Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008483.1 Hibiscus syriacus cultivar Beakdansim tig00111317_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: 262260
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:160958 original size:33 final size:33
Alignment explanation
Indices: 160901--160998 Score: 160
Period size: 33 Copynumber: 2.9 Consensus size: 33
160891 ACGAGATAAT
160901 GAGAATCGCAACGCGGAAATGACTATCGCAACAA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACAA
160935 GAGAATCGCAACGCGAAATGACTATCGCAACAA
1 GAGAATCGCAACGCGAAATGACTATCGCAACAA
* **
160968 GACAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
160999 CGCGAAATAA
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACAA
Found at i:160963 original size:19 final size:19
Alignment explanation
Indices: 160876--161060 Score: 183
Period size: 19 Copynumber: 10.1 Consensus size: 19
160866 TCTTTTGGTT
*
160876 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
160895 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
160915 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
160933 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
**
160949 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
160966 --AA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
160982 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
161002 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
161021 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
161040 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
161059 GA
1 GA
161061 TTTTGGTTTC
Statistics
Matches: 140, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
14 19 0.14
15 4 0.03
16 2 0.01
17 1 0.01
18 5 0.04
19 62 0.44
20 45 0.32
21 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:161025 original size:39 final size:38
Alignment explanation
Indices: 160876--161060 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
160866 TCTTTTGGTT
* * *
160876 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATAAAAATCGCAACGC
** * *
160915 GGAAATGACTATCGCAA--C--AA-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
** * *
160949 GAAATGACTATCGCAA--C--AA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
160982 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATAAAAATCGCAACGC
* *
161021 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
161059 GA
1 GA
161061 TTTTGGTTTC
Statistics
Matches: 129, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
33 46 0.36
34 14 0.11
35 2 0.02
36 1 0.01
38 24 0.19
39 28 0.22
40 14 0.11
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATAAAAATCGCAACGC
Found at i:161081 original size:19 final size:19
Alignment explanation
Indices: 161056--161100 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
161046 AAAATCGCAA
*
161056 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
161075 TGTGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
161094 TGCGATT
1 TGCGATT
161101 ATCTCATTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.13, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:161718 original size:41 final size:41
Alignment explanation
Indices: 161672--161749 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
161662 CGAAAGTCAG
* * *
161672 TATCGCGTTGCGAAAGTAAGTATCTCTTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
*
161713 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
161750 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:161746 original size:20 final size:20
Alignment explanation
Indices: 161653--161746 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
161643 TGCTATGTAA
* * *
161653 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
161673 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
161693 ATCTCTTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
161714 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
161734 ATCGCATTGCGAT
1 ATCGCATTGCGAT
161747 TTTCCCAATT
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
20 46 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Found at i:161765 original size:41 final size:41
Alignment explanation
Indices: 161672--161767 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
161662 CGAAAGTCAG
* * * ** *
161672 TATCGCGTTGCGAAAGTAAGTATCTCTTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
161713 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
161755 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
161768 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:162136 original size:22 final size:22
Alignment explanation
Indices: 162110--162152 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
162100 CGGCGACATC
162110 CGTCCCCATCT-TCGACAAAATT
1 CGTCCCCATCTCT-GACAAAATT
*
162132 CGTCCCTATCTCTGACAAAAT
1 CGTCCCCATCTCTGACAAAAT
162153 CCATCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.28, C:0.35, G:0.09, T:0.28
Consensus pattern (22 bp):
CGTCCCCATCTCTGACAAAATT
Found at i:162569 original size:19 final size:19
Alignment explanation
Indices: 162547--162590 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
162537 AAATCGCAAC
162547 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
162566 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
162585 GCGATT
1 GCGATT
162591 ATCTCGTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:164549 original size:20 final size:20
Alignment explanation
Indices: 164508--164576 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
164498 GAAACTTAAA
* **
164508 ATCGCAACGTGAAAATGGCT
1 ATCGCAACGCGAAAATAACT
*
164528 ATTGCAACGCGAAAATAACT
1 ATCGCAACGCGAAAATAACT
** *
164548 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATAACT
164568 ATCGCAACG
1 ATCGCAACG
164577 GGATAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:164701 original size:20 final size:20
Alignment explanation
Indices: 164678--164715 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
164668 TCAAATTTGC
164678 GTTGCGATTTTAAGTTTCGT
1 GTTGCGATTTTAAGTTTCGT
*
164698 GTTGTGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
164716 AGAAACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGT
Found at i:165265 original size:21 final size:20
Alignment explanation
Indices: 165193--165271 Score: 52
Period size: 21 Copynumber: 3.8 Consensus size: 20
165183 CCGACTCACC
165193 TGTCATCGTTCAAGAGGCCTCA
1 TGTCATCGTTCAAGA-GCC-CA
* ** *
165215 -ATCATCCCTCAAGAGTCACA
1 TGTCATCGTTCAAGAG-CCCA
* *
165235 TCTCACCGTTCAAGATGCCCA
1 TGTCATCGTTCAAGA-GCCCA
*
165256 TGTCATCGTTGAAGAG
1 TGTCATCGTTCAAGAG
165272 GTTCATCCCA
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
