Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009149.1 Hibiscus syriacus cultivar Beakdansim tig00112673_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1143513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 2 of 6
Found at i:265609 original size:14 final size:14
Alignment explanation
Indices: 265592--265648 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
265582 TTAACTTACA
265592 TTTTTTTTTATTTT
1 TTTTTTTTTATTTT
* *
265606 TTTTATTTT-CTTT
1 TTTTTTTTTATTTT
* *
265619 ATTTTATTTATTTT
1 TTTTTTTTTATTTT
265633 ATTTTTTTTCTATTTT
1 -TTTTTTTT-TATTTT
265649 CTTTGTATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
13 9 0.28
14 11 0.34
15 6 0.19
16 6 0.19
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTATTTT
Found at i:277378 original size:23 final size:20
Alignment explanation
Indices: 277324--277362 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
277314 ATTTTAAGAA
*
277324 TTATCTTTAGGAATTATCTC
1 TTATTTTTAGGAATTATCTC
277344 TTATTTTTAGGAATTATCT
1 TTATTTTTAGGAATTATCT
277363 TTTCTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (20 bp):
TTATTTTTAGGAATTATCTC
Found at i:281273 original size:21 final size:19
Alignment explanation
Indices: 281245--281290 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
281235 TCATTGAATC
281245 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
281265 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
281284 ACTTAGT
1 A-TTAGT
281291 AGGATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:298089 original size:20 final size:20
Alignment explanation
Indices: 298049--298087 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
298039 CATTGCAGGA
*
298049 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCCACAAAAG
298069 ATTTCATGGCCTCCACAAA
1 ATTT-ATGGCCTCCACAAA
298088 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Found at i:303629 original size:2 final size:2
Alignment explanation
Indices: 303622--303705 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
303612 ACTCCCCTAA
303622 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
303664 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
303706 GTTGATAAAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:306686 original size:20 final size:20
Alignment explanation
Indices: 306661--306699 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
306651 AGCACACTTT
*
306661 ATTTCATTTAAATTTATTTC
1 ATTTCATTCAAATTTATTTC
*
306681 ATTTCATTCAATTTTATTT
1 ATTTCATTCAAATTTATTT
306700 TTATTTTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTCATTCAAATTTATTTC
Found at i:307638 original size:22 final size:21
Alignment explanation
Indices: 307619--307664 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
307609 AGCTTATTTT
307619 TTATATTATAATTATATATTAA
1 TTATATTATAATTAT-TATTAA
*
307641 TTATATTATTATTATTATT-A
1 TTATATTATAATTATTATTAA
307661 TTAT
1 TTAT
307665 TAATAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 4 0.17
22 14 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATATTATAATTATTATTAA
Found at i:307652 original size:3 final size:3
Alignment explanation
Indices: 307622--307666 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
307612 TTATTTTTTA
*
307622 TAT TAT AAT TAT ATAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT -TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
307667 ATAAATAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:314178 original size:93 final size:93
Alignment explanation
Indices: 314019--314194 Score: 253
Period size: 93 Copynumber: 1.9 Consensus size: 93
314009 CATATTATAT
* * * * *
314019 TATTATATGCAATAAAGCTTGAGTTGTTCCTTTATAGGAATTGGTTAATCACCCTGACTTTATGG
1 TATTATATACAATAAAGCTTGAGTTGTCCCTCTAGAGGAATTGGTTAATCACCCCGACTTTATGG
* **
314084 ATAATATTCTGCTAGCCTATTATATTAC
66 ATAAGATTCAACTAGCCTATTATATTAC
* * *
314112 TATTATATACAATAAAGCTTGAGTTGTCCCTCTAGAGTAATTGGTTAATCGCCCCGCCTTTATGG
1 TATTATATACAATAAAGCTTGAGTTGTCCCTCTAGAGGAATTGGTTAATCACCCCGACTTTATGG
314177 ATAAGATTCAACTAGCCT
66 ATAAGATTCAACTAGCCT
314195 GATAGTGGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (93 bp):
TATTATATACAATAAAGCTTGAGTTGTCCCTCTAGAGGAATTGGTTAATCACCCCGACTTTATGG
ATAAGATTCAACTAGCCTATTATATTAC
Found at i:316801 original size:29 final size:29
Alignment explanation
Indices: 316769--316854 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
316759 ATTGTGTTAT
*
316769 CTCAAATCATCATTGGATAGCCAGATATC
1 CTCAAATCATCATTGGATAGCCAAATATC
* * *
316798 CTC--ATTA-CATAGGA-A-CCATATTAT-
1 CTCAAATCATCATTGGATAGCCA-AATATC
*
316822 CTCAAATCATCCTTGGATAGCCAAATATC
1 CTCAAATCATCATTGGATAGCCAAATATC
316851 CTCA
1 CTCA
316855 TCATGAAAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 6 0.14
25 4 0.10
26 9 0.21
27 8 0.19
28 5 0.12
29 10 0.24
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (29 bp):
CTCAAATCATCATTGGATAGCCAAATATC
Found at i:316802 original size:53 final size:53
Alignment explanation
Indices: 316722--317078 Score: 353
Period size: 53 Copynumber: 6.7 Consensus size: 53
316712 AACATACTCG
* **
316722 TCATCCTTAGATAGCCAGATGTCCTCATCATGAAGGAATTGTGTTATCTCAAA
1 TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAA
* * * * * *
316775 TCATCATTGGATAGCCAGATATCCTCATTAC-ATAGGAACCATATTATCTCAAA
1 TCATCCTTAGATAGCCAGATGTCCTCATCACGA-AGGAACCGTGTTATCTCAAA
* * * * *
316828 TCATCCTTGGATAGCCAAATATCCTCATCATGAAAGAACCGTGTTATCGT-AAA
1 TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATC-TCAAA
* * *
316881 TCATCCTTGGATAGCCAGATGTCCTCATCACGAAGAAACCGTGTTATCCCAAA
1 TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAA
* * * * *
316934 TCATCCTTAGAAATCCATATGTCCTCATCACGAAGAAACCATGTTATCTC-AA
1 TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAA
* * * * *
316986 TAATCCTTAGATAGCTAGACGTCCTCATCGCGAAGGAACTGTGTTATCTC-AA
1 TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAA
* * * * * *
317038 TTATCTTTAAACATGACCAGACGTCCTCATCATGAAGGAAC
1 TCATCCTTAGATA-G-CCAGATGTCCTCATCACGAAGGAAC
317079 AATGTCATAC
Statistics
Matches: 253, Mismatches: 45, Indels: 11
0.82 0.15 0.04
Matches are distributed among these distances:
52 54 0.21
53 175 0.69
54 24 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (53 bp):
TCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTATCTCAAA
Found at i:317287 original size:3 final size:3
Alignment explanation
Indices: 317259--317322 Score: 96
Period size: 3 Copynumber: 21.7 Consensus size: 3
317249 TATTGTTTTA
*
317259 TAT TAT AAT TA- TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT
317303 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
317323 ATAAATAATA
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:321531 original size:8 final size:7
Alignment explanation
Indices: 321500--321530 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
321490 AGCAAAAGTG
321500 AACACAAA
1 AACA-AAA
321508 AACAAAA
1 AACAAAA
321515 AACAAAA
1 AACAAAA
321522 AACAAAA
1 AACAAAA
321529 AA
1 AA
321531 AGGGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.83
8 4 0.17
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (7 bp):
AACAAAA
Found at i:322541 original size:73 final size:73
Alignment explanation
Indices: 322451--322596 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
322441 TGAAGGCTGT
322451 AAATACCTTCTCAGGGTAAGCCTTAAAACACATTCATAATTCATTTTTCTTCTTCCTCTGGGTTT
1 AAATACCTTCTCAGGGTAAGCCTTAAAACACATTCATAATTCATTTTTCTTCTTCCTCTGGGTTT
322516 TATAAAAG
66 TATAAAAG
*
322524 AAATACCTTCTTAGGGTAAGCCTTAAAACACATTCATAATTCATTTTTCTTCTTCCTCTGGGTTT
1 AAATACCTTCTCAGGGTAAGCCTTAAAACACATTCATAATTCATTTTTCTTCTTCCTCTGGGTTT
322589 TATAAAAG
66 TATAAAAG
322597 TTTTTTTTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (73 bp):
AAATACCTTCTCAGGGTAAGCCTTAAAACACATTCATAATTCATTTTTCTTCTTCCTCTGGGTTT
TATAAAAG
Found at i:324760 original size:20 final size:20
Alignment explanation
Indices: 324720--324763 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
324710 AAATTTTCAA
**
324720 TAAAAAATATATAATTTTTT
1 TAAAAAATATATAATAATTT
324740 TAAAAAATATATAATAATTT
1 TAAAAAATATATAATAATTT
324760 TAAA
1 TAAA
324764 TTTTCGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAAAAAATATATAATAATTT
Found at i:325976 original size:23 final size:23
Alignment explanation
Indices: 325931--325976 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
