Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 9 of 226
Found at i:3865316 original size:16 final size:16
Alignment explanation
Indices: 3865295--3865326 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3865285 GTCAAATAAG
3865295 TAAAAGAAAAAAGTAA
1 TAAAAGAAAAAAGTAA
*
3865311 TAAAAGACAAAAGTAA
1 TAAAAGAAAAAAGTAA
3865327 AACCAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (16 bp):
TAAAAGAAAAAAGTAA
Found at i:3866936 original size:407 final size:408
Alignment explanation
Indices: 3866180--3866997 Score: 1503
Period size: 407 Copynumber: 2.0 Consensus size: 408
3866170 AAACCCTATT
* * *
3866180 AATTGTATTGGGCTGATTCGGATATAGATGGCAGGCCATAGGATTGGAAAAGTTCAAAGATTTCT
1 AATTGTATTGAGCTAAGTCGGATATAGATGGCAGGCCATAGGATTGGAAAAGTTCAAAGATTTCT
*
3866245 TCGACTTCGAGTCGATGAGTCACTGGGTGCCAATTTACTTCGGTTTAACCGATGAGACACTGGGT
66 TCGACTTCGAGTCGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAACCGATGAGACACTGGGT
* * *
3866310 GTCAATTTACTACTTCGAATCATCCGATGAGGCACTTAGTGCCACACTGGTGTGTTTGGTTGGAT
131 GACAATTTACTACTTCGAATCATCCAATGAGGCACTGAGTGCCACACTGGTGTGTTTGGTTGGAT
* *
3866375 CCGTGTATCCGTCTAAGTCTGAGTCGTGTTAATAATGGTAAATAAATAATAAAGTTCTATAATTG
196 CCGTGTATCCGTCTAAGTCCGAGTCGTGTTAATAATGATAAATAAATAATAAAGTTCTATAATTG
3866440 ATATTGAAATGGCATGGTATGAGAAATGGAAGTGATATAGTGAATTGAAAATAGAATGTGAAATA
261 ATATTGAAATGGCATGGTATGAGAAATGGAAGTGATATAGTGAATTGAAAATAGAATGTGAAATA
3866505 TGTTGTAAATACATGGAATATATGAGTTATATACTCATGAATTTAATATGTAATGGATAATGCCA
326 TGTTGTAAATACATGGAATATATGAGTTATATACTCATGAATTTAATATGTAATGGATAATGCCA
3866570 TTGTTTAAATGAAATGTG
391 TTGTTTAAATGAAATGTG
* *
3866588 AATTGTATTGAGCTAAGTCGGATATAGATGGCATGCCATAGGATTGGAAAAGTTCAGAGATTTCT
1 AATTGTATTGAGCTAAGTCGGATATAGATGGCAGGCCATAGGATTGGAAAAGTTCAAAGATTTCT
3866653 TCGACTTCGAGTCGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAACCGATGAGACACTGGGT
66 TCGACTTCGAGTCGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAACCGATGAGACACTGGGT
* *
3866718 GACAATTTACTACTTCGAGTCATCCAATGAGGCACTGGGTGCCACA-TGGTGTGTTTGGTTGGAT
131 GACAATTTACTACTTCGAATCATCCAATGAGGCACTGAGTGCCACACTGGTGTGTTTGGTTGGAT
*
3866782 CTGTGTATCCGTCTAAGTCCGAGTCGTGTTAATAATGATAAATAAATAATAAAGTTCTATAATTG
196 CCGTGTATCCGTCTAAGTCCGAGTCGTGTTAATAATGATAAATAAATAATAAAGTTCTATAATTG
3866847 ATATTGAAATGGCATGGTATGAGAAATGGAAGTGATATAGTGAATTGAAAATAGAATGTGAAATA
261 ATATTGAAATGGCATGGTATGAGAAATGGAAGTGATATAGTGAATTGAAAATAGAATGTGAAATA
3866912 TGTTGTAAATACATGGAATATATGAGTTATATACTCATGAATTTAATATGTAATGGATAATGCCA
326 TGTTGTAAATACATGGAATATATGAGTTATATACTCATGAATTTAATATGTAATGGATAATGCCA
3866977 TTGTTTAAATGAAATGTG
391 TTGTTTAAATGAAATGTG
3866995 AAT
1 AAT
3866998 CAAATTGTGA
Statistics
Matches: 396, Mismatches: 14, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
407 231 0.58
408 165 0.42
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.33
Consensus pattern (408 bp):
AATTGTATTGAGCTAAGTCGGATATAGATGGCAGGCCATAGGATTGGAAAAGTTCAAAGATTTCT
TCGACTTCGAGTCGATGAGGCACTGGGTGCCAATTTACTTCGGTTTAACCGATGAGACACTGGGT
GACAATTTACTACTTCGAATCATCCAATGAGGCACTGAGTGCCACACTGGTGTGTTTGGTTGGAT
CCGTGTATCCGTCTAAGTCCGAGTCGTGTTAATAATGATAAATAAATAATAAAGTTCTATAATTG
ATATTGAAATGGCATGGTATGAGAAATGGAAGTGATATAGTGAATTGAAAATAGAATGTGAAATA
TGTTGTAAATACATGGAATATATGAGTTATATACTCATGAATTTAATATGTAATGGATAATGCCA
TTGTTTAAATGAAATGTG
Found at i:3867816 original size:41 final size:40
Alignment explanation
Indices: 3867750--3867881 Score: 187
Period size: 40 Copynumber: 3.3 Consensus size: 40
3867740 AAATTAAAAT
3867750 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTA
1 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTA
* *
3867790 AAAAATTAAAAAAAGTATTTTAAAAAAAATTTAAAATTAA
1 AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTA
** *
3867830 AAAAATTAAAAAAAAAGTATTTTAAAAGTATTTT-AAAGTTA
1 AAAAATT--AAAAAAAGTATTTTAAAAAAATTTTAAAATTTA
3867871 AAAAA-TAAAAA
1 AAAAATTAAAAA
3867882 TAAAAATATT
Statistics
Matches: 83, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
38 5 0.06
40 46 0.55
41 10 0.12
42 22 0.27
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (40 bp):
AAAAATTAAAAAAAGTATTTTAAAAAAATTTTAAAATTTA
Found at i:3867856 original size:11 final size:11
Alignment explanation
Indices: 3867842--3867866 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3867832 AAATTAAAAA
3867842 AAAAGTATTTT
1 AAAAGTATTTT
3867853 AAAAGTATTTT
1 AAAAGTATTTT
3867864 AAA
1 AAA
3867867 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:3867892 original size:41 final size:40
Alignment explanation
Indices: 3867733--3867892 Score: 162
Period size: 40 Copynumber: 3.8 Consensus size: 40
3867723 CCAAGAATTT
3867733 ATTTTAAAAATTAAAATAA-AAATTAAAAAAAGTATTTTAAAAAA
1 ATTTT-AAAATTAAAA-AATAAA--AAAAAAA-TATTTTAAAAAA
* *
3867777 ATTTTAAAATTTAAAAAAT-TAAAAAAAGTATTTTAAAAAA
1 ATTTTAAAA-TTAAAAAATAAAAAAAAAATATTTTAAAAAA
* * **
3867817 AATTTAAAATTAAAAAAATTAAAAAAAAAGTATTTTAAAAGT
1 ATTTTAAAATT-AAAAAA-TAAAAAAAAAATATTTTAAAAAA
*
3867859 ATTTTAAAGTTAAAAAATAAAAATAAAAATATTT
1 ATTTTAAAATTAAAAAATAAAAA-AAAAATATTT
3867893 ATTATTCGGG
Statistics
Matches: 101, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
39 2 0.02
40 32 0.32
41 22 0.22
42 27 0.27
43 7 0.07
44 11 0.11
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (40 bp):
ATTTTAAAATTAAAAAATAAAAAAAAAATATTTTAAAAAA
Found at i:3868121 original size:11 final size:11
Alignment explanation
Indices: 3868094--3868123 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
3868084 CATTTTAATA
3868094 TGTTTTGAATG
1 TGTTTTGAATG
3868105 TG-TTTGAATG
1 TGTTTTGAATG
3868115 TGTTTTGAA
1 TGTTTTGAA
3868124 CTGGTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (11 bp):
TGTTTTGAATG
Found at i:3872347 original size:20 final size:20
Alignment explanation
Indices: 3872322--3872359 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3872312 TTTAATTAGT
3872322 TTTTATTTTTTAAAGTATAG
1 TTTTATTTTTTAAAGTATAG
3872342 TTTTATTTTTTAAAGTAT
1 TTTTATTTTTTAAAGTAT
3872360 CATATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTTATTTTTTAAAGTATAG
Found at i:3874342 original size:28 final size:28
Alignment explanation
Indices: 3874296--3874351 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
3874286 TTATAATTTA
**
3874296 TCCACGTGTTGTTCAACATCCTATGTTG
1 TCCACGTGTCATTCAACATCCTATGTTG
*
3874324 TCCACGTGTCATTCGACATCCTATGTTG
1 TCCACGTGTCATTCAACATCCTATGTTG
3874352 AAAGCTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (28 bp):
TCCACGTGTCATTCAACATCCTATGTTG
Found at i:3887442 original size:13 final size:14
Alignment explanation
Indices: 3887424--3887452 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3887414 CTTGAAGACC
3887424 TTCTCTCCTT-CGA
1 TTCTCTCCTTCCGA
3887437 TTCTCTCCTTCCGA
1 TTCTCTCCTTCCGA
3887451 TT
1 TT
3887453 ATCTGCCTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.07, C:0.38, G:0.07, T:0.48
Consensus pattern (14 bp):
TTCTCTCCTTCCGA
Found at i:3893709 original size:31 final size:31
Alignment explanation
Indices: 3893674--3893733 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3893664 ATGATTGAAT
*
3893674 TATTCAAAAAATTTTATTCAAGTCCCTAAAC
1 TATTCAAAAAATTTTATTCAAGTCACTAAAC
** *
3893705 TATTCAAAAGTTTTTATTTAAGTCACTAA
1 TATTCAAAAAATTTTATTCAAGTCACTAA
3893734 GCGGTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (31 bp):
TATTCAAAAAATTTTATTCAAGTCACTAAAC
Found at i:3895979 original size:2 final size:2
Alignment explanation
Indices: 3895972--3896020 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3895962 GCACATACAG
3895972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3896014 AT AT AT A
1 AT AT AT A
3896021 ACCAAACATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3896960 original size:23 final size:21
Alignment explanation
Indices: 3896907--3896960 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 21
3896897 TATAATCATT
*
