Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008180.1 Hibiscus syriacus cultivar Beakdansim tig00110777_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: 2670214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:203070 original size:41 final size:41
Alignment explanation
Indices: 202984--203118 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
202974 GAATAAGTAA
* * *
202984 ATCGCAACGCGAATTGGGAAATTCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
203025 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
203066 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
203107 TTCGCAACGCGA
1 ATCGCAACGCGA
203119 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:203071 original size:20 final size:20
Alignment explanation
Indices: 203046--203140 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
203036 AATTGGGAAA
*
203046 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
203066 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
203087 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
203107 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
203127 TTCGCAACGCGATA
1 ATCGCAACGCGATA
203141 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:203356 original size:22 final size:22
Alignment explanation
Indices: 203328--203371 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
203318 CACTCTCTCA
203328 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
203350 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
203372 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:203661 original size:20 final size:20
Alignment explanation
Indices: 203636--203673 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
203626 CGATTCTCTC
203636 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
203656 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
203674 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:205013 original size:18 final size:18
Alignment explanation
Indices: 204992--205036 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
204982 TCCACTTCGG
*
204992 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
205010 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
205028 GAGCCATCA
1 GAGCCATCA
205037 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:205563 original size:19 final size:19
Alignment explanation
Indices: 205509--205593 Score: 91
Period size: 20 Copynumber: 4.4 Consensus size: 19
205499 TAGTTTACTT
*
205509 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGACTA
*
205529 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
205549 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
*
205568 TCGCAACGCGAAATGA-AA
1 TCGCAACGCGAAATGACTA
205586 TCGCAACG
1 TCGCAACG
205594 ACAAAATCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
18 10 0.18
19 22 0.39
20 24 0.42
21 1 0.02
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:205629 original size:19 final size:19
Alignment explanation
Indices: 205509--205629 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
205499 TAGTTTACTT
* **
205509 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
205529 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
205549 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
205568 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
205586 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
205600 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
205619 TCGCAATGCGA
1 TCGCAACGCGA
205630 TTTGTGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.12
16 4 0.05
18 10 0.12
19 35 0.42
20 24 0.29
21 1 0.01
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:205670 original size:19 final size:19
Alignment explanation
Indices: 205655--205758 Score: 111
Period size: 19 Copynumber: 5.4 Consensus size: 19
205645 GCGATTTTGT
205655 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
205673 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
205692 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
205712 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
205731 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
205751 TGTTGCGA
1 CGTTGCGA
205759 AAGTAAACTA
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 8 0.11
19 36 0.49
20 29 0.40
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:205716 original size:39 final size:38
Alignment explanation
Indices: 205666--205739 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
205656 GTTGCGATTT
**
205666 CATTTCGCGTTGCGATTTTCATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
*
205704 CATTTCCGCGTTGCGATAGTCATTTCGCGTTGCGAT
1 CATTT-CGCGTTGCGATAGTCATTTCGCATTGCGAT
205740 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 5 0.16
39 27 0.84
ACGTcount: A:0.15, C:0.24, G:0.23, T:0.38
Consensus pattern (38 bp):
CATTTCGCGTTGCGATAGTCATTTCGCATTGCGATAGC
Found at i:207627 original size:14 final size:14
Alignment explanation
Indices: 207608--207643 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
207598 ATTGTTTAAT
207608 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
207622 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
207636 TGATTTGT
1 TGATTTGT
207644 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:207769 original size:14 final size:15
Alignment explanation
Indices: 207750--207826 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
207740 CGAAATGGCT
207750 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
207764 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
207782 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
207801 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
207815 ATCGCAATGCGA
1 ATCGCAA-GCGA
207827 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:207782 original size:19 final size:19
Alignment explanation
Indices: 207760--207826 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
207750 ATCGCAACGA
207760 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
207779 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
207797 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
207811 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
207827 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:209555 original size:24 final size:24
Alignment explanation
Indices: 209528--209586 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
209518 AGTCAGTATT
* *
209528 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
*
209552 CGAACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
209576 CGAATTTTGAT
1 CGAAATTTGAT
209587 GATGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:209778 original size:12 final size:12
Alignment explanation
Indices: 209761--209785 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
209751 ATATAATCCT
209761 GAAGAAGAAAAA
1 GAAGAAGAAAAA
209773 GAAGAAGAAAAA
1 GAAGAAGAAAAA
209785 G
1 G
209786 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:212104 original size:19 final size:19
Alignment explanation
Indices: 212082--212140 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
