Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009583.1 Hibiscus syriacus cultivar Beakdansim tig00116960_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: 1341443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1155343 original size:16 final size:16
Alignment explanation
Indices: 1155324--1155384 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
1155314 AAGTGTTAAG
1155324 GTGTTAAAGGGGAGAA
1 GTGTTAAAGGGGAGAA
* *
1155340 GTGTTAAAGTAAGGGGGAGG
1 GTGTTAAAG---GGGAGA-A
*
1155360 GTGATAAAGGGGAGAA
1 GTGTTAAAGGGGAGAA
1155376 GTGTTAAAG
1 GTGTTAAAG
1155385 TAAGGGGGAG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
16 17 0.49
17 5 0.14
19 5 0.14
20 8 0.23
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (16 bp):
GTGTTAAAGGGGAGAA
Found at i:1155355 original size:20 final size:20
Alignment explanation
Indices: 1155330--1155391 Score: 69
Period size: 18 Copynumber: 3.3 Consensus size: 20
1155320 TAAGGTGTTA
1155330 AAGGGGAGAAGTGTTAAAGT
1 AAGGGGAGAAGTGTTAAAGT
* * *
1155350 AAGGGG-G-AGGGTGATA--
1 AAGGGGAGAAGTGTTAAAGT
1155366 AAGGGGAGAAGTGTTAAAGT
1 AAGGGGAGAAGTGTTAAAGT
1155386 AAGGGG
1 AAGGGG
1155392 GAGTAATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 6 0.19
17 1 0.03
18 12 0.38
19 1 0.03
20 12 0.38
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.16
Consensus pattern (20 bp):
AAGGGGAGAAGTGTTAAAGT
Found at i:1155375 original size:36 final size:36
Alignment explanation
Indices: 1155323--1155394 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1155313 GAAGTGTTAA
*
1155323 GGTGTTAAAGGGGAGAAGTGTTAAAGTAAGGGGGAG
1 GGTGATAAAGGGGAGAAGTGTTAAAGTAAGGGGGAG
1155359 GGTGATAAAGGGGAGAAGTGTTAAAGTAAGGGGGAG
1 GGTGATAAAGGGGAGAAGTGTTAAAGTAAGGGGGAG
1155395 TAATTTCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (36 bp):
GGTGATAAAGGGGAGAAGTGTTAAAGTAAGGGGGAG
Found at i:1157395 original size:201 final size:201
Alignment explanation
Indices: 1157049--1158404 Score: 1642
Period size: 201 Copynumber: 6.8 Consensus size: 201
1157039 CAAGAACAAT
* *
1157049 TATCTGTCAACGAAAACTTTCAAGTTCGATTCTATTCAGCTCAAGGGT-TATCAACCGCATGGTA
1 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
* * * *
1157113 GAAGCGAGGAACTACTTTCCGGTTGAAGTTTAAACCGATGTCTTTAAGCCAAGAAGAAGACCTAG
66 GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
* * *
1157178 GTTGGCTGTGATTTAGCGACAAGGAA-TAATCTCCCAGCCTAATTTACAACATAGCTTAAGTCGA
131 GTTGGCTGCGATTTAGCAACAAGGAACT-ATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGA
1157242 GAAAAGC
195 GAAAAGC
* * ** * * * *
1157249 TATCTGTTAATGAAAACTTTTGAGTTCAATTCCATTCAGCTTGAGGGCATATCAACCGTATGGTA
1 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
* * * * * * *
1157314 GCAGTGATGAAATTCTTTCCGGTTGAATTTTAAACTGAGGTATTTAAACCCAGAAGAAGACCTAG
66 GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
* * * * *
1157379 ATTGACTGCAATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTTGTG
131 GTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGAG
1157444 AAAAGC
196 AAAAGC
* * * *
1157450 TATCTGTCAATGAAAACTTTTAAGTTCGATTCCATTCAGGTCGATGGTATATCAACCGCATGGTA
1 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
* * * *
1157515 GCAGCAAGGAACTACTTTTCGTTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACTTAG
66 GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
* * * * * *
1157580 GTTGGCTGCGATTTAACAACAAGTAACTATCTCCCAGCCTAATATATAGCATATCTTAAGTTGAG
131 GTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGAG
1157645 AAAAGC
196 AAAAGC
* * * *
1157651 TATATGTCAACGAAAACTTTCAATTTCGATTCCATTCAGCTCGAGGATATATCAACTGCATGGTA
1 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
* * * * * *
1157716 GCAACGGGGAATTACTTTTCGGTTAAATTTTAAA-CGAGGTCTTTAAGCCTAGAAGAAGACCTAG
66 GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
* * * * *
1157780 GTTGGCTGCGATTTAGCAATAAGAAACTATCTCCTAGCCTAATTTACAGTATATCTTAAGTCGAG
131 GTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGAG
*
1157845 AAAAGT
196 AAAAGC
* *
1157851 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCATCTCGAGAGTATATCAACCGCATGGTA
1 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
* * *
1157916 GCAGCGAGGAACTACTTTTCAGTTGAATTTTAAACCGAGGTCTTTAAACCCAGAAGAAGACCTAG
66 GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
* * * *
1157981 GTTGGCTACGATTTAGCAACAATGAACTATCTCCCAGCCTAATTTACAGCATAGCTTGACTCGAG
131 GTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGAG
1158046 AAAAGC
196 AAAAGC
* * * * * * * *
1158052 TATCTGTCAACAAAAACTTTCTAGTTCTATTCCATTCAG--CAATGATATATCAACTGAATGGTA
1 TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
* ** * * *
1158115 GTAATGAGGAACTACTTTCTGGTTGAAGTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAG
66 GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
* * * * * *
1158180 GTTGACTGCGATTTAGCGACAAGGAACTATCTCTCAGTCTAGTTTACAGTATAGCTTAAGTCGAG
131 GTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGAG
*
1158245 AAAAGA
196 AAAAGC
* * * * * * * * ** * *
1158251 TGTATGTCAACAAAAAACTTTCGAGTTTGATTCCATTCAGTTCAATGGCGTATCTACTGCATGGT
1 TATCTGTCAAC-GAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGT
* * * * ** * * *
1158316 AGCAACAAGGAACTATTTTTCTATTGAATTTCAAACCGAGGTCTTTAAGCCAAGAAGAAGACATA
65 AGCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTA
* * *
1158381 GGTTGACTACGATTTGGCAACAAG
130 GGTTGGCTGCGATTTAGCAACAAG
1158405 AAGCCACTTT
Statistics
Matches: 991, Mismatches: 159, Indels: 10
0.85 0.14 0.01
Matches are distributed among these distances:
199 143 0.14
200 242 0.24
201 512 0.52
202 94 0.09
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (201 bp):
TATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCGAGGGTATATCAACCGCATGGTA
GCAGCGAGGAACTACTTTCCGGTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACCTAG
GTTGGCTGCGATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGAG
AAAAGC
Found at i:1157934 original size:401 final size:401
Alignment explanation
Indices: 1157048--1158404 Score: 1692
Period size: 401 Copynumber: 3.4 Consensus size: 401
1157038 GCAAGAACAA
* *
1157048 TTATCTGTCAACGAAAACTTTCAAGTTCGATTCTATTCAGCTCAAGGGT-TATCAACCGCATGGT
1 TTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCAATGGTATATCAACCGCATGGT
* * * * * *
1157112 AGAAGCGAGGAACTACTTTCCGGTTGAAGTTTAAACCGATGTCTTTAAGCCAAGAAGAAGACCTA
66 AGCAGCAAGGAACTACTTTTCGTTTGAATTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTA
** * * *
1157177 GGTTGGCTGTGATTTAGCGACAAGGAA-TAATCTCCCAGCCTAATTTACAACATAGCTTAAGTCG
131 GGTTGGCTACGATTTAGCAACAAGTAACT-ATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCG
* * ** * ** *
1157241 AGAAAAGCTATCTGTTAATGAAAACTTTTGAGTTCAATTCCATTCAGCTTGAGGGCATATCAACC
195 AGAAAAGCTATCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGGATATATCAACT
* * * * * * *
1157306 GTATGGTAGCAGTGATGAAATT-CTTTCCGGTTGAATTTTAAACTGAGGTATTTAAACCCAGAAG
260 GAATGGTAGCAATGA-GGAATTACTTTTCGGTTGAATTTTAAAC-GAGGTCTTTAAGCCAAGAAG
* * * *
1157370 AAGACCTAGATTGACTGCAATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCT
323 AAGACCTAGGTTGACTGCGATTTAGCAACAAGGAACTATCTCCTAGCCTAATTTACAGTATAGCT
* *
1157435 TAAGTTGTGAAAAG
388 TAAGTCGAGAAAAG
* * * * *
1157449 CTATCTGTCAATGAAAACTTTTAAGTTCGATTCCATTCAGGTCGATGGTATATCAACCGCATGGT
1 TTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCAATGGTATATCAACCGCATGGT
* *
1157514 AGCAGCAAGGAACTACTTTTCGTTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGAAGACTTA
66 AGCAGCAAGGAACTACTTTTCGTTTGAATTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTA
* * * * * *
1157579 GGTTGGCTGCGATTTAACAACAAGTAACTATCTCCCAGCCTAATATATAGCATATCTTAAGTTGA
131 GGTTGGCTACGATTTAGCAACAAGTAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGA
* * *
1157644 GAAAAGCTATATGTCAACGAAAACTTTCAATTTCGATTCCATTCAGCTCGAGGATATATCAACTG
196 GAAAAGCTATCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGGATATATCAACTG
* * * * *
1157709 CATGGTAGCAACGGGGAATTACTTTTCGGTTAAATTTTAAACGAGGTCTTTAAGCCTAGAAGAAG
261 AATGGTAGCAATGAGGAATTACTTTTCGGTTGAATTTTAAACGAGGTCTTTAAGCCAAGAAGAAG
* * * *
1157774 ACCTAGGTTGGCTGCGATTTAGCAATAAGAAACTATCTCCTAGCCTAATTTACAGTATATCTTAA
326 ACCTAGGTTGACTGCGATTTAGCAACAAGGAACTATCTCCTAGCCTAATTTACAGTATAGCTTAA
1157839 GTCGAGAAAAG
391 GTCGAGAAAAG
* *
1157850 TTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCATCTCGA-GAGTATATCAACCGCATGG
1 TTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCAATG-GTATATCAACCGCATGG
* * *
1157914 TAGCAGCGAGGAACTACTTTTCAG-TTGAATTTTAAACCGAGGTCTTTAAACCCAGAAGAAGACC
65 TAGCAGCAAGGAACTACTTTTC-GTTTGAATTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACC
* *
1157978 TAGGTTGGCTACGATTTAGCAACAA-TGAACTATCTCCCAGCCTAATTTACAGCATAGCTTGACT
129 TAGGTTGGCTACGATTTAGCAACAAGT-AACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGT
* * * * *
1158042 CGAGAAAAGCTATCTGTCAACAAAAACTTTCTAGTTCTATTCCATTCAG--CAATGATATATCAA
193 CGAGAAAAGCTATCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGGATATATCAA
* * *
1158105 CTGAATGGTAGTAATGAGGAACTAC-TTTCTGGTTGAAGTTTAAACCGAGGTCTTTAAGCCAAGA
258 CTGAATGGTAGCAATGAGGAATTACTTTTC-GGTTGAATTTTAAA-CGAGGTCTTTAAGCCAAGA
* * *
1158169 AGAAGACCTAGGTTGACTGCGATTTAGCGACAAGGAACTATCT-CTCAGTCTAGTTTACAGTATA
321 AGAAGACCTAGGTTGACTGCGATTTAGCAACAAGGAACTATCTCCT-AGCCTAATTTACAGTATA
1158233 GCTTAAGTCGAGAAAAG
385 GCTTAAGTCGAGAAAAG
* * * * * * * ** * *
1158250 ATGTATGTCAACAAAAAACTTTCGAGTTTGATTCCATTCAGTTCAATGGCGTATCTACTGCATGG
1 TTATCTGTCAAC-GAAAACTTTCAAGTTCGATTCCATTCAGCTCAATGGTATATCAACCGCATGG
* * * *
1158315 TAGCAACAAGGAACTATTTTTC-TATTGAATTTCAAACCGAGGTCTTTAAGCCAAGAAGAAGACA
65 TAGCAGCAAGGAACTACTTTTCGT-TTGAATTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACC
* *
1158379 TAGGTTGACTACGATTTGGCAACAAG
129 TAGGTTGGCTACGATTTAGCAACAAG
1158405 AAGCCACTTT
Statistics
Matches: 827, Mismatches: 115, Indels: 27
0.85 0.12 0.03
Matches are distributed among these distances:
398 4 0.00
399 46 0.06
400 100 0.12
401 465 0.56
402 211 0.26
403 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (401 bp):
TTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCAGCTCAATGGTATATCAACCGCATGGT
AGCAGCAAGGAACTACTTTTCGTTTGAATTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTA
GGTTGGCTACGATTTAGCAACAAGTAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTCGA
GAAAAGCTATCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGGATATATCAACTG
AATGGTAGCAATGAGGAATTACTTTTCGGTTGAATTTTAAACGAGGTCTTTAAGCCAAGAAGAAG
ACCTAGGTTGACTGCGATTTAGCAACAAGGAACTATCTCCTAGCCTAATTTACAGTATAGCTTAA
GTCGAGAAAAG
Found at i:1158358 original size:602 final size:599
Alignment explanation
Indices: 1157053--1158406 Score: 1723
Period size: 602 Copynumber: 2.2 Consensus size: 599
1157043 AACAATTATC
* * *
1157053 TGTCAACGAAAACTTTCAAGTTCGATTCTATTCAGCTCAAGGGTTATCAACCGCATGGTAG-AAG
1 TGTCAACGAAAACTTTC-AGTTTGATTCCATTCAGCTCAAGGG-TATCAACTGCATGGTAGCAA-
* *
1157117 CGAGGAACTACTTTCCGGTTGAAGTTTAAACCGATGTCTTTAAGCCAAGAAGAAGACCTAGGTTG
63 CGAGGAACTACTTTTCGGTTGAA-TTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTG
* * *
1157182 GCTGTGATTTAGCGACAAGGAATAATCTCCCAGCCTAATTTACAACATAGCTTAAGTCGAGAAAA
127 GCTGCGATTTAGCAACAAGAAATAATCTCCCAGCCTAATTTACAACATAGCTTAAGTCGAGAAAA
* * ** * * *
1157247 GCTATCTGTTAATGAAAACTTTTGAGTTCAATTCCATTCAGCTTGAGGGCATATCAACCGTATGG
192 GCTATCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGAGCATATCAACCGCATGG
* * * * *
1157312 TAGCAGTGATGAAATTCTTTCCGGTTGAATTTTAAACTGAGGTATTTAAACCCAGAAGAAGACCT
257 TAGCAGCGAGGAAATACTTTCCAGTTGAATTTTAAACCGAGGTATTTAAACCCAGAAGAAGACCT
* * *
1157377 AGATTGACTGCAATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAAGTTG
322 AGATTGACTACAATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAACTCG
* ** * *
1157442 TGAAAAGCTATCTGTCAATGAAAACTTTTAAGTTCGATTCCATTCAGGTCGATGGTATATCAACC
387 AGAAAAGCTATCTGTCAACAAAAACTTTTAAGTTCGATTCCATTCAGGTCAATGATATATCAACC
* * * * *
1157507 GCATGGTAGCAGCAAGGAACTACTTTTCGTTTGAATTTTAAACCGAGGTCTTTAAGCCCAGAAGA
452 GAATGGTAGCAACAAGGAACTACTTTTCGGTTGAAGTTTAAACCGAGGTCTTTAAGCCAAGAAGA
* * * * *
1157572 AGACTTAGGTTGGCTGCGATTTAACAACAAGTAACTATCTCCCAGCCTAATATATAGCATATCTT
517 AGACCTAGGTTGACTGCGATTTAACAACAAGGAACTATCTCCCAGCCTAATATACAGCATAGCTT
* *
1157637 AAGTTGAGAAAAGCTATA
582 AAGTCGAGAAAAGATATA
* * *
1157655 TGTCAACGAAAACTTTCAATTTCGATTCCATTCAGCTCGAGGATATATCAACTGCATGGTAGCAA
1 TGTCAACGAAAACTTTCAGTTT-GATTCCATTCAGCTCAAGG--GTATCAACTGCATGGTAGCAA
* * * *
1157720 CGGGGAATTACTTTTCGGTTAAATTTTAAA-CGAGGTCTTTAAGCCTAGAAGAAGACCTAGGTTG
63 CGAGGAACTACTTTTCGGTTGAA-TTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTG
* * ** *
1157784 GCTGCGATTTAGCAATAAGAAACT-ATCTCCTAGCCTAATTTACAGTATATCTTAAGTCGAGAAA
127 GCTGCGATTTAGCAACAAGAAA-TAATCTCCCAGCCTAATTTACAACATAGCTTAAGTCGAGAAA
* * * *
1157848 AGTTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTCATCTCGAGAGTATATCAACCGCATG
191 AGCTATCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGAGCATATCAACCGCATG
* * *
1157913 GTAGCAGCGAGGAACTACTTTTCAGTTGAATTTTAAACCGAGGTCTTTAAACCCAGAAGAAGACC
256 GTAGCAGCGAGGAAATACTTTCCAGTTGAATTTTAAACCGAGGTATTTAAACCCAGAAGAAGACC
* * * * *
1157978 TAGGTTGGCTACGATTTAGCAACAATGAACTATCTCCCAGCCTAATTTACAGCATAGCTTGACTC
321 TAGATTGACTACAATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAACTC
*
1158043 GAGAAAAGCTATCTGTCAACAAAAACTTTCT-AGTTCTATTCCATTCA-G-CAATGATATATCAA
386 GAGAAAAGCTATCTGTCAACAAAAACTTT-TAAGTTCGATTCCATTCAGGTCAATGATATATCAA
* * **
1158105 CTGAATGGTAGTAATGAGGAACTAC-TTTCTGGTTGAAGTTTAAACCGAGGTCTTTAAGCCAAGA
450 CCGAATGGTAGCAACAAGGAACTACTTTTC-GGTTGAAGTTTAAACCGAGGTCTTTAAGCCAAGA
* * * * * * *
1158169 AGAAGACCTAGGTTGACTGCGATTTAGCGACAAGGAACTATCTCTCAGTCTAGTTTACAGTATAG
514 AGAAGACCTAGGTTGACTGCGATTTAACAACAAGGAACTATCTCCCAGCCTAATATACAGCATAG
*
1158234 CTTAAGTCGAGAAAAGATGTA
579 CTTAAGTCGAGAAAAGATATA
* * *
1158255 TGTCAACAAAAAACTTTCGAGTTTGATTCCATTCAGTTCAATGGCGTATCTACTGCATGGTAGCA
1 TGTCAAC-GAAAACTTTC-AGTTTGATTCCATTCAGCTCAA-GG-GTATCAACTGCATGGTAGCA
* * ** *
1158320 ACAAGGAACTATTTTTCTATTGAATTTCAAACCGAGGTCTTTAAGCCAAGAAGAAGACATAGGTT
62 ACGAGGAACTACTTTTCGGTTGAATTT-AAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTT
* * *
1158385 GACTACGATTTGGCAACAAGAA
126 GGCTGCGATTTAGCAACAAGAA
1158407 GCCACTTTCT
Statistics
Matches: 642, Mismatches: 98, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
599 4 0.01
600 143 0.22
601 66 0.10
602 384 0.60
603 43 0.07
604 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (599 bp):
TGTCAACGAAAACTTTCAGTTTGATTCCATTCAGCTCAAGGGTATCAACTGCATGGTAGCAACGA
GGAACTACTTTTCGGTTGAATTTAAACCGAGGTCTTTAAGCCAAGAAGAAGACCTAGGTTGGCTG
CGATTTAGCAACAAGAAATAATCTCCCAGCCTAATTTACAACATAGCTTAAGTCGAGAAAAGCTA
TCTGTCAACGAAAACTTTCAAGTTCAATTCCATTCAGCTCGAGAGCATATCAACCGCATGGTAGC
AGCGAGGAAATACTTTCCAGTTGAATTTTAAACCGAGGTATTTAAACCCAGAAGAAGACCTAGAT
TGACTACAATTTAGCAACAAGGAACTATCTCCCAGCCTAATTTACAGCATAGCTTAACTCGAGAA
AAGCTATCTGTCAACAAAAACTTTTAAGTTCGATTCCATTCAGGTCAATGATATATCAACCGAAT
GGTAGCAACAAGGAACTACTTTTCGGTTGAAGTTTAAACCGAGGTCTTTAAGCCAAGAAGAAGAC
CTAGGTTGACTGCGATTTAACAACAAGGAACTATCTCCCAGCCTAATATACAGCATAGCTTAAGT
CGAGAAAAGATATA
Found at i:1158903 original size:2 final size:2
Alignment explanation
Indices: 1158898--1158926 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1158888 ATTTTTGAAA
1158898 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 A
1158927 GTTTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1158903 original size:21 final size:19
Alignment explanation
Indices: 1158870--1158947 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
1158860 CAATATATGG
1158870 TTTTTAAAAATATATATAA
1 TTTTTAAAAATATATATAA
*
1158889 TTTTTGAAAATATATATATA
1 TTTTTAAAAATATATATA-A
* * * * *
1158909 TATATATATATATATATAG
1 TTTTTAAAAATATATATAA
*
1158928 TTTTGAAAACATATAATATA