3896907 TAAATATTTTATTTTTTATAAA
1 TAAA-ATTTTATTTTTAATAAA
3896929 TAGATAATTTATATTTTTAATAAAA
1 TA-A-AATTT-TATTTTTAAT-AAA
3896954 TAAAATT
1 TAAAATT
3896961 AAATATTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 11 0.41
25 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAAATTTTATTTTTAATAAA
Found at i:3902970 original size:15 final size:15
Alignment explanation
Indices: 3902947--3902981 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3902937 TTTTTAACGT
* *
3902947 ATTAAAAATGATGAA
1 ATTATAAATGATAAA
3902962 ATTATAAATGATAAA
1 ATTATAAATGATAAA
3902977 ATTAT
1 ATTAT
3902982 GTTTTTAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (15 bp):
ATTATAAATGATAAA
Found at i:3907293 original size:18 final size:19
Alignment explanation
Indices: 3907265--3907303 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3907255 GGTTTTTTAC
3907265 AAAAATATTATAAAAAAAT
1 AAAAATATTATAAAAAAAT
* *
3907284 AAAAAT-TTATCAAAATAT
1 AAAAATATTATAAAAAAAT
3907302 AA
1 AA
3907304 TCTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATTATAAAAAAAT
Found at i:3907325 original size:27 final size:27
Alignment explanation
Indices: 3907288--3907356 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
3907278 AAAAATAAAA
**
3907288 ATTTATCAAAATATAATCTTTTTTTTT
1 ATTTATCAAAATATAATAATTTTTTTT
*
3907315 ATTTA-CTAAAATATTATAATTTTTTTT
1 ATTTATC-AAAATATAATAATTTTTTTT
3907342 ATTTATCAAAATATA
1 ATTTATCAAAATATA
3907357 CCAAAAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 34 0.94
28 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTATCAAAATATAATAATTTTTTTT
Found at i:3907927 original size:58 final size:58
Alignment explanation
Indices: 3907863--3907972 Score: 220
Period size: 58 Copynumber: 1.9 Consensus size: 58
3907853 CTGGTATTTC
3907863 TATTAATTTAAAATATAGTTATTAAATGAGAATAGTTTATTAAATTAAAATAGAGTTA
1 TATTAATTTAAAATATAGTTATTAAATGAGAATAGTTTATTAAATTAAAATAGAGTTA
3907921 TATTAATTTAAAATATAGTTATTAAATGAGAATAGTTTATTAAATTAAAATA
1 TATTAATTTAAAATATAGTTATTAAATGAGAATAGTTTATTAAATTAAAATA
3907973 ATAACGAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (58 bp):
TATTAATTTAAAATATAGTTATTAAATGAGAATAGTTTATTAAATTAAAATAGAGTTA
Found at i:3907954 original size:19 final size:20
Alignment explanation
Indices: 3907872--3907972 Score: 88
Period size: 18 Copynumber: 5.3 Consensus size: 20
3907862 CTATTAATTT
3907872 AAAATATAG-TTATTAAATG
1 AAAATATAGTTTATTAAATG
* *
3907891 -AGA-ATAGTTTATTAAATT
1 AAAATATAGTTTATTAAATG
* * *
3907909 AAAATAGAGTTATATTAATTT
1 AAAATATAGTT-TATTAAATG
3907930 AAAATATAG-TTATTAAATG
1 AAAATATAGTTTATTAAATG
* *
3907949 -AGA-ATAGTTTATTAAATT
1 AAAATATAGTTTATTAAATG
3907967 AAAATA
1 AAAATA
3907973 ATAACGAATA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
17 8 0.12
18 22 0.34
19 11 0.17
20 7 0.11
21 16 0.25
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
AAAATATAGTTTATTAAATG
Found at i:3908609 original size:27 final size:27
Alignment explanation
Indices: 3908579--3908631 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3908569 TTTTTTCTGT
* *
3908579 TTTTTTTGT-ATATTTTGGTAAATAAA
1 TTTTTTTATAATATTTTAGTAAATAAA
3908605 TTTTTTTATAATATTTTAGTAAATAAA
1 TTTTTTTATAATATTTTAGTAAATAAA
3908632 AAAAAGATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (27 bp):
TTTTTTTATAATATTTTAGTAAATAAA
Found at i:3908665 original size:18 final size:19
Alignment explanation
Indices: 3908639--3908677 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3908629 AAAAAAAAGA
3908639 TTATATTTTGATAA-ATTT
1 TTATATTTTGATAATATTT
* *
3908657 TTATTTTTTTATAATATTT
1 TTATATTTTGATAATATTT
3908676 TT
1 TT
3908678 GTAAAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (19 bp):
TTATATTTTGATAATATTT
Found at i:3948191 original size:24 final size:25
Alignment explanation
Indices: 3948135--3948223 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
3948125 CCATATAATA
* * *
3948135 GGAAGCTTATGTGAGCCATGTAA-CA
1 GGAAGCTCATGAGAGCCA-GTAATCG
*
3948160 GGAAGCTCATGAGAGTC-GTAATCG
1 GGAAGCTCATGAGAGCCAGTAATCG
** * *
3948184 GGAAGCTCCGGAGAGCCATTAATTG
1 GGAAGCTCATGAGAGCCAGTAATCG
3948209 GGAAGCTCATGAGAG
1 GGAAGCTCATGAGAG
3948224 AGCCTTTAAT
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
23 4 0.08
24 15 0.29
25 32 0.63
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.20
Consensus pattern (25 bp):
GGAAGCTCATGAGAGCCAGTAATCG
Found at i:3948212 original size:25 final size:27
Alignment explanation
Indices: 3948178--3948243 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
3948168 ATGAGAGTCG
*
3948178 TAATCGGGAAGCTC-CG-GAGAGCCAT
1 TAATTGGGAAGCTCACGAGAGAGCCAT
* *
3948203 TAATTGGGAAGCTCATGAGAGAGCCTT
1 TAATTGGGAAGCTCACGAGAGAGCCAT
*
3948230 TAATTGAGAAGCTC
1 TAATTGGGAAGCTC
3948244 GTAAGAGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 13 0.37
26 1 0.03
27 21 0.60
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (27 bp):
TAATTGGGAAGCTCACGAGAGAGCCAT
Found at i:3948250 original size:27 final size:27
Alignment explanation
Indices: 3948194--3948250 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
3948184 GGAAGCTCCG
* *
3948194 GAGAGCCATTAATTGGGAAGCTCATGA
1 GAGAGCCATTAATTGAGAAGCTCATAA
* *
3948221 GAGAGCCTTTAATTGAGAAGCTCGTAA
1 GAGAGCCATTAATTGAGAAGCTCATAA
3948248 GAG
1 GAG
3948251 CCATATGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (27 bp):
GAGAGCCATTAATTGAGAAGCTCATAA
Found at i:3948288 original size:25 final size:23
Alignment explanation
Indices: 3948260--3948336 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
3948250 GCCATATGTT
3948260 GGGATGCTCATAAGAGCTAAATAAC
1 GGGATGCTCA-AAGAGCT-AATAAC
* ** * *
3948285 GGGAAGCTCCGGAGAGCCAATATC
1 GGGATGCT-CAAAGAGCTAATAAC
3948309 GGGATGCTCAAGAGAGCTAATAAC
1 GGGATGCTCAA-AGAGCTAATAAC
3948333 GGGA
1 GGGA
3948337 CGTTCTTGCA
Statistics
Matches: 40, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
23 1 0.03
24 26 0.65
25 12 0.30
26 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (23 bp):
GGGATGCTCAAAGAGCTAATAAC
Found at i:3959279 original size:18 final size:18
Alignment explanation
Indices: 3959258--3959299 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3959248 AAGTTGATAA
*
3959258 AAAAAACACT-TTTGAGGT
1 AAAAAACACTATTT-AGAT
*
3959276 AAAAAGCACTATTTAGAT
1 AAAAAACACTATTTAGAT
3959294 AAAAAA
1 AAAAAA
3959300 ATTGTTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAAACACTATTTAGAT
Found at i:3966853 original size:24 final size:24
Alignment explanation
Indices: 3966808--3966854 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3966798 TATATATATC
3966808 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
3966832 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
3966855 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:3977272 original size:26 final size:26
Alignment explanation
Indices: 3977236--3977288 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3977226 CAAAAATTAT
3977236 GTTAAAACAGTCTGCACATGATACTA
1 GTTAAAACAGTCTGCACATGATACTA
3977262 GTTAAAACAGTCTGCACATGATACTA
1 GTTAAAACAGTCTGCACATGATACTA
3977288 G
1 G
3977289 AAGAATGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (26 bp):
GTTAAAACAGTCTGCACATGATACTA
Found at i:3980392 original size:30 final size:30
Alignment explanation
Indices: 3980358--3980417 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3980348 TTGTATGCTC
*
3980358 AATACATGCTTACTTGAGTATTGTGTGATT
1 AATACATGCATACTTGAGTATTGTGTGATT
*
3980388 AATACATGCATATTTGAGTATTGTGTGATT
1 AATACATGCATACTTGAGTATTGTGTGATT
3980418 TTTTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.43
Consensus pattern (30 bp):
AATACATGCATACTTGAGTATTGTGTGATT
Found at i:3980547 original size:14 final size:13
Alignment explanation
Indices: 3980528--3980558 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3980518 ATTAAGAAAA
3980528 TTGTATTTGTTTAT
