652942 ATTAATTTTT
*
16652952 TTAAAAATTTAA-AAATA
1 TTAAAAAATTAATAAATA
16652969 TTAAAAAATTAATTAAATA
1 TTAAAAAATTAA-TAAATA
16652988 TTAA
1 TTAA
16652992 TGTATCATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 11 0.55
19 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAAAAATTAATAAATA
Found at i:16661353 original size:105 final size:105
Alignment explanation
Indices: 16661169--16661374 Score: 331
Period size: 105 Copynumber: 2.0 Consensus size: 105
16661159 TTTTAATAAA
* *
16661169 ATATTTTCATCATTAAGTAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTTTAA
1 ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTGTAA
* * *
16661234 TATTTATTAAAAATAGAGTTTTATATTAATTGTATTAATT
66 TATTTATTAAAAATAAAATTTTATATTAATTATATTAATT
** *
16661274 ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAATGCATTTATATATATTAAGATTGTAA
1 ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTGTAA
*
16661339 TATTTATTAGAAATAAAATTTTATATTAATTATATT
66 TATTTATTAAAAATAAAATTTTATATTAATTATATT
16661375 TTTTATGTGC
Statistics
Matches: 92, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 92 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (105 bp):
ATATTTTCATCATTAAATAGATATTTATCAAAATTAAAAAACATTTATATACATTAAGATTGTAA
TATTTATTAAAAATAAAATTTTATATTAATTATATTAATT
Found at i:16662469 original size:43 final size:43
Alignment explanation
Indices: 16662422--16662509 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
16662412 GCCCTATTTA
*
16662422 ATCTATTAATCTCCATAGTACGTGAAAGAAAATAATCAAATAC
1 ATCTATTAATCTCCATAGTACGTGAAAGAAAAGAATCAAATAC
16662465 ATCTATTAATCTCCATAGTACGTGAAAGAAAAGAATCAAATAC
1 ATCTATTAATCTCCATAGTACGTGAAAGAAAAGAATCAAATAC
16662508 AT
1 AT
16662510 GGTTTTGAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (43 bp):
ATCTATTAATCTCCATAGTACGTGAAAGAAAAGAATCAAATAC
Found at i:16663251 original size:20 final size:18
Alignment explanation
Indices: 16663226--16663262 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
16663216 ATTGCTAAGT
16663226 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
16663246 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
16663263 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:16674108 original size:25 final size:25
Alignment explanation
Indices: 16674074--16674137 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
16674064 TCTGTAAAAT
16674074 CAATTGAAACGGTGCGTGGT-GGAAA
1 CAATTGAAACGGTGCGTGGTAGG-AA
16674099 CAATTGAAACGGTGCGTGGTAGGAA
1 CAATTGAAACGGTGCGTGGTAGGAA
16674124 CAATTGAAACGGTG
1 CAATTGAAACGGTG
16674138 AGTTTTGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 36 0.95
26 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (25 bp):
CAATTGAAACGGTGCGTGGTAGGAA
Found at i:16675244 original size:7 final size:7
Alignment explanation
Indices: 16675228--16675325 Score: 65
Period size: 7 Copynumber: 14.0 Consensus size: 7
16675218 TCATATCCTA
*
16675228 TAAACAC
1 TAAACCC
16675235 TAAACCC
1 TAAACCC
16675242 TAAACCC
1 TAAACCC
*
16675249 TTAACCC
1 TAAACCC
*
16675256 CAAACCC
1 TAAACCC
* *
16675263 TTACACCT
1 -TAAACCC
16675271 TAAACTCC
1 TAAAC-CC
16675279 --AACCC
1 TAAACCC
*
16675284 TAACCCC
1 TAAACCC
*
16675291 TAACCCC
1 TAAACCC
*
16675298 TAAACCT
1 TAAACCC
* *
16675305 TAAATCA
1 TAAACCC
*
16675312 TAATCCC
1 TAAACCC
16675319 TAAACCC
1 TAAACCC
16675326 ATAATTCATC
Statistics
Matches: 69, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
5 2 0.03
6 3 0.04
7 59 0.86
8 5 0.07
ACGTcount: A:0.39, C:0.42, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:16675405 original size:46 final size:46
Alignment explanation
Indices: 16675352--16675445 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
16675342 CTTCAAATAC
* * *
16675352 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
16675398 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
1 TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
16675444 TA
1 TA
16675446 AACCATAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.45, C:0.26, G:0.02, T:0.28
Consensus pattern (46 bp):
TAGTTAACTCATAAACCATAAACCCTAAACCATATATATTAAACCA
Found at i:16675419 original size:7 final size:7
Alignment explanation
Indices: 16675363--16675460 Score: 63
Period size: 7 Copynumber: 13.4 Consensus size: 7
16675353 AGTTAACTCC
*
16675363 TAAACCT
1 TAAACCA
*
16675370 TAAACCC
1 TAAACCA
16675377 TAAACCA
1 TAAACCA
* * *
16675384 TATATCT
1 TAAACCA
16675391 TAAACCA
1 TAAACCA
16675398 TAGTTAACTCA
