Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:363516 original size:19 final size:19
Alignment explanation
Indices: 363492--363543 Score: 60
Period size: 14 Copynumber: 3.0 Consensus size: 19
363482 GCGATTCTCT
363492 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
363511 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
363525 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
363544 TATTGCGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
14 10 0.38
16 3 0.12
17 3 0.12
19 10 0.38
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:363552 original size:19 final size:17
Alignment explanation
Indices: 363491--363544 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
363481 TGCGATTCTC
363491 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
*
363508 TCGCGTTGCGA--TTC-TC
1 T--CGTTGCGATTTTCATT
363524 TCGTTGCGATTTTCATT
1 TCGTTGCGATTTTCATT
363541 TCGT
1 TCGT
363545 ATTGCGATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 8 0.27
16 5 0.17
17 9 0.30
19 8 0.27
ACGTcount: A:0.09, C:0.22, G:0.20, T:0.48
Consensus pattern (17 bp):
TCGTTGCGATTTTCATT
Found at i:363678 original size:14 final size:14
Alignment explanation
Indices: 363659--363695 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
363649 CATCAATTAA
363659 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
363673 ACAAATCACCTTTT
1 ACAAATCAACTTTT
363687 ACAAATCAA
1 ACAAATCAA
363696 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:365118 original size:21 final size:21
Alignment explanation
Indices: 365052--365118 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
365042 GTGAATCGGG
*
365052 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
365072 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
365094 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
365115 CTCT
1 CTCT
365119 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:365137 original size:42 final size:41
Alignment explanation
Indices: 365052--365174 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
365042 GTGAATCGGG
* * * *
365052 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
365094 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
365136 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
365175 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:367236 original size:19 final size:19
Alignment explanation
Indices: 367172--367341 Score: 188
Period size: 19 Copynumber: 9.1 Consensus size: 19
367162 TCTTTTGGTT
*
367172 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
367191 GATAATGAGAATTGCAACGC
1 GA-AATGAAAATCGCAACGC
**
367211 AGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
** *
367231 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
367248 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
367264 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
367283 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
367302 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
367321 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
367340 GA
1 GA
367342 TTTTTGTTTC
Statistics
Matches: 130, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.06
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 86 0.66
20 28 0.22
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:367359 original size:19 final size:19
Alignment explanation
Indices: 367337--367382 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
367327 AAAATCGCAA
*
367337 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
367356 TGCGTTTTTTTATTTCGCGT
1 TGCG-ATTTTTATTTCGCGT
367376 TGCGATT
1 TGCGATT
367383 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.07, C:0.15, G:0.24, T:0.54
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:367371 original size:20 final size:20
Alignment explanation
Indices: 367342--367379 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
367332 CGCAATGCGA
*
367342 TTTTTGTTTCGCGTTGCGTT
1 TTTTTATTTCGCGTTGCGTT
367362 TTTTTATTTCGCGTTGCG
1 TTTTTATTTCGCGTTGCG
367380 ATTCTCTCGT
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:0.03, C:0.16, G:0.24, T:0.58
Consensus pattern (20 bp):
TTTTTATTTCGCGTTGCGTT
Found at i:368024 original size:20 final size:20
Alignment explanation
Indices: 367995--368048 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
367985 GATTTTGTAT
367995 TATCGCATTGCGATAATAAG
1 TATCGCATTGCGATAATAAG
* * *
368015 TATCGTATTGCGATAGTCAG
1 TATCGCATTGCGATAATAAG
368035 TATCGCATTGCGAT
1 TATCGCATTGCGAT
368049 TTTTCCAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAATAAG
Found at i:368159 original size:21 final size:21
Alignment explanation
Indices: 368119--368159 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
368109 ACTGTAGACC
**
368119 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
368140 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
368160 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:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:368742 original size:2 final size:2
Alignment explanation
Indices: 368731--368763 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
368721 ATTTTCGTCC
368731 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
368764 ATTTGCAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:368831 original size:40 final size:39
Alignment explanation
Indices: 368777--369050 Score: 237
Period size: 38 Copynumber: 7.1 Consensus size: 39
368767 TGCAAATTAT
* *
368777 TTTTG-AAACATATATATAATATATATAGTTTTTAGAATA
1 TTTTGAAAACATATATAT-ATATATATAGTTTTTAAAACA
* * * * *
368816 GTTTGAAAAC-T-TATATA-ATATATGGGTTTTAAAGCG
1 TTTTGAAAACATATATATATATATATAGTTTTTAAAACA
*
368852 TTTTGAAAATATATATATAT-TATATAG-TTTTAAAACA
1 TTTTGAAAACATATATATATATATATAGTTTTTAAAACA
*
368889 TTTTGAACTACATATATATATATTATATAGTTTTTAAAACA
1 TTTTGAA-AACATATATATATA-TATATAGTTTTTAAAACA
* * * ****
368930 TTTTGAAAATAAATATATA-ATATATTGTTTTTGAATTTT
1 TTTTGAAAACATATATATATATATATAGTTTTT-AAAACA
*
368969 TTTTGAAAAAATATATATA-ATATATAGTTTTTAAAAAAACA
1 TTTTGAAAACATATATATATATATATAGTTTTT---AAAACA
*
369010 TTTTTGAAAA-AT-TATATA-ATGTATAGTTTTTAAAACA
1 -TTTTGAAAACATATATATATATATATAGTTTTTAAAACA
369047 TTTT
1 TTTT
369051 TTGAAAACTC
Statistics
Matches: 192, Mismatches: 31, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
36 25 0.13
37 23 0.12
38 39 0.20
39 37 0.19
40 38 0.20
41 21 0.11
42 9 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (39 bp):
TTTTGAAAACATATATATATATATATAGTTTTTAAAACA
Found at i:368869 original size:38 final size:38
Alignment explanation
Indices: 368777--369050 Score: 254
Period size: 39 Copynumber: 7.1 Consensus size: 38
368767 TGCAAATTAT
* *
368777 TTTTGAAACATATATATA-ATATATATAGTTTTTAGAATA
1 TTTTGAAA-ATATATATATA-ATATATAGTTTTTAAAACA
* * * * * *
368816 GTTTGAAAA-CT-TATATAATATATGGGTTTTAAAGCG
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
368852 TTTTGAAAATATATATATATTATATAG-TTTTAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
*
368889 TTTTGAACTACATATATATATATTATATAGTTTTTAAAACA
1 TTTTGAA--A-ATATATATATAATATATAGTTTTTAAAACA
* * ****
368930 TTTTGAAAATAAATATATAATATATTGTTTTTGAATTTT
1 TTTTGAAAATATATATATAATATATAGTTTTT-AAAACA
*
368969 TTTTGAAAAAATATATATAATATATAGTTTTTAAAAAAACA
1 TTTTGAAAATATATATATAATATATAGTTTTT---AAAACA
*
369010 TTTTTGAAAA-AT-TATATAATGTATAGTTTTTAAAACA
1 -TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
369047 TTTT
1 TTTT
369051 TTGAAAACTC
Statistics
Matches: 194, Mismatches: 30, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
36 29 0.15
37 24 0.12
38 34 0.18
39 40 0.21
40 37 0.19
41 21 0.11
42 9 0.05
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (38 bp):
TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
Found at i:369085 original size:33 final size:32
Alignment explanation
Indices: 369004--369097 Score: 91
Period size: 33 Copynumber: 2.8 Consensus size: 32
368994 AGTTTTTAAA
* *
369004 AAAACATTTTTGAAAAATTATATAATGTATAGTTTTT
1 AAAACATTTTTTAAAAACTATAT-A-G--TA-TTTTT
*
369041 AAAACATTTTTTGAAAACTCATATAGTATTTTT
1 AAAACATTTTTTAAAAACT-ATATAGTATTTTT
369074 AAAATCA-TTTTTAAAAACTATATA
1 AAAA-CATTTTTTAAAAACTATATA
369098 ATATATAGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
32 5 0.10
33 20 0.39
34 4 0.08
36 1 0.02
37 17 0.33
38 4 0.08
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (32 bp):
AAAACATTTTTTAAAAACTATATAGTATTTTT
Found at i:369203 original size:16 final size:17
Alignment explanation
Indices: 369177--369208 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
369167 ATATAATCTA
369177 TATTATATTACTATTAG
1 TATTATATTACTATTAG
369194 TATT-TATTACTATTA
1 TATTATATTACTATTA
369209 TTAATTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTATATTACTATTAG
Found at i:370566 original size:41 final size:38
Alignment explanation
Indices: 370500--370577 Score: 86
Period size: 41 Copynumber: 2.0 Consensus size: 38
370490 TTTCGTAACG
* *
370500 TTTTATTATCTTTTATTACT-TATTTTTTTAGTTTTTAA
1 TTTTATTATCTTTTATTACTAAATTTTATTA-TTTTTAA
*
370538 TTTTATTATTCTTCTTTTTACTAAATTTTATTTATTTTTA
1 TTTTATTA-TCTT-TTATTACTAAATTTTA-TTATTTTTA
370578 CTTATCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
38 8 0.24
39 4 0.12
40 7 0.21
41 11 0.33
42 3 0.09
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.71
Consensus pattern (38 bp):
TTTTATTATCTTTTATTACTAAATTTTATTATTTTTAA
Found at i:373392 original size:94 final size:95
Alignment explanation
Indices: 373199--373460 Score: 357
Period size: 94 Copynumber: 2.7 Consensus size: 95
373189 AAATTATAAT
** * * *
373199 ATTATATATATACAATAAAGCTTGAACTGTCCCTTTATAGCAATTGGTTAAACGCCCCGACTTTA
1 ATTATA-ATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
373264 TGGATAAGATTCAGTTAGACTGATAAAGGTG
65 TGGATAAGATTCAGCTAGACTGATAAAGGTG
*
373295 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTTGTTAAAC-CCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
* *
373359 GGATAATATTCAGCTAGCCTGATAAAGGTG
66 GGATAAGATTCAGCTAGACTGATAAAGGTG
* * *
373389 ATTATAATAT-CTATATAATGACATTGAGTTGTCCTTCTAGAGCAATTGGTTAAACGCCCTGGCT
1 ATTATAATATAC-A-ATAAAG-C-TTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
373453 TTATGGAT
62 TTATGGAT
373461 TCAGTTAGCC
Statistics
Matches: 148, Mismatches: 13, Indels: 8
0.88 0.08 0.05
Matches are distributed among these distances:
93 1 0.01
94 49 0.33
95 46 0.31
96 7 0.05
97 30 0.20
98 15 0.10
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAGATTCAGCTAGACTGATAAAGGTG
Found at i:374511 original size:80 final size:80
Alignment explanation
Indices: 374143--375685 Score: 1740
Period size: 80 Copynumber: 18.9 Consensus size: 80
374133 TCAAAAGCAC
* * * * **
374143 GACCTTTGAGTTTGATTACACTCAGCTCAAAGGCATATCATTTACAGCATAACTCAAGGTGAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
374208 GGGTTATCTGTCAATCAA
66 GGGCTATCTG-CCA--AA
* * * *
374226 GACCTTCAAGTTCGATTACACTAAGCTCAAAGGCACATTATTTGCAGCATAACTCAAGGCGAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
374291 GGGTTATCTACGAACAATA
66 GGGCTATCT--G-CCAA-A
* * * * **
374310 GACCTTCGAGTTCGATTACACTCAACTCAAAGGAACATCATTTACAGTATAACTCAAGGTGAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * *
374375 GGGTTATCTATCAACCAA
66 GGGCTATCT-GC--CAAA
* ** * * * *
374393 GACCTTCGAGTTCGATTACACTCAGATCAAAGATACATCATTTTCAACATAGCTCAATGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * *
374458 GAGCTATATGGCAAA
66 GGGCTATCTGCCAAA
* * *
374473 GACCTTCGAGTTCGATTACACTCAGCTCGAAGGCACATCATTTGCAGTATAGCTCAAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
*
374538 AGGCTA-CTGCCAAA
