Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 51
Found at i:5598501 original size:61 final size:61
Alignment explanation
Indices: 5598386--5598505 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
5598376 TTCGTCTCTT
* * * * *
5598386 TTGAGACAACTTTCCTTTGAAACAAAATTTATCTCCCTTGAGATGGTTTTTCTTAAAACCC
1 TTGAGACAACTTTCCTTCGAAACAAAATTTATCTCACTCGAGATGGCTTCTCTTAAAACCC
*
5598447 TTGAGACAATTTTCCTTCGAAACAAAATTTATCTCACTCGAGA-GAGCTTCTCTTAAAAC
1 TTGAGACAACTTTCCTTCGAAACAAAATTTATCTCACTCGAGATG-GCTTCTCTTAAAAC
5598506 AAGTTTCTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 1 0.02
61 51 0.98
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.35
Consensus pattern (61 bp):
TTGAGACAACTTTCCTTCGAAACAAAATTTATCTCACTCGAGATGGCTTCTCTTAAAACCC
Found at i:5599097 original size:136 final size:136
Alignment explanation
Indices: 5598751--5599362 Score: 844
Period size: 136 Copynumber: 4.5 Consensus size: 136
5598741 AAACAGATCA
*
5598751 ACATTTTCAATGGAGAGTTCA-AATGAGAAGAACTTATCCGAAAGAGGGAGAAGAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
* ** *
5598815 GAGAAGAGCTTGTTTGACCTATCACTTGATTCACTG-CATTTCGAATCAGTGACACCTCGCTTGA
66 GAGAAGAGCTTGTTCGACCTATCACTCAATTCA-TGTCATTTCGAATCAGTAACACCTCGCTTGA
*
5598879 GGAATTG
130 GGGATTG
* * * * *
5598886 AGATTTT-AATAGAGAGTTCATAATTAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
* * * * *
5598950 GAGAAAAGCTTGTTCGACCTATCACTCGATTCATGTCATTTCGAGTCAGTAACGCCTCTCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCAATTCATGTCATTTCGAATCAGTAACACCTCGCTTGAG
5599015 GGATTG
131 GGATTG
* * *
5599021 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGTGGGAGAATAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
* * *
5599086 GAGAAGAGCTTGTTCGACCTATCACTCAATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCAATTCATGTCATTTCGAATCAGTAACACCTCGCTTGAG
5599151 GGATTG
131 GGATTG
* * *
5599157 ACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCAT-CTAACAGAGGGAGAAGAAGTTCATAA
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAA-AGAGGGAGAAGAAGTTCATAA
** * *
5599221 TGAGAAGAGCTTGTTCGACCTATCACTCAATTCCCGGT-ATTTCAAATCAGTGAA-GCCTCGCTT
65 TGAGAAGAGCTTGTTCGACCTATCACTCAATT-CATGTCATTTCGAATCAGT-AACACCTCGCTT
5599284 GAGGGATTG
128 GAGGGATTG
* **
5599293 ACATTTT-AGTGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGAAAGAAGAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
5599356 GAGAAGA
66 GAGAAGA
5599363 ATTTGTTCAA
Statistics
Matches: 424, Mismatches: 46, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
134 41 0.10
135 143 0.34
136 237 0.56
137 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (136 bp):
ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCAATTCATGTCATTTCGAATCAGTAACACCTCGCTTGAG
GGATTG
Found at i:5599308 original size:271 final size:271
Alignment explanation
Indices: 5598751--5599362 Score: 937
Period size: 271 Copynumber: 2.3 Consensus size: 271
5598741 AAACAGATCA
*
5598751 ACATTTTCAATGGAGAGTTCA-AATGAGAAGAACTTATCCGAAAGAGGGAGAAGAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
* ** *
5598815 GAGAAGAGCTTGTTTGACCTATCACTTGATTCACTGCATTTCGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCAATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
* * * *
5598880 GAATTGAGATTTTAATAGAGAGTTCATAATTAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
131 GAATTGACATTTCAATAGAGAGTTCATAATGAGAAGAACTCATCTAACAGAGGGAGAAGAAGTTC
* * * * *
5598945 ATAATGAGAAAAGCTTGTTCGACCTATCACTCGATTCATGTCATTTCGAGTCAGTAACGCCTCTC
196 ATAATGAGAAAAGCTTGTTCGACCTATCACTCAATTCAGGTCATTTCAAATCAGTAACGCCTCGC
5599010 TTGAGGGATTG
261 TTGAGGGATTG
* * *
5599021 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGTGGGAGAATAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
5599086 GAGAAGAGCTTGTTCGACCTATCACTCAATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
66 GAGAAGAGCTTGTTCGACCTATCACTCAATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
* * *
5599151 GGATTGACATTTCCAATGGAGAGTTTATAATGAGAAGAACTCATCTAACAGAGGGAGAAGAAGTT
131 GAATTGACATTT-CAATAGAGAGTTCATAATGAGAAGAACTCATCTAACAGAGGGAGAAGAAGTT
* *
5599216 CATAATGAGAAGAGCTTGTTCGACCTATCACTCAATTCCCGGT-ATTTCAAATCAGTGAA-GCCT
195 CATAATGAGAAAAGCTTGTTCGACCTATCACTCAATT-CAGGTCATTTCAAATCAGT-AACGCCT
5599279 CGCTTGAGGGATTG
258 CGCTTGAGGGATTG
* **
5599293 ACATTTT-AGTGGAGAGTTCATAATGAGAAGAACTCATCC-AAAGAGAAAGAAGAAGTTCATAAT
1 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
5599356 GAGAAGA
66 GAGAAGA
5599363 ATTTGTTCAA
Statistics
Matches: 310, Mismatches: 28, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
270 47 0.15
271 141 0.45
272 117 0.38
273 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (271 bp):
ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTGTTCGACCTATCACTCAATTCACGGCATTTCGAATCAGTGACACCTCGCTTGAG
GAATTGACATTTCAATAGAGAGTTCATAATGAGAAGAACTCATCTAACAGAGGGAGAAGAAGTTC
ATAATGAGAAAAGCTTGTTCGACCTATCACTCAATTCAGGTCATTTCAAATCAGTAACGCCTCGC
TTGAGGGATTG
Found at i:5599407 original size:91 final size:90
Alignment explanation
Indices: 5599300--5599554 Score: 431
Period size: 91 Copynumber: 2.8 Consensus size: 90
5599290 TTGACATTTT
5599300 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGAAAGAAGAAGTTCATAATGAGAAGAAT
1 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAG-AAGAAGAAGTTCATAATGAGAAGAAT
5599365 TTGTTCAACCTTGCATCAGTATTTCC
65 TTGTTCAACCTTGCATCAGTATTTCC
5599391 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGATGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGA-GAAGAAGAAGTTCATAATGAGAAGAAT
*
5599456 TTGTTCAACCTTGCATCAGTATTTCT
65 TTGTTCAACCTTGCATCAGTATTTCC
* **
5599482 AGTGAAGAGTTCATAATGAGAAGAACTCATTTAAAGAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGA-GAAGAAGAAGTTCATAATGAGAAGAA-
5599547 TTT-TTCAA
64 TTTGTTCAA
5599555 TCCAACGCTT
Statistics
Matches: 157, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
91 153 0.97
92 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (90 bp):
AGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGAAGAAGAAGTTCATAATGAGAAGAATT
TGTTCAACCTTGCATCAGTATTTCC
Found at i:5599735 original size:3 final size:3
Alignment explanation
Indices: 5599727--5599764 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5599717 ACATTATATG
5599727 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5599765 ATGTTATTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5600348 original size:20 final size:21
Alignment explanation
Indices: 5600309--5600351 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5600299 GGAGATCGGA
5600309 AAGTCTTAAAGCCAACCGTGG
1 AAGTCTTAAAGCCAACCGTGG
5600330 AAGTCTTAAA-CTC-ACCGTGG
1 AAGTCTTAAAGC-CAACCGTGG
5600350 AA
1 AA
5600352 CCACCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (21 bp):
AAGTCTTAAAGCCAACCGTGG
Found at i:5600667 original size:2 final size:2
Alignment explanation
Indices: 5600660--5600688 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5600650 CTATAATTTC
5600660 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5600689 TCAAAACGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5602375 original size:15 final size:15
Alignment explanation
Indices: 5602351--5602381 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5602341 GTCCCCGCCG
5602351 AAAAACGGTTACGAC
1 AAAAACGGTTACGAC
*
5602366 AAAAATGGTTACGAC
1 AAAAACGGTTACGAC
5602381 A
1 A
5602382 GGTATAATAA
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:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (15 bp):
AAAAACGGTTACGAC
Found at i:5604175 original size:7 final size:7
Alignment explanation
Indices: 5604163--5604205 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
5604153 AATAATTGGA
*
5604163 TTTAGGT
1 TTTAGGG
5604170 TTTAGGG
1 TTTAGGG
5604177 TTTAGGG
1 TTTAGGG
5604184 TTATA--G
1 TT-TAGGG
5604190 TTTAGGG
1 TTTAGGG
5604197 TTTAGGG
1 TTTAGGG
5604204 TT
1 TT
5604206 ATTGCAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
5 2 0.06
6 3 0.09
7 25 0.78
8 2 0.06
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (7 bp):
TTTAGGG
Found at i:5604195 original size:20 final size:20
Alignment explanation
Indices: 5604170--5604207 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5604160 GGATTTAGGT
5604170 TTTAGGGTTTAGGGTTATAG
1 TTTAGGGTTTAGGGTTATAG
5604190 TTTAGGGTTTAGGGTTAT
1 TTTAGGGTTTAGGGTTAT
5604208 TGCAAAGACA
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:0.00, G:0.34, T:0.47
Consensus pattern (20 bp):
TTTAGGGTTTAGGGTTATAG
Found at i:5604278 original size:14 final size:14
Alignment explanation
Indices: 5604257--5604290 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5604247 AAGTAAGTAC
5604257 AATTTAGGGCTTAT
1 AATTTAGGGCTTAT
* *
5604271 AGTTTAGGGTTTAT
1 AATTTAGGGCTTAT
5604285 AATTTA
1 AATTTA
5604291 TGATTTAGGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (14 bp):
AATTTAGGGCTTAT
Found at i:5605021 original size:12 final size:13
Alignment explanation
Indices: 5605000--5605041 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
5604990 TTTTTTAATG
5605000 TTTATTTTATATTA
1 TTTA-TTTATATTA
*
5605014 TTTA-TTATACTA
1 TTTATTTATATTA
*
5605026 TTTATTTATTTTA
1 TTTATTTATATTA
5605039 TTT
1 TTT
5605042 CTAAACTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 11 0.46
13 9 0.38
14 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATTTATATTA
Found at i:5614088 original size:22 final size:22
Alignment explanation
Indices: 5614063--5614104 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5614053 TGTATAAATT
* *
5614063 TGTCCCGAAGGACCTCTGTATA
1 TGTCCCGAAGAACCTATGTATA