325921 ACATATCTAG
**
325931 TTGTAAAATCTTGAATTGTGTTC
1 TTGTAAAATCTTGAATTACGTTC
* *
325954 TTGTTAAATCTTGGATTACGTTC
1 TTGTAAAATCTTGAATTACGTTC
325977 CGATAGATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (23 bp):
TTGTAAAATCTTGAATTACGTTC
Found at i:336971 original size:43 final size:42
Alignment explanation
Indices: 336900--337020 Score: 134
Period size: 43 Copynumber: 2.8 Consensus size: 42
336890 GCTAAAGTTC
*
336900 GCGGCGTTTGTTAACAAAAAATGCCGCAATAGGTGACGATATATA
1 GCGGCGTTTGTTAA-AAAACA--CCGCAATAGGTGACGATATATA
** * *
336945 GCGGCGTTTGTTGAAAAAACACCGCAATAGGTGTTGCTATTTA
1 GCGGCGTTTGTT-AAAAAACACCGCAATAGGTGACGATATATA
* *
336988 GCGGCGTTTGTCTTAAAAACGCCGCAATAGGTG
1 GCGGCGTTTGT-TAAAAAACACCGCAATAGGTG
337021 TTGTCGTTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
43 47 0.70
44 1 0.01
45 17 0.25
46 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (42 bp):
GCGGCGTTTGTTAAAAAACACCGCAATAGGTGACGATATATA
Found at i:337021 original size:43 final size:43
Alignment explanation
Indices: 336916--337213 Score: 201
Period size: 43 Copynumber: 6.9 Consensus size: 43
336906 TTTGTTAACA
* ** * *
336916 AAAAATGCCGCAATAGGTGACGATATATAGCGGCGTTTGT-TGA
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCT-C
* * *
336959 AAAAACACCGCAATAGGTGTTGCTATTTAGCGGCGTTTGTCTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * *
337002 AAAAACGCCGCAATAGGTGTTG-TCGTTTAGCGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGAT-ATTTAGCGGCGTTTGTCTC
** * * * * * * * *
337045 CCAAACGCCGCAGTAGGTATCGTTGTTTAGTGGCGTTTTTCCC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * * *
337088 AAAAATGTCGCAATAGGTGTTGTTGTTTAGCGGTGTTT-T-TC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * * *
337129 AAACAAGCGCCGCAATAAGCGTTGAGATTTAGCGGCGTTTTTATC
1 AAA-AA-CGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
* * * *
337174 GAAAACGCCGCTACATGT-TATGATATTTAGCGGCGTTTGT
1 AAAAACGCCGCAATAGGTGT-TGATATTTAGCGGCGTTTGT
337214 GGTAAAAAAA
Statistics
Matches: 204, Mismatches: 43, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
41 4 0.02
42 5 0.02
43 186 0.91
44 5 0.02
45 4 0.02
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTC
Found at i:337056 original size:86 final size:86
Alignment explanation
Indices: 336943--337168 Score: 229
Period size: 86 Copynumber: 2.6 Consensus size: 86
336933 TGACGATATA
* * * **
336943 TAGCGGCGTTTGTTGAAA-AAACACCGCAATAGGTGTTGCTATTTAGCGGCGTTTGTCTTAAAAA
1 TAGCGGCGTTT-TTCAAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCCAAAAA
337007 CGCCGCAATAGGTGTTGTCGTT
65 CGCCGCAATAGGTGTTGTCGTT
*** * * * * * * * *
337029 TAGCGGCGTTTTTCCCCCAAACGCCGCAGTAGGTATCGTTGTTTAGTGGCGTTTTTCCCAAAAAT
1 TAGCGGCGTTTTTCAAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCCAAAAAC
* *
337094 GTCGCAATAGGTGTTGTTGTT
66 GCCGCAATAGGTGTTGTCGTT
* * * * *
337115 TAGCGGTGTTTTTCAAACAAGCGCCGCAATAAGCGTTGAGATTTAGCGGCGTTT
1 TAGCGGCGTTTTTCAAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
337169 TTATCGAAAA
Statistics
Matches: 108, Mismatches: 31, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
85 2 0.02
86 106 0.98
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (86 bp):
TAGCGGCGTTTTTCAAACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCCCAAAAAC
GCCGCAATAGGTGTTGTCGTT
Found at i:338970 original size:22 final size:22
Alignment explanation
Indices: 338942--338988 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
338932 GCTTTACAAA
338942 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
338964 AAGTAAACATTCAAGGATCAAG
1 AAGTAAACATTCAAGGATCAAG
338986 AAG
1 AAG
338989 GCTTTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.51, C:0.13, G:0.19, T:0.17
Consensus pattern (22 bp):
AAGTAAACATTCAAGGATCAAG
Found at i:341083 original size:41 final size:41
Alignment explanation
Indices: 340906--341213 Score: 336
Period size: 42 Copynumber: 7.4 Consensus size: 41
340896 ACAATCAAAT
* * *
340906 TACGAGTCTATAGTGGTGTTTG-GTATTAAAACGCCACAAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTA--AAAACGCCACTAAAG
*
340948 TACGTGTCTATAGCGGCGTTTGTGTAAAAAACGCCACTAAAG
1 TACGAGTCTATAGCGGCGTTTGTGT-AAAAACGCCACTAAAG
* ** *
340990 TACGAATCTATAGTTGCGTTTG-GTATTAAAACGCCACAAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTA--AAAACGCCACTAAAG
* * *
341032 TACGTGTCTATAGCGGCGTTTGTGTAAAAATGTCACTAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
*
341073 TACGAGTCTATAGCGGCGTTTG-GTATTAAAACGCCACAAAAG
1 TACGAGTCTATAGCGGCGTTTGTGTA--AAAACGCCACTAAAG
*
341115 TAC-ATGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAA
1 TACGA-GTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
* * * * *
341156 TACTAGTTTATAGCGGCGTTTGTATAAAAACGCCACTACAT
1 TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
* *
341197 TACGATTCTTTAGCGGC
1 TACGAGTCTATAGCGGC
341214 TATATATAAA
Statistics
Matches: 226, Mismatches: 30, Indels: 21
0.82 0.11 0.08
Matches are distributed among these distances:
40 4 0.02
41 97 0.43
42 116 0.51
43 8 0.04
44 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.29
Consensus pattern (41 bp):
TACGAGTCTATAGCGGCGTTTGTGTAAAAACGCCACTAAAG
Found at i:341113 original size:83 final size:83
Alignment explanation
Indices: 340906--341191 Score: 448
Period size: 83 Copynumber: 3.4 Consensus size: 83
340896 ACAATCAAAT
* *
340906 TACGAGTCTATAGTGGTGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
340971 GTAAAAAACGCCACTAAAG
66 GT-AAAAACGCCACTAAAG
* **
340990 TACGAATCTATAGTTGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
* *
341055 GTAAAAATGTCACTAAAG
66 GTAAAAACGCCACTAAAG
*
341073 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACATGTCTATAGCGGCGTTTGT
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
*
341138 GTAAAAACGCCACTAAAA
66 GTAAAAACGCCACTAAAG
* * *
341156 TACTAGTTTATAGCGGCGTTT-GTATAAAAACGCCAC
1 TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCAC
341192 TACATTACGA
Statistics
Matches: 187, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
82 14 0.07
83 109 0.58
84 64 0.34
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (83 bp):
TACGAGTCTATAGCGGCGTTTGGTATTAAAACGCCACAAAAGTACGTGTCTATAGCGGCGTTTGT
GTAAAAACGCCACTAAAG
Found at i:349689 original size:21 final size:22
Alignment explanation
Indices: 349659--349699 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
349649 TATAGAGAAT
*
349659 TTGAGGAAATGCTT-CTAAAGA
1 TTGAGAAAATGCTTGCTAAAGA
349680 TTGAGAAAATGCTTGCTAAA
1 TTGAGAAAATGCTTGCTAAA
349700 ACTGAATCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (22 bp):
TTGAGAAAATGCTTGCTAAAGA
Found at i:351624 original size:22 final size:20
Alignment explanation
Indices: 351572--351629 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
351562 GATGCATGGG
351572 GTATCGATACCTGTAT-GAAAA
1 GTATCGATACC--TATGGAAAA
* *
351593 ATATCAATACCATATGGAATAA
1 GTATCGATACC-TATGGAA-AA
351615 GTATCGATACCTATG
1 GTATCGATACCTATG
351630 TGGAGGGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.10
21 16 0.53
22 11 0.37
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (20 bp):
GTATCGATACCTATGGAAAA
Found at i:352170 original size:31 final size:31
Alignment explanation
Indices: 352083--352179 Score: 113
Period size: 32 Copynumber: 3.1 Consensus size: 31
352073 AAGAGTCGAG
*
352083 GGTTACCTATGTCCTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGAGACATATGGACA
* **
352114 GTATTACCTATGTCCTTCTTGACATATGGACA
1 G-GTTACCTATGTCCTTCGAGACATATGGACA
* * * *
352146 GGTTACCTATGTTCTACGAAACATATGGATA
1 GGTTACCTATGTCCTTCGAGACATATGGACA
352177 GGT
1 GGT
352180 CCTTCAAAAC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 27 0.49
32 28 0.51
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGAGACATATGGACA
Found at i:355594 original size:22 final size:22
Alignment explanation
Indices: 355544--355598 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
355534 TGATGCATGG
*
355544 GGTATCGATACCTGTATGAACA
1 GGTATCGATACCTATATGAACA
*
355566 -GTATCGATACC-ATATGGAATA
1 GGTATCGATACCTATAT-GAACA
355587 GGTATCGATACC
1 GGTATCGATACC
355599 CGGGAAGCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 3 0.10
21 15 0.52
22 11 0.38
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (22 bp):
GGTATCGATACCTATATGAACA
Found at i:355646 original size:19 final size:21