66 GGGCTATCTGCCAAA
* * *
374552 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCATCTTAGCTCAAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
*
374617 GGGCTATCTTCCAAA
66 GGGCTATCTGCCAAA
** *
374632 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGAAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
374697 GGGTTATCTGTCAATCAA
66 GGGCTATCTG-CCA--AA
* * * * **
374715 GACCTACGAGTTCGATTACAATCAGCTCAAAGGCATATCATTTAG-AGCATAGCTCAAGATAAGA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT-GCAGCATAACTCAAGGCAAGA
*
374779 AGGGCTATATGCCAACAAA
65 AGGGCTATCTG-C--CAAA
* * * ** * *
374798 GACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATGGTTTGCAGCATAAATCAAGGCTAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
374863 GGGTTATATGCCAACAAAA
66 GGGCTATCTG-C--C-AAA
* * * * *
374882 GACCTTCGAGTTTGATTATACTCATCTCAAAGGAACATCATTTGCAGCATAACTCAAAGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
374947 GGGCTATCTGCCAAA
66 GGGCTATCTGCCAAA
* * * **
374962 GACCTTCGAGTTCGATTACACTTAGCTCAAAGGTACATCATTTACAGCATAACTCAAGGTGAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
375027 GGGTTATCTGTCAGTTAA
66 GGGCTATCTGCCA---AA
* * * *
375045 GACCTTCGAGTTCGATTACCCTCAGCTTAAAGGCACATCATTTGCAGTATAACTCAAGGCTAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
*
375110 GGGTTATCTGCCAACAAAA
66 GGGCTATCTG-C--C-AAA
* * * **
375129 GACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTTGAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
*
375194 GGGTTATCTGCCAAA
66 GGGCTATCTGCCAAA
* * * * * *
375209 GACCTTCGAGTTCGATTACACTCAACTCAAAGGTACATCATTTGTAACATAACTTAAGTCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
*
375274 GGGCTATCTACCAAA
66 GGGCTATCTGCCAAA
* * * *
375289 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGTACATCATTTACAGCATAGCTCAAGACAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
375354 GGGCTATCTACAAAA
66 GGGCTATCTGCCAAA
* * *
375369 GACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
375434 GGGCTATCTGCCAAA
66 GGGCTATCTGCCAAA
* * * *
375449 GATCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCATAGCTCAAGGTAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
375514 GGGTTATCAGCCAAA
66 GGGCTATCTGCCAAA
* *
375529 GACCTTCAAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
375594 GGGCTATCTGCCAAA
66 GGGCTATCTGCCAAA
* * * * * * * **
375609 GACCTTAGAGTTCGATTACATTCAACTCAGAGGCAAATCAAATTTACAGAATAGTTCAAGGCAAG
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAACTCAAGGCAAG
375674 AAGGGCTATCTG
64 AAGGGCTATCTG
375686 TCAACAAAAT
Statistics
Matches: 1261, Mismatches: 176, Indels: 47
0.85 0.12 0.03
Matches are distributed among these distances:
79 72 0.06
80 607 0.48
81 4 0.00
82 34 0.03
83 336 0.27
84 203 0.16
85 3 0.00
86 1 0.00
87 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (80 bp):
GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
GGGCTATCTGCCAAA
Found at i:375049 original size:247 final size:244
Alignment explanation
Indices: 374143--375685 Score: 1759
Period size: 247 Copynumber: 6.3 Consensus size: 244
374133 TCAAAAGCAC
* * * * **
374143 GACCTTTGAGTTTGATTACACTCAGCTCAAAGGCATATCATTTACAGCATAACTCAAGGTGAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * * * *
374208 GGGTTATCTGTCAATCAAGACCTTCAAGTTCGATTACACTAAGCTCAAAGGCACATTATTTGCAG
66 GGGCTATCTG-CCA--AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAG
** * * *
374273 CATAACTCAAGGCGAGAAGGGTTATCTACGAACAATAGACCTTCGAGTTCGATTACACTCAACTC
128 CATAACTCAAGGTAAGAAGGGCTATCT--G-CCAA-AGACCTTCGAGTTCGATTACACTCAGCTC
* * * ** ** *
374338 AAAGGAACATCATTTACAGTATAACTCAAGGTGAGAAGGGTTATCTATCAAC-CAA
189 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
* ** * * * *
374393 GACCTTCGAGTTCGATTACACTCAGATCAAAGATACATCATTTTCAACATAGCTCAATGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * * * *
374458 GAGCTATATGGCAAAGACCTTCGAGTTCGATTACACTCAGCTCGAAGGCACATCATTTGCAGTAT
66 GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCAT
* * *
374523 AGCTCAAGGCAAGAAAGGCTA-CTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
131 AACTCAAGGTAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
* * * * *
374587 CATCATTTGCATCTTAGCTCAAGGCAAGAAGGGCTATCT-TC--C-AAA
196 CATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
** *
374632 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTATAGCATAACTCAAGGAAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * * * *
374697 GGGTTATCTGTCAATCAAGACCTACGAGTTCGATTACAATCAGCTCAAAGGCATATCATTTAG-A
66 GGGCTATCTG-CCA--AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTT-GCA
* * * * *
374761 GCATAGCTCAAGATAAGAAGGGCTATATGCCAACAAAGACCTTCGAGTTTGATTACATTCAGCTC
127 GCATAACTCAAGGTAAGAAGGGCTATCTG-C--CAAAGACCTTCGAGTTCGATTACACTCAGCTC
* ** * * *
374826 AAAGGCATATGGTTTGCAGCATAAATCAAGGCTAGAAGGGTTATATGCCAACAAAA
189 AAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
* * * * *
374882 GACCTTCGAGTTTGATTATACTCATCTCAAAGGAACATCATTTGCAGCATAACTCAAAGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * *
374947 GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTTAGCTCAAAGGTACATCATTTACAGCAT
66 GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCAT
* * * * *
375012 AACTCAAGGTGAGAAGGGTTATCTGTCAGTTAAGACCTTCGAGTTCGATTACCCTCAGCTTAAAG
131 AACTCAAGGTAAGAAGGGCTATCTGCCA---AAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
* *
375077 GCACATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
193 GCACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
* * * **
375129 GACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATAGCTTGAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* * * * *
375194 GGGTTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGTACATCATTTGTAACAT
66 GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCAT
* * *
375259 AACTTAA-GTCAAGAAGGGCTATCTACCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGT
131 AACTCAAGGT-AAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC
* * * *
375323 ACATCATTTACAGCATAGCTCAAGACAAGAAGGGCTATCT----ACAAAA
195 ACATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
* * *
375369 GACCTTTGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAAGGCAAGAA
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
* *
375434 GGGCTATCTGCCAAAGATCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCATTTGCAGCAT
66 GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCAT
* * * *
375499 AGCTCAAGGTAAGAAGGGTTATCAGCCAAAGACCTTCAAGTTCGATTACACTCAGCTCAAAGGCA
131 AACTCAAGGTAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
* *
375564 CATCATTTGCAGCATAGCTCAAGGCAAGAAGGGCTATCTG-C--C-AAA
196 CATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
* * * * * * * **
375609 GACCTTAGAGTTCGATTACATTCAACTCAGAGGCAAATCAAATTTACAGAATAGTTCAAGGCAAG
1 GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC--ATTTGCAGCATAACTCAAGGCAAG
375674 AAGGGCTATCTG
64 AAGGGCTATCTG
375686 TCAACAAAAT
Statistics
Matches: 1108, Mismatches: 163, Indels: 52
0.84 0.12 0.04
Matches are distributed among these distances:
239 66 0.06
240 257 0.23
241 5 0.00
242 160 0.14
243 6 0.01
244 71 0.06
246 70 0.06
247 340 0.31
249 4 0.00
250 129 0.12
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (244 bp):
GACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAA
GGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCAT
AACTCAAGGTAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCA
CATCATTTGCAGCATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAA
Found at i:376194 original size:2 final size:2
Alignment explanation
Indices: 376184--376224 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
376174 TTTTTTATTT
*
376184 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
376225 ATTTGCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:376321 original size:2 final size:2
Alignment explanation
Indices: 376314--376350 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
376304 AGCGTTTTGA
376314 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
376351 ATTTTTAAAA
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:376323 original size:34 final size:34
Alignment explanation
Indices: 376247--376330 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 34
376237 TTTTTGAAAC
*
376247 ATATATATAT-ATATAGTTTTTAGAATATTTTGA
1 ATATATATATAATATAGTTTTTAGAACATTTTGA
* * *
376280 AAACT-TATATAATATGGTTTTTA-AAGCGTTTTGA
1 ATA-TATATATAATATAGTTTTTAGAA-CATTTTGA
376314 ATATATATATATATATA
1 ATATATATATA-ATATA
376331 TATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
33 10 0.25
34 26 0.65
35 4 0.10
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (34 bp):
ATATATATATAATATAGTTTTTAGAACATTTTGA
Found at i:376393 original size:37 final size:36
Alignment explanation
Indices: 376334--376517 Score: 217
Period size: 38 Copynumber: 4.9 Consensus size: 36
376324 ATATATATAT
*
376334 ATATATATATATATATAATTTTTAAAACATTTTGAAA
1 ATATATATA-ATATATAGTTTTTAAAACATTTTGAAA
* *
376371 TATATACATATTATATAGTTTTTAAAACATTTTGAAA
1 -ATATATATAATATATAGTTTTTAAAACATTTTGAAA
*
376408 ATAAATATAATATATAGTTTTTGAAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTT--AAAACATTTTGAAA
* *
376446 AAATATATAATATGTAGTTTTTAAAAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTT---AAAACA-TTTTGAAA
*
376486 A-ATTATATAATATATAGTTTTAAAAACATTTT
1 ATA-TATATAATATATAGTTTTTAAAACATTTT
376518 TTTTGAAAAC
Statistics
Matches: 129, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
36 23 0.18
37 31 0.24
38 41 0.32
39 8 0.06
40 26 0.20
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAACATTTTGAAA
Found at i:376597 original size:36 final size:35
Alignment explanation
Indices: 376336--376604 Score: 188
Period size: 37 Copynumber: 7.2 Consensus size: 35
376326 ATATATATAT
* * *
376336 ATATATATATATATAATTTTTAAAACATTTTGAAATA
1 ATATATA-ATATATAGTTTTAAAAACTTTTTGAAA-A
* * * *
376373 TATACATATTATATAGTTTTTAAAACATTTTGAAAA
1 -ATATATAATATATAGTTTTAAAAACTTTTTGAAAA
* *
376409 TAAATATAATATATAGTTTTTGAAAAACATTTTGAAAAA
1 -ATATATAATATATAG-TTTT-AAAAACTTTTTG-AAAA
*
376448 ATATATAATATGTAGTTTTTAAAAAAACATTTTTGAAAA
1 ATATATAATATATAG-TTTT--AAAAAC-TTTTTGAAAA
376487 ATTATATAATATATAGTTTTAAAAACATTTTTTTTGAAAA
1 A-TATATAATATATAGTTTTAAAAAC----TTTTTGAAAA
* * *
376527 CTCATAT-A-GTAT--TTTTAAAATCATTTTTGAAAA
1 AT-ATATAATATATAGTTTTAAAAAC-TTTTTGAAAA
*
376560 ATATATAATATATAGTTTTGGAAAA-TTTTTAGAAAA
1 ATATATAATATATAGTTTT-AAAAACTTTTT-GAAAA
376596 ATAGTATAA
1 ATA-TATAA
376605 AGTTTGAAAA
Statistics
Matches: 193, Mismatches: 21, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
32 4 0.02
33 12 0.06
34 3 0.02
35 5 0.03
36 35 0.18
37 43 0.22
38 38 0.20
39 21 0.11
40 32 0.17
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATAATATATAGTTTTAAAAACTTTTTGAAAA
Found at i:376667 original size:14 final size:14
Alignment explanation
Indices: 376636--376688 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
376626 TATATATATA
*
376636 TATTATATAATCTA-
1 TATTATATTAT-TAT
376650 TATTATATTATTAT
1 TATTATATTATTAT
* *
376664 TATTATCTTTTTAT
1 TATTATATTATTAT
376678 TATTATTATTA
1 TATTA-TATTA
376689 ATTTACTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 2 0.06
14 27 0.84
15 3 0.09
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTATATTATTAT
Found at i:378019 original size:17 final size:15
Alignment explanation
Indices: 377996--378046 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
377986 TTTCTTAACG
377996 TTTTATTATCTTTTAT
1 TTTTATTAT-TTTTAT
378012 TATTTATTA-TTTTAT
1 T-TTTATTATTTTTAT
* *
378027 TTTTATTATTCTTCT
1 TTTTATTATTTTTAT