1 TTGTATTTGTTT-T
3980542 TTGTATTTGTTTT
1 TTGTATTTGTTTT
3980555 TTGT
1 TTGT
3980559 CACTAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.10, C:0.00, G:0.16, T:0.74
Consensus pattern (13 bp):
TTGTATTTGTTTT
Found at i:3985434 original size:26 final size:26
Alignment explanation
Indices: 3985405--3985496 Score: 68
Period size: 26 Copynumber: 3.6 Consensus size: 26
3985395 CTTATGAGTG
3985405 TCCCGTTATATGGCTCTTCGTGAGCT
1 TCCCGTTATATGGCTCTTCGTGAGCT
* * *
3985431 TCCCGATTA-AAGGCACTTTGTGAGCT
1 TCCCG-TTATATGGCTCTTCGTGAGCT
* * *
3985457 T-TCGTGATTAATGGCTCATCG-GAGCT
1 TCCCGTTA-T-ATGGCTCTTCGTGAGCT
3985483 TCCCG--ATATGGCTC
1 TCCCGTTATATGGCTC
3985497 GCTTGAACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 13
0.69 0.14 0.18
Matches are distributed among these distances:
23 7 0.14
24 3 0.06
25 3 0.06
26 26 0.51
27 12 0.24
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (26 bp):
TCCCGTTATATGGCTCTTCGTGAGCT
Found at i:4000937 original size:19 final size:19
Alignment explanation
Indices: 4000913--4000951 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
4000903 AGCAAGGAAA
4000913 TCTTTTCAGCAATCCAATT
1 TCTTTTCAGCAATCCAATT
4000932 TCTTTTCAGCAATCCAATT
1 TCTTTTCAGCAATCCAATT
4000951 T
1 T
4000952 GGACCAACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.44
Consensus pattern (19 bp):
TCTTTTCAGCAATCCAATT
Found at i:4004520 original size:26 final size:26
Alignment explanation
Indices: 4004489--4004538 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
4004479 TTTCTTAGAA
4004489 TAGTATTGAAAATGTATATATAATAT
1 TAGTATTGAAAATGTATATATAATAT
4004515 TAGTATTGAAAATGTATATATAAT
1 TAGTATTGAAAATGTATATATAAT
4004539 TATTTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (26 bp):
TAGTATTGAAAATGTATATATAATAT
Found at i:4004764 original size:2 final size:2
Alignment explanation
Indices: 4004759--4004784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4004749 ACAAACTTGA
4004759 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4004785 TAAAGGATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4022581 original size:32 final size:32
Alignment explanation
Indices: 4022545--4022609 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4022535 GTTCGAAAAT
4022545 CTTTTCATTTGTGAATTCAGTCAAATACATGG
1 CTTTTCATTTGTGAATTCAGTCAAATACATGG
4022577 CTTTTCATTTGTGAATTCAGTCAAATACATGG
1 CTTTTCATTTGTGAATTCAGTCAAATACATGG
4022609 C
1 C
4022610 CCATGCTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (32 bp):
CTTTTCATTTGTGAATTCAGTCAAATACATGG
Found at i:4023723 original size:22 final size:22
Alignment explanation
Indices: 4023694--4023784 Score: 94
Period size: 22 Copynumber: 4.0 Consensus size: 22
4023684 TGCACTAATG
*
4023694 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAACGTGCTA
* *
4023716 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-ACGTGCTA
* *
4023738 AACAGAGAACACTGACGTGCTAA
1 AACAGAGAGCACTAACGTGCT-A
*
4023761 AATCAGAGAGCACCAACGTGCTA
1 AA-CAGAGAGCACTAACGTGCTA
4023784 A
1 A
4023785 TAATCAGAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.02
22 34 0.61
23 5 0.09
24 16 0.29
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (22 bp):
AACAGAGAGCACTAACGTGCTA
Found at i:4024878 original size:5 final size:5
Alignment explanation
Indices: 4024860--4024899 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
4024850 TGTTTTATGT
*
4024860 ATATA ATAATA ATATA ATATT ATAATA ATATA ATATA ATA
1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATA
4024900 ACTTACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.71
6 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:4024884 original size:16 final size:16
Alignment explanation
Indices: 4024860--4024900 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
4024850 TGTTTTATGT
4024860 ATATAATAATAATATA
1 ATATAATAATAATATA
*
4024876 ATATTATAATAATATA
1 ATATAATAATAATATA
4024892 ATATAATAA
1 ATATAATAA
4024901 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:4024900 original size:8 final size:8
Alignment explanation
Indices: 4024865--4024894 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
4024855 TATGTATATA
4024865 ATAATAAT
1 ATAATAAT
*
4024873 ATAATATT
1 ATAATAAT
4024881 ATAATAAT
1 ATAATAAT
4024889 ATAATA
1 ATAATA
4024895 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:4031656 original size:16 final size:16
Alignment explanation
Indices: 4031637--4031684 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
4031627 GTGAAAATTA
4031637 AATATTTTATTAATAT
1 AATATTTTATTAATAT
*
4031653 AATATTTTAACTAATAT
1 AATATTTT-ATTAATAT
*
4031670 CAT-TTTTATTTAATA
1 AATATTTTA-TTAATA
4031685 GATTATAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 17 0.63
17 9 0.33
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTTTATTAATAT
Found at i:4035833 original size:24 final size:24
Alignment explanation
Indices: 4035795--4035857 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
4035785 AAGAAAAACT
*
4035795 AATAATAATTCAAAAAAT-TTAAA
1 AATAATAATTAAAAAAATATTAAA
* *
4035818 AAGTAATACTTAAAAATATATTAAA
1 AA-TAATAATTAAAAAAATATTAAA
* *
4035843 AATTATATTTAAAAA
1 AATAATAATTAAAAA
4035858 CTAAGAGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
23 2 0.06
24 24 0.73
25 7 0.21
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAATAATTAAAAAAATATTAAA
Found at i:4036420 original size:20 final size:20
Alignment explanation
Indices: 4036395--4036434 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4036385 CGTAAAATGA
*
4036395 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
4036415 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
4036435 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:4044370 original size:50 final size:49
Alignment explanation
Indices: 4044306--4044488 Score: 215
Period size: 50 Copynumber: 3.6 Consensus size: 49
4044296 AGCTCCATAT
*
4044306 GGTCCCATGTAAGACCATGCCTAGGGCATGGCGTTGGCACCGAGATGAGA
1 GGTCCCATGTAAGACCATGTCT-GGGCATGGCGTTGGCACCGAGATGAGA
* *
4044356 GGTCCCATGCAAGACCATGTCTGAGACATGGCGTTGGCACCGAGATGAGA
1 GGTCCCATGTAAGACCATGTCTG-GGCATGGCGTTGGCACCGAGATGAGA
** * *
4044406 GGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGACG-TGAGAA
1 GGTCCCATGTAAGACCATGTCTGGG-CATGGCGTTGGCACCGA-GATGAG-A
** *
4044457 CATTCCATGTAAGACCATGTCTGGGACATGGC
1 GGTCCCATGTAAGACCATGTCTGGG-CATGGC
4044489 TTTGACATGT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.02
50 84 0.73
51 29 0.25
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.19
Consensus pattern (49 bp):
GGTCCCATGTAAGACCATGTCTGGGCATGGCGTTGGCACCGAGATGAGA
Found at i:4048622 original size:2 final size:2
Alignment explanation
Indices: 4048615--4048645 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4048605 CATTCATGTA
4048615 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4048646 AGTGATACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4057309 original size:23 final size:22
Alignment explanation
Indices: 4057283--4057326 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4057273 TAATTTAAAT
*
4057283 ATTATAATAATTTTTAACATATA
1 ATTAAAAT-ATTTTTAACATATA
* *
4057306 ATTAAAATGTTTTTACCATAT
1 ATTAAAATATTTTTAACATAT
4057327 TCAACATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTAAAATATTTTTAACATATA
Found at i:4065765 original size:22 final size:22
Alignment explanation
Indices: 4065737--4065781 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4065727 AAAAAGGAAG
4065737 TTTGTAATAACTGAGACCAAAC
1 TTTGTAATAACTGAGACCAAAC
4065759 TTTGTAATAACTGAGACCAAAC
1 TTTGTAATAACTGAGACCAAAC
4065781 T
1 T
4065782 GCTTCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (22 bp):
TTTGTAATAACTGAGACCAAAC
Found at i:4076808 original size:22 final size:22
Alignment explanation
Indices: 4076780--4076821 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4076770 ATTTTTTAAC
