Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 21 of 172
Found at i:6680911 original size:28 final size:28
Alignment explanation
Indices: 6680866--6680921 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
6680856 AAAAAAGATA
*
6680866 AAAATATATAGTATAAATTAAAAATTTT
1 AAAATATATAGTAAAAATTAAAAATTTT
* *
6680894 AAAATATTATA-TAAAAATTGAAATTTTT
1 AAAATA-TATAGTAAAAATTAAAAATTTT
6680922 TTATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (28 bp):
AAAATATATAGTAAAAATTAAAAATTTT
Found at i:6681193 original size:20 final size:21
Alignment explanation
Indices: 6681168--6681257 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 21
6681158 AAATTTTGAA
6681168 TTTTATATAAT-TTTTAAATT
1 TTTTATATAATATTTTAAATT
* *
6681188 TTTTATACAATATTTT-TATT
1 TTTTATATAATATTTTAAATT
* *
6681208 TTTTAAATTTATATTTTAGAATT
1 TTTTATA-TAATATTTTA-AATT
* * *
6681231 TGTTAAAT-A-ATTTTGAATT
1 TTTTATATAATATTTTAAATT
*
6681250 ATTTATAT
1 TTTTATAT
6681258 TTTATATATG
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
19 9 0.16
20 24 0.44
21 12 0.22
22 1 0.02
23 9 0.16
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.61
Consensus pattern (21 bp):
TTTTATATAATATTTTAAATT
Found at i:6683082 original size:84 final size:83
Alignment explanation
Indices: 6682728--6684063 Score: 1070
Period size: 84 Copynumber: 16.0 Consensus size: 83
6682718 GGGAGGAAAG
* * * * * ** * * *
6682728 GTAATCAGAGTCCGGTTTTAGCTCTCCTATCATCCATTTATGTCATGGTGTCACTGAAAGTTAGG
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
*
6682793 CTTTGTATAAGCTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * *
6682812 GTTAATCCGAGTTCGGGTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGTTAG
1 G-TAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAG
*
6682875 ACTTTGTATAAGCTGCATTT
65 ACTTTGTA-GAGCTGCATTT
** * * * * * *
6682895 GTAATCCGAGTTCAAGTTCAGCTCTCATATAATAGATTTACGATATGGTGTCGTTCAAAGTTAAG
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTT-AG
*
6682960 ACTTTGTTTA-AGCTGTATTT
65 ACTTTG--TAGAGCTGCATTT
* * * * * *
6682980 GTGATCCGAGTTCTGGTTTAGCCCTCATTTGATAGATTTATGTTATTGAGTCGCTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
*
6683045 CATTGTAGAAGCTGCATTT
66 CTTTGTAG-AGCTGCATTT
* * * *
6683064 GTAATCTGAGTTCGGGTTTGGCTCTCATATGATATATTTATGTTATGGTGTCACTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
* *
6683129 CTTTGTATAAGCTGTATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * * *
6683148 GTAACCCAATTTCGGGTTCAGCTCTCATATAATAGATTTATGTTATGATGTCACTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
* *
6683213 CTTTGGACAAGCTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * *
6683232 GTAATCCAAGTTCGGGTTCAGCTCTCATATAATATATTTATGTTGTGGTGTCACTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
* *
6683297 CTTTGTATAAGTTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * *
6683316 GTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
*
6683381 CTTTGCATGAGCTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * * * * *
6683400 ATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
*
6683465 CTTTGCATGAGCTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * * * * *
6683484 ATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
*
6683549 CTTTGCATGAGCTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * * * * * *
6683568 ATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTTA-A
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
*
6683632 CCTTTGCATGAGCTGCATTT
66 -CTTTGTA-GAGCTGCATTT
* * * * * *
6683652 ATAA-CCTGAGTTCGGGCTTAGCTCT-AT-TGTAATAGATTTAT-ATATGGTTTTGCTGAATGTT
1 GTAATCC-GAGTTCGGGTTTAGCTCTCATATG--ATAGATTTATGTTATGGTGTCGCTGAAAGTT
* * *
6683713 AGACTTTTTATGAGTTGTATTT
63 AGACTTTGTA-GAGCTGCATTT
* * * * * *
6683735 GTAATCCGATTTCAGGTTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAAAGTTA
1 GTAATCCGAGTTCGGGTTTAGCTC-TCATATGATAGA-TTTATGTTATGGTGTCGCTGAAAGTTA
*
6683799 GACTTTGTGTGAGCTGCATTT
64 GACTTTGT-AGAGCTGCATTT
* * * * * *
6683820 GCAATCTGATTTTGGGATTAGCTCTCGA-ATCATAGATTTATGTTA---TG--G-TG-AAGTTAG
1 GTAATCCGAGTTCGGGTTTAGCTCTC-ATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAG
6683877 ACTTTGTATGAGCTGCATTT
65 ACTTTGTA-GAGCTGCATTT
* * * * *** * * * * ** * *
6683897 GTAATCTGAGTTTGGGTTCAGCCCTCATGCCATAGATTTGTCTTATGGTATCACTGCCACTTGGA
1 GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
6683962 CTTTGTATGAGCTGCATTT
66 CTTTGTA-GAGCTGCATTT
* * * * * * *
6683981 CTAA-CCTCAGTTCGGGTTTAGCTCTCAAATCATAGATTTATATTATGTTGTTGCTGAAAGTTAG
1 GTAATCC-GAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAG
*
6684045 ACTTTGTATGTGCTGCATT
65 ACTTTGTA-GAGCTGCATT
6684064 CGTACTAAGA
Statistics
Matches: 1066, Mismatches: 154, Indels: 64
0.83 0.12 0.05
Matches are distributed among these distances:
76 1 0.00
77 59 0.06
78 2 0.00
79 1 0.00
80 1 0.00
81 2 0.00
82 37 0.03
83 104 0.10
84 702 0.66
85 155 0.15
87 2 0.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (83 bp):
GTAATCCGAGTTCGGGTTTAGCTCTCATATGATAGATTTATGTTATGGTGTCGCTGAAAGTTAGA
CTTTGTAGAGCTGCATTT
Found at i:6683227 original size:168 final size:167
Alignment explanation
Indices: 6682744--6684063 Score: 1194
Period size: 168 Copynumber: 7.9 Consensus size: 167
6682734 AGAGTCCGGT
* * ** * *
6682744 TTTAGCTCTCCTATCATCCATTTATGTCATGGTGTCACTGAAAGTTAGGCTTTGTATAAGCTGCA
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * *
6682809 TTTGTTAATCCGAGTTCGGGTTCAGCTCTCATATAATAGA-TT-TGTTATGGTGTCACTGAAAGT
66 TTTG-TAACCCGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTAT-GTGTCGCTGAAAGT
* *
6682872 TAGACTTTGTATAAGCTGCATTTGTAATCCGAGTTCAAG
129 TAGACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
* * * * ** * * *
6682911 TTCAGCTCTCATATAATAGATTTACGATATGGTGTCGTTCAAAGTTAAGACTTTGTTTAAGCTGT
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTT-AGACTTTGTATAAGCTGC
* * * * * * *
6682976 ATTTGTGATCCGAGTTCTGGTTTAGCCCTCATTTGATAGATTTATGTTATTGAGTCGCTGAAAGT
65 ATTTGTAACCCGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTA-TGTGTCGCTGAAAGT
* * *
6683041 TAGACATTGTA-GAAGCTGCATTTGTAATCTGAGTTCGGG
129 TAGACTTTGTATG-AGCTGCATTTGTAATCCGAGTTCAGG
* * *
6683080 TTTGGCTCTCATATGATATATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGTA
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * * *
6683145 TTTGTAACCCAATTTCGGGTTCAGCTCTCATATAATAGATTTATGTTATGATGTCACTGAAAGTT
66 TTTGTAACCCGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATG-TGTCGCTGAAAGTT
* ** * *
6683210 AGACTTTGGACAAGCTGCATTTGTAATCCAAGTTCGGG
130 AGACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
* * * * *
6683248 TTCAGCTCTCATATAATATATTTATGTTGTGGTGTCACTGAAAGTTAGACTTTGTATAAGTTGCA
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * * * * * *
6683313 TTTGTAATCCAAGTTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTT
66 TTTGTAACCCGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTA-TGTGTCGCTGAAAGTT
* * * * *
6683378 AGACTTTGCATGAGCTGCATTTATAACCCAAATTCAGG
130 AGACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
* * * * * * *
6683416 TTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTTAGACTTTGCATGAGCTGCA
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * * * * * * *
6683481 TTTATAACCCAAATTCAGGTTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCGCTGAAAGTT
66 TTTGTAACCCGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTA-TGTGTCGCTGAAAGTT
* * * * *
6683546 AGACTTTGCATGAGCTGCATTTATAACCCAAATTCAGG
130 AGACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
* * * * * *
6683584 TTTAGCCCTCGTTTGATAGATTTATGTTATTGTGTCACTGAAAGTTA-ACCTTTGCATGAGCTGC
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGA-CTTTGTATAAGCTGC
* * * * * * * *
6683648 ATTTATAACCTGAGTTCGGGCTTAGCTCT-ATTGTAATAGATTTAT-ATATGGTTTTGCTGAATG
65 ATTTGTAACCCGAGTTCGGGTTTAGCTCTCA-TATAATAGATTTATGTTAT-GTGTCGCTGAAAG
* * * *
6683711 TTAGACTTTTTATGAGTTGTATTTGTAATCCGATTTCAGG
128 TTAGACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
* * * ** * *
6683751 TTTAGCTCTTGA-ATTATAGATTTTATGTTACGGTGTTGCTGAAAGTTAGACTTTGTGTGAGCTG
1 TTTAGCTC-TCATATGATAGA-TTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTG
* * * * * * *
6683815 CATTTGCAATCTGATTTTGGGATTAGCTCTCGA-ATCATAGATTTATGTTA--TG--G-TG-AAG
64 CATTTGTAACCCGAGTTCGGGTTTAGCTCTC-ATATAATAGATTTATGTTATGTGTCGCTGAAAG
* **
6683873 TTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGG
128 TTAGACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
* * *** * * * ** * * *
6683913 TTCAGCCCTCATGCCATAGATTTGTCTTATGGTATCACTGCCACTTGGACTTTGTATGAGCTGCA
1 TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
* * * * *
6683978 TTTCTAACCTC-AGTTCGGGTTTAGCTCTCAAATCATAGATTTATATTATGTTGTTGCTGAAAGT
66 TTTGTAACC-CGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATG-TGTCGCTGAAAGT
*
6684042 TAGACTTTGTATGTGCTGCATT
129 TAGACTTTGTATGAGCTGCATT
6684064 CGTACTAAGA
Statistics
Matches: 959, Mismatches: 167, Indels: 53
0.81 0.14 0.04
Matches are distributed among these distances:
160 1 0.00
161 73 0.08
162 46 0.05
163 2 0.00
164 3 0.00
166 3 0.00
167 126 0.13
168 611 0.64
169 92 0.10
170 2 0.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (167 bp):
TTTAGCTCTCATATGATAGATTTATGTTATGGTGTCACTGAAAGTTAGACTTTGTATAAGCTGCA
TTTGTAACCCGAGTTCGGGTTTAGCTCTCATATAATAGATTTATGTTATGTGTCGCTGAAAGTTA
GACTTTGTATGAGCTGCATTTGTAATCCGAGTTCAGG
Found at i:6683931 original size:77 final size:76
Alignment explanation
Indices: 6683793--6683945 Score: 202
Period size: 77 Copynumber: 2.0 Consensus size: 76
6683783 GTGTTGCTGA
* * *
6683793 AAGTTAGACTTTGTGTGAGCTGCATTTGCAATCTGATTTTGGGATTAGCTCTCGAATCATAGATT
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATTAGCCCTC-AATCATAGATT
*
6683858 TATGTTATGGTG
65 TATCTTATGGTG
*
6683870 AAGTTAGACTTTGTATGAGCTGCATTTGTAATCTGAGTTTGGG-TTCAGCCCTC-ATGCCATAGA