Alignment explanation
Indices: 355622--355675 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 21
355612 AGCTATTTTT
*
355622 GGTATCGGTACCTAG-GTAG-
1 GGTATCGGTACCTAGCATAGA
355641 GGTATCGGTACCCTAGCATAGA
1 GGTATCGGTA-CCTAGCATAGA
355663 GGTATCGGTACCT
1 GGTATCGGTACCT
355676 TGAGGGTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 10 0.32
20 5 0.16
21 6 0.19
22 10 0.32
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.26
Consensus pattern (21 bp):
GGTATCGGTACCTAGCATAGA
Found at i:355669 original size:22 final size:20
Alignment explanation
Indices: 355622--355674 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
355612 AGCTATTTTT
*
355622 GGTATCGGTA-CCTAGGTAG
1 GGTATCGGTACCCTAGATAG
355641 GGTATCGGTACCCTAGCATAG
1 GGTATCGGTACCCTAG-ATAG
355662 AGGTATCGGTACC
1 -GGTATCGGTACC
355675 TTGAGGGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 10 0.33
20 5 0.17
21 3 0.10
22 12 0.40
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (20 bp):
GGTATCGGTACCCTAGATAG
Found at i:356020 original size:2 final size:2
Alignment explanation
Indices: 356013--356060 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
356003 GACTAGATGA
356013 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
356055 AT AT AT
1 AT AT AT
356061 CTAGAAGTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:357003 original size:32 final size:31
Alignment explanation
Indices: 356962--357051 Score: 117
Period size: 32 Copynumber: 2.9 Consensus size: 31
356952 GAGTCGAGAG
*
356962 TTACCTATGTCCTTCGGGACATATGGAAAGTA
1 TTACCTATGTCCTTCGGAACATATGGAAAG-A
* * *
356994 TTACCTATGTCCTTCCGAACATATGGACAGG
1 TTACCTATGTCCTTCGGAACATATGGAAAGA
* *
357025 TTACCTATGTTCTACGGAACATATGGA
1 TTACCTATGTCCTTCGGAACATATGGA
357052 TAGGTCCTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 24 0.47
32 27 0.53
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (31 bp):
TTACCTATGTCCTTCGGAACATATGGAAAGA
Found at i:357032 original size:31 final size:31
Alignment explanation
Indices: 356961--357056 Score: 120
Period size: 31 Copynumber: 3.1 Consensus size: 31
356951 AGAGTCGAGA
*
356961 GTTACCTATGTCCTTCGGGACATATGGAAAG
1 GTTACCTATGTCCTTCGGAACATATGGAAAG
* * *
356992 TATTACCTATGTCCTTCCGAACATATGGACAG
1 -GTTACCTATGTCCTTCGGAACATATGGAAAG
* * *
357024 GTTACCTATGTTCTACGGAACATATGGATAG
1 GTTACCTATGTCCTTCGGAACATATGGAAAG
357055 GT
1 GT
357057 CCTTTGGGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
31 28 0.51
32 27 0.49
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGGAACATATGGAAAG
Found at i:359265 original size:24 final size:23
Alignment explanation
Indices: 359235--359284 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
359225 GAAGAAAGAA
359235 AAAAATGA-AAATGAAAAAAAATAG
1 AAAAATGACAAA-GAAAAAAAA-AG
*
359259 AAAAATGACAAAGAAAGAAAAAG
1 AAAAATGACAAAGAAAAAAAAAG
359282 AAA
1 AAA
359285 GAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 5 0.21
24 16 0.67
25 3 0.12
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (23 bp):
AAAAATGACAAAGAAAAAAAAAG
Found at i:360305 original size:133 final size:132
Alignment explanation
Indices: 360118--360441 Score: 362
Period size: 133 Copynumber: 2.4 Consensus size: 132
360108 AATCGTACCT
* * **
360118 GATTAAATCTTCCAGAAGAACAGTGGAATGAATCAATGTTTCCAGATCTGATCTACCCTAAAGAA
1 GATTCAATCTTCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTAAAGAA
* ** * * * **
360183 GCAACGGAGCATATCATTTTTTTCCAGATTTGATATTCCCTGAGTAGCATTGGAACAAGTCTGCC
66 GCAACGGAGCAGATCACCTTTTTCCAGATTTAATATTCCCTGAGTAACAGTGGAACAAGTAAGCC
360248 TC
131 TC
* * * *
360250 GATTCAATCTTCTCTGAAGAACAATAGAATGAATCAACATTTACAGATCTTATCTACCCTAAAGA
1 GATTCAATCTTC-CTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTAAAGA
* * * * * * * *
360315 AGTAGCGGAGTAGATCCCCTTTTTCCATATTTAATCTTCCTTGAGTAATAGTGGAACAAGTAAGC
65 AGCAACGGAGCAGATCACCTTTTTCCAGATTTAATATTCCCTGAGTAACAGTGGAACAAGTAAGC
360380 CTC
130 CTC
* * * * *
360383 TATTCAATATTCCCTG-AGAATAGTGGAATCAATCAACATTTCCAGATCTGATTTACCCT
1 GATTCAATCTT-CCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCT
360442 GAAAAAACAG
Statistics
Matches: 157, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
132 47 0.30
133 109 0.69
134 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (132 bp):
GATTCAATCTTCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATCTGATCTACCCTAAAGAA
GCAACGGAGCAGATCACCTTTTTCCAGATTTAATATTCCCTGAGTAACAGTGGAACAAGTAAGCC
TC
Found at i:363037 original size:131 final size:131
Alignment explanation
Indices: 362796--363191 Score: 571
Period size: 131 Copynumber: 3.0 Consensus size: 131
362786 ATAAATAACA
* *
362796 CTCGAATCAATATTGAATTTTAGG-GGAAAATAGTAATATTTCTTCATTTCGATTGGAGTAATAA
1 CTCGAATCAATATTGAATTTTAGGACG-AAATAGTAATATCTCTTCATTTCGATTGGAGTAATAA
* *
362860 ATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCAATTGCAAATAATTAGATATTATCGTTTT
65 ATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTT
362925 CT
130 CT
* * * * *
362927 CTCGAATTAATATTGAATTTTAGGACGAAATTGTAATGTCTCTTCATTTCGAATGTAGTAATAAA
1 CTCGAATCAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA
* ** * * ***
362992 TGATTGCTTGAA-TAATTGAGAGGTCTTTTATTCTCTATTGGAAATAATTAGACGCTATCATTTT
66 TGATTGCTTTAAGGCA-TGAGAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTT
363056 CT
130 CT
*
363058 CTCGAATCAATATTGAATTTTAGGATGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA
1 CTCGAATCAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA
* * *
363123 TGACTGCTTTAAGGCATGAGATGTCATTTATTCTCAATTGGAAATAATTAGATATTATTATTTTC
66 TGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTC
363188 T
131 T
363189 CTC
1 CTC
363192 TTAAAATTCA
Statistics
Matches: 228, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
130 1 0.00
131 225 0.99
132 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
CTCGAATCAATATTGAATTTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA
TGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTC
T
Found at i:364717 original size:20 final size:21
Alignment explanation
Indices: 364692--364743 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
364682 TTTTCCCAAT
*
364692 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
364712 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
364733 TCGCAATGCGA
1 TCGCAATGCGA
364744 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:364757 original size:20 final size:20
Alignment explanation
Indices: 364732--364906 Score: 192
Period size: 20 Copynumber: 8.7 Consensus size: 20
364722 AATTGGGAAA
364732 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
364752 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
364772 ATCGCTATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
364792 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
364812 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
364833 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
364853 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
364873 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
364893 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
364907 TTTCAAAGCA
Statistics
Matches: 134, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.03
20 104 0.78
21 24 0.18
22 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:364837 original size:81 final size:82
Alignment explanation
Indices: 364731--364906 Score: 207
Period size: 81 Copynumber: 2.2 Consensus size: 82
364721 GAATTGGGAA
* * * * * *
364731 AATCGCAATGCGATACTGAC--TATCGCAATGCGATACTGACTATCGCTATGCGATACTGACTAT
1 AATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTAT
* *
364794 CGCAATGCGATACTTAC-T
65 CGCAACGCGATA-ATACAT
* * *
364812 -ATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTC
1 AATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATC
364876 GCAACGCGATAATACAT
66 GCAACGCGATAATACAT
364893 AATCGCAATGCGAT
1 AATCGCAATGCGAT
364907 TTTCAAAGCA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
79 2 0.03
80 18 0.22
81 47 0.59
82 13 0.16
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (82 bp):
AATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATC
GCAACGCGATAATACAT
Found at i:364878 original size:61 final size:60
Alignment explanation
Indices: 364732--364900 Score: 205
Period size: 61 Copynumber: 2.8 Consensus size: 60
