Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 77 of 378
Found at i:20693156 original size:56 final size:57
Alignment explanation
Indices: 20693031--20693176 Score: 156
Period size: 56 Copynumber: 2.6 Consensus size: 57
20693021 GAGTTTGCAT
* * * * *
20693031 GGACTACCTTTCAAGTAAGAG-TCTGCATGGACTATCTATCAAGCAAGAGTCCGCAT
1 GGACTATCTTTCAAGAAAGAGTTCTGCAAGGACTATCTATCAAGCAAGAGTCCACAA
* *
20693087 GGGCTATCTTTCAAGAAAGAGTTC-GCAAGGACTATCTTTCAAGCAAGAGTCCACAA
1 GGACTATCTTTCAAGAAAGAGTTCTGCAAGGACTATCTATCAAGCAAGAGTCCACAA
* * * *
20693143 GGATTGT-TCTTCAAGAAGGAG-TCTGCAAAGACTA
1 GGACTATCT-TTCAAGAAAGAGTTCTGCAAGGACTA
20693177 ACTAATGGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
55 3 0.04
56 70 0.93
57 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (57 bp):
GGACTATCTTTCAAGAAAGAGTTCTGCAAGGACTATCTATCAAGCAAGAGTCCACAA
Found at i:20693157 original size:84 final size:84
Alignment explanation
Indices: 20693012--20693165 Score: 186
Period size: 84 Copynumber: 1.8 Consensus size: 84
20693002 CCATGGCATA
* * * * ** *
20693012 TTCAAGTAAGAGTTTGCATGGACTACCTTTCAAGTAAGAGTCTGCATGGACTATCTATCAAGCAA
1 TTCAAGAAAGAGTTCGCAAGGACTACCTTTCAAGCAAGAGTCCACAAGGACTATCTATCAAG-AA
20693077 -GAGTCCGCATGGGCTATCT
65 GGAGTCCGCATGGGCTATCT
* * *
20693096 TTCAAGAAAGAGTTCGCAAGGACTATCTTTCAAGCAAGAGTCCACAAGGATTGTTCT-TCAAGAA
1 TTCAAGAAAGAGTTCGCAAGGACTACCTTTCAAGCAAGAGTCCACAAGGACT-ATCTATCAAGAA
20693160 GGAGTC
65 GGAGTC
20693166 TGCAAAGACT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
83 2 0.03
84 53 0.91
85 3 0.05
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (84 bp):
TTCAAGAAAGAGTTCGCAAGGACTACCTTTCAAGCAAGAGTCCACAAGGACTATCTATCAAGAAG
GAGTCCGCATGGGCTATCT
Found at i:20695302 original size:30 final size:30
Alignment explanation
Indices: 20695262--20695327 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
20695252 TATATTCAAA
*
20695262 TTATATTTTATTATATAACATTTATTATATT
1 TTATATTTTATTATATAACACTTATTAT-TT
* **
20695293 TTAT-TTTTATTTTATATTACTTATTATTT
1 TTATATTTTATTATATAACACTTATTATTT
20695322 TTATAT
1 TTATAT
20695328 ATGTTATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 6 0.20
30 20 0.67
31 4 0.13
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (30 bp):
TTATATTTTATTATATAACACTTATTATTT
Found at i:20695360 original size:19 final size:19
Alignment explanation
Indices: 20695336--20695375 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20695326 ATATGTTATG
20695336 TATATTATATATTATCTAT
1 TATATTATATATTATCTAT
* *
20695355 TATATTATTTATTATTTAT
1 TATATTATATATTATCTAT
20695374 TA
1 TA
20695376 AAGTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTATATATTATCTAT
Found at i:20695367 original size:7 final size:7
Alignment explanation
Indices: 20695292--20695375 Score: 52
Period size: 7 Copynumber: 12.0 Consensus size: 7
20695282 TTTATTATAT
20695292 TTTATT-
1 TTTATTA
20695298 TTTATT-
1 TTTATTA
20695304 TTATATTA
1 TT-TATTA
*
20695312 CTTATTA
1 TTTATTA
20695319 TTT-TTA
1 TTTATTA
*
20695325 TATATGTTA
1 T-T-TATTA
20695334 TGTATATTA
1 T-T-TATTA
*
20695343 TATATTA
1 TTTATTA
*
20695350 TCTATTA
1 TTTATTA
20695357 --TATTA
1 TTTATTA
20695362 TTTATTA
1 TTTATTA
20695369 TTTATTA
1 TTTATTA
20695376 AAGTATTTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
5 5 0.08
6 12 0.18
7 35 0.54
8 2 0.03
9 11 0.17
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTATTA
Found at i:20695382 original size:19 final size:19
Alignment explanation
Indices: 20695345--20695384 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20695335 GTATATTATA
* *
20695345 TATTATCTATTATATTATT
1 TATTATCTATTAAAGTATT
*
20695364 TATTATTTATTAAAGTATT
1 TATTATCTATTAAAGTATT
20695383 TA
1 TA
20695385 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TATTATCTATTAAAGTATT
Found at i:20695476 original size:23 final size:23
Alignment explanation
Indices: 20695450--20695499 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
20695440 AAATTATTAA
*
20695450 TTATTTATT-TATTATGTATTGTT
1 TTATTT-TTATATTATGTATTATT
*
20695473 TTATTTTTATATTATGTGTTATT
1 TTATTTTTATATTATGTATTATT
20695496 TTAT
1 TTAT
20695500 AAATTCTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (23 bp):
TTATTTTTATATTATGTATTATT
Found at i:20695831 original size:33 final size:33
Alignment explanation
Indices: 20695784--20695852 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 33
20695774 TGTATTACTT
*
20695784 TTTTTTGTATATCATACATTATTTAATTATTAC
1 TTTTTTGTACATCATACATTATTTAATTATTAC
*
20695817 TTTTTTGTACATCATGCATTATTTAATTATTAC
1 TTTTTTGTACATCATACATTATTTAATTATTAC
20695850 TTT
1 TTT
20695853 GTATGTTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.04, T:0.58
Consensus pattern (33 bp):
TTTTTTGTACATCATACATTATTTAATTATTAC
Found at i:20713431 original size:11 final size:11
Alignment explanation
Indices: 20713415--20713440 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20713405 TACTTATCTT
20713415 TTTTCTTATCA
1 TTTTCTTATCA
20713426 TTTTCTTATCA
1 TTTTCTTATCA
20713437 TTTT
1 TTTT
20713441 AACTTTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTCTTATCA
Found at i:20735209 original size:37 final size:37
Alignment explanation
Indices: 20735168--20735244 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
20735158 ATTCCCTGGA
* * *
20735168 AAAAGAAGATAG-GGATGAACATGAGTGATTCTCTGCC
1 AAAAGAA-ATAGAAGATGAACATGAGTGATTCCCCGCC
* * *
20735205 AAAAGCAATCGAAGATGAATATGAGTGATTCCCCGCC
1 AAAAGAAATAGAAGATGAACATGAGTGATTCCCCGCC
20735242 AAA
1 AAA
20735245 TGCGGACGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 3 0.09
37 30 0.91
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.19
Consensus pattern (37 bp):
AAAAGAAATAGAAGATGAACATGAGTGATTCCCCGCC
Found at i:20735552 original size:21 final size:21
Alignment explanation
Indices: 20735513--20735552 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20735503 AAATTTAATG
* *
20735513 TTAAAAAAATTTCTTAAATTA
1 TTAAAAAAATTTATAAAATTA
*
20735534 TTAAGAAAATTTATAAAAT
1 TTAAAAAAATTTATAAAAT
20735553 ATCAAAGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
TTAAAAAAATTTATAAAATTA
Found at i:20737808 original size:18 final size:18
Alignment explanation
Indices: 20737787--20737974 Score: 92
Period size: 18 Copynumber: 10.4 Consensus size: 18
20737777 TTTCAGTTTC
*
20737787 ATTCAGTAACATTCAATC
1 ATTCAGTAACATTCAATT
* *
20737805 ATTCAATAACAATT-AGTT
1 ATTCAGTAAC-ATTCAATT
* * * *
20737823 GTTCAATAATATTCAATC
1 ATTCAGTAACATTCAATT
* ** * *
20737841 ACTCTTTAACAGTCAGTT
1 ATTCAGTAACATTCAATT
*
20737859 ATTCAGTAACGA-TAAATT
1 ATTCAGTAAC-ATTCAATT
* *
20737877 ATTTAGTAACAATCAATT
1 ATTCAGTAACATTCAATT
* **
20737895 ATTCAGTAACAATCTTTT
1 ATTCAGTAACATTCAATT
** * * *
20737913 ACACAGTAGCAGTCAGTT
1 ATTCAGTAACATTCAATT
* * *
20737931 ATCCAGTAACAGTCAGTT
1 ATTCAGTAACATTCAATT
* *
20737949 ATTCAGTAGCAGTCAATT
1 ATTCAGTAACATTCAATT
20737967 ATTCAGTA
1 ATTCAGTA
20737975 CCTTTATTTA
Statistics
Matches: 129, Mismatches: 37, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
17 4 0.03
18 121 0.94
19 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (18 bp):
ATTCAGTAACATTCAATT
Found at i:20737938 original size:36 final size:36
Alignment explanation
Indices: 20737889--20737974 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
20737879 TTAGTAACAA
**
20737889 TCAATTATTCAGTAACAATCTTTTACACAGTAGCAG
1 TCAATTATTCAGTAACAATCAGTTACACAGTAGCAG
* * * **
20737925 TCAGTTATCCAGTAACAGTCAGTTATTCAGTAGCAG
1 TCAATTATTCAGTAACAATCAGTTACACAGTAGCAG
20737961 TCAATTATTCAGTA
1 TCAATTATTCAGTA
20737975 CCTTTATTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (36 bp):
TCAATTATTCAGTAACAATCAGTTACACAGTAGCAG
Found at i:20738171 original size:51 final size:54
Alignment explanation
Indices: 20738062--20738176 Score: 148
Period size: 51 Copynumber: 2.2 Consensus size: 54
20738052 GTGTAACGGT
* * * *
20738062 AACAGTAACAGTAACAGTAGCGGTACATAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAATAACAGTAGAGGTACATAGAGTACCTCATCGAAACAAATCCGA
*
20738116 AACAGTAACAATAACAGTA-AGGTACA-A-AGTACCTC-TCCGAAACGAATCCGA
1 AACAGTAACAATAACAGTAGAGGTACATAGAGTACCTCAT-CGAAACAAATCCGA
20738167 AACAGTAACA
1 AACAGTAACA
20738177 GTAAGGTGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 29 0.53
52 1 0.02
53 6 0.11
54 18 0.33
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (54 bp):
AACAGTAACAATAACAGTAGAGGTACATAGAGTACCTCATCGAAACAAATCCGA
Found at i:20739264 original size:14 final size:14
Alignment explanation
Indices: 20739247--20739276 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20739237 TTCTATTTTG
20739247 TTTCTTTCCTTATT
1 TTTCTTTCCTTATT
*
20739261 TTTCTTTCTTTATT
1 TTTCTTTCCTTATT
20739275 TT
1 TT
20739277 CATTAAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTCTTTCCTTATT
Found at i:20739295 original size:2 final size:2
Alignment explanation
Indices: 20739288--20739320 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20739278 ATTAAACTAT
20739288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20739321 TATTTATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20743933 original size:16 final size:18
Alignment explanation
Indices: 20743898--20743935 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20743888 ATCCTTATTT
*
20743898 AAATCAAATACAATAGTA
1 AAATAAAATACAATAGTA
20743916 AAATAAAATA-AA-AGTA
1 AAATAAAATACAATAGTA
20743932 AAAT
1 AAAT
20743936 TCATATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 9 0.47
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAATACAATAGTA
Found at i:20748341 original size:28 final size:28