20 4 0.10
21 37 0.88
22 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (20 bp):
TGTCATCGTTCAAGAGCCCA
Found at i:166688 original size:14 final size:14
Alignment explanation
Indices: 166666--166702 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
166656 GCTTGTTTAA
166666 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
166680 TTTATTTGTAAAAG
1 TTGATTTGTAAAAG
166694 TTGATTTGT
1 TTGATTTGT
166703 TTAATTGATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:166861 original size:20 final size:20
Alignment explanation
Indices: 166836--166899 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
166826 AATGCTAAAC
*
166836 TCAAAATCGCAATATGAAAG
1 TCAAAATCGCAATACGAAAG
*
166856 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATACGAAAG
* **
166876 CCAAAATCGCAACGCGAAAG
1 TCAAAATCGCAATACGAAAG
166896 TCAA
1 TCAA
166900 TTCGCGTTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.14
Consensus pattern (20 bp):
TCAAAATCGCAATACGAAAG
Found at i:166911 original size:19 final size:19
Alignment explanation
Indices: 166889--166930 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
166879 AAATCGCAAC
*
166889 GCGAAAGTCAATTCGCGTT
1 GCGAAAGTCAATCCGCGTT
*
166908 GCGAAAGTCAATCCGTGTT
1 GCGAAAGTCAATCCGCGTT
166927 GCGA
1 GCGA
166931 TTTTTGCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (19 bp):
GCGAAAGTCAATCCGCGTT
Found at i:169450 original size:24 final size:24
Alignment explanation
Indices: 169423--169476 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
169413 CTGAACCATC
169423 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
169447 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
169471 ATCAAA
1 ATCAAA
169477 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:169490 original size:24 final size:24
Alignment explanation
Indices: 169423--169490 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
169413 CTGAACCATC
* * *
169423 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
169447 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
169471 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
169491 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:170154 original size:17 final size:17
Alignment explanation
Indices: 170132--170164 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
170122 GATGGGGAAG
170132 GATGTCGTTGGATATAA
1 GATGTCGTTGGATATAA
170149 GATGTCGTTGGATATA
1 GATGTCGTTGGATATA
170165 GGAACGGATG
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:0.27, C:0.06, G:0.30, T:0.36
Consensus pattern (17 bp):
GATGTCGTTGGATATAA
Found at i:170177 original size:22 final size:20
Alignment explanation
Indices: 170127--170177 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
170117 TGCGGGATGG
170127 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
170147 --AA-GATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
170164 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
170178 CCGGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 15 0.58
18 2 0.08
20 2 0.08
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Found at i:170339 original size:20 final size:20
Alignment explanation
Indices: 170314--170380 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
170304 GAAATTCAGT
*
170314 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAAAATCGC
* * *
170334 GTTGCGAT-TTACATATTCGC
1 GTTGCGATAGT-CAAAATCGC
**
170354 AATGCGATAGTCAAAATCGC
1 GTTGCGATAGTCAAAATCGC
170374 GTTGCGA
1 GTTGCGA
170381 ATCTGGAAAC
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAAAATCGC
Found at i:171830 original size:20 final size:20
Alignment explanation
Indices: 171805--171846 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
171795 ACCAACAAAT
*
171805 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATATGTAAA
*
171825 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
171845 TC
1 TC
171847 ACATTGCGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:171854 original size:20 final size:20
Alignment explanation
Indices: 171812--171855 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
171802 AATTCGCAAC
* *
171812 GCGAATCTGTAAATCGCAAT
1 GCGAATATGTAAATCACAAT
*
171832 GCGAATATGTAAATCACATT
1 GCGAATATGTAAATCACAAT
171852 GCGA
1 GCGA
171856 TTTCCAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
GCGAATATGTAAATCACAAT
Found at i:171951 original size:20 final size:20
Alignment explanation
Indices: 171878--171952 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
171868 CAACACTGAA
* *
171878 TTTCAAATTCGCAACTC-GA
1 TTTCGAATTCGCAACTCGGT
*
171897 TTTCTGAATTCGCAACTCGAAT
1 TTTC-GAATTCGCAACTCG-GT
* *
171919 TTT-G-TTGTAGCAACTCGGT
1 TTTCGAAT-TCGCAACTCGGT
171938 TTTCGAATTCGCAAC
1 TTTCGAATTCGCAAC
171953 ACGAATTATA
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
19 9 0.21
20 29 0.69
21 1 0.02
22 3 0.07
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (20 bp):
TTTCGAATTCGCAACTCGGT
Found at i:171972 original size:40 final size:39
Alignment explanation
Indices: 171853--171972 Score: 107
Period size: 40 Copynumber: 3.0 Consensus size: 39
171843 AATCACATTG
** * *
171853 CGATTTCCAAATTCTCAACACTGAATTTCAAATTCGCAACT
1 CGATTTCTGAATTCGCAACAC-GAATTT-AATTTCGCAACT
* ** *
171894 CGATTTCTGAATTCGCAACTCGAATTTTGTTGTAGCAACT
1 CGATTTCTGAATTCGCAACACGAATTTAATT-TCGCAACT
*
171934 CGGTTT-TCGAATTCGCAACACGAATTATAATTTCGCAAC
1 CGATTTCT-GAATTCGCAACACGAATT-TAATTTCGCAAC
171973 AGGTTTTAGT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
39 2 0.03
40 41 0.65
41 20 0.32
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.33
Consensus pattern (39 bp):
CGATTTCTGAATTCGCAACACGAATTTAATTTCGCAACT
Found at i:172778 original size:12 final size:12
Alignment explanation
Indices: 172761--172795 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
172751 ACCACATTTC
*
172761 CAATATCAAACA
1 CAATATCAAAAA
172773 CAATATCAAAAA
1 CAATATCAAAAA
*
172785 CAATCTCAAAA
1 CAATATCAAAA
172796 CCCGCAACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.60, C:0.23, G:0.00, T:0.17
Consensus pattern (12 bp):
CAATATCAAAAA
Found at i:172933 original size:24 final size:23
Alignment explanation
Indices: 172918--172973 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 23
172908 CAGTATTCGA
*
172918 ATTTTGATCTTGGTCAATACCCG
1 ATTTTGATCTTGGTCAATACTCG
172941 ATCTTTGATCTTGGTCAATACTCGG
1 AT-TTTGATCTTGGTCAATACTC-G
172966 ATTTTGAT
1 ATTTTGAT
172974 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 25 0.83
25 3 0.10
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (23 bp):
ATTTTGATCTTGGTCAATACTCG
Found at i:175254 original size:18 final size:18
Alignment explanation