5614085 TGTCCCGAAGAACCTATGTA
1 TGTCCCGAAGAACCTATGTA
5614105 ACCCTCGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (22 bp):
TGTCCCGAAGAACCTATGTATA
Found at i:5614692 original size:20 final size:20
Alignment explanation
Indices: 5614652--5614692 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5614642 CGAAATTATT
*
5614652 TGGTATCGATACCCTCCGTA
1 TGGTATCGATACCCTACGTA
* *
5614672 TGGTATCGGTACCCTAGGTA
1 TGGTATCGATACCCTACGTA
5614692 T
1 T
5614693 CGATACCACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
TGGTATCGATACCCTACGTA
Found at i:5616198 original size:34 final size:33
Alignment explanation
Indices: 5616135--5616199 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5616125 TCAACAACTA
*
5616135 AAAATTTACTCTTCTTCTTCTCTCTAGTTTTAT
1 AAAATTTACTCTTCTTCTTCTCTCAAGTTTTAT
* * *
5616168 AAAATTTTCTCTTCTATTTTCTTTCAAGTTTT
1 AAAATTTACTCTTCT-TCTTCTCTCAAGTTTT
5616200 TTGCAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.22, C:0.18, G:0.03, T:0.57
Consensus pattern (33 bp):
AAAATTTACTCTTCTTCTTCTCTCAAGTTTTAT
Found at i:5625573 original size:33 final size:35
Alignment explanation
Indices: 5625536--5625613 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
5625526 CTTGTTCCAC
*
5625536 GAAAAAAAAAATG-A-AAAAAAAGTTCATTGTTTT
1 GAAAAAAAAAATGAAGAAAAAAAGTTCATTGTTTA
* * *
5625569 GAAAAAGAAATTGAAGAAAAAAATTTCATTGTTTA
1 GAAAAAAAAAATGAAGAAAAAAAGTTCATTGTTTA
*
5625604 GAACAAAAAA
1 GAAAAAAAAA
5625614 TGTTCACTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 11 0.30
34 1 0.03
35 25 0.68
ACGTcount: A:0.59, C:0.04, G:0.13, T:0.24
Consensus pattern (35 bp):
GAAAAAAAAAATGAAGAAAAAAAGTTCATTGTTTA
Found at i:5625614 original size:22 final size:23
Alignment explanation
Indices: 5625586--5625636 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5625576 AAATTGAAGA
*
5625586 AAAAAAT-TTCATTGTTTAGAAC
1 AAAAAATGTTCACTGTTTAGAAC
**
5625608 AAAAAATGTTCACTGTTTCTAAC
1 AAAAAATGTTCACTGTTTAGAAC
5625631 AAAAAA
1 AAAAAA
5625637 AAAGAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (23 bp):
AAAAAATGTTCACTGTTTAGAAC
Found at i:5627385 original size:17 final size:17
Alignment explanation
Indices: 5627360--5627393 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5627350 CTTTATCTCA
*
5627360 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
5627377 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
5627394 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:5632892 original size:23 final size:26
Alignment explanation
Indices: 5632839--5632887 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
5632829 ATATCACTGG
*
5632839 TTAATATGACATATTATTCTTTTAGA
1 TTAATATAACATATTATTCTTTTAGA
* *
5632865 ATAATATAACATA-TATTTTTTTA
1 TTAATATAACATATTATTCTTTTA
5632888 TTAATTTAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
TTAATATAACATATTATTCTTTTAGA
Found at i:5632943 original size:15 final size:14
Alignment explanation
Indices: 5632913--5632948 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
5632903 TACAAATGAT
5632913 AATATATATTTTAAA
1 AATAT-TATTTTAAA
5632928 AATATTATTTTAAA
1 AATATTATTTTAAA
5632942 AATATTA
1 AATATTA
5632949 AATCATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATATTATTTTAAA
Found at i:5633381 original size:19 final size:19
Alignment explanation
Indices: 5633354--5633393 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
5633344 TGCAATTTAA
*
5633354 TATATATATAACAAATTGT
1 TATAAATATAACAAATTGT
5633373 TATAAATATAACAAATTGT
1 TATAAATATAACAAATTGT
5633392 TA
1 TA
5633394 AGTTGAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TATAAATATAACAAATTGT
Found at i:5636951 original size:35 final size:35
Alignment explanation
Indices: 5636912--5636996 Score: 152
Period size: 35 Copynumber: 2.4 Consensus size: 35
5636902 AATACATAGC
*
5636912 AACTAACCAATCCCTGAAGTTTGCAACCTTATTTG
1 AACTAACCAATCCCTGAAGTTTGCAACCTCATTTG
*
5636947 AACTAACCAATCCTTGAAGTTTGCAACCTCATTTG
1 AACTAACCAATCCCTGAAGTTTGCAACCTCATTTG
5636982 AACTAACCAATCCCT
1 AACTAACCAATCCCT
5636997 AATTTAACAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.33, C:0.28, G:0.09, T:0.29
Consensus pattern (35 bp):
AACTAACCAATCCCTGAAGTTTGCAACCTCATTTG
Found at i:5646433 original size:52 final size:52
Alignment explanation
Indices: 5646371--5646473 Score: 197
Period size: 52 Copynumber: 2.0 Consensus size: 52
5646361 AAATTGGACA
5646371 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
*
5646423 CATAGAAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
1 CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAG
5646474 AATATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (52 bp):
CATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAAGG
Found at i:5655210 original size:9 final size:9
Alignment explanation
Indices: 5655183--5655233 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
5655173 TTATTTTATT
5655183 TATTATTAGC
1 TATTATTA-C
5655193 -ATTATTTAC
1 TATTA-TTAC
5655202 TATTATTAC
1 TATTATTAC
* *
5655211 TATTGTTAT
1 TATTATTAC
*
5655220 TATTATTAA
1 TATTATTAC
5655229 TATTA
1 TATTA
5655234 CCTATTACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 28 0.80
10 7 0.20
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (9 bp):
TATTATTAC
Found at i:5656055 original size:21 final size:21
Alignment explanation
Indices: 5656031--5656076 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5656021 AAAGAAAAAA
*
5656031 AGAAAAAGGGGAAGAGTAGAG
1 AGAAAAAGGAGAAGAGTAGAG
** *
5656052 AGAATGAGGAGAAGAGTTGAG
1 AGAAAAAGGAGAAGAGTAGAG
5656073 AGAA
1 AGAA
5656077 TTGTTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.41, T:0.09
Consensus pattern (21 bp):
AGAAAAAGGAGAAGAGTAGAG
Found at i:5660460 original size:4 final size:4
Alignment explanation
Indices: 5660451--5660477 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5660441 TCAAAGAAAA
5660451 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
5660478 AAACAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5662377 original size:66 final size:64
Alignment explanation
Indices: 5662244--5662378 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 64
5662234 GTTTTCTGAA
* **
5662244 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAATCTTTGAATTTGTTTCTTTGG
1 AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTCGAAAAAATCTTTGAATGAGTTTCTTTGG
* * * *
5662308 AAACAATA-TTTTTTCTCTTTTGAGACAGTTTCTTTCGAAGGAAAATCTTTGAGTGAGTTTCTCT
1 AAACAA-AGTTTTGTCTCTCTTGAGACAATTTCTTTCGAA--AAAATCTTTGAATGAGTTTCT-T
5662372 T-G
62 TGG
5662374 AAACA
1 AAACA
5662379 TCTGTCTATG
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
64 33 0.55
65 1 0.02
66 24 0.40
67 2 0.03
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (64 bp):
AAACAAAGTTTTGTCTCTCTTGAGACAATTTCTTTCGAAAAAATCTTTGAATGAGTTTCTTTGG
Found at i:5662463 original size:31 final size:31
Alignment explanation
Indices: 5662428--5662508 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 31
5662418 TCCCTTAACA
* *
5662428 GTTTCTCTGGAAACACAAAATCTTTGAGTTT
1 GTTTCACTGGAAACAAAAAATCTTTGAGTTT
*
5662459 GTTTCACTTGAAACAAAAAAAAAATCTTTGAGTTT
1 GTTTCACTGGAAAC----AAAAAATCTTTGAGTTT
5662494 GTTTCACTGGAAACA
1 GTTTCACTGGAAACA
5662509 GAATGAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
31 13 0.31
35 29 0.69
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (31 bp):
GTTTCACTGGAAACAAAAAATCTTTGAGTTT
Found at i:5662534 original size:37 final size:35
Alignment explanation
Indices: 5662444--5662548 Score: 129
Period size: 35 Copynumber: 2.9 Consensus size: 35
5662434 CTGGAAACAC
*
5662444 AAAATCTTTGAGTTTGTTTCACTTGAAACAAAAAA
1 AAAATCTTTGAGTTTGTTTCACTGGAAACAAAAAA
*
5662479 AAAATCTTTGAGTTTGTTTCACTGGAAACAGAATGAA
1 AAAATCTTTGAGTTTGTTTCACTGGAAACA-AA-AAA
** * **
5662516 ACTATCTTTGAGTATGTTTCTTTGGAAACAAAA
1 AAAATCTTTGAGTTTGTTTCACTGGAAACAAAA
5662549 TTTTGTCTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 29 0.48
36 4 0.07
37 27 0.45
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (35 bp):
AAAATCTTTGAGTTTGTTTCACTGGAAACAAAAAA
Found at i:5662637 original size:29 final size:29
Alignment explanation
Indices: 5662568--5662640 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
5662558 TCTCGAGACA
* * *
5662568 ATTTCTTTTGAGAAAATCATCTTTGAGTCT
1 ATTTCTTTTGA-AACATCATATTTGAGTCG
*
5662598 ATTTATTTTGAAACATCATATTTGAGTCG
1 ATTTCTTTTGAAACATCATATTTGAGTCG
* *
5662627 GTTTCTCTTGAAAC
1 ATTTCTTTTGAAAC
5662641 CATTATCCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 26 0.72
30 10 0.28
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (29 bp):
ATTTCTTTTGAAACATCATATTTGAGTCG
Found at i:5663209 original size:3 final size:3
Alignment explanation
Indices: 5663192--5663247 Score: 78
Period size: 3 Copynumber: 18.7 Consensus size: 3
5663182 CTACCAAAAA
*
5663192 TAT TAT T-T TATT TAT TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5663237 TAT TAA TAT TA
1 TAT TAT TAT TA
5663248 CCTATTATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5664036 original size:132 final size:132
Alignment explanation
Indices: 5663890--5664153 Score: 519
Period size: 132 Copynumber: 2.0 Consensus size: 132
5663880 AAGGAAAACC
5663890 ACAATATATTCAAAAAACACATAGAAACAAAATAGGAAAAAAACATTACCTTTCATTGTCTGGTG
1 ACAATATATTCAAAAAACACATAGAAACAAAATAGGAAAAAAACATTACCTTTCATTGTCTGGTG
5663955 GTTGTGGTTTTCATCAGAGGAGAAGAAGAGCCTCATCGAAGGTAAAGAGGGTTTTAGTTATGTGT
66 GTTGTGGTTTTCATCAGAGGAGAAGAAGAGCCTCATCGAAGGTAAAGAGGGTTTTAGTTATGTGT
5664020 GT
131 GT
5664022 ACAATATATTCAAAAAACACATAGAAACAAAATAGGAAAAAAACATTACCTTTCATTGTCTGGTG