1 TTTTTAAAA-ATAT-ATATA
1158948 TATAGCTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 21 0.48
20 18 0.41
21 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (19 bp):
TTTTTAAAAATATATATAA
Found at i:1158926 original size:39 final size:37
Alignment explanation
Indices: 1158879--1158951 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1158869 GTTTTTAAAA
* *
1158879 ATATATATA-ATTTTTGAAAATATATATATATATATAT
1 ATATATATATAGTTTTGAAAACATATA-ATATATATAT
1158916 ATATATATATAGTTTTGAAAACATATAATATATATA
1 ATATATATATAGTTTTGAAAACATATAATATATATA
1158952 GCTTTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATATATAGTTTTGAAAACATATAATATATATAT
Found at i:1158950 original size:25 final size:27
Alignment explanation
Indices: 1158912--1158962 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
1158902 ATATATATAT
1158912 ATATATATATATATAG-TTTTGAAAAC
1 ATATATATATATATAGCTTTTGAAAAC
1158938 ATATA-ATATATATAGCTTTTGAAAA
1 ATATATATATATATAGCTTTTGAAAA
1158963 TAGTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (27 bp):
ATATATATATATATAGCTTTTGAAAAC
Found at i:1159014 original size:19 final size:20
Alignment explanation
Indices: 1158990--1159030 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1158980 AAACATATAT
1158990 AATATA-TATAATTTTTGAA
1 AATATATTATAATTTTTGAA
*
1159009 AATATATTATAGTTTTTGAA
1 AATATATTATAATTTTTGAA
1159029 AA
1 AA
1159031 CAATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (20 bp):
AATATATTATAATTTTTGAA
Found at i:1159059 original size:14 final size:14
Alignment explanation
Indices: 1159040--1159095 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
1159030 ACAATATATG
1159040 TTATATAGTT-TTTA
1 TTATATA-TTATTTA
1159054 TTATATATTATTTA
1 TTATATATTATTTA
1159068 TTAT-TA-TATATTA
1 TTATATATTAT-TTA
*
1159081 TTATTTATTTATTTA
1 TTATATA-TTATTTA
1159096 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 11 0.30
14 17 0.46
15 3 0.08
16 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTATATATTATTTA
Found at i:1159072 original size:10 final size:10
Alignment explanation
Indices: 1159054--1159089 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1159044 ATAGTTTTTA
1159054 TTATATATTAT
1 TTAT-TATTAT
1159065 TTATTATTAT
1 TTATTATTAT
*
1159075 ATATTATTAT
1 TTATTATTAT
1159085 TTATT
1 TTATT
1159090 TATTTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (10 bp):
TTATTATTAT
Found at i:1159088 original size:17 final size:16
Alignment explanation
Indices: 1159048--1159103 Score: 71
Period size: 17 Copynumber: 3.5 Consensus size: 16
1159038 TGTTATATAG
1159048 TTTTTATTATATATTA
1 TTTTTATTATATATTA
1159064 TTTATTATTATATATTA
1 TTT-TTATTATATATTA
1159081 TTATTTATT-TAT-TTA
1 TT-TTTATTATATATTA
*
1159096 ATTTTATT
1 TTTTTATT
1159104 TTTTTTAGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.16
15 4 0.11
16 6 0.16
17 20 0.54
18 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTTATTATATATTA
Found at i:1162156 original size:11 final size:11
Alignment explanation
Indices: 1162127--1162160 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1162117 CCACCACCTG
*
1162127 TTTTTAATTTA
1 TTTTTAAATTA
1162138 TATTTTAAATTA
1 T-TTTTAAATTA
1162150 TTTTTAAATTA
1 TTTTTAAATTA
1162161 AATAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTTAAATTA
Found at i:1163245 original size:30 final size:32
Alignment explanation
Indices: 1163203--1163280 Score: 99
Period size: 31 Copynumber: 2.5 Consensus size: 32
1163193 CGGGGTCTAT
*
1163203 TTAAAAGTTTCAAAAA-TCTTGGAGG-TTTAAA
1 TTAAAAGTTTCAAAAAGT-TTGAAGGATTTAAA
*
1163234 TTAAAA-TTTCAAAAAGTTTGAAGGATTTAAT
1 TTAAAAGTTTCAAAAAGTTTGAAGGATTTAAA
*
1163265 TTAAAATTTTCAAAAA
1 TTAAAAGTTTCAAAAA
1163281 ATGGAGGTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 15 0.36
31 18 0.43
32 9 0.21
ACGTcount: A:0.46, C:0.05, G:0.12, T:0.37
Consensus pattern (32 bp):
TTAAAAGTTTCAAAAAGTTTGAAGGATTTAAA
Found at i:1165394 original size:27 final size:27
Alignment explanation
Indices: 1165356--1165408 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1165346 CTCGATTCGA
*
1165356 AAAAACTAATCTTTTCGGCTCAACTCG
1 AAAAACTAATCTTTTCGACTCAACTCG
*
1165383 AAAAACTGATCTTTTCGACTCAACTC
1 AAAAACTAATCTTTTCGACTCAACTC
1165409 AACAAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.30
Consensus pattern (27 bp):
AAAAACTAATCTTTTCGACTCAACTCG
Found at i:1168597 original size:167 final size:170
Alignment explanation
Indices: 1168411--1168748 Score: 655
Period size: 167 Copynumber: 2.0 Consensus size: 170
1168401 GAATAGATGT
1168411 TTAGTGTTGAAAATGATGAAATGTCAAGACAATGAAAAATGGTAAAAACAGTAAATAAAAGATAA
1 TTAGTGTTGAAAATGATGAAATGTCAAGACAATGAAAAATGGTAAAAACAGTAAATAAAAGATAA
1168476 ATAAAATGAAAA-AAGATAATCCTCACGTGACAAGC-TTCAATGGAATGAATGGTAGGGATTGAT
66 ATAAAATGAAAAGAAGATAATCCTCACGTGACAAGCTTTCAATGGAATGAATGGTAGGGATTGAT
1168539 CTAAGAATGCTAAACTGATCTCTCAGGAAGA-TTAAGCTA
131 CTAAGAATGCTAAACTGATCTCTCAGGAAGATTTAAGCTA
1168578 TTAGTGTTGAAAATGATGAAATGTCAAGACAATGAAAAATGGTAAAAACAGTAAATAAAAGATAA
1 TTAGTGTTGAAAATGATGAAATGTCAAGACAATGAAAAATGGTAAAAACAGTAAATAAAAGATAA
1168643 ATAAAATGAAAAGAAGATAATCCTCACGTGACAAGCTTTCAATGGAATGAATGGTAGGGATTGAT
66 ATAAAATGAAAAGAAGATAATCCTCACGTGACAAGCTTTCAATGGAATGAATGGTAGGGATTGAT
1168708 CTAAGAATGCTAAACTGATCTCTCAGGAAGATTTAAGCTA
131 CTAAGAATGCTAAACTGATCTCTCAGGAAGATTTAAGCTA
1168748 T
1 T
1168749 CTGGTCTTTA
Statistics
Matches: 168, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
167 77 0.46
168 23 0.14
169 59 0.35
170 9 0.05
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.25
Consensus pattern (170 bp):
TTAGTGTTGAAAATGATGAAATGTCAAGACAATGAAAAATGGTAAAAACAGTAAATAAAAGATAA
ATAAAATGAAAAGAAGATAATCCTCACGTGACAAGCTTTCAATGGAATGAATGGTAGGGATTGAT
CTAAGAATGCTAAACTGATCTCTCAGGAAGATTTAAGCTA
Found at i:1169183 original size:23 final size:23
Alignment explanation
Indices: 1169139--1169187 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1169129 ATAAAGAACC
*
1169139 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
1169162 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
1169185 AAA
1 AAA
1169188 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:1170943 original size:5 final size:5
Alignment explanation
Indices: 1170935--1170960 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1170925 ATGTGATACG
1170935 ATGCA ATGCA ATGCA ATGCA ATGCA A
1 ATGCA ATGCA ATGCA ATGCA ATGCA A
1170961 GGTACCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATGCA
Found at i:1174695 original size:23 final size:23
Alignment explanation
Indices: 1174651--1174697 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1174641 ATAAAGAACC
*
1174651 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
1174674 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
1174697 A
1 A
1174698 TACCAACCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:1182329 original size:15 final size:16
Alignment explanation
Indices: 1182303--1182334 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1182293 AACCAAAGGT
1182303 TCTCTATTTTATTTTC
1 TCTCTATTTTATTTTC
1182319 TCTCT-TTTTATTTTC
1 TCTCTATTTTATTTTC
1182334 T
1 T
1182335 TGTTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (16 bp):
TCTCTATTTTATTTTC
Found at i:1183006 original size:13 final size:13
Alignment explanation
Indices: 1182954--1183006 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1182944 ATAAATGAAG
*
1182954 ATGACACACATTTGT
1 ATGACATACA-TT-T
*
1182969 ATGACATAAATTT
1 ATGACATACATTT
*
1182982 ATGACATGCATTT
1 ATGACATACATTT
*
1182995 ATGACTTACATT
1 ATGACATACATT
1183007 GCGTGTCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 22 0.69
14 2 0.06
15 8 0.25
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (13 bp):
ATGACATACATTT
Found at i:1188721 original size:13 final size:13
Alignment explanation
Indices: 1188705--1188760 Score: 69