Alignment explanation
Indices: 20748301--20748370 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
20748291 GCAATCAAAT
*
20748301 ATGGCACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
20748329 ATGGCACTTAGTGTTCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
20748357 ACGACACTTAGTGT
1 ATGGCACTTAGTGT
20748371 GTGAATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:20748819 original size:21 final size:22
Alignment explanation
Indices: 20748788--20748828 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
20748778 GAATGTATTG
*
20748788 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
20748810 TGAT-TATGTGCTAATGAAA
1 TGATGTATGTGCAAATGAAA
20748829 CATAAATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.34
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:20751342 original size:33 final size:34
Alignment explanation
Indices: 20751273--20751339 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
20751263 AAAATAAAAC
20751273 AAAAAAAAAAATGAAAGACTAACAGGGAAATTTT
1 AAAAAAAAAAATGAAAGACTAACAGGGAAATTTT
*
20751307 AAAAAAGAAAATGAAAGACTAACAGGGAAATTT
1 AAAAAAAAAAATGAAAGACTAACAGGGAAATTT
20751340 AAAGAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.61, C:0.06, G:0.16, T:0.16
Consensus pattern (34 bp):
AAAAAAAAAAATGAAAGACTAACAGGGAAATTTT
Found at i:20752325 original size:20 final size:20
Alignment explanation
Indices: 20752287--20752325 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20752277 TTTAGAAACC
* *
20752287 ATACCAAAAATTACGAGTAA
1 ATACCAAAAAATACAAGTAA
*
20752307 ATACCAAAAAATATAAGTA
1 ATACCAAAAAATACAAGTA
20752326 TGTATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.21
Consensus pattern (20 bp):
ATACCAAAAAATACAAGTAA
Found at i:20752345 original size:20 final size:20
Alignment explanation
Indices: 20752292--20752360 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
20752282 AAACCATACC
** *
20752292 AAAAATTACGAGTAAATACCA
1 AAAAATTATAAGTAAATA-TA
**
20752313 AAAAA-TATAAGTATGTATA
1 AAAAATTATAAGTAAATATA
* *
20752332 AAAAATTATGAGTAAATATT
1 AAAAATTATAAGTAAATATA
20752352 AAAAATTAT
1 AAAAATTAT
20752361 TGATACTCAC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
19 6 0.16
20 27 0.71
21 5 0.13
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAGTAAATATA
Found at i:20752431 original size:20 final size:24
Alignment explanation
Indices: 20752393--20752441 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
20752383 TGTATTCCCT
*
20752393 ATTTTTTTTAGCATACCCTTAT-A
1 ATTTTTTTTAGCATACCCTAATAA
20752416 ATTTTTTTTA-C-T-CCCTAATAA
1 ATTTTTTTTAGCATACCCTAATAA
20752437 ATTTT
1 ATTTT
20752442 GATTTTGGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 7 0.29
22 1 0.04
23 10 0.42
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTTTTTTTAGCATACCCTAATAA
Found at i:20752439 original size:21 final size:23
Alignment explanation
Indices: 20752393--20752441 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 23
20752383 TGTATTCCCT
*
20752393 ATTTTTTTTAGCATACCCTTATA
1 ATTTTTTTTAGCATACCCTAATA
20752416 ATTTTTTTTA-C-T-CCCTAATA
1 ATTTTTTTTAGCATACCCTAATA
*
20752436 AATTTT
1 ATTTTT
20752442 GATTTTGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.50
21 1 0.04
22 1 0.04
23 10 0.42
ACGTcount: A:0.27, C:0.16, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTTTTTTAGCATACCCTAATA
Found at i:20752544 original size:21 final size:21
Alignment explanation
Indices: 20752499--20752545 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
20752489 GTATGCTTTT
* * * *
20752499 AAAATTAATTTTTTGTTTGAG
1 AAAATCAATTTTTTGTATAAA
20752520 AAAATCAATTTTTTGTATAAA
1 AAAATCAATTTTTTGTATAAA
20752541 AAAAT
1 AAAAT
20752546 TTGTACAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (21 bp):
AAAATCAATTTTTTGTATAAA
Found at i:20762206 original size:7 final size:7
Alignment explanation
Indices: 20762176--20762223 Score: 60
Period size: 7 Copynumber: 6.3 Consensus size: 7
20762166 CCAAAAGTTA
20762176 TATTTAT
1 TATTTAT
20762183 TATCTTAT
1 TAT-TTAT
20762191 TATCTTTTAT
1 TA---TTTAT
20762201 TATTTAT
1 TATTTAT
20762208 TATTTAT
1 TATTTAT
20762215 TATTTAT
1 TATTTAT
20762222 TA
1 TA
20762224 GTCTATTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
7 24 0.65
8 6 0.16
10 6 0.16
11 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTTAT
Found at i:20767246 original size:50 final size:50
Alignment explanation
Indices: 20767142--20767247 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
20767132 CTAATCGAGT
* * * *
20767142 GCTCGTCACGACTTCTAAGATACCACATCGCGACTTCACTCTCCGACTAA
1 GCTCGTCACGACTTCTAAGATACCACATCGCAACGTCACTCACCGAATAA
* *
20767192 GCTCGTCACGACTTC-AAGAGTACCACAAT-GCAACGTCACTCACTGAATAG
1 GCTCGTCACGACTTCTAAGA-TACCAC-ATCGCAACGTCACTCACCGAATAA
20767242 GCTCGT
1 GCTCGT
20767248 TGTGACTTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 4 0.08
50 42 0.88
51 2 0.04
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (50 bp):
GCTCGTCACGACTTCTAAGATACCACATCGCAACGTCACTCACCGAATAA
Found at i:20767964 original size:23 final size:23
Alignment explanation
Indices: 20767911--20768008 Score: 63
Period size: 23 Copynumber: 4.3 Consensus size: 23
20767901 AAAATCGATA
*
20767911 ATTTGCACCAGAGTGCCACTGTT
1 ATTTGCACCAGAGTGCCACTGTC
* * * * *
20767934 ATTCGCACGAGCGTGCTATTGTC
1 ATTTGCACCAGAGTGCCACTGTC
* *
20767957 ATTTGCA-CTGAAGTGCCACTATC
1 ATTTGCACCAG-AGTGCCACTGTC
* * * * *
20767980 ACTTGCATCATAGTGTCACTATC
1 ATTTGCACCAGAGTGCCACTGTC
20768003 ATTTGC
1 ATTTGC
20768009 GCACATAAAA
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
22 1 0.02
23 53 0.96
24 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (23 bp):
ATTTGCACCAGAGTGCCACTGTC
Found at i:20771105 original size:9 final size:9
Alignment explanation
Indices: 20771093--20771178 Score: 70
Period size: 9 Copynumber: 9.4 Consensus size: 9
20771083 AGTAAAAACT
20771093 ATTTTTATA
1 ATTTTTATA
20771102 ATTTTTATA
1 ATTTTTATA
*
20771111 TTTTTTAAATA
1 ATTTTT--ATA
*
20771122 ATTTTAATA
1 ATTTTTATA
20771131 ATTTTT-T-
1 ATTTTTATA
*
20771138 ATTTTTAAA
1 ATTTTTATA
20771147 ATATTTT-TA
1 AT-TTTTATA
*
20771156 TATTTTTTTA
1 -ATTTTTATA
*
20771166 ATTTTTAAA
1 ATTTTTATA
20771175 ATTT
1 ATTT
20771179 AATCGAATCC
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
7 6 0.10
8 1 0.02
9 40 0.65
10 8 0.13
11 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
ATTTTTATA
Found at i:20771114 original size:17 final size:17
Alignment explanation
Indices: 20771092--20771172 Score: 66
Period size: 17 Copynumber: 5.0 Consensus size: 17
20771082 TAGTAAAAAC
20771092 TATTTTTATAATTTTTA
1 TATTTTTATAATTTTTA
*
20771109 TATTTTT-TAA---ATA
1 TATTTTTATAATTTTTA
*
20771122 -ATTTTAATAATTTTT-
1 TATTTTTATAATTTTTA
*
20771137 TATTTTTAAAATATTTTTA
1 TATTTTT-ATA-ATTTTTA
*
20771156 TATTTTTTTAATTTTTA
1 TATTTTTATAATTTTTA
20771173 AAATTTAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
12 5 0.10
13 5 0.10
16 9 0.18
17 16 0.33
18 7 0.14
19 7 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTATAATTTTTA
Found at i:20771124 original size:20 final size:21
Alignment explanation
Indices: 20771099--20771138 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20771089 AACTATTTTT
*
20771099 ATAATTTTTAT-ATTTTTTAA
1 ATAATTTTAATAATTTTTTAA
20771119 ATAATTTTAATAATTTTTTA
1 ATAATTTTAATAATTTTTTA
20771139 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATAATTTTAATAATTTTTTAA
Found at i:20771135 original size:28 final size:27
Alignment explanation
Indices: 20771092--20771178 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
20771082 TAGTAAAAAC
20771092 TATTTTTATAATTTTTATATTTTTTAAA
1 TATTTTTATAATTTTT-TATTTTTTAAA
* *
20771120 TAATTTTAATAATTTTTTATTTTTAAAA
1 T-ATTTTTATAATTTTTTATTTTTTAAA
* *
20771148 TATTTTTATATTTTTTTAATTTTTAAA
1 TATTTTTATAATTTTTTATTTTTTAAA
20771175 -ATTT
1 TATTT
20771179 AATCGAATCC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.08
27 22 0.42
28 12 0.23
29 14 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTTTATAATTTTTTATTTTTTAAA
Found at i:20779319 original size:46 final size:46
Alignment explanation
Indices: 20779269--20779627 Score: 531
Period size: 46 Copynumber: 7.8 Consensus size: 46
20779259 CTATGATAGA
20779269 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
20779315 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
20779361 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
*
20779407 AAACGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
* * * *
20779453 AAACGTGTAAGACCATGGTTAAAAGATACCATGGCAACGTGACATG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
* ***
20779499 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACGGGG
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA-TATG
** * * *
20779546 AAATGAATAAGACCATGGTTGAATGATACCATGGCAACATGACA-G
1 AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
* * * *
20779591 AAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 -AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
20779628 TCATGTCGAA
Statistics
Matches: 291, Mismatches: 20, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
45 1 0.00
46 251 0.86
47 39 0.13
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (46 bp):
AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATG
Found at i:20784399 original size:34 final size:34
Alignment explanation
Indices: 20784360--20784460 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
20784350 CCATCCTATA
20784360 TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