364722 AATTGGGAAA
* * * * *
364732 ATCGCAATGCGATACTGACTATCGCAATGCGATACTGAC-TATCGCTATGCGATACTGACT
1 ATCGCAATGCGATACTGACTATCGCAATGCGATAAT-ACAAATCGCAACGAGATACTGACT
*
364792 ATCGCAATGCGATACTTACTATCGCAATGCGATAATACAAAATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACTATCGCAATGCGATAATAC-AAATCGCAACGAGATACTGACT
* * * * *
364853 TTCGCAACGCGATTCTGACTTTCGCAACGCGATAATACATAATCGCAA
1 ATCGCAATGCGATACTGACTATCGCAATGCGATAATACA-AATCGCAA
364901 TGCGATTTTC
Statistics
Matches: 94, Mismatches: 12, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
59 2 0.02
60 35 0.37
61 57 0.61
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (60 bp):
ATCGCAATGCGATACTGACTATCGCAATGCGATAATACAAATCGCAACGAGATACTGACT
Found at i:365419 original size:20 final size:20
Alignment explanation
Indices: 365380--365438 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
365370 GCGATTCTCT
* **
365380 CGTTGCAATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
365400 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
365420 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
365439 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:365629 original size:25 final size:24
Alignment explanation
Indices: 365575--365629 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
365565 TGTTTATTAT
* *
365575 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
365599 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
365625 TGTTT
1 TGTTT
365630 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:366778 original size:18 final size:18
Alignment explanation
Indices: 366757--366801 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
366747 CTCCACTTCG
*
366757 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
* *
366775 AGAGCTATCACCTCACCT
1 AGAGCCATCACCTCACCC
366793 AGAGCCATC
1 AGAGCCATC
366802 CTCTGATCGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:367311 original size:19 final size:20
Alignment explanation
Indices: 367257--367312 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
367247 TAGTTTACTT
* *
367257 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
367277 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
367297 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
367313 AAATCAAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:367350 original size:19 final size:19
Alignment explanation
Indices: 367326--367392 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
367316 TCAAAACGAC
367326 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
367345 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
* *
367359 AAAATCGCAACGCAAAATG
1 AAAATCGCAATGCGAAATG
367378 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
367393 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 1 0.03
17 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:367376 original size:13 final size:14
Alignment explanation
Indices: 367345--367376 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
367335 ATGCGAAATG
367345 AAAATCGCAACGAC
1 AAAATCGCAACGAC
367359 AAAATCGCAACG-C
1 AAAATCGCAACGAC
367372 AAAAT
1 AAAAT
367377 GAAAATCGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.53, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:367384 original size:33 final size:33
Alignment explanation
Indices: 367296--367387 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
367286 GGAAATGGCT
**
367296 ATCGCAATGCGAAATGAAAATCAAAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
367329 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
367362 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
367388 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.51, C:0.21, G:0.16, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:367463 original size:20 final size:19
Alignment explanation
Indices: 367429--367484 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
367419 GTTGCGATTT
*
367429 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
367448 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
367468 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
367485 TTTTAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:369374 original size:14 final size:14
Alignment explanation
Indices: 369355--369390 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
369345 ATTGTTTAAT
369355 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
369369 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
369383 TGATTTGT
1 TGATTTGT
369391 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:369572 original size:19 final size:19
Alignment explanation
Indices: 369527--369581 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 19
369517 ATCGCAACGA
*
369527 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
369546 GAAAAATCGCAATGCGAAAT
1 G-AAAATCGCAATGCGAAAT
369566 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
369582 TTTTCATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.16
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:369613 original size:20 final size:20
Alignment explanation
Indices: 369588--369641 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
369578 GCGATTTTCA
*
369588 TTTCGCATTGCGATAACCAT
1 TTTCGCGTTGCGATAACCAT
*
369608 TTTCGCGTTGCGATAGCCAT
1 TTTCGCGTTGCGATAACCAT
369628 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
369642 TTCCCCGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (20 bp):
TTTCGCGTTGCGATAACCAT
Found at i:369880 original size:20 final size:20
Alignment explanation
Indices: 369855--369946 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
369845 TTGAAGATGA
369855 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
369875 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
369895 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
369916 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
369936 TTGCGATTTTC
1 TTGCGATTTTC
369947 CAAATTCGCA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:370198 original size:12 final size:12
Alignment explanation
Indices: 370179--370212 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
370169 CTCTCTGACG
370179 ACATCCGTTCCT
1 ACATCCGTTCCT
*
370191 ATATCCGTTCCT
1 ACATCCGTTCCT
370203 ACATCC-TTCC
1 ACATCCGTTCC
370213 CCATCCGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:370794 original size:24 final size:24
Alignment explanation
Indices: 370767--370820 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
370757 GTATTTGAAA
*
370767 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
370791 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
370815 TTTGAT
1 TTTGAT
370821 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:371003 original size:3 final size:3
Alignment explanation
Indices: 370995--371037 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
370985 ATATAATCCT
* * *
370995 GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA GAA AAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
371038 GAAAAGTCCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:371012 original size:12 final size:12
Alignment explanation
Indices: 370995--371043 Score: 89
Period size: 12 Copynumber: 4.1 Consensus size: 12
370985 ATATAATCCT
370995 GAAGAAGAAAAA
1 GAAGAAGAAAAA
371007 GAAGAAGAAAAA
1 GAAGAAGAAAAA
371019 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
371031 GAAGAAGGAAAA
1 GAAGAAGAAAAA
371043 G
1 G
371044 TCCCCGAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:373357 original size:19 final size:19
Alignment explanation
Indices: 373335--373393 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
373325 GGAAATTACT
373335 ATCGCAATGAGAAATGAAA
1 ATCGCAATGAGAAATGAAA
*
373354 ATCGCAACGAG--A-G--A
1 ATCGCAATGAGAAATGAAA
*
373368 ATCGCAATGCGAAATGAAA
1 ATCGCAATGAGAAATGAAA
373387 ATCGCAA
1 ATCGCAA
373394 CGCTAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
16 2 0.06
17 2 0.06
19 18 0.56
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGAGAAATGAAA
Found at i:373382 original size:33 final size:33
Alignment explanation
Indices: 373335--373461 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
373325 GGAAATTACT
*
373335 ATCGCAATGAGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