Indices: 175231--175266 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
175221 AAGCAAAAGG
*
175231 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
175249 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
175267 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:175564 original size:20 final size:20
Alignment explanation
Indices: 175531--175635 Score: 138
Period size: 20 Copynumber: 5.2 Consensus size: 20
175521 AAATCGCAAC
*
175531 GCGAAGTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* * *
175551 GTGAATTTGGCTTTCACGTT
1 GCGAATTTGACTTTCGCGTT
*
175571 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCGCGTT
*
175591 GAGAATTTGACTTTCGCGTT
1 GCGAATTTGACTTTCGCGTT
* *
175611 GCGGATTTGACTTTTGCGTT
1 GCGAATTTGACTTTCGCGTT
175631 GCGAA
1 GCGAA
175636 AGCGTACCTT
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCGTT
Found at i:175766 original size:13 final size:13
Alignment explanation
Indices: 175745--175789 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
175735 AAGAATTATT
*
175745 AACACATCAATTA
1 AACAAATCAATTA
*
175758 AACAAATCAACTTT
1 AACAAATCAA-TTA
*
175772 TACAAATCAATTA
1 AACAAATCAATTA
175785 AACAA
1 AACAA
175790 GCAAAAAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (13 bp):
AACAAATCAATTA
Found at i:175795 original size:64 final size:64
Alignment explanation
Indices: 175694--175844 Score: 232
Period size: 64 Copynumber: 2.4 Consensus size: 64
175684 AATTTAAAAC
175694 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTAACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTAACACATCAATTA
*** ** *
175758 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTAACACATCAATTA
*
175822 AACAAATCAAC-TTTAAAAATCAA
1 AACAAATCAACTTTTACAAATCAA
175845 CTTTTACAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 11 0.14
64 69 0.86
ACGTcount: A:0.54, C:0.17, G:0.02, T:0.27
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTAACACATCAATTA
Found at i:177148 original size:21 final size:21
Alignment explanation
Indices: 177122--177189 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
177112 GTCGGGCATG
*
177122 TGAACGGTGGGAGGGACCTCT
1 TGAACGGTGGGAGGGGCCTCT
177143 TGAACGGTGGGAGGGGCCTCT
1 TGAACGGTGGGAGGGGCCTCT
**
177164 TGAA-GGATGATAGGGGCCTCT
1 TGAACGG-TGGGAGGGGCCTCT
177185 TGAAC
1 TGAAC
177190 AATATGAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.21, C:0.18, G:0.41, T:0.21
Consensus pattern (21 bp):
TGAACGGTGGGAGGGGCCTCT
Found at i:177606 original size:21 final size:22
Alignment explanation
Indices: 177511--177606 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 22
177501 ATAGAGCGGC
*
177511 TACCTCATCACGTAAAGTA-GA-
1 TACCTCATCACGTAAAG-ACCAT
* *
177532 TACCTCACCACGTAAAACACCAT
1 TACCTCATCACGT-AAAGACCAT
* *
177555 TA--TCATCGCGTAAA-ACCTT
1 TACCTCATCACGTAAAGACCAT
* *
177574 TACCTAACCACGTAAAGACC-T
1 TACCTCATCACGTAAAGACCAT
177595 TACCTCATCACG
1 TACCTCATCACG
177607 CCATGCACCA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
19 6 0.10
20 3 0.05
21 40 0.69
22 7 0.12
23 2 0.03
ACGTcount: A:0.35, C:0.32, G:0.09, T:0.23
Consensus pattern (22 bp):
TACCTCATCACGTAAAGACCAT
Found at i:177647 original size:21 final size:21
Alignment explanation
Indices: 177623--177672 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
177613 ACCATTGTCT
*
177623 TCACGTAAAGTATCGACCTCA
1 TCACGTAAAGCATCGACCTCA
* *
177644 TCACGCAAAGCATTGACCTCA
1 TCACGTAAAGCATCGACCTCA
177665 TCACGTAA
1 TCACGTAA
177673 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCATCGACCTCA
Found at i:179291 original size:20 final size:20
Alignment explanation
Indices: 179248--179291 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
179238 CGCAACGCGA
* * *
179248 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
179268 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
179288 TTTC
1 TTTC
179292 AAATAGTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:179521 original size:19 final size:20
Alignment explanation
Indices: 179491--179531 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
179481 CATCAATTTA
*
179491 AATATAAAAAATTTAATAAT
1 AATATAAAAAATTTAAAAAT
179511 AATAT-AAAAATTTAAAAAT
1 AATATAAAAAATTTAAAAAT
179530 AA
1 AA
179532 AAATAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATATAAAAAATTTAAAAAT
Found at i:179636 original size:20 final size:21
Alignment explanation
Indices: 179611--179653 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
179601 TCTGAGAGAT
*
179611 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATATCGCC
179631 GGAGATGGAGACGGATATCGCC
1 GGAGAT-GAGACGGATATCGCC
179653 G
1 G
179654 TAAAGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.26, C:0.19, G:0.40, T:0.16
Consensus pattern (21 bp):
GGAGATGAGACGGATATCGCC
Found at i:179830 original size:20 final size:20
Alignment explanation
Indices: 179801--179851 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
179791 TAAACGCGCT
*
179801 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
*
179821 TTGTGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
179841 TTGCGAATTTG
1 TTGCGAATTTG
179852 GAAAATCGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.10, G:0.25, T:0.47
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:180165 original size:31 final size:29
Alignment explanation
Indices: 180101--180201 Score: 141
Period size: 29 Copynumber: 3.4 Consensus size: 29
180091 TTTCATTTAA
*
180101 GTACCTAAAGTATTTGTTT-GTCAAAATAA
1 GTACCTAAAGTATTT-TTTGGTCAAAATAG
*
180130 GTACCTAAAGTTATCTTTTTGGTTAAAATAG
1 GTACCTAAAG-TAT-TTTTTGGTCAAAATAG
*
180161 GTACCTAAAGTATTTTTTGATCAAAATAG
1 GTACCTAAAGTATTTTTTGGTCAAAATAG
180190 GTACCTAAAGTA
1 GTACCTAAAGTA
180202 CTCAATTTTA
Statistics
Matches: 65, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
29 36 0.55
30 9 0.14
31 20 0.31
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (29 bp):
GTACCTAAAGTATTTTTTGGTCAAAATAG
Found at i:180225 original size:31 final size:31
Alignment explanation
Indices: 180190--180258 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
180180 ATCAAAATAG
180190 GTACCTAAAGTACTCAATTTTATTAATCTAA
1 GTACCTAAAGTACTCAATTTTATTAATCTAA
*
180221 GTACCTAAAGTACTCAATTTTTTTAATCTAA
1 GTACCTAAAGTACTCAATTTTATTAATCTAA
180252 GTACCTA
1 GTACCTA
180259 TAATCCTATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.39
Consensus pattern (31 bp):
GTACCTAAAGTACTCAATTTTATTAATCTAA
Found at i:180225 original size:60 final size:60
Alignment explanation
Indices: 180098--180232 Score: 168
Period size: 60 Copynumber: 2.2 Consensus size: 60
180088 CATTTTCATT
* *
180098 TAAGTACCTAAAGTATTTGTTTGTCAAAATAAGTACCTAAAGTTATCTTTTTGGTTAAAA