1 TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
*
20784394 TTCTC-A-----AATTTT-ATACTTTGTTT-TACA--
1 TTCTCAATCCTCAATTTTCA-A-TTTATTTCTA-ATT
20784421 -TCTCAATCCTCAATTTTCAATTTATTTCTAATT
1 TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
20784454 TTCTCAA
1 TTCTCAA
20784461 ATTGTATACT
Statistics
Matches: 51, Mismatches: 2, Indels: 28
0.63 0.02 0.35
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 9 0.18
29 7 0.14
31 7 0.14
32 9 0.18
33 2 0.04
34 11 0.22
ACGTcount: A:0.27, C:0.20, G:0.01, T:0.52
Consensus pattern (34 bp):
TTCTCAATCCTCAATTTTCAATTTATTTCTAATT
Found at i:20784434 original size:60 final size:60
Alignment explanation
Indices: 20784361--20784486 Score: 243
Period size: 60 Copynumber: 2.1 Consensus size: 60
20784351 CATCCTATAT
*
20784361 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTTTATACTTTGTTTTACA
1 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
20784421 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
1 TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
20784481 TCTCAA
1 TCTCAA
20784487 ATGTACAATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.27, C:0.19, G:0.02, T:0.52
Consensus pattern (60 bp):
TCTCAATCCTCAATTTTCAATTTATTTCTAATTTTCTCAAATTGTATACTTTGTTTTACA
Found at i:20789905 original size:3 final size:3
Alignment explanation
Indices: 20789897--20789956 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
20789887 ATATTACTAG
20789897 ATT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20789944 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
20789957 AATAAAATAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:20799262 original size:20 final size:21
Alignment explanation
Indices: 20799224--20799263 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
20799214 TTTATTAAGT
**
20799224 TAAATTTAAAATATTTTTTTA
1 TAAATTTAAAATAAGTTTTTA
20799245 TAAA-TTAAAATAAGTTTTT
1 TAAATTTAAAATAAGTTTTT
20799264 GTCTTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TAAATTTAAAATAAGTTTTTA
Found at i:20799262 original size:21 final size:21
Alignment explanation
Indices: 20799224--20799263 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20799214 TTTATTAAGT
*
20799224 TAAATTTAAAATATTTTTTTA
1 TAAATTTAAAATAGTTTTTTA
20799245 TAAA-TTAAAATAAGTTTTT
1 TAAATTTAAAAT-AGTTTTT
20799264 GTCTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TAAATTTAAAATAGTTTTTTA
Found at i:20801125 original size:38 final size:40
Alignment explanation
Indices: 20801074--20801156 Score: 134
Period size: 38 Copynumber: 2.1 Consensus size: 40
20801064 ATCATATGCA
20801074 TTTAATAATTTTATATTTC-AAAAA-AATAATATAATAGT
1 TTTAATAATTTTATATTTCAAAAAATAATAATATAATAGT
* *
20801112 TTTAATAATTTTATATTTCAAAAAATAATAATTTCATAGT
1 TTTAATAATTTTATATTTCAAAAAATAATAATATAATAGT
20801152 TTTAA
1 TTTAA
20801157 AATCATTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 19 0.46
39 5 0.12
40 17 0.41
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (40 bp):
TTTAATAATTTTATATTTCAAAAAATAATAATATAATAGT
Found at i:20801158 original size:23 final size:23
Alignment explanation
Indices: 20801114--20801158 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20801104 ATAATAGTTT
*
20801114 TAATAATTTTATATTTCAAAAAA
1 TAATAATTTCATATTTCAAAAAA
*
20801137 TAATAATTTCATAGTTTTAAAA
1 TAATAATTTCATA-TTTCAAAA
20801159 TCATTTGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (23 bp):
TAATAATTTCATATTTCAAAAAA
Found at i:20804875 original size:49 final size:50
Alignment explanation
Indices: 20804773--20804948 Score: 246
Period size: 49 Copynumber: 3.5 Consensus size: 50
20804763 CCATGGCAAC
* * *
20804773 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGAAAAATGA
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATAA
* * *
20804823 AAGTGATAAGTAATAGCTTCAGCTA-AATTATCTGATCAAGGACAAGTAA
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATAA
*
20804872 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGAC
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAAT-AA
* * *
20804923 AAGTGAAAAGTGGTAGCTTCTGCTAC
1 AAGTGATAAGTGATAGCTTCAGCTAC
20804949 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
49 44 0.40
50 43 0.39
51 24 0.22
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATAA
Found at i:20804962 original size:31 final size:31
Alignment explanation
Indices: 20804924--20805041 Score: 164
Period size: 31 Copynumber: 3.8 Consensus size: 31
20804914 ACAAATGACA
*
20804924 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
*
20804955 AGTGAAAAGTGGTAGCTTCAGCTACATGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * *
20804986 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
* * *
20805017 AGTGAATAGTTGTATCTTCAGCTAC
1 AGTGAAAAGTGGTAGCTTCAGCTAC
20805042 ATGTGACAAG
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
Found at i:20805021 original size:62 final size:62
Alignment explanation
Indices: 20804924--20805044 Score: 188
Period size: 62 Copynumber: 2.0 Consensus size: 62
20804914 ACAAATGACA
* * *
20804924 AGTGAAAAGTGGTAGCTTCTGCTACCTGATCAGTGAAAAGTGGTAGCTTCAGCTACATGATC
1 AGTGAAAAATGGTAGCTCCGGCTACCTGATCAGTGAAAAGTGGTAGCTTCAGCTACATGATC
* * *
20804986 AGTGAAAAATGGTAGCTCCGGCTACCTGATCAGTGAATAGTTGTATCTTCAGCTACATG
1 AGTGAAAAATGGTAGCTCCGGCTACCTGATCAGTGAAAAGTGGTAGCTTCAGCTACATG
20805045 TGACAAGTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (62 bp):
AGTGAAAAATGGTAGCTCCGGCTACCTGATCAGTGAAAAGTGGTAGCTTCAGCTACATGATC
Found at i:20805114 original size:47 final size:46
Alignment explanation
Indices: 20805059--20805231 Score: 184
Period size: 47 Copynumber: 3.7 Consensus size: 46
20805049 AAGTGATTTC
* * *
20805059 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATA
** * * *
20805105 CTGTATAAGACCATATTTGGGATATGGCATCAGTGAGATATGTGATT
1 C-GTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATA
* * * *
20805152 CGTGTAAGACCATAGCTGGGCTATGGCGTCGATATGTGATATGTGATTA
1 CGTATAAGACCATAGCTGGGATATGGCATCG--GTGTGATATGTGA-TA
* *
20805201 CGTGTAAGACCATAGCTGGGCTATGGCATCG
1 CGTATAAGACCATAGCTGGGATATGGCATCG
20805232 ATAGATGAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
46 25 0.23
47 40 0.37
48 11 0.10
49 31 0.29
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATAGCTGGGATATGGCATCGGTGTGATATGTGATA
Found at i:20809761 original size:11 final size:11
Alignment explanation
Indices: 20809745--20809792 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
20809735 ATTAGATAAA
20809745 TAATATTTTAT
1 TAATATTTTAT
20809756 TAATATTTTAAT
1 TAATATTTT-AT
* *
20809768 GAGATATTTTAC
1 TA-ATATTTTAT
20809780 TAATATTTTAT
1 TAATATTTTAT
20809791 TA
1 TA
20809793 TAAATAACTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 19 0.61
12 5 0.16
13 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (11 bp):
TAATATTTTAT
Found at i:20812481 original size:33 final size:32
Alignment explanation
Indices: 20812456--20812615 Score: 189
Period size: 33 Copynumber: 4.9 Consensus size: 32
20812446 AAAAGGTTAT
*
20812456 GTACACTTTGTGTATACCATATGAAAAAGAAAG
1 GTACACTTTGTGTATACCAT-TGAAAAGGAAAG
* *
20812489 GTATACTTTGTGTATACCATATGAATAGGAAAG
1 GTACACTTTGTGTATACCAT-TGAAAAGGAAAG
* *
20812522 GTATATTTTGTGTATACCATATGAAAAGGAAAG
1 GTACACTTTGTGTATACCAT-TGAAAAGGAAAG
*
20812555 GTATACTTTGTGTATACCACTTGAAAAGGAAAG
1 GTACACTTTGTGTATACCA-TTGAAAAGGAAAG
*
20812588 GTACACTATATGTGTA-AAC-TTGAAAAGG
1 GTACACT-T-TGTGTATACCATTGAAAAGG
20812616 TTAATGTGCA
Statistics
Matches: 116, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
32 9 0.08
33 97 0.84
34 4 0.03
35 6 0.05
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.31
Consensus pattern (32 bp):
GTACACTTTGTGTATACCATTGAAAAGGAAAG
Found at i:20812532 original size:66 final size:66
Alignment explanation
Indices: 20812462--20812590 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
20812452 TTATGTACAC
*
20812462 TTTGTGTATACCATATGAAAAAGAAAGGTATACTTTGTGTATACCA-TATGAATAGGAAAGGTAT
1 TTTGTGTATACCATATGAAAAAGAAAGGTATACTTTGTGTATACCACT-TGAAAAGGAAAGGTAT
20812526 AT
65 AT
*
20812528 TTTGTGTATACCATATGAAAAGGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAAGGTA
1 TTTGTGTATACCATATGAAAAAGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAAGGTA
20812591 CACTATATGT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 59 0.98
67 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.32
Consensus pattern (66 bp):
TTTGTGTATACCATATGAAAAAGAAAGGTATACTTTGTGTATACCACTTGAAAAGGAAAGGTATA
T
Found at i:20812629 original size:66 final size:66
Alignment explanation
Indices: 20812566--20812692 Score: 150
Period size: 66 Copynumber: 1.9 Consensus size: 66
20812556 TATACTTTGT
* * *
20812566 GTATACCACTTGAAAAGGAAAGGTACACTAT-ATGTGTAA-ACTTGAAAAGGTTAATGTGCACTT
1 GTATACAAATTGAAAAGGAAAGGTACACT-TCATGTGTAACACTTGAAAAGG-GAATGTGCACTT
20812629 TAA
64 TAA
* ** * *
20812632 GTGTACAAATTGAAAAGGGTATGTACACTTCGTGTGTAACACTTGAAAAGGGAATGTGCAC
1 GTATACAAATTGAAAAGGAAAGGTACACTTCATGTGTAACACTTGAAAAGGGAATGTGCAC
20812693 CTCGAGTGTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
65 1 0.02
66 39 0.76
67 11 0.22
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.28
Consensus pattern (66 bp):
GTATACAAATTGAAAAGGAAAGGTACACTTCATGTGTAACACTTGAAAAGGGAATGTGCACTTTA
A
Found at i:20812661 original size:33 final size:33
Alignment explanation
Indices: 20812575--20812688 Score: 90
Period size: 33 Copynumber: 3.5 Consensus size: 33
20812565 TGTATACCAC
* * * * *
20812575 TTGAAAA-GGAAAGGTACACTATATGTGTAAAC
1 TTGAAAAGGGTAATGTACACTTTAAGTGTAAAA
