Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005788.1 Hibiscus syriacus cultivar Beakdansim tig00013565_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: 403709
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:140230 original size:17 final size:18
Alignment explanation
Indices: 140193--140233 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
140183 ATATTCTGTA
*
140193 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
140211 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
140228 TTTACT
1 TTTACT
140234 AATATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:142466 original size:48 final size:46
Alignment explanation
Indices: 142389--142481 Score: 132
Period size: 48 Copynumber: 2.0 Consensus size: 46
142379 ACATCGATAG
* *
142389 ATTTTTTTTATTTATATTTGTATTTACTTTATTTTGTTAAATTGTA
1 ATTTTTTTTATTTATATTTATACTTACTTTATTTTGTTAAATTGTA
* *
142435 ATTTTTTTTATTTCTCATTTAATACTTACTTTATTTTGTTAATTTGT
1 ATTTTTTTTATTTAT-ATTT-ATACTTACTTTATTTTGTTAAATTGT
142482 TGGATTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 14 0.34
47 4 0.10
48 23 0.56
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (46 bp):
ATTTTTTTTATTTATATTTATACTTACTTTATTTTGTTAAATTGTA
Found at i:147005 original size:8 final size:8
Alignment explanation
Indices: 146994--147029 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
146984 ATATATTCTA
146994 TTTTATTT
1 TTTTATTT
*
147002 TTTTATATA
1 TTTTAT-TT
147011 TTTTATTT
1 TTTTATTT
147019 TTTTATTT
1 TTTTATTT
147027 TTT
1 TTT
147030 ATATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTATTT
Found at i:147011 original size:22 final size:24
Alignment explanation
Indices: 146984--147034 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
146974 AATCTAATTC
146984 ATATATTCTA-TTTTAT-TTTTTT
1 ATATATTCTATTTTTATATTTTTT
* *
147006 ATATATTTTATTTTTTTATTTTTT
1 ATATATTCTATTTTTATATTTTTT
147030 ATATA
1 ATATA
147035 ATAAAACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 5 0.20
24 11 0.44
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
ATATATTCTATTTTTATATTTTTT
Found at i:147014 original size:17 final size:17
Alignment explanation
Indices: 146992--147024 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
146982 TCATATATTC
146992 TATTTTATTTTTTTATA
1 TATTTTATTTTTTTATA
147009 TATTTTATTTTTTTAT
1 TATTTTATTTTTTTAT
147025 TTTTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTTATTTTTTTATA
Found at i:149360 original size:61 final size:61
Alignment explanation
Indices: 149256--149394 Score: 210
Period size: 62 Copynumber: 2.3 Consensus size: 61
149246 CATTAGACAT
* *
149256 TTCATA-CCGAAATCATCCATAACCATGTAGTAAAATATCATAT-AAAATGTATTGAGTAG
1 TTCATACCCAAAATCATCCATAACCATGTAGTAAAATATCATATAAAAATGTATTGAGTAA
* * *
149315 TTCGTACCCAAAATCATCCATAAACCATTTAGTAAAATATCATATAAAAATGTATTGGGTAA
1 TTCATACCCAAAATCATCCAT-AACCATGTAGTAAAATATCATATAAAAATGTATTGAGTAA
149377 TTCATACCCAAAATCATC
1 TTCATACCCAAAATCATC
149395 TGAATACAAT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
59 5 0.07
60 13 0.18
61 22 0.31
62 31 0.44
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (61 bp):
TTCATACCCAAAATCATCCATAACCATGTAGTAAAATATCATATAAAAATGTATTGAGTAA
Found at i:151328 original size:12 final size:12
Alignment explanation
Indices: 151287--151329 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
151277 TAAGATTTTC
*
151287 TTTGAAAATCATT
1 TTTG-AAATCAAT
*
151300 TTTGAATTCAA-
1 TTTGAAATCAAT
151311 TTTGAAATCAAT
1 TTTGAAATCAAT
151323 TTTGAAA
1 TTTGAAA
151330 ATTACTCCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 10 0.38
12 12 0.46
13 4 0.15
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (12 bp):
TTTGAAATCAAT
Found at i:151608 original size:19 final size:21
Alignment explanation
Indices: 151573--151616 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
151563 AATAAACATT
*
151573 AAATTCAAAATAATC-AAACC
1 AAATTCAAAACAATCAAAACC
151593 AAATTC-AAACAATCAAAACC
1 AAATTCAAAACAATCAAAACC
151613 AAAT
1 AAAT
151617 ATATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATTCAAAACAATCAAAACC
Found at i:155069 original size:15 final size:15
Alignment explanation
Indices: 155049--155080 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
155039 GTGAATGATA
155049 TGATAAGAAGCTATG
1 TGATAAGAAGCTATG
155064 TGATAAGAAGCTATG
1 TGATAAGAAGCTATG
155079 TG
1 TG
155081 CTTATGTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.28, T:0.28
Consensus pattern (15 bp):
TGATAAGAAGCTATG
Found at i:155217 original size:21 final size:21
Alignment explanation
Indices: 155193--155233 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
155183 TTCTATGTGG
155193 TCCTTCAGG-ACATATATGTAA
1 TCCTT-AGGAACATATATGTAA
*
155214 TCCTTTGGAACATATATGTA
1 TCCTTAGGAACATATATGTA
155234 GTACTTCGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
TCCTTAGGAACATATATGTAA
Found at i:155617 original size:2 final size:2
Alignment explanation
Indices: 155610--155651 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
155600 TAATATTAGC
155610 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
155652 GTATTTGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:158391 original size:25 final size:25
Alignment explanation
Indices: 158361--158421 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
158351 GATAATCATT
158361 TTAATAATTTTTAATTTATTGAAAA
1 TTAATAATTTTTAATTTATTGAAAA
*
158386 TTAATAATTTTTAATTTATTGAGAA
1 TTAATAATTTTTAATTTATTGAAAA
158411 TTAATAATTTT
1 TTAATAATTTT
158422 AGTATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (25 bp):
TTAATAATTTTTAATTTATTGAAAA
Found at i:158907 original size:16 final size:16
Alignment explanation
Indices: 158876--158926 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
158866 GTGCATGTTA
158876 TTTTCGGTTCGG-TTGC
1 TTTT-GGTTCGGATTGC
*
158892 TTTTGGTTCTGATTGC
1 TTTTGGTTCGGATTGC
*
158908 TTTTGGTTCGGATTAC
1 TTTTGGTTCGGATTGC
158924 TTT
1 TTT
158927 CAGTTCGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.06, C:0.14, G:0.25, T:0.55
Consensus pattern (16 bp):
TTTTGGTTCGGATTGC
Found at i:162462 original size:21 final size:20
Alignment explanation
Indices: 162419--162465 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
162409 AAAATGGAAA
162419 GAGAAG-AGAAGCCATCATC
1 GAGAAGCAGAAGCCATCATC
*
162438 --GAAGCAGCAGCCATCATC
1 GAGAAGCAGAAGCCATCATC
162456 GGAGAAGCAG
1 -GAGAAGCAG
162466 GAAAACCTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 4 0.17
18 12 0.52
21 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.30, T:0.09
Consensus pattern (20 bp):
GAGAAGCAGAAGCCATCATC
Found at i:162464 original size:18 final size:18
Alignment explanation
Indices: 162428--162465 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
162418 AGAGAAGAGA
*
162428 AGCCATCATCGAAGCAGC
1 AGCCATCATCGAAGAAGC
*
162446 AGCCATCATCGGAGAAGC
1 AGCCATCATCGAAGAAGC
162464 AG
1 AG
162466 GAAAACCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.26, T:0.11
Consensus pattern (18 bp):
AGCCATCATCGAAGAAGC
Found at i:167677 original size:28 final size:24
Alignment explanation
Indices: 167611--167667 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
167601 ATAGAGAAGC
* *
167611 AAGAGAAGCA-ATAAAGAAGTAGA
1 AAGAGAAGCAGAGAAATAAGTAGA
167634 AAGAGAAGCAGAGAAATAAGTAGA
1 AAGAGAAGCAGAGAAATAAGTAGA
167658 AAGAGAAGCA
1 AAGAGAAGCA
167668 AAGAGAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 10 0.32
24 21 0.68
ACGTcount: A:0.60, C:0.05, G:0.28, T:0.07
Consensus pattern (24 bp):
AAGAGAAGCAGAGAAATAAGTAGA
Found at i:167872 original size:28 final size:28
Alignment explanation
Indices: 167836--167907 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
167826 TTACTCTAGT
* * *
167836 TGTTAAACTATATTACATTTCCCTTGAA-
1 TGTTGAACTACATTACATTTCACTT-AAC
*
167864 TGTTGAACTACATTGCATTTCACTTAAC
1 TGTTGAACTACATTACATTTCACTTAAC
*
167892 TATTGAACTACATTAC
1 TGTTGAACTACATTAC
167908 TTGAATGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 2 0.05
28 35 0.95
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.40
Consensus pattern (28 bp):
TGTTGAACTACATTACATTTCACTTAAC
Found at i:168166 original size:43 final size:43
Alignment explanation
Indices: 168112--168287 Score: 160
Period size: 43 Copynumber: 4.1 Consensus size: 43
168102 TTTGTTTTAC
* * *
168112 AAACGCTGCTATAATTCTTAACCTATTGTGACATTTGTAAAAG
1 AAACGTTGCTATAATTCTTAACCTATTGCGACGTTTGTAAAAG
* *
168155 AAATGTTGCTAT-ATTTTGTAACCTATTGCGGA-GTTTGTAAAAG
1 AAACGTTGCTATAATTCT-TAACCTATTGC-GACGTTTGTAAAAG
* * * *
168198 AAACGTTACTATATTTCGTAACCTATTGCGGCGTTTGTAAAAG
1 AAACGTTGCTATAATTCTTAACCTATTGCGACGTTTGTAAAAG
** * * * * *
168241 AAACACAT-ATATAATCCGTAACCTATTGCAACGTTGGTAAAAG
1 AAAC-GTTGCTATAATTCTTAACCTATTGCGACGTTTGTAAAAG
168284 AAAC
1 AAAC
168288 CCCACTAAAA
Statistics
Matches: 109, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
42 5 0.05
43 99 0.91
44 5 0.05
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (43 bp):
AAACGTTGCTATAATTCTTAACCTATTGCGACGTTTGTAAAAG
Found at i:168317 original size:42 final size:43
Alignment explanation
Indices: 168172--168339 Score: 137
Period size: 43 Copynumber: 3.9 Consensus size: 43
168162 GCTATATTTT
*** * ***
168172 GTAACCTATTGCGGA-GTTTGTAAAAGAAACGTTACTATATTTC
1 GTAACCTATTGC-GACGTTTGTAAAAGAAACCCCACTAAAAGCC
* * *
168215 GTAACCTATTGCGGCGTTTGTAAAAGAAA-CACA-TATATAATCC
1 GTAACCTATTGCGACGTTTGTAAAAGAAACCCCACTA-A-AAGCC
* *
168258 GTAACCTATTGCAACGTTGGTAAAAGAAACCCCACTAAAAGCC
1 GTAACCTATTGCGACGTTTGTAAAAGAAACCCCACTAAAAGCC
* * * *
168301 -TAACCTGTTGCGACGTTTGTATAAGAAACGCCGCTAAAA
1 GTAACCTATTGCGACGTTTGTAAAAGAAACCCCACTAAAA
168340 ACCCTAACAT
Statistics
Matches: 102, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
41 2 0.02
42 35 0.34
43 59 0.58
44 4 0.04
45 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (43 bp):
GTAACCTATTGCGACGTTTGTAAAAGAAACCCCACTAAAAGCC
Found at i:181459 original size:23 final size:23
Alignment explanation
Indices: 181391--181451 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
181381 CAATCTTATA
* *
181391 TGGCACTACGATGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * *
181414 CGGTACTTCGGTGTAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