Period size: 13 Copynumber: 4.3 Consensus size: 13
1188695 CAATGCACGC
1188705 CATAAATGAGCGT
1 CATAAATGAGCGT
*
1188718 CATAAATGCGCGT
1 CATAAATGAGCGT
* *
1188731 CATAAATGTGTGT
1 CATAAATGAGCGT
1188744 CATAAAT-ACGCGT
1 CATAAATGA-GCGT
1188757 CATA
1 CATA
1188761 GATTTATGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (13 bp):
CATAAATGAGCGT
Found at i:1188726 original size:26 final size:26
Alignment explanation
Indices: 1188696--1188750 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1188686 AATGATGCTC
1188696 AATGCACGCCATAAATGAGCGTCATA
1 AATGCACGCCATAAATGAGCGTCATA
* * * *
1188722 AATGCGCGTCATAAATGTGTGTCATA
1 AATGCACGCCATAAATGAGCGTCATA
1188748 AAT
1 AAT
1188751 ACGCGTCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (26 bp):
AATGCACGCCATAAATGAGCGTCATA
Found at i:1188755 original size:26 final size:26
Alignment explanation
Indices: 1188705--1188760 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
1188695 CAATGCACGC
*
1188705 CATAAATGAGCGTCATAAATGCGCGT
1 CATAAATGAGCGTCATAAATACGCGT
* *
1188731 CATAAATGTGTGTCATAAATACGCGT
1 CATAAATGAGCGTCATAAATACGCGT
1188757 CATA
1 CATA
1188761 GATTTATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.27
Consensus pattern (26 bp):
CATAAATGAGCGTCATAAATACGCGT
Found at i:1189354 original size:16 final size:18
Alignment explanation
Indices: 1189333--1189374 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1189323 GGATATAAGA
1189333 GATATATGT-GT-TACGT
1 GATATATGTGGTATACGT
*
1189349 GATATATGTGGTATATGT
1 GATATATGTGGTATACGT
1189367 GATATATG
1 GATATATG
1189375 GAAAACACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
18 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (18 bp):
GATATATGTGGTATACGT
Found at i:1189365 original size:9 final size:9
Alignment explanation
Indices: 1189333--1189374 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1189323 GGATATAAGA
1189333 GATATATGT
1 GATATATGT
*
1189342 G-T-TACGT
1 GATATATGT
1189349 GATATATGT
1 GATATATGT
*
1189358 GGTATATGT
1 GATATATGT
1189367 GATATATG
1 GATATATG
1189375 GAAAACACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
7 5 0.19
8 2 0.07
9 20 0.74
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (9 bp):
GATATATGT
Found at i:1192869 original size:24 final size:24
Alignment explanation
Indices: 1192837--1192891 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
1192827 TTAGCTGGGT
1192837 AATGGATGATTTTCGGGTTTAAGG
1 AATGGATGATTTTCGGGTTTAAGG
1192861 AATGGATGATTTTCGGGTTTAAGG
1 AATGGATGATTTTCGGGTTTAAGG
1192885 AATGGAT
1 AATGGAT
1192892 TCTGGGTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.36
Consensus pattern (24 bp):
AATGGATGATTTTCGGGTTTAAGG
Found at i:1194474 original size:16 final size:18
Alignment explanation
Indices: 1194453--1194494 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1194443 GGATATAAGA
1194453 GATATATGT-GT-TATGT
1 GATATATGTGGTATATGT
1194469 GATATATGTGGTATATGT
1 GATATATGTGGTATATGT
*
1194487 TATATATG
1 GATATATG
1194495 GAAAACACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
18 12 0.52
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GATATATGTGGTATATGT
Found at i:1194476 original size:9 final size:9
Alignment explanation
Indices: 1194453--1194494 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
1194443 GGATATAAGA
1194453 GATATATGT
1 GATATATGT
1194462 G-T-TATGT
1 GATATATGT
1194469 GATATATGT
1 GATATATGT
*
1194478 GGTATATGT
1 GATATATGT
*
1194487 TATATATG
1 GATATATG
1194495 GAAAACACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
7 6 0.21
8 2 0.07
9 20 0.71
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (9 bp):
GATATATGT
Found at i:1194713 original size:32 final size:32
Alignment explanation
Indices: 1194667--1194761 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
1194657 GAGTCGATAG
* *
1194667 TTACATATGTCCTTCGGGACATATGGACAGGA
1 TTACCTATGTCCTTCGGGACATATGGACAAGA
1194699 TTACCTATGTCCTTCGGGACATATGGACAAGA
1 TTACCTATGTCCTTCGGGACATATGGACAAGA
*
1194731 TTACCTATGTCATTCGGGACATATGGACAAG
1 TTACCTATGTCCTTCGGGACATATGGACAAG
1194762 TCCTTTGGGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 60 1.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (32 bp):
TTACCTATGTCCTTCGGGACATATGGACAAGA
Found at i:1198039 original size:22 final size:23
Alignment explanation
Indices: 1198012--1198067 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
1198002 CTGTATGAAC
1198012 AGTATCGATACCATAAG-GAAGG
1 AGTATCGATACCATAAGTGAAGG
* *
1198034 AGTATCGATACC-TATGTGGAGG
1 AGTATCGATACCATAAGTGAAGG
1198056 -GTATCGATACCA
1 AGTATCGATACCA
1198068 GGGAACATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.34, C:0.16, G:0.27, T:0.23
Consensus pattern (23 bp):
AGTATCGATACCATAAGTGAAGG
Found at i:1199272 original size:32 final size:32
Alignment explanation
Indices: 1199231--1199294 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1199221 ATATAGTCAG
1199231 GTGAAATCCTTATGTGGTATGAGTATATGACA
1 GTGAAATCCTTATGTGGTATGAGTATATGACA
*
1199263 GTGAAATCCTTATGTGGTATGGGTATATGACA
1 GTGAAATCCTTATGTGGTATGAGTATATGACA
1199295 TTACTATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.34
Consensus pattern (32 bp):
GTGAAATCCTTATGTGGTATGAGTATATGACA
Found at i:1199532 original size:16 final size:18
Alignment explanation
Indices: 1199511--1199552 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1199501 GGATATAAGA
1199511 GATATATGT-GT-TACGT
1 GATATATGTGGTATACGT
*
1199527 GATATATGTGGTATAGGT
1 GATATATGTGGTATACGT
1199545 GATATATG
1 GATATATG
1199553 GAAAACACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
18 12 0.52
ACGTcount: A:0.29, C:0.02, G:0.29, T:0.40
Consensus pattern (18 bp):
GATATATGTGGTATACGT
Found at i:1199766 original size:32 final size:32
Alignment explanation
Indices: 1199725--1199815 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
1199715 GAGTCGAGGG
1199725 TTACCTATGTCCTTCGGGACATATGGACAGGA
1 TTACCTATGTCCTTCGGGACATATGGACAGGA
* *
1199757 TTACCTATGTCCTTCGGGATATATAGACAGGA
1 TTACCTATGTCCTTCGGGACATATGGACAGGA
*
1199789 TTACCTTTGTCCTTCGGGACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
1199816 TAGGTTGTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (32 bp):
TTACCTATGTCCTTCGGGACATATGGACAGGA
Found at i:1200176 original size:35 final size:35
Alignment explanation
Indices: 1200130--1200207 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
1200120 AAATATTTCT
1200130 GATCTGAACTTTGCGCGGAGATATGCTGCTTTACG
1 GATCTGAACTTTGCGCGGAGATATGCTGCTTTACG
1200165 GATCTGAACTTTGCGCGGAGATATGCTGCTTTACG
1 GATCTGAACTTTGCGCGGAGATATGCTGCTTTACG
1200200 GATCTGAA
1 GATCTGAA
1200208 GCTTGATCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (35 bp):
GATCTGAACTTTGCGCGGAGATATGCTGCTTTACG
Found at i:1200781 original size:18 final size:18
Alignment explanation
Indices: 1200760--1200947 Score: 232
Period size: 18 Copynumber: 10.4 Consensus size: 18
1200750 TTTGTCCCAT
*
1200760 AGGACCACTATGTCCTGA
1 AGGACCACTATGTCCCGA
1200778 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
* * *
1200796 ATGACCATTATATCCCGA
1 AGGACCACTATGTCCCGA
* * *
1200814 ATGAACATTATGTCCCGA
1 AGGACCACTATGTCCCGA
1200832 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
1200850 AGGACCACTATGTCCCGA
1 AGGACCACTATGTCCCGA
*
1200868 AGGACCATTATGTCCCGA
1 AGGACCACTATGTCCCGA
* *
1200886 AGGACCACTATGTCTCAA
1 AGGACCACTATGTCCCGA
* * **
1200904 ATGACCATTATGTCTTGA
1 AGGACCACTATGTCCCGA
* *
1200922 AAGACCACTATGTCCTGA
1 AGGACCACTATGTCCCGA
1200940 AGGACCAC
1 AGGACCAC
1200948 GTAGACCCTC
Statistics
Matches: 149, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 149 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (18 bp):
AGGACCACTATGTCCCGA
Found at i:1205433 original size:27 final size:27
Alignment explanation
Indices: 1205402--1205455 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1205392 TAAAAGTTCA