* *
20812607 TTGAAAAGGTTAATGTGCACTTTAAGTGTACAAA
1 TTGAAAAGGGTAATGTACACTTTAAGTGTA-AAA
*** *
20812641 TTGAAAAGGGT-ATGTACACTTCGTGTGTAACAC
1 TTGAAAAGGGTAATGTACACTTTAAGTGTAA-AA
20812674 TTGAAAAGGG-AATGT
1 TTGAAAAGGGTAATGT
20812689 GCACCTCGAG
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
32 8 0.12
33 45 0.69
34 12 0.18
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (33 bp):
TTGAAAAGGGTAATGTACACTTTAAGTGTAAAA
Found at i:20812702 original size:33 final size:33
Alignment explanation
Indices: 20812599--20812715 Score: 112
Period size: 33 Copynumber: 3.5 Consensus size: 33
20812589 TACACTATAT
* **
20812599 GTGTA-AACTTGAAAAGGTTAATGTGCACTTTAA
1 GTGTACAACTTGAAAAGG-GAATGTGCACTTCGA
* * * *
20812632 GTGTACAAATTGAAAAGGGTATGTACACTTCGT
1 GTGTACAACTTGAAAAGGGAATGTGCACTTCGA
*
20812665 GTGTA-ACACTTGAAAAGGGAATGTGCACCTCGA
1 GTGTACA-ACTTGAAAAGGGAATGTGCACTTCGA
* *
20812698 GTGTACGACTAGAAAAGG
1 GTGTACAACTTGAAAAGG
20812716 AAAAGTCCAT
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
32 1 0.01
33 55 0.82
34 11 0.16
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (33 bp):
GTGTACAACTTGAAAAGGGAATGTGCACTTCGA
Found at i:20816915 original size:25 final size:25
Alignment explanation
Indices: 20816881--20816935 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
20816871 TTGGACTTCG
*
20816881 ACCTCTGATCTTATCAAACACAATT
1 ACCTCTGATCTTATCAAACACAATC
*
20816906 ACCTTTGATCTTATCAAACACAATC
1 ACCTCTGATCTTATCAAACACAATC
20816931 ACCTC
1 ACCTC
20816936 GAAACCTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.31, G:0.04, T:0.31
Consensus pattern (25 bp):
ACCTCTGATCTTATCAAACACAATC
Found at i:20818756 original size:2 final size:2
Alignment explanation
Indices: 20818749--20818781 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20818739 TTAAACCTTT
20818749 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20818782 TATTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20818954 original size:9 final size:8
Alignment explanation
Indices: 20818938--20818962 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20818928 TATATACATA
20818938 TATTTTTT
1 TATTTTTT
20818946 TATTTTTT
1 TATTTTTT
20818954 TATTTTTT
1 TATTTTTT
20818962 T
1 T
20818963 CTAAATTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:20825583 original size:30 final size:30
Alignment explanation
Indices: 20825547--20825606 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
20825537 AAATGCAATA
* *
20825547 GACAAAGTAATGTAACACTGAAGTAATGTT
1 GACAAAGCAATGTAAAACTGAAGTAATGTT
*
20825577 GACAAAGCAATGTAAAATTGAAGTAATGTT
1 GACAAAGCAATGTAAAACTGAAGTAATGTT
20825607 CAATCCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (30 bp):
GACAAAGCAATGTAAAACTGAAGTAATGTT
Found at i:20826522 original size:15 final size:15
Alignment explanation
Indices: 20826498--20826550 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
20826488 AGAGTGTAAA
*
20826498 GAAAACTAAAAAGAT
1 GAAAAATAAAAAGAT
*
20826513 GAAAAATAAAAAAGGT
1 GAAAAAT-AAAAAGAT
* *
20826529 AGAAAATTAGAAAGAT
1 -GAAAAATAAAAAGAT
20826545 GAAAAA
1 GAAAAA
20826551 CATAAATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 11 0.37
16 13 0.43
17 6 0.20
ACGTcount: A:0.68, C:0.02, G:0.17, T:0.13
Consensus pattern (15 bp):
GAAAAATAAAAAGAT
Found at i:20834298 original size:18 final size:19
Alignment explanation
Indices: 20834275--20834318 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
20834265 TAAATAGGAA
20834275 AGAGGTTACAAG-AAGATG
1 AGAGGTTACAAGAAAGATG
*
20834293 AGAGGTT-TAAGAAAGATG
1 AGAGGTTACAAGAAAGATG
*
20834311 AAAGGTTA
1 AGAGGTTA
20834319 AAGGTTGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.20
Consensus pattern (19 bp):
AGAGGTTACAAGAAAGATG
Found at i:20836847 original size:27 final size:28
Alignment explanation
Indices: 20836810--20836949 Score: 166
Period size: 27 Copynumber: 5.2 Consensus size: 28
20836800 AGCATGGCTG
** *
20836810 CCAGA-ACAGATA-ATGTGATAGAGTCA
1 CCAGATACAGATATATGTGGCAGAGCCA
20836836 CCAGATACAGATA-ATCGTGGCAGAGCCA
1 CCAGATACAGATATAT-GTGGCAGAGCCA
20836864 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
20836891 CCAGAT-CAGATATTTGTGGTAGAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
* *
20836918 CCAGAT-CAGATATTTGTGGCATAGCCA
1 CCAGATACAGATATATGTGGCAGAGCCA
20836945 CCAGA
1 CCAGA
20836950 ATGCTTCCTC
Statistics
Matches: 103, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
26 5 0.05
27 82 0.80
28 16 0.16
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.19
Consensus pattern (28 bp):
CCAGATACAGATATATGTGGCAGAGCCA
Found at i:20838602 original size:26 final size:26
Alignment explanation
Indices: 20838566--20838675 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
20838556 CATGAAATTC
20838566 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
20838592 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
20838618 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
*
20838644 TTATCATTG-AACATTTACCTAACCTA
1 TTATCA-TGAAACATTTACCTAACCCA
20838670 TTATCA
1 TTATCA
20838676 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
26 79 0.98
27 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:20841162 original size:9 final size:9
Alignment explanation
Indices: 20841148--20841292 Score: 132
Period size: 9 Copynumber: 16.1 Consensus size: 9
20841138 ATTCCTTTCT
20841148 TAACTTACA
1 TAACTTACA
20841157 TAACTTACA
1 TAACTTACA
* *
20841166 TAA-ATATA
1 TAACTTACA
* *
20841174 TATCATATCA
1 TAACTTA-CA
20841184 TAACTTACA
1 TAACTTACA
*
20841193 TAACTTATA
1 TAACTTACA
20841202 TAACTTACA
1 TAACTTACA
*
20841211 TAATTTACA
1 TAACTTACA
20841220 TAACTTACA
1 TAACTTACA
* *
20841229 TAA-ATATA
1 TAACTTACA
* *
20841237 TATCATATCA
1 TAACTTA-CA
20841247 TAACTTACA
1 TAACTTACA
20841256 TAACTTACA
1 TAACTTACA
* *
20841265 CAATTTACA
1 TAACTTACA
*
20841274 TGACTTACA
1 TAACTTACA
*
20841283 TAAATTACA
1 TAACTTACA
20841292 T
1 T
20841293 GATTTAATTC
Statistics
Matches: 109, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
8 10 0.09
9 87 0.80
10 12 0.11
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (9 bp):
TAACTTACA
Found at i:20841195 original size:36 final size:36
Alignment explanation
Indices: 20841148--20841264 Score: 153
Period size: 36 Copynumber: 3.5 Consensus size: 36
20841138 ATTCCTTTCT
20841148 TAACTTACATAACTTACATAAATATATATCATATCA
1 TAACTTACATAACTTACATAAATATATATCATATCA
*
20841184 TAACTTACATAAC-T---T--ATATA-A-CTTA-CA
1 TAACTTACATAACTTACATAAATATATATCATATCA
*
20841211 TAATTTACATAACTTACATAAATATATATCATATCA
1 TAACTTACATAACTTACATAAATATATATCATATCA
20841247 TAACTTACATAACTTACA
1 TAACTTACATAACTTACA
20841265 CAATTTACAT
Statistics
Matches: 68, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.21
28 4 0.06
29 1 0.01
30 5 0.07
31 1 0.01
32 1 0.01
33 5 0.07
34 1 0.01
35 4 0.06
36 32 0.47
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (36 bp):
TAACTTACATAACTTACATAAATATATATCATATCA
Found at i:20841251 original size:63 final size:63
Alignment explanation
Indices: 20841148--20841292 Score: 236
Period size: 63 Copynumber: 2.3 Consensus size: 63
20841138 ATTCCTTTCT
* *
20841148 TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTATATAACTTACA
1 TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAACTTACA
* *
20841211 TAATTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAATTTACA
1 TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAACTTACA
* *
20841274 TGACTTACATAAATTACAT
1 TAACTTACATAACTTACAT
20841293 GATTTAATTC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.37
Consensus pattern (63 bp):
TAACTTACATAACTTACATAAATATATATCATATCATAACTTACATAACTTACACAACTTACA
Found at i:20845477 original size:15 final size:14
Alignment explanation
Indices: 20845459--20845508 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
20845449 ATATATATAT
20845459 TATAATTTCAATCAA
1 TATAATTT-AATCAA
20845474 TATAAATTTAATCAA
1 TAT-AATTTAATCAA
* *
20845489 AATGATTTTAATCAA
1 TAT-AATTTAATCAA
20845504 TATAA
1 TATAA
20845509 ATTTGATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 1 0.03
15 23 0.79
16 5 0.17
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (14 bp):
TATAATTTAATCAA
Found at i:20846269 original size:18 final size:17
Alignment explanation
Indices: 20846246--20846289 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
20846236 GTTTCTTCTT
20846246 TGTTTCGTTTCCACATTC
1 TGTTTC-TTTCCACATTC
*
20846264 TGTTTCTTT--TCATTC
1 TGTTTCTTTCCACATTC
20846279 TGTTTCTTTCC
1 TGTTTCTTTCC
20846290 TTTATTTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 14 0.61
17 3 0.13
18 6 0.26
ACGTcount: A:0.07, C:0.25, G:0.09, T:0.59
Consensus pattern (17 bp):
TGTTTCTTTCCACATTC
Found at i:20846279 original size:15 final size:15
Alignment explanation
Indices: 20846259--20846287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20846249 TTCGTTTCCA
20846259 CATTCTGTTTCTTTT
1 CATTCTGTTTCTTTT
20846274 CATTCTGTTTCTTT
1 CATTCTGTTTCTTT
20846288 CCTTTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (15 bp):
CATTCTGTTTCTTTT
Found at i:20846517 original size:21 final size:22
Alignment explanation
Indices: 20846464--20846520 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
20846454 CAATTTAAAT
*
20846464 AATAATAACAATAACAATAATA
1 AATAATAATAATAACAATAATA
* *
20846486 ATTAA-ATATAA-AACTATAATA
1 AATAATA-ATAATAACAATAATA
20846507 AATAATAATAATAA
1 AATAATAATAATAA
20846521 TTTAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAATAATAATAACAATAATA
Found at i:20847699 original size:45 final size:45