378042 TTTTA
1 TTTTA
378047 CTAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 7 0.23
15 16 0.52
16 1 0.03
17 7 0.23
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTATTTTTAT
Found at i:379067 original size:2 final size:2
Alignment explanation
Indices: 379060--379085 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
379050 TTTAATTTCC
379060 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
379086 GTCTTCCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:380972 original size:5 final size:5
Alignment explanation
Indices: 380931--380987 Score: 59
Period size: 5 Copynumber: 12.0 Consensus size: 5
380921 AAAAAGTTAC
* *
380931 TTTAT TTTCT TCTT-T TTTAT TTT-T TTTAT CTTA- -TTAT TTTAT TTTAT
1 TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
380978 TTTAT TTTAT
1 TTTAT TTTAT
380988 CTCGTTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 3 0.07
4 6 0.13
5 34 0.76
6 2 0.04
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:380980 original size:23 final size:22
Alignment explanation
Indices: 380945--380987 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
380935 TTTTCTTCTT
380945 TTTTATTTTTTTTATCTTATTA
1 TTTTATTTTTTTTATCTTATTA
*
380967 TTTTATTTTATTTTATTTTAT
1 TTTTATTTT-TTTTATCTTAT
380988 CTCGTTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTATTTTTTTTATCTTATTA
Found at i:381003 original size:28 final size:26
Alignment explanation
Indices: 380943--381009 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 26
380933 TATTTTCTTC
*
380943 TTTTTTATTTTTTTTATCTTATTATT
1 TTTTTTATTTTTTTTATCTCATTATT
* *
380969 TTATTTTATTTTATTTTATCTCGTTCTAT
1 TT-TTTTATTTT-TTTTATCTCATTAT-T
380998 TTTTTTATTTTT
1 TTTTTTATTTTT
381010 GATATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 10 0.29
28 20 0.57
29 3 0.09
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (26 bp):
TTTTTTATTTTTTTTATCTCATTATT
Found at i:393600 original size:29 final size:29
Alignment explanation
Indices: 393545--393600 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
393535 ACCAAGAAAG
* *
393545 AAACTAAGCTCTCCAAGATCTTTCAATGC
1 AAACTAAGCTCTCCAACAACTTTCAATGC
*
393574 AAACTCAGCTC-CCAACAACTTTGCAAT
1 AAACTAAGCTCTCCAACAACTTT-CAAT
393601 TTCTTCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (29 bp):
AAACTAAGCTCTCCAACAACTTTCAATGC
Found at i:399110 original size:14 final size:13
Alignment explanation
Indices: 399071--399111 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
399061 ATAAAAGAAG
399071 AAAT-GAAGATGGA
1 AAATAGAAGAT-GA
399084 AAATAGAAGATGA
1 AAATAGAAGATGA
399097 AAAGTAGAAGATGA
1 AAA-TAGAAGATGA
399111 A
1 A
399112 TACATAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.59, C:0.00, G:0.27, T:0.15
Consensus pattern (13 bp):
AAATAGAAGATGA
Found at i:399824 original size:31 final size:31
Alignment explanation
Indices: 399766--399830 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
399756 TAACTAACTA
* *
399766 TCTGAACAATATGATTTTTTAATTGTGACTG
1 TCTGAACAATATGATTTTTGAACTGTGACTG
* *
399797 TCTGAACGATAT-ATTTTCTGAACTGTGATTG
1 TCTGAACAATATGATTTT-TGAACTGTGACTG
399828 TCT
1 TCT
399831 ACCTCTGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (31 bp):
TCTGAACAATATGATTTTTGAACTGTGACTG
Found at i:401068 original size:96 final size:95
Alignment explanation
Indices: 400887--401140 Score: 285
Period size: 96 Copynumber: 2.6 Consensus size: 95
400877 AATCTGTGGA
** * * * * *
400887 AACCGGAAAACCTTTCGTCAAAGATTTTGAGTTTAGACATGATCATTTTGTCGTAATTTACTTGA
1 AACCGGAAAATATTTCGTCAAGGATTTCGAG-TGAGAGATGATCATTTTGTCGTAATTTACTCGA
* ** * *
400952 ACAATGATGCTCAATTTCAAGAACCTGCAGG
65 ACAAAGATAATAAATCTCAAGAACCTGCAGG
* *
400983 AATC-GATAAATATTTCGTCAAGGATTTCGAGCTGAGAGATGATCATTTTATCGTAATTTACTCG
1 AACCGGA-AAATATTTCGTCAAGGATTTCGAG-TGAGAGATGATCATTTTGTCGTAATTTACTCG
* **
401047 AGCAAAGATAATAAATCTCAAGAATTTGCAGG
64 AACAAAGATAATAAATCTCAAGAACCTGCAGG
* * *
401079 AACCGGAAAATTTTTCGTCAAGGATTTCAAGTCGAGAGATGATCATTTTGTCATAATTTACT
1 AACCGGAAAATATTTCGTCAAGGATTTCGAGT-GAGAGATGATCATTTTGTCGTAATTTACT
401141 TAAACAATGA
Statistics
Matches: 132, Mismatches: 23, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
95 3 0.02
96 127 0.96
97 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (95 bp):
AACCGGAAAATATTTCGTCAAGGATTTCGAGTGAGAGATGATCATTTTGTCGTAATTTACTCGAA
CAAAGATAATAAATCTCAAGAACCTGCAGG
Found at i:408472 original size:4 final size:4
Alignment explanation
Indices: 408463--408489 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
408453 CCTGCATCGT
408463 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
408490 TCTTTTTCTT
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:412494 original size:12 final size:12
Alignment explanation
Indices: 412477--412501 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
412467 AAATTGAAAG
412477 AAATCTTAAAAT
1 AAATCTTAAAAT
412489 AAATCTTAAAAT
1 AAATCTTAAAAT
412501 A
1 A
412502 CAAGGATGAA
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATCTTAAAAT
Found at i:413486 original size:30 final size:30
Alignment explanation
Indices: 413419--413550 Score: 119
Period size: 30 Copynumber: 4.4 Consensus size: 30
413409 TAGATCTAGC
* * *
413419 AAAACATG-AACTTAAAGGATTAAAAATGGTA
1 AAAACA-GAAACTTAAAAGACT-AAAATAGTA
* *
413450 AGAACAGAAACTTAAAAGACTAAAATAGTT
1 AAAACAGAAACTTAAAAGACTAAAATAGTA
* *
413480 AAAACAGAAATTTAAAGGAC-ATAAATAGTA
1 AAAACAGAAACTTAAAAGACTA-AAATAGTA
**
413510 AAAACAGAAACTTAAGTGACTAAAATA--A
1 AAAACAGAAACTTAAAAGACTAAAATAGTA
413538 AATAACAGAAACT
1 AA-AACAGAAACT
413551 AAAGTGTCAA
Statistics
Matches: 85, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
28 3 0.04
29 11 0.13
30 54 0.64
31 17 0.20
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (30 bp):
AAAACAGAAACTTAAAAGACTAAAATAGTA
Found at i:413984 original size:145 final size:146
Alignment explanation
Indices: 413810--414076 Score: 364
Period size: 145 Copynumber: 1.8 Consensus size: 146
413800 GTAAAAATGC
* * *
413810 CAAAAACCATTCGGATTTATTTTCTCCGATTTGCCA-C-CC-TCCACCGTCTGATCGTCCTGATT
1 CAAAAACCATTCGGATTTATTTTCTCCGA--T-CCATCGCCGTCCACCGTCCGATCATCCTGAAT
* * * * *
413872 TTTTAGTATGTTGTT-TGTGTTGGCCTTGTGCAACTTTTTACTGTTCAGAATTTTGATCGGTGTT
63 ATTCAGTATGTTGTTCT-TGTTGGCCTTGCGCAACTTTTTACTATTCAGAATGTTGATCGGTGTT
413936 GCCGATCGCCGTAAATAGGA
127 GCCGATCGCCGTAAATAGGA
* *
413956 CAAAAACCGTTTGGA-TTATTTTCTCCGATCCATCGCCGTCCACCGTCCGATCATCCTGAATATT
1 CAAAAACCATTCGGATTTATTTTCTCCGATCCATCGCCGTCCACCGTCCGATCATCCTGAATATT
*
414020 CAGTATGTTGTTCTTGTTGGCCTTGCGCAACTTTTTACTATTCGGAATGTTGATCGG
66 CAGTATGTTGTTCTTGTTGGCCTTGCGCAACTTTTTACTATTCAGAATGTTGATCGG
414077 ACATCTTGAT
Statistics
Matches: 106, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
142 3 0.03
143 2 0.02
144 2 0.02
145 85 0.80
146 14 0.13
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.38
Consensus pattern (146 bp):
CAAAAACCATTCGGATTTATTTTCTCCGATCCATCGCCGTCCACCGTCCGATCATCCTGAATATT
CAGTATGTTGTTCTTGTTGGCCTTGCGCAACTTTTTACTATTCAGAATGTTGATCGGTGTTGCCG
ATCGCCGTAAATAGGA
Found at i:414801 original size:564 final size:550
Alignment explanation
Indices: 413696--415174 Score: 1853
Period size: 564 Copynumber: 2.7 Consensus size: 550
413686 CCACTGTGCG
* ** *
413696 ACCGCCACCGGTGGCCAATGGTTGCCAAATTTTATCGGGAAGTCCGTCTTGGCCTCCTCATCTTG
1 ACCGCCACCGATGGCTGATGGTTACCAAATTTTATCGGGAAGTCCGTCTTGGCCTCCTCATCTTG
* * * *
413761 GATCTAGAGTCAGTTTTGCATGAATCGTCTTCGTTTATCGTAAAAATGCCAAAAACCATTCGGAT
66 GATCTAGAGTCGGTTTTGCATGAATCGACTCCGTTTATCGTAAAAAGGCCAAAAACCATTCGGAT
** * * *
413826 TTATTTTCTCCGATTTGCCACCCTCCACCGTCTGATCGTCCTGATTTTTTAGTATGTTGTTTGTG
131 TTATTTTCTCC-A--TGCCACTGTCCACCGTCCGATCGTCCTGATTTTTCAGTATGTTGTTCGTG
* * * * *
413891 TTGGCCTTGTGCAACTTTTT-ACTGTTCAGAATTTTGATCGGTGTTGCCGATCGCCGTAAATAGG
193 TTGGCCTTGCGCAACTTTTTCACTGTTCAGAATGTTGATCGGAGATCCCGATCGCCGTAAATAGG
* * * * *
413955 ACAAAAACCGTTTG-GATTATTTTCTCCGATCCATCGCCGTCCACCGTCCGATCATCCTGAATAT
258 CCAAAAACCG--TGCGATTATTTTCTCCGATCCGTCGCTGTCCACCGTCTGATCATCCTGAATTT
* * * * * *
414019 TCAGTATGTTGTTCTTGTTGGCCTTGCGCAACTTTTTACTATTCGGAATGTTGATCGGACATCTT
321 TCAGTATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACTGTTCAGAATGTTGATCGAACATCCT
* ** * * *
414084 GATCACCGACGAAATTTTGGCAGAATTCAAGACCTTTTTTTTCTTTCTATTTTTCCTTCAATTTG
386 GATCACCGACGAAATTTCGGCAGAATTCAAGACAATTTTTTTATTTCTATTTTTCATT-AATTTA
* * *
414149 CTTCTTCTTCTCTCTCACGTATGGCTTCCTCCCCCTTGTATGCCTGCAAAAATATATAACATCAT
450 CTTCTTCTTCTCTCTCACGTATGGCTTCCTCCCCCTTGTATGCCTCCAAAAATACATAAAATCAT
*
414214 CATAAAAGAGTTGCCAACCACCGTCGTTGCGCCGACG-TGCCACC
515 CATAAAAGAGTCGCCAACCA-C--CG-T-CGCCG-CGTTG---CC
* * ** * *
414258 ACCGTCACCGATGGTTGATGGTTATTAAATTTCATCGGGAAATCCGTCTTGGCCTCCTCATCTTG
1 ACCGCCACCGATGGCTGATGGTTACCAAATTTTATCGGGAAGTCCGTCTTGGCCTCCTCATCTTG
* * * * * *
414323 GATCTAGAGTCGGTTTTTCATGAATTGGCTCCATTTATCGTAAAAAGGCCAAAACCCATTCAGAT
66 GATCTAGAGTCGGTTTTGCATGAATCGACTCCGTTTATCGTAAAAAGGCCAAAAACCATTCGGAT
* * *
414388 TTATTTTCTCCAATCCGCCGCTGTCTACTGTCCGATCGTCCTGATTTTTCAGTATGTTGTTCGTG
131 TTATTTTCTCC-AT--GCCACTGTCCACCGTCCGATCGTCCTGATTTTTCAGTATGTTGTTCGTG
* ** * *
414453 TTAGCCTTGCGCAACTTTTTTCACCATTCAGAATGTTGATCGGAGATCCCAATCGCTGTAAATAG
193 TTGGCCTTGCGCAAC-TTTTTCACTGTTCAGAATGTTGATCGGAGATCCCGATCGCCGTAAATAG
* *
414518 GCCAAAAACCGTGCGACTTATTTTCTCCGATCCGCCGCTGTCCACCGTCTGATCATCCTAAATTT
257 GCCAAAAACCGTGCGA-TTATTTTCTCCGATCCGTCGCTGTCCACCGTCTGATCATCCTGAATTT
* *
414583 TTAGTATGTTGTTCGTGTTTGCCTTGCGCAACTTTTCACTGTTCAGAATGTTGATCGAACATCCT
321 TCAGTATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACTGTTCAGAATGTTGATCGAACATCCT
* *
414648 GATCACCGACGAAATTTCGGCAGAATTCAAGACAATTTTTTTATTTTTATTTTT-ATT-TTTCCT
386 GATCACCGACGAAATTTCGGCAGAATTCAAGACAATTTTTTTATTTCTATTTTTCATTAATT--T
*
414711 ACATTTTTCTTCTCTCTCACGTATGGCTTCCTCCCCCTTGTATGCCTCCAAAAATACATAAAATC
449 AC-TTCTTCTTCTCTCTCACGTATGGCTTCCTCCCCCTTGTATGCCTCCAAAAATACATAAAATC
***
414776 ATCATAAAAGAGTCGCTGGCCACCGTCGCCGCGTTGCC
513 ATCATAAAAGAGTCGCCAACCACCGTCGCCGCGTTGCC
* * * *
414814 ACCGCCACCGGTGGCTGATGGTTGCCAAATTTTATCGGGAAGTCCGTCTTGGCCTCATTATCTTG
1 ACCGCCACCGATGGCTGATGGTTACCAAATTTTATCGGGAAGTCCGTCTTGGCCTCCTCATCTTG
* * *
414879 GATCTAGAGTCGGCTTTGCATGAATCAACTCTGTTTATCGTAAAAAGGCCAAAAACCATTCGGAT
66 GATCTAGAGTCGGTTTTGCATGAATCGACTCCGTTTATCGTAAAAAGGCCAAAAACCATTCGGAT
*
414944 TTATTTTCT-C-TG--ATCTG-CCACCGTCCGATCGTCCTGATTTCTCAGTATGTTGTTCGTGTT
131 TTATTTTCTCCATGCCA-CTGTCCACCGTCCGATCGTCCTGATTTTTCAGTATGTTGTTCGTGTT
* * *
415004 GGCCTTACACAACTTTTTCACTGTTCAGAATGTTGATCGGAGATTCCGATCGCCGTAAATAGGCC
195 GGCCTTGCGCAACTTTTTCACTGTTCAGAATGTTGATCGGAGATCCCGATCGCCGTAAATAGGCC
** * * * * *
415069 AAAAACTATTCGGTTTATTTTCTCTGATCCGTCGCTGTCCACCATCTGATCATCATGAATTTTCA
260 AAAAACCGTGC-GATTATTTTCTCCGATCCGTCGCTGTCCACCGTCTGATCATCCTGAATTTTCA
* * *
415134 GTATGTTGTTCGTGCTGGCCTTGTGTAACTTTTCACTGTTC
324 GTATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACTGTTC
415175 GAAATATTGG
Statistics
Matches: 791, Mismatches: 114, Indels: 38
0.84 0.12 0.04
Matches are distributed among these distances:
548 137 0.17
549 51 0.06
550 3 0.00
551 1 0.00
553 1 0.00
555 1 0.00
556 122 0.15
558 2 0.00
559 7 0.01
560 2 0.00
561 4 0.01
562 179 0.23
563 12 0.02
564 269 0.34
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (550 bp):
ACCGCCACCGATGGCTGATGGTTACCAAATTTTATCGGGAAGTCCGTCTTGGCCTCCTCATCTTG
GATCTAGAGTCGGTTTTGCATGAATCGACTCCGTTTATCGTAAAAAGGCCAAAAACCATTCGGAT
TTATTTTCTCCATGCCACTGTCCACCGTCCGATCGTCCTGATTTTTCAGTATGTTGTTCGTGTTG
GCCTTGCGCAACTTTTTCACTGTTCAGAATGTTGATCGGAGATCCCGATCGCCGTAAATAGGCCA
AAAACCGTGCGATTATTTTCTCCGATCCGTCGCTGTCCACCGTCTGATCATCCTGAATTTTCAGT
ATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACTGTTCAGAATGTTGATCGAACATCCTGATCA
CCGACGAAATTTCGGCAGAATTCAAGACAATTTTTTTATTTCTATTTTTCATTAATTTACTTCTT
CTTCTCTCTCACGTATGGCTTCCTCCCCCTTGTATGCCTCCAAAAATACATAAAATCATCATAAA
AGAGTCGCCAACCACCGTCGCCGCGTTGCC
Found at i:415658 original size:129 final size:129
Alignment explanation
Indices: 415426--415995 Score: 757
Period size: 129 Copynumber: 4.4 Consensus size: 129
415416 AACTTCTATG
* * * * **
415426 TGACACAGTTCCTACGTGATGAGGACGGTAGACCATCATTAGGGATGATAACACGGTTCCTACAC
1 TGACACGGTTCCTACGTGATGAGGACGGCAGGCCATC-TAAGGG-TGATAACACGGTTCCTACGT
* * ** *
415491 GATGAGGACGACTGATTATCTAAGGTTGACA-GGACTCCTATGTGATGAGGAGATCAGGTCGGGT
64 GATGAGGACGGCTGGTTATCTGGGGTCGACACGG-CTCCTATGTGATGAGGAGATCAGGTCGGGT
415555 GA
128 GA
* ** * *
415557 TGACACGGTTCCTGCGTGATGAGGACGGCAAACCATCTATGGGTGATAACACGATTCCTACGTGA
1 TGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGA
* * * *
415622 TGAGGACGGTTGGTTATTTGGGGTCGACACGGCTCCTAAGTGATGAGGAGATCAGGTCAGGTGA
66 TGAGGACGGCTGGTTATCTGGGGTCGACACGGCTCCTATGTGATGAGGAGATCAGGTCGGGTGA
* * *
415686 TGTCACGGTTCCTACGTGATGAGGTCGGCATGCCATCTAAGGGTGATAACACGGTTCCTACGTGA
1 TGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGA
*** * *
415751 TGAGGACGGCTGGTTATCT-GGGTCGACATATCTCTTACGTGATGAGGAGATCAGGTCGGGTGA
66 TGAGGACGGCTGGTTATCTGGGGTCGACACGGCTCCTATGTGATGAGGAGATCAGGTCGGGTGA
* * *
415814 TGACACGGTTCCTACGTGATGAGGACGACATGCCATCTAAGGGTGATAACACGGTTCTTACGTGA
1 TGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGA
* * * * *
415879 TGAGGACGGCTGGTTATATGGGGTTGACACGACTCCTATGTGATGAGGATATCTGGTCGGGTGA
66 TGAGGACGGCTGGTTATCTGGGGTCGACACGGCTCCTATGTGATGAGGAGATCAGGTCGGGTGA
* *
415943 TGACATGGTTCCTACGTGATGAGAACGGCAGGCCATCTAAGGGTGATAACACG
1 TGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCTAAGGGTGATAACACG
415996 ATTTCAAGAG
Statistics
Matches: 387, Mismatches: 50, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
128 117 0.30
129 231 0.60
130 6 0.02
131 33 0.09
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (129 bp):
TGACACGGTTCCTACGTGATGAGGACGGCAGGCCATCTAAGGGTGATAACACGGTTCCTACGTGA
TGAGGACGGCTGGTTATCTGGGGTCGACACGGCTCCTATGTGATGAGGAGATCAGGTCGGGTGA
Found at i:415705 original size:40 final size:40
Alignment explanation
Indices: 415526--415965 Score: 131
Period size: 46 Copynumber: 10.3 Consensus size: 40
415516 TTGACAGGAC
* *
415526 TCCTATGTGATGAGGAGATCAGGTCGGGTGATGACACGGT
1 TCCTACGTGATGAGGAGATCAGGTCAGGTGATGACACGGT
* * * *
415566 TCCTGCGTGATGAGGACGGCAAACCA--TCTATGGGTGATAACACGAT
1 TCCTACGTGATGAGGA--G---ATCAGGTC-A--GGTGATGACACGGT
* * * * *
415612 TCCTACGTGATGAGGACGGT-TGGTTATTTGG-GGTCGACACGGC
1 TCCTACGTGATGAGGA-GATCAGGTCA---GGTGAT-GACACGGT
* *
415655 TCCTAAGTGATGAGGAGATCAGGTCAGGTGATGTCACGGT
1 TCCTACGTGATGAGGAGATCAGGTCAGGTGATGACACGGT
* ** * *
415695 TCCTACGTGATGAGGTCGGCATGCCATCTAAGGGTGATAACACGGT
1 TCCTACGTGATGAGG--AG-AT--CAGGTCA-GGTGATGACACGGT
* * * ** * **
415741 TCCTACGTGATGAGGACG-GCTGGTTATCTGGGTCGACA-TAT
1 TCCTACGTGATGAGGA-GATCAGGTCAGGT-GAT-GACACGGT
* *
415782 CTCTTACGTGATGAGGAGATCAGGTCGGGTGATGACACGGT
1 -TCCTACGTGATGAGGAGATCAGGTCAGGTGATGACACGGT
* *
415823 TCCTACGTGATGAGGACGA-CATGCCATCTAAGGGTGATAACACGGT
1 TCCTACGTGATGAGGA-GATCA-G--GTC--A-GGTGATGACACGGT
* * * * * * **
415869 TCTTACGTGATGAGGACG-GCTGGTTATATGGGGTTGACACGAC
1 TCCTACGTGATGAGGA-GATCAGG-T-CA-GGTGATGACACGGT
* * * * *
415912 TCCTATGTGATGAGGATATCTGGTCGGGTGATGACATGGT
1 TCCTACGTGATGAGGAGATCAGGTCAGGTGATGACACGGT
415952 TCCTACGTGATGAG
1 TCCTACGTGATGAG
415966 AACGGCAGGC
Statistics
Matches: 284, Mismatches: 79, Indels: 74
0.65 0.18 0.17
Matches are distributed among these distances:
40 80 0.28
41 15 0.05
42 31 0.11
43 62 0.22
44 1 0.00
45 10 0.04
46 85 0.30
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCAGGTCAGGTGATGACACGGT
Found at i:415748 original size:46 final size:45
Alignment explanation
Indices: 415551--415888 Score: 198
Period size: 46 Copynumber: 7.8 Consensus size: 45
415541 AGATCAGGTC
* * **
415551 GGGTGATGACACGGTTCCTGCGTGATGAGGACGGCAAACCATCTA
1 GGGTGATAACACGGTTCCTACGTGATGAGGACGGCATGCCATCTA
* * ** *
415596 TGGGTGATAACACGATTCCTACGTGATGAGGACGG-TTGGTTAT-TT
1 -GGGTGATAACACGGTTCCTACGTGATGAGGACGGCAT-GCCATCTA
* * *
415641 GGG-G-TCGACACGGCTCCTAAGTGATGAGGA--G-AT--CAGGTC-A
1 GGGTGAT-AACACGGTTCCTACGTGATGAGGACGGCATGCCA--TCTA
** *
415681 -GGTGATGTCACGGTTCCTACGTGATGAGGTCGGCATGCCATCTAA
1 GGGTGATAACACGGTTCCTACGTGATGAGGACGGCATGCCATCT-A
**
415726 GGGTGATAACACGGTTCCTACGTGATGAGGACGGC-TGGTTATCT-
1 GGGTGATAACACGGTTCCTACGTGATGAGGACGGCAT-GCCATCTA
** * ** *
415770 GGGTCG---ACA-TATCTCTTACGTGATGAGGA--G-AT--CAGGTC
1 GGGT-GATAACACGGT-TCCTACGTGATGAGGACGGCATGCCATCTA
* *
415808 GGGTGATGACACGGTTCCTACGTGATGAGGACGACATGCCATCTAA
1 GGGTGATAACACGGTTCCTACGTGATGAGGACGGCATGCCATCT-A
*
415854 GGGTGATAACACGGTTCTTACGTGATGAGGACGGC
1 GGGTGATAACACGGTTCCTACGTGATGAGGACGGC
415889 TGGTTATATG
Statistics
Matches: 221, Mismatches: 41, Indels: 60
0.69 0.13 0.19
Matches are distributed among these distances:
37 3 0.01
38 5 0.02
39 2 0.01
40 42 0.19
41 5 0.02
42 20 0.09
43 27 0.12
44 7 0.03
45 9 0.04
46 101 0.46
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.25
Consensus pattern (45 bp):
GGGTGATAACACGGTTCCTACGTGATGAGGACGGCATGCCATCTA
Found at i:415944 original size:257 final size:257
Alignment explanation
Indices: 415426--415995 Score: 793
Period size: 257 Copynumber: 2.2 Consensus size: 257
415416 AACTTCTATG
* * *
415426 TGACACAGTTCCTACGTGATGAGGACGGTAGACCATCATTAGGGATGATAACACGGTTCCTACAC
1 TGACACGGTTCCTACGTGATGAGGACGGCAG-CCATC-TAAGGG-TGATAACACGGTTCCTACAC
* *
415491 GATGAGGACGACTGATTATCTAAGGTTGACAGGACTCCTATGTGATGAGGAGATCAGGTCGGGTG
63 GATGAGGACGACTGATTATCTAAGGTCGACAGGACTCCTACGTGATGAGGAGATCAGGTCGGGTG
* * *
415556 ATGACACGGTTCCTGCGTGATGAGGACGGCAAACCATCTATGGGTGATAACACGATTCCTACGTG
128 ATGACACGGTTCCTACGTGATGAGGACGACAAACCATCTAAGGGTGATAACACGATTCCTACGTG
* * *
415621 ATGAGGACGGTTGGTTATTTGGGGTCGACACGGCTCCTAAGTGATGAGGAGATCAGGTCAGGTGA
193 ATGAGGACGGCTGGTTATATGGGGTCGACACGACTCCTAAGTGATGAGGAGATCAGGTCAGGTGA
* * **
415686 TGTCACGGTTCCTACGTGATGAGGTCGGCATGCCATCTAAGGGTGATAACACGGTTCCTACGTGA
1 TGACACGGTTCCTACGTGATGAGGACGGCA-GCCATCTAAGGGTGATAACACGGTTCCTACACGA
* * * * *
415751 TGAGGACGGCTGGTTATCT-GGGTCGACA-TATCTCTTACGTGATGAGGAGATCAGGTCGGGTGA
65 TGAGGACGACTGATTATCTAAGGTCGACAGGA-CTCCTACGTGATGAGGAGATCAGGTCGGGTGA
** * *
415814 TGACACGGTTCCTACGTGATGAGGACGACATGCCATCTAAGGGTGATAACACGGTTCTTACGTGA
129 TGACACGGTTCCTACGTGATGAGGACGACAAACCATCTAAGGGTGATAACACGATTCCTACGTGA
* * * * *
415879 TGAGGACGGCTGGTTATATGGGGTTGACACGACTCCTATGTGATGAGGATATCTGGTCGGGTGA
194 TGAGGACGGCTGGTTATATGGGGTCGACACGACTCCTAAGTGATGAGGAGATCAGGTCAGGTGA
* *
415943 TGACATGGTTCCTACGTGATGAGAACGGCAGGCCATCTAAGGGTGATAACACG
1 TGACACGGTTCCTACGTGATGAGGACGGCA-GCCATCTAAGGGTGATAACACG
415996 ATTTCAAGAG
Statistics
Matches: 274, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
256 1 0.00
257 199 0.73
258 37 0.14
259 5 0.02
260 31 0.11
261 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (257 bp):
TGACACGGTTCCTACGTGATGAGGACGGCAGCCATCTAAGGGTGATAACACGGTTCCTACACGAT
GAGGACGACTGATTATCTAAGGTCGACAGGACTCCTACGTGATGAGGAGATCAGGTCGGGTGATG
ACACGGTTCCTACGTGATGAGGACGACAAACCATCTAAGGGTGATAACACGATTCCTACGTGATG
AGGACGGCTGGTTATATGGGGTCGACACGACTCCTAAGTGATGAGGAGATCAGGTCAGGTGA
Found at i:416098 original size:33 final size:33
Alignment explanation
Indices: 416061--416187 Score: 105
Period size: 33 Copynumber: 3.8 Consensus size: 33
416051 GATAAAATAC
*
416061 GTTTCAAGGGAAACAATCTCAAAGATATTTGTT
1 GTTTCAAGAGAAACAATCTCAAAGATATTTGTT
* ** * **
416094 GTTTCATGAGAAATGATCTCAAAGAAAATAGGATTT
1 GTTTCAAGAGAAACAATCTCAAAG-ATATTTG--TT
*
416130 GTTTCAAGAGAAAC-ATCTCAAAG-TTTGGTTGTT
1 GTTTCAAGAGAAACAATCTCAAAGATAT--TTGTT
* *
416163 ATTTCATGAGAAACAATCTCAAAGA
1 GTTTCAAGAGAAACAATCTCAAAGA
416188 AACTAAAACT
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
33 35 0.49
34 13 0.18
35 10 0.14
36 14 0.19
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (33 bp):
GTTTCAAGAGAAACAATCTCAAAGATATTTGTT
Found at i:416134 original size:69 final size:67
Alignment explanation
Indices: 416061--416277 Score: 206
Period size: 69 Copynumber: 3.2 Consensus size: 67
416051 GATAAAATAC
**
416061 GTTTCAAGGGAAACAATCTCAAAGATATTTGTTGTTTCATGAGAAATGATCTCAAAGAAAATAGG
1 GTTTCAAGGGAAACAATCTCAAAG-T-TTTGTTGTTTCATGAGAAATGATCTCAAAGAAAATAAA
*
416126 ATTT
64 ACTT
* * ** *
416130 GTTTCAAGAGAAAC-ATCTCAAAGTTTGGTTGTTATTTCATGAGAAACAATCTCAAAGAAACTAA
1 GTTTCAAGGGAAACAATCTCAAAG-TT--TTGTTGTTTCATGAGAAATGATCTCAAAGAAAATAA
416194 AACTT
63 AACTT
* * * * * * *
416199 GTTTCAAGGGAAACAATATCAAAG-TTTGGTGTTTCATAAGAAACTG-TCTCAAGGGAGACAAAA
1 GTTTCAAGGGAAACAATCTCAAAGTTTTGTTGTTTCATGAGAAA-TGATCTCAAAGAAAATAAAA
*
416262 CAT
65 CTT
*
416265 GTTTCAAGAGAAA
1 GTTTCAAGGGAAA
416278 ATGTCTCAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
66 41 0.34
67 1 0.01
68 11 0.09
69 60 0.50
70 8 0.07
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (67 bp):
GTTTCAAGGGAAACAATCTCAAAGTTTTGTTGTTTCATGAGAAATGATCTCAAAGAAAATAAAAC
TT
Found at i:416262 original size:66 final size:65
Alignment explanation
Indices: 416061--416316 Score: 198
Period size: 66 Copynumber: 3.8 Consensus size: 65
416051 GATAAAATAC
* * *
416061 GTTTCAAGGGAAACAATCTCAAAGATATTTGTTGTTTCATGAGAAA-TGATCTCAAAGAAA-ATA
1 GTTTCAAGAGAAACAATCTCAAAG---TTTGGTGTTTCATGAGAAACTG-TCTCAAGGAAACA-A
* *
416124 GGATTT
61 -AACTT
** *
416130 GTTTCAAGAGAAAC-ATCTCAAAGTTTGGTTGTTATTTCATGAGAAACAATCTCAAAGAAACTAA
1 GTTTCAAGAGAAACAATCTCAAAGTTTGG-TG---TTTCATGAGAAACTGTCTCAAGGAAAC-AA
416194 AACTT
61 AACTT
* * * * *
416199 GTTTCAAGGGAAACAATATCAAAGTTTGGTGTTTCATAAGAAACTGTCTCAAGGGAGACAAAACA
1 GTTTCAAGAGAAACAATCTCAAAGTTTGGTGTTTCATGAGAAACTGTCTCAA-GGAAACAAAACT
416264 T
65 T
* * * *
416265 GTTTCAAGAGAAA-ATGTCTCAAA-TATGGGTGTTTCAAGAGAAACTATCTCAA
1 GTTTCAAGAGAAACA-ATCTCAAAGT-TTGGTGTTTCATGAGAAACTGTCTCAA
416317 AAGAGACAAA
Statistics
Matches: 155, Mismatches: 21, Indels: 25
0.77 0.10 0.12
Matches are distributed among these distances:
65 6 0.04
66 67 0.43
67 4 0.03
68 9 0.06
69 54 0.35
70 14 0.09
71 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (65 bp):
GTTTCAAGAGAAACAATCTCAAAGTTTGGTGTTTCATGAGAAACTGTCTCAAGGAAACAAAACTT
Found at i:416458 original size:36 final size:36
Alignment explanation
Indices: 416390--416638 Score: 140
Period size: 36 Copynumber: 7.0 Consensus size: 36
416380 TCAAAGTTTA
* * *
416390 TGTTTCAAGAGAAACTGTCTCAAGGGATACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
* *
416426 TGTTTCAAAAGAAACTATCTCAATAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
** * *
416462 CATTCCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
** * * * *
416498 CATTTTAAGGGAAAC-ATTTTC-A-A-AG-----TTT
1 TGTTTCAAGAGAAACTA-TCTCAAGAGAGACAAAATT
* * *
416526 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAGTTT
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAA-ATT
* * *
416564 ATGTTTCGAGGGAAACTGA-CTCAAGGGAGACAAAACTTT
1 -TGTTTCAAGAGAAACT-ATCTCAAGAGAGACAAAA--TT
* * *
416603 GTGTTTCGAGGGAAACTATCTCAAGCGAGACAAAAT
1 -TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAT
416639 CTTCTTTAAA
Statistics
Matches: 169, Mismatches: 28, Indels: 31
0.74 0.12 0.14
Matches are distributed among these distances:
28 2 0.01
29 14 0.08
30 1 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 2 0.01
36 77 0.46
37 1 0.01
38 34 0.20
39 33 0.20
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
Found at i:416569 original size:38 final size:38
Alignment explanation
Indices: 416518--416636 Score: 166
Period size: 38 Copynumber: 3.1 Consensus size: 38