181437 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
181452 TTTATACGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:182771 original size:27 final size:28
Alignment explanation
Indices: 182701--182829 Score: 154
Period size: 29 Copynumber: 4.6 Consensus size: 28
182691 TCGAAATGGA
* *
182701 TGCTATTTTAGGAATTTAATTCGAAAAG
1 TGCTATTTTGGGAATTTAATTCAAAAAG
*
182729 ATGTTATTTTGGGAATTTAATTC-AAAAG
1 -TGCTATTTTGGGAATTTAATTCAAAAAG
*
182757 TGCTATTTTGGGAATTTATTTCAAAAAG
1 TGCTATTTTGGGAATTTAATTCAAAAAG
* *
182785 TGTTATTTTGGGAA-TTAATTTAAAAAGGG
1 TGCTATTTTGGGAATTTAATTCAAAAA--G
*
182814 TGCTATTTTGGTAATT
1 TGCTATTTTGGGAATT
182830 AGTTTAAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 30 0.34
28 23 0.26
29 33 0.38
30 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (28 bp):
TGCTATTTTGGGAATTTAATTCAAAAAG
Found at i:182783 original size:28 final size:28
Alignment explanation
Indices: 182701--182850 Score: 146
Period size: 29 Copynumber: 5.3 Consensus size: 28
182691 TCGAAATGGA
* * *
182701 TGCTATTTTAGGAATTTAATTCGAAAAG
1 TGCTATTTTGGGAATTTATTTCAAAAAG
* *
182729 ATGTTATTTTGGGAATTTAATTC-AAAAG
1 -TGCTATTTTGGGAATTTATTTCAAAAAG
182757 TGCTATTTTGGGAATTTATTTCAAAAAG
1 TGCTATTTTGGGAATTTATTTCAAAAAG
* *
182785 TGTTATTTTGGGAATTAATTT-AAAAAGGG
1 TGCTATTTTGGGAATTTATTTCAAAAA--G
*
182814 TGCTATTTTGGTAA-TTAGTTT-AAAAATGG
1 TGCTATTTTGGGAATTTA-TTTCAAAAA--G
182843 TGCTATTT
1 TGCTATTT
182851 CTGTAAAATG
Statistics
Matches: 107, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
27 25 0.23
28 31 0.29
29 51 0.48
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (28 bp):
TGCTATTTTGGGAATTTATTTCAAAAAG
Found at i:189717 original size:17 final size:17
Alignment explanation
Indices: 189695--189729 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
189685 TGACCGGTTC
189695 CGACCCGACCCGTTGAT
1 CGACCCGACCCGTTGAT
189712 CGACCCGACCCGTTGAT
1 CGACCCGACCCGTTGAT
189729 C
1 C
189730 TTTGACCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (17 bp):
CGACCCGACCCGTTGAT
Found at i:189801 original size:30 final size:29
Alignment explanation
Indices: 189744--189864 Score: 134
Period size: 29 Copynumber: 4.1 Consensus size: 29
189734 ACCAAGTGAC
* ** *
189744 ATTTTAGGAATTAATTCGAAATGGGTGCT
1 ATTTTGGGAATTAATTTAAAAAGGGTGCT
*
189773 ATTTTGGGAATTTAATTTAAAAAAGGTGCT
1 ATTTTGGGAA-TTAATTTAAAAAGGGTGCT
* * *
189803 ATTTTTGGAAATAATTTGAAAAGGGTGCT
1 ATTTTGGGAATTAATTTAAAAAGGGTGCT
* * *
189832 ATTTTGGTAATTATTTTAAAAAGGGTGTT
1 ATTTTGGGAATTAATTTAAAAAGGGTGCT
189861 ATTT
1 ATTT
189865 CTGTAAAATG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
29 52 0.68
30 24 0.32
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.42
Consensus pattern (29 bp):
ATTTTGGGAATTAATTTAAAAAGGGTGCT
Found at i:189836 original size:59 final size:58
Alignment explanation
Indices: 189744--189864 Score: 161
Period size: 59 Copynumber: 2.1 Consensus size: 58
189734 ACCAAGTGAC
* *
189744 ATTTTAGGAATTAATTCGAAATGGGTGCTATTTTGGGAATTTAATTTAAAAAAGGTGCT
1 ATTTTAGGAAATAATTCGAAAAGGGTGCTATTTTGGGAA-TTAATTTAAAAAAGGTGCT
* * * * * *
189803 ATTTTTGGAAATAATTTGAAAAGGGTGCTATTTTGGTAATTATTTTAAAAAGGGTGTT
1 ATTTTAGGAAATAATTCGAAAAGGGTGCTATTTTGGGAATTAATTTAAAAAAGGTGCT
189861 ATTT
1 ATTT
189865 CTGTAAAATG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
58 20 0.37
59 34 0.63
ACGTcount: A:0.33, C:0.03, G:0.21, T:0.42
Consensus pattern (58 bp):
ATTTTAGGAAATAATTCGAAAAGGGTGCTATTTTGGGAATTAATTTAAAAAAGGTGCT
Found at i:194231 original size:18 final size:18
Alignment explanation
Indices: 194208--194252 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
194198 CTTAACATGT
194208 CATCAAGTTAAAGCTGAA
1 CATCAAGTTAAAGCTGAA
194226 CATCAAGTTAAAGCTGAA
1 CATCAAGTTAAAGCTGAA
194244 CATCAAGTT
1 CATCAAGTT
194253 CCGTCTGGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (18 bp):
CATCAAGTTAAAGCTGAA
Found at i:196871 original size:23 final size:23
Alignment explanation
Indices: 196840--196891 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
196830 ATGGTACTAT
*
196840 GGTGTAATTCTACGCGGCACTTC
1 GGTGCAATTCTACGCGGCACTTC
*
196863 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTCTACGCGGCACTTC
196886 GGTGCA
1 GGTGCA
196892 TTTATACGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (23 bp):
GGTGCAATTCTACGCGGCACTTC
Found at i:196899 original size:23 final size:23
Alignment explanation
Indices: 196840--196899 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
196830 ATGGTACTAT
* *
196840 GGTGTAATTCTACGCGGCACTTC
1 GGTGCAATTATACGCGGCACTTC
* *
196863 GGTGCAATTCTACGTGGCACTTC
1 GGTGCAATTATACGCGGCACTTC
*
196886 GGTGCATTTATACG
1 GGTGCAATTATACG
196900 AATTGTGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTGCAATTATACGCGGCACTTC
Found at i:198005 original size:21 final size:21
Alignment explanation
Indices: 197981--198035 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
197971 GTGTGAGTGA
197981 AGTTAGTTTAGCAGTGATATC
1 AGTTAGTTTAGCAGTGATATC
198002 AGTTAGTTTAGCAGTGATATC
1 AGTTAGTTTAGCAGTGATATC
198023 AGTTAGTTTAGCA
1 AGTTAGTTTAGCA
198036 ACTGAGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (21 bp):
AGTTAGTTTAGCAGTGATATC
Found at i:204395 original size:13 final size:13
Alignment explanation
Indices: 204377--204406 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
204367 CTTTATTGCG
*
204377 AAAATTAAAATTT
1 AAAATTAAAAATT
204390 AAAATTAAAAATT
1 AAAATTAAAAATT
204403 AAAA
1 AAAA
204407 ACCCGATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:204636 original size:25 final size:25
Alignment explanation
Indices: 204540--204636 Score: 60
Period size: 25 Copynumber: 3.9 Consensus size: 25
204530 AGAAGAATAG
* * *
204540 AAATAAAAAACAAAAGG-TTAAAATT
1 AAATAAATAA-AAAAGGATCAAAAAT
* * *
204565 AAA-AAATAAAAAATGTTAAGAAAAT
1 AAATAAATAAAAAAGGATCA-AAAAT
*
204590 AAAT-ATTAAAAAA--ATCGAAAAAAT
1 AAATAAATAAAAAAGGATC--AAAAAT
204614 AAATAAATAAAAAAGGATCAAAA
1 AAATAAATAAAAAAGGATCAAAA
204637 TGAATGATGT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
23 6 0.11
24 16 0.29
25 31 0.55
27 3 0.05
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (25 bp):
AAATAAATAAAAAAGGATCAAAAAT
Found at i:206426 original size:36 final size:35
Alignment explanation
Indices: 206332--206465 Score: 159
Period size: 36 Copynumber: 3.9 Consensus size: 35
206322 CAAAGATTGG
206332 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATT
* *
206366 TGTTT-AAG-GGAATTGTCTCAAGAGAGACAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA-TT
*
206400 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAATT
* * *
206436 TGTTTTAAGAG-AATTAGTCTCAAGCGAGAC
1 TGTTTCAAGAGAAACT-GTCTCAAGAGAGAC
206466 GACCCCTTGT
Statistics
Matches: 85, Mismatches: 9, Indels: 10
0.82 0.09 0.10
Matches are distributed among these distances:
32 18 0.21
33 5 0.06
34 12 0.14
35 6 0.07
36 41 0.48
37 3 0.04
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (35 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAATT
Found at i:210948 original size:6 final size:7
Alignment explanation
Indices: 210933--211082 Score: 56
Period size: 7 Copynumber: 19.6 Consensus size: 7
210923 ATTAGATTGT
210933 AAAATAA
1 AAAATAA
210940 AAAATAAA
1 AAAAT-AA
210948 AAAATATTA
1 AAAATA--A
210957 ATAGAAT-A
1 A-A-AATAA
*
210965 ATAATAA
1 AAAATAA
210972 TAAAATAA
1 -AAAATAA
210980 GAAGAAT-A
1 -AA-AATAA
*
210988 GAAATAA
1 AAAATAA
210995 AAAA-ACA
1 AAAATA-A
* *
211002 AAAGGTTA
1 AAA-ATAA
*
211010 AAATTAA
1 AAAATAA
211017 AAAAT-A
1 AAAATAA
211023 AAAATAA
1 AAAATAA
211030 AAAATGTTAA
1 AAAA---TAA
211040 GAAAATAA
1 -AAAATAA
* *
211048 ATATTAA
1 AAAATAA
211055 AAAATCAAA
1 AAAAT--AA
211064 AAAATAA
1 AAAATAA
211071 ATAAATAA
1 A-AAATAA
211079 AAAA
1 AAAA
211083 GGATCAAAAT
Statistics
Matches: 109, Mismatches: 14, Indels: 40
0.67 0.09 0.25
Matches are distributed among these distances:
6 13 0.12
7 41 0.38
8 32 0.29
9 12 0.11
10 4 0.04
11 7 0.06
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.20
Consensus pattern (7 bp):
AAAATAA
Found at i:211056 original size:24 final size:23
Alignment explanation
Indices: 211013--211082 Score: 70
Period size: 24 Copynumber: 2.9 Consensus size: 23
211003 AAGGTTAAAA
211013 TTAAAAAATAAAAATAAAAAATG
1 TTAAAAAATAAAAATAAAAAATG
*
211036 TTAAGAAAATAAATATTAAAAAAT-
1 TTAA-AAAATAAA-AATAAAAAATG
**
211060 CAAAAAAATAAATAAATAAAAAA
1 TTAAAAAAT-AA-AAATAAAAAA
211083 GGATCAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
23 9 0.23
24 20 0.51
25 10 0.26
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.21
Consensus pattern (23 bp):
TTAAAAAATAAAAATAAAAAATG
Found at i:211088 original size:27 final size:26
Alignment explanation
Indices: 211015--211091 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 26
211005 GGTTAAAATT
*
211015 AAAAAAT-AA-AAATAAAAAATG-TTA
1 AAAAAATAAATAAATAAAAAA-GATCA
* *
211039 AGAAAATAAAT--ATTAAAAA-ATCA
1 AAAAAATAAATAAATAAAAAAGATCA
211062 AAAAAATAAATAAATAAAAAAGGATCA
1 AAAAAATAAATAAATAAAAAA-GATCA
211089 AAA
1 AAA
211092 TGAATGATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
23 12 0.29
24 13 0.32
25 9 0.22
27 7 0.17
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (26 bp):
AAAAAATAAATAAATAAAAAAGATCA
Found at i:212283 original size:13 final size:12
Alignment explanation
Indices: 212265--212315 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
212255 GGGCCTAAAA
212265 AATAATAAATAAT
1 AATAA-AAATAAT
212278 AATAATAAAT-AT
1 AATAA-AAATAAT
212290 -ATAAAGAATAAT
1 AATAAA-AATAAT
212302 AATAAAATATAAT
1 AATAAAA-ATAAT
212315 A
1 A
212316 TTTTTTAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 7 0.21
12 5 0.15
13 21 0.62
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:219541 original size:31 final size:31
Alignment explanation
Indices: 219503--219562 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
219493 AATGACGATA
*
219503 TCTTAATTAAATAAAAACGAAAGTGACCACG
1 TCTTAATTAAATAAAAACAAAAGTGACCACG
219534 TCTTAATTAAATAAAAACAAAAGTGACCA
1 TCTTAATTAAATAAAAACAAAAGTGACCA
219563 AATATTATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.15, G:0.10, T:0.23
Consensus pattern (31 bp):
TCTTAATTAAATAAAAACAAAAGTGACCACG
Found at i:221589 original size:27 final size:27
Alignment explanation