Alignment explanation
Indices: 20847649--20847749 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 45
20847639 GTAGCAGTAG
* * *
20847649 CAGTAACAGTAACGGTATTCAACACACAAAGTG-CTGAATCTATAA
1 CAGTAACAGTAACAGTATTCAACACACAAAATGTC-GAATCGATAA
* * *
20847694 CAGTAACGGTAACAGTATTCGACACACAAAATGTCGAATCGGTAA
1 CAGTAACAGTAACAGTATTCAACACACAAAATGTCGAATCGATAA
20847739 CAGTAACAGTA
1 CAGTAACAGTA
20847750 GTCGGCACAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 47 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCAACACACAAAATGTCGAATCGATAA
Found at i:20852542 original size:43 final size:43
Alignment explanation
Indices: 20852481--20852834 Score: 304
Period size: 43 Copynumber: 8.3 Consensus size: 43
20852471 TGACTTGTAG
* *
20852481 TAGCGGCGTTTGTAG-AGAAAGCGTTGATAAAGGTCACGATCTA
1 TAGCGGCGTTTGTAGTA-AAAGCGTCGCTAAAGGTCACGATCTA
* * * * *
20852524 TAGCGGCGTTTGTAG-AGAAAGCGCCACTAAAGGTCATGTTTTA
1 TAGCGGCGTTTGTAGTA-AAAGCGTCGCTAAAGGTCACGATCTA
* * * * *
20852567 TAGCGACGTTTATAGTAAAAGTGCCGCTAAAGGTCACGTTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTA
* ** * * * *
20852610 TAGCAGTATTTGTAG-AAAAACGCCGCTAAAGGTCATGTTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTA
* *
20852652 TAGCCGCGTTTGTAGTAAAAACGTCGCTAAAGGTCAC-ATTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGA-TCTA
* * * * *
20852695 TAGCGGTGTTAGTAGTAAAAGTGCCACTAAAGGTCAC-ATTCTA
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGA-TCTA
* * *
20852738 TAGCGGCATTTGTAGTAAAAGCATCGGTAAAGGTCACGATCTA
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTA
* * * * * * *
20852781 TAACGGCCTTTGTAGTAGAAGCTTCGCTAAAGGTCATGTTTTA
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTA
*
20852824 TAGTGGCGTTT
1 TAGCGGCGTTT
20852835 TTTCAAATAA
Statistics
Matches: 254, Mismatches: 53, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
42 36 0.14
43 216 0.85
44 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTA
Found at i:20852737 original size:128 final size:127
Alignment explanation
Indices: 20852508--20852816 Score: 372
Period size: 128 Copynumber: 2.4 Consensus size: 127
20852498 AAAGCGTTGA
* * ** *
20852508 TAAAGGTCACGATCTATAGCGGCGTTTGTAG-AGAAAGCGCCACTAAAGGTCATGTTTTATAGCG
1 TAAAGGTCACGATCTATAGCGGCGTTTGTAGTA-AAAGCGTCGCTAAAGGTCACATTCTATAGCG
* * *
20852572 ACGTTTATAGTAAAAGTGCCGCTAAAGGTCACGTTCTATAGCAGTATTTGTAGAAAAACGC-CGC
65 A-GTTTATAGTAAAAGTGCCACTAAAGGTCACATTCTATAGCAGCATTTGTAGAAAAA-GCACGC
* * * *
20852636 TAAAGGTCATGTTCTATAGCCGCGTTTGTAGTAAAAACGTCGCTAAAGGTCACATTCTATAGCG-
1 TAAAGGTCACGATCTATAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACATTCTATAGCGA
* * *
20852700 GTGTTAGTAGTAAAAGTGCCACTAAAGGTCACATTCTATAGCGGCATTTGTAGTAAAAGCATCGG
66 GT-TTA-TAGTAAAAGTGCCACTAAAGGTCACATTCTATAGCAGCATTTGTAGAAAAAGCA-CGC
* * * *
20852765 TAAAGGTCACGATCTATAACGGCCTTTGTAGTAGAAGCTTCGCTAAAGGTCA
1 TAAAGGTCACGATCTATAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCA
20852817 TGTTTTATAG
Statistics
Matches: 153, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
126 2 0.01
127 5 0.03
128 99 0.65
129 47 0.31
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (127 bp):
TAAAGGTCACGATCTATAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACATTCTATAGCGA
GTTTATAGTAAAAGTGCCACTAAAGGTCACATTCTATAGCAGCATTTGTAGAAAAAGCACGC
Found at i:20852756 original size:86 final size:85
Alignment explanation
Indices: 20852481--20852834 Score: 370
Period size: 86 Copynumber: 4.1 Consensus size: 85
20852471 TGACTTGTAG
* * *
20852481 TAGCGGCGTTTGTAG-AGAAAGCGTTGATAAAGGTCACGATCTATAGCGGCGTTTGTAGAGAAAG
1 TAGCGGCGTTTGTAGTA-AAAGCGTCGCTAAAGGTCACGATCTATAGCGGTGTTTGTAGA-AAAG
*
20852545 CGCCACTAAAGGTCATGTTTTA
64 CGCCACTAAAGGTCATGTTCTA
* * * * * * * *
20852567 TAGCGACGTTTATAGTAAAAGTGCCGCTAAAGGTCACGTTCTATAGCAGTATTTGTAGAAAAACG
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTATAGCGGTGTTTGTAGAAAAGCG
*
20852632 CCGCTAAAGGTCATGTTCTA
66 CCACTAAAGGTCATGTTCTA
* * *
20852652 TAGCCGCGTTTGTAGTAAAAACGTCGCTAAAGGTCAC-ATTCTATAGCGGTGTTAGTAGTAAAAG
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGA-TCTATAGCGGTGTTTGTAG-AAAAG
* **
20852716 TGCCACTAAAGGTCACATTCTA
64 CGCCACTAAAGGTCATGTTCTA
* * * * ** *
20852738 TAGCGGCATTTGTAGTAAAAGCATCGGTAAAGGTCACGATCTATAACGGCCTTTGTAGTAGAAGC
1 TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTATAGCGGTGTTTGTAG-AAAAGC
** * *
20852803 TTCGCTAAAGGTCATGTTTTA
65 GCCACTAAAGGTCATGTTCTA
*
20852824 TAGTGGCGTTT
1 TAGCGGCGTTT
20852835 TTTCAAATAA
Statistics
Matches: 217, Mismatches: 47, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
85 70 0.32
86 145 0.67
87 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (85 bp):
TAGCGGCGTTTGTAGTAAAAGCGTCGCTAAAGGTCACGATCTATAGCGGTGTTTGTAGAAAAGCG
CCACTAAAGGTCATGTTCTA
Found at i:20852771 original size:171 final size:171
Alignment explanation
Indices: 20852481--20852826 Score: 394
Period size: 171 Copynumber: 2.0 Consensus size: 171
20852471 TGACTTGTAG
* * * *
20852481 TAGCGGCGTTTGTAGAGAAAGCGTTGATAAAGGTCACGATCTATAGCGGCGTTTGTAGAGAAAGC
1 TAGCCGCGTTTGTAGAGAAAACGTCGATAAAGGTCACGATCTATAGCGGCGTTAGTAGAGAAAGC
** * * ** *
20852546 GCCACTAAAGGTCATGTTTTATAGCGACGTTTATAGTAAAAGTGCCGCTAAAGGTCACGTTCTAT
66 GCCACTAAAGGTCACATTCTATAGCGACATTTATAGTAAAAGCACCGCTAAAGGTCACGATCTAT
* *
20852611 AGCAGTATTTGTAGAAAAACGC-CGCTAAAGGTCATGTTCTA
131 AACAGCATTTGTAGAAAAA-GCTCGCTAAAGGTCATGTTCTA
* *
20852652 TAGCCGCGTTTGTAGTA-AAAACGTCGCTAAAGGTCAC-ATTCTATAGCGGTGTTAGTAGTA-AA
1 TAGCCGCGTTTGTAG-AGAAAACGTCGATAAAGGTCACGA-TCTATAGCGGCGTTAGTAG-AGAA
* * * * *
20852714 AGTGCCACTAAAGGTCACATTCTATAGCGGCATTTGTAGTAAAAGCATCGGTAAAGGTCACGATC
63 AGCGCCACTAAAGGTCACATTCTATAGCGACATTTATAGTAAAAGCACCGCTAAAGGTCACGATC
* * * * *
20852779 TATAACGGCCTTTGTAGTAGAAGCTTCGCTAAAGGTCATGTTTTA
128 TATAACAGCATTTGTAGAAAAAGC-TCGCTAAAGGTCATGTTCTA
20852824 TAG
1 TAG
20852827 TGGCGTTTTT
Statistics
Matches: 145, Mismatches: 25, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
170 3 0.02
171 119 0.82
172 23 0.16
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (171 bp):
TAGCCGCGTTTGTAGAGAAAACGTCGATAAAGGTCACGATCTATAGCGGCGTTAGTAGAGAAAGC
GCCACTAAAGGTCACATTCTATAGCGACATTTATAGTAAAAGCACCGCTAAAGGTCACGATCTAT
AACAGCATTTGTAGAAAAAGCTCGCTAAAGGTCATGTTCTA
Found at i:20855665 original size:6 final size:6
Alignment explanation
Indices: 20855631--20855661 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20855621 CCTCGACTAT
*
20855631 GACCAC GACCAC GACCAC GACCAC GGCCAC G
1 GACCAC GACCAC GACCAC GACCAC GACCAC G
20855662 GCCATGGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.48, G:0.23, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:20855670 original size:12 final size:12
Alignment explanation
Indices: 20855633--20855671 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20855623 TCGACTATGA
*
20855633 CCACGACCACGA
1 CCACGACCACGG
20855645 CCACGACCACGG
1 CCACGACCACGG
* *
20855657 CCACGGCCATGG
1 CCACGACCACGG
20855669 CCA
1 CCA
20855672 TGTCCTTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.26, C:0.49, G:0.23, T:0.03
Consensus pattern (12 bp):
CCACGACCACGG
Found at i:20856401 original size:33 final size:35
Alignment explanation
Indices: 20856364--20856435 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
20856354 TAATATAAAT
* * * *
20856364 ATAAGTAGTTCCTTAAC-AAGCTTTTAAGCA-AAC
1 ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
20856397 ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
1 ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
20856432 ATAA
1 ATAA
20856436 CAGGAAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 15 0.45
34 11 0.33
35 7 0.21
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (35 bp):
ATAAGTAATTCATTAACAAAACTTTCAAGCATAAC
Found at i:20859379 original size:3 final size:3
Alignment explanation
Indices: 20859366--20859412 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
20859356 CAAATAGATG
*
20859366 AAT AGAT AAT AAT -AT AAT AAT AGAT AAT AA- AAT ACT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
20859411 AA
1 AA
20859413 AGGCATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
2 4 0.11
3 28 0.74
4 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20859387 original size:18 final size:18
Alignment explanation
Indices: 20859366--20859413 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
20859356 CAAATAGATG
*
20859366 AATAGATAATAATATAAT
1 AATAGATAATAAAATAAT
*
20859384 AATAGATAATAAAATACT
1 AATAGATAATAAAATAAT
20859402 AATA-ATAATAAA
1 AATAGATAATAAA
20859414 GGCATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (18 bp):
AATAGATAATAAAATAAT
Found at i:20862016 original size:12 final size:12
Alignment explanation
Indices: 20862001--20862032 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20861991 CCCGGCTAAG
20862001 TATTAATTTTTA
1 TATTAATTTTTA
20862013 TATTAA-TTTTA
1 TATTAATTTTTA
20862024 TA-TAATTTT
1 TATTAATTTT
20862033 GAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 10 0.53
12 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTAATTTTTA
Found at i:20862273 original size:22 final size:22
Alignment explanation
Indices: 20862248--20862290 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20862238 TATCCAAACA
20862248 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* *
20862270 ATAATAGTAAAATAGTAGCAA
1 ATAACAATAAAATAGTAGCAA
20862291 AATAGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:20862294 original size:11 final size:11
Alignment explanation