*
1205402 TTTTAGTCCTATAAAAAATATTTTAAT
1 TTTTAGTCCTATAAAAAATATTATAAT
*
1205429 TTTTAGTCCTATAAAAAGTATTATAAT
1 TTTTAGTCCTATAAAAAATATTATAAT
1205456 CCTTATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (27 bp):
TTTTAGTCCTATAAAAAATATTATAAT
Found at i:1205594 original size:14 final size:15
Alignment explanation
Indices: 1205575--1205604 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1205565 TTTCTATTTG
1205575 ACTTAAAT-ATTTTT
1 ACTTAAATGATTTTT
1205589 ACTTAAATGATTTTT
1 ACTTAAATGATTTTT
1205604 A
1 A
1205605 GGTTCTTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (15 bp):
ACTTAAATGATTTTT
Found at i:1209635 original size:17 final size:18
Alignment explanation
Indices: 1209602--1209635 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1209592 CCACTATTAA
1209602 TGAACCGGTCAGAACCGT
1 TGAACCGGTCAGAACCGT
*
1209620 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
1209636 AACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGT
Found at i:1213264 original size:23 final size:23
Alignment explanation
Indices: 1213238--1213286 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
1213228 TAAGTGGCAT
1213238 ATAAAATTATCCCGAAGGACCAC
1 ATAAAATTATCCCGAAGGACCAC
* *
1213261 ATAAAATTGTCCCTAAGGACCAC
1 ATAAAATTATCCCGAAGGACCAC
1213284 ATA
1 ATA
1213287 TATGTTCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.20
Consensus pattern (23 bp):
ATAAAATTATCCCGAAGGACCAC
Found at i:1213362 original size:21 final size:21
Alignment explanation
Indices: 1213247--1213365 Score: 123
Period size: 21 Copynumber: 5.6 Consensus size: 21
1213237 TATAAAATTA
*
1213247 TCCCGAAGGACCACATAAAATTG
1 TCCCGAAGGACCACAT-ATA-TG
*
1213270 TCCCTAAGGACCACATATATG
1 TCCCGAAGGACCACATATATG
* *
1213291 TTCC-ATAGGACCAAATATATG
1 TCCCGA-AGGACCACATATATG
* *
1213312 TCCCTAAGGACCGCATATATG
1 TCCCGAAGGACCACATATATG
* * *
1213333 TTCCAAAGGATCACATATATG
1 TCCCGAAGGACCACATATATG
1213354 TCCCGAAGGACC
1 TCCCGAAGGACC
1213366 GAGTAAAACC
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
20 1 0.01
21 61 0.76
22 3 0.04
23 15 0.19
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATG
Found at i:1213366 original size:42 final size:42
Alignment explanation
Indices: 1213268--1213366 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
1213258 CACATAAAAT
* *
1213268 TGTCCCTAAGGACCACATATATGTTCCATAGGACCAAATATA
1 TGTCCCTAAGGACCGCATATATGTTCCAAAGGACCAAATATA
* *
1213310 TGTCCCTAAGGACCGCATATATGTTCCAAAGGATCACATATA
1 TGTCCCTAAGGACCGCATATATGTTCCAAAGGACCAAATATA
*
1213352 TGTCCCGAAGGACCG
1 TGTCCCTAAGGACCG
1213367 AGTAAAACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (42 bp):
TGTCCCTAAGGACCGCATATATGTTCCAAAGGACCAAATATA
Found at i:1216094 original size:6 final size:6
Alignment explanation
Indices: 1216083--1216107 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1216073 GACACGTATT
1216083 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
1216108 GCTGAGCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1222124 original size:33 final size:33
Alignment explanation
Indices: 1222082--1222147 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
1222072 ACTCCGCTGA
1222082 TATCTTTTTCATCTTGTCACGTGCCCCAACCCC
1 TATCTTTTTCATCTTGTCACGTGCCCCAACCCC
1222115 TATCTTTTTCATCTTGTCACGTGCCCCAACCCC
1 TATCTTTTTCATCTTGTCACGTGCCCCAACCCC
1222148 ACCATCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.15, C:0.39, G:0.09, T:0.36
Consensus pattern (33 bp):
TATCTTTTTCATCTTGTCACGTGCCCCAACCCC
Found at i:1223713 original size:59 final size:59
Alignment explanation
Indices: 1223619--1223756 Score: 181
Period size: 59 Copynumber: 2.4 Consensus size: 59
1223609 CCTTACCAGC
* * **
1223619 TGTCCCTCCACGTTGCAACTCCAACCGACGATTCCAGTAGCTTCTAGAGGAACACCAAT
1 TGTCCCTCCACGTTGCAGCTCCAACCGACGATTCCAGCAAATTCTAGAGGAACACCAAT
* * * *
1223678 TGTCCCTCAACATTGCAGCTCCAGCCGACTG-TTCCAGCAAATTCTAGAGGAACACCAGT
1 TGTCCCTCCACGTTGCAGCTCCAACCGAC-GATTCCAGCAAATTCTAGAGGAACACCAAT
1223737 TGT-CCTCCACGTTGCAGCTC
1 TGTCCCTCCACGTTGCAGCTC
1223757 TACCAACAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
58 15 0.22
59 52 0.76
60 1 0.01
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (59 bp):
TGTCCCTCCACGTTGCAGCTCCAACCGACGATTCCAGCAAATTCTAGAGGAACACCAAT
Found at i:1224059 original size:7 final size:7
Alignment explanation
Indices: 1224049--1224075 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1224039 TTCAGCTTTG
1224049 TATTTTA
1 TATTTTA
1224056 TATTTTA
1 TATTTTA
1224063 TATTTTA
1 TATTTTA
1224070 TATTTT
1 TATTTT
1224076 TCTTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TATTTTA
Found at i:1224998 original size:2 final size:2
Alignment explanation
Indices: 1224991--1225016 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1224981 AGTCACATGA
1224991 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
1225017 GAAAGACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1226864 original size:16 final size:16
Alignment explanation
Indices: 1226840--1226870 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1226830 ATTTTCCAAA
1226840 TCATGCATTAAAATAT
1 TCATGCATTAAAATAT
*
1226856 TCATTCATTAAAATA
1 TCATGCATTAAAATA
1226871 ATAATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (16 bp):
TCATGCATTAAAATAT
Found at i:1228930 original size:3 final size:3
Alignment explanation
Indices: 1228922--1228977 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1228912 AGGTTAATAA
1228922 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1228970 ATT ATT AT
1 ATT ATT AT
1228978 AGATTATACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1231578 original size:19 final size:18
Alignment explanation
Indices: 1231551--1231589 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1231541 AGGTTTTATA
*
1231551 TTTTATATATTTTTCACTT
1 TTTTATATAATTTTCA-TT
*
1231570 TTTTTTATAATTTTCATT
1 TTTTATATAATTTTCATT
1231588 TT
1 TT
1231590 GTCTATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATATAATTTTCATT
Found at i:1231774 original size:27 final size:27
Alignment explanation
Indices: 1231723--1231786 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
1231713 ATATGTTTAA
1231723 ATTATTACTTTAATCATTATTTTTA-TT
1 ATTATTA-TTTAATCATTATTTTTATTT
*
1231750 ATTATTATTTAGTCA-TATTCATTTATTT
1 ATTATTATTTAATCATTATT--TTTATTT
1231778 ATT-TTATTT
1 ATTATTATTT
1231787 GTTTTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 17 0.52
28 5 0.15
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (27 bp):
ATTATTATTTAATCATTATTTTTATTT
Found at i:1237989 original size:32 final size:32
Alignment explanation
Indices: 1237949--1238010 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1237939 TCTGGAAACA
* * *
1237949 AGAAGTATCTCTGCGAGATGAGCATAACAACG
1 AGAAGTATCTCTACCAGATAAGCATAACAACG
1237981 AGAAGTATCTCTACCAGATAAGCATAACAA
1 AGAAGTATCTCTACCAGATAAGCATAACAA
1238011 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACCAGATAAGCATAACAACG
Found at i:1240544 original size:75 final size:73
Alignment explanation
Indices: 1240410--1240649 Score: 228
Period size: 75 Copynumber: 3.3 Consensus size: 73
1240400 AACAAGAAGA
* * * *
1240410 AAATGTTGGGGTATGCTGAAAGCCCATTTCAATCA-TAATTAGGAATATCGACGTGTTTTGAATG
1 AAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAAATT-GGAATATCGA-GTGTTTTGAACG
1240474 TTCACGTCA-A-C
64 -TC-CGT-ATAGC
* *
1240485 AAATGCTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTG-GTGCATTTTGAACG
1 AAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATCGAGTG--TTTTGAACG
* *
1240549 TCTGTATTAGT
64 TCCGTA-TAGC
* *
1240560 AAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATAAC-A---TTTTGAACGTT
1 AAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATCGAGTGTTTTGAACGTC
*
1240621 CATATCAGC
66 CGTAT-AGC
1240630 AAAT-ATTGGGGCATGCTGAA