Indices: 221551--221612 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
221541 GTATAAGAAA
221551 GTTAAATGTATTTTTTAATATTTTAAT
1 GTTAAATGTATTTTTTAATATTTTAAT
221578 GTTAAATGTATTTTTTAATATTTTAAT
1 GTTAAATGTATTTTTTAATATTTTAAT
221605 GTTAAATG
1 GTTAAATG
221613 ATTATATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (27 bp):
GTTAAATGTATTTTTTAATATTTTAAT
Found at i:222708 original size:13 final size:13
Alignment explanation
Indices: 222690--222727 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
222680 AGAAGTCTAG
222690 AATTTA-AAGTTTA
1 AATTTATAA-TTTA
222703 AATTTATAATTTA
1 AATTTATAATTTA
*
222716 AATTTATGATTT
1 AATTTATAATTT
222728 TATCTAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (13 bp):
AATTTATAATTTA
Found at i:222965 original size:13 final size:13
Alignment explanation
Indices: 222942--222975 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
222932 AGACCACTAT
222942 TTTTTATTTTTTTA
1 TTTTTA-TTTTTTA
222956 TTTTTATTTTTTA
1 TTTTTATTTTTTA
*
222969 TCTTTAT
1 TTTTTAT
222976 AATTGAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:223050 original size:21 final size:21
Alignment explanation
Indices: 223003--223052 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
222993 TTTGTAATTT
*
223003 TACTTATTATTTTTATAAATGA
1 TACTT-TTAATTTTATAAATGA
*
223025 AACTTTTAATTTTATAAAT-A
1 TACTTTTAATTTTATAAATGA
223045 CTACTTTT
1 -TACTTTT
223053 TTACATTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (21 bp):
TACTTTTAATTTTATAAATGA
Found at i:229480 original size:43 final size:43
Alignment explanation
Indices: 229430--229694 Score: 241
Period size: 43 Copynumber: 6.1 Consensus size: 43
229420 AACGAAAAAT
229430 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATACAAAC
* * * *
229473 GCCGCAATACGTGTTAATTTTTAGCGGCGTTTTTC-CACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATACAAAC
* * *
229515 ACCGCAATAGGTGTTGAGATTTAGCGGCGTTTTT-ATCACAAAT
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCAT-ACAAAC
* * * * * *
229558 GCAGCAATATGTCTTG-TAATTTAGCGACGTTTTTCTTGCAAAC
1 GCCGCAATAGGTGTTGAT-ATTTAGCGGCGTTTTTCATACAAAC
* * * *
229601 GCCGCAATAGGTGTTGAGATTTCGCGGCGTTTTTTTGATACAAAA
1 GCCGCAATAGGTGTTGATATTTAGCGGCG--TTTTTCATACAAAC
* * * * * *
229646 GCCGCAAAAGGT-CTGGTATATAGCGGCATTTTTAGGATACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTT--CATACAAAC
229690 GCCGC
1 GCCGC
229695 TAAATGTAAG
Statistics
Matches: 175, Mismatches: 38, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
42 40 0.23
43 90 0.51
44 24 0.14
45 21 0.12
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (43 bp):
GCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATACAAAC
Found at i:229581 original size:85 final size:85
Alignment explanation
Indices: 229431--229634 Score: 261
Period size: 85 Copynumber: 2.4 Consensus size: 85
229421 ACGAAAAATG
* *
229431 CCGCAATAGGTGTTGATATTTAGCGGCGTTTTTCATACAAACGCCGCAATACGTGTTAATTTTTA
1 CCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCATACAAACGCAGCAATACGTGTTAA-TTTTA
*
229496 GCGGCGTTTTTC-CACAAACA
65 GCGACGTTTTTCTCACAAACA
* * *
229516 CCGCAATAGGTGTTGAGATTTAGCGGCGTTTTT-ATCACAAATGCAGCAATATGTCTTGTAA-TT
1 CCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCAT-ACAAACGCAGCAATACGT-GT-TAATTT
** *
229579 TAGCGACGTTTTTCTTGCAAACG
63 TAGCGACGTTTTTCTCACAAACA
*
229602 CCGCAATAGGTGTTGAGATTTCGCGGCGTTTTT
1 CCGCAATAGGTGTTGAGATTTAGCGGCGTTTTT
229635 TTGATACAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
84 2 0.02
85 62 0.59
86 38 0.36
87 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (85 bp):
CCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCATACAAACGCAGCAATACGTGTTAATTTTAG
CGACGTTTTTCTCACAAACA
Found at i:229733 original size:44 final size:44
Alignment explanation
Indices: 229624--229743 Score: 134
Period size: 44 Copynumber: 2.7 Consensus size: 44
229614 TTGAGATTTC
* * * **
229624 GCGGCGTTTTTTTGATACAAAAGCCGCAAAAGGTCTGGTATATA
1 GCGGCGTTTTTTTGATACAAACGCCGCTAAATGTAAGGTATATA
* **
229668 GCGGCATTTTTAGGATACAAACGCCGCTAAATGTAAGGTATATTA
1 GCGGCGTTTTTTTGATACAAACGCCGCTAAATGTAAGGTATA-TA
* *
229713 -CGGCGTTTTTTTGTTACAAACGTCGCTAAAT
1 GCGGCGTTTTTTTGATACAAACGCCGCTAAAT
229744 AATGCATAAT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
44 60 0.97
45 2 0.03
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.32
Consensus pattern (44 bp):
GCGGCGTTTTTTTGATACAAACGCCGCTAAATGTAAGGTATATA
Found at i:233029 original size:42 final size:42
Alignment explanation
Indices: 232924--233033 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
232914 CTACTATATA
* * *
232924 GCGGCATTT-TTGGATACAAACGCCGCTAAATGACTACTCTTTG
1 GCGGCGTTTGTTGGA-A-AAACGCCGCAAAATGACCACTCTTTG
* * *
232967 GCGGCGTTTG-TGCCATAAACGCCGCAAAATTACCACTCTATT-
1 GCGGCGTTTGTTG-GAAAAACGCCGCAAAATGACCACTCT-TTG
233009 GCGGCGTTTGTTGGAAAAACGCCGC
1 GCGGCGTTTGTTGGAAAAACGCCGC
233034 TAAAGTATCA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
42 40 0.73
43 14 0.25
44 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (42 bp):
GCGGCGTTTGTTGGAAAAACGCCGCAAAATGACCACTCTTTG
Found at i:234441 original size:17 final size:16
Alignment explanation
Indices: 234411--234450 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
234401 GGTGTATAAT
*
234411 AATTCTATAAATTTAAC
1 AATT-TATAAATTTAAA
234428 AATTTATAATATTTAAA
1 AATTTATAA-ATTTAAA
234445 AATTTA
1 AATTTA
234451 ATAACTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTATAAATTTAAA
Found at i:235507 original size:57 final size:57
Alignment explanation
Indices: 235437--235729 Score: 462
Period size: 57 Copynumber: 5.1 Consensus size: 57
235427 TGCGGAGCTT
*
235437 GACCCTGAGAAGAGGCTCTA-CCCGGGTGGCTACTTTGGCCCACTTGGCTTAGCCTCC
1 GACCCTGAGAAGAGGCTCTATCCC-GGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
* *
235494 CACCCTGAGAAGAGGCTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGACTCC
1 GACCCTGAGAAGAGGCTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
*
235551 GACCCTGAGAAGAGGTTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
1 GACCCTGAGAAGAGGCTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
* * * *
235608 GACCCTGAGAAGAGCCTCTATCCCGGTGACTGCTTTGACCCACTTGACTTAGCCTCC
1 GACCCTGAGAAGAGGCTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
** * *
235665 GACCCTGAGAAGAGGCTCTGCCCCGGTGGCTGCTTTGACCCACTTGGCCTAGCCTCC
1 GACCCTGAGAAGAGGCTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
235722 GACCCTGA
1 GACCCTGA
235730 CAACATTGAT
Statistics
Matches: 218, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
57 215 0.99
58 3 0.01
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.24
Consensus pattern (57 bp):
GACCCTGAGAAGAGGCTCTATCCCGGTGGCTGCTTTGGCCCACTTGGCTTAGCCTCC
Found at i:236656 original size:23 final size:22
Alignment explanation
Indices: 236603--236656 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
236593 TTTTTGTACC
236603 AAAAA-ATATTATTATAATATA
1 AAAAATATATTATTATAATATA
** *
236624 ATCGAGTATATTATTATAATATTA
1 A-AAAATATATTATTATAATA-TA
236648 AAAAATATA
1 AAAAATATA
236657 ATATCGTATT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 19 0.79
24 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (22 bp):
AAAAATATATTATTATAATATA
Found at i:242364 original size:30 final size:31
Alignment explanation
Indices: 242330--242391 Score: 108
Period size: 30 Copynumber: 2.0 Consensus size: 31
242320 GCTAACGAAC
*
242330 AATAAATAAACGAATATAAACACT-TTAAAA
1 AATAAATAAACAAATATAAACACTATTAAAA
242360 AATAAATAAACAAATATAAACACTATTAAAA
1 AATAAATAAACAAATATAAACACTATTAAAA
242391 A
1 A
242392 TTTAAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.23
Consensus pattern (31 bp):
AATAAATAAACAAATATAAACACTATTAAAA
Found at i:243431 original size:22 final size:20
Alignment explanation
Indices: 243397--243447 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
243387 ATAATTATTT
243397 AAAAAATTAAATAAAAATATCA
1 AAAAAATTAAATAAAAA-AT-A
* *
243419 AAAACATTTAATAAAAAATA
1 AAAAAATTAAATAAAAAATA
243439 AAAAAATTA
1 AAAAAATTA
243448 GGTTGAACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 15 0.60
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAATA
Found at i:243435 original size:23 final size:21
Alignment explanation
Indices: 243397--243447 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
243387 ATAATTATTT
243397 AAAAAATTAAATAAAAATATC
1 AAAAAATTAAATAAAAATATC
* *
243418 AAAAACATTTAATAAAAA-ATA
1 AAAAA-ATTAAATAAAAATATC
243439 AAAAAATTA
1 AAAAAATTA
243448 GGTTGAACCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 3 0.12
21 12 0.46
22 11 0.42
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATATC
Found at i:244205 original size:39 final size:41
Alignment explanation
Indices: 244160--244248 Score: 103
Period size: 43 Copynumber: 2.2 Consensus size: 41
244150 ACTAAGAATC
*
244160 AGGTTGCGA-TCT-A-TAATGTTAATATTTTATTAAGAAAGT
1 AGGTTGCGATTCTAAGTAATGTTAATATTTT-TTAAGAAAAT
* *
244199 AGGTTGCGATTTGTAATGTAATGTTAATATTTTTTAATAAAAT
1 AGGTTGCGA-TTCTAA-GTAATGTTAATATTTTTTAAGAAAAT
244242 AGGTTGC
1 AGGTTGC
244249 ATCCAAGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 9 0.21
41 2 0.05
42 1 0.02
43 15 0.36
44 15 0.36
ACGTcount: A:0.34, C:0.04, G:0.19, T:0.43
Consensus pattern (41 bp):
AGGTTGCGATTCTAAGTAATGTTAATATTTTTTAAGAAAAT
Found at i:244437 original size:73 final size:72
Alignment explanation
Indices: 244350--244591 Score: 238
Period size: 73 Copynumber: 3.3 Consensus size: 72
244340 AAAGGTTCAA
* * * *
244350 AAATTT-AAATATCGATACTTAATATATTATTATCGATACTTTTAAATATTAAAAAAATTGAAGA
1 AAATTTAAAATATCGATACTT-ATATATAATGATTGATACTTTTAAATATTAAAAAAGTTGAAGA
244414 TAAGATCG
65 TAAGATCG
*** *
244422 AAATTTAAAATATCGATACTTATGCGGTAATGATTGATACTTTTAAA-ATTTGAAAAAGTTGATA
1 AAATTTAAAATATCGATACTTAT-ATATAATGATTGATACTTTTAAATA-TTAAAAAAGTTGA-A
244486 GA-AAGATCG
63 GATAAGATCG
* * *** * * *
244495 AAATTTAAAATATTGATACTTATGTGAGGGTGATTGATACTTTTAGATATTAAACAAGTTGATGA
1 AAATTTAAAATATCGATACTTATAT-ATAATGATTGATACTTTTAAATATTAAAAAAGTTGAAG-
*
244560 ATATGATCG
64 ATAAGATCG
* *
244569 ATAGTTAAAATATCGATACTTAT
1 AAATTTAAAATATCGATACTTAT
244592 GTTATGAGGT
Statistics
Matches: 139, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
72 10 0.07
73 99 0.71
74 30 0.22