4076780 AGATTTAATAAATAAATTCACG
1 AGATTTAATAAATAAATTCACG
*
4076802 AGATTTAATGAATAAATTCA
1 AGATTTAATAAATAAATTCA
4076822 ATATTTCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (22 bp):
AGATTTAATAAATAAATTCACG
Found at i:4079196 original size:116 final size:116
Alignment explanation
Indices: 4078992--4079225 Score: 450
Period size: 116 Copynumber: 2.0 Consensus size: 116
4078982 CAAGTCCAAC
4078992 TGATGATGGGAGCTTGTCATTGGTAGCATGCCTACAGACCCCTCATATGAAACCCTTCGAGGAAC
1 TGATGATGGGAGCTTGTCATTGGTAGCATGCCTACAGACCCCTCATATGAAACCCTTCGAGGAAC
4079057 AACTATACCAAGGCTTGACGTCATCTGAGAACAAAAAGGCTCGATATTAGT
66 AACTATACCAAGGCTTGACGTCATCTGAGAACAAAAAGGCTCGATATTAGT
4079108 TGATGATGGGAGCTTGTCATTGGTAGCATGCCTACAGACCCCTCATATGAAACCCTTCGAGGAAC
1 TGATGATGGGAGCTTGTCATTGGTAGCATGCCTACAGACCCCTCATATGAAACCCTTCGAGGAAC
* *
4079173 ATCTATACCAAGGCTTGATGTCATCTGAGAACAAAAAGGCTCGATATTAGT
66 AACTATACCAAGGCTTGACGTCATCTGAGAACAAAAAGGCTCGATATTAGT
4079224 TG
1 TG
4079226 TTCTTACTCT
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (116 bp):
TGATGATGGGAGCTTGTCATTGGTAGCATGCCTACAGACCCCTCATATGAAACCCTTCGAGGAAC
AACTATACCAAGGCTTGACGTCATCTGAGAACAAAAAGGCTCGATATTAGT
Found at i:4088597 original size:2 final size:2
Alignment explanation
Indices: 4088590--4088636 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
4088580 TTATTAGAAA
4088590 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4088632 TC TC T
1 TC TC T
4088637 AGTTCTGGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4097534 original size:17 final size:17
Alignment explanation
Indices: 4097513--4097544 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4097503 TTCGATTTTA
4097513 AAAAAAATAA-AGATTG
1 AAAAAAATAAGAGATTG
4097529 AAAAAAATAAGAGATT
1 AAAAAAATAAGAGATT
4097545 TGGTGGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
AAAAAAATAAGAGATTG
Found at i:4124990 original size:33 final size:32
Alignment explanation
Indices: 4124918--4124993 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
4124908 TAGATACATG
* * **
4124918 TGTAAGACCATACCTGGGCTATGGCATTCTGA
1 TGTAAGACCATAACTGGGCTATGGCATACAAA
*
4124950 TGATAAGACCATAACTGGGTTATGGCACTACAAA
1 TG-TAAGACCATAACTGGGCTATGGCA-TACAAA
4124984 TGTAAGACCA
1 TGTAAGACCA
4124994 CGGCAGGGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 30 0.81
34 5 0.14
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGGCATACAAA
Found at i:4125006 original size:105 final size:105
Alignment explanation
Indices: 4124813--4125007 Score: 232
Period size: 105 Copynumber: 1.9 Consensus size: 105
4124803 AATGTTTAAA
* * ** **
4124813 TGTAAGACCATAGCTGGGCTATGACATTTTAATGAAAAGACCATAGTTAGGTTATGGCACCTTGA
1 TGTAAGACCATACCTGGGCTATGACATTCTAATGAAAAGACCATAACTAGGTTATGGCACCTACA
* **
4124878 ACATAAGACCATGGTTGGACCATGGTAGTATAGATACATG
66 ACATAAGACCACGGCAGGACCATGGTAGTATAGATACATG
* * * *
4124918 TGTAAGACCATACCTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGGCA-CTACA
1 TGTAAGACCATACCTGGGCTATGACATTCTAATGAAAAGACCATAACTAGGTTATGGCACCTACA
*
4124982 A-ATGTAAGACCACGGCAGGGCCATGG
66 ACA--TAAGACCACGGCAGGACCATGG
4125008 CAATGCATGT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
103 1 0.01
104 4 0.05
105 69 0.93
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (105 bp):
TGTAAGACCATACCTGGGCTATGACATTCTAATGAAAAGACCATAACTAGGTTATGGCACCTACA
ACATAAGACCACGGCAGGACCATGGTAGTATAGATACATG
Found at i:4128622 original size:16 final size:16
Alignment explanation
Indices: 4128597--4128630 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4128587 CTCACTCTTC
*
4128597 CATAGTTTACTTGTCT
1 CATAGATTACTTGTCT
4128613 CATAGATTACTTGTCT
1 CATAGATTACTTGTCT
4128629 CA
1 CA
4128631 CTCTTCCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (16 bp):
CATAGATTACTTGTCT
Found at i:4129466 original size:24 final size:24
Alignment explanation
Indices: 4129434--4129499 Score: 123
Period size: 24 Copynumber: 2.8 Consensus size: 24
4129424 TAAAAGGTAA
4129434 CATAGTTTACTTGTCTCAATCTTC
1 CATAGTTTACTTGTCTCAATCTTC
*
4129458 CATAGTTTACTTGTCTCACTCTTC
1 CATAGTTTACTTGTCTCAATCTTC
4129482 CATAGTTTACTTGTCTCA
1 CATAGTTTACTTGTCTCA
4129500 TGGTTTACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.20, C:0.26, G:0.09, T:0.45
Consensus pattern (24 bp):
CATAGTTTACTTGTCTCAATCTTC
Found at i:4150044 original size:16 final size:15
Alignment explanation
Indices: 4150025--4150058 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4150015 TATTTAAATC
4150025 ATTAAAAATTAAAAAA
1 ATTAAAAA-TAAAAAA
*
4150041 ATTATAAATAAAAAA
1 ATTAAAAATAAAAAA
4150056 ATT
1 ATT
4150059 CCAATAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAAATAAAAAA
Found at i:4180120 original size:6 final size:6
Alignment explanation
Indices: 4180109--4180142 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
4180099 TGATGGCCCC
*
4180109 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCC GAGG
1 GAGGCG GAGGCG GAGGCG GAGGCG GAGGCG GAGG
4180143 ATGTGCCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.65, T:0.00
Consensus pattern (6 bp):
GAGGCG
Found at i:4189355 original size:16 final size:16
Alignment explanation
Indices: 4189324--4189360 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4189314 TAGTAAAGAA
4189324 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
4189340 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
4189356 TATTA
1 TATTA
4189361 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:4194341 original size:4 final size:4
Alignment explanation
Indices: 4194332--4194370 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
4194322 TTATATTACT
*
4194332 CATA CATA CATA CATA CATA CATA CTTA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
4194371 GATATATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:4194489 original size:26 final size:27
Alignment explanation
Indices: 4194439--4194499 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 27
4194429 AAAAATAACT
4194439 AAAATATTATAACTTTTTTTTATTTACC
1 AAAATATTATAAC-TTTTTTTATTTACC
4194467 AAAATATTATAA-TTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
4194493 AAAATAT
1 AAAATAT
4194500 ACAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 21 0.64
28 12 0.36
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (27 bp):
AAAATATTATAACTTTTTTTATTTACC
Found at i:4194514 original size:19 final size:18
Alignment explanation
Indices: 4194490--4194527 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
4194480 TTTTTTATTT
4194490 ACCAAAATATACA-AAAAAA
1 ACCAAAA-A-ACAGAAAAAA
4194509 ACCAAAAAACAGAAAAAA
1 ACCAAAAAACAGAAAAAA
4194527 A
1 A
4194528 AAACCTGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 8 0.44
19 7 0.39
ACGTcount: A:0.76, C:0.16, G:0.03, T:0.05
Consensus pattern (18 bp):
ACCAAAAAACAGAAAAAA
Found at i:4194590 original size:27 final size:27
Alignment explanation
Indices: 4194560--4194611 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4194550 GGCCAATCAC
4194560 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
4194587 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
4194612 GACTAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:4194910 original size:15 final size:15
Alignment explanation
Indices: 4194892--4194935 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
4194882 TTTAAAAAAA
4194892 TTAAATTAAAATAGT
1 TTAAATTAAAATAGT
* * **
4194907 TTAATTTTAAATTTT
1 TTAAATTAAAATAGT
4194922 TTAAATTAAAATAG
1 TTAAATTAAAATAG
4194936 AGTTATTAAA
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (15 bp):
TTAAATTAAAATAGT
Found at i:4194911 original size:30 final size:30
Alignment explanation
Indices: 4194876--4194935 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4194866 ATAACTCTAT
4194876 TTTAATTTTAAAAAAATTAAATTAAAATAG
1 TTTAATTTTAAAAAAATTAAATTAAAATAG