212072 GGAAATTACT
212082 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
212101 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
212115 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
212134 ATCGCAA
1 ATCGCAA
212141 CGAGGGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:212124 original size:33 final size:33
Alignment explanation
Indices: 212082--212171 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
212072 GGAAATTACT
212082 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
212115 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
212148 ATCGCAATGCGAAATGAAATTCGC
1 ATCGCAATGCGAAATGAAAATCGC
212172 GTTGCGATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.42, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:212189 original size:19 final size:19
Alignment explanation
Indices: 212167--212231 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
212157 CGAAATGAAA
*
212167 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
212186 TTCGCATTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
212202 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
212219 TTCGCATTGCGAT
1 TTCGCATTGCGAT
212232 AGTACTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
14 6 0.17
16 6 0.17
17 6 0.17
19 18 0.50
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:212357 original size:14 final size:15
Alignment explanation
Indices: 212338--212374 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
212328 CATCAATTAA
212338 ACAAATCAAC-TTTT
1 ACAAATCAACATTTT
212352 ACAAATC-ACATTTT
1 ACAAATCAACATTTT
212366 ACAAATCAA
1 ACAAATCAA
212375 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
ACAAATCAACATTTT
Found at i:213797 original size:21 final size:21
Alignment explanation
Indices: 213731--213797 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
213721 GTGAATTGGG
*
213731 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
213751 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
213773 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
213794 CTCT
1 CTCT
213798 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:213816 original size:42 final size:42
Alignment explanation
Indices: 213770--213851 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
213760 CGATGACAGT
* * *
213770 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAAG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
* * *
213812 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATA
213852 GGCGAGTCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAAG
Found at i:215972 original size:19 final size:19
Alignment explanation
Indices: 215855--216039 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
215845 TCTTTTGGTT
*
215855 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
215874 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
215894 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
215912 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
215928 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
215946 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
215961 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
215981 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
216000 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
216019 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
216038 GA
1 GA
216040 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:215993 original size:39 final size:38
Alignment explanation
Indices: 215855--216039 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
215845 TCTTTTGGTT
* *
215855 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
215894 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
215928 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
215961 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
216000 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
216038 GA
1 GA
216040 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
33 42 0.33
34 16 0.13
35 2 0.02
38 24 0.19
39 28 0.22
40 14 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:216061 original size:19 final size:19
Alignment explanation
Indices: 216039--216075 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
216029 TCGCAATGCG
*
216039 ATTTTGGTTTCGCGTTGCA
1 ATTTTGATTTCGCGTTGCA
*
216058 ATTTTTATTTCGCGTTGC
1 ATTTTGATTTCGCGTTGC
216076 GATTATCTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (19 bp):
ATTTTGATTTCGCGTTGCA
Found at i:216714 original size:20 final size:20
Alignment explanation
Indices: 216629--216722 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
216619 CGCTAAGTAA
*
216629 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
216649 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
216669 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
216690 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
216710 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
216723 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:216741 original size:41 final size:41
Alignment explanation
Indices: 216711--216806 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
216701 ATAGTCAGTA
* * *
216711 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
216752 TCGCATTGCGAATTTCCCAATTCGTGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
216793 TCGCATTGCGAATT
1 TCGCATTGCGAATT
216807 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:216755 original size:20 final size:20
Alignment explanation
Indices: 216711--216803 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
216701 ATAGTCAGTA
* **
216711 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
216732 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
216752 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
**
216773 TCGTGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
216793 TCGCATTGCGA
1 TCGCATTGCGA
216804 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:222030 original size:15 final size:15
Alignment explanation
Indices: 222010--222050 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
222000 AATAAGTTTG
222010 AAAAACAATTAAATC
1 AAAAACAATTAAATC
222025 AAAAACAACGATTAAATC
1 AAAAAC-A--ATTAAATC
222043 AAAAACAA
1 AAAAACAA
222051 ATAATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 1 0.04
18 14 0.61
ACGTcount: A:0.68, C:0.15, G:0.02, T:0.15
Consensus pattern (15 bp):
AAAAACAATTAAATC
Found at i:222597 original size:22 final size:21
Alignment explanation
Indices: 222572--222621 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
222562 ATACTAATAG
222572 TCGATACCTAACAAGAGTAGTA
1 TCGATACCT-ACAAGAGTAGTA
***
222594 TCGATA-CTATGTGAGTAGTA
1 TCGATACCTACAAGAGTAGTA
222614 TCGATACC
1 TCGATACC
222622 AAGTGCACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 15 0.62
21 3 0.12
22 6 0.25
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (21 bp):
TCGATACCTACAAGAGTAGTA
Found at i:228761 original size:23 final size:23
Alignment explanation
Indices: 228735--228778 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