1 AAATGA-TGGGGCATGCTGAA
1240650 GGCACACATC
Statistics
Matches: 142, Mismatches: 14, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
69 2 0.01
70 32 0.23
72 1 0.01
73 5 0.04
74 3 0.02
75 95 0.67
76 4 0.03
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (73 bp):
AAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATCGAGTGTTTTGAACGTC
CGTATAGC
Found at i:1242015 original size:22 final size:22
Alignment explanation
Indices: 1241987--1242065 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
1241977 ACATCTACAT
1241987 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1242009 TCTTCAAATATGGTAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
1242031 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1242053 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1242066 AAGCCTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1242799 original size:45 final size:45
Alignment explanation
Indices: 1242735--1242870 Score: 209
Period size: 45 Copynumber: 3.0 Consensus size: 45
1242725 CTATTTCCCA
*
1242735 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
* * *
1242780 CATCTGTAAGCCCTTCAGTGCCTGATGTTTTTAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
*
1242825 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAGCCTTCGGG
1242871 AGCTTTCTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 70 0.86
47 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
Found at i:1242929 original size:45 final size:45
Alignment explanation
Indices: 1242880--1243432 Score: 759
Period size: 45 Copynumber: 12.2 Consensus size: 45
1242870 GAGCTTTCTT
*
1242880 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
1242925 ATGTTTTCAAAACCTTC-AGTCATCTGTAAGCCCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
1242969 ATGTTTTCAAAACCTTCAGGTCATCTGTAAAG-CCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGT-AAGCCCTTCAGTGCATG
* *
1243014 ATGTTTTCAAAACCTTCGGGTAATCTGTAAGCTCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
1243059 ATGTTTTCAAAACCTTCGGGTCATCTGTAAACCCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * *
1243104 ATGTTTTCAAAGCCTTCGGGCCATCTATAAGCCCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1243149 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * *
1243194 ATGTTTTCAAAATCTTTGGGTCATCTGTAAGCCTTTCAGTGCATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* *
1243239 ATGTTTTTTCAAAACCTTTGGGTCATCTGTAAGACCTTCAGTGCATG
1 ATG--TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * *
1243286 ATGTTTTCAAAACCTTCGGGTCCTCTGTAAGACCTTCAGTACATG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * ** * *
1243331 ATTTTTTCAAAACCTTCAGGTCATCCATAAGACCTTCAGTGCAGG
1 ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
* * ** * ** * *
1243376 ATGTTTTTAAAGTCCTTCAAGCCATCCATAAGACCTTCAGTGCAGG
1 ATGTTTTCAAA-ACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
*
1243422 ATATTTTCAAA
1 ATGTTTTCAAA
1243433 GGAAATCTTA
Statistics
Matches: 463, Mismatches: 39, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
44 46 0.10
45 332 0.72
46 43 0.09
47 42 0.09
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (45 bp):
ATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATG
Found at i:1243455 original size:227 final size:224
Alignment explanation
Indices: 1242880--1243432 Score: 603
Period size: 227 Copynumber: 2.5 Consensus size: 224
1242870 GAGCTTTCTT
* * * ** * *
1242880 ATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTC-AG
1 ATGTTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCAAG
* ** * * * * * * * *
1242944 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTTCAGGTCATCTGTAAAGCC-TTCA
66 CCATCCATAAGACCTTCAGTGCAGGATATTTTCAAAATCTTTGA-GTAAAC-G-CAAGCCTTTCA
1243007 GTGCATGATGTTTTCAAAACCTTCGGGTAATCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAAC
128 GTGCATGATGTTTTCAAAACCTTCGGGTAATCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAAC
*
1243072 CTTCGGGTCATCTGTAAACCCTTCAGTGCATG
193 CTTCGGGTCATCTGTAAACCCTTCAGTACATG
* * * * * **
1243104 ATGTTTTCAAAGCCTTCGGGCCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
1 ATGTTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCAAG
* ** * * * * * * *
1243169 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAATCTTTGGGTCATCTGTAAGCCTTTCAGT
66 CCATCCATAAGACCTTCAGTGCAGGATATTTTCAAAATCTTTGAGTAAAC-GCAAGCCTTTCAGT
* *
1243234 GCATGATGTTTTTTCAAAACCTTTGGGTCATCTGTAAGAC-CTTCAGTGCATGATGTTTTCAAAA
130 GCATGATG--TTTTCAAAACCTTCGGGTAATCTGTAAG-CTCTTCAGTGCATGATGTTTTCAAAA
*
1243298 CCTTCGGGTCCTCTGTAAGA-CCTTCAGTACATG
192 CCTTCGGGTCATCTGTAA-ACCCTTCAGTACATG
* * * *
1243331 ATTTTTTCAAAACCTTCAGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTTAAAGTCCTTCAA
1 ATGTTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAA-ACCTTCAA
1243396 GCCATCCATAAGACCTTCAGTGCAGGATATTTTCAAA
65 GCCATCCATAAGACCTTCAGTGCAGGATATTTTCAAA
1243433 GGAAATCTTA
Statistics
Matches: 293, Mismatches: 28, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
224 65 0.22
225 60 0.20
226 3 0.01
227 127 0.43
228 38 0.13
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (224 bp):
ATGTTTTCAAAACCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAAACCTTCAAG
CCATCCATAAGACCTTCAGTGCAGGATATTTTCAAAATCTTTGAGTAAACGCAAGCCTTTCAGTG
CATGATGTTTTCAAAACCTTCGGGTAATCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAACCTT
CGGGTCATCTGTAAACCCTTCAGTACATG
Found at i:1243765 original size:23 final size:23
Alignment explanation
Indices: 1243739--1243807 Score: 120
Period size: 23 Copynumber: 3.0 Consensus size: 23
1243729 TCCAGCCGTT
*
1243739 CCTCTACTCCAACTGCTCTGCCG
1 CCTCTACTCCAACTGCTCCGCCG
*
1243762 CCTCTACTCCAACTACTCCGCCG
1 CCTCTACTCCAACTGCTCCGCCG
1243785 CCTCTACTCCAACTGCTCCGCCG
1 CCTCTACTCCAACTGCTCCGCCG
1243808 TTATGTTCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.14, C:0.51, G:0.12, T:0.23
Consensus pattern (23 bp):
CCTCTACTCCAACTGCTCCGCCG
Found at i:1251346 original size:36 final size:36
Alignment explanation
Indices: 1251274--1251346 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
1251264 TCCTATTATT
** * *
1251274 TAAAATTCAAATTTTAGCCTTATTCTCAACAGCTAA
1 TAAAATTCAAATTCCAACCTTATTCTCAACAACTAA
*
1251310 TAAAATTCAAATTCCAACCTTA-TCTTCAGCAACTAA
1 TAAAATTCAAATTCCAACCTTATTC-TCAACAACTAA
1251346 T
1 T
1251347 CAATTCTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (36 bp):
TAAAATTCAAATTCCAACCTTATTCTCAACAACTAA
Found at i:1259170 original size:19 final size:21
Alignment explanation
Indices: 1259142--1259198 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
1259132 GAACCTGTGG
1259142 GGGGGTATCGATTCCCC-TC-
1 GGGGGTATCGATTCCCCTTCA
* *
1259161 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTTC-A
1259183 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
1259199 TCTGCACCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 15 0.48
20 2 0.06
22 14 0.45
ACGTcount: A:0.14, C:0.28, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTTCA
Found at i:1262969 original size:21 final size:20
Alignment explanation
Indices: 1262944--1262985 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1262934 GACTATTTTC
*
1262944 ATTTTTTAATTTTGAAATATA
1 ATTTTTGAATTTTGAAA-ATA
*
1262965 ATTTTTGCATTTTGAAAATA
1 ATTTTTGAATTTTGAAAATA
1262985 A
1 A
1262986 AGTCTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTTGAATTTTGAAAATA
Found at i:1265217 original size:21 final size:20
Alignment explanation
Indices: 1265193--1265234 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1265183 GACTATTTTC
*
1265193 ATTTTTTAATTTTGAAATATA
1 ATTTTTGAATTTTGAAA-ATA
*
1265214 ATTTTTGCATTTTGAAAATA
1 ATTTTTGAATTTTGAAAATA
1265234 A
1 A
1265235 AGTCTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTTGAATTTTGAAAATA
Found at i:1267459 original size:21 final size:20