1 TAAGTACCTAAAGTATTTGTTTGTCAAAATAAGTACCTAAAGTTATCATTTTGATTAAAA
* * **
180158 TAGGTACCTAAAGTATTT-TTTGATCAAAATAGGTACCTAAAG-TACTCAATTTT-ATTAATC
1 TAAGTACCTAAAGTATTTGTTTG-TCAAAATAAGTACCTAAAGTTA-TC-ATTTTGATTAAAA
180218 TAAGTACCTAAAGTA
1 TAAGTACCTAAAGTA
180233 CTCAATTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 6 0.09
60 55 0.85
61 4 0.06
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.38
Consensus pattern (60 bp):
TAAGTACCTAAAGTATTTGTTTGTCAAAATAAGTACCTAAAGTTATCATTTTGATTAAAA
Found at i:180589 original size:30 final size:30
Alignment explanation
Indices: 180527--180598 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
180517 TATAGAATAC
180527 TTTAGGTA-TCTATTTTAACCAAAGAGATAA
1 TTTAGGTACT-TATTTTAACCAAAGAGATAA
*
180557 TTTTAGGTACTTATTTTGACACAAA-A-ATAA
1 -TTTAGGTACTTATTTTAAC-CAAAGAGATAA
*
180587 TTTAGATACTTA
1 TTTAGGTACTTA
180599 AATAAAAAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 11 0.30
30 4 0.11
31 17 0.46
32 5 0.14
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (30 bp):
TTTAGGTACTTATTTTAACCAAAGAGATAA
Found at i:180949 original size:31 final size:31
Alignment explanation
Indices: 180914--181006 Score: 73
Period size: 31 Copynumber: 3.1 Consensus size: 31
180904 TGAAGATTGA
180914 TATAAAATATTTTAAAGTTTAAGGATCAATT
1 TATAAAATATTTTAAAGTTTAAGGATCAATT
* * ** * * *
180945 TATAATAGAAGTTATAGTTTAGGGATTAA--
1 TATAAAATATTTTAAAGTTTAAGGATCAATT
* * * *
180974 AATAAAATATTTTAAATTTTAAGAACCAATT
1 TATAAAATATTTTAAAGTTTAAGGATCAATT
181005 TA
1 TA
181007 AAATAAATAT
Statistics
Matches: 41, Mismatches: 19, Indels: 4
0.64 0.30 0.06
Matches are distributed among these distances:
29 18 0.44
31 23 0.56
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (31 bp):
TATAAAATATTTTAAAGTTTAAGGATCAATT
Found at i:181902 original size:16 final size:16
Alignment explanation
Indices: 181883--181915 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
181873 ATATTTAAAC
181883 ACTAAAATATTTTTCG
1 ACTAAAATATTTTTCG
181899 ACTAAAATATTTTTCG
1 ACTAAAATATTTTTCG
181915 A
1 A
181916 AATAAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
ACTAAAATATTTTTCG
Found at i:181921 original size:17 final size:16
Alignment explanation
Indices: 181885--181921 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
181875 ATTTAAACAC
*
181885 TAAAATATTTTTCGAC
1 TAAAATATTTTTCGAA
181901 TAAAATATTTTTCGAAA
1 TAAAATATTTTTCG-AA
181918 TAAA
1 TAAA
181922 GTTTAAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (16 bp):
TAAAATATTTTTCGAA
Found at i:182857 original size:251 final size:240
Alignment explanation
Indices: 182235--182821 Score: 810
Period size: 251 Copynumber: 2.4 Consensus size: 240
182225 CTTATTCATA
*
182235 TATTGAATAAAAATATTTTCTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
** *
182300 CGGGTGAAACTTTATTTTGGTAAGGTCGGGTCGTTTTTTTAAGTGTGATATTC--G-GGTCGGG-
66 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTC-TTTTTTTAAGTTTGATATTCGGGTGGTCGGGT
* * * *
182361 TCGAGTTAAAAATACCCGACCTGAAAATATATATAATTTTACCTTATATATTTAGAAATAATTAC
130 TAGAGTGAAAAATACCCGACCGGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTAC
182426 AATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTT
195 AATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTT
* * *
182472 TATTGAATAAAAAATACTTTTTTATTATTTCATGTCGGGTCGGATTTCTAATTTATATATTCGGG
1 TATTGAAT-AAAAATA--TTTTT-TTA-TT-ATTTCGGGTCGGGTTTCTAATTCATATATTCGGG
* * *
182537 TCGGGTCAGATGAAACTTTATTTTGGTCGGGTC-GAT-TTTTTTTAAGTTTGATATTCGGGTCGG
60 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTTTTTTTAAGTTTGATATTCGGGT--G
*
182600 GTCGGGTTTAGGGTGAAAAATACCCGACCCGGCCAAAAAAATATATAATTTTACCTTATATATTT
123 GTCGGG-TTAGAGTGAAAAATACCCGA-CCGG---AAAAAATATATAATTTTACCTTATATATTT
* **
182665 AGGAATAATTACAATAATACTTCTCTATATATAATATTTTTTCAATTAAGTCACTG-TTT
183 AGAAATAATTACAATAATACCCCTCTATATAT-A-ATTTTTTCAATTAAGTCACTGTTTT
*
182724 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTTGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
182789 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTCT
66 CGGGTGAAACTTTATTTTGGTCGGGTCGGGTCT
182822 CGGATGGAGG
Statistics
Matches: 304, Mismatches: 25, Indels: 31
0.84 0.07 0.09
Matches are distributed among these distances:
237 8 0.03
238 7 0.02
240 23 0.08
241 3 0.01
242 5 0.02
243 60 0.20
245 7 0.02
246 61 0.20
247 20 0.07
248 7 0.02
249 5 0.02
251 65 0.21
252 12 0.04
253 21 0.07
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (240 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGGGTTTCTAATTCATATATTCGGGTCGGGT
CGGGTGAAACTTTATTTTGGTCGGGTCGGGTCTTTTTTTAAGTTTGATATTCGGGTGGTCGGGTT
AGAGTGAAAAATACCCGACCGGAAAAAATATATAATTTTACCTTATATATTTAGAAATAATTACA
ATAATACCCCTCTATATATAATTTTTTCAATTAAGTCACTGTTTT
Found at i:183204 original size:17 final size:17
Alignment explanation
Indices: 183184--183222 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
183174 ATTGGATTTC
*
183184 AATTCTTGACAGATTCT
1 AATTCCTGACAGATTCT
*
183201 AATTCCTGACAGATTTT
1 AATTCCTGACAGATTCT
183218 AATTC
1 AATTC
183223 ATTCACATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (17 bp):
AATTCCTGACAGATTCT
Found at i:189576 original size:23 final size:23
Alignment explanation
Indices: 189529--189576 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
189519 AATAACATAT
**
189529 TAGGTAGCGTTTATATAATGTAA
1 TAGGTAGCGTTTATATAATAAAA
189552 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCGTTTATATAATAAAA
189575 TA
1 TA
189577 AAGATTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (23 bp):
TAGGTAGCGTTTATATAATAAAA
Found at i:189642 original size:23 final size:23
Alignment explanation
Indices: 189607--189654 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
189597 TTCAAATACA
*
189607 ATAACATATTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
*
189630 ATAATATAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
189653 AT
1 AT
189655 TGATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGTTTAT
Found at i:189957 original size:16 final size:15
Alignment explanation
Indices: 189934--189972 Score: 69
Period size: 15 Copynumber: 2.5 Consensus size: 15
189924 TATGGGTTTT
189934 GATGTTTTTGGGATC
1 GATGTTTTTGGGATC
189949 GATGTTTTTGGGATC
1 GATGTTTTTGGGATC
189964 GATAGTTTT
1 GAT-GTTTT
189973 AATAAATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.15, C:0.05, G:0.31, T:0.49
Consensus pattern (15 bp):
GATGTTTTTGGGATC
Found at i:190060 original size:214 final size:205
Alignment explanation
Indices: 189678--190356 Score: 646
Period size: 214 Copynumber: 3.3 Consensus size: 205
189668 AAGTAAACCA
* * *
189678 GTATATTTATATCGGTAACATTATAAATTTATC-TTTTACATTATAATTATCGGTTTTGATG---