1 AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATT-AGCCCTCAAT--CATAGA
*
6683933 TTTGTCTTATGGT
63 TTTATCTTATGGT
6683946 ATCACTGCCA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
75 2 0.03
76 2 0.03
77 63 0.94
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (76 bp):
AAGTTAGACTTTGTATGAGCTGCATTTGCAATCTGAGTTTGGGATTAGCCCTCAATCATAGATTT
ATCTTATGGTG
Found at i:6689948 original size:23 final size:22
Alignment explanation
Indices: 6689922--6689972 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
6689912 AATATGAATT
*
6689922 AAATTAATATTT-TTAATAAATAA
1 AAATTAA-ATTTCTAAAT-AATAA
6689945 AAATTTAAATTTCTAAATAATAA
1 AAA-TTAAATTTCTAAATAATAA
6689968 AAATT
1 AAATT
6689973 TTGAAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 15 0.60
24 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTAAATTTCTAAATAATAA
Found at i:6690379 original size:17 final size:18
Alignment explanation
Indices: 6690351--6690384 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
6690341 TTAAAAATAA
6690351 TTTAACAATAATAAATTT
1 TTTAACAATAATAAATTT
*
6690369 TTTAA-AATAATTAATT
1 TTTAACAATAATAAATT
6690385 CGATTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAACAATAATAAATTT
Found at i:6694537 original size:28 final size:26
Alignment explanation
Indices: 6694506--6694568 Score: 63
Period size: 26 Copynumber: 2.3 Consensus size: 26
6694496 TATTTTTTCA
*
6694506 ATTTTTAAATAATACTTTTAATTTATAT
1 ATTTTTAAATAATAATTTT--TTTATAT
* * **
6694534 ATTTCTAATTTCTAATTTTTTTATAT
1 ATTTTTAAATAATAATTTTTTTATAT
6694560 ATTTTTAAA
1 ATTTTTAAA
6694569 AGTTTTGTGC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 14 0.50
28 14 0.50
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTTTTAAATAATAATTTTTTTATAT
Found at i:6694601 original size:19 final size:19
Alignment explanation
Indices: 6694579--6694615 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6694569 AGTTTTGTGC
6694579 ATTTT-TTATTTCTATATAG
1 ATTTTATTATTT-TATATAG
6694598 ATTTTATTATTTTATATA
1 ATTTTATTATTTTATATA
6694616 TTTTTATTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
ATTTTATTATTTTATATAG
Found at i:6697551 original size:42 final size:42
Alignment explanation
Indices: 6697492--6697575 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
6697482 CTTGCCTAAA
6697492 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
1 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
6697534 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
1 TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
6697576 ACTTTAGTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.45
Consensus pattern (42 bp):
TATTTCCTAAGGGTTGCCAATCCTAAGTTTTTATGTTCTTAC
Found at i:6701395 original size:38 final size:38
Alignment explanation
Indices: 6701314--6701466 Score: 164
Period size: 38 Copynumber: 4.1 Consensus size: 38
6701304 TTCAGGCTAT
** ** * **
6701314 GTGCCTAGTAGGCTTTGTATCGGTGAT-TTCGGGCTAT
1 GTGCCTAACAGGCTTTGTGCCGGTGATATTCGAGCTCC
* * *
6701351 GTGCCTAGCAGGCTTTATGCCGGTAATATTCGAGCTCC
1 GTGCCTAACAGGCTTTGTGCCGGTGATATTCGAGCTCC
* * * *
6701389 GTGCCTAACAGACTTTGTACCAGTGATATTCGACCTCC
1 GTGCCTAACAGGCTTTGTGCCGGTGATATTCGAGCTCC
*
6701427 GTGCCTAACAGGCTTTGTGCCGGTGATATTCGGGCTCC
1 GTGCCTAACAGGCTTTGTGCCGGTGATATTCGAGCTCC
6701465 GT
1 GT
6701467 ACCGGTGATA
Statistics
Matches: 95, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
37 22 0.23
38 73 0.77
ACGTcount: A:0.17, C:0.24, G:0.27, T:0.31
Consensus pattern (38 bp):
GTGCCTAACAGGCTTTGTGCCGGTGATATTCGAGCTCC
Found at i:6701471 original size:22 final size:22
Alignment explanation
Indices: 6701446--6701491 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
6701436 AGGCTTTGTG
*
6701446 CCGGTGATATTCGGGCTCCGTA
1 CCGGTGATATTCAGGCTCCGTA
*
6701468 CCGGTGATATTCAGGCTCTGTA
1 CCGGTGATATTCAGGCTCCGTA
6701490 CC
1 CC
6701492 TAACAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.28
Consensus pattern (22 bp):
CCGGTGATATTCAGGCTCCGTA
Found at i:6701573 original size:25 final size:25
Alignment explanation
Indices: 6701536--6701624 Score: 124
Period size: 25 Copynumber: 3.5 Consensus size: 25
6701526 TTGTGCCTAG
*
6701536 CAGGCTTCATGCCAGTGTACTATAT
1 CAGGCTTCGTGCCAGTGTACTATAT
*
6701561 CAGGCTTTGTGCCAGTGTACTATAT
1 CAGGCTTCGTGCCAGTGTACTATAT
**
6701586 CAGGCTTCGTGTGAGTGTACTATTAT
1 CAGGCTTCGTGCCAGTGTACTA-TAT
*
6701612 CAGGCTTGGTGCC
1 CAGGCTTCGTGCC
6701625 TAGTAGGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
25 42 0.76
26 13 0.24
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (25 bp):
CAGGCTTCGTGCCAGTGTACTATAT
Found at i:6715728 original size:27 final size:27
Alignment explanation
Indices: 6715695--6715818 Score: 185
Period size: 27 Copynumber: 4.6 Consensus size: 27
6715685 TAAATTGTGC
6715695 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
6715722 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGT
* *
6715749 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-ATTGACTATGT
* * *
6715777 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACTATGT
*
6715804 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6715819 GACTTAATAT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 66 0.73
28 25 0.27
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAATTGACTATGT
Found at i:6715787 original size:55 final size:54
Alignment explanation
Indices: 6715695--6715818 Score: 185
Period size: 55 Copynumber: 2.3 Consensus size: 54
6715685 TAAATTGTGC
*
6715695 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATAT
* * * *
6715749 AGCACTAAGTGTGCGAGTTTGATTATGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-ATTGACTATGTAGCACTAAGTGTGCGAATTGACTATAT
*
6715804 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
6715819 GACTTAATAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 16 0.25
55 47 0.75
ACGTcount: A:0.27, C:0.14, G:0.28, T:0.31
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAATTGACTATAT
Found at i:6720808 original size:48 final size:50
Alignment explanation
Indices: 6720734--6720869 Score: 168
Period size: 48 Copynumber: 2.8 Consensus size: 50
6720724 TCATTACGGG
* * *
6720734 ATACATTGATTTGACTTCGGGCCATGATATTGGCACTTCCGGTGCGAGCT
1 ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCCGGTGCAAGAT
* *
6720784 -T-CATTGATTTGGCTTCGGGCCATGATATTAGCACTTCGGGTGCAAGAT
1 ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCCGGTGCAAGAT
* * * * *
6720832 ATATATTAAGTTGGCTTCGAGCCATAATATTGGCACTT
1 ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTT
6720870 AGTGTGTGAG
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
48 42 0.58
49 2 0.03
50 29 0.40
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (50 bp):
ATACATTGATTTGGCTTCGGGCCATGATATTGGCACTTCCGGTGCAAGAT
Found at i:6750420 original size:105 final size:105
Alignment explanation
Indices: 6750233--6750553 Score: 633
Period size: 105 Copynumber: 3.1 Consensus size: 105
6750223 GAAGAACTAG
*
6750233 AGTGACATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
1 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
6750298 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
66 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
6750338 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
1 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
6750403 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
66 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
6750443 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
1 AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
6750508 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
66 AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
6750548 AGTGGC
1 AGTGGC
6750554 CTCAACAATT
Statistics
Matches: 215, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 215 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (105 bp):
AGTGGCATAGATCAGTAAGCATTCAAATGATGTTCTAAGAAGTTTGAAGCTAAAAACCAAAGGCA
AAAAAATTCGGTGAATGTATCTGAGAGGTCTCTCTATTAT
Found at i:6754274 original size:19 final size:19
Alignment explanation
Indices: 6754231--6754267 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6754221 ATTTTCAATT
6754231 TTTTATATTTTTTAATTATA
1 TTTT-TATTTTTTAATTATA
6754251 TTTTTATTTTTT-ATTAT
1 TTTTTATTTTTTAATTAT
6754268 TGTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTTTTTAATTATA
Found at i:6757991 original size:12 final size:12
Alignment explanation
Indices: 6757976--6758019 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
6757966 TTAAGGTTGG
6757976 AATTAAAAATAA
1 AATTAAAAATAA
6757988 AATTAAAAATTAA
1 AATTAAAAA-TAA
* *
6758001 AAATAAAATTTAA
1 AATTAAAA-ATAA
6758014 AATTAA
1 AATTAA
6758020 GGGATCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTAAAAATAA
Found at i:6757998 original size:7 final size:7
Alignment explanation
Indices: 6757976--6758019 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
6757966 TTAAGGTTGG
6757976 AATTAAA
1 AATTAAA
6757983 AA-T-AA
1 AATTAAA
6757988 AATTAAA
1 AATTAAA
6757995 AATTAAA
1 AATTAAA
6758002 AA-T-AA
1 AATTAAA
*
6758007 AATTTAA
1 AATTAAA
6758014 AATTAA
1 AATTAA
6758020 GGGATCTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
5 8 0.25
6 4 0.12
7 20 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AATTAAA
Found at i:6758000 original size:19 final size:19
Alignment explanation
Indices: 6757976--6758019 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
6757966 TTAAGGTTGG
6757976 AATTAAAAATAAAATTAAA
1 AATTAAAAATAAAATTAAA
*
6757995 AATTAAAAATAAAATTTAA
1 AATTAAAAATAAAATTAAA
6758014 AATTAA
1 AATTAA
6758020 GGGATCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATTAAAAATAAAATTAAA
Found at i:6766002 original size:12 final size:12