373368 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
373400 TTTCGCAAAGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
373434 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
373462 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:373426 original size:19 final size:19
Alignment explanation
Indices: 373335--373465 Score: 58
Period size: 19 Copynumber: 7.7 Consensus size: 19
373325 GGAAATTACT
* *
373335 ATCGCAATGAGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
373354 ATCGC-AA-CG--A-GAGA
1 ATCGCAAAGCGAAATGAAA
*
373368 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
* *
373387 ATCGC-AA-CG--CT-AAT
1 ATCGCAAAGCGAAATGAAA
*
373401 TTCGCAAAGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
**
373420 ATCGC-AA-CG--A-GGGA
1 ATCGCAAAGCGAAATGAAA
*
373434 ATCGCAATGCGAAATGAAA
1 ATCGCAAAGCGAAATGAAA
*
373453 ATCGCAACGCGAA
1 ATCGCAAAGCGAA
373466 TTTAATTTCG
Statistics
Matches: 79, Mismatches: 18, Indels: 30
0.62 0.14 0.24
Matches are distributed among these distances:
14 21 0.27
15 7 0.09
16 6 0.08
17 5 0.06
18 7 0.09
19 33 0.42
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAAAGCGAAATGAAA
Found at i:373442 original size:66 final size:66
Alignment explanation
Indices: 373336--373468 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
373326 GAAATTACTA
* *
373336 TCGCAATGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAAAGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
373401 T
66 T
* *
373402 TCGCAAAGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAAAGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
373467 T
66 T
373468 T
1 T
373469 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (66 bp):
TCGCAAAGAGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:373483 original size:19 final size:19
Alignment explanation
Indices: 373461--373502 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
373451 AAATCGCAAC
373461 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
* *
373480 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
373499 GCGA
1 GCGA
373503 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:373503 original size:19 final size:19
Alignment explanation
Indices: 373470--373536 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
373460 CGCGAATTTA
373470 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
373489 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
373506 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
373522 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
373537 AGTACTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
16 3 0.08
17 3 0.08
19 24 0.60
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:373662 original size:14 final size:14
Alignment explanation
Indices: 373643--373679 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
373633 CATCAATTAA
373643 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
373657 ACAAATCACCTTTT
1 ACAAATCAACTTTT
373671 ACAAATCAA
1 ACAAATCAA
373680 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:374044 original size:19 final size:19
Alignment explanation
Indices: 374020--374087 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
374010 ATCGCAACGA
*
374020 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
374039 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
374058 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
374072 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
374088 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 29 0.64
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:374139 original size:34 final size:36
Alignment explanation
Indices: 374094--374181 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
374084 GCGATTTTCA
* * *
374094 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAG
374128 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAG
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAG
374168 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
374182 AGTCAAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
34 12 0.27
35 5 0.11
38 1 0.02
39 1 0.02
40 26 0.58
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAG
Found at i:374406 original size:20 final size:20
Alignment explanation
Indices: 374381--374472 Score: 67
Period size: 20 Copynumber: 4.5 Consensus size: 20
374371 TTGAAGATGA
374381 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
374401 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* * **
374421 TTGTGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
374442 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
374462 TTGCGATTTTC
1 TTGCGATTTTC
374473 CAAATTCGCA
Statistics
Matches: 52, Mismatches: 19, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:374501 original size:20 final size:21
Alignment explanation
Indices: 374457--374506 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
374447 ATAGTCAGTA
*
374457 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
374478 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
374498 TCGCATTGC
1 TCGCATTGC
374507 TAATTAGGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:374724 original size:12 final size:12
Alignment explanation
Indices: 374705--374738 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
374695 CTCTCTGACG
374705 ACATCCGTTCCT
1 ACATCCGTTCCT
*
374717 ATATCCGTTCCT
1 ACATCCGTTCCT
374729 ACATCC-TTCC
1 ACATCCGTTCC
374739 CCATCCGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:375320 original size:24 final size:24
Alignment explanation
Indices: 375293--375346 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
375283 GTATTCGAAA
* *
375293 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGATCAATACCCGGAC
* *
375317 TTTGATATTGATCAATACTCGGAT
1 TTTGATATTGATCAATACCCGGAC
375341 TTTGAT
1 TTTGAT
375347 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGATCAATACCCGGAC
Found at i:375538 original size:12 final size:12
Alignment explanation
Indices: 375521--375545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
375511 ATATAATCCT
375521 GAAGAAGAAAAA
1 GAAGAAGAAAAA
375533 GAAGAAGAAAAA
1 GAAGAAGAAAAA
375545 G
1 G
375546 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:377859 original size:19 final size:19
Alignment explanation
Indices: 377837--377895 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
377827 GGAAATTACT
377837 ATCGCAATGAGAAATGAAA
1 ATCGCAATGAGAAATGAAA
*
377856 ATCGCAACGAG--A-G--A
1 ATCGCAATGAGAAATGAAA
377870 ATCGCAATGCA-AAATGAAA
1 ATCGCAATG-AGAAATGAAA
377889 ATCGCAA
1 ATCGCAA
377896 CACTAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
19 18 0.56
ACGTcount: A:0.49, C:0.17, G:0.20, T:0.14
Consensus pattern (19 bp):
ATCGCAATGAGAAATGAAA
Found at i:377885 original size:33 final size:33
Alignment explanation
Indices: 377837--377963 Score: 143
Period size: 33 Copynumber: 3.8 Consensus size: 33
377827 GGAAATTACT
377837 ATCGCAATG-AGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCA-AAATGAAAATCGCAACGAGAGA
*
377870 ATCGCAATGCAAAATGAAAATCGCAAC-ACTA-A
1 ATCGCAATGCAAAATGAAAATCGCAACGA-GAGA
* * * * *
377902 TTTTGCAATACGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
*
377936 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCAAAATGAAAATCGCAACG
377964 CGAATTTAAT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
32 2 0.03
33 74 0.94
34 3 0.04
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
Found at i:377970 original size:66 final size:66
Alignment explanation
Indices: 377847--377970 Score: 212
Period size: 66 Copynumber: 1.9 Consensus size: 66
377837 ATCGCAATGA
*
377847 GAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACACTAATTTTGCAATA
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACACGAATTTTGCAATA
377912 C
66 C
* * *
377913 GAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 GAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACACGAATTT
377971 AATTTCGCGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.17
Consensus pattern (66 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACACGAATTTTGCAATA
C
Found at i:377985 original size:19 final size:19
Alignment explanation
Indices: 377972--378016 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