1 GTATATTTATACCGGTTACATTATAAATTTA-CATATTACATTATAATTATCGGTTTTGATGTTT
* * * *
189739 ---TTTT-TT-GGATCGATACAATTT--GAAATATATCGACACTTTATGCGTGCATCTCG-TTGG
65 TTATTTTATTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCA-CCCGTTTGG
* * * * * * *
189796 ACATTTATTTTGAAAAAAAAATATCGACATAAACTTAAAAAGCGTCGATACATTAT-TTAGATCT
128 -CATTCATTTTG-AACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTT-GA-CT
189860 ATTTTCTCATAAAATCG
189 ATTTTCTCATAAAATCG
* * * * * *
189877 GTATATTTCTATCGGGTATATTATAAATTTACATATTACATTGTAATTATGGGTTTTGATGTTTT
1 GTATATTTATACCGGTTACATTATAAATTTACATATTACATTATAATTATCGGTTTTGATGTTTT
* * * *
189942 TGGGATCGATGTTTTTGGGATCGATAGTTTTAATAAATGTATCGACACTTTATGTGTGTACCCGT
66 T---AT---T-TTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCGT
* *
190007 TTGGCATTCATTATGAACAAAATGTATCGACACAAATTTAACAAGTGTCGATACTTTATGTTGAC
124 TTGGCATTCATTTTGAACAAAA-GTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGA-
190072 CTATTTTCTCATAAAATCG
187 CTATTTTCTCATAAAATCG
* * * *
190091 ATATATTTATACCGGTTACACTGTAAATTTACATATTACATTATAATTATCGG-TTTCA------
1 GTATATTTATACCGGTTACATTATAAATTTACATATTACATTATAATTATCGGTTTTGATGTTTT
*
190149 -ATTTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTTGGGC
66 TATTTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CGTTT-GGC
* ** * *
190213 ATTCATTTTGGACAATAAGTATCGACACAAATTGCACAAGTGTTGATACATTATGTTGACTTGTT
129 ATTCATTTTGAACAA-AAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGAC-TATT
* * *
190278 TTCTAAT-TAATCA
192 TTCTCATAAAATCG
* * *
190291 GTATATTTATACCGGTTACATTATTAATTTACATATTACATTATAATTATTGGTTTCGATGTTTT
1 GTATATTTATACCGGTTACATTATAAATTTACATATTACATTATAATTATCGGTTTTGATGTTTT
190356 T
66 T
190357 TGGGTTGATA
Statistics
Matches: 391, Mismatches: 56, Indels: 57
0.78 0.11 0.11
Matches are distributed among these distances:
198 1 0.00
199 99 0.25
200 58 0.15
201 65 0.17
202 2 0.01
203 2 0.01
208 1 0.00
211 1 0.00
212 2 0.01
213 15 0.04
214 116 0.30
215 29 0.07
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (205 bp):
GTATATTTATACCGGTTACATTATAAATTTACATATTACATTATAATTATCGGTTTTGATGTTTT
TATTTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCGTTTGGCAT
TCATTTTGAACAAAAGTATCGACACAAATTTAACAAGTGTCGATACATTATGTTGACTATTTTCT
CATAAAATCG
Found at i:190339 original size:200 final size:200
Alignment explanation
Indices: 189950--190388 Score: 595
Period size: 200 Copynumber: 2.2 Consensus size: 200
189940 TTTGGGATCG
* * * *
189950 ATGTTT-TTGGGATCGATAGTTTTAATAAATGTATCGACACTTTATGTGTGTACCCGTTTGGCAT
1 ATGTTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCATTTGGCAT
* *
190014 TCATTATGAACAAAATGTATCGACACAAATTTAACAAGTGTCGATACTTTATGTTGACCTATTTT
66 TCATTATGAACAAAATGTATCGACACAAATTGAACAAGTGTCGATACATTATGTTGACCTATTTT
* *
190079 CTCATAAAATCGATATATTTATACCGGTTACACTGTAAATTTACATATTACATTATAATTATCGG
131 CTAATAAAATCGATATATTTATACCGGTTACACTATAAATTTACATATTACATTATAATTATCGG
190144 TTTCA
196 TTTCA
190149 AT-TTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTTGGGC
1 ATGTTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACC-CATTT-GGC
* * * * * *
190213 ATTCATTTTGGACAATAA-GTATCGACACAAATTGCACAAGTGTTGATACATTATGTTGACTTGT
64 ATTCATTATGAACAA-AATGTATCGACACAAATTGAACAAGTGTCGATACATTATGTTGACCTAT
* * *
190277 TTTCTAAT-TAATC-AGTATATTTATACCGGTTACATTATTAATTTACATATTACATTATAATTA
128 TTTCTAATAAAATCGA-TATATTTATACCGGTTACACTATAAATTTACATATTACATTATAATTA
* *
190340 TTGGTTTCG
192 TCGGTTTCA
* *
190349 ATGTTTTTTGGG-TTGATACTTTTAGA-AAATGTATCGACAC
1 ATGTTTATTGGGATCGATACTTTTA-ATAAATGTATCGACAC
190389 ATATTTAGAT
Statistics
Matches: 212, Mismatches: 21, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
198 3 0.01
199 48 0.23
200 87 0.41
201 72 0.34
202 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (200 bp):
ATGTTTATTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCCATTTGGCAT
TCATTATGAACAAAATGTATCGACACAAATTGAACAAGTGTCGATACATTATGTTGACCTATTTT
CTAATAAAATCGATATATTTATACCGGTTACACTATAAATTTACATATTACATTATAATTATCGG
TTTCA
Found at i:194997 original size:200 final size:198
Alignment explanation
Indices: 194527--195488 Score: 1178
Period size: 200 Copynumber: 4.8 Consensus size: 198
194517 ATTTAAACAA
* * **
194527 TATCGACACAAATT-TAAAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATTGGTATA
1 TATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* *
194591 TTTATACCGGTTACATTGTAAATTTACCTATTACGTTATAATTATC-AGTTTCGATATTTTTGGG
66 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGA-TTTCGATGTTTTTGGG
** * * * * **
194655 ATCGATACAATTTCAAATGTATCGACACTTTGTTCCTGCACCCCGTTTGACATTCATTTTGGACA
130 ATCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCA-CCATTTTGACATTCATTTTGGACA
*
194720 AAATG
194 AAAAG
* * ** * * *
194725 TATCGACACAAA-TCTAAAACGTGTCGATATATTATGTTCACCTATTTTCTTATAAAACCGGTAA
1 TATCGACACAAATTCCAAAA-GTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
194789 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGG
65 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGG
* *
194854 ATCGATACTTTTTAAAACTGTATCGATACTTTATGCGTGCAACCCTTTTGACATTCATTTTGGAC
130 ATCGATACTTTTTAAAA-TGTATCGACACTTTATGCGTGC-ACCATTTTGACATTCATTTTGGAC
194919 AAAAAG
193 AAAAAG
* *
194925 TATCGACACAAATTCCACAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAATCGGTATA
1 TATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* * * * * *
194990 GTTATACCGGTTACATTGTAAATTTATCTATTACATTATAATTATGGGTTTCGATGTTTCTAGGA
66 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGGA
* * ** * *
195055 TCGATACTTTTTATAAATATATCGACACTTTATGCGTTCACCATTTTGGGTAATCATTCTGGACA
131 TCGATACTTTTTA-AAATGTATCGACACTTTATGCGTGCACCATTTT-GACATTCATTTTGGACA
195120 AAAAG
194 AAAAG
* * * *
195125 TATCGACACAAAATT-CAAAAGTGTCGACACATTATATAGACCTATTCTCACATAAAACCGATAT
1 TATCGACAC-AAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTAT
* ** * ** * * * *
195189 ATTTATGCCGGTTACATTACAAAATTATGTATTACATTATAATTATTGGTTTCGATGGTTTTGAG
65 ATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGG
* * *
195254 ATCAATCCTTTTTAAAAATGTATCGACACTTTATGCGTGCACCATATTTGGCATTCATTTTGGAC
130 ATCGATACTTTTT-AAAATGTATCGACACTTTATGCGTGCACCAT-TTTGACATTCATTTTGGAC
195319 AAAAAG
193 AAAAAG
* *** * * *
195325 TATCGACACAAATTCCACAAGTGTCGATACATTATGTATTTCTATTTTCTCAAAAAACTGGTATA
1 TATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
* * * * *
195390 TGTATACCGGTGACATTGTAAATTTACCTATTATATTATAATTTTC-AGTTTCGATATTTTTGGG
66 TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGA-TTTCGATGTTTTTGGG
195454 ATCGATACTTTTTAAACATGTATCGACACTTTATG
130 ATCGATACTTTTTAAA-ATGTATCGACACTTTATG
195489 GGAAACTTTA
Statistics
Matches: 657, Mismatches: 93, Indels: 26
0.85 0.12 0.03