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.37
Consensus pattern (72 bp):
AAATTTAAAATATCGATACTTATATATAATGATTGATACTTTTAAATATTAAAAAAGTTGAAGAT
AAGATCG
Found at i:246890 original size:32 final size:31
Alignment explanation
Indices: 246801--246895 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 31
246791 GTGAGATCAG
* * *
246801 ATACTAATCAAGGTACATTTAGATAATGCATA
1 ATAC-AATCAGGGTGCATTCAGATAATGCATA
* * *
246833 ATACAATCATGGTGTATTCAAATAATGCATA
1 ATACAATCAGGGTGCATTCAGATAATGCATA
* *
246864 TTACAATTAGGGTTGCATTCAGATAATGCATA
1 ATACAATCAGGG-TGCATTCAGATAATGCATA
246896 GGAGTTGATA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 31 0.60
32 21 0.40
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (31 bp):
ATACAATCAGGGTGCATTCAGATAATGCATA
Found at i:250033 original size:21 final size:20
Alignment explanation
Indices: 250001--250039 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
249991 CATTGCATGA
*
250001 ATTTATGACTTCGACAAAAG
1 ATTTATGACTTCAACAAAAG
*
250021 ATTTCATGGCTTCAACAAA
1 ATTT-ATGACTTCAACAAA
250040 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTTATGACTTCAACAAAAG
Found at i:258891 original size:25 final size:25
Alignment explanation
Indices: 258863--258914 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
258853 ATTTAAGTAC
258863 AACATTTGAATAGTTGGGGTACTTA
1 AACATTTGAATAGTTGGGGTACTTA
258888 AACATTTGAATAGTTGGGGTACTTA
1 AACATTTGAATAGTTGGGGTACTTA
258913 AA
1 AA
258915 TGTAATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (25 bp):
AACATTTGAATAGTTGGGGTACTTA
Found at i:259907 original size:45 final size:45
Alignment explanation
Indices: 259838--260165 Score: 471
Period size: 45 Copynumber: 7.3 Consensus size: 45
259828 TGGTATATGG
* * *
259838 TTATGGAA-AAATGGAAAGTGTATTGGTAAAATGAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
259882 TTATGGAATAAATGGTAAGTATATTGATAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
** * *
259927 TTATGGAATAAATGACAAGTATATTGATAAAATACGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
259972 TTATGGAAT-AATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
260016 TTATGGAACAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * * *
260061 TTATGAGATTAAATGGTAAGTATATTGGTAAATTAAGTTTACGATC
1 TTATG-GAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
260107 TTATGGAACAAATGGTAAGTATGTTGGTAAAATAAGCTTATGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
*
260152 TTATGGGATAAATG
1 TTATGGAATAAATG
260166 ATAAATTATT
Statistics
Matches: 253, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
44 47 0.19
45 167 0.66
46 39 0.15
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:260006 original size:89 final size:90
Alignment explanation
Indices: 259838--260165 Score: 464
Period size: 89 Copynumber: 3.7 Consensus size: 90
259828 TGGTATATGG
* *
259838 TTATGGAA-AAATGGA-AAGTGTATTGGTAAAATGAGCTTACGAGCTTATGGAATAAATGGTAAG
1 TTATGGAACAAAT-GATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
*
259901 TATATTGATAAAATAAGCTTACGAGC
65 TATATTGGTAAAATAAGCTTACGAGC
* * * *
259927 TTATGGAATAAATGACAAGTATATTGATAAAATACGCTTACGAGCTTATGGAAT-AATGGTAAGT
1 TTATGGAACAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGT
259991 ATATTGGTAAAATAAGCTTACGAGC
66 ATATTGGTAAAATAAGCTTACGAGC
* * *
260016 TTATGGAACAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGCTTATGAGATTAAATGGTAAG
1 TTATGGAACAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATG-GAATAAATGGTAAG
* * *
260081 TATATTGGTAAATTAAGTTTACGATC
65 TATATTGGTAAAATAAGCTTACGAGC
* * * *
260107 TTATGGAACAAATGGTAAGTATGTTGGTAAAATAAGCTTATGAGCTTATGGGATAAATG
1 TTATGGAACAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATG
260166 ATAAATTATT
Statistics
Matches: 215, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
89 88 0.41
90 48 0.22
91 79 0.37
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (90 bp):
TTATGGAACAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGT
ATATTGGTAAAATAAGCTTACGAGC
Found at i:260009 original size:134 final size:134
Alignment explanation
Indices: 259838--260180 Score: 481
Period size: 134 Copynumber: 2.5 Consensus size: 134
259828 TGGTATATGG
* * *
259838 TTATGGAAAAATGGAAAGTGTATTGGTAAAATGAGCTTACGAGCTTATGGAATAAATGGTAAGTA
1 TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGT-
*
259903 TATTGATAAAATAAGCTTACGAGCTTATG-GAATAAATGACAAGTATATTGATAAAATACGCTTA
65 TATTGATAAAATAAGCTTACGAGCTTATGAGAATAAATGACAAGTATATTGATAAAATAAGCTTA
259967 CGAGC
130 CGAGC
* *
259972 TTATGGAATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTG
1 TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGT-
* * ** * * *
260037 TATTGGTAAAATAAGCTTACGAGCTTATGAGATTAAATGGTAAGTATATTGGTAAATTAAGTTTA
65 TATTGATAAAATAAGCTTACGAGCTTATGAGAATAAATGACAAGTATATTGATAAAATAAGCTTA
*
260102 CGATC
130 CGAGC
* * * * *
260107 TTATGGAACAAATGGTAAGTATGTTGGTAAAATAAGCTTATGAGCTTATGGGATAAATGATAAAT
1 TTATGGAA-AAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGT
260172 TATTGATAA
65 TATTGATAA
260181 GAAATGTTAT
Statistics
Matches: 184, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
134 87 0.47
135 48 0.26
136 49 0.27
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (134 bp):
TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTT
ATTGATAAAATAAGCTTACGAGCTTATGAGAATAAATGACAAGTATATTGATAAAATAAGCTTAC
GAGC
Found at i:262896 original size:29 final size:29
Alignment explanation
Indices: 262856--263055 Score: 149
Period size: 29 Copynumber: 6.8 Consensus size: 29
262846 ATTTAAAATT
**
262856 AAATACTTTTTATAAATTACATTTAA-GGAC
1 AAAT-CTTTTTATAAATTA-AAATAATGGAC
262886 AAAGT-TTTTTATAAATTAAAATAATGGAC
1 AAA-TCTTTTTATAAATTAAAATAATGGAC
* * *
262915 AAATCTTTTTATAAATTATAATAGA-AGAT
1 AAATCTTTTTATAAATTAAAATA-ATGGAC
* * *
262944 AAATCTTCTTATAAATTACAATAAAGGAC
1 AAATCTTTTTATAAATTAAAATAATGGAC
* * * **
262973 ACATTTTTTTATAATTTAAAATAGA-AAAC
1 AAATCTTTTTATAAATTAAAATA-ATGGAC
*
263002 AAATCTTTTTTATAAATTAAAATAAT-GTC
1 AAATC-TTTTTATAAATTAAAATAATGGAC
* * *
263031 ATATACTTTTTACAAATTACAATAA
1 AAAT-CTTTTTATAAATTAAAATAA
263056 CAACTCATAT
Statistics
Matches: 137, Mismatches: 24, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
28 6 0.04
29 107 0.78
30 23 0.17
31 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (29 bp):
AAATCTTTTTATAAATTAAAATAATGGAC
Found at i:262930 original size:58 final size:58
Alignment explanation
Indices: 262856--263054 Score: 190
Period size: 58 Copynumber: 3.4 Consensus size: 58
262846 ATTTAAAATT
* *
262856 AAATACTTTTTATAAATTACATTTA-AGGACAAAGTTTTTTATAAATTAAAATAATGGAC
1 AAATACTTTTTATAAATTACA-ATAGAAGACAAA-TTTTTTATAAATTAAAATAATGGAC
* * * * *
262915 AAAT-CTTTTTATAAATTATAATAGAAGATAAATCTTCTTATAAATTACAATAAAGGAC
1 AAATACTTTTTATAAATTACAATAGAAGACAAAT-TTTTTATAAATTAAAATAATGGAC
* * * * * *
262973 ACAT-TTTTTTATAATTTAAAATAGAAAACAAATCTTTTTTATAAATTAAAATAAT-GTC
1 AAATACTTTTTATAAATTACAATAGAAGACAAA--TTTTTTATAAATTAAAATAATGGAC
* *
263031 ATATACTTTTTACAAATTACAATA
1 AAATACTTTTTATAAATTACAATA
263055 ACAACTCATA
Statistics
Matches: 113, Mismatches: 22, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
57 3 0.03
58 73 0.65
59 36 0.32
60 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (58 bp):
AAATACTTTTTATAAATTACAATAGAAGACAAATTTTTTATAAATTAAAATAATGGAC
Found at i:263011 original size:87 final size:89
Alignment explanation
Indices: 262855--263055 Score: 232
Period size: 87 Copynumber: 2.3 Consensus size: 89
262845 AATTTAAAAT
* * * **
262855 TAAATACTTTTTATAAATTACATTTAAGGACAAAGTTTTTTATAAATTAAAATAATGGACAAATC
1 TAAATACTTCTTATAAATTACAATAAAGGACAAAGTTTTTTATAAATTAAAATAATAAACAAATC
*
262920 -TTTTTATAAATTATAATAGAAGA
66 TTTTTTATAAATTAAAATAGAAGA
* * *
262943 TAAAT-CTTCTTATAAATTACAATAAAGGACACATTTTTTTATAATTTAAAATAGA-AAACAAAT
1 TAAATACTTCTTATAAATTACAATAAAGGACAAAGTTTTTTATAAATTAAAATA-ATAAACAAAT
*
263006 CTTTTTTATAAATTAAAATA-ATG-
65 CTTTTTTATAAATTAAAATAGAAGA
* * *
263029 TCATATACTTTTTACAAATTACAATAA
1 T-AAATACTTCTTATAAATTACAATAA
263056 CAACTCATAT
Statistics
Matches: 96, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
86 1 0.01
87 54 0.56
88 41 0.43
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.40
Consensus pattern (89 bp):
TAAATACTTCTTATAAATTACAATAAAGGACAAAGTTTTTTATAAATTAAAATAATAAACAAATC
TTTTTTATAAATTAAAATAGAAGA
Found at i:263069 original size:87 final size:86
Alignment explanation
Indices: 262891--263083 Score: 198
Period size: 87 Copynumber: 2.2 Consensus size: 86
262881 AGGACAAAGT
* ** * *
262891 TTTTTATAAATTAAAATAATGGACAAATCTTTTTATAAATTATAATAGAAGATAAATCTTCTTAT
1 TTTTTATAATTTAAAATAATAAACAAATCTTTTTATAAATTAAAATAGAAGATAAATCTTCTTAC
*
262956 AAATTACAATAAAGGACACATT
66 AAATTACAATAAA-GACACATA
* * *
262978 TTTTTATAATTTAAAATAGA-AAACAAATCTTTTTTATAAATTAAAATA-ATG-TCATATACTTT
1 TTTTTATAATTTAAAATA-ATAAACAAATC-TTTTTATAAATTAAAATAGAAGAT-AAAT-CTTC
*
263040 TTACAAATTACAATAACA-ACTCATA
62 TTACAAATTACAATAA-AGACACATA
263065 TTTTTAT-ATATTAAAATAA
1 TTTTTATAAT-TTAAAATAA
263084 CAACCTATAT
Statistics
Matches: 90, Mismatches: 10, Indels: 13
0.80 0.09 0.12
Matches are distributed among these distances:
86 4 0.04
87 49 0.54
88 36 0.40
89 1 0.01
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.40
Consensus pattern (86 bp):
TTTTTATAATTTAAAATAATAAACAAATCTTTTTATAAATTAAAATAGAAGATAAATCTTCTTAC
AAATTACAATAAAGACACATA
Found at i:263077 original size:28 final size:28
Alignment explanation
Indices: 263008--263101 Score: 91
Period size: 28 Copynumber: 3.3 Consensus size: 28
262998 AAACAAATCT
* *** *
263008 TTTTTATAAATTAAAATAATGTCATATA
1 TTTTTACAAATTAAAATAACAACCTATA
*
263036 CTTTTTACAAATTACAATAACAA-CTCATA
1 -TTTTTACAAATTAAAATAACAACCT-ATA
* *
263065 TTTTTATATATTAAAATAACAACCTATA
1 TTTTTACAAATTAAAATAACAACCTATA
263093 TTTTTACAA
1 TTTTTACAA
263102 TCACTACATT
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
28 30 0.58
29 22 0.42
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.43
Consensus pattern (28 bp):
TTTTTACAAATTAAAATAACAACCTATA
Found at i:265957 original size:99 final size:99
Alignment explanation
Indices: 265723--266102 Score: 469
Period size: 99 Copynumber: 3.8 Consensus size: 99
265713 TTTAAGGTGT
* * ** * *
265723 GTTA-CATGAGCAACATGTTTTGTCTTA-TTTCTGCATAATGTAAACAATTTCATATTTATAATT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTT-TGCATAATATAAACGGTTTCATACTTATAACT