Alignment explanation
Indices: 6765985--6766062 Score: 86
Period size: 12 Copynumber: 6.2 Consensus size: 12
6765975 GCTTAAGTTT
6765985 TTCTTCTTCCTC
1 TTCTTCTTCCTC
6765997 TTCTTCTT-CTGC
1 TTCTTCTTCCT-C
*
6766009 TTCTGCTTCTGCTTC
1 TTCTTCTTC--C-TC
6766024 TTCTTCTTCCTC
1 TTCTTCTTCCTC
*
6766036 TTCCTCTTCCTC
1 TTCTTCTTCCTC
*
6766048 TTCCTCTTCCTC
1 TTCTTCTTCCTC
6766060 TTC
1 TTC
6766063 GGATTCTCCA
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
11 2 0.03
12 44 0.76
13 1 0.02
15 10 0.17
16 1 0.02
ACGTcount: A:0.00, C:0.41, G:0.04, T:0.55
Consensus pattern (12 bp):
TTCTTCTTCCTC
Found at i:6766004 original size:6 final size:6
Alignment explanation
Indices: 6765985--6766062 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
6765975 GCTTAAGTTT
* * * *
6765985 TTCTTC TTCCTC TTCTTC TTCTGC TTCTGC TTCTGC TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
* * * * *
6766033 CTCTTC CTCTTC CTCTTC CTCTTC CTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC
6766063 GGATTCTCCA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.00, C:0.41, G:0.04, T:0.55
Consensus pattern (6 bp):
TTCTTC
Found at i:6766011 original size:18 final size:18
Alignment explanation
Indices: 6765985--6766062 Score: 86
Period size: 18 Copynumber: 4.2 Consensus size: 18
6765975 GCTTAAGTTT
*
6765985 TTCTTCTTCCTCTTCTTC
1 TTCTTCTTCCTCTTCCTC
*
6766003 TTCTGCTT-CTGCTTCTGCTTC
1 TTCTTCTTCCT-CTTC--C-TC
6766024 TTCTTCTTCCTCTTCCTC
1 TTCTTCTTCCTCTTCCTC
*
6766042 TTCCTCTTCCTCTTCCTC
1 TTCTTCTTCCTCTTCCTC
6766060 TTC
1 TTC
6766063 GGATTCTCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
17 2 0.04
18 33 0.65
19 1 0.02
21 13 0.25
22 2 0.04
ACGTcount: A:0.00, C:0.41, G:0.04, T:0.55
Consensus pattern (18 bp):
TTCTTCTTCCTCTTCCTC
Found at i:6776710 original size:5 final size:6
Alignment explanation
Indices: 6776694--6776720 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6776684 AAAGCTCACC
6776694 ATTTTT ATTTTT ATTTTT ATTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATT
6776721 CTCTGCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:6777649 original size:3 final size:3
Alignment explanation
Indices: 6777643--6777672 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6777633 GGCGGAGGTA
*
6777643 TGG TGG TGC TGG TGG TGG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
6777673 CAGGCCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.63, T:0.33
Consensus pattern (3 bp):
TGG
Found at i:6778809 original size:19 final size:20
Alignment explanation
Indices: 6778785--6778834 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
6778775 AAATATAAAT
*
6778785 TTTGGAATTTTTAT-AATTA
1 TTTGGAATTTTTATAAATCA
*
6778804 TTTGG-ATTTTAATAAATCA
1 TTTGGAATTTTTATAAATCA
*
6778823 TTTTGAATTTTT
1 TTTGGAATTTTT
6778835 TTTAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (20 bp):
TTTGGAATTTTTATAAATCA
Found at i:6778832 original size:20 final size:19
Alignment explanation
Indices: 6778783--6778833 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
6778773 TTAAATATAA
* *
6778783 ATTTTGGAATTTTTATAATT
1 ATTTT-GAATTTTAATAATC
*
6778803 A-TTTGGATTTTAATAAATC
1 ATTTTGAATTTTAAT-AATC
6778822 ATTTTGAATTTT
1 ATTTTGAATTTT
6778834 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.32
19 7 0.28
20 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
ATTTTGAATTTTAATAATC
Found at i:6780281 original size:12 final size:12
Alignment explanation
Indices: 6780264--6780295 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
6780254 TCATCTATAC
6780264 TTGAAATTGCTT
1 TTGAAATTGCTT
6780276 TTGAAATTGCTT
1 TTGAAATTGCTT
6780288 TTGAAATT
1 TTGAAATT
6780296 TAAGATGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.50
Consensus pattern (12 bp):
TTGAAATTGCTT
Found at i:6781154 original size:18 final size:18
Alignment explanation
Indices: 6781119--6781154 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6781109 GTTTGTGATG
* *
6781119 TTTTATATTATGTTATTT
1 TTTTATATTATATAATTT
6781137 TTTTATATTATATAATTT
1 TTTTATATTATATAATTT
6781155 ATAACACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTATATTATATAATTT
Found at i:6781264 original size:30 final size:27
Alignment explanation
Indices: 6781207--6781274 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
6781197 TAATATGGCT
*
6781207 ATATATAAAATTTTAATAAATTAAAAAA
1 ATATATAAATTTTTAATAAATT-AAAAA
6781235 ATATATAAATTTATTAAATCAAATT-AAAA
1 ATATATAAATTT-TT-AAT-AAATTAAAAA
6781264 ATAATATAAAT
1 AT-ATATAAAT
6781275 ATAATTTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
28 11 0.31
29 8 0.23
30 11 0.31
31 5 0.14
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (27 bp):
ATATATAAATTTTTAATAAATTAAAAA
Found at i:6781868 original size:28 final size:28
Alignment explanation
Indices: 6781836--6781892 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
6781826 TACAAATGTG
*
6781836 TTAAAATTATTAATTAAAAATAAAAAAA
1 TTAAAATCATTAATTAAAAATAAAAAAA
6781864 TTAAAATCATTAATTAAAAATAAAAAAA
1 TTAAAATCATTAATTAAAAATAAAAAAA
6781892 T
1 T
6781893 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (28 bp):
TTAAAATCATTAATTAAAAATAAAAAAA
Found at i:6782228 original size:13 final size:13
Alignment explanation
Indices: 6782212--6782249 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
6782202 TTTAAACTAA
6782212 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
6782225 ACTTTCTCATAA-C
1 ACTTT-TCAAAAGC
6782238 ACTTTTCAAAAG
1 ACTTTTCAAAAG
6782250 TATTGCCCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:6782952 original size:25 final size:24
Alignment explanation
Indices: 6782868--6782965 Score: 69
Period size: 26 Copynumber: 4.0 Consensus size: 24
6782858 TATTAAATAT
* *
6782868 ATATAAACCTTAAAATAATTATAAAA
1 ATATAAA--TTAAAATAAATAAAAAA
6782894 ATA-AAA-T-AAATAAAT-AAAAA
1 ATATAAATTAAAATAAATAAAAAA
* *
6782914 ATCTTAAAAATAAAATAAATAAAAAA
1 AT-AT-AAATTAAAATAAATAAAAAA
*
6782940 ATATATAATTAAATATTAATAAAAAA
1 ATATA-AATTAAA-ATAAATAAAAAA
6782966 GAAAAATCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
20 6 0.10
21 7 0.12
22 1 0.02
23 3 0.05
24 2 0.03
25 18 0.31
26 21 0.36
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
ATATAAATTAAAATAAATAAAAAA
Found at i:6782954 original size:29 final size:28
Alignment explanation
Indices: 6782879--6782947 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
6782869 TATAAACCTT
*
6782879 AAAATAATTATAAAAATAAAATAAATAAA
1 AAAAT-ATCATAAAAATAAAATAAATAAA
* *
6782908 TAAAAAATCTTAAAAATAAAATAAATAAA
1 -AAAATATCATAAAAATAAAATAAATAAA
6782937 AAAATAT-ATAA
1 AAAATATCATAA
6782948 TTAAATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 3 0.09
28 6 0.18
29 21 0.62
30 4 0.12
ACGTcount: A:0.74, C:0.01, G:0.00, T:0.25
Consensus pattern (28 bp):
AAAATATCATAAAAATAAAATAAATAAA
Found at i:6795170 original size:16 final size:17
Alignment explanation
Indices: 6795149--6795184 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
6795139 TTATGCTTAA
*
6795149 TTAATAATTT-TTATTT
1 TTAATAATTTATTAATT
6795165 TTAATAATTTATTAATT
1 TTAATAATTTATTAATT
6795182 TTA
1 TTA
6795185 TTTTAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATAATTTATTAATT
Found at i:6798043 original size:13 final size:14
Alignment explanation
Indices: 6798029--6798083 Score: 60
Period size: 14 Copynumber: 4.1 Consensus size: 14
6798019 GTACCCTTCT
*
6798029 ACGA-TACCTTCCT
1 ACGAGTACCTTCCC
*
6798042 ACGAGTACCCTCCC
1 ACGAGTACCTTCCC
*
6798056 ATGAGTACCTTCCC
1 ACGAGTACCTTCCC
*
6798070 ACGACTACC-TCCC
1 ACGAGTACCTTCCC
6798083 A
1 A
6798084 AAGTACCCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.24, C:0.44, G:0.11, T:0.22
Consensus pattern (14 bp):
ACGAGTACCTTCCC
Found at i:6798093 original size:27 final size:28
Alignment explanation
Indices: 6798033--6798095 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
6798023 CCTTCTACGA
* * *
6798033 TACCTTCCTACGAGTACCCTCCCATGAG
1 TACCTTCCCACGACTACCCTCCCATAAG
6798061 TACCTTCCCACGACTA-CCTCCCA-AAG
1 TACCTTCCCACGACTACCCTCCCATAAG
6798087 TACCCTTCC
1 TA-CCTTCC
6798096 ACGGAACCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 13 0.42
28 14 0.45
ACGTcount: A:0.22, C:0.44, G:0.10, T:0.24
Consensus pattern (28 bp):
TACCTTCCCACGACTACCCTCCCATAAG
Found at i:6801995 original size:26 final size:26
Alignment explanation
Indices: 6801959--6802010 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
6801949 TAAACTAGAC
6801959 TGCCTGTATATCTGTTTCAAATATAT
1 TGCCTGTATATCTGTTTCAAATATAT
6801985 TGCCTGTATATCTGTTTCAAATATAT
1 TGCCTGTATATCTGTTTCAAATATAT
6802011 CTTTGAGTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (26 bp):
TGCCTGTATATCTGTTTCAAATATAT
Found at i:6809477 original size:16 final size:16
Alignment explanation
Indices: 6809456--6809488 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
6809446 ACATGGATAT
6809456 GTTCAAAATTTTAAGA
1 GTTCAAAATTTTAAGA
6809472 GTTCAAAATTTTAAGA
1 GTTCAAAATTTTAAGA
6809488 G
1 G
6809489 ACGTCTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (16 bp):
GTTCAAAATTTTAAGA
Found at i:6812240 original size:77 final size:76
Alignment explanation
Indices: 6812137--6812286 Score: 203
Period size: 77 Copynumber: 2.0 Consensus size: 76
6812127 GCTAGTCTTC
* * * * *
6812137 AAGAAACTCGATAATGATTCTGATACTCAAGCAACTGGCAGTCAAGAAGCTTTATCTCAGACTGT
1 AAGAAACTCGACAATGATTCTGATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACTGT
6812202 CTGAAAGTTGG
66 CTGAAAGTTGG
** *
6812213 AAGAAACTCAGACAATGATT-TGGATACTTGAGCAACCGGCAGTCGAGAAGCTTCATCACAAACT
1 AAGAAACTC-GACAATGATTCT-GATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACT
6812277 GTCTGAAAGT
64 GTCTGAAAGT
6812287 GAATAACTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
76 10 0.16
77 54 0.84
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (76 bp):