416508 GAAACATTTT
* *
416518 CAAAGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAAAGTTTATGTTTCGAGGGAAACTGTCTCAAGGGAGA
*
416556 CAAAGTTTATGTTTCGAGGGAAACTGACTCAAGGGAGA
1 CAAAGTTTATGTTTCGAGGGAAACTGTCTCAAGGGAGA
* * * *
416594 CAAAACTTTGTGTTTCGAGGGAAACTATCTCAAGCGAGA
1 C-AAAGTTTATGTTTCGAGGGAAACTGTCTCAAGGGAGA
416633 CAAA
1 CAAA
416637 ATCTTCTTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 39 0.54
39 33 0.46
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (38 bp):
CAAAGTTTATGTTTCGAGGGAAACTGTCTCAAGGGAGA
Found at i:416619 original size:39 final size:39
Alignment explanation
Indices: 416523--416637 Score: 153
Period size: 39 Copynumber: 3.0 Consensus size: 39
416513 ATTTTCAAAG
* * * *
416523 TTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAG
1 TTTATGTTTCGAGGGAAACTGACTCAAGGGAGACAAAAC
416561 TTTATGTTTCGAGGGAAACTGACTCAAGGGAGACAAAAC
1 TTTATGTTTCGAGGGAAACTGACTCAAGGGAGACAAAAC
* *
416600 TTTGTGTTTCGAGGGAAACT-ATCTCAAGCGAGACAAAA
1 TTTATGTTTCGAGGGAAACTGA-CTCAAGGGAGACAAAA
416638 TCTTCTTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
38 32 0.46
39 37 0.54
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (39 bp):
TTTATGTTTCGAGGGAAACTGACTCAAGGGAGACAAAAC
Found at i:416987 original size:124 final size:124
Alignment explanation
Indices: 416767--416993 Score: 375
Period size: 124 Copynumber: 1.8 Consensus size: 124
416757 TTCTTGATGG
** *
416767 TGGACATGATATCCTTAGTTTTGAAGTTGAAATCGTGGATGGCCCCTTCGACGTGAAGTCGAGCC
1 TGGACATGATATCCTTAGTCATGAAGTTGAAATCATGGATGGCCCCTTCGACGTGAAGTCGAGCC
416832 TCAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTGAAATATGAATGTTGTTGA
66 TCAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTGAAATATGAATGTTGTTGA
* * * *
416891 TGGACATGATATCCTTCA-TCATGAAGTTGAAATCATGTATGGTCCCTTCGTCTTGAAGTCGAGC
1 TGGACATGATATCCTT-AGTCATGAAGTTGAAATCATGGATGGCCCCTTCGACGTGAAGTCGAGC
416955 CTCAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
65 CTCAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA
416994 GAACTGTTTT
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
124 94 0.99
125 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.32
Consensus pattern (124 bp):
TGGACATGATATCCTTAGTCATGAAGTTGAAATCATGGATGGCCCCTTCGACGTGAAGTCGAGCC
TCAAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATTGAAATATGAATGTTGTTGA
Found at i:417383 original size:15 final size:15
Alignment explanation
Indices: 417350--417383 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
417340 AATCTCCAAA
*
417350 GATGCCCCAATATTC
1 GATGCCCCAACATTC
*
417365 GATGCCCCAACATTT
1 GATGCCCCAACATTC
417380 GATG
1 GATG
417384 TTGAATCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.26
Consensus pattern (15 bp):
GATGCCCCAACATTC
Found at i:418458 original size:15 final size:15
Alignment explanation
Indices: 418432--418490 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
418422 GCTTCTTGTC
418432 TCTTTT-TCTTTG-T
1 TCTTTTCTCTTTGCT
418445 TCATTTTCTCTTTGCT
1 TC-TTTTCTCTTTGCT
* *
418461 TCTTTTCTTTTTGAT
1 TCTTTTCTCTTTGCT
418476 T-TTTGT-TCTTTGCT
1 TCTTT-TCTCTTTGCT
418490 T
1 T
418491 TTCTTTATGC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.05
14 14 0.37
15 19 0.50
16 3 0.08
ACGTcount: A:0.03, C:0.17, G:0.08, T:0.71
Consensus pattern (15 bp):
TCTTTTCTCTTTGCT
Found at i:421506 original size:16 final size:18
Alignment explanation
Indices: 421485--421522 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
421475 AATGTCTTTT
421485 AAAAAT-AATTTTAAGA-
1 AAAAATCAATTTTAAGAC
*
421501 AAAAATCATTTTTAAGAC
1 AAAAATCAATTTTAAGAC
421519 AAAA
1 AAAA
421523 GTTGGTACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 9 0.47
18 4 0.21
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:422364 original size:145 final size:145
Alignment explanation
Indices: 422162--422574 Score: 469
Period size: 145 Copynumber: 2.8 Consensus size: 145
422152 GTAAAAAAGC
* * * *
422162 CAAAAACCATTCAGATTTATTTTCTCCGATCTACAGTCT-TCCACCGTCCGATAGTCCTAATTTT
1 CAAAAACCGTTCAGA-TTATTTTCTCCGATCTGCCG-CTGTCCACAGTCCGATAGTCCTAATTTT
* * * *
422226 TCAGTATGTTGTTCGTGTTGGCCTTGTGCAACTTTTAACCGTTCAAAATGTTGATCGGAGT-TCT
64 TCAGTATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACCGTTCAGAATGTTGATCGGA-TATCC
422290 CGATCGCCGTAAATAGGA
128 CGATCGCCGTAAATAGGA
* ** * * *
422308 CAAAAACCGTTCAGATTATTTTCTCCGATCCGCCGCTGTCCATTGTCTGATCGTCCTGATTTTTC
1 CAAAAACCGTTCAGATTATTTTCTCCGATCTGCCGCTGTCCACAGTCCGATAGTCCTAATTTTTC
**
422373 AGTATGTTGTTCGTGTTGGCCTTGCGCAA-TGTTTCACTATTCAGAATGTTGATCGGATATCCCG
66 AGTATGTTGTTCGTGTTGGCCTTGCGCAACT-TTTCACCGTTCAGAATGTTGATCGGATATCCCG
** *
422437 ATCGTTGTAAATAGGC
130 ATCGCCGTAAATAGGA
** * * *
422453 CAAAAACCGTTTGGATTATTTTCTCCGATCTGTCG-TCGTCCACAGTCCGATTGTCTTGAA-TTT
1 CAAAAACCGTTCAGATTATTTTCTCCGATCTGCCGCT-GTCCACAGTCCGATAGTCCT-AATTTT
* * * *
422516 TCAGTATGTTGTTTGTATTGGCCTTGCGCAACATTTCA-CGATTCGGAATGTTGATCGGA
64 TCAGTATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACCG-TTCAGAATGTTGATCGGA
422575 CTTCCTGATC
Statistics
Matches: 226, Mismatches: 34, Indels: 15
0.82 0.12 0.05
Matches are distributed among these distances:
144 5 0.02
145 206 0.91
146 15 0.07
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (145 bp):
CAAAAACCGTTCAGATTATTTTCTCCGATCTGCCGCTGTCCACAGTCCGATAGTCCTAATTTTTC
AGTATGTTGTTCGTGTTGGCCTTGCGCAACTTTTCACCGTTCAGAATGTTGATCGGATATCCCGA
TCGCCGTAAATAGGA
Found at i:422778 original size:37 final size:37
Alignment explanation
Indices: 422725--422829 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
422715 CATTTTCGTC
422725 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
422762 TTTCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
422799 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
422830 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:423193 original size:15 final size:15
Alignment explanation
Indices: 423173--423232 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
423163 TAGTCCCTTT
423173 ATTTATTATATATTC
1 ATTTATTATATATTC
*
423188 ATTTATTTTTATTATTC
1 ATTTA-TTATA-TATTC
423205 ATATTATTAT-TATT-
1 AT-TTATTATATATTC
*
423219 ATATATATATATAT
1 ATTTAT-TATATAT
423233 ATTTCTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.08
14 5 0.14
15 12 0.32
16 4 0.11
17 10 0.27
18 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTATTATATATTC
Found at i:423226 original size:18 final size:18
Alignment explanation
Indices: 423175--423226 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 18
423165 GTCCCTTTAT
*
423175 TTATTATATATTCATTTATTT
1 TTATTATATA-T-A-TTATTA
423196 TTATTAT-TCATATTATTA
1 TTATTATAT-ATATTATTA
423214 TTATTATATATAT
1 TTATTATATATAT
423227 ATATATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 16 0.57
19 2 0.07
20 2 0.07
21 8 0.29
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATTATATATATTATTA
Found at i:423677 original size:2 final size:2
Alignment explanation
Indices: 423670--423707 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
423660 TAATACTTTG
423670 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
423708 TTTCCTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:428965 original size:183 final size:183
Alignment explanation
Indices: 428432--428970 Score: 945
Period size: 183 Copynumber: 2.9 Consensus size: 183
428422 ATTAAATCCG
428432 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
428497 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* * *
428562 TTGTCAGGCCAAAGACTTTTTGATGAGATGAACCCTTAAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTTATTTGTCCCTC
428615 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
428680 ATAAATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
428745 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTTATTTGTCCCTT
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTTATTTGTCCCTC
*
428798 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * * *
428863 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTACT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
428927 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGTTA
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTTA
428971 AACCTGATAA
Statistics
Matches: 341, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 340 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (183 bp):
TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTTATTTGTCCCTC
Found at i:430154 original size:36 final size:35
Alignment explanation
Indices: 430114--430239 Score: 101
Period size: 36 Copynumber: 3.5 Consensus size: 35
430104 CACTCAAATT
430114 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACATA-TTTGTCTCACTTGAGAC
* * * * ** *
430150 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACATATTTGTCTCACTTGAGAC
* *
430186 TGTTTTTCTTAAAACAAGATTTGTCTCCCTTGAGAC
1 TGTTTTTCTTAAAAC-ATATTTGTCTCACTTGAGAC
* * *
430222 AGTTTCTCTTGAAACATA
1 TGTTTTTCTTAAAACATA
430240 AACATTGAAA
Statistics
Matches: 68, Mismatches: 18, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
34 1 0.01
35 5 0.07
36 56 0.82
37 5 0.07
38 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (35 bp):
TGTTTTTCTTAAAACATATTTGTCTCACTTGAGAC
Found at i:430190 original size:72 final size:72
Alignment explanation
Indices: 430098--430235 Score: 190
Period size: 72 Copynumber: 1.9 Consensus size: 72
430088 ATGCAGATGA
* * *
430098 TTATCTCACTCAAATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTTTCTCGA
1 TTATCTCACTCAAATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACAGTTTCTCTCGA
430162 AAGAAGAT
65 AAGAAGAT
* * *
430170 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCCCTTGAGACAGTTTCTCTTGA
1 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTCTCTCGA
430234 AA
65 AA
430236 CATAAACATT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
71 1 0.02
72 56 0.97
73 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.43
Consensus pattern (72 bp):
TTATCTCACTCAAATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACAGTTTCTCTCGAA
AGAAGAT
Found at i:430343 original size:105 final size:101
Alignment explanation
Indices: 430205--430458 Score: 375
Period size: 105 Copynumber: 2.5 Consensus size: 101
430195 TAAAACAAGA
*
430205 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGATT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGA-A
* *
430270 TTTTTTCTCTCTTGAGATAGTTTCCCTTGAAACAGAAAAT
65 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
*
430310 TTTGTCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTG-AAACAATTTCCCTTGAAATGAA
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC-ATTTCCCTTGAAATGAA
* *
430374 TTTTATCTCGCTTGGGATAGTTTTCCTTGAAACGAAT
65 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAACGAAT
** *
430411 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACTTTGAAAACA
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
430459 ATTTAACGAA
Statistics
Matches: 137, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
101 42 0.31
102 4 0.03
103 1 0.01
104 33 0.24
105 57 0.42
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
TTTATCTCGCTTGAGATAGTTTCCCTTGAAACGAAT
Found at i:430411 original size:36 final size:36
Alignment explanation
Indices: 430362--430432 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
430352 AAACAATTTC
* * * *
430362 CCTTGAAATGAATTTTATCTCGCTTGGGATAGTTTT
1 CCTTGAAACGAATTTTATCTCCCTTGAGACAGTTTT
*
430398 CCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTT
1 CCTTGAAACGAATTTTATCTCCCTTGAGACAGTTT
430433 CTCTCCAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (36 bp):