Indices: 20862256--20862295 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
20862246 CAATAACAAT
20862256 AAAATAGTAGC
1 AAAATAGTAGC
* * *
20862267 AACATAATAGT
1 AAAATAGTAGC
20862278 AAAATAGTAGC
1 AAAATAGTAGC
20862289 AAAATAG
1 AAAATAG
20862296 GAAAAAAACA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.07, G:0.15, T:0.20
Consensus pattern (11 bp):
AAAATAGTAGC
Found at i:20864726 original size:4 final size:4
Alignment explanation
Indices: 20864717--20864743 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
20864707 GGCTTCAACC
20864717 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
20864744 AAGGCATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:20866659 original size:26 final size:25
Alignment explanation
Indices: 20866620--20866688 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 25
20866610 CAGTAGACTA
20866620 TTTTT-ATTTAAGTTTAATTTAAATTG
1 TTTTTAATTT-AGTTT-ATTTAAATTG
20866646 TTTTTAATTTAG----TTTAAATTG
1 TTTTTAATTTAGTTTATTTAAATTG
*
20866667 TTTTTAATTTAGTTTATATAAA
1 TTTTTAATTTAGTTTATTTAAA
20866689 AGAAAAACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 21 0.57
25 5 0.14
26 7 0.19
27 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (25 bp):
TTTTTAATTTAGTTTATTTAAATTG
Found at i:20866661 original size:21 final size:21
Alignment explanation
Indices: 20866626--20866682 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
20866616 ACTATTTTTA
*
20866626 TTTAAGTTTAATTTAAATTGTT
1 TTTAA-TTTAGTTTAAATTGTT
20866648 TTTAATTTAGTTTAAATTGTT
1 TTTAATTTAGTTTAAATTGTT
20866669 TTTAATTTAGTTTA
1 TTTAATTTAGTTTA
20866683 TATAAAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 29 0.85
22 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (21 bp):
TTTAATTTAGTTTAAATTGTT
Found at i:20870768 original size:10 final size:10
Alignment explanation
Indices: 20870755--20870779 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20870745 ATATATAAAA
20870755 ATAAAATATT
1 ATAAAATATT
20870765 ATAAAATATT
1 ATAAAATATT
20870775 ATAAA
1 ATAAA
20870780 CTTTAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
ATAAAATATT
Found at i:20879127 original size:18 final size:20
Alignment explanation
Indices: 20879093--20879138 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
20879083 TTAATTATTT
20879093 TATATTAATTGATATAAAAA
1 TATATTAATTGATATAAAAA
*
20879113 TATATT-ATTGA-ATAAAAG
1 TATATTAATTGATATAAAAA
20879131 TA-ATTAAT
1 TATATTAAT
20879139 GGTGCATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 3 0.12
18 10 0.42
19 5 0.21
20 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (20 bp):
TATATTAATTGATATAAAAA
Found at i:20879933 original size:53 final size:53
Alignment explanation
Indices: 20879841--20879945 Score: 131
Period size: 53 Copynumber: 2.0 Consensus size: 53
20879831 AATAACAATT
** * * *
20879841 TTAATCTTCAACTTTTACATATTATATTAAATTAGTCTTAATTTTAAAAAAAA
1 TTAATCTTCAAAATTTACAAATAATATTAAATTAGTCTTAATTATAAAAAAAA
* *
20879894 TTAATCTTCAAAATTTACAAATAATCTT-AATTTGATCTTAATTATAAAAAAA
1 TTAATCTTCAAAATTTACAAATAATATTAAATTAG-TCTTAATTATAAAAAAA
20879946 GAAATATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 5 0.11
53 39 0.89
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.43
Consensus pattern (53 bp):
TTAATCTTCAAAATTTACAAATAATATTAAATTAGTCTTAATTATAAAAAAAA
Found at i:20883127 original size:13 final size:13
Alignment explanation
Indices: 20883109--20883134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20883099 ATACAAGTCA
20883109 AGGTGGAGATTTG
1 AGGTGGAGATTTG
20883122 AGGTGGAGATTTG
1 AGGTGGAGATTTG
20883135 TGGGGCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (13 bp):
AGGTGGAGATTTG
Found at i:20884198 original size:16 final size:17
Alignment explanation
Indices: 20884177--20884216 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20884167 CTCCCCTTAA
**
20884177 AATTTTTATT-TTTATT
1 AATTTTTATTATAAATT
20884193 AATTTTTATTATAAATT
1 AATTTTTATTATAAATT
20884210 AATTTTT
1 AATTTTT
20884217 TTAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
AATTTTTATTATAAATT
Found at i:20892468 original size:40 final size:40
Alignment explanation
Indices: 20892419--20892513 Score: 181
Period size: 40 Copynumber: 2.4 Consensus size: 40
20892409 CGGATGTAAC
*
20892419 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
20892459 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
20892499 AACCCGCACGAATGC
1 AACCCGCACGAATGC
20892514 TATGCACATA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:20900971 original size:39 final size:40
Alignment explanation
Indices: 20900860--20900992 Score: 234
Period size: 40 Copynumber: 3.4 Consensus size: 40
20900850 CGGATGTAAC
*
20900860 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
20900900 AACCCACACGAATGCCTTCGGGACTTAA-CCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
20900939 AA-CCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
20900978 AACCCGCACGAATGC
1 AACCCGCACGAATGC
20900993 TATGCACATA
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
38 24 0.27
39 26 0.30
40 38 0.43
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:20904720 original size:675 final size:675
Alignment explanation
Indices: 20903430--20904782 Score: 2544
Period size: 675 Copynumber: 2.0 Consensus size: 675
20903420 TTTTTTTTCC
20903430 ATTGTGTTGTTGAATTTCAAGTTTCGATTTCCTGGGTTTTTGGTCTCTTGTGTTTCATTTTTCTT
1 ATTGTGTTGTTGAATTTCAAGTTTCGATTTCCTGGGTTTTTGGTCTCTTGTGTTTCATTTTTCTT
20903495 GATAAGGTCTTTTTGCTTAAGATTTGAAGGCTGAATCATGCTTTTCTTTTTTTGTCATATTTTTC
66 GATAAGGTCTTTTTGCTTAAGATTTGAAGGCTGAATCATGCTTTTCTTTTTTTGTCATATTTTTC
20903560 TCTATACTATTTTGATATTATGGTCGAGACAAAGTTGTAAATTGATCATCAAAGCACCTAGGAAG
131 TCTATACTATTTTGATATTATGGTCGAGACAAAGTTGTAAATTGATCATCAAAGCACCTAGGAAG
*
20903625 GTGGTTGAAGATTAGCAAGTTGAGAGGAAGGAAAATGAACTTATCAGCAATGCTTCCTACAAGTC
196 GTGGTTGAAGATTAGCAAGTTGAGAGGAAGGAAAATGAACCTATCAGCAATGCTTCCTACAAGTC
*
20903690 CACCACCATCGATATGGAGATGAGGAGATTGTTGAGGTGCCTGGGGCTTGCCTAAAATAATCACA
261 CACCACCATCGATATGGAGATGAGGAGATTGTTAAGGTGCCTGGGGCTTGCCTAAAATAATCACA
20903755 AGTATGAATTTAGCATACCGAAAGGATCTTATCCCCTCAGTGGGGTTTTAAGGCCTAGATATAGG
326 AGTATGAATTTAGCATACCGAAAGGATCTTATCCCCTCAGTGGGGTTTTAAGGCCTAGATATAGG
* *
20903820 GGAGGAAGTCCAGGATACTACCTCTCATTGTACTTACTTGAACTTGGGTTCTACCTTCCTTTCTA
391 GGAGGAAGTCCAGGATACTACCTCTCATTGTACTTACTTGAACCTGGGTTCTACCTTCCTTCCTA
* *
20903885 TTCTTTTGCTTGTGACTTGCTCAGAAGCTATAACGTGACACCCAAGCAACTGACAGAGCTGTCAT
456 TTCTTTTGCTTGTGACTTACTCAGAAGCTATAACGTGACACCCAAGCAACTGACAGAACTGTCAT
**
20903950 AGTGCGTGATCATAGGCTATCTTATCCTCTATTGCAAGCAAGGAATATGGCCTAAGATGAGGGTG
521 AGTGCGTGATCATAGGCTATCTTATCCTCTATCACAAGCAAGGAATATGGCCTAAGATGAGGGTG
* *
20904015 TTTTAGTATAATACTATCCAAAAGAGGGAGTTAATCCAGACCATTTAGGCTTTCTGCACATCGCG
586 TTTTAGTATAATACTATCCAAAAGAGGGAGTTAATCCAGACCATTTAAGCTTTCTACACATCGCG
20904080 AGGAGGCCATAAGCTCTACAACCTT
651 AGGAGGCCATAAGCTCTACAACCTT
* *
20904105 ATTGTGTTGTTGATTTTCAAGTTTCGATTTCCTGGGTTTTTGTTCTCTTGTGTTTCATTTTTCTT
1 ATTGTGTTGTTGAATTTCAAGTTTCGATTTCCTGGGTTTTTGGTCTCTTGTGTTTCATTTTTCTT
*
20904170 GATAAGGTCTTTTTGCTTAAGATTTGAAGGTTGAATCATGCTTTTCTTTTTTTGTCATATTTTTC
66 GATAAGGTCTTTTTGCTTAAGATTTGAAGGCTGAATCATGCTTTTCTTTTTTTGTCATATTTTTC
*
20904235 TCTATACTATTTTGATATTATGGTCGATACAAAGTTGTAAATTGATCATCAAAGCACCTAGGAAG
131 TCTATACTATTTTGATATTATGGTCGAGACAAAGTTGTAAATTGATCATCAAAGCACCTAGGAAG
20904300 GTGGTTGAAGATTAGCAAGTTGAGAGGAAGGAAAATGAACCTATCAGCAATGCTTCCTACAAGTC
196 GTGGTTGAAGATTAGCAAGTTGAGAGGAAGGAAAATGAACCTATCAGCAATGCTTCCTACAAGTC
20904365 CACCACCATCGATATGGAGATGAGGAGATTGTTAAGGTGCCTGGGGCTTGCCTAAAATAATCACA
261 CACCACCATCGATATGGAGATGAGGAGATTGTTAAGGTGCCTGGGGCTTGCCTAAAATAATCACA
20904430 AGTATGAATTTAGCATACCGAAAGGATCTTATCCCCTCAGTGGGGTTTTAAGGCCTAGATATAGG
326 AGTATGAATTTAGCATACCGAAAGGATCTTATCCCCTCAGTGGGGTTTTAAGGCCTAGATATAGG
*
20904495 GGAGGAAGTCCAGGATTCTACCTCTCATTGTACTTACTTGAACCTGGGTTCTACCTTCCTTCCTA
391 GGAGGAAGTCCAGGATACTACCTCTCATTGTACTTACTTGAACCTGGGTTCTACCTTCCTTCCTA
* *
20904560 TTCTTTTGCTTGTGACTTACTCAGAAGCTATAATGTGGCACCCAAGCAACTGACAGAACTGTCAT
456 TTCTTTTGCTTGTGACTTACTCAGAAGCTATAACGTGACACCCAAGCAACTGACAGAACTGTCAT
*
20904625 AGTGCGTGATCATAGGCTATCTTATCCTCTATCACAAGTAAGGAATATGGCCTAAGATGAGGGTG
521 AGTGCGTGATCATAGGCTATCTTATCCTCTATCACAAGCAAGGAATATGGCCTAAGATGAGGGTG
20904690 TTTTAGTATAATACTATCCAAAAGAGGGAGTTAATCCAGACCATTTAAGCTTTCTACACATCGCG
586 TTTTAGTATAATACTATCCAAAAGAGGGAGTTAATCCAGACCATTTAAGCTTTCTACACATCGCG
20904755 AGGAGGCCATAAGCTCTACAACCTT
651 AGGAGGCCATAAGCTCTACAACCTT
20904780 ATT
1 ATT
20904783 AGAAAATACA
Statistics
Matches: 660, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
675 660 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (675 bp):
ATTGTGTTGTTGAATTTCAAGTTTCGATTTCCTGGGTTTTTGGTCTCTTGTGTTTCATTTTTCTT
GATAAGGTCTTTTTGCTTAAGATTTGAAGGCTGAATCATGCTTTTCTTTTTTTGTCATATTTTTC
TCTATACTATTTTGATATTATGGTCGAGACAAAGTTGTAAATTGATCATCAAAGCACCTAGGAAG
GTGGTTGAAGATTAGCAAGTTGAGAGGAAGGAAAATGAACCTATCAGCAATGCTTCCTACAAGTC
CACCACCATCGATATGGAGATGAGGAGATTGTTAAGGTGCCTGGGGCTTGCCTAAAATAATCACA
AGTATGAATTTAGCATACCGAAAGGATCTTATCCCCTCAGTGGGGTTTTAAGGCCTAGATATAGG
GGAGGAAGTCCAGGATACTACCTCTCATTGTACTTACTTGAACCTGGGTTCTACCTTCCTTCCTA
TTCTTTTGCTTGTGACTTACTCAGAAGCTATAACGTGACACCCAAGCAACTGACAGAACTGTCAT
AGTGCGTGATCATAGGCTATCTTATCCTCTATCACAAGCAAGGAATATGGCCTAAGATGAGGGTG
TTTTAGTATAATACTATCCAAAAGAGGGAGTTAATCCAGACCATTTAAGCTTTCTACACATCGCG
AGGAGGCCATAAGCTCTACAACCTT
Found at i:20909189 original size:14 final size:14
Alignment explanation
Indices: 20909170--20909206 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20909160 TAAAATATCC