228725 ACCACAGTTT
*
228735 TCCC-TTTTGTTTGTTGTATGTCA
1 TCCCTTTTTGTTT-TTGCATGTCA
228758 TCCCTTTTTGTTTTTGCATGT
1 TCCCTTTTTGTTTTTGCATGT
228779 TTATCCCGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.07, C:0.18, G:0.16, T:0.59
Consensus pattern (23 bp):
TCCCTTTTTGTTTTTGCATGTCA
Found at i:228784 original size:24 final size:24
Alignment explanation
Indices: 228731--228785 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
228721 TTTGACCACA
*
228731 GTTT-TCCCTTTTGTTTGTTGTAT
1 GTTTATCCCTTTTGTTTGTTGCAT
*
228754 G-TCATCCCTTTTTGTTT-TTGCAT
1 GTTTATCCC-TTTTGTTTGTTGCAT
228777 GTTTATCCC
1 GTTTATCCC
228786 GAATATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.04
23 11 0.42
24 14 0.54
ACGTcount: A:0.07, C:0.20, G:0.15, T:0.58
Consensus pattern (24 bp):
GTTTATCCCTTTTGTTTGTTGCAT
Found at i:233954 original size:12 final size:12
Alignment explanation
Indices: 233937--233961 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
233927 ATTTTTTACG
233937 AGGTTACTATTC
1 AGGTTACTATTC
233949 AGGTTACTATTC
1 AGGTTACTATTC
233961 A
1 A
233962 TATGAATAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (12 bp):
AGGTTACTATTC
Found at i:249872 original size:232 final size:232
Alignment explanation
Indices: 249459--249893 Score: 816
Period size: 232 Copynumber: 1.9 Consensus size: 232
249449 ATTGATATCT
*
249459 TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCC
1 TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGCTAGTATGGCTGCC
*
249524 ATTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
66 AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
249589 GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
131 GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
249654 CTTGCATATATCTTGACAATACGTTTACAGAAATGTA
196 CTTGCATATATCTTGACAATACGTTTACAGAAATGTA
* *
249691 TTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTATGGCTGCC
1 TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGCTAGTATGGCTGCC
249756 AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
66 AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
* *
249821 TTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGACAATATGTTAGCACTGTCATATCA
131 GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
249886 CTTGCATA
196 CTTGCATA
249894 GATACTTCAA
Statistics
Matches: 197, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
232 197 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (232 bp):
TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGCTAGTATGGCTGCC
AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
CTTGCATATATCTTGACAATACGTTTACAGAAATGTA
Found at i:250631 original size:830 final size:830
Alignment explanation
Indices: 249033--251127 Score: 4145
Period size: 830 Copynumber: 2.5 Consensus size: 830
249023 TATCAAAAAA
249033 AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
1 AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
249098 ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
66 ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
249163 ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
131 ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
249228 AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
196 AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
249293 TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
261 TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
249358 TTTTGACACTGCTGCTTGCAAGAATTTAGTTTGTTACAGTCTTAAGCGTATGTTACTTAATGGCA
326 TTTTGACACTGCTGCTTGCAAGAATTTAGTTTGTTACAGTCTTAAGCGTATGTTACTTAATGGCA
249423 TAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCCCTCTTTGATGTATTGAATTGTTG
391 TAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCCCTCTTTGATGTATTGAATTGTTG
249488 AGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCCATTCTCATAGTTCCACCTGTTCGAGTTTG
456 AGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCCATTCTCATAGTTCCACCTGTTCGAGTTTG
249553 AAATTCATAACGATCAGTTAGCAGCCTTGACAATGTGTTTCGGGATTTGCAAGAAGCCCTTGTAG
521 AAATTCATAACGATCAGTTAGCAGCCTTGACAATGTGTTTCGGGATTTGCAAGAAGCCCTTGTAG
249618 GATATATCTTGACAATATGTTAGCACTGTCATATCACTTGCATATATCTTGACAATACGTTTACA
586 GATATATCTTGACAATATGTTAGCACTGTCATATCACTTGCATATATCTTGACAATACGTTTACA
249683 GAAATGTATTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTA
651 GAAATGTATTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTA
249748 TGGCTGCCAGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTT
716 TGGCTGCCAGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTT
249813 GACAATGTTTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGAC
781 GACAATGTTTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGAC
249863 AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
1 AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
249928 ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
66 ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
249993 ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
131 ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
250058 AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
196 AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
250123 TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
261 TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
250188 TTTTGACACTGCTGCTTGCAAGAATTTAGTTTGTTACAGTCTTAAGCGTATGTTACTTAATGGCA
326 TTTTGACACTGCTGCTTGCAAGAATTTAGTTTGTTACAGTCTTAAGCGTATGTTACTTAATGGCA
250253 TAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCCCTCTTTGATGTATTGAATTGTTG
391 TAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCCCTCTTTGATGTATTGAATTGTTG
250318 AGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCCATTCTCATAGTTCCACCTGTTCGAGTTTG
456 AGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCCATTCTCATAGTTCCACCTGTTCGAGTTTG
250383 AAATTCATAACGATCAGTTAGCAGCCTTGACAATGTGTTTCGGGATTTGCAAGAAGCCCTTGTAG
521 AAATTCATAACGATCAGTTAGCAGCCTTGACAATGTGTTTCGGGATTTGCAAGAAGCCCTTGTAG
250448 GATATATCTTGACAATATGTTAGCACTGTCATATCACTTGCATATATCTTGACAATACGTTTACA
586 GATATATCTTGACAATATGTTAGCACTGTCATATCACTTGCATATATCTTGACAATACGTTTACA
250513 GAAATGTATTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTA
651 GAAATGTATTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTA
250578 TGGCTGCCAGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTT
716 TGGCTGCCAGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTT
250643 GACAATGTTTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGAC
781 GACAATGTTTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGAC
250693 AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
1 AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
250758 ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
66 ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
250823 ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
131 ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
250888 AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
196 AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