CCTTGAAACGAATTTTATCTCCCTTGAGACAGTTTT
Found at i:430839 original size:105 final size:104
Alignment explanation
Indices: 430633--431158 Score: 709
Period size: 105 Copynumber: 5.0 Consensus size: 104
430623 ATATCGTGAT
* * * * *
430633 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
430698 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
430739 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTTCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
430804 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
430844 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAATAAAAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
430909 ATCTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
430949 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTACTTGCCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* * *
431010 ATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
431049 ACTCGAGACAACACAAGTTCCACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
431114 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
431155 ACTC
1 ACTC
431159 GGAACAATGC
Statistics
Matches: 373, Mismatches: 40, Indels: 14
0.87 0.09 0.03
Matches are distributed among these distances:
100 77 0.21
101 4 0.01
102 3 0.01
103 4 0.01
104 4 0.01
105 200 0.54
106 81 0.22
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:430959 original size:210 final size:205
Alignment explanation
Indices: 430633--431158 Score: 784
Period size: 210 Copynumber: 2.5 Consensus size: 205
430623 ATATCGTGAT
*
430633 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
*
430698 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACT
66 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * *
430763 TCACGACGAAGGGACCGCTTCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCA
130 CCACGACGAAGGGACCGCTACTTGCCAACAA-AA-TT-CC-AT-TCAGAGCCAATTTCAACTTCA
430828 CAACGAAGGATATTGG
190 CAACGAAGGATATTGG
* * * * *
430844 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAATAAA-AACTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
*
430908 AATCTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
* * * *
430973 CCACGACGAAGGGACCGCTACTTGCCAACAAAATTTCATTTAGAGTCAATTTCAACTTCACAGCG
130 CCACGACGAAGGGACCGCTACTTGCCAACAAAATTCCATTCAGAGCCAATTTCAACTTCACAACG
431038 AAGGATATTGG
195 AAGGATATTGG
* *
431049 ACTCGAGACAACACAAGTTCCACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
** * *
431114 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 AATT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
431159 GGAACAATGC
Statistics
Matches: 285, Mismatches: 27, Indels: 11
0.88 0.08 0.03
Matches are distributed among these distances:
205 85 0.30
206 47 0.16
207 1 0.00
208 2 0.01
209 3 0.01
210 96 0.34
211 51 0.18
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (205 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
AATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTC
CACGACGAAGGGACCGCTACTTGCCAACAAAATTCCATTCAGAGCCAATTTCAACTTCACAACGA
AGGATATTGG
Found at i:431754 original size:37 final size:37
Alignment explanation
Indices: 431701--431805 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
431691 CATTTTTTTC
431701 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
431738 TTGCTAGGATTCAAACTACTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
431775 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
431806 CCACAAGTAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:432647 original size:2 final size:2
Alignment explanation
Indices: 432640--432669 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
432630 TAATACTTTG
*
432640 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432670 TTGTTTTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:433291 original size:3 final size:3
Alignment explanation
Indices: 433283--433322 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
433273 GTGGGTAGGG
433283 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
433323 TATATTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:434358 original size:31 final size:30
Alignment explanation
Indices: 434323--434384 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 30
434313 GGTTCGGGTA
* *
434323 TCAGGTCAGG-TCAATATCGGATGGGTTGATT
1 TCAGGT-AGGATCAA-ATCAGATCGGTTGATT
*
434354 TCAGGTTGGATCAAATCAGATCGGTTGATT
1 TCAGGTAGGATCAAATCAGATCGGTTGATT
434384 T
1 T
434385 TCAGTTGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.24, C:0.13, G:0.29, T:0.34
Consensus pattern (30 bp):
TCAGGTAGGATCAAATCAGATCGGTTGATT
Found at i:434672 original size:47 final size:47
Alignment explanation
Indices: 434603--434696 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
434593 CAAACTTGAC
434603 CTAAAAGATATGTTAAAGTTTGTGATATTTTTGTATTGATCAAGACT
1 CTAAAAGATATGTTAAAGTTTGTGATATTTTTGTATTGATCAAGACT
* * *
434650 CTAAAATATATGTTAAAGTTTGTGATATTTTTGTGTTGATCAGGACT
1 CTAAAAGATATGTTAAAGTTTGTGATATTTTTGTATTGATCAAGACT
434697 GAAAAGTTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (47 bp):
CTAAAAGATATGTTAAAGTTTGTGATATTTTTGTATTGATCAAGACT
Found at i:434805 original size:19 final size:19
Alignment explanation
Indices: 434769--434822 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
434759 CTATTAAAAT
*
434769 TTTAATTATTAACTTAATG
1 TTTAATTATTAAATTAATG
*
434788 TTTAATTA-TAAATATAATA
1 TTTAATTATTAAAT-TAATG
434807 TTT--TTATTAAACTTAA
1 TTTAATTATTAAA-TTAA
434823 AAGTAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 11 0.37
19 16 0.53
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTATTAAATTAATG
Found at i:435219 original size:60 final size:60
Alignment explanation
Indices: 435143--435314 Score: 193
Period size: 60 Copynumber: 2.9 Consensus size: 60
435133 TGTAAATTAT
* * *
435143 GACTCTCATT-TCAAATTAATCCTTAAACTTTTAAATATTTCAATTTCATTCTTAAACTAC
1 GACTCTCATTCT-AAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCCCTAAACTAC
* * * * *
435203 GACTCTCATTCTAAATTAGTCCTTAAGCTTTTGAACATTTGAATTTCATCCCTAAACTAT
1 GACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCCCTAAACTAC
* * * * * * *
435263 GAATATCATTCTAAATTGGTGCTTAAACCTTTAGATCTTTCAATTTCATCCC
1 GACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCCC
435315 CAAATTCATC
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (60 bp):
GACTCTCATTCTAAATTAGTCCTTAAACTTTTAAATATTTCAATTTCATCCCTAAACTAC
Found at i:435811 original size:19 final size:19
Alignment explanation
Indices: 435775--435828 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
435765 CTATTAAAAT
*
435775 TTTAATTATTAACTTAATG
1 TTTAATTATTAAATTAATG
*
435794 TTTAATTA-TAAATATAATA
1 TTTAATTATTAAAT-TAATG
435813 TTT--TTATTAAACTTAA
1 TTTAATTATTAAA-TTAA
435829 AAGTAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 11 0.37
19 16 0.53
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTATTAAATTAATG
Found at i:436216 original size:60 final size:60
Alignment explanation
Indices: 436142--436321 Score: 191
Period size: 60 Copynumber: 3.0 Consensus size: 60
436132 CATATGTCCA
* * * * *
436142 TAAACTATGACTCTCATT-TCAAATTAATTCTTAAACTTTTAAATATTTCAATTTCATTCT
1 TAAACTACGACTCTCATTCT-AAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
* * * *
436202 TAAACTACGACTCTCATTCTAAATTAGTCCTTAATCTTTTGAACATTTGAATTTCATCCC
1 TAAACTACGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
* * * ** * * *
436262 TAAACTATGAATATCATTCTAAATTGGTCCTTAAACCTTTAGACCTTTCAATTTCATCCC
1 TAAACTACGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
436322 CAAATTCATC
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
60 99 0.99
61 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (60 bp):
TAAACTACGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTTCATCCC
Found at i:436818 original size:19 final size:19
Alignment explanation
Indices: 436782--436835 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
436772 CTATTAAAGT
*
436782 TTTAATTATTAACTTAATG
1 TTTAATTATTAAATTAATG
*
436801 TTTAATTA-TAAATATAATA
1 TTTAATTATTAAAT-TAATG
436820 TTT--TTATTAAACTTAA
1 TTTAATTATTAAA-TTAA
436836 AAGTAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.10
18 11 0.37
19 16 0.53
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTATTAAATTAATG
Found at i:437183 original size:31 final size:31
Alignment explanation
Indices: 437148--437244 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
437138 CATATGTCCG
437148 TAAACTATGACTCTCATTTCAAATTAATCCT
1 TAAACTATGACTCTCATTTCAAATTAATCCT
* * ** * * *
437179 TAAACTTTTA-AAT-ATTTCAATTTCATTCT
1 TAAACTATGACTCTCATTTCAAATTAATCCT
* * *
437208 TAAACTACGACTCTCA-TTCTAAATTAGTCTT
1 TAAACTATGACTCTCATTTC-AAATTAATCCT
437239 TAAACT
1 TAAACT
437245 TTTGAACATT
Statistics
Matches: 46, Mismatches: 17, Indels: 6
0.67 0.25 0.09
Matches are distributed among these distances:
29 20 0.43
30 5 0.11
31 21 0.46
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (31 bp):
TAAACTATGACTCTCATTTCAAATTAATCCT
Found at i:437273 original size:60 final size:60
Alignment explanation
Indices: 437149--437331 Score: 181
Period size: 60 Copynumber: 3.0 Consensus size: 60
437139 ATATGTCCGT
* * * **
437149 AAACTATGACTCTCATT-TCAAATTAATCCTTAAACTTTTAAATATTTCAATTTCATTCTT
1 AAACTATGACTCTCATTCT-AAATTAATCCTTAAACTTTTAAACATTTCAATTCCATCCCC
* * * * *
437209 AAACTACGACTCTCATTCTAAATTAGTCTTTAAACTTTTGAACATTTGAATTCCATCCCC
1 AAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTCCATCCCC
* ** * * * *
437269 AAACTATGAATCTCATTCTAAATTGGTCCCTAAACCTTTAGATCA-TTCAATTTCATCCCC
1 AAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTA-AACATTTCAATTCCATCCCC
437329 AAA
1 AAA
437332 TTCATCCAAA
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
60 97 0.96
61 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (60 bp):
AAACTATGACTCTCATTCTAAATTAATCCTTAAACTTTTAAACATTTCAATTCCATCCCC
Found at i:443783 original size:16 final size:17
Alignment explanation
Indices: 443762--443795 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
443752 CGATCAAATT
443762 TTTACTATTCATA-AAA
1 TTTACTATTCATATAAA
443778 TTTACTATTCATATAAA
1 TTTACTATTCATATAAA
443795 T
1 T
443796 AGTAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTACTATTCATATAAA
Found at i:445373 original size:15 final size:15
Alignment explanation
Indices: 445330--445361 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
445320 ATTAAAACTC
*
445330 AACTCAAACTCAAAA
1 AACTCAAATTCAAAA
445345 AACTCAAATTCAAAA
1 AACTCAAATTCAAAA
445360 AA
1 AA
445362 GCTCGAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (15 bp):
AACTCAAATTCAAAA
Found at i:445624 original size:14 final size:15
Alignment explanation
Indices: 445605--445637 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
445595 ATATAATATT
445605 AAAACTC-AACTCAA
1 AAAACTCAAACTCAA
*
445619 AAAACTCAAATTCAA
1 AAAACTCAAACTCAA
445634 AAAA
1 AAAA
445638 ATATCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.64, C:0.21, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAACTCAAACTCAA
Found at i:445685 original size:23 final size:23
Alignment explanation
Indices: 445640--445712 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
445630 TCAAAAAAAT
445640 ATCAAACTCAAT-TTGAGCTCGA
1 ATCAAACTCAATATTGAGCTCGA
* *
445662 ATCAAACTCGATATTAAGCTCGA
1 ATCAAACTCAATATTGAGCTCGA
445685 ATCAAACTCAATATTGAGCTCGA
1 ATCAAACTCAATATTGAGCTCGA
445708 ATCAA
1 ATCAA
445713 GCCACTAGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 11 0.24
23 35 0.76
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (23 bp):
ATCAAACTCAATATTGAGCTCGA