20909170 AAATAATAACAAAA
1 AAATAATAACAAAA
* *
20909184 AAATAATAGCAATA
1 AAATAATAACAAAA
20909198 AAATAATAA
1 AAATAATAA
20909207 AATAACAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAATAACAAAA
Found at i:20916553 original size:9 final size:9
Alignment explanation
Indices: 20916539--20916610 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 9
20916529 TAAGTATAAT
20916539 TAAGTTATG
1 TAAGTTATG
20916548 TAAGTTATG
1 TAAGTTATG
* * *
20916557 ATATGATATA
1 -TAAGTTATG
*
20916567 T-ATTTATG
1 TAAGTTATG
*
20916575 T-A-TTATT
1 TAAGTTATG
20916582 TAAGTTATG
1 TAAGTTATG
*
20916591 TAAATTATG
1 TAAGTTATG
20916600 TAAGTTATG
1 TAAGTTATG
20916609 TA
1 TA
20916611 TAATGTACGA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
7 5 0.10
8 6 0.12
9 32 0.65
10 6 0.12
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (9 bp):
TAAGTTATG
Found at i:20916757 original size:9 final size:9
Alignment explanation
Indices: 20916743--20916901 Score: 84
Period size: 9 Copynumber: 17.7 Consensus size: 9
20916733 TGTGTTAATT
20916743 TTATGTAAA
1 TTATGTAAA
*
20916752 TTATGTAAG
1 TTATGTAAA
20916761 TTATG-AAA
1 TTATGTAAA
*
20916769 TTTGATCTTTAAA
1 -TT-A--TGTAAA
* *
20916782 TAATGTAAG
1 TTATGTAAA
*
20916791 TCATGT--A
1 TTATGTAAA
20916798 TTATGTAAGA
1 TTATGTAA-A
20916808 -TATGT--A
1 TTATGTAAA
*
20916814 TTATGTAAG
1 TTATGTAAA
20916823 TTATGTAAA
1 TTATGTAAA
*
20916832 TTATGTAAG
1 TTATGTAAA
20916841 TTATG-AAA
1 TTATGTAAA
*
20916849 TTCGAACTTTAAA
1 TT---A-TGTAAA
*
20916862 TTATGTAAG
1 TTATGTAAA
20916871 TTATGT--A
1 TTATGTAAA
20916878 TTATGTAAA
1 TTATGTAAA
*
20916887 TTAAGTAAA
1 TTATGTAAA
20916896 TTATGT
1 TTATGT
20916902 GAGTTGCTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 36
0.67 0.11 0.21
Matches are distributed among these distances:
6 1 0.01
7 16 0.14
8 6 0.05
9 74 0.65
10 3 0.03
11 2 0.02
12 3 0.03
13 8 0.07
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (9 bp):
TTATGTAAA
Found at i:20916805 original size:16 final size:15
Alignment explanation
Indices: 20916784--20916841 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 15
20916774 TCTTTAAATA
20916784 ATGTAAGTCATGTATT
1 ATGTAAGT-ATGTATT
20916800 ATGTAAGATATGTATT
1 ATGTAAG-TATGTATT
20916816 ATGTAAGTTATGTAAATT
1 ATGTAAG-TATGT--ATT
20916834 ATGTAAGT
1 ATGTAAGT
20916842 TATGAAATTC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
16 26 0.68
17 2 0.05
18 10 0.26
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (15 bp):
ATGTAAGTATGTATT
Found at i:20917252 original size:99 final size:99
Alignment explanation
Indices: 20916999--20917469 Score: 795
Period size: 99 Copynumber: 4.8 Consensus size: 99
20916989 AATTAAAGTG
20916999 AAATAAAAT-AGAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAA
1 AAATAAAATGA-AATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAA
20917063 ATAAAATAAAATATTGAAATTATTTTTCGTGATTC
65 ATAAAATAAAATATTGAAATTATTTTTCGTGATTC
* *
20917098 AAA-AAAATGAAATATTTAAAATGAAACTTTAAATACAATTTAATTTAATTAGGTAATATTAAAA
1 AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
20917162 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
*
20917196 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
*
20917261 TAAAATAAAACATTGAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
* *
20917295 AAATTAAATGAAATATTTAAAATAAAACTTTAAATACGATTTAATTTAATTAGGTAATGTTAAAA
1 AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
*
20917360 TAAAATAAAATATTAAAATTATTTTTCGTGATTC
66 TAAAATAAAATATTGAAATTATTTTTCGTGATTC
* * * *
20917394 AAAAAAAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAAT-TTGAA
1 -AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTT-AA
20917458 AATAAAATAAAA
64 AATAAAATAAAA
20917470 GATAATAAAA
Statistics
Matches: 353, Mismatches: 15, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
98 94 0.27
99 193 0.55
100 66 0.19
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.38
Consensus pattern (99 bp):
AAATAAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTTAAAA
TAAAATAAAATATTGAAATTATTTTTCGTGATTC
Found at i:20917393 original size:198 final size:198
Alignment explanation
Indices: 20916921--20917469 Score: 800
Period size: 197 Copynumber: 2.7 Consensus size: 198
20916911 GTGAACTTGA
* * **
20916921 AAATAAAATTTAATTTAATTAGGTAAT-TTGAAAATAAAATTAAATAAAAAAAATT-TTTTTCGT
1 AAATACAATTTAATTTAATTAGGTAATATT-AAAATAAAATAAAAT-ATTAAAATTATTTTTCGT
* *
20916984 GGTTAAATTAAAGTGAAATAAAATAGAATATTTAAAATAAAACTTTAAATACAATTTAATTTAAT
64 -G----ATTCAA---AAA-AAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAAT
*
20917049 TAGGTAATGTTAAAATAAAATAAAATATTGAAATTATTTTTCGTGATTCAAAAAAATGAAATATT
120 TAGGTAATGTTAAAATAAAATAAAACATTGAAATTATTTTTCGTGATTCAAAAAAATGAAATATT
*
20917114 TAAAATGAAACTTT
185 TAAAATAAAACTTT
*
20917128 AAATACAATTTAATTTAATTAGGTAATATTAAAATAAAATAAAATATTGAAATTATTTTTCGTGA
1 AAATACAATTTAATTTAATTAGGTAATATTAAAATAAAATAAAATATTAAAATTATTTTTCGTGA
** *
20917193 TTC-AAATTAAATGAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTT
66 TTCAAAAAAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTT
*
20917257 AAAATAAAATAAAACATTGAAATTATTTTTCGTGATTCAAATTAAATGAAATATTTAAAATAAAA
131 AAAATAAAATAAAACATTGAAATTATTTTTCGTGATTCAAA-AAAATGAAATATTTAAAATAAAA
20917322 CTTT
195 CTTT
* *
20917326 AAATACGATTTAATTTAATTAGGTAATGTTAAAATAAAATAAAATATTAAAATTATTTTTCGTGA
1 AAATACAATTTAATTTAATTAGGTAATATTAAAATAAAATAAAATATTAAAATTATTTTTCGTGA
* *
20917391 TTCAAAAAAAAATAAAATATTTAAAATGAAACTTTAAATATAATTTAATTTAATTAGGTAAT-TT
66 TTCAAAAAAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTT
20917455 GAAAATAAAATAAAA
131 -AAAATAAAATAAAA
20917470 GATAATAAAA
Statistics
Matches: 316, Mismatches: 21, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
197 94 0.30
198 94 0.30
199 67 0.21
201 1 0.00
202 3 0.01
206 7 0.02
207 48 0.15
208 2 0.01
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (198 bp):
AAATACAATTTAATTTAATTAGGTAATATTAAAATAAAATAAAATATTAAAATTATTTTTCGTGA
TTCAAAAAAAAATAAAATATTTAAAATAAAACTTTAAATACAATTTAATTTAATTAGGTAATGTT
AAAATAAAATAAAACATTGAAATTATTTTTCGTGATTCAAAAAAATGAAATATTTAAAATAAAAC
TTT
Found at i:20920467 original size:12 final size:12
Alignment explanation
Indices: 20920450--20920475 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20920440 CAAGTTAAAT
20920450 TAAGTCACCAAA
1 TAAGTCACCAAA
20920462 TAAGTCACCAAA
1 TAAGTCACCAAA
20920474 TA
1 TA
20920476 TGCAAATCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.23, G:0.08, T:0.19
Consensus pattern (12 bp):
TAAGTCACCAAA
Found at i:20921777 original size:77 final size:77
Alignment explanation
Indices: 20921684--20921857 Score: 271
Period size: 77 Copynumber: 2.3 Consensus size: 77
20921674 TTTAGCGGCG
*
20921684 TTTTTCAAAAAGCGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACTA
1 TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACT-
20921749 TTTTTTGCGAC-A
65 TTTTTTGCGACGA
* *
20921761 TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGATGTCGTTTTGTTCAACTT
1 TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACTT
* *
20921826 TTTTTGCGGCGC
66 TTTTTGCGACGA
*
20921838 TTTTT-AAAAAACGTCGCTAA
1 TTTTTCAAAAAACGCCGCTAA
20921858 TGCTTGATCT
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
76 24 0.27
77 66 0.73
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (77 bp):
TTTTTCAAAAAACGCCGCTAAAGATCGATCTTCTAAACAAAGGGCGACGTCGTTTTGGTCAACTT
TTTTTGCGACGA
Found at i:20921994 original size:41 final size:40
Alignment explanation
Indices: 20921827--20922043 Score: 159
Period size: 40 Copynumber: 5.3 Consensus size: 40
20921817 GTTCAACTTT
* * * *
20921827 TTTTGCGGCGCTTTTTAAAAAACGTCGCTAATGCTTGATC
1 TTTTGCGGCGTTTTTTCAAAAACGCCGCTAATTCTTGATC
* * *** * * *
20921867 TTTAGCGGCGCTTTTGGGAAAACGCCGTTAATGCTTTATC
1 TTTTGCGGCGTTTTTTCAAAAACGCCGCTAATTCTTGATC
* * * *
20921907 TTTAGCGGCGCTTTTT-AAAAAGCGCCGCTAATTATCGATC
1 TTTTGCGGCGTTTTTTCAAAAA-CGCCGCTAATTCTTGATC
* * *
20921947 TATTGCGGCGTTTGTTTCATAAACGCCGCTAATTCTTGACC
1 TTTTGCGGCGTTT-TTTCAAAAACGCCGCTAATTCTTGATC
* * * * *
20921988 TTTTGCGGCTTTTTTGTCACAAACGCCACT-ATAACTCTAATC
1 TTTTGCGGCGTTTTT-TCAAAAACGCCGCTAAT-TCT-TGATC
20922030 TTTTGCGGCGTTTT
1 TTTTGCGGCGTTTT
20922044 GTTATAGGCG
Statistics
Matches: 142, Mismatches: 29, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
39 4 0.03
40 75 0.53
41 43 0.30
42 20 0.14
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.37
Consensus pattern (40 bp):
TTTTGCGGCGTTTTTTCAAAAACGCCGCTAATTCTTGATC
Found at i:20923132 original size:14 final size:15
Alignment explanation
Indices: 20923099--20923133 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20923089 TTTTAAGGAA
20923099 AAAAATAAATATTGT
1 AAAAATAAATATTGT
* *
20923114 AAAAATAAATGTTTT
1 AAAAATAAATATTGT
20923129 AAAAA
1 AAAAA
20923134 GCTTAGTTTT
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:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:20925280 original size:5 final size:5
Alignment explanation
Indices: 20925270--20925300 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
20925260 TGTTTGGAGT
*
20925270 GAAGA GAAGA GAAGA GAAGG GAAGA GAAGA G
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA G
20925301 CGAGTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:20930620 original size:6 final size:6
Alignment explanation
Indices: 20930609--20930635 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20930599 TTAAAGAATT
20930609 TGTATA TGTATA TGTATA TGTATA TGT
1 TGTATA TGTATA TGTATA TGTATA TGT
20930636 TTTCATTAAA