250953 TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
261 TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
* *
251018 TTTTGACACTGCTGCTTGCAAGAATTTAGTTTGTTTGTACAGCCTTAAGGGTATGTTACTTAATG
326 TTTTGACACTGCTGCTTGCAAGAATTTAGTTTG--T-TACAGTCTTAAGCGTATGTTACTTAATG
251083 GCATAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCC
388 GCATAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCC
251128 TACTTTTAAG
Statistics
Matches: 1260, Mismatches: 2, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
830 1188 0.94
832 1 0.00
833 71 0.06
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (830 bp):
AATATGTTAGCACTGTCATATCACTTGCATAGATACTTCAAAGTTCTTGGGAGTTGACGTTAGAT
ATTTAATGGGAAAAGAATGGAAACCACTGTTTACTTGTACAATTATATATTTTTCTTTTCATAAT
ATACTCCAAAAATCTTCTTGAGAGTTGAAATTGAGAAATTTAAACAATAATGTTTCTACTAGAAG
AATTGAGGTTTCCTGCTTGCATTTGGTTTAGAGTTCTGTTTGGAAGATTCCTTTACTTATCCTTC
TGTGCATCATTAGTAGCGAAAATGTAATTAGAGAGAAGTAATCTACATTTCATTTGGTGTAAATT
TTTTGACACTGCTGCTTGCAAGAATTTAGTTTGTTACAGTCTTAAGCGTATGTTACTTAATGGCA
TAGAGTGAATGATATTTCTGATGCTGATTGATATCTTTTCCCCTCTTTGATGTATTGAATTGTTG
AGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCCATTCTCATAGTTCCACCTGTTCGAGTTTG
AAATTCATAACGATCAGTTAGCAGCCTTGACAATGTGTTTCGGGATTTGCAAGAAGCCCTTGTAG
GATATATCTTGACAATATGTTAGCACTGTCATATCACTTGCATATATCTTGACAATACGTTTACA
GAAATGTATTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTA
TGGCTGCCAGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTT
GACAATGTTTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGAC
Found at i:250702 original size:232 final size:232
Alignment explanation
Indices: 250289--250723 Score: 816
Period size: 232 Copynumber: 1.9 Consensus size: 232
250279 ATTGATATCT
*
250289 TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCGTTGTGGGCTAGTATGGCTGCC
1 TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGCTAGTATGGCTGCC
*
250354 ATTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
66 AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
250419 GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
131 GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
250484 CTTGCATATATCTTGACAATACGTTTACAGAAATGTA
196 CTTGCATATATCTTGACAATACGTTTACAGAAATGTA
* *
250521 TTTCCCGTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGTTAGTATGGCTGCC
1 TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGCTAGTATGGCTGCC
250586 AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
66 AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
* *
250651 TTTTCGGGATTTGCAAGAAGCCCTTGTAGGGTATATCTTGACAATATGTTAGCACTGTCATATCA
131 GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
250716 CTTGCATA
196 CTTGCATA
250724 GATACTTCAA
Statistics
Matches: 197, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
232 197 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (232 bp):
TTTCCCCTCTTTGATGTATTGAATTGTTGAGGCGAGCCCTTCCCTTGTGGGCTAGTATGGCTGCC
AGTCTCATAGTTCCACCTGTTCGAGTTTGAAATTCATAACGATCAGTTAGCAGCCTTGACAATGT
GTTTCGGGATTTGCAAGAAGCCCTTGTAGGATATATCTTGACAATATGTTAGCACTGTCATATCA
CTTGCATATATCTTGACAATACGTTTACAGAAATGTA
Found at i:252570 original size:26 final size:27
Alignment explanation
Indices: 252541--252598 Score: 91
Period size: 26 Copynumber: 2.1 Consensus size: 27
252531 CCTAAACCCG
*
252541 AACCCGACCTGAATATCAC-TTAAAAA
1 AACCCGACCCGAATATCACATTAAAAA
252567 AACCCGACCCGAATATCACATTTAAAAA
1 AACCCGACCCGAATATCACA-TTAAAAA
252595 AACC
1 AACC
252599 GACTCGACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 18 0.62
28 11 0.38
ACGTcount: A:0.47, C:0.29, G:0.07, T:0.17
Consensus pattern (27 bp):
AACCCGACCCGAATATCACATTAAAAA
Found at i:256156 original size:29 final size:30
Alignment explanation
Indices: 256118--256175 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
256108 AATTTAAGTA
256118 AAAATGGTTTTTGGACTTAATTGAATTTAC
1 AAAATGGTTTTTGGACTTAATTGAATTTAC
256148 AAAAT-GTTTTTGGACTTAATTGAATTTA
1 AAAATGGTTTTTGGACTTAATTGAATTTA
256176 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (30 bp):
AAAATGGTTTTTGGACTTAATTGAATTTAC
Found at i:257632 original size:19 final size:20
Alignment explanation
Indices: 257608--257654 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
257598 AACGATTTTC
*
257608 TTTTGAAAGCAAAAAT-AGA
1 TTTTGAAAGCAAAAATGAAA
*
257627 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAGCAAAAATGAAA
257647 TTTTGAAA
1 TTTTGAAA
257655 AAGGATTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (20 bp):
TTTTGAAAGCAAAAATGAAA
Found at i:258855 original size:20 final size:19
Alignment explanation
Indices: 258797--258854 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
258787 CCAACAATTG
258797 GTAATAATTGGTTATCTTTT
1 GTAATAATTGG-TATCTTTT
* *
258817 -TAACAATTAGTATCATTTT
1 GTAATAATTGGTATC-TTTT
258836 GTAATAATTGGTATCTTTT
1 GTAATAATTGGTATCTTTT
258855 TCATTAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.12
19 16 0.50
20 12 0.38
ACGTcount: A:0.29, C:0.07, G:0.12, T:0.52
Consensus pattern (19 bp):
GTAATAATTGGTATCTTTT
Found at i:258995 original size:34 final size:30
Alignment explanation
Indices: 258957--259025 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
258947 TTGATATAAC
258957 AATTTAAGGAAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--AAAAAT-GTTTTTGGACTT-AATTG
*
258991 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAAAAAAATGTTTTTGGACTTAATTG
259020 AATTTA
1 AATTTA
259026 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 12 0.36
31 5 0.15
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAAAAAAATGTTTTTGGACTTAATTG
Found at i:259036 original size:29 final size:30
Alignment explanation
Indices: 258967--259025 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
258957 AATTTAAGGA
258967 AAAATGGTTTTTGGACTTGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAC
258998 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
259026 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAC
Found at i:259623 original size:34 final size:32
Alignment explanation
Indices: 259584--259653 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
259574 TTTTGTAAAT
* *
259584 GGGAAAAGTTCTAGCTTATCCCGTATAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCGGA-AAAA-CTA
*
259618 GGGAAAAGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
259650 GGGA
1 GGGA
259654 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 22 0.67
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.23
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:263022 original size:19 final size:21
Alignment explanation
Indices: 262998--263039 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
262988 TCTCTTTCAT
262998 ATATCTCGT-ATCATGT-ATC
1 ATATCTCGTGATCATGTAATC
*
263017 ATATCTTGTGATCATGTAATC
1 ATATCTCGTGATCATGTAATC
263038 AT
1 AT
263040 GTTACTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATATCTCGTGATCATGTAATC
Found at i:267999 original size:23 final size:23
Alignment explanation
Indices: 267965--268027 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
267955 TAGCTCATAT
267965 AAATGCA-CGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* *