1 ACAATATATTCAAAAAACACATAGAAACAAAATAGGAAAAAAACATTACCTTTCATTGTCTGGTG
*
5664087 GTTGTGGTTTTCATCAGAGGAGAAGAAGAGCCTCATCGAAGGTCAAGAGGGTTTTAGTTATGTGT
66 GTTGTGGTTTTCATCAGAGGAGAAGAAGAGCCTCATCGAAGGTAAAGAGGGTTTTAGTTATGTGT
5664152 GT
131 GT
5664154 CTCGATTTAA
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 131 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (132 bp):
ACAATATATTCAAAAAACACATAGAAACAAAATAGGAAAAAAACATTACCTTTCATTGTCTGGTG
GTTGTGGTTTTCATCAGAGGAGAAGAAGAGCCTCATCGAAGGTAAAGAGGGTTTTAGTTATGTGT
GT
Found at i:5681103 original size:16 final size:16
Alignment explanation
Indices: 5681060--5681106 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5681050 TTTTATATAT
5681060 TATTT-TCAT-TAATA
1 TATTTATCATATAATA
*
5681074 TCTTTTACTCATATAATA
1 T-ATTTA-TCATATAATA
5681092 TATTTATCATATAAT
1 TATTTATCATATAAT
5681107 TCATGTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 3 0.11
16 9 0.33
17 8 0.30
18 6 0.22
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTATCATATAATA
Found at i:5689536 original size:14 final size:15
Alignment explanation
Indices: 5689517--5689557 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
5689507 TCTTCCTCCG
*
5689517 TCTTTGGTAA-CTGT
1 TCTTTGGAAAGCTGT
5689531 TCTTTGGAAAGTCTGT
1 TCTTTGGAAAG-CTGT
5689547 TCTTTGGAAAG
1 TCTTTGGAAAG
5689558 TCTGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.38
16 15 0.62
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (15 bp):
TCTTTGGAAAGCTGT
Found at i:5689548 original size:16 final size:16
Alignment explanation
Indices: 5689527--5689561 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5689517 TCTTTGGTAA
5689527 CTGTTCTTTGGAAAGT
1 CTGTTCTTTGGAAAGT
5689543 CTGTTCTTTGGAAAGT
1 CTGTTCTTTGGAAAGT
5689559 CTG
1 CTG
5689562 AAATAAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (16 bp):
CTGTTCTTTGGAAAGT
Found at i:5694535 original size:16 final size:16
Alignment explanation
Indices: 5694507--5694559 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
5694497 TAAATAAACG
*
5694507 AACACAAACGAACACA
1 AACATAAACGAACACA
* *
5694523 AACATAAATGAACACG
1 AACATAAACGAACACA
*
5694539 AACATAAACGAACATA
1 AACATAAACGAACACA
5694555 AACAT
1 AACAT
5694560 TGGAGACCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.60, C:0.23, G:0.08, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:5694541 original size:32 final size:30
Alignment explanation
Indices: 5694496--5694559 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
5694486 CGTTCATTTA
5694496 ATAAATAAACGAACACAAACGAACACAAAC
1 ATAAATAAACGAACACAAACGAACACAAAC
* *
5694526 ATAAATGAACACGAACATAAACGAACATAAAC
1 ATAAAT-AA-ACGAACACAAACGAACACAAAC
5694558 AT
1 AT
5694560 TGGAGACCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.20
31 2 0.07
32 22 0.73
ACGTcount: A:0.61, C:0.20, G:0.08, T:0.11
Consensus pattern (30 bp):
ATAAATAAACGAACACAAACGAACACAAAC
Found at i:5694549 original size:10 final size:10
Alignment explanation
Indices: 5694500--5694557 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
5694490 CATTTAATAA
5694500 ATAAACGAAC
1 ATAAACGAAC
*
5694510 ACAAACGAAC
1 ATAAACGAAC
* *
5694520 ACAAAC-ATAA
1 ATAAACGA-AC
5694530 ATGAACACGAAC
1 AT-AA-ACGAAC
5694542 ATAAACGAAC
1 ATAAACGAAC
5694552 ATAAAC
1 ATAAAC
5694558 ATTGGAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 1 0.03
10 29 0.73
11 4 0.10
12 5 0.12
13 1 0.03
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:5694810 original size:23 final size:23
Alignment explanation
Indices: 5694756--5694835 Score: 99
Period size: 23 Copynumber: 3.4 Consensus size: 23
5694746 AAAAAATTAA
*
5694756 GAGCTCGATTAAAACTCGAG-ACT
1 GAGCTCGATTAAAACTCG-GTTCT
5694779 CGAGCTCGATTAAAACTCGGTTCT
1 -GAGCTCGATTAAAACTCGGTTCT
* *
5694803 GAGCTCGATTGAAGCTCGGTTCT
1 GAGCTCGATTAAAACTCGGTTCT
*
5694826 GAGCTTGATT
1 GAGCTCGATT
5694836 CTGAGCTCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 31 0.61
24 20 0.39
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (23 bp):
GAGCTCGATTAAAACTCGGTTCT
Found at i:5694837 original size:12 final size:12
Alignment explanation
Indices: 5694794--5694848 Score: 60
Period size: 12 Copynumber: 4.7 Consensus size: 12
5694784 TCGATTAAAA
*
5694794 CTCGGTTCTGAG
1 CTCGATTCTGAG
5694806 CTCGA-T-TGAAG
1 CTCGATTCTG-AG
*
5694817 CTCGGTTCTGAG
1 CTCGATTCTGAG
*
5694829 CTTGATTCTGAG
1 CTCGATTCTGAG
5694841 CTCGATTC
1 CTCGATTC
5694849 AAGCTCAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 2 0.06
11 7 0.20
12 24 0.69
13 2 0.06
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.35
Consensus pattern (12 bp):
CTCGATTCTGAG
Found at i:5695743 original size:14 final size:14
Alignment explanation
Indices: 5695726--5695757 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5695716 AATGAACATA
*
5695726 AACGAACATAATCG
1 AACGAACATAACCG
5695740 AACGAACATAACCG
1 AACGAACATAACCG
5695754 AACG
1 AACG
5695758 TTCACGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:5695746 original size:24 final size:24
Alignment explanation
Indices: 5695706--5695756 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
5695696 AATTGGGTTA
*
5695706 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
5695730 AACAT-AATCGAACGAACATAACCG
1 AACATAAAT-GAACGAACATAAACG
5695754 AAC
1 AAC
5695757 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:5698814 original size:23 final size:22
Alignment explanation
Indices: 5698776--5698818 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5698766 CAATTCCTTT
5698776 ATCTTTTATTTATCTTGTTTTA
1 ATCTTTTATTTATCTTGTTTTA
*
5698798 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTATTTATCTTGTTT
5698819 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTATTTATCTTGTTTTA
Found at i:5703419 original size:23 final size:22
Alignment explanation
Indices: 5703381--5703423 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
5703371 CAATTCCTTT
5703381 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
5703403 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
5703424 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:5706055 original size:15 final size:15
Alignment explanation
Indices: 5706037--5706066 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5706027 GTTGTCGCTT
*
5706037 CCATCACTGCTATTG
1 CCATCACCGCTATTG
5706052 CCATCACCGCTATTG
1 CCATCACCGCTATTG
5706067 ATGCTACCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.37, G:0.13, T:0.30
Consensus pattern (15 bp):
CCATCACCGCTATTG
Found at i:5706147 original size:21 final size:21
Alignment explanation
Indices: 5706123--5706163 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5706113 CGCTATTGTC
*
5706123 GCTATCACTGCTGCTGTCATT
1 GCTATCACTGATGCTGTCATT
*
5706144 GCTATCACTGATGTTGTCAT
1 GCTATCACTGATGCTGTCAT
5706164 CGTCGTCGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
GCTATCACTGATGCTGTCATT
Found at i:5709323 original size:23 final size:22
Alignment explanation
Indices: 5709286--5709349 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
5709276 CAACTCATAT
5709286 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCA-GTAG
* * *
5709309 AATTGCACCGTAGTGTCGAGTAG
1 AAATGCACCGAAGTG-CCAGTAG
*
5709332 AAATACACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
5709350 TATAAGGTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.25, T:0.17
Consensus pattern (22 bp):
AAATGCACCGAAGTGCCAGTAG
Found at i:5709747 original size:2 final size:2
Alignment explanation
Indices: 5709740--5709783 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5709730 ATGTCTTATC
5709740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5709782 AT
1 AT
5709784 GTATGTATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5709867 original size:2 final size:2
Alignment explanation
Indices: 5709860--5709922 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
5709850 ATTCATCTTC
5709860 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5709901 AT AT AT -T AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
5709923 CATTTTTCCT
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5714595 original size:23 final size:23
Alignment explanation
Indices: 5714569--5714633 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
5714559 CACCACAGCT
*
5714569 CATATAAATGCACCGAAGTACCA
1 CATAGAAATGCACCGAAGTACCA
* * * *
5714592 CATAGAATTACACCGTAGTACCG
1 CATAGAAATGCACCGAAGTACCA
*
5714615 CGTAGAAATGCACCGAAGT
1 CATAGAAATGCACCGAAGT
5714634 GCCATATAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTACCA
Found at i:5715110 original size:2 final size:2
Alignment explanation
Indices: 5715103--5715145 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5715093 ATTCATCTTC
5715103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5715145 A
1 A
5715146 ATTTTTCCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5716381 original size:63 final size:63
Alignment explanation
Indices: 5716241--5716401 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 63
5716231 TTCCCTTGAT
5716241 GTGCATCGATGCACTACC-CATGCATCGATGCACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATGCACAAATCA-CTTCGATGTTTTCATTTTAAGGGG
* * * *
5716305 GTGCATCGATGCACTCCTTATGCATTGATGCACTAATGCA-TTCGATG-TTTCAATTTTTAA-TG
1 GTGCATCGATGCACTCCTCATGCATCGATGCACAAAT-CACTTCGATGTTTTC-A-TTTTAAGGG
5716367 G
63 G
* *
5716368 GTGCATCGATGCACGTCCT-GTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTCATGCATCGATGCACA
5716402 CTGAAGAATT
Statistics
Matches: 84, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
62 4 0.05