AAGAAACTCGACAATGATTCTGATACTCAAGCAACCGGCAGTCAAGAAGCTTCATCACAAACTGT
CTGAAAGTTGG
Found at i:6813083 original size:31 final size:31
Alignment explanation
Indices: 6813045--6813103 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
6813035 TGGACAAAAA
6813045 AATTCAAACCCTAATATGA-AAATAATTACCT
1 AATTCAAACCCTAATATGAGAAA-AATTACCT
* *
6813076 AATTCAAACCTTAATGTGAGAAAAATTA
1 AATTCAAACCCTAATATGAGAAAAATTA
6813104 TTAAATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (31 bp):
AATTCAAACCCTAATATGAGAAAAATTACCT
Found at i:6813265 original size:10 final size:10
Alignment explanation
Indices: 6813250--6813279 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6813240 TGCCTTTGTG
6813250 ATAAAATTTT
1 ATAAAATTTT
6813260 ATAAAATTTT
1 ATAAAATTTT
6813270 A-AAAATTTT
1 ATAAAATTTT
6813279 A
1 A
6813280 ACCCTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
ATAAAATTTT
Found at i:6817197 original size:27 final size:27
Alignment explanation
Indices: 6817167--6817228 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
6817157 GAAAAGATGA
6817167 AGAATCAAAGGAAGTAAAGGAAGGAGT
1 AGAATCAAAGGAAGTAAAGGAAGGAGT
6817194 AGAATCAAAGGAAGTAAAGGAAGGAGT
1 AGAATCAAAGGAAGTAAAGGAAGGAGT
*
6817221 AGCATCAA
1 AGAATCAA
6817229 TAGCATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.52, C:0.06, G:0.31, T:0.11
Consensus pattern (27 bp):
AGAATCAAAGGAAGTAAAGGAAGGAGT
Found at i:6817649 original size:28 final size:29
Alignment explanation
Indices: 6817605--6817659 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
6817595 TCTAAGAAGG
*
6817605 TGAATCAATTGGTTCC-TCTACTATTACA
1 TGAATCAATTAGTTCCTTCTACTATTACA
*
6817633 TGAATCAATTTAG-TCCTTTTACTATTA
1 TGAATCAA-TTAGTTCCTTCTACTATTA
6817660 AAAGGAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (29 bp):
TGAATCAATTAGTTCCTTCTACTATTACA
Found at i:6818397 original size:2 final size:2
Alignment explanation
Indices: 6818390--6818426 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6818380 TTCCACAAAA
6818390 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
6818427 ACACACACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:6827536 original size:18 final size:20
Alignment explanation
Indices: 6827513--6827556 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
6827503 AATTCTTTTT
*
6827513 TTTTGCT-ATTTT-TTACTA
1 TTTTGCTCATTTTCTCACTA
6827531 TTTTGCTGCATTTTCTCACTA
1 TTTTGCT-CATTTTCTCACTA
6827552 TTTTG
1 TTTTG
6827557 TTACCATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.14, C:0.16, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTTGCTCATTTTCTCACTA
Found at i:6829476 original size:25 final size:25
Alignment explanation
Indices: 6829444--6829599 Score: 120
Period size: 25 Copynumber: 6.3 Consensus size: 25
6829434 GCCCTCTCTT
6829444 GAGCCATATAATAGGAAGCTCATCA
1 GAGCCATATAATAGGAAGCTCATCA
* *
6829469 GAGCCATATAATAGGAAGCTTATCC
1 GAGCCATATAATAGGAAGCTCATCA
* ** * *
6829494 GAGCTATATAACGGGAAGCTTATAA
1 GAGCCATATAATAGGAAGCTCATCA
* * ***
6829519 GAGCCATA-ATTGGGAAGCTCAAGT
1 GAGCCATATAATAGGAAGCTCATCA
* *
6829543 GAGCCATA-AATAGGAAGCTTATCC
1 GAGCCATATAATAGGAAGCTCATCA
* ** *
6829567 GGGTTATATAAT-GAGAAGCTCATAA
1 GAGCCATATAATAG-GAAGCTCATCA
6829592 GAGCCATA
1 GAGCCATA
6829600 ATTGGGAAGT
Statistics
Matches: 100, Mismatches: 29, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
24 34 0.34
25 66 0.66
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (25 bp):
GAGCCATATAATAGGAAGCTCATCA
Found at i:6829562 original size:73 final size:74
Alignment explanation
Indices: 6829469--6829634 Score: 237
Period size: 73 Copynumber: 2.3 Consensus size: 74
6829459 AAGCTCATCA
* *
6829469 GAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGGGAAGCTTATAAGAGCCATAATTGGGA
1 GAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGAGAAGCTCATAAGAGCCATAATTGGGA
6829534 AGCTCAAGT
66 AGCTCAAGT
* * *
6829543 GAGCCATA-AATAGGAAGCTTATCCGGGTTATATAATGAGAAGCTCATAAGAGCCATAATTGGGA
1 GAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGAGAAGCTCATAAGAGCCATAATTGGGA
* *
6829607 AGTTCATGT
66 AGCTCAAGT
* *
6829616 GAGCCA-ATAACAGGTAGCT
1 GAGCCATATAATAGGAAGCT
6829635 CCAAAGAGCC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
72 1 0.01
73 73 0.89
74 8 0.10
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (74 bp):
GAGCCATATAATAGGAAGCTTATCCGAGCTATATAACGAGAAGCTCATAAGAGCCATAATTGGGA
AGCTCAAGT
Found at i:6829748 original size:26 final size:26
Alignment explanation
Indices: 6829719--6829769 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
6829709 TGGAGAACCA
6829719 TTAATCAGGAAGCTCACAAAGAGCCT
1 TTAATCAGGAAGCTCACAAAGAGCCT
* **
6829745 TTAATCGGGAAGCTCATGAAGAGCC
1 TTAATCAGGAAGCTCACAAAGAGCC
6829770 ATATAACGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (26 bp):
TTAATCAGGAAGCTCACAAAGAGCCT
Found at i:6830730 original size:16 final size:16
Alignment explanation
Indices: 6830711--6830743 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6830701 TTTGTTTACG
6830711 TTATTTT-TCCCATTTT
1 TTATTTTAT-CCATTTT
6830727 TTATTTTATCCATTTT
1 TTATTTTATCCATTTT
6830743 T
1 T
6830744 CTTTTGTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTATCCATTTT
Found at i:6832220 original size:34 final size:34
Alignment explanation
Indices: 6832097--6832215 Score: 114
Period size: 34 Copynumber: 3.5 Consensus size: 34
6832087 TTCTGATATG
* * * **
6832097 ATATAACATTTTGATATATTATATGTTTCTAAAA
1 ATATGACATTCTGATATAGTATATGTTTCTGGAA
* *
6832131 ATATGACATTCTAATCTAGTATATGTTTCTGGAA
1 ATATGACATTCTGATATAGTATATGTTTCTGGAA
* * * *
6832165 ATATGACATTTTGGT-TTGATATATGTTTCTGGTA
1 ATATGACATTCTGATATAG-TATATGTTTCTGGAA
*
6832199 ATCTGACATTCTGATAT
1 ATATGACATTCTGATAT
6832216 GATATTGTAT
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
33 2 0.03
34 65 0.96
35 1 0.01
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.45
Consensus pattern (34 bp):
ATATGACATTCTGATATAGTATATGTTTCTGGAA
Found at i:6840215 original size:15 final size:15
Alignment explanation
Indices: 6840195--6840260 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 15
6840185 ACTGCAAAAA
6840195 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
6840210 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
6840229 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
6840244 ATTCA-TATTAA-AT
1 ATTTATTATTAATAT
6840257 ATTT
1 ATTT
6840261 TCAATAATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 6 0.14
15 13 0.31
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:6840307 original size:16 final size:16
Alignment explanation
Indices: 6840279--6840315 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
6840269 ATGTGAAGAA
6840279 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
6840295 TATT-TTTACAAATTAT
1 TATTATTTA-AAATTAT
6840311 TATTA
1 TATTA
6840316 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:6841931 original size:13 final size:13
Alignment explanation
Indices: 6841913--6841937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6841903 ATTTCACAAG
6841913 ATAAAAATAAAAA
1 ATAAAAATAAAAA
6841926 ATAAAAATAAAA
1 ATAAAAATAAAA
6841938 CCCCCTAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
ATAAAAATAAAAA
Found at i:6844209 original size:6 final size:6
Alignment explanation
Indices: 6844198--6844233 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
6844188 ATAAGACGCA
* *
6844198 ATATGT ATATGT ATATGT ATATGT ACATGT ACATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
6844234 TTTTGTATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (6 bp):
ATATGT
Found at i:6844904 original size:7 final size:7
Alignment explanation
Indices: 6844892--6844924 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
6844882 ATTTCCGATC
6844892 GGCAAAT
1 GGCAAAT
6844899 GGCAAAT
1 GGCAAAT
6844906 GGCAAAT
1 GGCAAAT
6844913 GGCAAAT
1 GGCAAAT
6844920 GGCAA
1 GGCAA
6844925 TGAGGGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.30, T:0.12
Consensus pattern (7 bp):
GGCAAAT
Found at i:6845173 original size:34 final size:34
Alignment explanation
Indices: 6845130--6845199 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
6845120 TGACCTTTGT
*
6845130 TACACTCTTTGAAGATGAAGGATGAACGTATATA
1 TACACTCTTTGAAGATGAAGGATGAACATATATA
6845164 TACACTCTTTGAAGATGAAGGATGAACATATATA
1 TACACTCTTTGAAGATGAAGGATGAACATATATA
6845198 TA
1 TA
6845200 TATACACATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (34 bp):
TACACTCTTTGAAGATGAAGGATGAACATATATA
Found at i:6845210 original size:6 final size:6
Alignment explanation
Indices: 6845201--6845243 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
6845191 ATATATATAT
6845201 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC A
1 ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC ATACAC A
6845244 GGGACCTTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.51, C:0.33, G:0.00, T:0.16
Consensus pattern (6 bp):
ATACAC
Found at i:6848587 original size:21 final size:21
Alignment explanation
Indices: 6848561--6848621 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
6848551 CAACACAAGG
*
6848561 TTGTGTGTTGCAACACAGACA
1 TTGTGTGTTGCAACACACACA
* **
6848582 TTGTGTGTCGCATGACACACA
1 TTGTGTGTTGCAACACACACA
6848603 TTGTGTGTCATGCAACACA
1 TTGTGTGT--TGCAACACA
6848622 AGGCATTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 25 0.81
23 6 0.19
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGTGTGTTGCAACACACACA
Found at i:6853152 original size:168 final size:168
Alignment explanation
Indices: 6852863--6853206 Score: 616
Period size: 168 Copynumber: 2.0 Consensus size: 168
6852853 CCTAGAACAT
6852863 GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
1 GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