267987 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
268010 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
268028 TATAAGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 6 0.17
23 30 0.83
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.14
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:274625 original size:13 final size:13
Alignment explanation
Indices: 274607--274633 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
274597 TTACATATAT
274607 TATATATGAGAAG
1 TATATATGAGAAG
274620 TATATATGAGAAG
1 TATATATGAGAAG
274633 T
1 T
274634 TTTATAGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (13 bp):
TATATATGAGAAG
Found at i:275097 original size:253 final size:254
Alignment explanation
Indices: 274647--275157 Score: 765
Period size: 253 Copynumber: 2.0 Consensus size: 254
274637 ATAGTGTGAC
* * *
274647 ATATTTGATATATAATTAAAATAAGTGTTATTGATTTTGTTATTATTTAAATAATAAAATTAGTA
1 ATATTTGATATACAATTAAAATAAGTGTTACTGATTTTGTTATTATTTAAATAATAAAATCAGT-
* * * ** * * *
274712 AAAAAAAATTATCTAATATATTATTATTTTTATTTGAAACATTAATATTTTTTAATATTTCCGGT
65 AAAAAAAATTATCTAAAACATTATTATTTCTACATAAAACATCAATATTTTTTAACATTTCCGGT
* * * **
274777 TAAGTGCCCATCAATAATAAAATCGATAGAAAAAATAACAAAATCGGTAAAACGTTTAATAATAA
130 TAAGTACCCAACAATAATAAAATCGATAGAAAAAATAACAAAATCGATAAAACGTCCAATAATAA
* *
274842 TAAAACCGGTAGAAATAATAATGTTTCCGATAATTTTTTACTGATTTTATTATTTAAATA
195 TAAAACCGATAGAAATAATAATGTTTCCGATAACTTTTTACTGATTTTATTATTTAAATA
* * *
274902 ATATTTGATATACAATTAAAATAGGTGTTACTGGTTTTGTTATTATTTAAATAATAAAATCGGT-
1 ATATTTGATATACAATTAAAATAAGTGTTACTGATTTTGTTATTATTTAAATAATAAAATCAGTA
*
274966 AAAAAAATTATCTAAAACATTATTATTTCTACATAAAACATCAATATTTTTTAACATTTCGGGTT
66 AAAAAAATTATCTAAAACATTATTATTTCTACATAAAACATCAATATTTTTTAACATTTCCGGTT
*
275031 AAGTACCCAACAATAATAAAATTGATAGAAAAAATAACAAAA-CTGATAAAACGTCCAATAATAA
131 AAGTACCCAACAATAATAAAATCGATAGAAAAAATAACAAAATC-GATAAAACGTCCAATAATAA
* *
275095 TAAAACTGATAGAAATAATAATGTTTCCGATAACTTTTTATTGATTTTATTATTTAAATA
195 TAAAACCGATAGAAATAATAATGTTTCCGATAACTTTTTACTGATTTTATTATTTAAATA
275155 ATA
1 ATA
275158 ATAAAAACGA
Statistics
Matches: 230, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
252 1 0.00
253 171 0.74
255 58 0.25
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.39
Consensus pattern (254 bp):
ATATTTGATATACAATTAAAATAAGTGTTACTGATTTTGTTATTATTTAAATAATAAAATCAGTA
AAAAAAATTATCTAAAACATTATTATTTCTACATAAAACATCAATATTTTTTAACATTTCCGGTT
AAGTACCCAACAATAATAAAATCGATAGAAAAAATAACAAAATCGATAAAACGTCCAATAATAAT
AAAACCGATAGAAATAATAATGTTTCCGATAACTTTTTACTGATTTTATTATTTAAATA
Found at i:278816 original size:30 final size:30
Alignment explanation
Indices: 278761--278817 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
278751 ATCTCTCTAA
* *
278761 TTAAAAATTTATTTTAAAATTTTAATATTT
1 TTAAAAATTAATTTTAAAATGTTAATATTT
278791 TTAAACAATTAATTTTAAAA-GTTAATA
1 TTAAA-AATTAATTTTAAAATGTTAATA
278818 AACATTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
TTAAAAATTAATTTTAAAATGTTAATATTT
Found at i:281658 original size:23 final size:24
Alignment explanation
Indices: 281623--281674 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
281613 CTTAATAAAC
*
281623 ATGTATAATAATTATTAAATACGA
1 ATGTCTAATAATTATTAAATACGA
**
281647 ATGTCTAA-AATTATTAAATTTGA
1 ATGTCTAATAATTATTAAATACGA
281670 ATGTC
1 ATGTC
281675 CAAACTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (24 bp):
ATGTCTAATAATTATTAAATACGA
Found at i:282098 original size:21 final size:23
Alignment explanation
Indices: 282059--282101 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
282049 TGTTGTGTTT
*
282059 TTTGTGTTTGGTTCTTCTTCTTC
1 TTTGTGTTTGGTTCATCTTCTTC
282082 TTTGTG-TT-GTTCATCTTCTT
1 TTTGTGTTTGGTTCATCTTCTT
282102 TGACTTGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.02, C:0.16, G:0.16, T:0.65
Consensus pattern (23 bp):
TTTGTGTTTGGTTCATCTTCTTC
Found at i:282294 original size:15 final size:15
Alignment explanation
Indices: 282271--282300 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
282261 AAAAATTTAG
282271 ACACAATTCTAGATA
1 ACACAATTCTAGATA
*
282286 ACACTATTCTAGATA
1 ACACAATTCTAGATA
282301 TATTTTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (15 bp):
ACACAATTCTAGATA
Found at i:289118 original size:15 final size:16
Alignment explanation
Indices: 289088--289118 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
289078 TAATACTTAC
289088 TATTAATTTATTAATA
1 TATTAATTTATTAATA
289104 TATTAATTT-TTAATA
1 TATTAATTTATTAATA
289119 AACAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATTTATTAATA
Found at i:289255 original size:29 final size:29
Alignment explanation
Indices: 289212--289267 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
289202 TATATTGAGC
* *
289212 TTAACGAGCAACGAGTTGAGTAATAATTTT
1 TTAACAAGCAACGAGTCGAGTAA-AATTTT
289242 TTAACAAGC-ACGAGTCGAGTAAAATT
1 TTAACAAGCAACGAGTCGAGTAAAATT
289268 GTAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 12 0.50
30 8 0.33
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (29 bp):
TTAACAAGCAACGAGTCGAGTAAAATTTT
Found at i:289321 original size:17 final size:17
Alignment explanation
Indices: 289279--289312 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
289269 TAACGAGCTT
289279 AACAAGCAATGAGTCGG
1 AACAAGCAATGAGTCGG
289296 AACAAGCAATGAGTCGG
1 AACAAGCAATGAGTCGG
289313 GTCAAGCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.29, T:0.12
Consensus pattern (17 bp):
AACAAGCAATGAGTCGG
Found at i:289533 original size:11 final size:11
Alignment explanation
Indices: 289517--289541 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
289507 GAGATTTTTT
289517 AAAAAATATTA
1 AAAAAATATTA
289528 AAAAAATATTA
1 AAAAAATATTA
289539 AAA
1 AAA
289542 TTTAATGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAATATTA
Found at i:296564 original size:21 final size:22
Alignment explanation
Indices: 296529--296571 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
296519 TTTATTATAA
*
296529 TGTGTCATGTTATGCATTAGGC
1 TGTGTCATCTTATGCATTAGGC
*
296551 TGTGTC-TCTTATGCTTTAGGC
1 TGTGTCATCTTATGCATTAGGC
296572 ATTACGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (22 bp):
TGTGTCATCTTATGCATTAGGC
Found at i:297416 original size:118 final size:117
Alignment explanation
Indices: 297201--297465 Score: 316
Period size: 118 Copynumber: 2.2 Consensus size: 117
297191 GTGCCAAAAT
* * *
297201 AATATAGACGATAACATAA-CTAGTTAATTATTGGAAACATTAACAATCACAATAACATATTAGG
1 AATAT-GACGATAACATAATC-GGTTAATTACTGGAAACATTAACAAGCACAATAACATATTAGG
* * * * *
297265 TAATGCTTATGTAACGTAATAGATAACGTCTTTTTAAAGCTGATGGGGCTTTGGA
64 CAACGCTTATATAACGTAATAGATAACGGCTTTTT-AAGCTGATGGGACTTTGGA
** *
297320 AATATGACGATAACATAATCGGTTAATTACTGGAAACATTATGAAGCATAATAACATATTAGGCA
1 AATATGACGATAACATAATCGGTTAATTACTGGAAACATTAACAAGCACAATAACATATTAGGCA
* * ** *
297385 ACGTTTATATAACGTAATAGGTAGTGGCTTTTTAAGCTGATGGGATTTTGGA
66 ACGCTTATATAACGTAATAGATAACGGCTTTTTAAGCTGATGGGACTTTGGA
** * *
297437 AATCCGACGATAACAAAATAGGTTAATTA
1 AATATGACGATAACATAATCGGTTAATTA
297466 ATTAATTTGT
Statistics
Matches: 125, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