377962 CGCGAATTTA
377972 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
377991 ATTTCACGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
378010 ATTTCGC
1 ATTTCGC
378017 ATTGTGATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:378150 original size:14 final size:14
Alignment explanation
Indices: 378131--378167 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
378121 CATCAATTAA
378131 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
378145 ACAAATCACCTTTT
1 ACAAATCAACTTTT
378159 ACAAATCAA
1 ACAAATCAA
378168 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:378355 original size:14 final size:14
Alignment explanation
Indices: 378336--378371 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
378326 ATTGTTTAAT
378336 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
378350 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
378364 TGATTTGT
1 TGATTTGT
378372 TTAGTTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:378582 original size:19 final size:19
Alignment explanation
Indices: 378508--378575 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
378498 ATCGCAACGA
378508 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGTGAAAT
378527 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGTGAAAT
*
378546 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGTGAAAT
378565 GAAAATCGCAA
1 GAAAATCGCAA
378576 CGAGAAAATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.49, C:0.13, G:0.21, T:0.18
Consensus pattern (19 bp):
GAAAATCGCAATGTGAAAT
Found at i:378638 original size:20 final size:20
Alignment explanation
Indices: 378621--378708 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
378611 CGATTTTCTA
378621 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
378641 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
378661 ATTGCGATAGCCAGTTTCGC
1 GTTGCGATAGCCATTTTCGC
378681 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
378701 GTTGCGAT
1 GTTGCGAT
378709 TTCCCCGTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
19 3 0.05
20 49 0.89
21 3 0.05
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:378646 original size:34 final size:36
Alignment explanation
Indices: 378601--378688 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
378591 GCGATTTTCA
* * *
378601 TTTCGCATTGCGATTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAG
378635 TTTCGCGTTGCGATTTTTCATTTCGAATTGCGATAGCCAG
1 TTTCGCGTTGCGA-TTTTC--TTC-AATTGCGATAGCCAG
378675 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
378689 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
34 12 0.27
35 5 0.11
38 1 0.02
39 1 0.02
40 26 0.58
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (36 bp):
TTTCGCGTTGCGATTTTCTTCAATTGCGATAGCCAG
Found at i:378947 original size:20 final size:20
Alignment explanation
Indices: 378922--378971 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
378912 TTGAAGATGA
378922 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
378942 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
*
378962 TTGTGATTTT
1 TTGCGATTTT
378972 GTATTATCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:379042 original size:20 final size:21
Alignment explanation
Indices: 378998--379049 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
378988 ATAGTCAGTA
*
378998 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
379019 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
379039 TCGCATTGCGA
1 TCGCATTGCGA
379050 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:379265 original size:12 final size:12
Alignment explanation
Indices: 379246--379279 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
379236 CTCTCCGGCG
379246 ACATCCGTTCCT
1 ACATCCGTTCCT
*
379258 ATATCCGTTCCT
1 ACATCCGTTCCT
379270 ACATCC-TTCC
1 ACATCCGTTCC
379280 CCATCCGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:379861 original size:24 final size:24
Alignment explanation
Indices: 379834--379887 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
379824 GTATTCGAAA
* *
379834 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGATCAATACCCGGAC
* *
379858 TTTGATATTGATCAATACTCGGAT
1 TTTGATATTGATCAATACCCGGAC
379882 TTTGAT
1 TTTGAT
379888 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGATCAATACCCGGAC
Found at i:380079 original size:12 final size:12
Alignment explanation
Indices: 380062--380086 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
380052 ATATAATCCT
380062 GAAGAAGAAAAA
1 GAAGAAGAAAAA
380074 GAAGAAGAAAAA
1 GAAGAAGAAAAA
380086 G
1 G
380087 TCCACGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:382420 original size:33 final size:33
Alignment explanation
Indices: 382378--382504 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
382368 GGAAATTACT
382378 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
382411 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
382443 TTTCGTAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
382477 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
382505 CGAATTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 81 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:382489 original size:66 final size:66
Alignment explanation
Indices: 382383--382511 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
382373 TTACTATCGC
*
382383 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
382448 T
66 T
*
382449 AATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTT
382512 AATTTCGCGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.43, C:0.18, G:0.22, T:0.17
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAATTTCG
T
Found at i:382526 original size:19 final size:19
Alignment explanation
Indices: 382504--382545 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
382494 AAATCGCAAC
*
382504 GCGAATTTAATTTCGCGTT
1 GCGAATTTAATTTCGCATT
* *
382523 GCGATTTTCATTTCGCATT
1 GCGAATTTAATTTCGCATT
382542 GCGA
1 GCGA
382546 TAGTACTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (19 bp):
GCGAATTTAATTTCGCATT
Found at i:382672 original size:14 final size:14
Alignment explanation
Indices: 382653--382689 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
382643 CATCAATTAA
382653 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
382667 ACAAATCACCTTTT
1 ACAAATCAACTTTT
382681 ACAAATCAA
1 ACAAATCAA
382690 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:384111 original size:21 final size:21
Alignment explanation
Indices: 384045--384111 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
384035 GTGAATCGGG
*
384045 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
384065 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
384087 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
384108 CTCT
1 CTCT
384112 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:384130 original size:42 final size:41
Alignment explanation
Indices: 384045--384167 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
384035 GTGAATCGGG
* * * *
384045 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
384087 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
384129 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
384168 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:384563 original size:91 final size:92
Alignment explanation
Indices: 384385--384569 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 92
384375 ATTTCAAACT
384385 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAAATACATAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAAATACA-AGTTTAGC
*
384450 AGAATTGGCAGCAACCGAATAAATTTAC
65 AGAATTGGCAGAAACCGAATAAATTTAC
*
384478 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-AC-AGTTTAG
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAAAATACAAGTTTAG
*
384540 CAGTATTGGCAGAAACCGAATAAATTTAC
64 CAGAATTGGCAGAAACCGAATAAATTTAC
384569 T
1 T
384570 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 35 0.40
93 21 0.24
94 4 0.05
95 27 0.31
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (92 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAAAATACAAGTTTAGCA
GAATTGGCAGAAACCGAATAAATTTAC
Found at i:386300 original size:14 final size:14
Alignment explanation