6852928 AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATAATGACATCATAGTCAGAGAGT
66 AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATAATGACATCATAGTCAGAGAGT
6852993 TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
131 TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
* **
6853031 GGGCGTGTGCCTAGGCCGTGTGAAGTCTGCACCTGATTTTAGAATTTAATTCACCACACGGCCTA
1 GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
* * **
6853096 AGCACACGAGTGTGTGATTTGGCCGTGTGACCTTATTTTGGATGATGAGGTCATAGTCAGAGAGT
66 AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATAATGACATCATAGTCAGAGAGT
*
6853161 TACACGGGTTGAGGACACGGGCGTGTCCCAAACCACAC
131 TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
6853199 GGGCGTGT
1 GGGCGTGT
6853207 ATGACCACAC
Statistics
Matches: 168, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (168 bp):
GGGCGTGTGCCTAGGCCGTGTGAAGTCTACACCAAATTTTAGAATTTAATTCACCACACGGCCTA
AGCACACGAGTGTGTGATTTGGCCGTATGACCTTATTTTGGATAATGACATCATAGTCAGAGAGT
TACACGGGTTGAGGACACGAGCGTGTCCCAAACCACAC
Found at i:6854167 original size:11 final size:11
Alignment explanation
Indices: 6854154--6854208 Score: 67
Period size: 11 Copynumber: 5.1 Consensus size: 11
6854144 GACAAAAAGT
* *
6854154 AGCAGCAAAAT
1 AGCACCAAAAC
6854165 AGCACCAAAAC
1 AGCACCAAAAC
*
6854176 AGCAGCAAAAC
1 AGCACCAAAAC
6854187 AGCACC-AAAC
1 AGCACCAAAAC
*
6854197 AGCAACAAAAC
1 AGCACCAAAAC
6854208 A
1 A
6854209 ACACAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
10 9 0.24
11 29 0.76
ACGTcount: A:0.56, C:0.29, G:0.13, T:0.02
Consensus pattern (11 bp):
AGCACCAAAAC
Found at i:6854198 original size:21 final size:22
Alignment explanation
Indices: 6854154--6854217 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
6854144 GACAAAAAGT
*
6854154 AGCAGCAAAATAGCACCAAAAC
1 AGCAGCAAAACAGCACCAAAAC
6854176 AGCAGCAAAACAGCACC-AAAC
1 AGCAGCAAAACAGCACCAAAAC
* * *
6854197 AGCAACAAAACAACACAAAAA
1 AGCAGCAAAACAGCACCAAAA
6854218 ACAACATCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.59, C:0.28, G:0.11, T:0.02
Consensus pattern (22 bp):
AGCAGCAAAACAGCACCAAAAC
Found at i:6854214 original size:10 final size:10
Alignment explanation
Indices: 6854154--6854216 Score: 63
Period size: 11 Copynumber: 5.9 Consensus size: 10
6854144 GACAAAAAGT
*
6854154 AGCAGCAAAAT
1 AGCA-CAAAAC
6854165 AGCACCAAAAC
1 AGCA-CAAAAC
6854176 AGCAGCAAAAC
1 AGCA-CAAAAC
*
6854187 AGCACCAAAC
1 AGCACAAAAC
6854197 AGCAACAAAAC
1 AGC-ACAAAAC
*
6854208 AACACAAAA
1 AGCACAAAA
6854217 AACAACATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
10 14 0.31
11 31 0.69
ACGTcount: A:0.59, C:0.29, G:0.11, T:0.02
Consensus pattern (10 bp):
AGCACAAAAC
Found at i:6855112 original size:26 final size:26
Alignment explanation
Indices: 6855083--6855133 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
6855073 GATAAAAATT
*
6855083 GATAATGGGTTAGGTAAATGTTCCAC
1 GATAATAGGTTAGGTAAATGTTCCAC
6855109 GATAATAGGTTAGGTAAATGTTCCA
1 GATAATAGGTTAGGTAAATGTTCCA
6855134 TGATGGGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (26 bp):
GATAATAGGTTAGGTAAATGTTCCAC
Found at i:6856671 original size:26 final size:26
Alignment explanation
Indices: 6856619--6856671 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6856609 ATTACAATTT
*
6856619 TACCCCTAGGAGATAAATTATCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
6856645 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
6856671 T
1 T
6856672 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:6860448 original size:26 final size:26
Alignment explanation
Indices: 6860412--6860807 Score: 747
Period size: 26 Copynumber: 15.2 Consensus size: 26
6860402 CATGAAATTC
*
6860412 TTATCATGAAACATTTACCGAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860438 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
6860464 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
6860490 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860516 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860542 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860568 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860594 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860620 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860646 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860672 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860698 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860724 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6860750 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
6860776 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
6860802 TTATCA
1 TTATCA
6860808 ATTTGTATCA
Statistics
Matches: 363, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 363 1.00
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6865238 original size:67 final size:67
Alignment explanation
Indices: 6865130--6865263 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
6865120 CCTAATTTTC
6865130 ACGTACTAACAGAATCACTACCGAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAAT
1 ACGTACTAACAGAATCACTACCGAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAAT
6865195 TT
66 TT
* *
6865197 ACGTACTAACAGAATCACTACCGAGGGTTTTTACCGAATTGGGCCCGTTGGTCCATCATTCCAAT
1 ACGTACTAACAGAATCACTACCGAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAAT
6865262 TT
66 TT
6865264 TGGCCCATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (67 bp):
ACGTACTAACAGAATCACTACCGAGGGTTCTTACCGAATTGGGCCCGTTGGCCCATCATTCCAAT
TT
Found at i:6883052 original size:14 final size:14
Alignment explanation
Indices: 6883033--6883071 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
6883023 TTGTTTCACT
6883033 GAAAATGACTTTC-A
1 GAAAATGA-TTTCTA
6883047 GAAAATGATTTCTA
1 GAAAATGATTTCTA
*
6883061 GAAAATAATTT
1 GAAAATGATTT
6883072 ACTTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (14 bp):
GAAAATGATTTCTA
Found at i:6883523 original size:148 final size:148
Alignment explanation
Indices: 6883255--6883552 Score: 596
Period size: 148 Copynumber: 2.0 Consensus size: 148
6883245 ATATTTTACA
6883255 TTTTTTGCATATATTAAAAATATTTGTTAAATTCAGGTTCATTACAAATTGTTTTTTAATTACAT
1 TTTTTTGCATATATTAAAAATATTTGTTAAATTCAGGTTCATTACAAATTGTTTTTTAATTACAT
6883320 GACTACTAAGTGAGTATTTTTATTTAAAAATGTGACATCAACAAAATTTACAAAAAAAAATTAAC
66 GACTACTAAGTGAGTATTTTTATTTAAAAATGTGACATCAACAAAATTTACAAAAAAAAATTAAC
6883385 GATGTCAACAATTGGACT
131 GATGTCAACAATTGGACT
6883403 TTTTTTGCATATATTAAAAATATTTGTTAAATTCAGGTTCATTACAAATTGTTTTTTAATTACAT
1 TTTTTTGCATATATTAAAAATATTTGTTAAATTCAGGTTCATTACAAATTGTTTTTTAATTACAT
6883468 GACTACTAAGTGAGTATTTTTATTTAAAAATGTGACATCAACAAAATTTACAAAAAAAAATTAAC
66 GACTACTAAGTGAGTATTTTTATTTAAAAATGTGACATCAACAAAATTTACAAAAAAAAATTAAC
6883533 GATGTCAACAATTGGACT
131 GATGTCAACAATTGGACT
6883551 TT
1 TT
6883553 GTAATAACCC
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
148 150 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (148 bp):
TTTTTTGCATATATTAAAAATATTTGTTAAATTCAGGTTCATTACAAATTGTTTTTTAATTACAT
GACTACTAAGTGAGTATTTTTATTTAAAAATGTGACATCAACAAAATTTACAAAAAAAAATTAAC
GATGTCAACAATTGGACT
Found at i:6886543 original size:19 final size:19
Alignment explanation
Indices: 6886507--6886545 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6886497 TATTATTAAT
**
6886507 ATATTTATAATTGTAATAA
1 ATATTTATAATTAAAATAA
*
6886526 ATATTTATTATTAAAATAA
1 ATATTTATAATTAAAATAA
6886545 A
1 A
6886546 CTTGAAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:6886586 original size:21 final size:20
Alignment explanation
Indices: 6886552--6886605 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
6886542 TAAACTTGAA
6886552 ATATTAAATAATTTA-TTA-T
1 ATATT-AATAATTTATTTAGT
6886571 -T-TTAATAATTATATTTAGT
1 ATATTAATAATT-TATTTAGT
6886590 ATATTAATAATTTATT
1 ATATTAATAATTTATT
6886606 ATATGACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.23
17 4 0.13
18 4 0.13
19 1 0.03
20 5 0.17
21 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTAATAATTTATTTAGT
Found at i:6889599 original size:44 final size:45
Alignment explanation
Indices: 6889495--6889609 Score: 142
Period size: 45 Copynumber: 2.6 Consensus size: 45
6889485 ATTTCGCNAT
* * * * *
6889495 CTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAAAGATAGCAAAT
1 CTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGATAGCAAAC
* * * *
6889540 ATTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTA-TAAAC
1 CTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGATAGCAAAC
6889584 CTTATCTCTCTGAAGTTGTAGTAGAG
1 CTTATCTCTCTGAAGTTGTAGTAGAG
6889610 TAGGTTGAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
44 27 0.46
45 32 0.54
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (45 bp):
CTTATCTCTCTGAAGTTGTAGTAGAGCAGATTAAAGATAGCAAAC
Found at i:6889632 original size:44 final size:44
Alignment explanation
Indices: 6889493--6889917 Score: 156
Period size: 44 Copynumber: 9.5 Consensus size: 44
6889483 CGATTTCGCN
* * *
6889493 ATCTTATCTCCCTAAAGTTGTAGTGGAGTAGATTAAAGATAGCAA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAGATA-CAA
* * * * *
6889538 ATATTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAGATACAA
* * * * *
6889582 ACCTTATCTCTCTGAAGTTGTAGTAGAGTAGGTTGAAGTTACGA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAGATACAA
* * * * ** * * *
6889626 GTCTTATTTCCCTAAAGTTACAGTGGAGTAG-TCTAAAGACAGCGA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGAT-TAAAGATA-CAA
* * * * ** * *
6889671 ATCTTATTTTTCTGAAGTTGCAGTGGAACAAATCAAAGCTACAAATTACAA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAG------A-TACAA
* * * * * * *
6889722 ATCTTATCTCCCTAAAGTTGCAGTGGAGCATATTGAAGATAGCAA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAGATA-CAA
* * * * * *