* * *
265786 TAAACGGTTGACATTAAAAA-ACGCTACCTAGTAC
65 TAAACGGTTGACAATAAAAAGGCGCTACCTACTAC
* * * *
265820 GTTATCATGAGCAACATGCTTTGTCTTATTTTTGCATAATATAAACGGTTTCGTACTTATAACTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
* *
265885 AAACGGGTGACAATAAAAAGGCGCTACATACTAC
66 AAACGGTTGACAATAAAAAGGCGCTACCTACTAC
* * * *
265919 GTTATCACGATAAACATGTTTTGTCTTACTTTTCCATAATATAAACGGTTTCATACTTATAATTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
* * *
265984 AAACGGTTGACAAAAAAAAAGGTGTTACCTACTAC
66 AAACGGTTGAC-AATAAAAAGGCGCTACCTACTAC
* * *
266019 GTTATCATGAGAAACATTTTTTATCTTACTTTTGCATCATATAAACGGTTTCATACTTATAACTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
* * *
266084 AAATGATTGACATTAAAAA
66 AAACGGTTGACAATAAAAA
266103 AAACGTTACC
Statistics
Matches: 243, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
97 4 0.02
98 66 0.27
99 87 0.36
100 86 0.35
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (99 bp):
GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
AAACGGTTGACAATAAAAAGGCGCTACCTACTAC
Found at i:266066 original size:100 final size:98
Alignment explanation
Indices: 265723--266122 Score: 462
Period size: 100 Copynumber: 4.0 Consensus size: 98
265713 TTTAAGGTGT
* * ** * *
265723 GTTA-CATGAGCAACATGTTTTGTCTTA-TTTCTGCATAATGTAAACAATTTCATATTTATAATT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTT-TGCATAATATAAACGGTTTCATACTTATAACT
** *
265786 TAAACGGTTGACATTAAAAAACGCTACCTAGTAC
65 TAAACGGTTGACAAAAAAAAACGCTACCTACTAC
* * * *
265820 GTTATCATGAGCAACATGCTTTGTCTTATTTTTGCATAATATAAACGGTTTCGTACTTATAACTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
* ** *
265885 AAACGGGTGACAATAAAAAGGCGCTACATACTAC
66 AAACGGTTGACAA-AAAAAAACGCTACCTACTAC
* * * *
265919 GTTATCACGATAAACATGTTTTGTCTTACTTTTCCATAATATAAACGGTTTCATACTTATAATTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
* *
265984 AAACGGTTGACAAAAAAAAAGGTGTTACCTACTAC
66 AAACGGTTGACAAAAAAAAA--CGCTACCTACTAC
* * *
266019 GTTATCATGAGAAACATTTTTTATCTTACTTTTGCATCATATAAACGGTTTCATACTTATAACTT
1 GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
* * * *
266084 AAATGATTGACATTAAAAAAAACGTTACCTGCTAC
66 AAACGGTTGACA--AAAAAAAACGCTACCTACTAC
266119 GTTA
1 GTTA
266123 AAAGCTTAAA
Statistics
Matches: 257, Mismatches: 39, Indels: 11
0.84 0.13 0.04
Matches are distributed among these distances:
97 4 0.02
98 65 0.25
99 87 0.34
100 93 0.36
102 8 0.03
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (98 bp):
GTTATCATGAGAAACATGTTTTGTCTTACTTTTGCATAATATAAACGGTTTCATACTTATAACTT
AAACGGTTGACAAAAAAAAACGCTACCTACTAC
Found at i:266267 original size:20 final size:20
Alignment explanation
Indices: 266230--266268 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
266220 TCTTTAATTC
*
266230 AAAAGTATCAATATTTTTGG
1 AAAAGTATCAATACTTTTGG
**
266250 AAAAGTATTTATACTTTTG
1 AAAAGTATCAATACTTTTG
266269 AATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (20 bp):
AAAAGTATCAATACTTTTGG
Found at i:266420 original size:84 final size:81
Alignment explanation
Indices: 266225--266431 Score: 279
Period size: 84 Copynumber: 2.5 Consensus size: 81
266215 GTTTTTCTTT
* * ** *
266225 AATTCAAAAGTATCAATATTTTTGGAAAAGTATTTATACTTTTGAATTTTAAAAAAATGGAAAAT
1 AATTCAAAAGTATCGATACTTTTGGAAAAGTATAAATACTTTTGAATTTTAAAAAAATGAAAAAT
266290 GATATTTTAACTTTCA
66 GATATTTTAACTTTCA
* * *
266306 AATTTAAAAATATCGGTACTTTTGGAAAAGTATAAATACTTTTGAATTTTAAAAAATACATGAAA
1 AATTCAAAAGTATCGATACTTTTGGAAAAGTATAAATACTTTTGAATTTT-AAAAA-A-ATGAAA
*
266371 AATGATATTTTAACTTTCG
63 AATGATATTTTAACTTTCA
* **
266390 AATTCAAAAGTATCGATACTTTTGGGAAAGTATCGATACTTT
1 AATTCAAAAGTATCGATACTTTTGGAAAAGTATAAATACTTT
266432 GCAACCTTCT
Statistics
Matches: 108, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
81 43 0.40
82 5 0.05
83 1 0.01
84 59 0.55
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.39
Consensus pattern (81 bp):
AATTCAAAAGTATCGATACTTTTGGAAAAGTATAAATACTTTTGAATTTTAAAAAAATGAAAAAT
GATATTTTAACTTTCA
Found at i:266488 original size:18 final size:19
Alignment explanation
Indices: 266465--266504 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
266455 TTTCTTTAAA
266465 TTTG-AAAGTATAGATACT
1 TTTGAAAAGTATAGATACT
*
266483 TTTGAAAAAGTATTGATACT
1 TTTG-AAAAGTATAGATACT
266503 TT
1 TT
266505 CAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
20 15 0.79
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (19 bp):
TTTGAAAAGTATAGATACT
Found at i:266625 original size:19 final size:20
Alignment explanation
Indices: 266601--266639 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
266591 TTTAAATTCG
266601 AAAGTAT-CATACTTTTGAA
1 AAAGTATCCATACTTTTGAA
*
266620 AAAGTATCCATATTTTTGAA
1 AAAGTATCCATACTTTTGAA
266640 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
AAAGTATCCATACTTTTGAA
Found at i:266806 original size:76 final size:77
Alignment explanation
Indices: 266641--266828 Score: 224
Period size: 76 Copynumber: 2.5 Consensus size: 77
266631 ATTTTTGAAT
* * * *
266641 TTTTA-TAATAGAAAA-ATTAATATTCTAGATCGCAACTTAGTTTCTCATGAATCATAACAATCT
1 TTTTATTAATA-AAAATATTAACATTCCAGATCGCAACCTAGTTTCTCATGAACCATAACAATCT
*
266704 TGTGCGCAATCTA
65 TGTGCGAAATCTA
* * *
266717 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTA-TTTCTTAGTGAACCATGACATTCT
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTAGTTTCTCA-TGAACCATAACAATCT
266781 TG-GCGAAA-CTCA
65 TGTGCGAAATCT-A
* *
266793 TTTTATTAATAAAAATGTTAACATTCCAGATTGCAA
1 TTTTATTAATAAAAATATTAACATTCCAGATCGCAA
266829 ACATCAAAAT
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
75 2 0.02
76 55 0.56
77 41 0.42
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.36
Consensus pattern (77 bp):
TTTTATTAATAAAAATATTAACATTCCAGATCGCAACCTAGTTTCTCATGAACCATAACAATCTT
GTGCGAAATCTA
Found at i:272205 original size:174 final size:173
Alignment explanation
Indices: 271833--273034 Score: 1113
Period size: 174 Copynumber: 6.9 Consensus size: 173
271823 TCCTCAAATT
* ** *
271833 GTGAATCATAACCAGAACATCCTTCAGA-TCCTGGTTTCTCTGTACTCAGGTCATCAGGCCCAAC
1 GTGAATCATAACCAGAGCATCCTTCAGATTCCT-GTTTCTCTGTACTCAAATCATCAGTCCCAAC
* * * * * *
271897 AGGAATGGTTCTCAAATCTGAAGTCGTCCTACTACCCC--CAACATCAGATGAAACCACTGCGAT
65 AGGCATGGTTCTCAAGTCTGAAGTCATCCTATTACCCCATCAACATCAGATGAAACCACTTCTAT
* * * * *
271960 TGTAGTGTCAT-TTTCTATAACTTGAGATTCCTTAGACTGCAA-A
130 CGTAGTATCATCTTT-TATATCTTGAGGTTCCTTAGTCTGCAAGA
* *
272003 TGTGAATCATAACCATAGCATCCTTCAGATCCCTGTTTCTCTGTACTCAAATCATCAGTCCCAAC
1 -GTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAATCATCAGTCCCAAC
* ** * *
272068 AAGCATTATTCT-AGAGTCTGAAGTCAACCTATTACCTCCATCAACATCAGGTGAAACCACTTCT
65 AGGCATGGTTCTCA-AGTCTGAAGTCATCCTATTACC-CCATCAACATCAGATGAAACCACTTCT
* * * * * * *
272132 CTCATAGCATCATGTTTTGTATCTTGAGGTTCATTACTCTGCAAGA
128 ATCGTAGTATCATCTTTTATATCTTGAGGTTCCTTAGTCTGCAAGA
* * *
272178 GTAAATCATAAACAGAGCATCCTTCAGATTCCTGTTTCTCGGTAC-CAAATCATCAGTCCCAACA
1 GTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAATCATCAGTCCCAACA
* * * * * * *
272242 GCCATCGTTCTCATGTCTGAAGTTAACCTATTACCCCCATCAACATCAGAAGAAACCACTTCTTT
66 GGCATGGTTCTCAAGTCTGAAGTCATCCTATTA-CCCCATCAACATCAGATGAAACCACTTCTAT
* ** * * * * *
272307 CTTAGTATCAGGTATCATATCTTGACGTTCATTAGTCTGCAAGT
130 CGTAGTATCATCTTTTATATCTTGAGGTTCCTTAGTCTGCAAGA
* * *
272351 GTGAATCATAACCAGAGCATGCTTCAGATTCATGTTTCTCTGTACTCAACTCATCAGTCCCAACA
1 GTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAATCATCAGTCCCAACA
* ** * * * *
272416 GGAATGGTTCTCTCGTCTGAAGTCATCCTATTACCCC--CATCATCAGATGAAACTA-TTTTGTT
66 GGCATGGTTCTCAAGTCTGAAGTCATCCTATTACCCCATCAACATCAGATGAAACCACTTCT-AT
* * * * *
272478 TGTAGTATCATCTTTTGTACCTTGAGGTTCCTCAGTCTGCAAGT
130 CGTAGTATCATCTTTTATATCTTGAGGTTCCTTAGTCTGCAAGA
* * * * * * * * **
272522 GTAAATCATAATCAG-GACATCCTTCACATTCCTGTTTCTCTGTACTCGAGTCATAACTACCGGC
1 GTGAATCATAACCAGAG-CATCCTTCAGATTCCTGTTTCTCTGTACTCAAATCATCAGTCCCAAC
* *
272586 AGTCATGGTTCTCAAGTCTGAAGTCATCATATTAACCCCATCAACATCAGATGAAACCACTTCGT
65 AGGCATGGTTCTCAAGTCTGAAGTCATCCTATT-ACCCCATCAACATCAGATGAAACCACTTC-T
* * * * * * *
272651 -TTGTAGAAACATTTTTTATATCTTGATGTTTCTTAGTCTGCAAGT
128 ATCGTAGTATCATCTTTTATATCTTGAGGTTCCTTAGTCTGCAAGA
* * * *
272696 GGGAATCATAACCAGAGCATCCTTCACACTCCTGTTTCTCT-TCACTCAAATCATCGGTCCCAAC
1 GTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGT-ACTCAAATCATCAGTCCCAAC
* * * * * * ** *
272760 AGGGAAGGTTCCCAAGTCTGAAGCCGTCCTATTATCTCCATCGGCATCTA-ATGAAACCA-TTTT
65 AGGCATGGTTCTCAAGTCTGAAGTCATCCTATTA-CCCCATCAACATC-AGATGAAACCACTTCT
* * * *
272823 ATCTGTATTATCATCTTTTATATCTCGAGGTTCCTGAATCTGCAAGTGTGA
128 ATC-GTAGTATCATCTTTTATATCTTGAGGTTCCTTAGTCTGCAA----GA
* * *
272874 CTGTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAGTCGTCAGTCTCAA
1 --GTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAATCATCAGTCCCAA
* * * *
272939 CAGGCATGGTTCTCATGTCTGAAGTCATCCTATTACCCCCATCGACATCAGATGAAATCTCTTC-
64 CAGGCATGGTTCTCAAGTCTGAAGTCATCCTATTA-CCCCATCAACATCAGATGAAACCACTTCT
** * *
273003 ATTCAAAGTGTCATTTTTTATATCTTGAGGTT
128 A-TCGTAGTATCATCTTTTATATCTTGAGGTT
273035 TTGTAATCTG
Statistics
Matches: 832, Mismatches: 166, Indels: 57
0.79 0.16 0.05
Matches are distributed among these distances:
170 5 0.01
171 208 0.25
172 11 0.01
173 154 0.19
174 314 0.38
175 8 0.01
176 1 0.00
178 1 0.00
179 1 0.00
180 124 0.15
181 5 0.01
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (173 bp):
GTGAATCATAACCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAATCATCAGTCCCAACA
GGCATGGTTCTCAAGTCTGAAGTCATCCTATTACCCCATCAACATCAGATGAAACCACTTCTATC
GTAGTATCATCTTTTATATCTTGAGGTTCCTTAGTCTGCAAGA
Found at i:275184 original size:15 final size:15
Alignment explanation
Indices: 275155--275202 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
275145 GTAGGAAGAG
275155 AGAAGAGAAGAAGAAAA
1 AGAAGAG-AG-AGAAAA
275172 AGAAGAGAGAGAAAA
1 AGAAGAGAGAGAAAA
275187 AGAAGA-ATGAGAAAA
1 AGAAGAGA-GAGAAAA
275202 A
1 A
275203 AAAAGGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.03
15 20 0.67
16 2 0.07
17 7 0.23
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (15 bp):
AGAAGAGAGAGAAAA
Found at i:278222 original size:174 final size:173
Alignment explanation
Indices: 277932--278580 Score: 805