Alignment explanation
Indices: 1267435--1267476 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1267425 GACTATTTTC
*
1267435 ATTTTTTAATTTTGAAATATA
1 ATTTTTGAATTTTGAAA-ATA
*
1267456 ATTTTTGCATTTTGAAAATA
1 ATTTTTGAATTTTGAAAATA
1267476 A
1 A
1267477 AGTCTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTTGAATTTTGAAAATA
Found at i:1269713 original size:21 final size:20
Alignment explanation
Indices: 1269689--1269730 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1269679 GACTATTTTC
*
1269689 ATTTTTTAATTTTGAAATATA
1 ATTTTTGAATTTTGAAA-ATA
*
1269710 ATTTTTGCATTTTGAAAATA
1 ATTTTTGAATTTTGAAAATA
1269730 A
1 A
1269731 AGTCTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTTGAATTTTGAAAATA
Found at i:1273478 original size:180 final size:180
Alignment explanation
Indices: 1273176--1273499 Score: 594
Period size: 180 Copynumber: 1.8 Consensus size: 180
1273166 AAAAATTAAG
*
1273176 GATAAGGTATTTCACTTAGTGAAATGGATGCAATGTGTAGGCTTTGCTAACTACAATAATGCTTC
1 GATAAGGTATTTCACTTAGTGAAATGGATACAATGTGTAGGCTTTGCTAACTACAATAATGCTTC
* *
1273241 AAGCACTGCCCATTAACTTTGAATGTGCTTCTATCCACTAGATTCTTCAGAAGAACTACATCATG
66 AAGCACTGCCCATTAACTATGAATGTGCTTCTATCCACTAGATTCTTCAGAAGAACTACAGCATG
1273306 AGGGTAGAATTCTTGTATCTCAAAAAGACCAAACTAATGAGACTTCAATC
131 AGGGTAGAATTCTTGTATCTCAAAAAGACCAAACTAATGAGACTTCAATC
*
1273356 GATAAGGTATTTCACTTAGTGAAATGGATACAATGTGTAGGCTTTGCTGACTACAATAATGCTTC
1 GATAAGGTATTTCACTTAGTGAAATGGATACAATGTGTAGGCTTTGCTAACTACAATAATGCTTC
* *
1273421 AAGCACTGCCCATTAACTATGAATGTTCTTCTATCCTCTAGATTCTTCAGAAGAACTACAGCATG
66 AAGCACTGCCCATTAACTATGAATGTGCTTCTATCCACTAGATTCTTCAGAAGAACTACAGCATG
1273486 AGGGTAGAATTCTT
131 AGGGTAGAATTCTT
1273500 CAATCGAGAG
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
180 138 1.00
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (180 bp):
GATAAGGTATTTCACTTAGTGAAATGGATACAATGTGTAGGCTTTGCTAACTACAATAATGCTTC
AAGCACTGCCCATTAACTATGAATGTGCTTCTATCCACTAGATTCTTCAGAAGAACTACAGCATG
AGGGTAGAATTCTTGTATCTCAAAAAGACCAAACTAATGAGACTTCAATC
Found at i:1275320 original size:15 final size:15
Alignment explanation
Indices: 1275300--1275330 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1275290 CTATCATTTC
*
1275300 ATTATTATTATTAAT
1 ATTATTATCATTAAT
1275315 ATTATTATCATTAAT
1 ATTATTATCATTAAT
1275330 A
1 A
1275331 GCATGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTATCATTAAT
Found at i:1275582 original size:18 final size:18
Alignment explanation
Indices: 1275559--1275593 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1275549 TCGCATAGAA
1275559 ATGTCCCCAAGGACCACT
1 ATGTCCCCAAGGACCACT
* *
1275577 ATGTCCCGAATGACCAC
1 ATGTCCCCAAGGACCAC
1275594 ATATCACATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (18 bp):
ATGTCCCCAAGGACCACT
Found at i:1286537 original size:36 final size:36
Alignment explanation
Indices: 1286490--1286562 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
1286480 TCCTTTTATT
* * *
1286490 TAAAATTCAAATTCTAGCCTTACCTTTAGTAGCTAA
1 TAAAATTCAAATTCCAGACTTACCTTTAGCAGCTAA
*
1286526 TAAAATTCAAATTCCAGACTTATCTTTAGCAGCTAA
1 TAAAATTCAAATTCCAGACTTACCTTTAGCAGCTAA
1286562 T
1 T
1286563 CGATTCCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (36 bp):
TAAAATTCAAATTCCAGACTTACCTTTAGCAGCTAA
Found at i:1289399 original size:14 final size:15
Alignment explanation
Indices: 1289373--1289420 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
1289363 CTATTTCAGA
*
1289373 TTAA-TTTTCATAAT
1 TTAATTTTTTATAAT
1289387 TT-ATTTTTTATAAT
1 TTAATTTTTTATAAT
1289401 TTAATTTATTT-TAA-
1 TTAATTT-TTTATAAT
1289415 TTAATT
1 TTAATT
1289421 GTATTGTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.03
14 19 0.63
15 7 0.23
16 3 0.10
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (15 bp):
TTAATTTTTTATAAT
Found at i:1289419 original size:19 final size:19
Alignment explanation
Indices: 1289383--1289450 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
1289373 TTAATTTTCA
*
1289383 TAATTTATTTT-TTATAATT
1 TAATTTATTTTAAT-TAATT
1289402 TAATTTATTTTAATTAATT
1 TAATTTATTTTAATTAATT
* *
1289421 GT-ATTGTGTTTTCA-TAATT
1 -TAATT-TATTTTAATTAATT
1289440 TAA-TTATTTTA
1 TAATTTATTTTA
1289451 TTTTCTTGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 5 0.12
18 2 0.05
19 25 0.62
20 8 0.20
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (19 bp):
TAATTTATTTTAATTAATT
Found at i:1291014 original size:89 final size:89
Alignment explanation
Indices: 1290863--1291028 Score: 296
Period size: 89 Copynumber: 1.9 Consensus size: 89
1290853 GAAGGTCTTA
1290863 ATTTGATCGCAATCCCTAGGAGAGCCTAAAAGATGATGCCGATCTCTTCTCCTTGTCTTGCCCAA
1 ATTTGATCGCAATCCCTAGGAGAGCCTAAAAGATGATGCCGATCTCTTCTCCTTGTCTTGCCCAA
1290928 GGTACCCATCATGATTTGAAAATG
66 GGTACCCATCATGATTTGAAAATG
* * * *
1290952 ATTTGATGGCAGTCCCTAGGAGAGCCTAAAAGATGATGCCGGTCTCTTCTCCTTGTGTTGCCCAA
1 ATTTGATCGCAATCCCTAGGAGAGCCTAAAAGATGATGCCGATCTCTTCTCCTTGTCTTGCCCAA
1291017 GGTACCCATCAT
66 GGTACCCATCAT
1291029 ATCTTGTTTC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (89 bp):
ATTTGATCGCAATCCCTAGGAGAGCCTAAAAGATGATGCCGATCTCTTCTCCTTGTCTTGCCCAA
GGTACCCATCATGATTTGAAAATG
Found at i:1291953 original size:10 final size:10
Alignment explanation
Indices: 1291938--1291986 Score: 62
Period size: 10 Copynumber: 4.7 Consensus size: 10
1291928 CATTTAATAA
1291938 ATAAACGAAC
1 ATAAACGAAC
1291948 ATAAACGAAC
1 ATAAACGAAC
*
1291958 ACGAACACGAAC
1 A-TAA-ACGAAC
*
1291970 ATAAACAAAC
1 ATAAACGAAC
1291980 ATAAACG
1 ATAAACG
1291987 TTGGAGACCC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 22 0.67
11 4 0.12
12 7 0.21
ACGTcount: A:0.59, C:0.22, G:0.10, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1292226 original size:12 final size:12
Alignment explanation
Indices: 1292209--1292251 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1292199 CTCGAGACTC
1292209 GAGCTCGATTCT
1 GAGCTCGATTCT
*
1292221 GAGCTCAATTC-
1 GAGCTCGATTCT
*
1292232 AAGCTCGATTCT
1 GAGCTCGATTCT
1292244 GAGCTCGA
1 GAGCTCGA
1292252 CATTGCCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (12 bp):
GAGCTCGATTCT
Found at i:1292778 original size:10 final size:10
Alignment explanation
Indices: 1292763--1292810 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
1292753 ATAAATGAAT
1292763 GAACATAAAC
1 GAACATAAAC
1292773 GAACATAACCGAAC
1 GAACAT-A---AAC
1292787 GAACATAAAC
1 GAACATAAAC
*
1292797 GAACATAACC
1 GAACATAAAC
1292807 GAAC
1 GAAC
1292811 GTTCACGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:1292787 original size:14 final size:14
Alignment explanation
Indices: 1292770--1292811 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1292760 AATGAACATA
1292770 AACGAACATAACCG
1 AACGAACATAACCG
1292784 AACGAACAT-A---
1 AACGAACATAACCG
1292794 AACGAACATAACCG
1 AACGAACATAACCG
1292808 AACG
1 AACG
1292812 TTCACGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1292790 original size:24 final size:24
Alignment explanation
Indices: 1292763--1292811 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1292753 ATAAATGAAT
1292763 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
1292787 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
1292811 G
1 G
1292812 TTCACGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.24, G:0.14, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:1293589 original size:18 final size:19
Alignment explanation
Indices: 1293566--1293602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1293556 CCAGTAATCC
1293566 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
1293584 TATTCCCATTGGTAATCTT
1 TATTCCCA-TGGTAATCTT
1293603 ACATTCCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:1295607 original size:2 final size:2
Alignment explanation
Indices: 1295600--1295629 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1295590 TGCATGTTAC