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:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:20938535 original size:16 final size:16
Alignment explanation
Indices: 20938514--20938544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20938504 TTCACTATTA
*
20938514 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
20938530 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
20938545 GCATGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:20941147 original size:29 final size:29
Alignment explanation
Indices: 20941115--20941211 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 29
20941105 TACTAATATT
20941115 ATGGCTCGAAGCCAAATCAGCCGATATGC
1 ATGGCTCGAAGCCAAATCAGCCGATATGC
* **
20941144 ATGGC-C----CGAAAT-A-CTAATAT-C
1 ATGGCTCGAAGCCAAATCAGCCGATATGC
*
20941165 ATGGCTCGAAGCCAAATCAGTCGATATGC
1 ATGGCTCGAAGCCAAATCAGCCGATATGC
20941194 ATGG-TCCGAAGCCAAATC
1 ATGGCT-CGAAGCCAAATC
20941212 GGTTTATCTC
Statistics
Matches: 52, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
21 6 0.12
22 6 0.12
23 1 0.02
24 5 0.10
26 5 0.10
27 1 0.02
28 6 0.12
29 22 0.42
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.20
Consensus pattern (29 bp):
ATGGCTCGAAGCCAAATCAGCCGATATGC
Found at i:20941163 original size:50 final size:50
Alignment explanation
Indices: 20941101--20941203 Score: 179
Period size: 50 Copynumber: 2.1 Consensus size: 50
20941091 ACTTATCCCA
*
20941101 GAAATACTAATATTATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
1 GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
* *
20941151 GAAATACTAATATCATGGCTCGAAGCCAAATCAGTCGATATGCATGGTCC
1 GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
20941201 GAA
1 GAA
20941204 GCCAAATCGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (50 bp):
GAAATACTAATATCATGGCTCGAAGCCAAATCAGCCGATATGCATGGCCC
Found at i:20942725 original size:20 final size:20
Alignment explanation
Indices: 20942700--20942792 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 20
20942690 ATGATATTAT
20942700 TTTAATATTTTAATATTAAA
1 TTTAATATTTTAATATTAAA
* *
20942720 TTTAAT-TTAATACTTATCTTAATA
1 TTTAATATT--T--TAATATTAA-A
* *
20942744 TTTTATTAATTTAATATTAAA
1 -TTTAATATTTTAATATTAAA
* * *
20942765 GTGAATATCTTAATATTAAA
1 TTTAATATTTTAATATTAAA
20942785 TTTAATAT
1 TTTAATAT
20942793 AATTTTTCTA
Statistics
Matches: 53, Mismatches: 13, Indels: 14
0.66 0.16 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.51
21 2 0.04
22 7 0.13
23 7 0.13
24 2 0.04
25 5 0.09
26 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTAATATTTTAATATTAAA
Found at i:20942757 original size:5 final size:6
Alignment explanation
Indices: 20942709--20942848 Score: 51
Period size: 5 Copynumber: 24.8 Consensus size: 6
20942699 TTTTAATATT
* *
20942709 TTAATA TTAA-A TTTAAT- TTAATA CTT-ATC TTAATA TT-TTA TTAAT-
1 TTAATA TTAATA -TTAATA TTAATA -TTAATA TTAATA TTAATA TTAATA
* * **
20942754 TTAATA TTAA-A GTGAATA TCTTAATA TTAA-A TTTAATA -TAATT TTTCTA
1 TTAATA TTAATA -TTAATA --TTAATA TTAATA -TTAATA TTAATA TTAATA
20942803 TT-AT- TTAATA --AGAT- TTAATA TT-ATA TTAAT- TTAATA TTAA-A
1 TTAATA TTAATA TTA-ATA TTAATA TTAATA TTAATA TTAATA TTAATA
20942844 TTAAT
1 TTAAT
20942849 TAAGTTTAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 44
0.64 0.08 0.28
Matches are distributed among these distances:
4 3 0.03
5 45 0.45
6 43 0.43
7 4 0.04
8 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
TTAATA
Found at i:20942836 original size:16 final size:16
Alignment explanation
Indices: 20942815--20942849 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
20942805 ATTTAATAAG
*
20942815 ATTTAATATTATATTA
1 ATTTAATATTAAATTA
20942831 ATTTAATATTAAATTA
1 ATTTAATATTAAATTA
20942847 ATT
1 ATT
20942850 AAGTTTAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAATATTAAATTA
Found at i:20946789 original size:32 final size:32
Alignment explanation
Indices: 20946753--20946815 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
20946743 GGAATTGAAT
* *
20946753 TTTTTTAATACACATGACAAAATTTGATTGAG
1 TTTTTAAATACACATGACAAAATTTAATTGAG
* * *
20946785 TTTTTAAATATATATGACATAATTTAATTGA
1 TTTTTAAATACACATGACAAAATTTAATTGA
20946816 TTAAATACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (32 bp):
TTTTTAAATACACATGACAAAATTTAATTGAG
Found at i:20946789 original size:33 final size:32
Alignment explanation
Indices: 20946745--20946815 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
20946735 ATTGGAAGGG
*
20946745 AATTGAATTTTTTTAATACACATGACAAAATTT
1 AATTGAA-TTTTTAAATACACATGACAAAATTT
* * * * *
20946778 GATTGAGTTTTTAAATATATATGACATAATTT
1 AATTGAATTTTTAAATACACATGACAAAATTT
20946810 AATTGA
1 AATTGA
20946816 TTAAATACAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
32 26 0.84
33 5 0.16
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.44
Consensus pattern (32 bp):
AATTGAATTTTTAAATACACATGACAAAATTT
Found at i:20948030 original size:7 final size:7
Alignment explanation
Indices: 20948018--20948047 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
20948008 TAGCCTATTT
20948018 ATTAGCC
1 ATTAGCC
20948025 ATTAGCC
1 ATTAGCC
20948032 ATTAGCC
1 ATTAGCC
20948039 ATTAGCC
1 ATTAGCC
20948046 AT
1 AT
20948048 GGCCAATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (7 bp):
ATTAGCC
Found at i:20951842 original size:19 final size:19
Alignment explanation
Indices: 20951815--20951853 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
20951805 AAAATAATCT
20951815 TAAAAAATC-AAAATTTTA
1 TAAAAAATCTAAAATTTTA
20951833 TAAAATAATCTTAAAATTTTA
1 TAAAA-AATC-TAAAATTTTA
20951854 AATTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 4 0.22
21 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAATCTAAAATTTTA
Found at i:20957130 original size:50 final size:51
Alignment explanation
Indices: 20957063--20957172 Score: 170
Period size: 50 Copynumber: 2.2 Consensus size: 51
20957053 CCATTTCAAT
20957063 CCTTTTCATAATTTCATGACATAGTTTATTTGAAT-TCATACCTTTCCTTTC
1 CCTTTTCATAATTTCATGACATAGTTTATTTGAATGT-ATACCTTTCCTTTC
* *
20957114 CCTTTT-ATAATTTCATGACATAGTTTATTTGAATGTATACTTTTCCTTTA
1 CCTTTTCATAATTTCATGACATAGTTTATTTGAATGTATACCTTTCCTTTC
*
20957164 CTTTTTCAT
1 CCTTTTCAT
20957173 GGTCGTTGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
50 45 0.83
51 9 0.17
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (51 bp):
CCTTTTCATAATTTCATGACATAGTTTATTTGAATGTATACCTTTCCTTTC
Found at i:20971525 original size:2 final size:2
Alignment explanation
Indices: 20971518--20971554 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20971508 AACACAATTA
20971518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20971555 AAATTCAAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20972366 original size:21 final size:21
Alignment explanation
Indices: 20972322--20972367 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
20972312 TTTCTTTTTG
*
20972322 AAAAAGAACAAAATGAATTAT
1 AAAAAGAACAAAATGAATCAT
*
20972343 AAAAA-AATAAAATGAATCACT
1 AAAAAGAACAAAATGAATCA-T
20972364 AAAA
1 AAAA
20972368 CTAAAATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAAGAACAAAATGAATCAT
Found at i:20974049 original size:17 final size:17
Alignment explanation
Indices: 20974027--20974062 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20974017 AAGAGTAGAT
20974027 TTTTAGTCTAAATATTA
1 TTTTAGTCTAAATATTA
* *
20974044 TTTTAGTTTAAATTTTA
1 TTTTAGTCTAAATATTA
20974061 TT
1 TT
20974063 ATTTATGGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTAGTCTAAATATTA
Found at i:20974254 original size:15 final size:16
Alignment explanation
Indices: 20974234--20974275 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
20974224 TTAATTATTT
20974234 TAAAAATTATA-AAAA
1 TAAAAATTATATAAAA
*
20974249 TAAAAATTA-ATATAA
1 TAAAAATTATATAAAA
20974264 TAAAAA-TATATA
1 TAAAAATTATATA
20974276 TTAACTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 3 0.12
15 21 0.88
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
TAAAAATTATATAAAA
Found at i:20974278 original size:21 final size:22
Alignment explanation
Indices: 20974242--20974296 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 22
20974232 TTTAAAAATT
* *
20974242 ATAAAAATAAAAATTAA-TATA
1 ATAAAAATATATATTAACTATA
* *
20974263 ATAAAAATATATATTAACTTTT
1 ATAAAAATATATATTAACTATA
20974285 AT-AAAATATATA
1 ATAAAAATATATA
20974297 ACATAATTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAAAAATATATATTAACTATA
Found at i:20974529 original size:3 final size:3
Alignment explanation
Indices: 20974521--20974553 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20974511 CAAGGATTTC
20974521 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20974554 TACCTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20974694 original size:16 final size:16
Alignment explanation
Indices: 20974673--20974712 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
20974663 TTTTCCTTTT
*
20974673 TTCACTCCCTCCCT-CC
1 TTCACTCCCT-CATGCC
20974689 TTCACTCCCTCATGCC
1 TTCACTCCCTCATGCC
20974705 TTCACTCC
1 TTCACTCC
20974713 ACAAAACGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 2 0.09
16 20 0.91
ACGTcount: A:0.10, C:0.55, G:0.03, T:0.33
Consensus pattern (16 bp):
TTCACTCCCTCATGCC
Found at i:20983208 original size:3 final size:3
Alignment explanation
Indices: 20983202--20983226 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20983192 TTATTATTAT
20983202 TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC T
20983227 TCTTCTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TAC
Done.