117 42 0.34
118 77 0.62
119 6 0.05
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (117 bp):
AATATGACGATAACATAATCGGTTAATTACTGGAAACATTAACAAGCACAATAACATATTAGGCA
ACGCTTATATAACGTAATAGATAACGGCTTTTTAAGCTGATGGGACTTTGGA
Found at i:297739 original size:226 final size:224
Alignment explanation
Indices: 297325--297978 Score: 902
Period size: 226 Copynumber: 2.9 Consensus size: 224
297315 TTGGAAATAT
* * * * * *
297325 GACGATAACATAATCGGTTAATTACTGGAAACATTATGAAGCATAATAACATATTAGGCAACGTT
1 GACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGG-TAGGCT
* *
297390 TATATAACGTAATAGGTAG-TGGCTTTTT-AAGCTGATGGGATTTTGGAAATCCGACGATAACAA
65 TATATAACGTAATAGGTAGCT-CCTTTTTAAAGCTGATGGG-CTTTGGAAATCCGACGATAACAA
* * * *
297453 AATAGGTTAATTAATTAATTTGTTATTAGTATTATCAACATATTAGGTAACACATAAAATGTTAT
128 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAA
297518 CAAAATTTAAGCTGATAGAGCCTTAGAAATCC
193 CAAAATTTAAGCTGATAGAGCCTTAGAAATCC
* *
297550 GACGATAATATAACCGGTTAATTATTGGAAACACTATCAAGCATAATAACATATTAGGTATGGCT
1 GACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTA-GGCT
* *
297615 TATATAACGTAATAGGTAGCTCCTTTTTAAAGCTGACGAGGCTTTGGAAATCCGACGAAAACAAA
65 TATATAACGTAATAGGTAGCTCCTTTTTAAAGCTGATG-GGCTTTGGAAATCCGACGATAACAAA
* * *
297680 ATAGGTTAATTACTTAATTTGTTATTTGTATTATCAACATATTAGGTAATGCCTAAAATGTTACC
129 ATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAAC
* * *
297745 AAAGTTTAAGCTGATAGAGCCTTGGAAATTC
194 AAAATTTAAGCTGATAGAGCCTTAGAAATCC
*
297776 GACGATAACATAACCGGTTAATTATTGGAAACATTATCGAA-CATAATAACATATTAGGTAGAAC
1 GACGATAACATAACCGGTTAATTATTGGAAACATTATC-AAGCATAATAACATATTAGGTAG-GC
* * * * * * * * *
297840 TTATGTAACATAATAGGTTGCACATTATTAAAGCTGATGGGGCCTTAGAAATCCAACGATAACAA
64 TTATATAACGTAATAGGTAGCTCCTTTTTAAAGCTGAT-GGGCTTTGGAAATCCGACGATAACAA
* *
297905 AATAGGTTAATTACTTAATTTGTTATCAGTATTATCAACATATTAGGTAACGTCT-AAATGTTAA
128 AATAGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAA
297969 CAAAATTTAA
193 CAAAATTTAA
297979 TGTTGAGTTA
Statistics
Matches: 381, Mismatches: 41, Indels: 14
0.87 0.09 0.03
Matches are distributed among these distances:
224 1 0.00
225 98 0.26
226 277 0.73
227 5 0.01
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (224 bp):
GACGATAACATAACCGGTTAATTATTGGAAACATTATCAAGCATAATAACATATTAGGTAGGCTT
ATATAACGTAATAGGTAGCTCCTTTTTAAAGCTGATGGGCTTTGGAAATCCGACGATAACAAAAT
AGGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGGTAACGCCTAAAATGTTAACAA
AATTTAAGCTGATAGAGCCTTAGAAATCC
Found at i:298767 original size:19 final size:19
Alignment explanation
Indices: 298743--298795 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
298733 AAATAGCCAG
298743 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGGCT
*
298762 AGTGCATCGATTCATGGCT
1 AGTGCATCGATGCATGGCT
*
298781 GGTGCATCGATGCAT
1 AGTGCATCGATGCAT
298796 CAAATGCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (19 bp):
AGTGCATCGATGCATGGCT
Found at i:299540 original size:14 final size:15
Alignment explanation
Indices: 299521--299549 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
299511 TCAAGCATTT
299521 AACAATCCA-AAACA
1 AACAATCCAGAAACA
299535 AACAATCCAGAAACA
1 AACAATCCAGAAACA
299550 TAAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:307433 original size:64 final size:65
Alignment explanation
Indices: 307347--307491 Score: 188
Period size: 64 Copynumber: 2.2 Consensus size: 65
307337 TTCACTAAGA
*
307347 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATGG-C
1 GTGCATCGATGCATCAAATGCATTCGATG-TTCAAAATAAGCCATG-GTGCATCGATGCATGGAC
307409 TG
64 TG
** ** *
307411 GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATGGATTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAAAATAAGCCATGGTGCATCGATGCATGGACTG
*
307476 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
307492 CTTTGATAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
63 6 0.08
64 47 0.66
65 18 0.25
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCAAAATAAGCCATGGTGCATCGATGCATGGACTG
Found at i:309624 original size:183 final size:183
Alignment explanation
Indices: 309405--309819 Score: 704
Period size: 183 Copynumber: 2.3 Consensus size: 183
309395 ACTTATTAAA
* * *
309405 GTATCGATACCTTTAACATATATGGTAGCGCTTTACCGATTTTGTCATAATGAAACCGGTTTTGT
1 GTATCGATACCTTTAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGT
*
309470 CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGG
66 CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATACTTTATAGG
* * *
309535 CGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTAATTGAATG
131 CGCTATTATTATTTTTCTTTTAAATTCCAAAAGCATCAATACTTAATTGAATG
* *
309588 GTATCGATACCTTTAACATATCTGGTAGCGCTTTACCGGTTTTGACATAATGAAATCGATTTTGT
1 GTATCGATACCTTTAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGT
309653 CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATACTTTATAGG
66 CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATACTTTATAGG
*
309718 CGCTATTATTATTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATG
131 CGCTATTATTATTTTTCTTTTAAATTCCAAAAGCATCAATACTTAATTGAATG
* * * *
309771 ATATCGATACCTTCAACATATCTGGTAACACTTTACCGGTTTTGTCATA
1 GTATCGATACCTTTAACATATCTGGTAGCGCTTTACCGGTTTTGTCATA
309820 TTTTTACCTG
Statistics
Matches: 217, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 217 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (183 bp):
GTATCGATACCTTTAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGT
CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATACTTTATAGG
CGCTATTATTATTTTTCTTTTAAATTCCAAAAGCATCAATACTTAATTGAATG
Found at i:309833 original size:163 final size:163
Alignment explanation
Indices: 309644--309982 Score: 516
Period size: 163 Copynumber: 2.1 Consensus size: 163
309634 ATAATGAAAT
*
309644 CGATTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATA
1 CGATTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCAATA
* * *
309709 CTTTATAGGCGCTATTATTATTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATA
66 CTTTAAAAGCGCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATA
* *
309774 TCGATACCTTCAACATATCTGGTAACACTTTAC
131 TCGATACCTTCAACATATCCGGCAACACTTTAC
* * * *
309807 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATATATGTTTATAAAGTATCAATA
1 CGATTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCAATA
* * * * *
309872 CTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTGAATGATG
66 CTTTAAAAGCGCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATA
* *
309937 TCGATACCTTCAACATATCCGGCAGCGCTTTAC
131 TCGATACCTTCAACATATCCGGCAACACTTTAC
*
309970 CGATTTTTTCATA
1 CGATTTTGTCATA
309983 ATGAAATCGT
Statistics
Matches: 157, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
163 157 1.00
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (163 bp):
CGATTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCAATA
CTTTAAAAGCGCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATA
TCGATACCTTCAACATATCCGGCAACACTTTAC
Found at i:310092 original size:346 final size:346
Alignment explanation
Indices: 309459--310875 Score: 1748
Period size: 346 Copynumber: 4.0 Consensus size: 346