63 37 0.44
64 41 0.49
65 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATGCACAAATCACTTCGATGTTTTCATTTTAAGGGG
Found at i:5719849 original size:23 final size:23
Alignment explanation
Indices: 5719805--5719864 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
5719795 CAGCTCATAT
*
5719805 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTACCACGTAG
* * *
5719828 AATTGCACCGTAGTACCGCGTAG
1 AAATGCACCGAAGTACCACGTAG
5719851 AAATGCACCGAAGT
1 AAATGCACCGAAGT
5719865 GCCATATAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTACCACGTAG
Found at i:5720267 original size:2 final size:2
Alignment explanation
Indices: 5720260--5720287 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5720250 ATGTATAATC
5720260 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
5720288 TCACATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5720353 original size:2 final size:2
Alignment explanation
Indices: 5720346--5720397 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
5720336 ATTCATCTTC
5720346 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5720388 AT AT AT AT AT
1 AT AT AT AT AT
5720398 CATTTTTCCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5721088 original size:20 final size:19
Alignment explanation
Indices: 5721065--5721102 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5721055 TCTTTTATAT
5721065 TCATATAATTTATTATCATA
1 TCATATAATTTA-TATCATA
*
5721085 TCATATAGTTTATATCAT
1 TCATATAATTTATATCAT
5721103 CATAACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (19 bp):
TCATATAATTTATATCATA
Found at i:5721647 original size:64 final size:64
Alignment explanation
Indices: 5721495--5721656 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
5721485 TTCCCTTGAA
** * *
5721495 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTACATATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
* * * * ** *
5721559 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAA-TGG
1 GTGCATCGATGCACTACATATGCATCGATACACAAATCACATTCGATGTTTCCA-TTTTAAGGGG
* * *
5721623 GTGCATCGATGCACTTCATGTGCATTGATACACA
1 GTGCATCGATGCACTACATATGCATCGATACACA
5721657 CTGAATAATT
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTACATATGCATCGATACACAAATCACATTCGATGTTTCCATTTTAAGGGG
Found at i:5722967 original size:19 final size:19
Alignment explanation
Indices: 5722945--5722981 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
5722935 ATTTAGTTGC
5722945 CTAAATTATAGCCTAATTA
1 CTAAATTATAGCCTAATTA
5722964 CTAAATTATAGCCTAATT
1 CTAAATTATAGCCTAATT
5722982 GTTAGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (19 bp):
CTAAATTATAGCCTAATTA
Found at i:5727677 original size:274 final size:271
Alignment explanation
Indices: 5726931--5727724 Score: 900
Period size: 274 Copynumber: 2.9 Consensus size: 271
5726921 ATTTAAGTTT
* * * *
5726931 TTTTGTAAAAATAAGGAATTTTTAGAAGATTTTCTGTTTGCTCTTTCTATAGAGTCTGGAAAGTC
1 TTTTGTAAAACTAAGGAATTTTCAGAAGATTTTCTGTTTGCTCTTTCTAAACAGTCTGG-AAGTC
* * * * * * * * *
5726996 ACCAGTTCCTATCCACCACTCACGCCACCATTGTCATCGTCTCTGGCCGCTATTGCTAGAAAATA
65 AGCAGTTCCTATCCCCCACTCATGTCATCATTGTCATCGTCTTTGGCCGCTATCGCCAAAAAATA
* * * *
5727061 TTGAAGGCTTGT-TTAGGCTTCTTGATCACTATTCTAATGTTGTATTCGCT-GAAAAATATTAAA
130 TTGAAGGCTTGTCTCA-GCTTCTTGATCACTATTTTGATGTTGCATTCGCTAG-AAAATATTAAA
* * * * *
5727124 GGTCTCGTTTGAACATCAACTTAGATCAGGTATCTTATTCTTGTAATTGCTATTTCTTTCGTGTC
193 -GTCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTTCGTGTC
5727189 TTTACATTTCTTTCA
257 TTTACATTTCTTTCA
* * * *
5727204 TTTTGTAAAACTAATGAATTTTCAAAAGATTTTATGTTTTCTCTTTCTAAACAGTCTGGAAGTCA
1 TTTTGTAAAACTAAGGAATTTTCAGAAGATTTTCTGTTTGCTCTTTCTAAACAGTCTGGAAGTCA
* * * * * * * * *
5727269 GC-GATTCATGT-ACTCAGCTCATGTCGTCATCGTCATCGTCTTTGGTCGTTATCGCCGAAAAAT
66 GCAG-TTCCTATCCCCCA-CTCATGTCATCATTGTCATCGTCTTTGGCCGCTATCGCCAAAAAAT
* * * *
5727332 ATTGAAGGCTTGTCTCGGCTTCTTGATCGCTATTTTGATGTTGCATTCGCCAAAAAATATTAAAA
129 ATTGAAGGCTTGTCTCAGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAGAAAATATT--AA
*
5727397 AGTCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTCTC-TTT
192 AGTCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTT-TCGTGT
**
5727461 CTTTACATTTCCTTTTG
256 CTTTACATTT-CTTTCA
* * **
5727478 TTTTGTTAAACTAAGGAATTTTCAGAAGATTTTCTGTTTGCT-TTTTTCAAACAGTCCAGAAGTC
1 TTTTGTAAAACTAAGGAATTTTCAGAAGATTTTCTGTTTGCTCTTTCT-AAACAGTCTGGAAGTC
* * * * *
5727542 AGCAGTCCCTATCCCCCACTCATGTTATCGTTGTCATCATCTTTGACCGCTATCGTCCAAAAAAT
65 AGCAGTTCCTATCCCCCACTCATGTCATCATTGTCATCGTCTTTGGCCGCTATCG-CCAAAAAAT
* * *
5727607 ATCGAAGTCTTGTCTCAACTTCTTGATCACTATTTTGATGTTGCATTCGCTAGAAAATATTGAAA
129 ATTGAAGGCTTGTCTCAGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAGAAAATATT-AAA
* * *
5727672 GTCTCGTTTGAGCATCAACTCAGATTATGTATCTCATT-TTCGTAATTCTTATT
193 GTCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTT-GTAATTGTTATT
5727725 ATTTCTTTTG
Statistics
Matches: 433, Mismatches: 75, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
271 3 0.01
272 96 0.22
273 122 0.28
274 146 0.34
275 66 0.15
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (271 bp):
TTTTGTAAAACTAAGGAATTTTCAGAAGATTTTCTGTTTGCTCTTTCTAAACAGTCTGGAAGTCA
GCAGTTCCTATCCCCCACTCATGTCATCATTGTCATCGTCTTTGGCCGCTATCGCCAAAAAATAT
TGAAGGCTTGTCTCAGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAGAAAATATTAAAGTC
TCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTTCGTGTCTTTA
CATTTCTTTCA
Found at i:5728340 original size:19 final size:19
Alignment explanation
Indices: 5728316--5728365 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5728306 TACTCAAATC
5728316 AATATTATTTTATGTA-TTT
1 AATATTATTTTAT-TATTTT
* *
5728335 AATATTAATATATTATTTT
1 AATATTATTTTATTATTTT
*
5728354 AATACTATTTTA
1 AATATTATTTTA
5728366 GTAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTATTTT
Found at i:5728553 original size:33 final size:28
Alignment explanation
Indices: 5728485--5728542 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
5728475 TATTGCATGT
*
5728485 ATATTTTTATTTTAATAATTAATAATTA
1 ATATTTTTATTTTAAAAATTAATAATTA
5728513 ATATTTTTATTTTAGTAAAATATAATAATT
1 ATATTTTTATTTTA--AAAAT-TAATAATT
5728543 TTCATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 14 0.54
30 4 0.15
31 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
ATATTTTTATTTTAAAAATTAATAATTA
Found at i:5738297 original size:6 final size:6
Alignment explanation
Indices: 5738286--5738344 Score: 61
Period size: 6 Copynumber: 9.8 Consensus size: 6
5738276 GAACCCACTT
5738286 TTTTTC TTTTTC TTTTTC -TTTTC TTTTCATC TTCTTT- TTTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT--TC TT-TTTC TTTTTC TTTTTC
*
5738334 TTCTTC TTTTT
1 TTTTTC TTTTT
5738345 TCAATTTAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
5 13 0.28
6 26 0.57
7 1 0.02
8 4 0.09
9 2 0.04
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:5738344 original size:17 final size:17
Alignment explanation
Indices: 5738286--5738345 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
5738276 GAACCCACTT
*
5738286 TTTTTCTTTTTCTTTTTC
1 TTTTT-TTTTTCTTCTTC
* *
5738304 TTTTCTTTTCATCTTCTTT
1 TTTT-TTTT-TTCTTCTTC
5738323 TTTTTTTTTTCTTCTTC
1 TTTTTTTTTTCTTCTTC
5738340 TTTTTT
1 TTTTTT
5738346 CAATTTAGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.37
18 11 0.31
19 11 0.31
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTCTTCTTC
Found at i:5738415 original size:6 final size:7
Alignment explanation
Indices: 5738383--5738414 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
5738373 ACCCTAAATA
5738383 TTTTTTC
1 TTTTTTC
5738390 -TTTTTC
1 TTTTTTC
5738396 TTTTTTC
1 TTTTTTC
5738403 TTTTTTC
1 TTTTTTC
5738410 TTTTT
1 TTTTT
5738415 CGACTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:5738442 original size:69 final size:70
Alignment explanation
Indices: 5738317--5738448 Score: 162
Period size: 69 Copynumber: 1.9 Consensus size: 70
5738307 TCTTTTCATC
* * * *
5738317 TTCTTTTTTTTTTTTTCTTCTTCTTTTTTCAATTTAGGACGCCCTTTCGGGATTTCACCCTAAAT
1 TTCTTTTTTTTTTTTTCTTCTTCTTTTTTCAACTTAGGACGCCATCTCGCGATTTCACCCTAAAT
5738382 ATTTT
66 ATTTT
* * *
5738387 TTCTTTTTCTTTTTTCTT-TT-TTC-TTTTTCGACTTAGGACGCCATCTCGCGTTTTCATCCTAA
1 TTCTTTTT-TTTTTT-TTCTTCTTCTTTTTTCAACTTAGGACGCCATCTCGCGATTTCACCCTAA
5738449 GCGAAGTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
69 32 0.60
70 11 0.21
71 8 0.15
72 2 0.04
ACGTcount: A:0.13, C:0.22, G:0.09, T:0.56
Consensus pattern (70 bp):
TTCTTTTTTTTTTTTTCTTCTTCTTTTTTCAACTTAGGACGCCATCTCGCGATTTCACCCTAAAT
ATTTT
Found at i:5744707 original size:23 final size:20
Alignment explanation
Indices: 5744684--5744721 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5744674 ATAAATGTAA
5744684 AAACATGGAAAATATAAAAAT
1 AAACAT-GAAAATATAAAAAT
5744705 AAACATGAAAA-ATAAAA
1 AAACATGAAAATATAAAA
5744722 TGCAAAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (20 bp):
AAACATGAAAATATAAAAAT
Found at i:5748042 original size:29 final size:29
Alignment explanation
Indices: 5748003--5748080 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
5747993 TAAAGTAATG
* *
5748003 AAAAATAAATAAAT-AAAATACAAAAAATC
1 AAAAAGAAATAAATCAAAAAACAAAAAA-C
*
5748032 AAAAAGAAATAAATCAAAAAACCAAAAAC
1 AAAAAGAAATAAATCAAAAAACAAAAAAC
**
5748061 AAAAATCAA-AAATCAAAAAA
1 AAAAAGAAATAAATCAAAAAA
5748081 AATAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.26
29 21 0.49
30 11 0.26
ACGTcount: A:0.77, C:0.10, G:0.01, T:0.12
Consensus pattern (29 bp):
AAAAAGAAATAAATCAAAAAACAAAAAAC
Found at i:5748045 original size:15 final size:15
Alignment explanation