Matches are distributed among these distances:
197 1 0.00
198 17 0.03
199 127 0.19
200 494 0.75
201 18 0.03
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (198 bp):
TATCGACACAAATTCCAAAAGTGTCGATACATTATGTAGACCTATTCTCTCATAAAACCGGTATA
TTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGGA
TCGATACTTTTTAAAATGTATCGACACTTTATGCGTGCACCATTTTGACATTCATTTTGGACAAA
AAG
Found at i:200201 original size:202 final size:200
Alignment explanation
Indices: 199703--200523 Score: 922
Period size: 202 Copynumber: 4.2 Consensus size: 200
199693 CGCGATTTTT
* * * * *
199703 AAAATGGTATCGACACAAATTTAAAAATTATTGATAC-TTTATGCT-GACCTATTTTCTCATAAA
1 AAAAT-GTATCGACACAAATTTCAAAAGTGTCGATACATTT-TG-TAGACCTATTCTCTCATAAA
* * **
199766 ACCGGTATATTTATACCAGTTACATTGGAAATTTACCTATTACATTATAATTACCGGTTTCGATG
63 ACCGGTATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATG
* * * * * *
199831 TTTTTGGGATCGAAACATTTTAAAAATGTATCGACACTTAATGGGTACACCCTTTT-GGCATTCC
128 TTTTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCA
*
199895 TTATGGAC
193 TTCTGGAC
* * * * * *
199903 AAAAAGTATCGACACAAATTTCAGAAGTGTCGATATATTTTCTAGACCTATTCTCGCATAAAACT
1 AAAATGTATCGACACAAATTTCAAAAGTGTCGATACATTTTGTAGACCTATTCTCTCATAAAACC
* *
199968 GGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATAATCATAGGTTTCGATGTTT
66 GGTATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTT
* **
200033 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCAACATTTTTTGGGCATTCAT
131 TTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGC-AC-CCTTTTGGGCATTCAT
*
200098 TCTGGAT
194 TCTGGAC
*
200105 AAAATGTATCGACACATAA-TT-AAAATGTGTCGATACATTTTGTAGACCTATTCTCACATAAAA
1 AAAATGTATCGACACA-AATTTCAAAA-GTGTCGATACATTTTGTAGACCTATTCTCTCATAAAA
* * * *
200168 CCAGTATATTTATACCAGTTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTTCGACG
64 CCGGTATATTTATACCAGTTACATTGA-AAAATTACCTATTACATTATAATTATAGGTTTCGATG
* ** ** *
200232 TTTTTGGGATCTATACTTTAAAAAAATGTATCGACACTTTATTTGTGCACCCTTTTGGGCATTCC
128 TTTTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCA
200297 TTCTGGAC
193 TTCTGGAC
* * * * * *
200305 AAACAT-CATCAACACAAATTTCATAAGTGTCGATATATTATATAGACCTATTCTCTCATAAAAC
1 AAA-ATGTATCGACACAAATTTCAAAAGTGTCGATACATTTTGTAGACCTATTCTCTCATAAAAC
* * * * *
200369 TGATATAGTTGTACCAATTACATTGAAAAATTACCTATTACATTATAATTAT--G----G--G--
65 CGGTATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTT
* * * *
200424 -TTGGGATCAATACTTTTTATAAATGTATCGACACTTTATGCGTTCACCATTTTGGGCATTCATT
130 TTTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATT
200488 CTGGAC
195 CTGGAC
* * *
200494 AAAAAGTATCGACGCTAATTTCAAAAGTGT
1 AAAATGTATCGACACAAATTTCAAAAGTGT
200524 TTTTGGGATG
Statistics
Matches: 529, Mismatches: 79, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
188 1 0.00
189 83 0.16
192 1 0.00
194 1 0.00
198 2 0.00
199 144 0.27
200 118 0.22
201 16 0.03
202 161 0.30
203 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (200 bp):
AAAATGTATCGACACAAATTTCAAAAGTGTCGATACATTTTGTAGACCTATTCTCTCATAAAACC
GGTATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATAGGTTTCGATGTTT
TTGGGATCGATACTTTTTAAAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCATTC
TGGAC
Found at i:204134 original size:182 final size:182
Alignment explanation
Indices: 203785--204635 Score: 1182
Period size: 182 Copynumber: 4.7 Consensus size: 182
203775 TATGCGTACT
* * * * * * *
203785 TATTAAAGTATCGACAGTTTCAATATATCCGGT-AGCGCTTTACCGGTTTTGTCATTTCGAGACT
1 TATTAAAGTATCGACACTTTCAATATATCTGGTCA-CTCTATACCGGTTTTGTCCTTTAGAGACC
* *
203849 GGTTTTGTCATATTTTTACCTG----ATCGTTGTGGA-CGATACATTGTTATAAAGTATCGACAT
65 GGTTTTGTCATATTTTTACCTGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACAC
* *
203909 TTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACCTA
130 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
203962 TATTAAAGTATCGACACTTTAAATATATCTGGTCATTCTATACCGGTTTTGTCCTTTAGAGATCG
1 TATTAAAGTATCGACACTTTCAATATATCTGGTCACTCTATACCGGTTTTGTCCTTTAGAGACCG
*
204027 GTTTTGTCATATTTTTACCTGTTATATCATTTTGGATCGATACATTGTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACACT
* * * *
204092 TTATGGGCGCTAAAATTGCTTCTCTTTTAAATTCAAAAAGTGTTGATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * *
204144 TATTAAAGTATCGACACTTTCAATATATCAGGTCTCTCTATACCGATTATGTCTTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCTGGTCACTCTATACCGGTTTTGTCCTTTAGAGACCG
* * * *
204209 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATTGATACATTATTAGAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACACT
* *
204274 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCAATACTTA
131 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* *
204326 TATTAAAGTATCGACACTTTCAATATATTTGGTCGCTCTATACCGGTTTTGTCCTTTAGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCTGGTCACTCTATACCGGTTTTGTCCTTTAGAGACCG
* *
204391 ATTTTGTCATATTTTTACCTGTTATATCAGTT-TGGATCGATACATTGTTATAAAGTATCGACAG
66 GTTTTGTCATATTTTTACCTGTTATATCA-TTGTGGATCGATACATTGTTATAAAGTATCGACAC
* *
204455 TTTATAGGCTCTAAAACTGCTTCTCTTTTAAATTCACAGAGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * *
204508 TATTAAAGTATCGACACTTTCAATATATCTGGT-ACCGCTTTACTGATTTTGTCTTTTCGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCTGGTCA-CTCTATACCGGTTTTGTCCTTTAGAGACC
* * *
204572 GGTTTTGTCATATTTTCACTTGTTATATTGA-TGTGGATCGATACAATT-TTATAAAGTATCGAC
65 GGTTTTGTCATATTTTTACCTGTTATA-TCATTGTGGATCGATAC-ATTGTTATAAAGTATCGAC
204635 A
128 A
204636 TAAACCGACA
Statistics
Matches: 597, Mismatches: 66, Indels: 17
0.88 0.10 0.03
Matches are distributed among these distances:
177 74 0.12
178 1 0.00
181 10 0.02
182 505 0.85
183 7 0.01
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCTGGTCACTCTATACCGGTTTTGTCCTTTAGAGACCG
GTTTTGTCATATTTTTACCTGTTATATCATTGTGGATCGATACATTGTTATAAAGTATCGACACT
TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:208979 original size:15 final size:15
Alignment explanation
Indices: 208947--208983 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
208937 ACTTTGAGAT
208947 TTTTTAA-CCAATTG
1 TTTTTAATCCAATTG
208961 TTTTTAATCC-ATTG
1 TTTTTAATCCAATTG
208975 TTTTTAATC
1 TTTTTAATC
208984 GAATATTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 20 0.91
15 2 0.09
ACGTcount: A:0.24, C:0.14, G:0.05, T:0.57
Consensus pattern (15 bp):
TTTTTAATCCAATTG
Found at i:212342 original size:20 final size:21
Alignment explanation
Indices: 212293--212342 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
212283 TATAATTTTT
*
212293 TAATTTTTTTAATATTAAAAA
1 TAATTTTTTTAATAATAAAAA
* *
212314 T-ATTATTTT-CTAATAAAAA
1 TAATTTTTTTAATAATAAAAA
212333 TAATTTTTTT
1 TAATTTTTTT
212343 TAAAAATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.38