1 TA---AAC-CA
16675409 TAAACCA
1 TAAACCA
*
16675416 TAAACCC
1 TAAACCA
16675423 TAAACCA
1 TAAACCA
* *
16675430 TATA-TA
1 TAAACCA
16675436 TTAAACCA
1 -TAAACCA
16675444 TAAACCA
1 TAAACCA
*
16675451 TAAACTA
1 TAAACCA
16675458 TAA
1 TAA
16675461 TGATAATTAA
Statistics
Matches: 70, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
6 1 0.01
7 58 0.83
8 4 0.06
10 3 0.04
11 4 0.06
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (7 bp):
TAAACCA
Found at i:16675662 original size:41 final size:41
Alignment explanation
Indices: 16675617--16675777 Score: 268
Period size: 41 Copynumber: 3.9 Consensus size: 41
16675607 GTTATATGAC
*
16675617 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
16675658 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
* *
16675699 TTTTAGCGGCGCTTTGCCAAAAGCGCCACTAATGCTCTGGT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
* **
16675740 TTTTAGCGGCGTTTTTCCAAAAGCATCGCTAATGCTCT
1 TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCT
16675778 ATTTTTCACG
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.33
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTGCCAAAAGCGCCGCTAATGCTCTGGT
Found at i:16675817 original size:41 final size:40
Alignment explanation
Indices: 16675635--16675856 Score: 112
Period size: 41 Copynumber: 5.4 Consensus size: 40
16675625 GCGTTTTTCC
* * * **
16675635 AAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTT-TTGCC
1 AAAA-CGCCGCTATTGCTCT-ATTTTTAGCGGCATTCTTGGT
* * ** **
16675676 AAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGCT-TTGCC
1 AAAA-CGCCGCTATTGCTCT-ATTTTTAGCGGCATTCTTGGT
* * * * ***
16675717 AAAAGCGCCACTAATGCTCTGGTTTTTAGCGGCGTT-TTTCC
1 AAAA-CGCCGCTATTGCTCT-ATTTTTAGCGGCATTCTTGGT
* *
16675758 AAAA-GCATCGCTAATGCTCTATTTTTCA-CGGCATTTTTGGT
1 AAAACGC--CGCTATTGCTCTATTTTT-AGCGGCATTCTTGGT
* * *
16675799 AAAAACGCTGCTATTGCTCTATTTTTAGTGGCGTTCTTGGT
1 -AAAACGCCGCTATTGCTCTATTTTTAGCGGCATTCTTGGT
16675840 AAAACGCCGCTATTGCT
1 AAAACGCCGCTATTGCT
16675857 ATGTGTTTTA
Statistics
Matches: 158, Mismatches: 16, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.01
40 28 0.18
41 122 0.77
42 4 0.03
43 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (40 bp):
AAAACGCCGCTATTGCTCTATTTTTAGCGGCATTCTTGGT
Found at i:16675905 original size:12 final size:12
Alignment explanation
Indices: 16675890--16675915 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16675880 GTTTTTTGAT
16675890 AAAACGCCGCTA
1 AAAACGCCGCTA
16675902 AAAACGCCGCTA
1 AAAACGCCGCTA
16675914 AA
1 AA
16675916 GCCTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:16676540 original size:17 final size:17
Alignment explanation
Indices: 16676518--16676552 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16676508 GAAAAGAAGA
**
16676518 AAAAGAAGGTAAAGACG
1 AAAAGAAGAAAAAGACG
16676535 AAAAGAAGAAAAAGACG
1 AAAAGAAGAAAAAGACG
16676552 A
1 A
16676553 GGATATTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.26, T:0.03
Consensus pattern (17 bp):
AAAAGAAGAAAAAGACG
Found at i:16678153 original size:14 final size:15
Alignment explanation
Indices: 16678110--16678171 Score: 58
Period size: 14 Copynumber: 4.1 Consensus size: 15
16678100 TTAGATTTTA
16678110 ATTATAATATATATT-T
1 ATTATAAT-TA-ATTAT
*
16678126 ATTAGTAATAAATTAT
1 ATTA-TAATTAATTAT
16678142 ATTA-AATTAATT-T
1 ATTATAATTAATTAT
16678155 ATTATAATTATATTAT
1 ATTATAATTA-ATTAT
16678171 A
1 A
16678172 AGATATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.13
14 12 0.31
15 6 0.15
16 12 0.31
17 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTATAATTAATTAT
Found at i:16678297 original size:18 final size:19
Alignment explanation
Indices: 16678276--16678325 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 19
16678266 ATGTATTAGA
16678276 TATTAAATAA-ATATTTAT
1 TATTAAATAAGATATTTAT
16678294 TATTTTATAA-AAGATATTTAT
1 TA--TTA-AATAAGATATTTAT
16678315 TAATTAAATAA
1 T-ATTAAATAA
16678326 TTATATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 2 0.08
19 2 0.08
20 10 0.38
21 11 0.42
22 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTAAATAAGATATTTAT
Found at i:16680374 original size:13 final size:13
Alignment explanation
Indices: 16680358--16680389 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
16680348 ATAGTTTATT
16680358 AATAAAATAAAGA
1 AATAAAATAAAGA
16680371 AATAAAATAAAGA
1 AATAAAATAAAGA
16680384 AATAAA
1 AATAAA
16680390 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Done.