Indices: 5748003--5748085 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 15
5747993 TAAAGTAATG
*
5748003 AAAAATAAATAAAT-
1 AAAAACAAATAAATC
5748017 AAAATACAAA-AAATC
1 AAAA-ACAAATAAATC
*
5748032 AAAAAGAAATAAATC
1 AAAAACAAATAAATC
*
5748047 AAAAAACCAA-AAA-C
1 -AAAAACAAATAAATC
5748061 AAAAATC-AA-AAATC
1 AAAAA-CAAATAAATC
5748075 AAAAA-AAATAA
1 AAAAACAAATAA
5748086 TAAAAGAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 12 0.21
14 22 0.39
15 16 0.28
16 7 0.12
ACGTcount: A:0.77, C:0.10, G:0.01, T:0.12
Consensus pattern (15 bp):
AAAAACAAATAAATC
Found at i:5748063 original size:6 final size:7
Alignment explanation
Indices: 5748025--5748079 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
5748015 ATAAAATACA
5748025 AAAAATC
1 AAAAATC
**
5748032 AAAAAGA
1 AAAAATC
5748039 AATAAATC
1 AA-AAATC
*
5748047 AAAAAACC
1 -AAAAATC
5748055 AAAAA-C
1 AAAAATC
5748061 AAAAATC
1 AAAAATC
5748068 AAAAATC
1 AAAAATC
5748075 AAAAA
1 AAAAA
5748080 AAATAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 6 0.15
7 25 0.62
8 7 0.17
9 2 0.05
ACGTcount: A:0.76, C:0.13, G:0.02, T:0.09
Consensus pattern (7 bp):
AAAAATC
Found at i:5748063 original size:14 final size:15
Alignment explanation
Indices: 5748025--5748080 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
5748015 ATAAAATACA
5748025 AAAAATCAAAAAGA--
1 AAAAATCAAAAA-ACC
5748039 AATAAATCAAAAAACC
1 AA-AAATCAAAAAACC
*
5748055 AAAAA-C-AAAAATC
1 AAAAATCAAAAAACC
5748068 AAAAATCAAAAAA
1 AAAAATCAAAAAA
5748081 AATAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 11 0.31
14 5 0.14
15 18 0.50
16 2 0.06
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.09
Consensus pattern (15 bp):
AAAAATCAAAAAACC
Found at i:5748070 original size:13 final size:14
Alignment explanation
Indices: 5748025--5748079 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
5748015 ATAAAATACA
**
5748025 AAAAATCAAAAAGA
1 AAAAATCAAAAACC
5748039 AATAAATCAAAAAACC
1 AA-AAATC-AAAAACC
*
5748055 AAAAA-CAAAAATC
1 AAAAATCAAAAACC
5748068 AAAAATCAAAAA
1 AAAAATCAAAAA
5748080 AAATAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 11 0.31
14 9 0.26
15 8 0.23
16 7 0.20
ACGTcount: A:0.76, C:0.13, G:0.02, T:0.09
Consensus pattern (14 bp):
AAAAATCAAAAACC
Found at i:5748080 original size:8 final size:8
Alignment explanation
Indices: 5748017--5748080 Score: 50
Period size: 7 Copynumber: 8.5 Consensus size: 8
5748007 ATAAATAAAT
5748017 AAAATACAA
1 AAAAT-CAA
5748026 AAAATCAA
1 AAAATCAA
5748034 AAAGA--AA
1 AAA-ATCAA
*
5748041 TAAATCAA
1 AAAATCAA
*
5748049 AAAA-CCA
1 AAAATCAA
5748056 AAAA-C-A
1 AAAATCAA
5748062 AAAATC-A
1 AAAATCAA
5748069 AAAATCAA
1 AAAATCAA
5748077 AAAA
1 AAAA
5748081 AATAATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.13
7 19 0.40
8 16 0.34
9 6 0.13
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.09
Consensus pattern (8 bp):
AAAATCAA
Found at i:5748194 original size:34 final size:34
Alignment explanation
Indices: 5748151--5748216 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
5748141 TGTAATTGGT
5748151 TTTCTGGAAAACCAATTCCAGAAAACCAATTATA
1 TTTCTGGAAAACCAATTCCAGAAAACCAATTATA
5748185 TTTCTGGAAAACCAATTCCAGAAAACCAATTA
1 TTTCTGGAAAACCAATTCCAGAAAACCAATTA
5748217 CGTTGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (34 bp):
TTTCTGGAAAACCAATTCCAGAAAACCAATTATA
Found at i:5750606 original size:33 final size:33
Alignment explanation
Indices: 5750517--5750608 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
5750507 AAATTATATA
* * *
5750517 TTCAATGTCTAACAATCTAAAAAAAATTTCAAT
1 TTCAATATCCAACAATCTAAAAACAATTTCAAT
*
5750550 TTCAATATCCAACAATCTAAAAACATTTTCAAT
1 TTCAATATCCAACAATCTAAAAACAATTTCAAT
*
5750583 TTCAATATCCAACAAACTAAAAACAA
1 TTCAATATCCAACAATCTAAAAACAA
5750609 CAATATTCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.50, C:0.20, G:0.01, T:0.29
Consensus pattern (33 bp):
TTCAATATCCAACAATCTAAAAACAATTTCAAT
Found at i:5752427 original size:13 final size:13
Alignment explanation
Indices: 5752409--5752446 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
5752399 CAATTCTAAA
*
5752409 CAATTTTATTTTT
1 CAATTTTATTTCT
5752422 CAATTTTATTTCT
1 CAATTTTATTTCT
5752435 CAATTTTATTTC
1 CAATTTTATTTC
5752447 ATAAGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
CAATTTTATTTCT
Found at i:5752500 original size:36 final size:36
Alignment explanation
Indices: 5752454--5752585 Score: 223
Period size: 36 Copynumber: 3.7 Consensus size: 36
5752444 TTCATAAGTA
5752454 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
* *
5752490 ATT-ATCTTTTACCTAAAGATAAAGTTCATATTACGT
1 -TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
5752526 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
5752562 TTAAGCTTTTACCT-AAGCTAAAGT
1 TTAAGCTTTTACCTAAAGCTAAAGT
5752586 GGATGTAATT
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
35 12 0.13
36 76 0.84
37 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (36 bp):
TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
Found at i:5753423 original size:34 final size:34
Alignment explanation
Indices: 5753384--5753462 Score: 140
Period size: 34 Copynumber: 2.3 Consensus size: 34
5753374 TCATATAACA
5753384 GAAATATTAATCGATGAGAACAAATTGAAAATAC
1 GAAATATTAATCGATGAGAACAAATTGAAAATAC
* *
5753418 GAAATATTAATCTATGAGAACAAATTGAGAATAC
1 GAAATATTAATCGATGAGAACAAATTGAAAATAC
5753452 GAAATATTAAT
1 GAAATATTAAT
5753463 TTTTGCGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.27
Consensus pattern (34 bp):
GAAATATTAATCGATGAGAACAAATTGAAAATAC
Found at i:5754600 original size:14 final size:14
Alignment explanation
Indices: 5754581--5754610 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5754571 GAATCTGACG
5754581 AATGGTAATATGGA
1 AATGGTAATATGGA
*
5754595 AATGGTAATCTGGA
1 AATGGTAATATGGA
5754609 AA
1 AA
5754611 AGTTGAGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (14 bp):
AATGGTAATATGGA
Found at i:5755199 original size:2 final size:2
Alignment explanation
Indices: 5755192--5755216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5755182 AATAAATTTA
5755192 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 A
5755217 ATGTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5757644 original size:2 final size:2
Alignment explanation
Indices: 5757637--5757725 Score: 160
Period size: 2 Copynumber: 44.5 Consensus size: 2
5757627 GGATGTTTTA
5757637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5757679 AT AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5757721 AT AT A
1 AT AT A
5757726 CACACACACA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5758842 original size:14 final size:15
Alignment explanation
Indices: 5758811--5758851 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
5758801 TCAAACATTA
5758811 TAAAT-TTTAAAATG
1 TAAATATTTAAAATG
*
5758825 TAAATATTTAATAT-
1 TAAATATTTAAAATG
*
5758839 TAAATAATTAAAA
1 TAAATATTTAAAA
5758852 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TAAATATTTAAAATG
Found at i:5761256 original size:25 final size:24
Alignment explanation
Indices: 5761203--5761256 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
5761193 TGTCCGTTCG
* *
5761203 ATTTTAAAAATATTTATTGTTTTA
1 ATTTTAAAAATATTTATTATTTCA
*
5761227 TTTTTAGAAAATAATTT-TTATTTCA
1 ATTTTA-AAAAT-ATTTATTATTTCA
5761252 ATTTT
1 ATTTT
5761257 CTTTTGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 5 0.21
25 15 0.62
26 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTTTAAAAATATTTATTATTTCA
Found at i:5761553 original size:183 final size:183
Alignment explanation
Indices: 5761208--5761558 Score: 514
Period size: 183 Copynumber: 1.9 Consensus size: 183
5761198 GTTCGATTTT
5761208 AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAATTTTCTTTTGAAAATAAGAG
1 AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAATTTTCTTTTGAAAATAAGAG
5761273 AATACGTTTGATTAATATAAATAAAAATTCAAATTCAGAAATAAAAAAACAAAAATATATTTAGT
66 AATACGTTTGATTAATATAAATAAAAATTCAAATTCAGAAAT-----AACAAAAATATATTTAGT
5761338 ATCTAACTTTTTAAAATAGAAATAAATAAATAGTTATTTTAAGGGTCCATTCAGTTTA
126 ATCTAACTTTTTAAAATAGAAATAAATAAATAGTTATTTTAAGGGTCCATTCAGTTTA
* *
5761396 AAAAATATTTATTGTTTTATTTTTAGAAAATAA-TTTTATTTCAATTTTGTTTTTTGAAAATTAG
1 AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAA-TTT-TCTTTTGAAAATAAG
* * *
5761460 AGAATATGTTTGATTAATATAAATCAAAAATTTAAATTCA-ACAAT-A-AAAAGTATATTT-GAT
64 AGAATACGTTTGATTAATATAAAT-AAAAATTCAAATTCAGA-AATAACAAAAATATATTTAG-T
* *
5761521 ATCTAACTTTTTAAAATGGAGATAAATAAATAGTTATT
126 ATCTAACTTTTTAAAATAGAAATAAATAAATAGTTATT
5761559 AAATAATTAA
Statistics
Matches: 151, Mismatches: 7, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
182 1 0.01
183 48 0.32
184 1 0.01
187 11 0.07
188 36 0.24
189 37 0.25
190 17 0.11
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (183 bp):
AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAATTTTCTTTTGAAAATAAGAG
AATACGTTTGATTAATATAAATAAAAATTCAAATTCAGAAATAACAAAAATATATTTAGTATCTA
ACTTTTTAAAATAGAAATAAATAAATAGTTATTTTAAGGGTCCATTCAGTTTA
Found at i:5763285 original size:28 final size:26
Alignment explanation
Indices: 5763247--5763302 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5763237 AAACATTTCA
*
5763247 AATATATTTATTAATTTATTAATAATGT
1 AATATAATTATT-ATTT-TTAATAATGT
*
5763275 AATATAATTATTATTTTTAATATTGT
1 AATATAATTATTATTTTTAATAATGT
5763301 AA
1 AA
5763303 CAGTATACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.42
27 4 0.15
28 11 0.42
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
AATATAATTATTATTTTTAATAATGT
Found at i:5763539 original size:30 final size:31