****
4194906 TTTAATTTTAAATTTTTTAAATTAAAATAG
1 TTTAATTTTAAAAAAATTAAATTAAAATAG
4194936 AGTTATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTAATTTTAAAAAAATTAAATTAAAATAG
Found at i:4195108 original size:134 final size:137
Alignment explanation
Indices: 4194829--4195122 Score: 524
Period size: 134 Copynumber: 2.2 Consensus size: 137
4194819 ATAAGCTCTT
4194829 AAATAGAGCTATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
1 AAATAGAG-TATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
*
4194894 AAATTAAAATAGTTTAATTTTAAATTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
65 AAATTAAAATAGTTTAATCTTAAATTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
4194959 TTAAATTA
130 TTAAATTA
4194967 AAATAGAGTAATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAA-TTTAAAAAAATT
1 AAATAGAGT-ATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATT
4195031 AAATTAAAATAGTTT-A-CTT-AATTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
65 AAATTAAAATAGTTTAATCTTAAATTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
4195093 TTAAATTA
130 TTAAATTA
4195101 AAATAGAGTTATTACTTAATTA
1 AAATAGAG-TATTACTTAATTA
4195123 CGGTGTTTTG
Statistics
Matches: 153, Mismatches: 1, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
134 71 0.46
135 3 0.02
136 1 0.01
137 28 0.18
138 50 0.33
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (137 bp):
AAATAGAGTATTACTTAATTAGAATTCTCTCATTTAATAACTCTATTTTAATTTTAAAAAAATTA
AATTAAAATAGTTTAATCTTAAATTTTTTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTAT
TAAATTA
Found at i:4195119 original size:18 final size:19
Alignment explanation
Indices: 4195056--4195114 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
4195046 ACTTAATTTT
4195056 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
4195075 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
4195093 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
4195112 TTA
1 TTA
4195115 CTTAATTACG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:4195706 original size:27 final size:27
Alignment explanation
Indices: 4195665--4195716 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4195655 CATTTTAGTC
4195665 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
*
4195692 CTTTGGCACCTTTGGTGCCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
4195717 GTGATTAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.33, G:0.23, T:0.31
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:4201937 original size:19 final size:20
Alignment explanation
Indices: 4201913--4201950 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4201903 TAATTTTAAT
4201913 ATTTAT-TTAAAAATAAAAA
1 ATTTATATTAAAAATAAAAA
4201932 ATTTATATTAAAAATAAAA
1 ATTTATATTAAAAATAAAA
4201951 TAATATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTTATATTAAAAATAAAAA
Found at i:4208403 original size:20 final size:20
Alignment explanation
Indices: 4208378--4208417 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4208368 CGTAAAATGA
*
4208378 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
4208398 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
4208418 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:4208407 original size:34 final size:35
Alignment explanation
Indices: 4208363--4208429 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
4208353 CAGTAAAATA
*
4208363 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
4208397 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
4208430 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:4208433 original size:14 final size:15
Alignment explanation
Indices: 4208357--4208433 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
4208347 GATTGCCAGT
* *
4208357 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
4208371 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
4208385 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
4208405 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
4208420 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
4208434 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:4228453 original size:43 final size:41
Alignment explanation
Indices: 4228399--4228554 Score: 188
Period size: 43 Copynumber: 3.7 Consensus size: 41
4228389 TATCGTAACA
* * *
4228399 ATGCCATATCCCAGATATGGTCTTACATGTAATACTGTATCG
1 ATGCCATATCCCAGACATGGTCTTACACG-AATACTATATCG
*
4228441 ATGCCAATATCCCAGCCATGGTCTTACACGAAATCAC-ATATCG
1 ATGCC-ATATCCCAGACATGGTCTTACACG-AAT-ACTATATCG
* *
4228484 ATGCCAATGTCCCAGACATGGTCTTACACGAATTCTCATATCG
1 ATGCC-ATATCCCAGACATGGTCTTACACGAATACT-ATATCG
*
4228527 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGACATGGTCTTACAC
4228555 ATAATCTCGG
Statistics
Matches: 100, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
41 1 0.01
42 29 0.29
43 68 0.68
44 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (41 bp):
ATGCCATATCCCAGACATGGTCTTACACGAATACTATATCG
Found at i:4228526 original size:86 final size:84
Alignment explanation
Indices: 4228399--4228554 Score: 215
Period size: 85 Copynumber: 1.8 Consensus size: 84
4228389 TATCGTAACA
* * * *
4228399 ATGCCATATCCCAGATATGGTCTTACATGTAATACTGTATCGATGCCAATATCCCAGCCATGGTC
1 ATGCCATATCCCAGACATGGTCTTACACGTAATACTATATCGATGCC-ATATCCCAGACATGGTC
4228464 TTACACGAAATCACATATCG
65 TTACACGAAATCACATATCG
* * *
4228484 ATGCCAATGTCCCAGACATGGTCTTACACG-AATTCTCATATCGATGCCATATCCCAGATATGGT
1 ATGCC-ATATCCCAGACATGGTCTTACACGTAATACT-ATATCGATGCCATATCCCAGACATGGT
4228548 CTTACAC
64 CTTACAC
4228555 ATAATCTCGG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
85 31 0.50
86 31 0.50
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (84 bp):
ATGCCATATCCCAGACATGGTCTTACACGTAATACTATATCGATGCCATATCCCAGACATGGTCT
TACACGAAATCACATATCG
Found at i:4260080 original size:2 final size:2
Alignment explanation
Indices: 4260073--4260118 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
4260063 TCGATCTGTT
4260073 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4260115 AG AG
1 AG AG
4260119 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4261699 original size:12 final size:12
Alignment explanation
Indices: 4261668--4261700 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
4261658 AATTCATTAT
*
4261668 TTTTAAAAATAA
1 TTTTATAAATAA
4261680 TTTT-TAAATAA
1 TTTTATAAATAA
4261691 TTTTATAAAT
1 TTTTATAAAT
4261701 CAAATTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTATAAATAA
Found at i:4262154 original size:2 final size:2
Alignment explanation
Indices: 4262147--4262186 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4262137 CGTCTCATTT
4262147 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4262187 CTTACTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4266868 original size:2 final size:2
Alignment explanation
Indices: 4266861--4266894 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4266851 AGACTTCAGA
4266861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4266895 CAAAGGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4268167 original size:21 final size:21
Alignment explanation
Indices: 4268141--4268182 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4268131 ATGGAAGTGA
4268141 ACAACCCTGTTTGTTAACAAT
1 ACAACCCTGTTTGTTAACAAT
4268162 ACAACCCTGTTTGTTAACAAT
1 ACAACCCTGTTTGTTAACAAT
4268183 CATTTGTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (21 bp):
ACAACCCTGTTTGTTAACAAT
Found at i:4268868 original size:30 final size:30
Alignment explanation
Indices: 4268832--4268891 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4268822 CATCTGCAAA
4268832 TGATGTTTTAACTCTATAGTTATTCAGGAT
1 TGATGTTTTAACTCTATAGTTATTCAGGAT
4268862 TGATGTTTTAACTCTATAGTTATTCAGGAT
1 TGATGTTTTAACTCTATAGTTATTCAGGAT
4268892 AACCAGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (30 bp):