Period size: 174 Copynumber: 3.8 Consensus size: 173
277922 CTCAAATTGA
* * * * ***
277932 GAATCATAATCAGAGCATCCTTCAGTTTCATGTTTCTCCGTATTGAAGTCATCAGTCCCAACAGG
1 GAATCATGACCAGAGCATCCTTCAGATTCATGTTTCTCTGTAACAAAGTCATCAGTCCCAACAGG
* * * * *
277997 AATGGTTCTCA-AGTCTGAAGTCATCCTATTAACCCCATCAACGTCAGATGAAACCACTCCGTTT
66 CATGATTCT-AGAGTCTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCGTTT
*
278061 GTAGTGTCACTTTTCATATCTTGAGGTTCCTTAGTCCGCAAGCAT
130 GTAGTGTCA-TTTTCATATCTTGAGGTTCCTTAGTCTGCAAGCAT
* * *
278106 GAATCATGATCAAAGCATCCTTCAGAATCATGTTTCTCTGTAACAAAGTCATCAGTCCCAACAGG
1 GAATCATGACCAGAGCATCCTTCAGATTCATGTTTCTCTGTAACAAAGTCATCAGTCCCAACAGG
* * *
278171 CATGATTCTGGAGTCTGAAGTCATCCTATTGCCCCCATCAACATCAGATGAAACCACTTTGTTTG
66 CATGATTCTAGAGTCTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCGTTTG
* * * *
278236 TAGTGTTATTTCTCATATCTTGAGGCTCCGTGGTCTGCAAGCAT
131 TAGTGTCATTT-TCATATCTTGAGGTTCCTTAGTCTGCAAGCAT
* * ***
278280 GAATCAT-AGCCAGAGCATCCTTCAGATTCCTGTTTATCTGTAATGCAGTCATCAGTCCCAACAG
1 GAATCATGA-CCAGAGCATCCTTCAGATTCATGTTTCTCTGTAACAAAGTCATCAGTCCCAACAG
* * * *
278344 GCATGATTCTAGAGTCAGAAATCA-CTCTATTACCCACATCAACATCAGATGAAACCACTTCGAT
65 GCATGATTCTAGAGTCTGAAGTCATC-CTATTACCCCCATCAACATCAGATGAAACCACTTCGTT
278408 TGTAGTGTCATTTTTCATATCTTGAGGTTCCTTAGTCTGCAA--AT
129 TGTAGTGTCA-TTTTCATATCTTGAGGTTCCTTAGTCTGCAAGCAT
* * * *
278452 -CAT-A-G-CCAGAGCATCCTTCAGATTCCTGTTTCTCTGTACTCAAA-TCATAAGTCCCAACAG
1 GAATCATGACCAGAGCATCCTTCAGATTCATGTTTCTCTGTA-ACAAAGTCATCAGTCCCAACAG
* * * *
278512 GCATGATTCTAGAGTCTGAAGTCACCCTATTACCTCCATCAACATCAGAGGAAACCACTTCTTTT
65 GCATGATTCTAGAGTCTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCGTTT
278577 GTAG
130 GTAG
278581 CATAATTTTT
Statistics
Matches: 413, Mismatches: 54, Indels: 22
0.84 0.11 0.04
Matches are distributed among these distances:
168 107 0.26
169 2 0.00
170 1 0.00
171 2 0.00
172 2 0.00
173 5 0.01
174 291 0.70
175 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (173 bp):
GAATCATGACCAGAGCATCCTTCAGATTCATGTTTCTCTGTAACAAAGTCATCAGTCCCAACAGG
CATGATTCTAGAGTCTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCGTTTG
TAGTGTCATTTTCATATCTTGAGGTTCCTTAGTCTGCAAGCAT
Found at i:278878 original size:141 final size:141
Alignment explanation
Indices: 278470--278881 Score: 533
Period size: 141 Copynumber: 2.9 Consensus size: 141
278460 GAGCATCCTT
*
278470 CAGATTCCTGTTTCTCTGTACTCAAATCATAAGTCCCAACAGGCATGATTCT-AGAGTCTGAAGT
1 CAGATTCCTGTTTCTCTGTACTCAAATCATAAGTCCCAACAGGCATGCTTCTCA-AGTCTGAAGT
* * * * * *
278534 CACCCTATTACCTCCATCAACATCAGAGGAAACCACTTCTTTTGTAGCATAATTTTTTATATATT
65 CATCCTATTACCTCCATCTACATCAGATGAAACCACTTCATTTGTAGCATCATTTTTTATATCTT
* *
278599 CTGAATCATAAC
130 GTGAACCATAAC
* * * * *
278611 CAGATTCCTGTTCCTCTGCACTCAAATCATTAGTCCAAACAGGCATGCTTCTCAATTCTGAAGTC
1 CAGATTCCTGTTTCTCTGTACTCAAATCATAAGTCCCAACAGGCATGCTTCTCAAGTCTGAAGTC
* * * * * *
278676 ATCCTATTACCCCCATCATTC-TCAGATGAAACAACTCCATTTGTAGTATCATCTTTTATATCTT
66 ATCCTATTACCTCCATC-TACATCAGATGAAACCACTTCATTTGTAGCATCATTTTTTATATCTT
278740 GTGAACCATAAC
130 GTGAACCATAAC
* * ** *
278752 CAGATTCCTGTTTCTCTGTACCCAAGTCAGCAGTCCCAGCA-GCAATGCTTCTCAAGTCTGAAGT
1 CAGATTCCTGTTTCTCTGTACTCAAATCATAAGTCCCAACAGGC-ATGCTTCTCAAGTCTGAAGT
* *
278816 CATCCTGTTACCTCCATCTACATCAGATGAAACCACTTCGTTTGTAGCATCATTTTTTATATCTT
65 CATCCTATTACCTCCATCTACATCAGATGAAACCACTTCATTTGTAGCATCATTTTTTATATCTT
278881 G
130 G
278882 AGATTCCATA
Statistics
Matches: 230, Mismatches: 37, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
140 4 0.02
141 224 0.97
142 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.33
Consensus pattern (141 bp):
CAGATTCCTGTTTCTCTGTACTCAAATCATAAGTCCCAACAGGCATGCTTCTCAAGTCTGAAGTC
ATCCTATTACCTCCATCTACATCAGATGAAACCACTTCATTTGTAGCATCATTTTTTATATCTTG
TGAACCATAAC
Found at i:287091 original size:20 final size:20
Alignment explanation
Indices: 287063--287104 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
287053 AATTTATTAG
* *
287063 TTTTTGAAACTTATAGGCAA
1 TTTTAGAAACTTATAGGAAA
*
287083 TTTTAGAAAGTTATAGGAAA
1 TTTTAGAAACTTATAGGAAA
287103 TT
1 TT
287105 CAGGGACCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTTAGAAACTTATAGGAAA
Found at i:287951 original size:14 final size:14
Alignment explanation
Indices: 287932--287968 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
287922 CAACCCGGAC
287932 TGAGTCAACTCGTA
1 TGAGTCAACTCGTA
*
287946 TGAGTCAACTCGTC
1 TGAGTCAACTCGTA
287960 TGAGTCAAC
1 TGAGTCAAC
287969 CAGTTAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (14 bp):
TGAGTCAACTCGTA
Found at i:304404 original size:34 final size:34
Alignment explanation
Indices: 304361--304426 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
304351 ATAAAAAAGA
304361 GTATTTTTAGGTGTCTTGTTTGCTGCTCGGTTGG
1 GTATTTTTAGGTGTCTTGTTTGCTGCTCGGTTGG
304395 GTATTTTTAGGTGTCTTGTTTGCTGCTCGGTT
1 GTATTTTTAGGTGTCTTGTTTGCTGCTCGGTT
304427 TATCTGAAAT
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:0.06, C:0.12, G:0.30, T:0.52
Consensus pattern (34 bp):
GTATTTTTAGGTGTCTTGTTTGCTGCTCGGTTGG
Found at i:306675 original size:35 final size:35
Alignment explanation
Indices: 306609--306676 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
306599 ATCAAGAAAG
* *
306609 ACTAAATCTGAGAGAAACCGAAATCCGACATCTAA
1 ACTAAAACTGAGAGAAACCGAAATCCAACATCTAA
* *
306644 ACTAAAACTGAGAGAAACTGAAATCTAACATCT
1 ACTAAAACTGAGAGAAACCGAAATCCAACATCT
306677 GAATTTCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (35 bp):
ACTAAAACTGAGAGAAACCGAAATCCAACATCTAA
Found at i:309212 original size:11 final size:11
Alignment explanation
Indices: 309181--309220 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
309171 TATATAGTTT
*
309181 ATATATAAAAC
1 ATATATAAACC
*
309192 ATACATAAACC
1 ATATATAAACC
*
309203 ATATATAAACT
1 ATATATAAACC
309214 ATATATA
1 ATATATA
309221 TAGTTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (11 bp):
ATATATAAACC
Found at i:309306 original size:9 final size:9
Alignment explanation
Indices: 309294--309338 Score: 60
Period size: 9 Copynumber: 5.2 Consensus size: 9
309284 AATTTATAAC
309294 TATATACTA
1 TATATACTA
309303 TATATAACTA
1 TATAT-ACTA
309313 TA-A-ACTA
1 TATATACTA
309320 TATATACTA
1 TATATACTA
309329 TATATA-TA
1 TATATACTA
309337 TA
1 TA
309339 GACTATATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 6 0.18
8 5 0.15
9 16 0.48
10 6 0.18
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (9 bp):
TATATACTA
Found at i:309309 original size:26 final size:26
Alignment explanation
Indices: 309280--309334 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
309270 TATATAAACG
*
309280 ATAAAATTTATAAC-TATATACTATAT
1 ATAAAATATA-AACATATATACTATAT
*
309306 AT-AACTATAAACTATATATACTATAT
1 ATAAAATATAAAC-ATATATACTATAT
309332 ATA
1 ATA
309335 TATAGACTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
24 3 0.12
25 5 0.21
26 16 0.67
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (26 bp):
ATAAAATATAAACATATATACTATAT
Found at i:309310 original size:17 final size:17
Alignment explanation
Indices: 309288--309338 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
309278 CGATAAAATT
309288 TATAACTATATACTATA
1 TATAACTATATACTATA
*
309305 TATAACTATAAACTATA
1 TATAACTATATACTATA
309322 TAT-ACTATATA-TATA
1 TATAACTATATACTATA
309337 TA
1 TA
309339 GACTATATGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.19
16 7 0.22
17 19 0.59
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAACTATATACTATA
Found at i:309314 original size:15 final size:15
Alignment explanation
Indices: 309296--309345 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
309286 TTTATAACTA
309296 TATACTATATATAAC
1 TATACTATATATAAC
309311 TATAAACTATATAT-AC
1 TAT--ACTATATATAAC
309327 TATA-TATATATAGAC
1 TATACTATATATA-AC
309342 TATA
1 TATA
309346 TGATGCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.23
14 1 0.03
15 9 0.29
16 5 0.16
17 9 0.29
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (15 bp):
TATACTATATATAAC
Found at i:309318 original size:24 final size:24
Alignment explanation
Indices: 309294--309346 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 24
309284 AATTTATAAC
309294 TATATACTATATATAACTATAAACTA
1 TATATACTATATAT-A-TATAAACTA
*
309320 TATATACTATATATATATAGACTA
1 TATATACTATATATATATAAACTA
309344 TAT
1 TAT
309347 GATGCATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 11 0.42
25 1 0.04
26 14 0.54
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (24 bp):
TATATACTATATATATATAAACTA
Found at i:309416 original size:26 final size:26
Alignment explanation
Indices: 309352--309442 Score: 87
Period size: 26 Copynumber: 3.4 Consensus size: 26
309342 TATATGATGC
*
309352 ATGTAT-ATAGTTATACTTAGATATAT
1 ATGTATCAT-GTTATACTTAGATATGT
*
309378 ATGTTATATATGTTATACTTAGATATGT
1 ATG-TAT-CATGTTATACTTAGATATGT
** *
309406 ATGTATCATG-TATGTTATACATATGT
1 ATGTATCATGTTATACT-TAGATATGT
309432 ATGTATCATGT
1 ATGTATCATGT
309443 ATCATGTATC
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
25 4 0.07
26 24 0.44
27 6 0.11
28 19 0.35
29 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.47
Consensus pattern (26 bp):
ATGTATCATGTTATACTTAGATATGT
Found at i:309422 original size:30 final size:30
Alignment explanation
Indices: 309361--309444 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 30
309351 CATGTATATA
* *
309361 GTTATACTTAGATATATATGT-T-ATATAT
1 GTTATACTTAGATATGTATGTATCATGTAT
309389 GTTATACTTAGATATGTATGTATCATGTAT
1 GTTATACTTAGATATGTATGTATCATGTAT
309419 GTTATAC----ATATGTATGTATCATGTAT
1 GTTATACTTAGATATGTATGTATCATGTAT
309445 CATGTATCAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
26 19 0.37
28 20 0.38
29 1 0.02
30 12 0.23
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (30 bp):
GTTATACTTAGATATGTATGTATCATGTAT
Found at i:309444 original size:7 final size:7
Alignment explanation
Indices: 309432--309477 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
309422 ATACATATGT
309432 ATGTATC
1 ATGTATC
309439 ATGTATC
1 ATGTATC
309446 ATGTATC
1 ATGTATC
309453 ATGTATC
1 ATGTATC
309460 ATGTATC
1 ATGTATC
309467 ATGTATC
1 ATGTATC
309474 ATGT
1 ATGT
309478 CTATATATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (7 bp):
ATGTATC
Found at i:309518 original size:22 final size:21