Alignment explanation
Indices: 5763505--5763565 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5763495 ATATTGACAC
*
5763505 TATTA-ATCTAATATTTTAAAATAAAAATTT
1 TATTATATCTAATATTATAAAATAAAAATTT
* * *
5763535 TATTATATTTGATATTATAATATAAAAATTT
1 TATTATATCTAATATTATAAAATAAAAATTT
5763566 ATGGGTAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (31 bp):
TATTATATCTAATATTATAAAATAAAAATTT
Found at i:5764130 original size:22 final size:21
Alignment explanation
Indices: 5764088--5764132 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
5764078 TTTTGAAAAC
***
5764088 CATTTTTCATAAAATGTAATT
1 CATTTTTCATAAAAAAAAATT
5764109 CATTTTTACATAAAAAAAAATT
1 CATTTTT-CATAAAAAAAAATT
5764131 CA
1 CA
5764133 GGTAATTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (21 bp):
CATTTTTCATAAAAAAAAATT
Found at i:5764153 original size:30 final size:30
Alignment explanation
Indices: 5764103--5764212 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
5764093 TTCATAAAAT
* * *
5764103 GTAATTCATTTTTACATAAAAAAAAATTCAG
1 GTAATTCA-TTTTACGTAAAAAAATATTCAA
* * * *
5764134 GTAATTCATTTTACGTAAAACAGTTTTCAT
1 GTAATTCATTTTACGTAAAAAAATATTCAA
* * *
5764164 GTAATTTATTTTACGTAAAATAATGTTCAA
1 GTAATTCATTTTACGTAAAAAAATATTCAA
* *
5764194 ATGATTCATTTTACGTAAA
1 GTAATTCATTTTACGTAAA
5764213 TTATTTTTCA
Statistics
Matches: 65, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
30 57 0.88
31 8 0.12
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTACGTAAAAAAATATTCAA
Found at i:5764223 original size:30 final size:30
Alignment explanation
Indices: 5764135--5764224 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
5764125 AAAATTCAGG
* * **
5764135 TAATTCATTTTACGTAAAACAGTTTTCATG
1 TAATTCATTTTACGTAAAATAATTTTCAAA
* *
5764165 TAATTTATTTTACGTAAAATAATGTTCAAA
1 TAATTCATTTTACGTAAAATAATTTTCAAA
* * *
5764195 TGATTCATTTTACGTAAATTATTTTTCAAA
1 TAATTCATTTTACGTAAAATAATTTTCAAA
5764225 AAATAAATTA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (30 bp):
TAATTCATTTTACGTAAAATAATTTTCAAA
Found at i:5772712 original size:29 final size:29
Alignment explanation
Indices: 5772669--5772733 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
5772659 TATTAAAAAA
* *
5772669 TTATTTTGTTTCAGTTTGGTG-CTTAACGT
1 TTATTTCGTTCCAGTTTGGTGTC-TAACGT
5772698 TTATTTCGTTCCAGTTTGGTGTCTAACGT
1 TTATTTCGTTCCAGTTTGGTGTCTAACGT
*
5772727 TTCTTTC
1 TTATTTC
5772734 TCTCTCTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 31 0.97
30 1 0.03
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.54
Consensus pattern (29 bp):
TTATTTCGTTCCAGTTTGGTGTCTAACGT
Found at i:5772750 original size:6 final size:6
Alignment explanation
Indices: 5772734--5772768 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
5772724 CGTTTCTTTC
5772734 TCTCTCT TCTCCT TCTCCT TCTCCT TCTCCT TCTC
1 TCTC-CT TCTCCT TCTCCT TCTCCT TCTCCT TCTC
5772769 GACCCAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
TCTCCT
Found at i:5772799 original size:20 final size:20
Alignment explanation
Indices: 5772773--5772821 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5772763 CTTCTCGACC
* *
5772773 CAAGAACTCTAAATTGAATT
1 CAAGAACCCTAAATTAAATT
*
5772793 TAAGAACCCTAAATTAAATT
1 CAAGAACCCTAAATTAAATT
5772813 CAAGAACCC
1 CAAGAACCC
5772822 ACTATTCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (20 bp):
CAAGAACCCTAAATTAAATT
Found at i:5773327 original size:18 final size:17
Alignment explanation
Indices: 5773304--5773337 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5773294 GTTCTTAGAT
5773304 GGAGAAGGAGAAGGAAAA
1 GGAGAA-GAGAAGGAAAA
*
5773322 GGAGAAGAGAGGGAAA
1 GGAGAAGAGAAGGAAA
5773338 GAAACGTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (17 bp):
GGAGAAGAGAAGGAAAA
Found at i:5793594 original size:33 final size:31
Alignment explanation
Indices: 5793557--5793621 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 31
5793547 AGTTCTCACC
*
5793557 ATCCATAAATCCAAACAAATT-CAAAATCAATCA
1 ATCCACAAATCCAAAC--ATTCCAAAAT-AATCA
*
5793590 ATCCACAAATTCAAACATTCCAAAATAATCA
1 ATCCACAAATCCAAACATTCCAAAATAATCA
5793621 A
1 A
5793622 AATGTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 9 0.31
32 6 0.21
33 14 0.48
ACGTcount: A:0.54, C:0.25, G:0.00, T:0.22
Consensus pattern (31 bp):
ATCCACAAATCCAAACATTCCAAAATAATCA
Found at i:5795612 original size:20 final size:21
Alignment explanation
Indices: 5795562--5795620 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 21
5795552 TAGAACCCCA
**
5795562 GGGGGTATCGATTCCCTTGTG
1 GGGGGTATCGATTCCCTCATG
*
5795583 GGGGGAATCGATTCCCTCAT-
1 GGGGGTATCGATTCCCTCATG
5795603 GGGGGTATCGATTCCCTC
1 GGGGGTATCGATTCCCTC
5795621 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.29
Consensus pattern (21 bp):
GGGGGTATCGATTCCCTCATG
Found at i:5799145 original size:22 final size:21
Alignment explanation
Indices: 5799103--5799142 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5799093 GAGTTTATTT
*
5799103 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
5799124 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
5799143 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:5812325 original size:39 final size:39
Alignment explanation
Indices: 5812271--5812409 Score: 165
Period size: 39 Copynumber: 3.6 Consensus size: 39
5812261 TCTATGACTT
*
5812271 GTAAATCCTTACCGCATGCTCCTCGACTTTTTGCTCAGG
1 GTAAATCCTTACCGCATGCTCCTCGACTTTGTGCTCAGG
* * *
5812310 GTAAATCCTTACCGCAAGCTCCTCGGCTTTGTGCTTAGG
1 GTAAATCCTTACCGCATGCTCCTCGACTTTGTGCTCAGG
* * * *
5812349 GTAAGTCCTTACCACA-GACTTCTCGACTTTGTGCTCATG
1 GTAAATCCTTACCGCATG-CTCCTCGACTTTGTGCTCAGG
* *
5812388 GTGAGTCCTTACCGCATG-TCCT
1 GTAAATCCTTACCGCATGCTCCT
5812410 TATTCTATGT
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
38 4 0.05
39 80 0.94
40 1 0.01
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.32
Consensus pattern (39 bp):
GTAAATCCTTACCGCATGCTCCTCGACTTTGTGCTCAGG
Found at i:5819043 original size:39 final size:39
Alignment explanation
Indices: 5818995--5819103 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 39
5818985 GGTTTCTCGA
* * * *
5818995 CTTTATTCTCAAGGTAAATCCTTATCGTAGGCTACTCT-G
1 CTTTGTTCTCAAGGTAAGTCCTTACCGCAGGCTACT-TGG
* *
5819034 CTTTGTTCTC-AGAGTAAGTTCTTACCGCAGGCTCCTTGG
1 CTTTGTTCTCAAG-GTAAGTCCTTACCGCAGGCTACTTGG
* * *
5819073 CTTTGTGCTCAGGGTAAGTCCTTACTGCAGG
1 CTTTGTTCTCAAGGTAAGTCCTTACCGCAGG
5819104 TCTTTATGCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
38 3 0.05
39 53 0.93
40 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (39 bp):
CTTTGTTCTCAAGGTAAGTCCTTACCGCAGGCTACTTGG
Found at i:5821264 original size:2 final size:2
Alignment explanation
Indices: 5821257--5821299 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5821247 AAAATCCTTC
5821257 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5821298 AT
1 AT
5821300 GTGCATGGCC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5822420 original size:19 final size:19
Alignment explanation
Indices: 5822373--5822421 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
5822363 CTTAGAGATT
*
5822373 TCGAAACCTAAAAAGGGGC
1 TCGAAACCTTAAAAGGGGC
*
5822392 TCGAAACCTTAAAAGGGGT
1 TCGAAACCTTAAAAGGGGC
*
5822411 TTGAAACCTTA
1 TCGAAACCTTA
5822422 CTCCAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (19 bp):
TCGAAACCTTAAAAGGGGC
Found at i:5825383 original size:11 final size:11
Alignment explanation
Indices: 5825343--5825455 Score: 57
Period size: 11 Copynumber: 9.6 Consensus size: 11
5825333 TTGGGGCAAT
5825343 TCGAGCTTGAA
1 TCGAGCTTGAA
*
5825354 TCGAG-TTCAAAA
1 TCGAGCTT--GAA
*
5825366 TCAAGCTTGAA
1 TCGAGCTTGAA
* *
5825377 TCGAGCTCGAGTC
1 TCGAGCTTGA--A
5825390 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
5825401 TCGAGCTCGAGTC
1 TCGAGCTTGA--A
*
5825414 TCGAGCTTCAA
1 TCGAGCTTGAA
* *
5825425 TCGAGCTCGAGTC
1 TCGAGCTTGA--A
*
5825438 TCGAGCTTCAA
1 TCGAGCTTGAA
5825449 TCGAGCT
1 TCGAGCT
5825456 CTTGAAATTT
Statistics
Matches: 74, Mismatches: 19, Indels: 18
0.67 0.17 0.16
Matches are distributed among these distances:
10 2 0.03
11 39 0.53
12 6 0.08
13 27 0.36
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:5825395 original size:13 final size:13
Alignment explanation
Indices: 5825377--5825444 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
5825367 CAAGCTTGAA
5825377 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
* *
5825390 TCGAGCTTGA--A
1 TCGAGCTCGAGTC
5825401 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
*
5825414 TCGAGCTTC-A--A
1 TCGAGC-TCGAGTC
5825425 TCGAGCTCGAGTC
1 TCGAGCTCGAGTC
5825438 TCGAGCT
1 TCGAGCT
5825445 TCAATCGAGC
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.05
11 16 0.37
13 23 0.53
14 2 0.05
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (13 bp):
TCGAGCTCGAGTC
Found at i:5825401 original size:24 final size:24
Alignment explanation
Indices: 5825343--5825456 Score: 158
Period size: 24 Copynumber: 4.8 Consensus size: 24
5825333 TTGGGGCAAT
* ***
5825343 TCGAGCTTGAATCGAGTTC-AAAA
1 TCGAGCTTGAATCGAGCTCGAGTC
*
5825366 TCAAGCTTGAATCGAGCTCGAGTC
1 TCGAGCTTGAATCGAGCTCGAGTC
5825390 TCGAGCTTGAATCGAGCTCGAGTC
1 TCGAGCTTGAATCGAGCTCGAGTC
*
5825414 TCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTGAATCGAGCTCGAGTC
*
5825438 TCGAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
5825457 TTGAAATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
23 17 0.20
24 66 0.80
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (24 bp):
TCGAGCTTGAATCGAGCTCGAGTC
Found at i:5834723 original size:55 final size:55