Indices: 386281--386307 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
386271 ACGAGATAAT
386281 GAGAATCGCAACGA
1 GAGAATCGCAACGA
386295 GAGAATCGCAACG
1 GAGAATCGCAACG
386308 CGAAATGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.30, T:0.07
Consensus pattern (14 bp):
GAGAATCGCAACGA
Found at i:386322 original size:19 final size:19
Alignment explanation
Indices: 386256--386381 Score: 119
Period size: 19 Copynumber: 7.1 Consensus size: 19
386246 TCTTTTGGTT
*
386256 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
386275 GATAATGAGAATCGCAA--C
1 GA-AATGAAAATCGCAACGC
*
386293 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
386309 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
386328 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
386345 G--A-GAGAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
386361 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
386380 GA
1 GA
386382 TTTTGGTTTT
Statistics
Matches: 88, Mismatches: 8, Indels: 22
0.75 0.07 0.19
Matches are distributed among these distances:
14 20 0.23
15 2 0.02
16 4 0.05
17 2 0.02
18 3 0.03
19 44 0.50
20 13 0.15
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:386348 original size:52 final size:53
Alignment explanation
Indices: 386256--386382 Score: 211
Period size: 52 Copynumber: 2.4 Consensus size: 53
386246 TCTTTTGGTT
* * *
386256 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGAGAGAATCACAACGC
386309 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGAGAGAATCACAACGC
1 GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGAGAGAATCACAACGC
*
386361 GAAATGAAAATCGCAATGCGAT
1 GAAATGAAAATCGCAACGCGAT
386383 TTTGGTTTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 49 0.71
53 20 0.29
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (53 bp):
GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGAGAGAATCACAACGC
Found at i:386415 original size:19 final size:20
Alignment explanation
Indices: 386393--386443 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
386383 TTTGGTTTTG
386393 CGTTGCGATTTTTATTT-CA
1 CGTTGCGATTTTTATTTCCA
** *
386412 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATTTTTATTTCCA
386432 CGTTGCGATTTT
1 CGTTGCGATTTT
386444 CATTCTCGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.14, C:0.18, G:0.22, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTTTATTTCCA
Found at i:386960 original size:20 final size:20
Alignment explanation
Indices: 386935--386987 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
386925 GCGCTATGTA
386935 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
386955 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
386975 TATCTCGTTGCGA
1 AATCGCGTTGCGA
386988 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:387021 original size:20 final size:20
Alignment explanation
Indices: 386996--387049 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
386986 GATTTTGTAT
386996 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
387016 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
387036 TATCGCATTGCGAT
1 TATCGCATTGCGAT
387050 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:387034 original size:61 final size:61
Alignment explanation
Indices: 386936--387052 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
386926 CGCTATGTAA
* * * * *
386936 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
386997 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
387053 CCCAATTCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:387068 original size:61 final size:61
Alignment explanation
Indices: 386936--387070 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
386926 CGCTATGTAA
* * * * * ** *
386936 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
386997 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
*
387059 -TCGTGTTGCGAT
1 ATCGCGTTGCGAT
387071 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:387160 original size:21 final size:21
Alignment explanation
Indices: 387120--387160 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
387110 ACTGTAGACC
** *
387120 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
387141 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
387161 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:391202 original size:35 final size:34
Alignment explanation
Indices: 391158--391250 Score: 91
Period size: 34 Copynumber: 2.7 Consensus size: 34
391148 GGTAAGAAAT
* * * *
391158 TTATTTTTATGTTAGTAT-TTTTTTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
391192 TTATATTTTATATTAATATATTTATGTAAATATTA
1 TTAT-TTTTATATTAATATATTTATGTAAATATTA
* *
391227 TT-TTTTTAATATTTATATAATTAT
1 TTATTTTT-ATATTAATATATTTAT
391251 TATTTATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
33 4 0.08
34 19 0.38
35 17 0.34
36 10 0.20
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:391241 original size:26 final size:26
Alignment explanation
Indices: 391209--391260 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
391199 TTATATTAAT
* *
391209 ATATTTATGTAAATATTATTTTTTTA
1 ATATTTATATAAATATTATTTATTTA
*
391235 ATATTTATATAATTATTATTTATTTA
1 ATATTTATATAAATATTATTTATTTA
391261 GAATTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATATTTATATAAATATTATTTATTTA
Found at i:391243 original size:40 final size:44
Alignment explanation
Indices: 391198--391277 Score: 107
Period size: 41 Copynumber: 1.9 Consensus size: 44
391188 GTTATTATAT
391198 TTTATATTAA-TA-TATTTATGTA-AA-TATT-ATTTTTTTAATA
1 TTTATA-TAATTATTATTTATGTAGAATTATTAATTTTTTTAATA
*
391238 TTTATATAATTATTATTTATTTAGAATTATTAATTTTTTT
1 TTTATATAATTATTATTTATGTAGAATTATTAATTTTTTT
391278 TGTTCTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
39 3 0.09
40 8 0.24
41 9 0.26
42 2 0.06
43 4 0.12
44 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (44 bp):
TTTATATAATTATTATTTATGTAGAATTATTAATTTTTTTAATA
Found at i:396301 original size:18 final size:19
Alignment explanation
Indices: 396260--396301 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
396250 AAATTGTCAA
396260 TAAAAATATATAAAAAATT
1 TAAAAATATATAAAAAATT
* *
396279 T-AAAATATAT-TATAATT
1 TAAAAATATATAAAAAATT
396296 TAAAAA
1 TAAAAA
396302 GAGAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 6 0.30
18 13 0.65
19 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
TAAAAATATATAAAAAATT
Found at i:396496 original size:21 final size:21
Alignment explanation
Indices: 396467--396519 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
396457 ATTCTGACTA
396467 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
396488 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
396509 TCGCAATGCGA
1 TCGCATTGCGA
396520 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:396534 original size:20 final size:20
Alignment explanation
Indices: 396509--396602 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
396499 TTTTCCTAAT
396509 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
396529 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
396549 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
396570 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
396590 TCGCAATGCGAAT
1 TCGCAATGCGAAT
396603 CTGACTATCG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
20 47 0.72
21 18 0.28
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:396540 original size:41 final size:40
Alignment explanation
Indices: 396509--396602 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 40
396499 TTTTCCTAAT
*
396509 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGAAAATCGCAACGCGATTACGTAAA
* * *
396549 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGAAAATCGCAACGCGATTACGTAAA
396590 TCGCAATGCGAAT
1 TCGCAATGCGAAT
396603 CTGACTATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 13 0.27
41 36 0.73
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGAAAATCGCAACGCGATTACGTAAA
Found at i:396851 original size:25 final size:27
Alignment explanation
Indices: 396829--396881 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
396819 GTCCCCATCG
396829 CCGAC-GAAATCCCTCACAACCATTCA
1 CCGACAGAAATCCCTCACAACCATTCA
* * *
396855 CGGTCAGAAATCCCTCACAATCATTCA
1 CCGACAGAAATCCCTCACAACCATTCA