20 14 0.58
21 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TAATTTTTTTAATAATAAAAA
Found at i:217910 original size:8 final size:8
Alignment explanation
Indices: 217897--217944 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
217887 ACGGAAAAAT
217897 AAATTTTA
1 AAATTTTA
217905 AAATTTTA
1 AAATTTTA
217913 AAATTTTA
1 AAATTTTA
* *
217921 AAATATAA
1 AAATTTTA
217929 AAATTATTA
1 AAATT-TTA
217938 AATATTT
1 AA-ATTT
217945 AATCAAGTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 26 0.76
9 5 0.15
10 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:221353 original size:17 final size:16
Alignment explanation
Indices: 221333--221372 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
221323 AAATTCTTAT
221333 TTTTATTGAATAAATAA
1 TTTTATTGAATAAAT-A
* *
221350 TTTTTTTTAATAAATA
1 TTTTATTGAATAAATA
221366 TTTTATT
1 TTTTATT
221373 TCGGGTCGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTTATTGAATAAATA
Found at i:221373 original size:21 final size:20
Alignment explanation
Indices: 221312--221373 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
221302 CTATATATTA
221312 TTTTTTTAATTAAAT-TCTTAT
1 TTTTTTTAA-TAAATAT-TTAT
*
221333 TTTTATTGAATAAATA---AT
1 TTTT-TTTAATAAATATTTAT
221351 TTTTTTTAATAAATATTTTAT
1 TTTTTTTAATAAATA-TTTAT
221372 TT
1 TT
221374 CGGGTCGTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 10 0.30
18 6 0.18
21 13 0.39
22 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTTTAATAAATATTTAT
Found at i:222041 original size:15 final size:15
Alignment explanation
Indices: 222021--222058 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
222011 AATTTTAATC
222021 AAAATATTAATTATT
1 AAAATATTAATTATT
222036 AAAATATTAATTATT
1 AAAATATTAATTATT
222051 AAAATATT
1 AAAATATT
222059 TAAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATATTAATTATT
Found at i:222088 original size:16 final size:17
Alignment explanation
Indices: 222064--222096 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
222054 ATATTTAAAA
*
222064 TATATTAAT-TAATATT
1 TATAATAATATAATATT
222080 TATAATAATATAATATT
1 TATAATAATATAATATT
222097 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAATAATATAATATT
Found at i:222097 original size:23 final size:23
Alignment explanation
Indices: 222053--222120 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
222043 TAATTATTAA
*
222053 AATATTTAAAAT-ATATTA-ATT
1 AATATTTATAATAATATTATATT
*
222074 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATTATATT
* *
222097 -ATATTTTTTAATATTATTATATT
1 AATA-TTTATAATAATATTATATT
222120 A
1 A
222121 TACTCAATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.29
22 8 0.21
23 19 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATTTATAATAATATTATATT
Found at i:224862 original size:22 final size:24
Alignment explanation
Indices: 224823--224886 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
224813 ATTATCCAAA
* *
224823 AATAATAATCTAATAATATTTTAA-T
1 AATAAT-ATTTAA-AATATATTAATT
224848 AA-AATATTTAAAATATATTAATT
1 AATAATATTTAAAATATATTAATT
*
224871 AATAATTTTTAAAATA
1 AATAATATTTAAAATA
224887 GAGTAGAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 9 0.26
23 8 0.24
24 15 0.44
25 2 0.06
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
AATAATATTTAAAATATATTAATT
Found at i:225396 original size:13 final size:15
Alignment explanation
Indices: 225373--225404 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
225363 CATTTTACAG
225373 AAAATATTTTTCAA-
1 AAAATATTTTTCAAT
225387 AAAATA-TTTTCAAT
1 AAAATATTTTTCAAT
225401 AAAA
1 AAAA
225405 CAAATAGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAATATTTTTCAAT
Found at i:225749 original size:46 final size:46
Alignment explanation
Indices: 225677--225835 Score: 187
Period size: 46 Copynumber: 3.5 Consensus size: 46
225667 ATATTGGATC
* * * * *
225677 GTTGGTTTCAGTTCGGGTCAAGCTTTAGATTTTCGAGTCAATTCGG
1 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
* *
225723 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTACGGGTTAATTCGG
1 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
* * * *
225769 GTTGGTTTTGGTTTAGATCAACCTTTAGATTTTTGAGTTAATTCGA
1 GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
*
225815 GTT-GTTTCTGTTTAGG-TCAAC
1 GTTGGTTTCGGTTT-GGATCAAC
225836 AATCTTCACT
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
45 13 0.14
46 83 0.86
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.43
Consensus pattern (46 bp):
GTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGAGTTAATTCGG
Found at i:233182 original size:67 final size:66
Alignment explanation
Indices: 233105--233232 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
233095 AATAAAAAAA
* * * *
233105 ATATTATGAAAAGCAAGGTCATTAATGAATATCTGAATAAATTCTGAAGTAATCAATTAATAAGA
1 ATATTATGAAAAACAAAGTCATTAATGAATATCTAAAT-AATTCGGAAGTAATCAATTAATAAGA
233170 AT
65 AT
* * * *
233172 ATATTCTGAAAAATAAAGTCGTTAATGAGTATCTAAATAATTCGGAAGTAATCAATTAATA
1 ATATTATGAAAAACAAAGTCATTAATGAATATCTAAATAATTCGGAAGTAATCAATTAATA
233233 TCGCATTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
66 22 0.42
67 31 0.58
ACGTcount: A:0.47, C:0.08, G:0.13, T:0.32
Consensus pattern (66 bp):
ATATTATGAAAAACAAAGTCATTAATGAATATCTAAATAATTCGGAAGTAATCAATTAATAAGAA
T
Found at i:239986 original size:20 final size:20
Alignment explanation
Indices: 239963--240001 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
239953 TACTTTTCTG
239963 GAAATTAATGTTAGAATGTT
1 GAAATTAATGTTAGAATGTT
*
239983 GAAATTGATGTTAGAATGT
1 GAAATTAATGTTAGAATGT
240002 GAGATAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (20 bp):
GAAATTAATGTTAGAATGTT
Found at i:240628 original size:22 final size:21
Alignment explanation
Indices: 240571--240647 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
240561 AGAATGCTCG
*
240571 GATGATACCGATACCCCC-CA
1 GATGGTACCGATACCCCCTCA
*
240591 GA--GTATCGATACCCCCATGCA
1 GATGGTACCGATACCCCC-T-CA
*
240612 -ATGGTACCGATAGCCCCTCA
1 GATGGTACCGATACCCCCTCA
*
240632 GGTGGTACCGATACCC
1 GATGGTACCGATACCC
240648 TAAGGCATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
18 12 0.27
20 5 0.11
21 16 0.36
22 12 0.27
ACGTcount: A:0.26, C:0.35, G:0.21, T:0.18
Consensus pattern (21 bp):
GATGGTACCGATACCCCCTCA
Found at i:242576 original size:22 final size:21
Alignment explanation
Indices: 242552--242591 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
242542 GAGAAATTGT
242552 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
242573 TTTTAAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
242592 AAACAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:246427 original size:21 final size:19
Alignment explanation