TGATGTTTTAACTCTATAGTTATTCAGGAT
Found at i:4273746 original size:9 final size:9
Alignment explanation
Indices: 4273722--4273768 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
4273712 TGGCTGAAGC
4273722 TCTTCCTCT
1 TCTTCCTCT
* *
4273731 TCATCCTCG
1 TCTTCCTCT
4273740 TCTTCCTCT
1 TCTTCCTCT
*
4273749 TCTTCTTCT
1 TCTTCCTCT
*
4273758 TCCTCCTCT
1 TCTTCCTCT
4273767 TC
1 TC
4273769 CTCACCATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.51
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:4273755 original size:24 final size:24
Alignment explanation
Indices: 4273721--4273771 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4273711 GTGGCTGAAG
*
4273721 CTCTTCCTCTTCATCCTCGTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
* *
4273745 CTCTTCTTCTTCTTCCTCCTCTTC
1 CTCTTCCTCTTCATCCTCCTCTTC
4273769 CTC
1 CTC
4273772 ACCATCATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.02, C:0.47, G:0.02, T:0.49
Consensus pattern (24 bp):
CTCTTCCTCTTCATCCTCCTCTTC
Found at i:4273788 original size:9 final size:9
Alignment explanation
Indices: 4273776--4273822 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
4273766 TTCCTCACCA
4273776 TCATCGTCG
1 TCATCGTCG
4273785 TCATCGTCG
1 TCATCGTCG
* *
4273794 TCATCATCC
1 TCATCGTCG
*
4273803 TCGTCGTCG
1 TCATCGTCG
*
4273812 TCATCCTCG
1 TCATCGTCG
4273821 TC
1 TC
4273823 TCCACTGGCA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.11, C:0.38, G:0.17, T:0.34
Consensus pattern (9 bp):
TCATCGTCG
Found at i:4273794 original size:12 final size:12
Alignment explanation
Indices: 4273774--4273822 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
4273764 TCTTCCTCAC
4273774 CATCATCGTCGT
1 CATCATCGTCGT
* *
4273786 CATCGTCGTCAT
1 CATCATCGTCGT
*
4273798 CATCCTCGTCGT
1 CATCATCGTCGT
* *
4273810 CGTCATCCTCGT
1 CATCATCGTCGT
4273822 C
1 C
4273823 TCCACTGGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.12, C:0.39, G:0.16, T:0.33
Consensus pattern (12 bp):
CATCATCGTCGT
Found at i:4273808 original size:15 final size:15
Alignment explanation
Indices: 4273788--4273822 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
4273778 ATCGTCGTCA
4273788 TCGTCGTCATCATCC
1 TCGTCGTCATCATCC
*
4273803 TCGTCGTCGTCATCC
1 TCGTCGTCATCATCC
4273818 TCGTC
1 TCGTC
4273823 TCCACTGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.09, C:0.40, G:0.17, T:0.34
Consensus pattern (15 bp):
TCGTCGTCATCATCC
Found at i:4273920 original size:21 final size:21
Alignment explanation
Indices: 4273896--4273935 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4273886 TGCATCCTCC
4273896 TCATCTGCAT-CTTCATCTTGA
1 TCATCT-CATGCTTCATCTTGA
*
4273917 TCATCTCCTGCTTCATCTT
1 TCATCTCATGCTTCATCTT
4273936 TCTCATCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.15, C:0.33, G:0.07, T:0.45
Consensus pattern (21 bp):
TCATCTCATGCTTCATCTTGA
Found at i:4279270 original size:93 final size:93
Alignment explanation
Indices: 4279111--4279296 Score: 354
Period size: 93 Copynumber: 2.0 Consensus size: 93
4279101 ATCTACGTCC
* *
4279111 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATGAATAAATAACT
1 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
4279176 ATTCAATCATAACTAACCTTGATGGTCT
66 ATTCAATCATAACTAACCTTGATGGTCT
4279204 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
1 CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
4279269 ATTCAATCATAACTAACCTTGATGGTCT
66 ATTCAATCATAACTAACCTTGATGGTCT
4279297 TGTCATCACC
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (93 bp):
CACACCTAAACTCAAGAAATCAGTGTAGAAGATCTATTTTTCTTCATATCAATAAAGAAATAACT
ATTCAATCATAACTAACCTTGATGGTCT
Found at i:4284047 original size:19 final size:20
Alignment explanation
Indices: 4284003--4284048 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
4283993 TAGACAAAAT
*
4284003 TTATTTTTAAAAATTAATAA
1 TTATTTTAAAAAATTAATAA
*
4284023 TT-TTTTAAAAAATTTA-AA
1 TTATTTTAAAAAATTAATAA
4284041 TTATTTTA
1 TTATTTTA
4284049 CTATTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 17 0.74
20 2 0.09
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTTTAAAAAATTAATAA
Found at i:4297691 original size:3 final size:3
Alignment explanation
Indices: 4297683--4297716 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
4297673 AGGAGTGTAC
4297683 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
4297717 AATAGTTAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:4304665 original size:2 final size:2
Alignment explanation
Indices: 4304660--4304695 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4304650 AAAATGGACA
4304660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4304696 CTTTATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4310394 original size:19 final size:17
Alignment explanation
Indices: 4310372--4310423 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
4310362 ATAAAAATAA
4310372 TATAAAATTTTAAAGTATT
1 TATAAAATTTTAAA-T-TT
*
4310391 TATAAAAATTTCAAATTT
1 TAT-AAAATTTTAAATTT
*
4310409 TCATAATATTTTAAA
1 T-ATAAAATTTTAAA
4310424 AATGTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 12 0.43
19 6 0.21
20 10 0.36
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (17 bp):
TATAAAATTTTAAATTT
Found at i:4310729 original size:27 final size:27
Alignment explanation
Indices: 4310679--4310731 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
4310669 TCACTTTCTT
*
4310679 TTTTGTGTATCTTTTTTTTCTGAAAGC
1 TTTTGTGTATCTTTTTTATCTGAAAGC
*
4310706 TTTTGTTTATCTTTTTTAAT-TGAAAG
1 TTTTGTGTATCTTTTTT-ATCTGAAAG
4310732 TCTACAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.19, C:0.08, G:0.13, T:0.60
Consensus pattern (27 bp):
TTTTGTGTATCTTTTTTATCTGAAAGC
Found at i:4311903 original size:21 final size:19
Alignment explanation
Indices: 4311873--4311913 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
4311863 GTGGAGATTT
*
4311873 TAATTTTATTTAATATTAATA
1 TAATTATATTT-AT-TTAATA
4311894 TAATTATATTTATTTAATA
1 TAATTATATTTATTTAATA
4311913 T
1 T
4311914 TAATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 2 0.11
21 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATTATATTTATTTAATA
Found at i:4312421 original size:20 final size:19
Alignment explanation
Indices: 4312396--4312435 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
4312386 ACTGCCAGAA
4312396 ATAATTACTTTGTTCAGTGG
1 ATAATTACTTTGTTC-GTGG
*
4312416 ATAATTATTTTGTTCGTGG
1 ATAATTACTTTGTTCGTGG
4312435 A
1 A
4312436 ACAAAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (19 bp):
ATAATTACTTTGTTCGTGG
Found at i:4316176 original size:14 final size:14
Alignment explanation
Indices: 4316157--4316184 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4316147 TTGTTGTTGT
4316157 TTTTTTTTTTTTGG
1 TTTTTTTTTTTTGG
4316171 TTTTTTTTTTTTGG
1 TTTTTTTTTTTTGG
4316185 GGGGGGGGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTTGG
Found at i:4318077 original size:24 final size:24
Alignment explanation
Indices: 4318050--4318101 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
4318040 AATCAAAGTC
* *
4318050 AAATATATGATGCTAATAAATGCT
1 AAATATATGATACTAATAAATACT
* *
4318074 AAATATATTATACTCATAAATACT
1 AAATATATGATACTAATAAATACT
4318098 AAAT
1 AAAT
4318102 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATATATGATACTAATAAATACT
Found at i:4320930 original size:29 final size:30
Alignment explanation
Indices: 4320871--4320928 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
4320861 TCTGAGCCTT
*
4320871 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
4320901 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
4320929 AGAGTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:4321159 original size:13 final size:13
Alignment explanation
Indices: 4321141--4321171 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