Alignment explanation
Indices: 309486--309526 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
309476 GTCTATATAT
309486 TATATTTAGATATGTATGTTA
1 TATATTTAGATATGTATGTTA
309507 TATATGTTAGATATGTATGT
1 TATAT-TTAGATATGTATGT
309527 ATCATGTCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (21 bp):
TATATTTAGATATGTATGTTA
Found at i:309567 original size:95 final size:95
Alignment explanation
Indices: 309384--309556 Score: 214
Period size: 91 Copynumber: 1.9 Consensus size: 95
309374 ATATATGTTA
* * *
309384 TATATGTTATACTTAGATATGTATGTATCATGTATGTTATACATATGTATGTATCATGTATCATG
1 TATATATTATACTTAGATATGTATGTATCATATATGTTATACATATGTATGTATCATGTATCATA
* *
309449 TATCATGTATCATGTATCATGTATCATGTC
66 CATCATGTATCATATATCATGTATCATGTC
* * *
309479 TATATATTATATTTAGATATGTATGT-T-ATATATG-T-TAGATATGTATGTATCATGTCTGACA
1 TATATATTATACTTAGATATGTATGTATCATATATGTTATACATATGTATGTATCATGTAT--CA
309540 TACAT-ATGTAT-ATATAT
64 TACATCATGTATCATATAT
309557 GATGCATGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
91 25 0.37
92 7 0.10
93 11 0.16
94 1 0.01
95 24 0.35
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (95 bp):
TATATATTATACTTAGATATGTATGTATCATATATGTTATACATATGTATGTATCATGTATCATA
CATCATGTATCATATATCATGTATCATGTC
Found at i:309646 original size:36 final size:35
Alignment explanation
Indices: 309597--309667 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
309587 ATGAATATAT
*
309597 GTATAATGCATGTATATATGTATGATGTATGTATGA
1 GTATAATGCATGTATATATGTA-CATGTATGTATGA
* * *
309633 GTATGATGGATGTATATATTTACATGTATGTATGA
1 GTATAATGCATGTATATATGTACATGTATGTATGA
309668 TAAATGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 12 0.39
36 19 0.61
ACGTcount: A:0.32, C:0.03, G:0.23, T:0.42
Consensus pattern (35 bp):
GTATAATGCATGTATATATGTACATGTATGTATGA
Found at i:315408 original size:56 final size:56
Alignment explanation
Indices: 315322--315433 Score: 206
Period size: 56 Copynumber: 2.0 Consensus size: 56
315312 TAAATCCATG
*
315322 AAAGCAGCTGGTGCATTCATAACTTTAAACGGCTTTACGATAAACTCATAGTGACC
1 AAAGCAGCTGGTGCATTCATAACTCTAAACGGCTTTACGATAAACTCATAGTGACC
*
315378 AAAGCAGCTGGTGCATTCGTAACTCTAAACGGCTTTACGATAAACTCATAGTGACC
1 AAAGCAGCTGGTGCATTCATAACTCTAAACGGCTTTACGATAAACTCATAGTGACC
315434 GTATCTTGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (56 bp):
AAAGCAGCTGGTGCATTCATAACTCTAAACGGCTTTACGATAAACTCATAGTGACC
Found at i:318183 original size:20 final size:20
Alignment explanation
Indices: 318143--318183 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
318133 TTTGATCATG
*
318143 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
318163 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
318183 A
1 A
318184 ACTAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:318426 original size:15 final size:15
Alignment explanation
Indices: 318402--318451 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
318392 CCGTAGGACC
*
318402 ACTACATCCCGAATG
1 ACTACGTCCCGAATG
*
318417 ACTACGTCCCGATTG
1 ACTACGTCCCGAATG
*
318432 ACTACGTCCCGAATA
1 ACTACGTCCCGAATG
318447 ACTAC
1 ACTAC
318452 AATACCCTCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.22
Consensus pattern (15 bp):
ACTACGTCCCGAATG
Found at i:323118 original size:64 final size:64
Alignment explanation
Indices: 322997--323138 Score: 146
Period size: 64 Copynumber: 2.2 Consensus size: 64
322987 CACATTGAAT
* *
322997 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAATGGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAATGCAAATGGGTGCATCAATGCAT-AGGTA
* ** ** * *
323061 GTGCATCGATGCATCCCTTTAAA-ATGAAACCATCGAA-GGTAATTTGTGTATCAATGCATGGGT
1 GTGCATCGATGCA-CCCTTTAAAGAAGAAA-CATCGAATGCAAATGGGTGCATCAATGCATAGGT
323124 A
64 A
*
323125 GCGCATCGATGCAC
1 GTGCATCGATGCAC
323139 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
63 3 0.05
64 47 0.72
65 15 0.23
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (64 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAATGCAAATGGGTGCATCAATGCATAGGTA
Found at i:323797 original size:31 final size:31
Alignment explanation
Indices: 323759--323818 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
323749 AGAGTCGAGG
*
323759 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
*
323790 GTTTACCTAGGTTCTTCGAGACCTATGGA
1 GTTTACCTAGGTTCTTCGAGACATATGGA
323819 TAATTGTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:323874 original size:29 final size:30
Alignment explanation
Indices: 323809--323880 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
323799 GGTTCTTCGA
* * *
323809 GACCTATGGATAATTGTCGAGGTTCTTTAT
1 GACCTCTGGATAGTTGTCGAGGGTCTTTAT
* *
323839 GGCCTCTGGATAGTTGTCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGTCGAGGGTCTTTAT
323868 GACCTCTGGATAG
1 GACCTCTGGATAG
323881 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.17, C:0.17, G:0.31, T:0.36
Consensus pattern (30 bp):
GACCTCTGGATAGTTGTCGAGGGTCTTTAT
Found at i:324349 original size:4 final size:4
Alignment explanation
Indices: 324342--324687 Score: 629
Period size: 4 Copynumber: 86.5 Consensus size: 4
324332 TGATAATGAC
324342 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
324390 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
324438 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
324486 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
324534 ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * *
324582 ATAT ATAT ATGT ATAT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
324630 ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
324678 ATGT ATGT AT
1 ATGT ATGT AT
324688 TTGTTACATA
Statistics
Matches: 330, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 330 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:327413 original size:64 final size:63
Alignment explanation
Indices: 327318--327455 Score: 161
Period size: 64 Copynumber: 2.2 Consensus size: 63
327308 CACATTGAAT
* *
327318 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGAAAATGGTGCATCGATGCATAAGGA
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGAAAATGGTGCATCGATGCATAAGGA
* * * * * ** *
327381 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGTGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCGAAGGAAAATGGTGCATCGATGCATAAGGA
327445 GTGCATCGATG
1 GTGCATCGATG
327456 TACATGTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
63 15 0.24
64 48 0.76
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGAAAATGGTGCATCGATGCATAAGGA
Found at i:328115 original size:31 final size:31
Alignment explanation
Indices: 328080--328144 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
328070 AGAGTCGATG
*
328080 GTTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTTACCTAGGTTC-TTCGAGACATATGGACA
* *
328111 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTAGGTTCTTCGAGACATATGGACA
328142 GTT
1 GTT
328145 GCCGAGGTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (31 bp):
GTTTACCTAGGTTCTTCGAGACATATGGACA
Found at i:328155 original size:30 final size:31
Alignment explanation
Indices: 328094--328156 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
328084 ACCTATGTCT
*
328094 TTCGAGACATATGGACAGTTTACCTAGGTTC
1 TTCGAGACATATGGACAGTTTACCGAGGTTC
* * *
328125 TTCGGGACCTATGGACAG-TTGCCGAGGTTC
1 TTCGAGACATATGGACAGTTTACCGAGGTTC
328155 TT
1 TT
328157 TATGACCTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 12 0.43
31 16 0.57
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (31 bp):
TTCGAGACATATGGACAGTTTACCGAGGTTC
Found at i:328164 original size:30 final size:30
Alignment explanation
Indices: 328103--328198 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
328093 TTTCGAGACA
* * * *
328103 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTGCCGAGGTTCTTTGTGACC
*
328134 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTGCCGAGGTTCTTTGTGACC
* * * *
328164 TCTGGATAGTTGTCG-GGGTCTTTGTGACC
1 TATGGACAGTTGCCGAGGTTCTTTGTGACC
*
328193 TCTGGA
1 TATGGA
328199 TAGGTCATTC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
29 18 0.33
30 28 0.51
31 9 0.16
ACGTcount: A:0.17, C:0.20, G:0.29, T:0.34
Consensus pattern (30 bp):
TATGGACAGTTGCCGAGGTTCTTTGTGACC
Found at i:328192 original size:29 final size:30
Alignment explanation
Indices: 328130--328201 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
328120 GGTTCTTCGG
* * *
328130 GACCTATGGACAGTTGCCGAGGTTCTTTAT
1 GACCTCTGGATAGTTGCCGAGGGTCTTTAT
* *
328160 GACCTCTGGATAGTTGTCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGCCGAGGGTCTTTAT
328189 GACCTCTGGATAG
1 GACCTCTGGATAG
328202 GTCATTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTGCCGAGGGTCTTTAT
Found at i:328679 original size:2 final size:2
Alignment explanation
Indices: 328674--328792 Score: 238
Period size: 2 Copynumber: 59.5 Consensus size: 2
328664 TATGTATATA
328674 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
328716 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
328758 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
328793 ATTTGTTACA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 117 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:333078 original size:35 final size:33
Alignment explanation
Indices: 333009--333073 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
332999 GAATGTGTGT
333009 CATCTTTTTTTAATGGCGTGTGCTTCAATGACG
1 CATCTTTTTTTAATGGCGTGTGCTTCAATGACG
333042 CATCTTTTTTTAATGGCGTGTGCTTCAATGAC
1 CATCTTTTTTTAATGGCGTGTGCTTCAATGAC
333074 ACGCAATGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.43
Consensus pattern (33 bp):
CATCTTTTTTTAATGGCGTGTGCTTCAATGACG
Found at i:333214 original size:13 final size:13
Alignment explanation
Indices: 333173--333217 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
333163 AATGAACGTT
*
333173 ATAAATGCACGTC
1 ATAAATGCGCGTC
* * *
333186 ATAAATGTGTGCC
1 ATAAATGCGCGTC
333199 ATAAATGCGCGTC
1 ATAAATGCGCGTC
333212 ATAAAT
1 ATAAAT
333218 TTATGTCGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (13 bp):
ATAAATGCGCGTC
Found at i:333999 original size:23 final size:25
Alignment explanation
Indices: 333963--334009 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
333953 CATAAATTTT
333963 TGTTATTCAAATTTT-CA-ATCAAA