396882 GAAATGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.34, C:0.38, G:0.09, T:0.19
Consensus pattern (27 bp):
CCGACAGAAATCCCTCACAACCATTCA
Found at i:397215 original size:21 final size:20
Alignment explanation
Indices: 397156--397225 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
397146 CTAAACTTAA
*
397156 AATCGCAACATGAAAATGAC
1 AATCGCAACACGAAAATGAC
397176 AATCGCAACACGAAAATGAC
1 AATCGCAACACGAAAATGAC
* *
397196 TATCGCAACGA-GAGAAATGAA
1 AATCGCAAC-ACGA-AAATGAC
397217 AATCGCAAC
1 AATCGCAAC
397226 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.49, C:0.21, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACACGAAAATGAC
Found at i:397293 original size:19 final size:19
Alignment explanation
Indices: 397266--397392 Score: 85
Period size: 20 Copynumber: 7.1 Consensus size: 19
397256 AAAACCAAAA
*
397266 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
397285 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
397299 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
397318 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
397332 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
397351 TCCGCGTTGCAATTTTTATT
1 T-CGCGTTGCGATTTTCATT
*
397371 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
397391 TC
1 TC
397393 AACCAAGAGA
Statistics
Matches: 81, Mismatches: 15, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 5 0.06
19 23 0.28
20 28 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:397313 original size:33 final size:33
Alignment explanation
Indices: 397271--397392 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
397261 CAAAATCGCA
397271 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
397304 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
397337 TTGCGATAGTCATTTCCGCGTTGCAATTTTTATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGC------GATTCTCTCG
397377 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
397393 AACCAAGAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 44 0.59
34 8 0.11
39 1 0.01
40 22 0.29
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:399282 original size:94 final size:94
Alignment explanation
Indices: 399084--399459 Score: 584
Period size: 94 Copynumber: 4.1 Consensus size: 94
399074 TAGATTGCTT
* *
399084 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
399145 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
399174 ATTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
399239 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
399268 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
399333 ATTTGTCTTTGTTTTGTCTTTTGGTTAAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
399362 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAAATGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
399427 ATTTGTCTTTGTTTTGTCTTTTGGTT-AA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
399455 AGTAA
1 AGTAA
399460 TGCAATCCAT
Statistics
Matches: 265, Mismatches: 16, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
90 34 0.13
92 3 0.01
93 29 0.11
94 199 0.75
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:399581 original size:20 final size:20
Alignment explanation
Indices: 399556--399613 Score: 91
Period size: 19 Copynumber: 3.0 Consensus size: 20
399546 GGTTGAAATA
399556 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGAGAGAATG
* *
399576 AAAATCGCAACGCGA-AACG
1 AAAATCGCAACGAGAGAATG
399595 AAAATCGCAACGAGAGAAT
1 AAAATCGCAACGAGAGAAT
399614 CGCAACGTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGAGAGAATG
Found at i:399620 original size:33 final size:33
Alignment explanation
Indices: 399576--399673 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
399566 CGAGAGAATG
*
399576 AAAATCGCAACGCGAAACGAAAATCGCAACGAG
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
* * * *
399609 AGAATCGCAACGTGAAATGAAAATCACAACGAC
1 AAAATCGCAACGCGAAACGAAAATCGCAACGAC
*
399642 AAAATCGCAACGCGAAACCAAAAATCGCAACG
1 AAAATCGCAACGCGAAA-CGAAAATCGCAACG
399674 CTAAACTATA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 43 0.80
34 11 0.20
ACGTcount: A:0.49, C:0.24, G:0.18, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACGAAAATCGCAACGAC
Found at i:399665 original size:20 final size:20
Alignment explanation
Indices: 399642--399679 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
399632 TCACAACGAC
399642 AAAATCGCAACGCGAAACCA
1 AAAATCGCAACGCGAAACCA
*
399662 AAAATCGCAACGCTAAAC
1 AAAATCGCAACGCGAAAC
399680 TATAATCGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.29, G:0.13, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAACCA
Found at i:399756 original size:19 final size:19
Alignment explanation
Indices: 399685--399748 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
399675 TAAACTATAA
399685 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
399704 TCGCATTGCGA--TTCA--
1 TCGCGTTGCGATTTTCATT
*
399719 -CTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
399737 TCGCGTTGCGAT
1 TCGCGTTGCGAT
399749 AGTCATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 8 0.22
16 4 0.11
17 4 0.11
19 20 0.56
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:400229 original size:42 final size:42
Alignment explanation
Indices: 400169--400291 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
400159 GCCCGACTCG
* * *
400169 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
400211 CCTATCATTCTTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
400253 ACTGTCATCGTTGAAGATGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
400292 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:400249 original size:21 final size:21
Alignment explanation
Indices: 400225--400291 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
400215 TCATTCTTCG
400225 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
400246 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
400267 AGATGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
400288 AGAG
1 AGAG
400292 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:401661 original size:14 final size:14
Alignment explanation
Indices: 401642--401677 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
401632 ATTGTTTAAT
401642 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
401656 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
401670 TGATTTGT
1 TGATTTGT
401678 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:401822 original size:14 final size:14
Alignment explanation
Indices: 401801--401838 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
401791 ATGCGAAATG
*
401801 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
401815 AGAATCGCAACGAC
1 AAAATCGCAACGAC
401829 AAAATCGCAA
1 AAAATCGCAA
401839 TGCGAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.18, T:0.08
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:401873 original size:19 final size:19
Alignment explanation
Indices: 401851--402001 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
401841 CGAAATTAAA
401851 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
401870 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
401885 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
401903 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
401918 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
401936 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
401951 -TCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
401969 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
401988 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
402002 AGACATTAAG
Statistics
Matches: 96, Mismatches: 20, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 43 0.45
20 10 0.10
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:401897 original size:33 final size:33
Alignment explanation
Indices: 401855--401981 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
401845 ATTAAATTCG
* *
401855 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
401888 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
401921 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
401954 CGTTGCAATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
401982 AGTCATTTCC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Done.