4321131 TTCCAGCAAC
4321141 TATGAATTTATTT
1 TATGAATTTATTT
4321154 TATGAATTTATTT
1 TATGAATTTATTT
*
4321167 GATGA
1 TATGA
4321172 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:4321361 original size:56 final size:53
Alignment explanation
Indices: 4321270--4321569 Score: 337
Period size: 56 Copynumber: 5.7 Consensus size: 53
4321260 GGGTAAAAGA
4321270 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--AAGATCATAAGAGG
*
4321326 TCCCCTGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--AAGATCATAAGAGG
* * * *
4321382 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGA-C--GAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATCATAAGAGG
* * * *
4321432 TCCCATGGAAGACCATGTCTGGGACATGGCGTTGGCACC--GA-GATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATCATAAGAGG
* * * * * * *
4321482 TCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATCATAAGAGG
*
4321533 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4321570 TGTTATTATC
Statistics
Matches: 217, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
48 2 0.01
50 80 0.37
51 33 0.15
52 2 0.01
53 7 0.03
55 2 0.01
56 91 0.42
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (53 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATCATAAGAGG
Found at i:4321519 original size:100 final size:103
Alignment explanation
Indices: 4321277--4321570 Score: 351
Period size: 100 Copynumber: 2.8 Consensus size: 103
4321267 AGATCCCATG
* * *
4321277 TAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCCCTGTAAGACCAT
1 TAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--GAGAGGTCCCATGTAAGACCAT
*
4321342 GTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCCCTG
60 GTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCCCTA
* *
4321389 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGGTCCCATGGAAGACCATGTCTGG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCAAGACGAGAGGTCCCATGTAAGACCATGTCTGG
* * *
4321454 GACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
66 GACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
* * **
4321489 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATGAGAACATCCCATGTAAGACCATGTCTG
1 TAAGACCATGTCTGGGACATGGCATGGGCACCAAGACGAG-AGGTCCCATGTAAGACCATGTCTG
*
4321554 GGACATGGCTTTGGCAT
65 GGACATGGCATTGGCAT
4321571 GTTATTATCA
Statistics
Matches: 164, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
100 50 0.30
101 38 0.23
105 2 0.01
106 39 0.24
108 1 0.01
109 3 0.02
111 2 0.01
112 29 0.18
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (103 bp):
TAAGACCATGTCTGGGACATGGCATGGGCACCAAGACGAGAGGTCCCATGTAAGACCATGTCTGG
GACATGGCATTGGCATCCAGATCATAAGAGGTCCCCTA
Found at i:4323773 original size:13 final size:13
Alignment explanation
Indices: 4323755--4323787 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
4323745 TCAAAATTCC
4323755 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
4323768 CTTTTCTTTCTTT
1 CTTTTCTTTCTTT
*
4323781 CCTTTCT
1 CTTTTCT
4323788 CCTTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTCTTTCTTT
Found at i:4327631 original size:162 final size:162
Alignment explanation
Indices: 4327364--4327687 Score: 621
Period size: 162 Copynumber: 2.0 Consensus size: 162
4327354 GAAATGAAAG
* *
4327364 GAAAAAGACTATTGAAGACTCAAAAATTGATATTTATTTAGGGTTTTAACTTTTTAAGATAGTAA
1 GAAAAAGACTATTGAAGACTCAAAAATTGATATTTATTTACGGTTTTAACCTTTTAAGATAGTAA
4327429 AACAACATGCCAACAACATCCCTTGACGAACATTTTCACATACTAATTCTTAGCATATTTATTAG
66 AACAACATGCCAACAACATCCCTTGACGAACATTTTCACATACTAATTCTTAGCATATTTATTAG
4327494 GAAAGCGTAAAGCATCGAATTTTACAATAAAT
131 GAAAGCGTAAAGCATCGAATTTTACAATAAAT
4327526 GAAAAAGACTATTGAAGACTCAAAAATTGATATTTATTTACGGTTTTAACCTTTTAAGATAGTAA
1 GAAAAAGACTATTGAAGACTCAAAAATTGATATTTATTTACGGTTTTAACCTTTTAAGATAGTAA
*
4327591 AACAACATGCCAACAACATCCTTTGACGAACATTTTCACATACTAATTCTTAGCATATTTATTAG
66 AACAACATGCCAACAACATCCCTTGACGAACATTTTCACATACTAATTCTTAGCATATTTATTAG
4327656 GAAAGCGTAAAGCATCGAATTTTACAATAAAT
131 GAAAGCGTAAAGCATCGAATTTTACAATAAAT
4327688 TTAAGGGTTT
Statistics
Matches: 159, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 159 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (162 bp):
GAAAAAGACTATTGAAGACTCAAAAATTGATATTTATTTACGGTTTTAACCTTTTAAGATAGTAA
AACAACATGCCAACAACATCCCTTGACGAACATTTTCACATACTAATTCTTAGCATATTTATTAG
GAAAGCGTAAAGCATCGAATTTTACAATAAAT
Found at i:4347945 original size:5 final size:5
Alignment explanation
Indices: 4347937--4347970 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
4347927 TGGTGCAGTG
*
4347937 CATGC CATGC CATGC CATGC CATGC CATGT CATG
1 CATGC CATGC CATGC CATGC CATGC CATGC CATG
4347971 GTCTTCCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.24
Consensus pattern (5 bp):
CATGC
Found at i:4374229 original size:3 final size:3
Alignment explanation
Indices: 4374221--4374246 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4374211 TCTAGCAACC
4374221 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
4374247 GATTTGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:4375705 original size:96 final size:96
Alignment explanation
Indices: 4375541--4375733 Score: 314
Period size: 96 Copynumber: 2.0 Consensus size: 96
4375531 TCAAGTGTAG
* *
4375541 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATGGTCCAAC
1 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
*
4375606 CTAGCCGACAGGGAATTTACATTCCTGATAA
66 CTAGCCGACAGGGAAGTTACATTCCTGATAA
* *
4375637 TGAAGGTGAAAACTTTGCTATGGAACCATCGGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
1 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
* * *
4375702 CTAGGCGACAGGGAAGTTATATTCCTGGTAA
66 CTAGCCGACAGGGAAGTTACATTCCTGATAA
4375733 T
1 T
4375734 CTTGGCTCAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 89 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (96 bp):
TGAAGGTGAAAACTTAGCTATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
CTAGCCGACAGGGAAGTTACATTCCTGATAA
Found at i:4386945 original size:13 final size:13
Alignment explanation
Indices: 4386927--4386963 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
4386917 AGTTCTTCAT
4386927 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
4386940 TGCTTTTCAAAAG
1 TGCTTTTGAGAAG
4386953 TGCTTTTGAGA
1 TGCTTTTGAGA
4386964 TATTTGAGTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:4388137 original size:21 final size:21
Alignment explanation
Indices: 4388113--4388157 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4388103 TAAGCTGACA
4388113 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
4388134 ACAAATTGAACAGCATTGCCT
1 ACAAATTGAACAGCATTGCCT
4388155 ACA
1 ACA
4388158 TACCAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.24, G:0.13, T:0.22
Consensus pattern (21 bp):
ACAAATTGAACAGCATTGCCT
Found at i:4404640 original size:20 final size:21
Alignment explanation
Indices: 4404615--4404654 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4404605 CGTTGAGTTT
*
4404615 GTGGCA-GGGTCTCAAGGATA
1 GTGGCATGGATCTCAAGGATA
4404635 GTGGCATTGGATCTCAAGGA
1 GTGGCA-TGGATCTCAAGGA
4404655 ATCACCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (21 bp):
GTGGCATGGATCTCAAGGATA
Found at i:4407120 original size:5 final size:5
Alignment explanation
Indices: 4407112--4407139 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
4407102 TTAAGTTAAA
4407112 ATATT ATATT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATA
4407140 ACAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:4407242 original size:12 final size:12
Alignment explanation
Indices: 4407203--4407250 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
4407193 AGAAAGGGAA
4407203 AGAAAGAAAAAG
1 AGAAAGAAAAAG
*
4407215 AAAAAGAAAAAG
1 AGAAAGAAAAAG
4407227 AGAAAGAAAGAA-
1 AGAAAGAAA-AAG
4407239 AGAAAGGAAAAA