Indices: 246401--246475 Score: 78
Period size: 19 Copynumber: 3.6 Consensus size: 19
246391 TGTGCATAGA
*
246401 GTATCGATACCCCTAAGACTG
1 GTATCGATACCCCT-TGA-TG
246422 GTATCGATACCCCCTTTGAATAG
1 GTATCGATA-CCCC-TTG-AT-G
246445 GTATCGATACCCCTTGATG
1 GTATCGATACCCCTTGATG
*
246464 GTATTGATACCC
1 GTATCGATACCC
246476 TCCACGGGGT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
19 12 0.25
20 2 0.04
21 12 0.25
22 10 0.21
23 12 0.25
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (19 bp):
GTATCGATACCCCTTGATG
Found at i:246451 original size:23 final size:23
Alignment explanation
Indices: 246396--246457 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
246386 ATTTTTGTGC
246396 ATAGAGTATCGATA-CCCCTAAGA
1 ATAG-GTATCGATACCCCCTAAGA
* **
246419 CT-GGTATCGATACCCCCTTTGA
1 ATAGGTATCGATACCCCCTAAGA
246441 ATAGGTATCGATACCCC
1 ATAGGTATCGATACCCC
246458 TTGATGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.27
22 9 0.27
23 15 0.45
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (23 bp):
ATAGGTATCGATACCCCCTAAGA
Found at i:247168 original size:6 final size:6
Alignment explanation
Indices: 247157--247186 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
247147 CCATCCAATA
247157 AATCCT AATCCT AATCCT AATCCT AATCCT
1 AATCCT AATCCT AATCCT AATCCT AATCCT
247187 GATATGATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
AATCCT
Found at i:250994 original size:29 final size:30
Alignment explanation
Indices: 250924--250983 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
250914 CAATTTAAGG
250924 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
250955 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
250984 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:251090 original size:13 final size:13
Alignment explanation
Indices: 251072--251096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
251062 AGTTCATCTA
251072 TGCATCCCTGCAG
1 TGCATCCCTGCAG
251085 TGCATCCCTGCA
1 TGCATCCCTGCA
251097 CCTGCACTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:251118 original size:22 final size:23
Alignment explanation
Indices: 251083--251125 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
251073 GCATCCCTGC
*
251083 AGTGCATCCCTGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
251105 AGTGCATCGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
251126 GTGCATCATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.23, C:0.35, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:251235 original size:21 final size:21
Alignment explanation
Indices: 251159--251235 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
251149 AATGCAATTA
**
251159 GTGCATCGATGCATC-ATTCT
1 GTGCATCGATGCATCAAGGCT
*
251179 GTGCATCGATGCATTAAGGCT
1 GTGCATCGATGCATCAAGGCT
251200 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCAAGGCT
251221 GTGCATCGATGCATC
1 GTGCATCGATGCATC
251236 CTGTTGTGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 14 0.27
21 38 0.73
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (21 bp):
GTGCATCGATGCATCAAGGCT
Found at i:251642 original size:34 final size:32
Alignment explanation
Indices: 251604--251673 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
251594 ATTTTTAAAG
* *
251604 GGGAAAGGTTCTAGATTATCCCGTATAAAAGCTA
1 GGGAAAGGTTCTAGATTAGCCCG-A-AAAAACTA
* *
251638 GGGAAATGTTCTAGTTTAGCCCGAAAAAACTA
1 GGGAAAGGTTCTAGATTAGCCCGAAAAAACTA
251670 GGGA
1 GGGA
251674 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGATTAGCCCGAAAAAACTA
Found at i:252339 original size:19 final size:19
Alignment explanation
Indices: 252315--252367 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
252305 TATGCATTGG
* *
252315 GCTATGGATTTGAAAGTAA
1 GCTATGAATCTGAAAGTAA
252334 GCTATGAATCTGAAAGTAA
1 GCTATGAATCTGAAAGTAA
* * *
252353 GTTCTGAATCAGAAA
1 GCTATGAATCTGAAA
252368 ATGAATTATG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (19 bp):
GCTATGAATCTGAAAGTAA
Found at i:253473 original size:42 final size:40
Alignment explanation
Indices: 253416--253504 Score: 108
Period size: 42 Copynumber: 2.2 Consensus size: 40
253406 GGTTTTTAAG
* * *
253416 AAACACCACTAAAGTACTAGTTTGTCA-CGGCGTTTGTGAAA
1 AAACGCCACTAAAGTACAAG-TTGT-AGCGGCGTTCGTGAAA
*
253457 TAAACGCCACTAAAGTACAAGTTGTAGCGGCGTTCGTGGAA
1 -AAACGCCACTAAAGTACAAGTTGTAGCGGCGTTCGTGAAA
253498 AAACGCC
1 AAACGCC
253505 GTTAATGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 8 0.19
41 16 0.38
42 18 0.43
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (40 bp):
AAACGCCACTAAAGTACAAGTTGTAGCGGCGTTCGTGAAA
Found at i:261458 original size:20 final size:20
Alignment explanation
Indices: 261433--261471 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
261423 CTAAATAAAT
*
261433 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
261453 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
261472 TTATTCTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:261502 original size:46 final size:48
Alignment explanation
Indices: 261431--261559 Score: 185
Period size: 46 Copynumber: 2.7 Consensus size: 48
261421 ATCTAAATAA
261431 ATATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTTATT-CT
1 ATATTAGATAGGATCA-TTTTAATTAGATAGAATCAGTTTTTTATTACT
*
261479 ATAGGTTAGATA-GA-CA-TTTAATTAGATAGAATCAGTTTTTTATTATT
1 ATA--TTAGATAGGATCATTTTAATTAGATAGAATCAGTTTTTTATTACT
261526 ATATTAGATAGGATCATTTTTAATTAGATAGAAT
1 ATATTAGATAGGATCA-TTTTAATTAGATAGAAT
261560 TATTTTTATT
Statistics
Matches: 73, Mismatches: 1, Indels: 13
0.84 0.01 0.15
Matches are distributed among these distances:
45 7 0.10
46 30 0.41
47 6 0.08
48 5 0.07
49 18 0.25
50 7 0.10
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (48 bp):
ATATTAGATAGGATCATTTTAATTAGATAGAATCAGTTTTTTATTACT
Found at i:261551 original size:25 final size:27
Alignment explanation
Indices: 261499--261551 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
261489 TAGACATTTA
261499 ATTAGATAGAATCAGTTTTTTATTATTAT
1 ATTAGATAGAATCAG-TTTTTA-TATTAT
*
261528 ATTAGATAGGATCA-TTTTTA-ATTA
1 ATTAGATAGAATCAGTTTTTATATTA
261552 GATAGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
27 6 0.26
29 13 0.57
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (27 bp):
ATTAGATAGAATCAGTTTTTATATTAT
Found at i:261553 original size:20 final size:20
Alignment explanation
Indices: 261528--261567 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
261518 TTATTATTAT
*
261528 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
*
261548 ATTAGATAGAATTATTTTTA
1 ATTAGATAGAATCATTTTTA
261568 TTTGTTGCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.47
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Done.