6889767 ACCTTATCTCTCTAAAGTTGCAGTAAAG-AGGTTGAAA-TTACAA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATT-AAAGATACAA
* * * * * * **
6889810 GTCTTATCTCCCT-AAGGTTGCAGTGGGGTAGACTAAAGATACCG
1 ATCTTATCTCTCTGAA-GTTGTAGTAGAGTAGATTAAAGATACAA
* * * * * * * *
6889854 ATCTTATCTCCCTGAAGTTGCAGTGGAATAGATTGAAGCTTCTA
1 ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAGATACAA
* *
6889898 ATCCTATCTCCCTGAAGTTG
1 ATCTTATCTCTCTGAAGTTG
6889918 CAATGGAGCG
Statistics
Matches: 288, Mismatches: 76, Indels: 33
0.73 0.19 0.08
Matches are distributed among these distances:
42 2 0.01
43 26 0.09
44 129 0.45
45 96 0.33
46 1 0.00
51 33 0.11
52 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (44 bp):
ATCTTATCTCTCTGAAGTTGTAGTAGAGTAGATTAAAGATACAA
Found at i:6889830 original size:43 final size:44
Alignment explanation
Indices: 6889713--6889833 Score: 138
Period size: 45 Copynumber: 2.8 Consensus size: 44
6889703 TCAAAGCTAC
** *
6889713 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCATATTG
1 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTAAAGCAGATTG
* * *
6889757 AAGA-TAGCAAACCTTATCTCTCTAAAGTTGCAGTAAAG-AGGTTG
1 AA-ATTA-CAAATCTTATCTCCCTAAAGTTGCAGTAAAGCAGATTG
* *
6889801 AAATTACAAGTCTTATCTCCCTAAGGTTGCAGT
1 AAATTACAAATCTTATCTCCCTAAAGTTGCAGT
6889834 GGGGTAGACT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 24 0.38
44 12 0.19
45 28 0.44
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (44 bp):
AAATTACAAATCTTATCTCCCTAAAGTTGCAGTAAAGCAGATTG
Found at i:6889890 original size:88 final size:88
Alignment explanation
Indices: 6889713--6889926 Score: 216
Period size: 88 Copynumber: 2.4 Consensus size: 88
6889703 TCAAAGCTAC
* * * *
6889713 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCATATTGAAGATAGCAAACCTTATCTCT
1 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGATAGCAAACCTTATCTCC
*
6889778 CTAAAGTTGCAGTAAAGAGGTTG
66 CTAAAGTTGCAGTAAAGAGATTG
* * * * ** *
6889801 AAATTACAAGTCTTATCTCCCTAAGGTTGCAGTGGGGTAGACTAAAGATA-CCGATCTTATCTCC
1 AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGATAGCAAACCTTATCTCC
* * *
6889865 CTGAAGTTGCAGTGGAATAGATTG
66 CTAAAGTTGCAGT-AAAGAGATTG
* * * * *
6889889 AAGCTT-CTAATCCTATCTCCCTGAAGTTGCAATGGAGC
1 AA-ATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGC
6889927 GGGTTAAAGC
Statistics
Matches: 100, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
87 22 0.22
88 76 0.76
89 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (88 bp):
AAATTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTAAAGATAGCAAACCTTATCTCC
CTAAAGTTGCAGTAAAGAGATTG
Found at i:6891604 original size:23 final size:22
Alignment explanation
Indices: 6891560--6891619 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
6891550 TTTAGATTAT
*
6891560 TTATTATT-TTATTATTACTAA
1 TTATTATTCTTATTTTTACTAA
6891581 -TATTATTCTTATTTTTCACTTAA
1 TTATTATTCTTATTTTT-AC-TAA
6891604 TTATT-TTCTT-TTTTTA
1 TTATTATTCTTATTTTTA
6891620 TCATTTCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 7 0.21
23 8 0.24
24 4 0.12
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTATTCTTATTTTTACTAA
Found at i:6894378 original size:14 final size:13
Alignment explanation
Indices: 6894349--6894387 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
6894339 AAAAGTTTAA
*
6894349 TAAATAAAAATGT
1 TAAATAAAAATAT
6894362 TAAATAATAAATAT
1 TAAATAA-AAATAT
*
6894376 TAAATTAAAATA
1 TAAATAAAAATA
6894388 ACATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
TAAATAAAAATAT
Found at i:6904438 original size:3 final size:3
Alignment explanation
Indices: 6904430--6904494 Score: 50
Period size: 3 Copynumber: 23.0 Consensus size: 3
6904420 TGATATTTTC
* * * *
6904430 TAT TAT TAT TCAC CAT TAT T-T T-T TAT TGT AAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6904474 TAT TAT T-T TA- TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
6904495 GTATATATCT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
2 10 0.20
3 38 0.78
4 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6911247 original size:26 final size:25
Alignment explanation
Indices: 6911209--6911292 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 25
6911199 CATGAAATTC
*
6911209 TTATCATGAAACATTTACCTAACCCA
1 TTATCATG-AACATTTACCTAACCTA
6911235 TTATCATCGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
6911261 TTATCATGGAACATTTACCTAACCTA
1 TTATCAT-GAACATTTACCTAACCTA
6911287 TTATCA
1 TTATCA
6911293 ATTTGTATCA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
26 54 0.98
27 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (25 bp):
TTATCATGAACATTTACCTAACCTA
Found at i:6912476 original size:12 final size:12
Alignment explanation
Indices: 6912459--6912483 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6912449 AGTGTCGAAT
6912459 CGGTAACAGTAA
1 CGGTAACAGTAA
6912471 CGGTAACAGTAA
1 CGGTAACAGTAA
6912483 C
1 C
6912484 AGTAGTCGGC
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:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:6913563 original size:5 final size:5
Alignment explanation
Indices: 6913553--6913595 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
6913543 TGTCTCTTTT
6913553 ATATA ATATA ATATA ATATA ATATA ATAT- A-ATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
6913596 CTTAATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 32 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:6914750 original size:26 final size:26
Alignment explanation
Indices: 6914714--6914795 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
6914704 TGATACAAAT
*
6914714 TGATAATGGGTTAGGTAAATATTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
6914740 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
6914766 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
6914792 TGAT
1 TGAT
6914796 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:6917054 original size:34 final size:34
Alignment explanation
Indices: 6917011--6917079 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
6917001 TTATTTTAAA
6917011 CAACTTTAAATTGATGGATACTAATTCAAATGGG
1 CAACTTTAAATTGATGGATACTAATTCAAATGGG
6917045 CAACTTTAAATTGATGGATACTAATTCAAATGGG
1 CAACTTTAAATTGATGGATACTAATTCAAATGGG
6917079 C
1 C
6917080 TAGACTTAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (34 bp):
CAACTTTAAATTGATGGATACTAATTCAAATGGG
Found at i:6917075 original size:20 final size:20
Alignment explanation
Indices: 6917018--6917075 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 20
6917008 AAACAACTTT
6917018 AAATTGATGGATACTAATTC
1 AAATTGATGGATACTAATTC
6917038 AAA-TG--GGCA-ACT--TT-
1 AAATTGATGG-ATACTAATTC
6917052 AAATTGATGGATACTAATTC
1 AAATTGATGGATACTAATTC
6917072 AAAT
1 AAAT
6917076 GGGCTAGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 16
0.65 0.00 0.35
Matches are distributed among these distances:
14 3 0.10
15 4 0.13
16 1 0.03
17 10 0.33
18 1 0.03
19 4 0.13
20 7 0.23
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (20 bp):
AAATTGATGGATACTAATTC
Found at i:6919702 original size:20 final size:20
Alignment explanation
Indices: 6919664--6919711 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
6919654 TAAATTCTAA
* **
6919664 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
6919684 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
6919704 AAA-ATAAA
1 AAAGATAAA
6919712 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:6921250 original size:7 final size:7
Alignment explanation
Indices: 6921229--6921291 Score: 53
Period size: 7 Copynumber: 9.1 Consensus size: 7
6921219 GAAATTTATT
6921229 AATATAAA
1 AATA-AAA
6921237 AAT-AAA
1 AATAAAA
6921243 AAT-AAA
1 AATAAAA
6921249 AAT--AA
1 AATAAAA
6921254 AATAAAA
1 AATAAAA
*
6921261 TAATAAAT
1 -AATAAAA
*
6921269 AATAAAT
1 AATAAAA
6921276 AATAAATA
1 AATAAA-A
6921284 AATAAAA
1 AATAAAA
6921291 A
1 A
6921292 GATTGGGTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
5 5 0.10
6 12 0.24
7 17 0.35
8 15 0.31
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (7 bp):
AATAAAA
Found at i:6921255 original size:11 final size:10
Alignment explanation
Indices: 6921232--6921291 Score: 61
Period size: 10 Copynumber: 5.7 Consensus size: 10
6921222 ATTTATTAAT
6921232 ATAAAAATAAAA
1 ATAAAAAT--AA
6921244 ATAAAAATAA
1 ATAAAAATAA
6921254 A-ATAAAAT-A
1 ATA-AAAATAA
6921263 ATAAATAATAA
1 ATAAA-AATAA
6921274 ATAATAAATAA
1 ATAA-AAATAA
6921285 ATAAAAA
1 ATAAAAA
6921292 GATTGGGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.12
10 15 0.35
11 14 0.33
12 9 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:6932438 original size:27 final size:26
Alignment explanation
Indices: 6932408--6932469 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
6932398 AGATAATTAA
6932408 AATAAAATCCTAA-ATGTGAATAATCCT
1 AATAAAATCCTAATAT-T-AATAATCCT
* * *
6932435 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAATATTAATAATCCT
6932462 AATAAAAT
1 AATAAAAT
6932470 AAAATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 18 0.62
28 7 0.24
29 2 0.07
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.37
Consensus pattern (26 bp):
AATAAAATCCTAATATTAATAATCCT
Found at i:6932907 original size:47 final size:48
Alignment explanation
Indices: 6932853--6932984 Score: 185
Period size: 47 Copynumber: 2.8 Consensus size: 48
6932843 CACAATCGAT
* *
6932853 AAGTACCTATACCATGACCCATAGCCAAATCAAGGTAACTTATCCCAG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCAG
* ** *
6932901 -AGTACCTATACCATGGCTCATAGCCAAATCAAGGTAACTCATTTCTG
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCAG
* *
6932948 AAATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
6932985 TCACTCGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 41 0.55
48 33 0.45
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCAG
Found at i:6934047 original size:40 final size:40
Alignment explanation
Indices: 6933985--6934060 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
6933975 GCTATACTAG
* *
6933985 CATTAGTGGCGTTTGTTGT-AAAACGCCGCAATATATCTGT
1 CATTAGCGGCGTTTGTAGTAAAAACGCCGCAA-ATATCTGT
6934025 CATTAGCGGCGTTT-TAGCTAAAAACGCCGCAAATAT
1 CATTAGCGGCGTTTGTAG-TAAAAACGCCGCAAATAT
6934061 GTTTAAGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 2 0.06
40 18 0.56
41 12 0.38
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (40 bp):
CATTAGCGGCGTTTGTAGTAAAAACGCCGCAAATATCTGT
Found at i:6934727 original size:21 final size:22
Alignment explanation
Indices: 6934682--6934737 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
6934672 TAAGGGTTGG
* * **
6934682 GGTTTAAGGGTTATGGGTTTGT
1 GGTTTAGGGGTTATGGATTAAT
6934704 GG-TTAGGGGTTATGGATTAAT
1 GGTTTAGGGGTTATGGATTAAT
*
6934725 GGTTTAGGTGTTA
1 GGTTTAGGGGTTA
6934738 AGGCTTAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.18, C:0.00, G:0.39, T:0.43
Consensus pattern (22 bp):
GGTTTAGGGGTTATGGATTAAT
Found at i:6934759 original size:29 final size:29
Alignment explanation
Indices: 6934727--6934786 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
6934717 GGATTAATGG
* *
6934727 TTTA-GGTGTTAAGGCTTAGGGGTTATTGT
1 TTTATGGT-TTAAGGCTTAGGGGATATAGT
* *
6934756 TTTATGGTTTAGGGTTTAGGGGATATAGT
1 TTTATGGTTTAAGGCTTAGGGGATATAGT
6934785 TT
1 TT
6934787 AGGGTACTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.18, C:0.02, G:0.33, T:0.47
Consensus pattern (29 bp):
TTTATGGTTTAAGGCTTAGGGGATATAGT
Found at i:6934968 original size:29 final size:29
Alignment explanation
Indices: 6934909--6934984 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
6934899 AATTCATACA
* * * *
6934909 TTTTGT-GTTTAAGGCTTAGGGGTTATTG
1 TTTTGTGGTTTAAGGTTTAAGGGATATAG
*
6934937 TTTTGTGGTTTATGGTTTAAGGGATATAG
1 TTTTGTGGTTTAAGGTTTAAGGGATATAG
**
6934966 TTTAATGGTTTAAGGTTTA
1 TTTTGTGGTTTAAGGTTTA
6934985 GGGTTTTGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 6 0.15
29 33 0.85
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.50
Consensus pattern (29 bp):
TTTTGTGGTTTAAGGTTTAAGGGATATAG
Found at i:6934990 original size:22 final size:21
Alignment explanation
Indices: 6934943--6934990 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
6934933 ATTGTTTTGT
*
6934943 GGTTTATGGTTTAAGGGATAT
1 GGTTTATGGTTTAAGGGATAG
* **
6934964 AGTTTAATGGTTTAAGGTTTAG
1 GGTTT-ATGGTTTAAGGGATAG
6934986 GGTTT
1 GGTTT
6934991 TGATTAATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
GGTTTATGGTTTAAGGGATAG
Found at i:6937176 original size:25 final size:25
Alignment explanation
Indices: 6937143--6937214 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 25
6937133 TAGTCCTCCG
* *
6937143 CATCGTCGTCGGCAGCCCTCTGCTA
1 CATCTTCGTCGGCATCCCTCTGCTA
* *
6937168 CATTTTCGTCAGCATCCCTCTGCTA
1 CATCTTCGTCGGCATCCCTCTGCTA
* *
6937193 CATCTCCGTCGACATCCCTCTG
1 CATCTTCGTCGGCATCCCTCTG
6937215 TTGCTTCTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.14, C:0.40, G:0.17, T:0.29
Consensus pattern (25 bp):
CATCTTCGTCGGCATCCCTCTGCTA
Found at i:6937930 original size:23 final size:23
Alignment explanation
Indices: 6937900--6937944 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6937890 AAGTATTTTC
* *
6937900 TTAAGAAATTTTATTTGATAATG
1 TTAAGAAAATTCATTTGATAATG
6937923 TTAAGAAAATTCATTTGATAAT
1 TTAAGAAAATTCATTTGATAAT
6937945 AATAATAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (23 bp):
TTAAGAAAATTCATTTGATAATG
Found at i:6938662 original size:9 final size:9
Alignment explanation
Indices: 6938650--6938912 Score: 205
Period size: 9 Copynumber: 29.6 Consensus size: 9
6938640 CATATCATAT
6938650 CATAACTTA
1 CATAACTTA
*
6938659 CATAATTTA
1 CATAACTTA
6938668 CATAACTTA
1 CATAACTTA
*
6938677 TATAACTTA
1 CATAACTTA
* *
6938686 GATAA-ATA
1 CATAACTTA
*
6938694 TATAACTTA
1 CATAACTTA
6938703 CATAACTTA
1 CATAACTTA
*
6938712 CATAA-ATA
1 CATAACTTA
* * *
6938720 TATATCATA
1 CATAACTTA
6938729 TCATAACTTA
1 -CATAACTTA
6938739 CATAACTTA
1 CATAACTTA
6938748 CATAACTTA
1 CATAACTTA
*
6938757 TATAACTTA
1 CATAACTTA
* *
6938766 GATAA-ATA
1 CATAACTTA
*
6938774 TATAACTTA
1 CATAACTTA
6938783 CATAAC-TA
1 CATAACTTA
* * *
6938791 TATATCATA
1 CATAACTTA
*
6938800 TCATAGCTTA
1 -CATAACTTA
6938810 CATAACTTA
1 CATAACTTA
*
6938819 TATAACTTA
1 CATAACTTA
* *
6938828 GATAA-ATA
1 CATAACTTA
*
6938836 TATAACTTA
1 CATAACTTA
6938845 CATAACTTA
1 CATAACTTA
*
6938854 CATAA-ATA
1 CATAACTTA
* * *
6938862 TATATCATA
1 CATAACTTA
*
6938871 TCATATCTTA
1 -CATAACTTA
6938881 CATAACTTA
1 CATAACTTA
*
6938890 CAAAACTTA
1 CATAACTTA
*
6938899 CTTAACTTA
1 CATAACTTA
6938908 CATAA
1 CATAA
6938913 TACATAAATA
Statistics
Matches: 203, Mismatches: 42, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
8 34 0.17
9 150 0.74
10 19 0.09
ACGTcount: A:0.46, C:0.16, G:0.02, T:0.37
Consensus pattern (9 bp):
CATAACTTA
Found at i:6938697 original size:17 final size:17
Alignment explanation
Indices: 6938660--6938849 Score: 104
Period size: 17 Copynumber: 11.8 Consensus size: 17
6938650 CATAACTTAC
* *
6938660 ATAATTTACATAACTTAT
1 ATAACTTACATAA-ATAT
*
6938678 ATAACTTAGATAAATAT
1 ATAACTTACATAAATAT
6938695 ATAACTTAC------AT
1 ATAACTTACATAAATAT
6938706 A--ACTTACATAAATAT
1 ATAACTTACATAAATAT
* * * *
6938721 ATATCATATCATAACTTAC
1 ATAACTTA-CATAA-ATAT
*
6938740 ATAACTTACATAACTTAT
1 ATAACTTACATAA-ATAT
*
6938758 ATAACTTAGATAAATAT
1 ATAACTTACATAAATAT
*
6938775 ATAACTTACATAACTAT
1 ATAACTTACATAAATAT
*
6938792 AT-A--T-CAT--AT-C
1 ATAACTTACATAAATAT
* *
6938802 ATAGCTTACATAACTTAT
1 ATAACTTACATAA-ATAT
*
6938820 ATAACTTAGATAAATAT
1 ATAACTTACATAAATAT
6938837 ATAACTTACATAA
1 ATAACTTACATAA
6938850 CTTACATAAA
Statistics
Matches: 130, Mismatches: 24, Indels: 37
0.68 0.13 0.19
Matches are distributed among these distances:
9 6 0.05
10 2 0.02
11 4 0.03
13 4 0.03
14 4 0.03
15 3 0.02
16 1 0.01
17 50 0.38
18 48 0.37
19 8 0.06
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (17 bp):
ATAACTTACATAAATAT
Found at i:6938740 original size:80 final size:81
Alignment explanation
Indices: 6938632--6938926 Score: 316
Period size: 80 Copynumber: 3.8 Consensus size: 81
6938622 TTAATGTTAA
*
6938632 ATAT-ATATCATATCATATCATAACTTACATAATTTACATAACTTATATAACTTAGATAAATATA
1 ATATAATATCATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATA
6938696 TAACTTACATAACTTAC
66 TAACTTACATAAC-TAC
6938713 ATA-AATAT-ATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATA
1 ATATAATATCATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATA
*
6938776 TAACTTACATAACTAT
66 TAACTTACATAACTAC
* * * * * * *
6938792 ATATCATATCATAGCTTA-CATAACTTATATAACTTAGATAA-ATATATAAC-----T---TACA
1 ATATAATATCATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATA
* *
6938847 TAACTTACATAAATAT
66 TAACTTACATAACTAC
* * * * * *
6938863 ATATCATATCATATCTTA-CATAACTTACAAAACTTACTTAACTTACATAA--TACATAAATATA
1 ATATAATATCATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATA
6938925 TA
66 TA
6938927 CTTGAAAATC
Statistics
Matches: 185, Mismatches: 18, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
71 54 0.29
72 6 0.03
74 1 0.01
75 1 0.01
78 5 0.03
79 13 0.07
80 92 0.50
81 13 0.07
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.37
Consensus pattern (81 bp):
ATATAATATCATATCATATCATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATA
TAACTTACATAACTAC
Found at i:6938779 original size:71 final size:71
Alignment explanation
Indices: 6938659--6938898 Score: 356
Period size: 71 Copynumber: 3.4 Consensus size: 71
6938649 TCATAACTTA
* *
6938659 CATAATTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
1 CATAACTTACATAACTTACATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
6938724 TCATAT
66 TCATAT
* * * * * *
6938730 CATAACTTACATAACTTACATAACTTATATAACTTAGATAA-ATATATAACTTACATAACTATAT
1 CATAACTTACATAACTTACATAACTTAGATAA-ATATATAACTTACATAACTTACATAAATATAT
6938794 ATCATAT
65 ATCATAT
* *
6938801 CATAGCTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
1 CATAACTTACATAACTTACATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
6938866 TCATAT
66 TCATAT
* *
6938872 CATATCTTACATAACTTACAAAACTTA
1 CATAACTTACATAACTTACATAACTTA
6938899 CTTAACTTAC
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
70 6 0.04
71 136 0.92
72 6 0.04
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (71 bp):
CATAACTTACATAACTTACATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATA
TCATAT
Found at i:6938840 original size:26 final size:26
Alignment explanation
Indices: 6938811--6938912 Score: 105
Period size: 26 Copynumber: 3.8 Consensus size: 26
6938801 CATAGCTTAC
* *
6938811 ATAACTTATATAACTTAGATAAATAT
1 ATAACTTACATAACTTACATAAATAT
6938837 ATAACTTACATAACTTACATAAATAT
1 ATAACTTACATAACTTACATAAATAT
* * * * *
6938863 ATATCATATCATATCTTACATAACTTAC
1 ATAACTTA-CATAACTTACATAA-ATAT
* *
6938891 AAAACTTACTTAACTTACATAA
1 ATAACTTACATAACTTACATAA
6938913 TACATAAATA
Statistics
Matches: 62, Mismatches: 12, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
26 30 0.48
27 25 0.40
28 7 0.11
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (26 bp):
ATAACTTACATAACTTACATAAATAT
Found at i:6938973 original size:142 final size:142
Alignment explanation
Indices: 6938665--6938919 Score: 424
Period size: 142 Copynumber: 1.8 Consensus size: 142
6938655 CTTACATAAT
6938665 TTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATATCATAT
1 TTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATATCATAT
* * * * *
6938730 CATAACTTACATAACTTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTATATA
66 CATAACTTACATAACTTACAAAACTTATATAACTTACATAAATACATAACATACATAACTATAAA
*
6938795 TCATATCATAGC
131 TCACATCATAGC