309449 TCATAATGAA
*
309459 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCAA
* * * *
309524 TACTTTATAGGCGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTAATTGAATGG
66 TACTTTATAAGCGCTATTATTGCTTTTCTTTTAAATTCTAAAAGTATCGATACTTATTTGAATGG
* * * * *
309589 TATCGATACCTTTAACATATCTGGTAGCGCTTTACCGGTTTTGACATAATGAAATCGATTTTGTC
131 TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAATCGGTTTTGTC
*
309654 ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATACTTTATAGGC
196 ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
*
309719 GCTATTATTATTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCTT
261 GCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCTT
*
309784 CAACATATCTGGTAACACTTT
326 CAACATATCCGGTAACACTTT
* *
309805 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATATATGTTTATAAAGTATCAA
1 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCAA
*
309870 TACTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATT-TCAAAAGTATCGATACTTATTTGAATG
66 TACTTTATAAGCGCTATTATTGCTTTTCTTTTAAATTCT-AAAAGTATCGATACTTATTTGAATG
* * * * *
309934 ATGTCGATACCTTCAACATATCCGGCAGCGCTTTACCGATTTTTTCATAATGAAATCGTTTTTGT
130 GTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAATCGGTTTTGT
* *
309999 CATATTTTTACCTATTATATTGTTATGTATCGATACATGTTTATAAAGTATCAATACTTTATAGG
195 CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGG
**
310064 CGCTATTATTGTTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCT
260 CGCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCT
*
310129 TCAACATATCTGGTAGCACTTTACCGGTTGTCATAAT
325 TCAACATATCCGGTA--AC---A-C-----T--T--T
* * * *
310166 GAAACAGGTTTTGTCATATTTTTACCTGTTATATTGTTATATATTGATATATGTTTATAAAGTAT
1 ---ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTAT
* * * *
310231 CAATATTTTATAAGAGCTATTATTGTTTTTCTTTTAAATTCTAAAAGTATCGATACTTACTTGAA
63 CAATACTTTATAAGCGCTATTATTGCTTTTCTTTTAAATTCTAAAAGTATCGATACTTATTTGAA
** * *
310296 TGGTATTAATACCTTTAACATATCCGATAGCGCTTTACCTG-TTTTGTCATAATGAAATCGGTTT
128 TGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACC-GATTTTGTCATAATGAAATCGGTTT
310360 TGTCATATTTTTACC-G-------G---T-TAT--AT---TG-TTAT---GTATCGATACTTTAT
192 TGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTAT
* * * *
310404 AGGCGTTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATATCGATA
257 AGGCGCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATA
* *
310469 CCTTCAACATATCCGGTAGCGCTTT
322 CCTTCAACATATCCGGTAACACTTT
*
310494 ACCGGTTTTTTCTTAATGAAACTGATTTTGTCATATTTCTACATGTTATATTGTTATGTATCGAT
1 ACCGGTTTTGTC--------A-T-A-TTT-T--TA---C--C-TGTTATATTGTTATGTATCGAT
* * * *
310559 ACAT-TTTATAAATTATCGATATTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCTAAAAGT
46 ACATGTTTATAAAGTATCAATACTTTATAAGCGCTATTATTGCTTTTCTTTTAAATTCTAAAAGT
* * **
310623 ATCGATACTTATTTAAATGGTATTGATACCTTCAACATATCAAGTAGCGCTTTACCGATTTTGTC
111 ATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTC
* *
310688 ATAATGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATGTTTATAA
176 ATAATGAAATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAA
* * *
310753 AGTATCGATACTTTATAGGCGCCATTATTACTTTTCTTTTAAATTCCAAAAGTATCGATACTTAT
241 AGTATCGATACTTTATAGGCGCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTAT
* * *
310818 TTGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTT
306 TTGAATGATATCGATACCTTCAACATATCCGGTAACACTTT
*
310859 ACCGATTTTGTCATATT
1 ACCGGTTTTGTCATATT
310876 GAACCCGATT
Statistics
Matches: 938, Mismatches: 70, Indels: 118
0.83 0.06 0.10
Matches are distributed among these distances:
325 10 0.01
328 1 0.00
330 1 0.00
332 1 0.00
333 1 0.00
334 1 0.00
335 1 0.00
336 3 0.00
337 2 0.00
339 2 0.00
341 1 0.00
342 1 0.00
343 93 0.10
344 142 0.15
345 24 0.03
346 321 0.34
347 2 0.00
348 2 0.00
350 2 0.00
351 1 0.00
352 5 0.01
353 1 0.00
354 2 0.00
355 2 0.00
356 5 0.01
357 2 0.00
358 2 0.00
359 1 0.00
361 3 0.00
362 4 0.00
364 186 0.20
365 113 0.12
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (346 bp):
ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCAA
TACTTTATAAGCGCTATTATTGCTTTTCTTTTAAATTCTAAAAGTATCGATACTTATTTGAATGG
TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAATCGGTTTTGTC
ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
GCTATTATTACTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCTT
CAACATATCCGGTAACACTTT
Found at i:310253 original size:181 final size:182
Alignment explanation
Indices: 309807--310397 Score: 889
Period size: 183 Copynumber: 3.2 Consensus size: 182
309797 AACACTTTAC
*
309807 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATATATGTTTATAAAGTATCAATA
1 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATATATGTTTATAAAGTATCAATA
* * * *
309872 CTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATTTCAAAAGTATCGATACTTATTTGAATGATG
66 CTTTATAAGCGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATA
* *
309937 TCGATACCTTCAACATATCCGGCAGCGCTTTACCGATTTTTTCATAATGAAAT
131 TCGATACCTTCAACATATCCGGTAGCGCTTTACCG-TTTTGTCATAATGAAAT
* * *
309990 CGTTTTTGTCATATTTTTACCTATTATATTGTTATGTATCGATACATGTTTATAAAGTATCAATA
1 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATATATGTTTATAAAGTATCAATA
* * *
310055 CTTTATAGGCGCTATTATTGTTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATA
66 CTTTATAAGCGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATA
* * *
310120 TCGATACCTTCAACATATCTGGTAGCACTTTACCG-GTTGTCATAATGAAA-
131 TCGATACCTTCAACATATCCGGTAGCGCTTTACCGTTTTGTCATAATGAAAT
* *
310170 CAGGTTTTGTCATATTTTTACCTGTTATATTGTTATATATTGATATATGTTTATAAAGTATCAAT
1 C-GGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATATATGTTTATAAAGTATCAAT
* * * * *
310235 ATTTTATAAGAGCTATTATTGTTTTTCTTTTAAATTCTAAAAGTATCGATACTTACTTGAATGGT
65 ACTTTATAAGCGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGAT
** * *
310300 ATTAATACCTTTAACATATCCGATAGCGCTTTACCTGTTTTGTCATAATGAAAT
130 ATCGATACCTTCAACATATCCGGTAGCGCTTTACC-GTTTTGTCATAATGAAAT
*
310354 CGGTTTTGTCATATTTTTACCGGTTATATTGTTATGTATCGATA
1 CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATA
310398 CTTTATAGGC
Statistics
Matches: 365, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
180 1 0.00
181 157 0.43
182 1 0.00
183 205 0.56
184 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (182 bp):
CGGTTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATATATGTTTATAAAGTATCAATA
CTTTATAAGCGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATA
TCGATACCTTCAACATATCCGGTAGCGCTTTACCGTTTTGTCATAATGAAAT
Found at i:310425 original size:162 final size:169
Alignment explanation
Indices: 310262--310922 Score: 689
Period size: 183 Copynumber: 3.8 Consensus size: 169
310252 ATTGTTTTTC
* * ** *
310262 TTTTAAATTCTAAAAGTATCGATACTTACTTGAATGGTATTAATACCTTTAACATATCCGATAGC
1 TTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGATAGC
* * *
310327 GCTTTACCTG-TTTTGTCATAATGAAATCGGTTTTGTCATATTTTTACCGGTTATATTGTTATGT
66 GCTTTACC-GATTTTGTCATAATGAAACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGT
* *
310391 ATCGATAC-TTTAT-AGGCGTTATTAT-TGC-TT-TT-C-
130 ATCGATACATTTATAAGTCGTTATTATGCGCATTATTACT
* *