Alignment explanation
Indices: 5834646--5835236 Score: 668
Period size: 55 Copynumber: 10.9 Consensus size: 55
5834636 GAAGGAGAAT
* * * *
5834646 CATT-GCAGAAGATTGTTTGAGTTCTATACTTCCTGAAGTAATAGGGATCGAACC
1 CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
** * * *
5834700 TGTTGGTAGAAGATTATTCGAGTTCTATACTCCCTGAAGCAATAGAGAGCGAACC
1 CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * *
5834755 CATTGGCAAAAGATTGTTCGAGTTCTATACTCCTTGAAGTAATAGGGAGAGAACA
1 CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* *
5834810 CATTGGTAGAAGATTGTTCGAGTTCTATACTCTCTGAAGCAATA--G-G-G-ACC
1 CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * *
5834860 C-GTGTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGTAATAGGGAGCGAACC
1 CATTG-GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
** *
5834915 CATTTTCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGTGAACC
1 CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * *
5834970 CATAT-TCAAAAGATTGTTCGAGTTTTATACTCCCTGAAGTAATAGGGAGCGAACC
1 CAT-TGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
* * * *
5835025 CGTTTGCAGAAGATTGTTCGAGTTCTATACTCCCTAAAGCAATAGGGAGTGAACC
1 CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
**
5835080 TGTTGGCAGAAGATTGTTCGAGTT-TCATACTCCCTGAAGCAATAGGGAGCGAACC
1 CATTGGCAGAAGATTGTTCGAGTTCT-ATACTCCCTGAAGCAATAGGGAGCGAACC
* * * * * *
5835135 C-GTGTTCAAAATATTGTTTGAGTTCTATACTCCCTTAAGCAATAGGGAGCGAACC
1 CATTG-GCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
** *
5835190 CATT-TTAGAAGATTGTTCAAG-TCTTATACTCCCTGAAAG-AATAGGGA
1 CATTGGCAGAAGATTGTTCGAGTTC-TATACTCCCTG-AAGCAATAGGGA
5835237 ACATACACGT
Statistics
Matches: 458, Mismatches: 63, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.00
50 38 0.08
51 1 0.00
52 2 0.00
53 4 0.01
54 37 0.08
55 370 0.81
56 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (55 bp):
CATTGGCAGAAGATTGTTCGAGTTCTATACTCCCTGAAGCAATAGGGAGCGAACC
Found at i:5840143 original size:30 final size:29
Alignment explanation
Indices: 5840044--5840203 Score: 105
Period size: 30 Copynumber: 5.4 Consensus size: 29
5840034 CAGGAATTGA
*
5840044 AAAGG-CT-AAATAGTAAATACAGAAAGTT
1 AAAGGACTAAAATAGTAAA-ATAGAAAGTT
* * * **
5840072 AAAGGACCAATATAGCAAATATAGAAACCT
1 AAAGGACTAAAATAGTAAA-ATAGAAAGTT
5840102 AAAGGACTAAAATAGATAAAATAGAAAGTT
1 AAAGGACTAAAATAG-TAAAATAGAAAGTT
* *
5840132 AAAGGATTAAAAAAGTAAAAATCA-AAAGTT
1 AAAGGACTAAAATAGT-AAAAT-AGAAAGTT
* * * * *
5840162 AAGGGTCT-AAATAG-AAATTACATATATTT
1 AAAGGACTAAAATAGTAAAATAGA-A-AGTT
5840191 AAAGGACTAAAAT
1 AAAGGACTAAAAT
5840204 GGTATTAACA
Statistics
Matches: 102, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
26 1 0.01
27 5 0.05
28 6 0.06
29 16 0.16
30 70 0.69
31 4 0.04
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (29 bp):
AAAGGACTAAAATAGTAAAATAGAAAGTT
Found at i:5843465 original size:28 final size:29
Alignment explanation
Indices: 5843406--5843466 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
5843396 CGGGTTCAAT
**
5843406 TTTTTTTGCCATCCCTAATAAATATTATG
1 TTTTTTTGCCATCCCTAATAAATAACATG
*
5843435 TTTTTTTGCCATCCCTAATTAATAACA-G
1 TTTTTTTGCCATCCCTAATAAATAACATG
5843463 TTTT
1 TTTT
5843467 AATATCTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (29 bp):
TTTTTTTGCCATCCCTAATAAATAACATG
Found at i:5846590 original size:16 final size:16
Alignment explanation
Indices: 5846569--5846602 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5846559 ATTTGTTATA
*
5846569 AAATAAAAATATTGAT
1 AAATAAAAATATTAAT
*
5846585 AAATAAATATATTAAT
1 AAATAAAAATATTAAT
5846601 AA
1 AA
5846603 TTGTTCCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATAAAAATATTAAT
Found at i:5849140 original size:229 final size:227
Alignment explanation
Indices: 5848735--5849183 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 227
5848725 GTAAATTATC
* * *
5848735 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
5848800 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
5848865 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
5848930 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
5848963 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
5849028 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
5849093 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
5849158 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
5849184 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 40 0.19
229 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:5849272 original size:20 final size:19
Alignment explanation
Indices: 5849249--5849294 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
5849239 CGATATACCA
5849249 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
5849269 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
5849289 GGTAAA
1 GGTAAA
5849295 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:5851823 original size:32 final size:32
Alignment explanation
Indices: 5851769--5851829 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
5851759 AAATAGATGG
*
5851769 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
***
5851801 AGTGGTGAAAGAAGTTTCGGTGTTAAGGG
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGG
5851830 GTGATATTAA
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:0.30, C:0.02, G:0.44, T:0.25
Consensus pattern (32 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGTGA
Found at i:5853643 original size:19 final size:19
Alignment explanation
Indices: 5853619--5853666 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
5853609 AATGTCGAGT
5853619 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
5853638 TAA-TTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
5853656 TATTTTTGTAT
1 TAATTTTGTAT
5853667 GTGAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 16 0.62
19 10 0.38
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5854127 original size:199 final size:199
Alignment explanation
Indices: 5853785--5855347 Score: 2892
Period size: 199 Copynumber: 7.9 Consensus size: 199
5853775 CAATATGGCC
* * *
5853785 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
5853850 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
* *
5853915 AGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
5853980 ATGGAA
194 ATGGAA
*
5853986 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854051 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
5854116 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
**
5854181 TAAA
196 GGAA
5854185 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854250 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5854315 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
5854380 GGAA
196 GGAA
*
5854384 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAA--ATCGAAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG-AAC
5854445 CC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
*
5854509 GGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAA
5854573 TGGAA
195 TGGAA
*
5854578 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854643 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5854708 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
5854773 GGAA
196 GGAA
*
5854777 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854842 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5854907 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
5854972 GGAA
196 GGAA
5854976 AACAAGGTGCACCCATAAAGTGTCGATCC--ATAT-AAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5855038 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5855103 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
5855168 GGAA
196 GGAA
5855172 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
* *
5855237 CAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTGTGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5855302 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
5855348 CTAATTTAAA
Statistics
Matches: 1332, Mismatches: 20, Indels: 22
0.97 0.01 0.02
Matches are distributed among these distances:
194 49 0.04
195 134 0.10
196 198 0.15
197 11 0.01
198 138 0.10
199 743 0.56
200 24 0.02
201 35 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
GGAA
Found at i:5854979 original size:592 final size:593
Alignment explanation
Indices: 5853785--5855347 Score: 2909
Period size: 592 Copynumber: 2.6 Consensus size: 593
5853775 CAATATGGCC
* *
5853785 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT--AAAAGTGTCGATCCC--AAA-ATCGAAA
5853850 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
61 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
5853915 AGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
126 AGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGA
5853980 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
190 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
5854045 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
255 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
*
5854110 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
320 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGA
* *
5854175 ATGAATTAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAA
385 ATGAATGAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAA
5854240 TCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
450 TCATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGT
5854305 TTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCC
515 TTTATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCC
5854370 CAGAATGAATGGAA
580 CAGAATGAATGGAA
5854384 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCGAAAACC-A
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCGAAAACCAA
5854448 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
66 AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
5854513 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAA
131 ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAA
5854578 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
196 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854643 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
261 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5854708 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
326 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
*
5854773 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCG
391 GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCG
5854838 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
456 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
5854903 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAAT
521 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAAT
5854968 GAATGGAA
586 GAATGGAA
*
5854976 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAGTGTCGATCCCAAAATC-ATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCGA---AAAC
5855038 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
63 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
5855103 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
128 GATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAAT
*
5855168 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
192 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
* *
5855233 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTGTG
257 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
5855298 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
322 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
5855348 CTAATTTAAA
Statistics
Matches: 948, Mismatches: 11, Indels: 15
0.97 0.01 0.02
Matches are distributed among these distances:
589 1 0.00
590 25 0.03
592 449 0.47
593 224 0.24
594 198 0.21
595 3 0.00
597 14 0.01
599 34 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (593 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCGAAAACCAA
AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGGAT
ATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAA
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
GAAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCG
AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAAT
GAATGGAA
Found at i:5855208 original size:395 final size:396
Alignment explanation
Indices: 5853785--5855347 Score: 2870
Period size: 395 Copynumber: 3.9 Consensus size: 396
5853775 CAATATGGCC
* * *
5853785 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAAGGTGCACCCATAAAGTGTCGATCCA-ATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
*
5853850 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
63 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
* *
5853915 AGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGA
128 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
*
5853980 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
193 ATGGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
5854045 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
258 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
5854110 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
323 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGA
**
5854175 ATGAATTAAA
387 ATGAATGGAA
5854185 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854250 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5854315 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
5854380 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAA--ATCG
195 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
*
5854441 AAAACC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
260 -AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
*
5854505 GAGAGGATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
324 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
5854570 GAATGGAA
389 GAATGGAA
*
5854578 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCA-ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
5854643 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
65 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
5854708 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
130 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
*
5854773 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAACTGTCGATCCCAAAATCATCG
195 GGAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
5854838 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
260 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
5854903 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAAT
325 AGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAAT
5854968 GAATGGAA
389 GAATGGAA
5854976 AACAAGGTGCACCCATAAAGTGTCGATCC-ATAT-AAAAGTGTCGATCCCAAAATCATCGAACCC
1 AACAAGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
5855039 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
66 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
5855104 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
131 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
5855169 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
196 GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
* *
5855234 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATATAACCGGTACAATTATACCGGTTTTGTGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
5855299 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
326 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
5855348 CTAATTTAAA
Statistics
Matches: 1137, Mismatches: 19, Indels: 19
0.97 0.02 0.02
Matches are distributed among these distances:
393 253 0.22
394 126 0.11
395 343 0.30
396 11 0.01
397 134 0.12
398 212 0.19
399 24 0.02
400 34 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (396 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCAATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATG
GAAAACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
ATGGAA
Found at i:5855833 original size:23 final size:23
Alignment explanation
Indices: 5855802--5855865 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5855792 TAAGGTAAAC
*
5855802 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5855825 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5855848 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5855866 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5855872 original size:23 final size:23
Alignment explanation
Indices: 5855802--5855874 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5855792 TAAGGTAAAC
* **
5855802 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5855825 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5855848 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5855871 ATAT
1 ATAT
5855875 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:5856177 original size:25 final size:25
Alignment explanation
Indices: 5856143--5856193 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5856133 ACAACAAATC
*
5856143 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
5856168 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
5856193 A
1 A
5856194 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:5856463 original size:18 final size:18
Alignment explanation
Indices: 5856442--5856478 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5856432 GTAATTGGAG
5856442 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
5856460 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
5856478 T
1 T
5856479 ATATTTCGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:5856820 original size:39 final size:39
Alignment explanation
Indices: 5856735--5856859 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
5856725 TCCGATGCTC
* *
5856735 ATCAAAATCCAAAGCTCATATGGTGCCAAGC-AAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
5856773 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
5856812 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
5856851 ATCAAAATC
1 ATCAAAATC
5856860 TACAACTTGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
38 29 0.35
39 55 0.65
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
Found at i:5857294 original size:23 final size:23
Alignment explanation
Indices: 5857263--5857326 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
5857253 ATAGGTAAAC
*
5857263 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
5857286 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
5857309 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
5857327 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:5857333 original size:23 final size:23
Alignment explanation
Indices: 5857263--5857335 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
5857253 ATAGGTAAAC
* **
5857263 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
5857286 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
5857309 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
5857332 ATAT
1 ATAT
5857336 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Done.