Found at i:447812 original size:7 final size:7
Alignment explanation
Indices: 447800--447867 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
447790 CAAATTAAGT
447800 GTTTAGG
1 GTTTAGG
447807 GTTTAGG
1 GTTTAGG
*
447814 GCTTAGG
1 GTTTAGG
*
447821 GCTTAGG
1 GTTTAGG
*
447828 GTTTATG
1 GTTTAGG
* *
447835 GCTTAGA
1 GTTTAGG
447842 GTTT-GAG
1 GTTTAG-G
* *
447849 ATTGAGG
1 GTTTAGG
447856 GTTTAGG
1 GTTTAGG
447863 GTTTA
1 GTTTA
447868 TAGTTAAGGG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
6 1 0.02
7 45 0.96
8 1 0.02
ACGTcount: A:0.18, C:0.04, G:0.38, T:0.40
Consensus pattern (7 bp):
GTTTAGG
Found at i:447972 original size:7 final size:7
Alignment explanation
Indices: 447949--448049 Score: 100
Period size: 7 Copynumber: 14.9 Consensus size: 7
447939 AATCGGATTA
447949 AGGGTTT
1 AGGGTTT
*
447956 AGAGTTT
1 AGGGTTT
447963 AGGGTTT
1 AGGGTTT
*
447970 AGGGCTT
1 AGGGTTT
*
447977 AGTGTTT
1 AGGGTTT
* *
447984 ATGGTCT
1 AGGGTTT
447991 AGGGTTT
1 AGGGTTT
*
447998 -GAGTTT
1 AGGGTTT
*
448004 GGGGTTT
1 AGGGTTT
*
448011 AAGGTTT
1 AGGGTTT
448018 AGGGTTT
1 AGGGTTT
*
448025 -GGATTT
1 AGGGTTT
448031 -GGGTTT
1 AGGGTTT
448037 AGGGTTT
1 AGGGTTT
448044 AGGGTT
1 AGGGTT
448050 AGTGTGTAAT
Statistics
Matches: 75, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
6 15 0.20
7 60 0.80
ACGTcount: A:0.15, C:0.02, G:0.40, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:448020 original size:27 final size:26
Alignment explanation
Indices: 447980--448049 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
447970 AGGGCTTAGT
* *
447980 GTTTATGGTCTAGGGTTT-GAGTTTGGG
1 GTTTAAGGTTTAGGGTTTGGA-TTT-GG
448007 GTTTAAGGTTTAGGGTTTGGATTTGG
1 GTTTAAGGTTTAGGGTTTGGATTTGG
*
448033 GTTTAGGGTTTAGGGTT
1 GTTTAAGGTTTAGGGTT
448050 AGTGTGTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 18 0.46
27 19 0.49
28 2 0.05
ACGTcount: A:0.13, C:0.01, G:0.40, T:0.46
Consensus pattern (26 bp):
GTTTAAGGTTTAGGGTTTGGATTTGG
Found at i:450075 original size:20 final size:20
Alignment explanation
Indices: 450050--450087 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
450040 TTACATCTCC
450050 CTTAGGTATTTGTTTATTCA
1 CTTAGGTATTTGTTTATTCA
450070 CTTAGGTATTTGTTTATT
1 CTTAGGTATTTGTTTATT
450088 TCCGTTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.16, T:0.58
Consensus pattern (20 bp):
CTTAGGTATTTGTTTATTCA
Found at i:453287 original size:23 final size:22
Alignment explanation
Indices: 453259--453315 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
453249 TTCTACCAAT
453259 TTATATATATTTTTATAAAAACA
1 TTATATATATTTTTATAAAAA-A
* *
453282 TTATATATACATTTTATTAAAAA
1 TTATATATA-TTTTTATAAAAAA
*
453305 GTATATATATT
1 TTATATATATT
453316 AAAAATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.03
23 18 0.62
24 10 0.34
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATATATATTTTTATAAAAAA
Found at i:454683 original size:25 final size:25
Alignment explanation
Indices: 454649--454697 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
454639 AATTAAGAGA
* *
454649 TCTCTACCCATTATTAGGGTTTTTC
1 TCTCCACCCATTATTAGAGTTTTTC
454674 TCTCCACCCATTATTAGAGTTTTT
1 TCTCCACCCATTATTAGAGTTTTT
454698 TGACCGACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.24, G:0.10, T:0.47
Consensus pattern (25 bp):
TCTCCACCCATTATTAGAGTTTTTC
Found at i:458445 original size:17 final size:17
Alignment explanation
Indices: 458423--458457 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
458413 ACAACATATA
458423 TTTATTCATGTATTTTT
1 TTTATTCATGTATTTTT
458440 TTTATTCATGTATTTTT
1 TTTATTCATGTATTTTT
458457 T
1 T
458458 AATATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTATTCATGTATTTTT
Found at i:458463 original size:18 final size:17
Alignment explanation
Indices: 458425--458463 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
458415 AACATATATT
*
458425 TATTCATGTATTTTTTT
1 TATTCATGTATTTTTTA
458442 TATTCATGTATTTTTTAA
1 TATTCATGTATTTTTT-A
458460 TATT
1 TATT
458464 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (17 bp):
TATTCATGTATTTTTTA
Found at i:458620 original size:3 final size:3
Alignment explanation
Indices: 458592--458652 Score: 86
Period size: 3 Copynumber: 19.3 Consensus size: 3
458582 ATTTTATTTT
*
458592 TTA TTA CTA TTA TATA CTTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
458640 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
458653 ATTTTATATG
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 46 0.87
4 5 0.09
5 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:458685 original size:21 final size:21
Alignment explanation
Indices: 458659--458723 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
458649 TTATATTTTA
*
458659 TATGTTTTATGTTTTATGTTT
1 TATGTTTTATGTTTTATCTTT
458680 TATGTTTTA-GCTTTTATCTTT
1 TATGTTTTATG-TTTTATCTTT
*
458701 TAT-TTTTATTTTTTTATCATTT
1 TATGTTTTA-TGTTTTATC-TTT
458723 T
1 T
458724 TAAAAAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
20 6 0.16
21 28 0.74
22 4 0.11
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (21 bp):
TATGTTTTATGTTTTATCTTT
Found at i:458712 original size:5 final size:6
Alignment explanation
Indices: 458613--458713 Score: 67
Period size: 7 Copynumber: 15.3 Consensus size: 6
458603 ATATACTTCA
* * * * *
458613 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTAT TATATTT TATATGTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATT-T T-TATTT T-TAT-TT
*
458665 TTATGTT TTATGTT TTATGTT TTAGCTT TTATCTT TTATTT TTATTT TT
1 TTAT-TT TTAT-TT TTAT-TT TTA-TTT TTAT-TT TTATTT TTATTT TT
458714 TTATCATTTT
Statistics
Matches: 87, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
6 39 0.45
7 41 0.47
8 7 0.08
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (6 bp):
TTATTT
Found at i:458714 original size:7 final size:7
Alignment explanation
Indices: 458659--458713 Score: 71
Period size: 7 Copynumber: 8.1 Consensus size: 7
458649 TTATATTTTA
458659 TATGTTT
1 TATGTTT
458666 TATGTTT
1 TATGTTT
458673 TATGTTT
1 TATGTTT
458680 TATGTTT
1 TATGTTT
458687 TA-GCTTT
1 TATG-TTT
*
458694 TATCTTT
1 TATGTTT
458701 TAT-TTT
1 TATGTTT
458707 TAT-TTT
1 TATGTTT
458713 T
1 T
458714 TTATCATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
6 11 0.24
7 34 0.76
ACGTcount: A:0.15, C:0.04, G:0.09, T:0.73
Consensus pattern (7 bp):
TATGTTT
Found at i:458912 original size:23 final size:23
Alignment explanation
Indices: 458886--458943 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
458876 TATTGTTCTT
* *
458886 TTTCTTTTCTTTA-TTTTACTTTA
1 TTTCTTTTATTTACTTTT-CTTGA
458909 TTTCTTTTATTTACTTTTCTTGA
1 TTTCTTTTATTTACTTTTCTTGA
*
458932 TTTTTTATTATT
1 TTTCTT-TTATT
458944 GTTATTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 21 0.70
24 9 0.30
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTCTTTTATTTACTTTTCTTGA
Found at i:458961 original size:11 final size:11
Alignment explanation
Indices: 458945--458973 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
458935 TTTATTATTG
458945 TTATTTTTGCT
1 TTATTTTTGCT
458956 TTATTTTTGCT
1 TTATTTTTGCT
458967 TT-TTTTT
1 TTATTTTT
458974 ATTTTCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (11 bp):
TTATTTTTGCT
Found at i:458978 original size:9 final size:9
Alignment explanation
Indices: 458884--458996 Score: 50
Period size: 9 Copynumber: 12.1 Consensus size: 9
458874 TATATTGTTC
*
458884 TTTTTCTTT
1 TTTTTATTT
*
458893 TCTTTATTT
1 TTTTTATTT
*
458902 TACTTTATTT
1 T-TTTTATTT
*
458912 CTTTTATTT
1 TTTTTATTT
* *
458921 ACTTTTCTTGAT
1 -TTTTTATT--T
*
458933 TTTTTATTA
1 TTTTTATTT
*
458942 TTGTTATTT
1 TTTTTATTT
458951 TTGCTTTA--T
1 TT--TTTATTT
**
458960 TTTTGCTTT
1 TTTTTATTT
458969 TTTTTATTT
1 TTTTTATTT
*
458978 TCTTTATTT
1 TTTTTATTT
*
458987 TATTTATTT
1 TTTTTATTT
458996 T
1 T
458997 CATTTTTTCC
Statistics
Matches: 79, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
7 2 0.03
9 52 0.66
10 15 0.19
11 9 0.11
12 1 0.01
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.76
Consensus pattern (9 bp):
TTTTTATTT
Found at i:458987 original size:14 final size:14
Alignment explanation
Indices: 458846--458991 Score: 65
Period size: 14 Copynumber: 10.5 Consensus size: 14
458836 CATTTTTGCC
*
458846 TTTATTTTCTTTAC
1 TTTATTTTCTTTAT
* *
458860 CTTA-TTTATTTAT
1 TTTATTTTCTTTAT
458873 TTATATTGTTC--T-T
1 TT-TATT-TTCTTTAT
*
458886 TTTCTTTTCTTTAT
1 TTTATTTTCTTTAT
* * *
458900 TTTACTTTATTTCT
1 TTTATTTTCTTTAT
*
458914 TTTATTTACTTT-T
1 TTTATTTTCTTTAT
* *
458927 CTTGATTTTTTATTAT
1 -TTTATTTTCT-TTAT
458943 TGTTATTTTTGCTTTA-
1 T-TTA-TTTT-CTTTAT
* *
458959 -TT-TTTGCTTTTT
1 TTTATTTTCTTTAT
458971 TTTATTTTCTTTAT
1 TTTATTTTCTTTAT
458985 TTTATTT
1 TTTATTT
458992 ATTTTCATTT
Statistics
Matches: 95, Mismatches: 22, Indels: 30
0.65 0.15 0.20
Matches are distributed among these distances:
11 7 0.07
12 6 0.06
13 15 0.16
14 50 0.53
15 4 0.04
16 5 0.05
17 7 0.07
18 1 0.01
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTATTTTCTTTAT
Found at i:462858 original size:95 final size:95
Alignment explanation
Indices: 462686--462884 Score: 256
Period size: 95 Copynumber: 2.1 Consensus size: 95
462676 TATATATATA
* * * * * *
462686 TATATATACACAATAAAGCTTGAGTTGTCCCTCTAAAGAAATTTATTAAATGCCCCAGGTTTATA
1 TATA-ATACACAATAAAGCATGAGTTGTCCCTATAAAGAAACTGATTAAACGCCCCAGCTTTATA
462751 GATAAGATTCAGCTAGCCTGATAAAGGTGAT
65 GATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * * * *
462782 TATAATATACAATAAAGCATGAGTTGTCCCTATAGAGAAACTGGTTAAACG-CCCTGACTTTATG
1 TATAATACACAATAAAGCATGAGTTGTCCCTATAAAGAAACTGATTAAACGCCCCAG-CTTTATA
* *
462846 GATAATATTCAGCTAGCTTGATAAAGGTGAT
65 GATAAGATTCAGCTAGCCTGATAAAGGTGAT
462877 TATAATAC
1 TATAATAC
462885 TAAGCTGTCC
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
94 4 0.05
95 80 0.91
96 4 0.05
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (95 bp):
TATAATACACAATAAAGCATGAGTTGTCCCTATAAAGAAACTGATTAAACGCCCCAGCTTTATAG
ATAAGATTCAGCTAGCCTGATAAAGGTGAT
Found at i:463995 original size:66 final size:66
Alignment explanation
Indices: 463911--464057 Score: 240
Period size: 66 Copynumber: 2.2 Consensus size: 66
463901 GCTAGAGTCA
* **
463911 ATTTCAACTTCACAACGAAGGACATCCAATTAAAATCTCAATTTCATAGCGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGACATCCAATTAAAAGATCAATTTCATAGCGAATGAGCCATCCAC
463976 G
66 G
* *
463977 ATTTCAATTTCACGACGAAGGATATCCAATTAAAAGATCAATTTCATAGCGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGACATCCAATTAAAAGATCAATTTCATAGCGAATGAGCCATCCAC
*
464042 T
66 G
464043 ATTTCAACTTCACGA
1 ATTTCAACTTCACGA
464058 AAAAGGATAT
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (66 bp):
ATTTCAACTTCACGACGAAGGACATCCAATTAAAAGATCAATTTCATAGCGAATGAGCCATCCAC
G
Found at i:464307 original size:36 final size:36
Alignment explanation
Indices: 464252--464439 Score: 331
Period size: 36 Copynumber: 5.2 Consensus size: 36
464242 AATTTACTCA
* * * *
464252 AAACAAAGTTTTGTTTCTCTTGAGGCAGTTTCTCTTT
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTCCCTTG
464289 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
464325 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
464361 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
464397 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
464433 AAACAAA
1 AAACAAA
464440 ATCTTTGAAT
Statistics
Matches: 147, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
36 140 0.95
37 7 0.05
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:464537 original size:137 final size:137
Alignment explanation
Indices: 464325--464677 Score: 548
Period size: 137 Copynumber: 2.6 Consensus size: 137