6938807 TTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATATCATAT
1 TTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATATCATAT
*
6938872 CATATCTTACATAACTTACAAAACTTACT-TAACTTACAT-AATACATAA
66 CATAACTTACATAACTTACAAAACTTA-TATAACTTACATAAATACATAA
6938920 ATATATACTT
Statistics
Matches: 108, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
141 8 0.07
142 99 0.92
143 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.36
Consensus pattern (142 bp):
TTACATAACTTATATAACTTAGATAAATATATAACTTACATAACTTACATAAATATATATCATAT
CATAACTTACATAACTTACAAAACTTATATAACTTACATAAATACATAACATACATAACTATAAA
TCACATCATAGC
Found at i:6941142 original size:26 final size:26
Alignment explanation
Indices: 6941106--6941189 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
6941096 CATGAAATTC
6941106 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
6941132 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
6941158 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
6941184 TTATCA
1 TTATCA
6941190 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:6947221 original size:25 final size:24
Alignment explanation
Indices: 6947193--6947240 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
6947183 TCATTTAATA
*
6947193 TTTTTATCTATTTTATTAATTTTGC
1 TTTTTATCTATATTATT-ATTTTGC
* *
6947218 TTTTTTTTTATATTATTATTTTG
1 TTTTTATCTATATTATTATTTTG
6947241 AAGTTGGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTTATCTATATTATTATTTTGC
Found at i:6948374 original size:131 final size:131
Alignment explanation
Indices: 6948188--6948650 Score: 648
Period size: 131 Copynumber: 3.6 Consensus size: 131
6948178 TAATTATTCA
* * * * * *
6948188 TTTAAAAATT-TTCAAAACGAAGGCAATATTCGAGGTTTGGGAATTTGGGGAATCGTGCCCAATC
1 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
*
6948252 GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATTGAATATTCCTTTGGAATTTCAATCATGT
66 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTGGAATTTCAATCATGT
6948317 C
131 C
* *
6948318 TTTAAAAATTCTTTAAAACGAAGGCAATGTTTGATGTTTGGCAATTCAGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
* * * * * * * *
6948383 GTGCTGGGTTGCGATTTCTCGTTTGTTCAAATTAATCGAACATCCCTTTGGAATTTCATTCATGC
66 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTGGAATTTCAATCATGT
6948448 C
131 C
*
6948449 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATTGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
* *
6948514 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTAGAATTTCACTCATGT
66 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTGGAATTTCAATCATGT
6948579 -
131 C
* * * * * * *
6948579 TTTCAAGATTC--TAAAGCG-AGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTACC
1 TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
6948641 GTGCTGGGTT
66 GTGCTGGGTT
6948651 TCGATTTTTT
Statistics
Matches: 295, Mismatches: 37, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
127 49 0.17
128 6 0.02
130 19 0.06
131 221 0.75
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (131 bp):
TTTAAAAATTCTTTAAAACGAAGGCAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATTGAATATTCCTTTGGAATTTCAATCATGT
C
Found at i:6949506 original size:13 final size:14
Alignment explanation
Indices: 6949490--6949521 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
6949480 TTATTATAAA
6949490 TAATTATAAT-GTT
1 TAATTATAATGGTT
6949503 TAATTATAATGGTT
1 TAATTATAATGGTT
6949517 TAATT
1 TAATT
6949522 CGCCGTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (14 bp):
TAATTATAATGGTT
Found at i:6950214 original size:33 final size:33
Alignment explanation
Indices: 6950166--6950244 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 33
6950156 TCATTTAATG
* *
6950166 TTTTTTGTTGCATTTTTTATGCTATATTTGCTA
1 TTTTTGGTTGGATTTTTTATGCTATATTTGCTA
* *
6950199 TTTTTGGTTGGA--TTTTATGTTATATTTGCTG
1 TTTTTGGTTGGATTTTTTATGCTATATTTGCTA
*
6950230 TTTTTGGTTCGATTT
1 TTTTTGGTTGGATTT
6950245 AATGCAGGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
31 28 0.72
33 11 0.28
ACGTcount: A:0.13, C:0.06, G:0.18, T:0.63
Consensus pattern (33 bp):
TTTTTGGTTGGATTTTTTATGCTATATTTGCTA
Found at i:6950223 original size:31 final size:31
Alignment explanation
Indices: 6950180--6950249 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
6950170 TTGTTGCATT
*
6950180 TTTTATGCTATATTTGCTATTTTTGGTTGGA
1 TTTTATGCTATATTTGCTATTTTTGGTTCGA
* *
6950211 TTTTATGTTATATTTGCTGTTTTTGGTTCGA
1 TTTTATGCTATATTTGCTATTTTTGGTTCGA
*
6950242 TTTAATGC
1 TTTTATGC
6950250 AGGAAGGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.16, C:0.07, G:0.19, T:0.59
Consensus pattern (31 bp):
TTTTATGCTATATTTGCTATTTTTGGTTCGA
Found at i:6959144 original size:29 final size:29
Alignment explanation
Indices: 6959083--6959148 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
6959073 ATGTGGCCTC
* *
6959083 TGTTATATGTGAGCCCTAGTTGCAAAATC
1 TGTTATATGTGAGCCCTAGTGGCAAAATA
* * **
6959112 TGTTATATGTGAGCCTTTGTGGCTGAATA
1 TGTTATATGTGAGCCCTAGTGGCAAAATA
6959141 TGTTATAT
1 TGTTATAT
6959149 ACGGAAGCCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (29 bp):
TGTTATATGTGAGCCCTAGTGGCAAAATA
Found at i:6961665 original size:24 final size:24
Alignment explanation
Indices: 6961620--6961665 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
6961610 TAATATTTAG
** *
6961620 TATTTATTAGCATAGTATATTTGA
1 TATTTATTAGCATAAAACATTTGA
*
6961644 TATTTATTAGTATAAAACATTT
1 TATTTATTAGCATAAAACATTT
6961666 TTTATTTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.50
Consensus pattern (24 bp):
TATTTATTAGCATAAAACATTTGA
Found at i:6965058 original size:39 final size:39
Alignment explanation
Indices: 6965004--6965078 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
6964994 TGTATAAGTC
*
6965004 AATAGCGACACGACTTGATATTATGTACACAGTTGATTT
1 AATAGCAACACGACTTGATATTATGTACACAGTTGATTT
*
6965043 AATAGCAACACGACTTGATATTATGTACGCAGTTGA
1 AATAGCAACACGACTTGATATTATGTACACAGTTGA
6965079 CTTGTTAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (39 bp):
AATAGCAACACGACTTGATATTATGTACACAGTTGATTT
Found at i:6965731 original size:18 final size:18
Alignment explanation
Indices: 6965708--6965753 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
6965698 CAAACACACT
6965708 TGGCGAACTCTCCAAGAA
1 TGGCGAACTCTCCAAGAA
* * *
6965726 TGGCGAACTCTTCGAGAG
1 TGGCGAACTCTCCAAGAA
6965744 TGGCGAACTC
1 TGGCGAACTC
6965754 ACAGCACATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (18 bp):
TGGCGAACTCTCCAAGAA
Found at i:6967564 original size:21 final size:20
Alignment explanation
Indices: 6967538--6967582 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
6967528 TTGCACATTT
6967538 TTTTTAATTCAATTCAATTCA
1 TTTTTAATTCAATTCAATT-A
* *
6967559 TTTTTAATTTAATTTAATTA
1 TTTTTAATTCAATTCAATTA
6967579 TTTT
1 TTTT
6967583 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAATTCAATTCAATTA
Found at i:6967890 original size:3 final size:3
Alignment explanation
Indices: 6967884--6967941 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
6967874 GTTACCATCA
*
6967884 AAG AAG -AG AAG -AG CAG AACG ACAG A-G AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AA-G A-AG AAG AAG AAG AAG AAG AAG AAG
*
6967928 AAG AAA AAG AAG AA
1 AAG AAG AAG AAG AA
6967942 ATGGATGCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
2 6 0.13
3 36 0.77
4 4 0.09
5 1 0.02
ACGTcount: A:0.64, C:0.05, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6968429 original size:14 final size:15
Alignment explanation
Indices: 6968411--6968454 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
6968401 ATTAATTTAG
6968411 AAAATTCAATTAATT
1 AAAATTCAATTAATT
* *
6968426 -AAATTTATTTAATT
1 AAAATTCAATTAATT
*
6968440 AAAAATCAATTAATT
1 AAAATTCAATTAATT
6968455 TACTTGGTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTCAATTAATT
Found at i:6969045 original size:30 final size:29
Alignment explanation
Indices: 6968983--6969047 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
6968973 ATAGTAAAAT
* *
6968983 AGTCACTAAACTTTGAAAAGTTACAACTC
1 AGTCACTAAACTTTGAAAAATAACAACTC
6969012 AGTCACTAAACTTTAGAAAAATAACAAAC-C
1 AGTCACTAAACTTT-GAAAAATAAC-AACTC
6969042 AGTCAC
1 AGTCAC
6969048 CAATAACCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 14 0.44
30 15 0.47
31 3 0.09
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (29 bp):
AGTCACTAAACTTTGAAAAATAACAACTC
Found at i:6969885 original size:30 final size:31
Alignment explanation
Indices: 6969851--6969923 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
6969841 TTTGATAACA
* **
6969851 TTAGTGACTGTTTTGTTATTTTTGT-AAAGT
1 TTAGTGACTATTTTGTTATTTTAATCAAAGT
6969881 TTAGTGACTATTTTGTTATTTTAATCAAAGT
1 TTAGTGACTATTTTGTTATTTTAATCAAAGT
*
6969912 TGAGTGACTATT
1 TTAGTGACTATT
6969924 GGTGTACTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
30 22 0.58
31 16 0.42
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (31 bp):
TTAGTGACTATTTTGTTATTTTAATCAAAGT
Found at i:6972643 original size:27 final size:27
Alignment explanation
Indices: 6972605--6972659 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
6972595 ATATATTTTT
*
6972605 TACCCCCATTTTCATCTAGTTTGACTA
1 TACCCCCATTTTCATCTAGTTTAACTA
6972632 TACCCCCATTTTCATCTAGTTTAACTA
1 TACCCCCATTTTCATCTAGTTTAACTA
6972659 T
1 T
6972660 CTTTAAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.29, G:0.05, T:0.42
Consensus pattern (27 bp):
TACCCCCATTTTCATCTAGTTTAACTA
Found at i:6975984 original size:10 final size:10
Alignment explanation
Indices: 6975969--6975996 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6975959 ATATTACATG
6975969 TTTACTTTGT
1 TTTACTTTGT
6975979 TTTACTTTGT
1 TTTACTTTGT
6975989 TTTACTTT
1 TTTACTTT
6975997 TTCCCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Done.