1295600 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
1295630 TTAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1301907 original size:58 final size:58
Alignment explanation
Indices: 1301844--1301958 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
1301834 GAACTTGTGT
* ** * *
1301844 TTTTTTTAAAAAAGAATCAATGGTGATGTGACATTATCTTATGGTGGCATATCAACAC
1 TTTTTTTAAAAAAAAATCAATAATGATATGACATTATCTTATGGTGACATATCAACAC
* *
1301902 TTTTTTTAAAAAAAAATCAATAATGATATGTCATTATCTTATGGTGATATATCAACA
1 TTTTTTTAAAAAAAAATCAATAATGATATGACATTATCTTATGGTGACATATCAACA
1301959 TTATTGTTAA
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (58 bp):
TTTTTTTAAAAAAAAATCAATAATGATATGACATTATCTTATGGTGACATATCAACAC
Found at i:1306242 original size:23 final size:23
Alignment explanation
Indices: 1306212--1306261 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1306202 TATTATTTTT
*
1306212 AATTTATATA-CT-TTTTAATAA
1 AATTTATATATATATTTTAATAA
*
1306233 AATTTATATATATATTTTTATAA
1 AATTTATATATATATTTTAATAA
1306256 AATTTA
1 AATTTA
1306262 AAAGATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 14 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTATATATATATTTTAATAA
Found at i:1306329 original size:16 final size:16
Alignment explanation
Indices: 1306308--1306347 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1306298 ATGTATTATT
1306308 TTAATTTTAATTAATA
1 TTAATTTTAATTAATA
1306324 TTAATTTTAATTAATA
1 TTAATTTTAATTAATA
1306340 TTAATTTT
1 TTAATTTT
1306348 TACATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAATTTTAATTAATA
Found at i:1311186 original size:24 final size:24
Alignment explanation
Indices: 1311134--1311186 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1311124 TTCTTTTCTT
1311134 TTTTTCTTCTTTTGAGTGCTTGCA
1 TTTTTCTTCTTTTGAGTGCTTGCA
*
1311158 ATTTTCTTCTTTTGAGTGCTT-CA
1 TTTTTCTTCTTTTGAGTGCTTGCA
1311181 GTTTTT
1 -TTTTT
1311187 TTGCTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.09, C:0.15, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTTTCTTCTTTTGAGTGCTTGCA
Found at i:1324173 original size:2 final size:2
Alignment explanation
Indices: 1324166--1324232 Score: 68
Period size: 2 Copynumber: 34.0 Consensus size: 2
1324156 ATAATATGTA
1324166 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT GAT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* * *
1324207 AC AT ACT AT AA AT AT AA AT A- AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT
1324233 GTACCATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
1 3 0.06
2 47 0.87
3 4 0.07
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1324926 original size:21 final size:21
Alignment explanation
Indices: 1324845--1324928 Score: 70
Period size: 21 Copynumber: 4.1 Consensus size: 21
1324835 AGAAGTTTAT
1324845 ATTTAAATTTT-AATAATTAA
1 ATTTAAATTTTAAATAATTAA
*
1324865 A--TAAA-TATAAATAATTTTAA
1 ATTTAAATTTTAAATAA--TTAA
* **
1324885 ATTGT-ATTTTTAAATTTTTAA
1 ATT-TAAATTTTAAATAATTAA
1324906 ATTTAAATTTTAAATAATTAA
1 ATTTAAATTTTAAATAATTAA
1324927 AT
1 AT
1324929 ACATATAAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
17 2 0.04
18 9 0.19
20 7 0.15
21 22 0.46
22 1 0.02
23 7 0.15
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTTAAATAATTAA
Found at i:1326435 original size:38 final size:38
Alignment explanation
Indices: 1326393--1326466 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
1326383 CAATCTGTCG
*
1326393 AACAGATTGTCTCCCCTTTCCCTCTTTTTCCTCTTCGA
1 AACAGATTGTCTCCCCTTCCCCTCTTTTTCCTCTTCGA
*
1326431 AACAGATTGTCTTCCCTTCCCCTCTTTTTCCTCTTC
1 AACAGATTGTCTCCCCTTCCCCTCTTTTTCCTCTTC
1326467 CGTTTCATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.12, C:0.38, G:0.07, T:0.43
Consensus pattern (38 bp):
AACAGATTGTCTCCCCTTCCCCTCTTTTTCCTCTTCGA
Found at i:1327190 original size:27 final size:28
Alignment explanation
Indices: 1327160--1327224 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
1327150 TCGGGTCGGG
1327160 TCGGGTCGGG-TTTTTTAAGTGTAATAT
1 TCGGGTCGGGTTTTTTTAAGTGTAATAT
*
1327187 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTAATAT
1327215 TCGGGTCGGG
1 TCGGGTCGGG
1327225 GTCGGGTTCG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 10 0.28
28 26 0.72
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTAATAT
Found at i:1327830 original size:17 final size:18
Alignment explanation
Indices: 1327808--1327855 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1327798 ATATGGAATT
*
1327808 AGATTTCAATTCC-TGAC
1 AGATTTCAATTCCTTCAC
1327825 AGATTTCAATTCCTTCAC
1 AGATTTCAATTCCTTCAC
1327843 AGATTTCAATTCC
1 AGATTTCAATTCC
1327856 CTCATAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.38
Consensus pattern (18 bp):
AGATTTCAATTCCTTCAC
Found at i:1328441 original size:32 final size:32
Alignment explanation
Indices: 1328381--1328441 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1328371 TACTGACCTG
* *
1328381 GTATGTGTCACATCATCTAAAATAATGATTTT
1 GTATGTGTCACATCATCCAAAACAATGATTTT
* *
1328413 GTATGTGTCACGTCATCCAAAACGATGAT
1 GTATGTGTCACATCATCCAAAACAATGAT
1328442 GTGGCATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
GTATGTGTCACATCATCCAAAACAATGATTTT
Found at i:1328653 original size:2 final size:2
Alignment explanation
Indices: 1328646--1328702 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1328636 ATTATACCTT
1328646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1328688 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1328703 TCATTTCAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1331394 original size:18 final size:18
Alignment explanation
Indices: 1331371--1331405 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1331361 TTCCATCCGG
*
1331371 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1331389 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1331406 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1332742 original size:18 final size:18
Alignment explanation
Indices: 1332716--1332786 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
1332706 AACGGTCAAT
1332716 GGGTAAACGGGTCGGGTC
1 GGGTAAACGGGTCGGGTC
*
1332734 GGGTCAA-----CGGGTC
1 GGGTAAACGGGTCGGGTC
* *
1332747 GGGTAAATGGGTTGGGTC
1 GGGTAAACGGGTCGGGTC
*
1332765 GGGTTAACGGGTCGGGTC
1 GGGTAAACGGGTCGGGTC
1332783 GGGT
1 GGGT
1332787 TGTGACCGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
13 12 0.29
18 30 0.71
ACGTcount: A:0.14, C:0.14, G:0.51, T:0.21
Consensus pattern (18 bp):
GGGTAAACGGGTCGGGTC
Found at i:1332764 original size:31 final size:31
Alignment explanation
Indices: 1332716--1332781 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
1332706 AACGGTCAAT
1332716 GGGTAAACGGGTCGGGTCGGGTCAACGGGTC
1 GGGTAAACGGGTCGGGTCGGGTCAACGGGTC
* * *
1332747 GGGTAAATGGGTTGGGTCGGGTTAACGGGTC
1 GGGTAAACGGGTCGGGTCGGGTCAACGGGTC
1332778 GGGT
1 GGGT
1332782 CGGGTTGTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.15, C:0.14, G:0.50, T:0.21
Consensus pattern (31 bp):
GGGTAAACGGGTCGGGTCGGGTCAACGGGTC
Found at i:1336584 original size:15 final size:15
Alignment explanation
Indices: 1336560--1336591 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1336550 TAGCAGATCG
*
1336560 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1336575 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1336590 AA
1 AA
1336592 GAAAGATTTT
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:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1341280 original size:22 final size:22
Alignment explanation
Indices: 1341252--1341297 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1341242 TCAATACTTC
1341252 AAAGTTGAAGGACTAAATTTAT
1 AAAGTTGAAGGACTAAATTTAT
*
1341274 AAAGTTGAATGACTAAATTTAT
1 AAAGTTGAAGGACTAAATTTAT
1341296 AA
1 AA
1341298 TTAAACCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (22 bp):
AAAGTTGAAGGACTAAATTTAT
Done.