464315 GTTTCCCTTG
* *
464325 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 AAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
464390 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTA-T
66 TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATT
464454 TTACTCA
131 TTACTCA
* * * * * *
464461 AAACAAATTTCGCCTCCCTTGGGACAGTTT-CTTTTAGAACTAAGTTTTGTCTCTTTTGAGACAG
1 AAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGA-AAC-AAATTTTGTCTCTCTTGAGACAG
* *
464525 TTTTCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTA
64 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTA
* **
464590 TTTTCCTTG
129 TTTTACTCA
*
464599 AAACAAATTTCGTCTCCCTTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
1 AAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
464664 TCCCTTGAAACAAA
66 TCCCTTGAAACAAA
464678 ACCTTTGAAA
Statistics
Matches: 191, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
135 4 0.02
136 29 0.15
137 119 0.62
138 35 0.18
139 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (137 bp):
AAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTT
TCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATT
TTACTCA
Found at i:464548 original size:36 final size:36
Alignment explanation
Indices: 464461--464576 Score: 117
Period size: 36 Copynumber: 3.2 Consensus size: 36
464451 TATTTACTCA
* * * * * *
464461 AAACAAATTTCGCCTCCCTTGGGACAGTTT-CTTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * *
464496 AGAACTAAGTTTTGTCTCTTTTGAGACAGTTTTCATTG
1 A-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
464534 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
464570 AAACAAA
1 AAACAAA
464577 ATCTTTGAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
35 1 0.02
36 38 0.58
37 23 0.35
38 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
Found at i:464637 original size:36 final size:36
Alignment explanation
Indices: 464594--464677 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
464584 AATCTATTTT
*
464594 CCTTGAAACAAATTTCGTCTCCCTTGAGATAGTTTC
1 CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC
* *
464630 CCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTC
1 CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC
464666 CCTTGAAACAAA
1 CCTTGAAACAAA
464678 ACCTTTGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.35
Consensus pattern (36 bp):
CCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTC
Found at i:464700 original size:101 final size:101
Alignment explanation
Indices: 464516--464704 Score: 301
Period size: 101 Copynumber: 1.9 Consensus size: 101
464506 TTTGTCTCTT
* *
464516 TTGAGACAGTTTTCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCT
1 TTGAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACCT
*
464581 TTGAATCTATTTTCCTTGAAACAAATTTCGTCTCCC
66 TTGAATCTATCTTCCTTGAAACAAATTTCGTCTCCC
* *
464617 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACCT
1 TTGAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACCT
464682 TTGAAAT-T-TCTTCTCTTGAAACA
66 TTG-AATCTATCTTC-CTTGAAACA
464705 CAAAAAAAAC
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
100 4 0.05
101 74 0.91
102 3 0.04
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (101 bp):
TTGAGACAGTTTCCATTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACCT
TTGAATCTATCTTCCTTGAAACAAATTTCGTCTCCC
Found at i:464715 original size:35 final size:34
Alignment explanation
Indices: 464675--464743 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
464665 CCCTTGAAAC
* *
464675 AAAACCTTT-GAAATTTCTTCTCTTGAAACACAAAA
1 AAAACCTTTAAAAATGT-TTCTCTTGAAACA-AAAA
464710 AAAACCTTTAAAAATGTTTCTCTTGAAACAAAAA
1 AAAACCTTTAAAAATGTTTCTCTTGAAACAAAAA
464744 CCCTTCGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 4 0.13
35 22 0.71
36 5 0.16
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.30
Consensus pattern (34 bp):
AAAACCTTTAAAAATGTTTCTCTTGAAACAAAAA
Found at i:466644 original size:19 final size:18
Alignment explanation
Indices: 466620--466656 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
466610 CAAAGTATAT
466620 TTATTCACGTATTTTTTTA
1 TTATTCA-GTATTTTTTTA
*
466639 TTATTCATTATTTTTTTA
1 TTATTCAGTATTTTTTTA
466657 ATAGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.68
Consensus pattern (18 bp):
TTATTCAGTATTTTTTTA
Found at i:466731 original size:2 final size:2
Alignment explanation
Indices: 466682--466712 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
466672 TTTTATTATT
466682 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 T
466713 TTACATGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:466804 original size:3 final size:3
Alignment explanation
Indices: 466778--466841 Score: 62
Period size: 3 Copynumber: 21.3 Consensus size: 3
466768 TTAGTTTCTT
* *
466778 TTA TTT TTA TT- TT- TTA TT- TTA TTA TTA CTA TTA TATA CTTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TT-A TTA
466823 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
466842 ATTTTATATG
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 6 0.12
3 39 0.75
4 5 0.10
5 2 0.04
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:466857 original size:25 final size:24
Alignment explanation
Indices: 466820--466880 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
466810 ATATACTTCA
* *
466820 TTATTATTATTATTATTATTATATT
1 TTATCATTTTTATTATTATT-TATT
* *
466845 TTAT-ATGTTTTATTTTTATTTTTT
1 TTATCAT-TTTTATTATTATTTATT
466869 TTATCATTTTTA
1 TTATCATTTTTA
466881 AAACATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 14 0.45
25 17 0.55
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (24 bp):
TTATCATTTTTATTATTATTTATT
Found at i:466947 original size:21 final size:21
Alignment explanation
Indices: 466921--466965 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
466911 ATTTGTTCCT
466921 TTTATTTTATT-TTATTTTCTC
1 TTTA-TTTATTATTATTTTCTC
*
466942 TTTATTTATTATTATTTTTTC
1 TTTATTTATTATTATTTTCTC
466963 TTT
1 TTT
466966 TACATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATTTATTATTATTTTCTC
Found at i:467080 original size:10 final size:10
Alignment explanation
Indices: 467016--467131 Score: 55
Period size: 10 Copynumber: 11.4 Consensus size: 10
467006 TTATTTACCT
467016 TTTTTATTTA
1 TTTTTATTTA
*
467026 TTTATATTTA
1 TTTTTATTTA
467036 TATTTATATTT-
1 T-TTT-TATTTA
*
467047 TCTTTTTTTTA
1 T-TTTTATTTA
*
467058 -CTTTATTT-
1 TTTTTATTTA
*
467066 CTTTTATTTA
1 TTTTTATTTA
* *
467076 TTTTTCTTAA
1 TTTTTATTTA
467086 TTTTT-TATTA
1 TTTTTAT-TTA
*
467096 TTGTTATTT-
1 TTTTTATTTA
467105 TTGCTTTATTTTA
1 TT--TTTA-TTTA
467118 TTTGTT-TTTA
1 TTT-TTATTTA
467128 TTTT
1 TTTT
467132 CTTTATTCTA
Statistics
Matches: 81, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
9 17 0.21
10 41 0.51
11 11 0.14
12 10 0.12
13 2 0.02
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:467106 original size:50 final size:50
Alignment explanation
Indices: 467017--467115 Score: 119
Period size: 50 Copynumber: 2.0 Consensus size: 50
467007 TATTTACCTT
* *
467017 TTTTATTTATTTATATTTATATTTATATTTTCTTTTTTTTACTTTATTTC
1 TTTTATTTATTTATATTAATATTTATATTTTCTTATTTTTACTTTATTTC
* * * * *
467067 TTTTATTTATTTTTCTTAAT-TTTTTATTATTGTTATTTTTGCTTTATTT
1 TTTTATTTATTTATATTAATATTTATATT-TTCTTATTTTTACTTTATTT
467116 TATTTGTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 7 0.17
50 34 0.83
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (50 bp):
TTTTATTTATTTATATTAATATTTATATTTTCTTATTTTTACTTTATTTC
Found at i:467149 original size:24 final size:25
Alignment explanation
Indices: 467103--467149 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
467093 TTATTGTTAT
* **
467103 TTTTGCTTTATTTTATTTGTTTTTA
1 TTTTGCTTTATTCTATTCATTTTTA
467128 TTTT-CTTTATTCTATTCATTTT
1 TTTTGCTTTATTCTATTCATTTT
467150 CGTTTTTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGCTTTATTCTATTCATTTTTA
Found at i:469003 original size:35 final size:37
Alignment explanation
Indices: 468961--469032 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
468951 AATTGGATGT
* *
468961 AATTTAAAATATTA-A-TCTTTTTAATATTTTTGGTTA
1 AATTAAAAATATTACATTC-TTGTAATATTTTTGGTTA
*
468997 AATTAAAAATGTTACATTCTTGTAATATTTTTGGTT
1 AATTAAAAATATTACATTCTTGTAATATTTTTGGTT
469033 GACAATCGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 12 0.39
37 17 0.55
38 2 0.06
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (37 bp):
AATTAAAAATATTACATTCTTGTAATATTTTTGGTTA
Found at i:469815 original size:10 final size:10
Alignment explanation
Indices: 469802--469856 Score: 56
Period size: 10 Copynumber: 5.2 Consensus size: 10
469792 CAAATGAACA
469802 AACATAAATG
1 AACATAAATG
469812 AACACAATAAATG
1 -A-AC-ATAAATG
*
469825 AACATAAATA
1 AACATAAATG
* *
469835 AACGTAAACG
1 AACATAAATG
469845 AACATAAATG
1 AACATAAATG
469855 AA
1 AA
469857 AATATACTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 23 0.64
11 3 0.08
12 3 0.08
13 7 0.19
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.16
Consensus pattern (10 bp):
AACATAAATG
Found at i:469823 original size:13 final size:14
Alignment explanation
Indices: 469784--469856 Score: 69
Period size: 14 Copynumber: 5.1 Consensus size: 14
469774 AACGGATGTA
*
469784 AACAAACACAAATG
1 AACAAACATAAATG
469798 AACAAACATAAATG
1 AACAAACATAAATG
*
469812 AACACA-ATAAATG
1 AACAAACATAAATG
*
469825 AACATAA-ATAAACGTA
1 AACA-AACATAAA--TG
*
469841 AACGAACATAAATG
1 AACAAACATAAATG
469855 AA
1 AA
469857 AATATACTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
13 11 0.22
14 27 0.55
15 2 0.04
16 9 0.18
ACGTcount: A:0.63, C:0.15, G:0.08, T:0.14
Consensus pattern (14 bp):
AACAAACATAAATG
Found at i:470137 original size:24 final size:23
Alignment explanation
Indices: 470025--470142 Score: 112
Period size: 24 Copynumber: 5.0 Consensus size: 23
470015 TGGGCTAAAT
* *
470025 ATAAATGAACGCACATAAATGAAC
1 ATAAATGAAC-AACATAAACGAAC
*
470049 ATAAACGAACAAACA-AAACGAAC
1 ATAAATGAAC-AACATAAACGAAC
*
470072 ATTAATGAACATACATAAACGAAC
1 ATAAATGAACA-ACATAAACGAAC
* * *
470096 ATAAATGAATGACCATAAACAAAC
1 ATAAATGAA-CAACATAAACGAAC
*
470120 ATAAATGAACAAGTATAAACGAA
1 ATAAATGAACAA-CATAAACGAA
470143 TATATTACCG
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
22 1 0.01
23 19 0.25
24 55 0.72
25 1 0.01
ACGTcount: A:0.58, C:0.16, G:0.10, T:0.15
Consensus pattern (23 bp):
ATAAATGAACAACATAAACGAAC
Found at i:472108 original size:17 final size:17
Alignment explanation
Indices: 472086--472127 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
472076 TTTTGTACTA
472086 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
472103 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
472120 TTAATGAA
1 TAAATGAA
472128 CAACACACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:482855 original size:10 final size:11
Alignment explanation
Indices: 482840--482868 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
482830 CGATTATGAA
482840 TTAAGTATG-T
1 TTAAGTATGTT
482850 TTAAGTATGTT
1 TTAAGTATGTT
482861 TTAAGTAT
1 TTAAGTAT
482869 AAACATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (11 bp):
TTAAGTATGTT
Found at i:488659 original size:21 final size:22
Alignment explanation
Indices: 488635--488689 Score: 94
Period size: 21 Copynumber: 2.5 Consensus size: 22
488625 AAACCATTCA
488635 GGGGGAATCGGTAACCCCTT-G
1 GGGGGAATCGGTAACCCCTTGG
*
488656 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTAACCCCTTGG
488678 GGGGGAATCGGT
1 GGGGGAATCGGT
488690 TCCCTCTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (22 bp):
GGGGGAATCGGTAACCCCTTGG
Done.