1 TGTTATTCAAATTTTGCATATCAAA
* *
333986 TGTTATTTAGATTTTGCATATCAA
1 TGTTATTCAAATTTTGCATATCAA
334010 TTAAATTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.47
Consensus pattern (25 bp):
TGTTATTCAAATTTTGCATATCAAA
Found at i:338264 original size:34 final size:34
Alignment explanation
Indices: 338221--338292 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
338211 AACCGAGTAG
338221 AAACCAGCCGAAGAAAAAGAAGGCACCGGAATAT
1 AAACCAGCCGAAGAAAAAGAAGGCACCGGAATAT
*
338255 AAACCAGCCGAAGAAAAAGAAGGCATCGGAATAT
1 AAACCAGCCGAAGAAAAAGAAGGCACCGGAATAT
338289 AAAC
1 AAAC
338293 GTTTAATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.51, C:0.19, G:0.22, T:0.07
Consensus pattern (34 bp):
AAACCAGCCGAAGAAAAAGAAGGCACCGGAATAT
Found at i:356428 original size:35 final size:37
Alignment explanation
Indices: 356357--356429 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
356347 GTTGGAAAAT
* * *
356357 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAATTAAAAATCATAAA
*
356394 ATTTATATAATTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAATTAAAAATCATAAA
356429 A
1 A
356430 AAAGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 6 0.19
36 14 0.44
37 12 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAATTAAAAATCATAAA
Found at i:370422 original size:12 final size:12
Alignment explanation
Indices: 370405--370438 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
370395 CTTAAAGCCA
370405 AGGAGAGAGAGG
1 AGGAGAGAGAGG
370417 AGGAGAGAGA-G
1 AGGAGAGAGAGG
370428 A-GAGAGAGAGG
1 AGGAGAGAGAGG
370439 TTCTTCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 3 0.14
12 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
AGGAGAGAGAGG
Found at i:370975 original size:15 final size:15
Alignment explanation
Indices: 370955--371005 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
370945 GAGACATTAG
370955 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
370970 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
*
370985 CCGCCCCACATCCGC
1 CCGCCCCGCATCCGC
371000 CCGCCC
1 CCGCCC
371006 AGCTAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.08, C:0.69, G:0.18, T:0.06
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:376214 original size:18 final size:17
Alignment explanation
Indices: 376156--376236 Score: 64
Period size: 18 Copynumber: 4.8 Consensus size: 17
376146 AAAACAAGTA
*
376156 AAATAAAGCAAAAGAAAT
1 AAATAAAGTAAAA-AAAT
376174 -AAT-AAG-ATAAAAAAT
1 AAATAAAGTA-AAAAAAT
*
376189 AAGA-AAAGTGAATAAAAT
1 AA-ATAAAGT-AAAAAAAT
376207 AAATAAAGTAAAATAAAT
1 AAATAAAGTAAAA-AAAT
376225 AAATAAA-TAAAA
1 AAATAAAGTAAAA
376237 TAAGAAAACA
Statistics
Matches: 53, Mismatches: 2, Indels: 17
0.74 0.03 0.24
Matches are distributed among these distances:
15 5 0.09
16 7 0.13
17 16 0.30
18 24 0.45
19 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (17 bp):
AAATAAAGTAAAAAAAT
Found at i:376220 original size:14 final size:13
Alignment explanation
Indices: 376134--376235 Score: 63
Period size: 12 Copynumber: 7.8 Consensus size: 13
376124 AAAAGAAGTG
376134 AATAAAATAAA-A
1 AATAAAATAAATA
376146 AA-AACAAGTAAAATA
1 AATAA-AA-T-AAATA
* *
376161 AAGCAAAAGAAAT-
1 AA-TAAAATAAATA
*
376174 AATAAGATAAA-A
1 AATAAAATAAATA
* *
376186 AATAAGAA-AAGTG
1 AATAA-AATAAATA
376199 AATAAAATAAATA
1 AATAAAATAAATA
376212 AAGTAAAATAAATA
1 AA-TAAAATAAATA
376226 AAT-AAATAAA
1 AATAAAATAAA
376236 ATAAGAAAAC
Statistics
Matches: 70, Mismatches: 9, Indels: 22
0.69 0.09 0.22
Matches are distributed among these distances:
11 2 0.03
12 26 0.37
13 15 0.21
14 20 0.29
15 3 0.04
16 2 0.03
17 2 0.03
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.17
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:376235 original size:22 final size:21
Alignment explanation
Indices: 376174--376235 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
376164 CAAAAGAAAT
376174 AATAAGATAAA-AAAT-AAGAA
1 AATAA-ATAAATAAATAAAGAA
*
376194 AAGTGAATAAAATAAATAAAGTAA
1 AA-TAAAT-AAATAAATAAAG-AA
376218 AATAAATAAATAAATAAA
1 AATAAATAAATAAATAAA
376236 ATAAGAAAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 4 0.11
21 5 0.14
22 15 0.43
23 7 0.20
24 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (21 bp):
AATAAATAAATAAATAAAGAA
Found at i:376437 original size:3 final size:3
Alignment explanation
Indices: 376429--376479 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
376419 CATGTAAAAT
376429 ATA ATA ATA ATA ATA AT- ATA AT- ATA TATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
376473 ATA ATA A
1 ATA ATA A
376480 ATAAAAAACC
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:376516 original size:12 final size:13
Alignment explanation
Indices: 376490--376523 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
376480 ATAAAAAACC
376490 AAAAAGAATGAAA
1 AAAAAGAATGAAA
376503 AAAAAGAATGAAA
1 AAAAAGAATGAAA
376516 AAAAAGAA
1 AAAAAGAA
376524 ATATAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (13 bp):
AAAAAGAATGAAA
Found at i:378433 original size:36 final size:36
Alignment explanation
Indices: 378383--378836 Score: 361
Period size: 36 Copynumber: 12.9 Consensus size: 36
378373 CAAAGGTTGG
* *
378383 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
378419 TGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
378456 AGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
378492 TGTTTAAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
378521 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
378557 TGATTCGAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
378593 TGTTTCAAAAGAAATTGTCTAAAGAGAGCCAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
378630 AGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* **
378666 TGTTTCAAGGAAAACACAT-TCT----A-AG----TTTT
1 TGTTTCAA-GAGAA-AC-TGTCTCAAGAGAGACAAAATT
* * *
378695 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
378731 TGTTTTAAGAGAAAATGTCTAAAGAGATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
378767 TGTTTTACGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
378803 TGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
378837 CTTTATTTTG
Statistics
Matches: 331, Mismatches: 61, Indels: 52
0.75 0.14 0.12
Matches are distributed among these distances:
26 1 0.00
27 5 0.02
28 5 0.02
29 27 0.08
30 2 0.01
31 2 0.01
32 4 0.01
33 4 0.01
34 1 0.00
35 2 0.01
36 210 0.63
37 62 0.19
38 5 0.02
39 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:378597 original size:101 final size:103
Alignment explanation
Indices: 378418--378606 Score: 285
Period size: 102 Copynumber: 1.9 Consensus size: 103
378408 GAGACAAAAC
*
378418 TTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
* *
378483 GACGAAATTTGTTT-AAAGGAAAACATATTCAAAGATT
66 GACAAAATTTGTTTCAAAAGAAAACATATTCAAAGATT
* * **
378520 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGATT-CGAGGGAAACTGTCTCAAGAG
1 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAG-TTCCAAAAGAAACTGTCTCAAGAG
378583 AGACAAAATTTGTTTCAAAAGAAA
65 AGACAAAATTTGTTTCAAAAGAAA
378607 TTGTCTAAAG
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
101 35 0.45
102 43 0.55
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (103 bp):
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACAAAATTTGTTTCAAAAGAAAACATATTCAAAGATT
Found at i:378698 original size:174 final size:174
Alignment explanation
Indices: 378386--378832 Score: 608
Period size: 174 Copynumber: 2.6 Consensus size: 174
378376 AGGTTGGTGT
* * * *
378386 TTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* *
378451 AACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACATATTCAAA
66 AACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACACATTCAAA
* *
378516 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGA
131 GATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGA
* * * * * *
378560 TTCGAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTAAAGAGAGCCAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* * *
378625 AACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAGGAAAACACATTCTAA
66 AACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACACATTCAAA
* *
378690 GTTTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGT
131 GATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGA
* * * * * *
378734 TTTAAGAGAAAATGTCTAAAGAGATACAAAATTTGTTTTACGAGAAACTGTCTCAAGAGAGACAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
* ** * * *
378799 AA-TTTGTTTTAAGAGAAATTGTCTCAAGAGAGAC
66 AACTTAGTTCCAAAAGAAACTATCTCAAGAGAGAC
378833 AAAACTTTAT
Statistics
Matches: 235, Mismatches: 38, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
173 25 0.11
174 210 0.89
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (174 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
AACTTAGTTCCAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACACATTCAAA
GATTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGA
Found at i:378706 original size:138 final size:138
Alignment explanation
Indices: 378555--378816 Score: 346
Period size: 138 Copynumber: 1.9 Consensus size: 138
378545 AGAGACAAAA
* * * *
378555 TTTGATTCGAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAGAAATTGTCTAAAGAGA
1 TTTGATTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAAAGAAAATGTCTAAAGAGA
* * *
378620 GCCAAAACTTAGTTCCAAAAGAAACTATCTCAAGGGAGACGAAATTTGTTTCAAG-GAAAACACA
66 GACAAAA-TTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACACA
378684 TTCTAAGTT
130 TTCTAAGTT
* * *
378693 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGTTTTAAGAGAAAATGTCTAAAGAGA
1 TTTGATTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAAAGAAAATGTCTAAAGAGA
* * ** ** * *
378758 TACAAAATTTGTTTTACGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAA
66 GACAAAATTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
378817 TTGTCTCAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
137 38 0.36
138 67 0.64
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (138 bp):
TTTGATTCAAGGGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAAAGAAAATGTCTAAAGAGA
GACAAAATTAGTTCCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAACACAT
TCTAAGTT
Done.