1 AGAAA-GAAAAA
4407251 TTAGGGCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 26 0.81
13 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAG
Found at i:4407928 original size:24 final size:24
Alignment explanation
Indices: 4407900--4407946 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
4407890 ATTGAAATGA
4407900 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
4407924 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
4407947 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:4408149 original size:41 final size:41
Alignment explanation
Indices: 4408102--4408248 Score: 176
Period size: 41 Copynumber: 3.7 Consensus size: 41
4408092 CGACTTTGAG
*
4408102 TCGATGAGACACTGGGTGTCAATTTACTACTTTGGATTAAT
1 TCGATGAGACACTGGGTGCCAATTTACTACTTTGGATTAAT
* * * * *
4408143 TTGATGAGGCACTGGGTGCCAA-TT--TACTTCGG-TTTAG
1 TCGATGAGACACTGGGTGCCAATTTACTACTTTGGATTAAT
* * *
4408180 CCAATGAGACACTGGGTGTCAATTTACTACTTTGGATTAAT
1 TCGATGAGACACTGGGTGCCAATTTACTACTTTGGATTAAT
*
4408221 TCGATGAGGCACTGGGTGCCAATTTACT
1 TCGATGAGACACTGGGTGCCAATTTACT
4408249 TCGGTTTAGC
Statistics
Matches: 84, Mismatches: 18, Indels: 8
0.76 0.16 0.07
Matches are distributed among these distances:
37 20 0.24
38 9 0.11
40 9 0.11
41 46 0.55
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (41 bp):
TCGATGAGACACTGGGTGCCAATTTACTACTTTGGATTAAT
Found at i:4408196 original size:37 final size:38
Alignment explanation
Indices: 4408145--4408316 Score: 177
Period size: 37 Copynumber: 4.4 Consensus size: 38
4408135 GGATTAATTT
4408145 GATGAGGCACTGGGTGCCAA-TTTACTTCGGTTTAGCC
1 GATGAGGCACTGGGTGCCAATTTTACTTCGGTTTAGCC
* * * * * **
4408182 AATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTC
1 GATGAGGCACTGGGTGCCAATTT--TACTTCGG-TTTAGCC
4408223 GATGAGGCACTGGGTGCCAA-TTTACTTCGGTTTAGCC
1 GATGAGGCACTGGGTGCCAATTTTACTTCGGTTTAGCC
* * ** *
4408260 GATGAGACACTGGGTGTCATATTATTACTTCGAATTATCC
1 GATGAGGCACTGGGTGCCA-ATT-TTACTTCGGTTTAGCC
4408300 GATGAGGCACTGGGTGC
1 GATGAGGCACTGGGTGC
4408317 TAAACTGGTG
Statistics
Matches: 107, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
37 38 0.36
38 10 0.09
39 1 0.01
40 37 0.35
41 21 0.20
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (38 bp):
GATGAGGCACTGGGTGCCAATTTTACTTCGGTTTAGCC
Found at i:4408234 original size:78 final size:78
Alignment explanation
Indices: 4408105--4408316 Score: 347
Period size: 78 Copynumber: 2.7 Consensus size: 78
4408095 CTTTGAGTCG
*
4408105 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTTGATGAGGCACTGGGTGCCAATTTAC
1 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCGATGAGGCACTGGGTGCCAATTTAC
4408170 TTCGGTTTAGCCA
66 TTCGGTTTAGCCA
4408183 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCGATGAGGCACTGGGTGCCAATTTAC
1 ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCGATGAGGCACTGGGTGCCAATTTAC
*
4408248 TTCGGTTTAGCCG
66 TTCGGTTTAGCCA
* * * *
4408261 ATGAGACACTGGGTGTC-ATATTATTACTTCGAATT-ATCCGATGAGGCACTGGGTGC
1 ATGAGACACTGGGTGTCAAT-TTACTACTTTGGATTAATTCGATGAGGCACTGGGTGC
4408317 TAAACTGGTG
Statistics
Matches: 127, Mismatches: 6, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
77 22 0.17
78 105 0.83
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.33
Consensus pattern (78 bp):
ATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATTCGATGAGGCACTGGGTGCCAATTTAC
TTCGGTTTAGCCA
Found at i:4410514 original size:4 final size:4
Alignment explanation
Indices: 4410491--4410530 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
4410481 TTAATAAAAT
* *
4410491 ATTA ATTA AATA A-TA TTTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
4410531 AAATATCACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
3 2 0.06
4 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:4411372 original size:13 final size:13
Alignment explanation
Indices: 4411354--4411380 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4411344 TGAATGATAT
4411354 TTTGATGATATAA
1 TTTGATGATATAA
4411367 TTTGATGATATAA
1 TTTGATGATATAA
4411380 T
1 T
4411381 CGTGGTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TTTGATGATATAA
Found at i:4411998 original size:23 final size:23
Alignment explanation
Indices: 4411971--4412023 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
4411961 TAAATCGTCG
4411971 AACGTCTTCCTAAATACCTACAA
1 AACGTCTTCCTAAATACCTACAA
4411994 AACGTCTTCCTAAATACCTACAA
1 AACGTCTTCCTAAATACCTACAA
4412017 AACGTCT
1 AACGTCT
4412024 AATAAATGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.06, T:0.26
Consensus pattern (23 bp):
AACGTCTTCCTAAATACCTACAA
Found at i:4429399 original size:38 final size:38
Alignment explanation
Indices: 4429303--4429415 Score: 163
Period size: 39 Copynumber: 2.9 Consensus size: 38
4429293 TAATAAATAA
*
4429303 AATTATCCAACCCAATAAAACTAAAACTGAAGTCTACCC
1 AATTA-CCAACCCAATAAAACTAAAACTAAAGTCTACCC
* * *
4429342 AATTGCCCAACCCAATAAAACTAAAATTAAAGTCTATCC
1 AATT-ACCAACCCAATAAAACTAAAACTAAAGTCTACCC
*
4429381 AATTACCAACCCAATAAAAATAAAACTAAAGTCTA
1 AATTACCAACCCAATAAAACTAAAACTAAAGTCTA
4429416 ACTCTAAGTC
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 28 0.42
39 38 0.58
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.21
Consensus pattern (38 bp):
AATTACCAACCCAATAAAACTAAAACTAAAGTCTACCC
Found at i:4436938 original size:42 final size:42
Alignment explanation
Indices: 4436891--4436976 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
4436881 TGGAAACTGT
4436891 AAGCCTGCAATGCTGTCCTTATTCCTTTCTATAAAACCCACC
1 AAGCCTGCAATGCTGTCCTTATTCCTTTCTATAAAACCCACC
4436933 AAGCCTGCAATGCTGTCCTTATTCCTTTCTATAAAACCCACC
1 AAGCCTGCAATGCTGTCCTTATTCCTTTCTATAAAACCCACC
4436975 AA
1 AA
4436977 ACCAATGGTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (42 bp):
AAGCCTGCAATGCTGTCCTTATTCCTTTCTATAAAACCCACC
Found at i:4449348 original size:45 final size:45
Alignment explanation
Indices: 4449284--4449377 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
4449274 ATTAAACTTT
*
4449284 ATTTTCATTATATATTAATTAGGTGTTTAAGTCGTTTTTAATTTC
1 ATTTTCATTATATATTAATTAGGTATTTAAGTCGTTTTTAATTTC
* *
4449329 ATTTTCATTATATATTAATTAGGTATTTAGGTCGTTTTTAATTTT
1 ATTTTCATTATATATTAATTAGGTATTTAAGTCGTTTTTAATTTC
4449374 ATTT
1 ATTT
4449378 AGGAAAATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (45 bp):
ATTTTCATTATATATTAATTAGGTATTTAAGTCGTTTTTAATTTC
Found at i:4453692 original size:21 final size:21
Alignment explanation
Indices: 4453668--4453712 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4453658 TCCTGCTTGG
4453668 AGCTTGCTTTCACCTGAATCT
1 AGCTTGCTTTCACCTGAATCT
4453689 AGCTTGCTTTCACCTGAATCT
1 AGCTTGCTTTCACCTGAATCT
4453710 AGC
1 AGC
4453713 AGAATCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.36
Consensus pattern (21 bp):
AGCTTGCTTTCACCTGAATCT
Found at i:4461615 original size:5 final size:5
Alignment explanation
Indices: 4461605--4461637 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
4461595 ATAAACCACT
4461605 GCATA GCATA GCATA GCATA GCATA GCA-A GCAT
1 GCATA GCATA GCATA GCATA GCATA GCATA GCAT
4461638 TATAGCTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (5 bp):
GCATA
Found at i:4464406 original size:6 final size:6
Alignment explanation
Indices: 4464395--4464421 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4464385 TAATTCACAC
4464395 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
4464422 ATTGATATAT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:4485604 original size:17 final size:18
Alignment explanation
Indices: 4485568--4485605 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
4485558 TATCCTTCTT
*
4485568 TTATTTTGATTTAGGGTA
1 TTATTTTGATTCAGGGTA
*
4485586 TTATTTTG-TTCATGGTA
1 TTATTTTGATTCAGGGTA
4485603 TTA
1 TTA
4485606 ACTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (18 bp):
TTATTTTGATTCAGGGTA
Done.