310424 TTTTAAATTCCAAAAGTATCGATACTTATTTGAATGATATCGATACCTTCAACATATCCGGTAGC
1 TTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGATAGC
* * * * * *
310489 GCTTTACCGGTTTTTTCTTAATGAAACTGATTTTGTCATATTTCTACATGTTATATTGTTATGTA
66 GCTTTACCGATTTTGTCATAATGAAACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGTA
* * *
310554 TCGATACATTTTATAAATTATCGATATTTTATAGGCGCTATTATTGCTTTT
131 TCGATACA-TTTAT-AA--GTCG-T-TATTAT--GCGC-ATTATTAC---T
* * * *
310605 CTTTTAAATTCTAAAAGTATCGATACTTATTTAAATGGTATTGATACCTTCAACATAT-CAAGTA
1 -TTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGA-TA
*
310669 GCGCTTTACCGATTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATG
64 GCGCTTTACCGATTTTGTCATAATGAAACCGATTTTGTCATATTTTTACCTGTTATATTGTTATG
* *
310734 TATTGATACATGTTTATAAAGTATCGATACTTTATAGGCGCCATTATTACTTTT
129 TATCGATACA--TTTAT-AAG--TCGTTA--TTAT--GCG-CATTATTAC---T
*
310788 CTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGGTAG
1 -TTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGATAG
* * *
310853 CGCTTTACCGATTTTGTCATATTGAACCCGATTTTGTCATATTTTTACATG--ATA-TGTTATGT
65 CGCTTTACCGATTTTGTCATAATGAAACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGT
310915 ATCGATAC
130 ATCGATAC
310923 TTATTTGAAT
Statistics
Matches: 422, Mismatches: 48, Indels: 40
0.83 0.09 0.08
Matches are distributed among these distances:
161 1 0.00
162 120 0.28
164 5 0.01
166 1 0.00
168 2 0.00
169 1 0.00
170 5 0.01
173 2 0.00
175 2 0.00
176 2 0.00
177 1 0.00
180 15 0.04
181 5 0.01
182 122 0.29
183 136 0.32
184 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (169 bp):
TTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGATAGC
GCTTTACCGATTTTGTCATAATGAAACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGTA
TCGATACATTTATAAGTCGTTATTATGCGCATTATTACT
Found at i:310653 original size:182 final size:183
Alignment explanation
Indices: 310389--310922 Score: 851
Period size: 182 Copynumber: 2.9 Consensus size: 183
310379 ATATTGTTAT
*
310389 GTATCGATACTTTATAGGCGTTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATT
1 GTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATT
* * * * *
310454 TGAATGATATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTTTCTTAATGAAACTGA
66 TGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAACCGA
*
310519 TTTTGTCATATTTCTACATGTTATATTGTTATGTATCGATACAT-TTTATAAA
131 TTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATGTTTATAAA
* * *
310571 TTATCGATATTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCTAAAAGTATCGATACTTATT
1 GTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATT
* * ** *
310636 TAAATGGTATTGATACCTTCAACATATCAAGTAGCGCTTTACCGATTTTGTCATAATGAAACCGG
66 TGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAACCGA
* *
310701 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATGTTTATAAA
131 TTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATGTTTATAAA
* *
310754 GTATCGATACTTTATAGGCGCCATTATTACTTTTCTTTTAAATTCCAAAAGTATCGATACTTATT
1 GTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATT
* *
310819 TGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATATTGAACCCGA
66 TGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAACCGA
310884 TTTTGTCATATTTTTACATG--ATA-TGTTATGTATCGATAC
131 TTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATAC
310923 TTATTTGAAT
Statistics
Matches: 320, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
180 15 0.05
181 3 0.01
182 157 0.49
183 145 0.45
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (183 bp):
GTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATT
TGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTGTCATAATGAAACCGA
TTTTGTCATATTTTTACATGTTATATTGTTATGTATCGATACATGTTTATAAA
Found at i:310713 original size:527 final size:523
Alignment explanation
Indices: 309406--310924 Score: 2163
Period size: 527 Copynumber: 2.9 Consensus size: 523
309396 CTTATTAAAG
* ** * * *
309406 TATCGATACCTTTAACATATATGGTAGCGCTTTACCGATTTTGTCATAATGAAACCGGTTTTGTC
1 TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTTTCATAATGAAACTGATTTTGTC
309471 ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
66 ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
*
309536 GCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTAATTGAATGGTATCGATACCTT
131 GCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTT
* * * *
309601 TAACATATCTGGTAGCGCTTTACCGGTTTTGACATAATGAAATCGATTTTGTCATATTTTTACCT
196 CAACATATCTGGTAGCGCTTTACC-GTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCT
* *
309666 GTTATATTGTTATGTATCGATACATGTATATAAAGTATCGATACTTTATAGGCGCTATTATTATT
260 GTTATATTGTTATGTATTGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTATT
* * * *
309731 TTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCTTCAACATATCTGG
325 TTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGG
* * *** * * * *
309796 TAACACTTTACCGGTTTTGTCATATTTTTAC---CTGTTATATTGTTATGTATTGATATATGTTT
390 TAGCGCTTTACC-GTTTTGTCATATTGAAACGTTTTGTCATATTTTTACG-ATT-ATAT-TG-TT
* *
309858 ATAAAGTATCAATACTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATTTCAAAAGTATCGATAC
450 AT---GTATCGATACTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATAC
309923 TTATTTGAATGA
512 TTATTTGAATGA
* * *
309935 TGTCGATACCTTCAACATATCCGGCAGCGCTTTACCGATTTTTTCATAATGAAA-TCGTTTTTGT
1 TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTTTCATAATGAAACT-GATTTTGT
* *
309999 CATATTTTTACCTATTATATTGTTATGTATCGATACATGTTTATAAAGTATCAATACTTTATAGG
65 CATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGG
* * *
310064 CGCTATTATTGTTTTTCTTTTAAATTCCAAAAGCATCAATACTTATTTGAATGATATCGATACCT
130 CGCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCT
* * *
310129 TCAACATATCTGGTAGCACTTTACCG-GTTGTCATAATGAAACAGGTTTTGTCATATTTTTACCT
195 TCAACATATCTGGTAGCGCTTTACCGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCT
* * * * * * *
310193 GTTATATTGTTATATATTGATATATGTTTATAAAGTATCAATATTTTATAAGAGCTATTATTGTT
260 GTTATATTGTTATGTATTGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTATT
* * ** * *
310258 TTTCTTTTAAATTCTAAAAGTATCGATACTTACTTGAATGGTATTAATACCTTTAACATATCCGA
325 TTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGG
* *
310323 TAGCGCTTTACCTGTTTTGTCATAATGAAATCGGTTTTGTCATATTTTTACCGGTTATATTGTTA
390 TAGCGCTTTACC-GTTTTGTCATATTGAAA-C-GTTTTGTCATATTTTTA-CGATTATATTGTTA
* * *
310388 TGTATCGATACTTTATAGGCGTTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTAT
451 TGTATCGATACTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTAT
310453 TTGAATGA
516 TTGAATGA
* *
310461 TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTTTCTTAATGAAACTGATTTTGTC
1 TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTTTCATAATGAAACTGATTTTGTC
* * * *
310526 ATATTTCTACATGTTATATTGTTATGTATCGATACAT-TTTATAAATTATCGATATTTTATAGGC
66 ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
* * * *
310590 GCTATTATTGCTTTTCTTTTAAATTCTAAAAGTATCGATACTTATTTAAATGGTATTGATACCTT
131 GCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTT
**
310655 CAACATATCAAGTAGCGCTTTACCGATTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCT
196 CAACATATCTGGTAGCGCTTTACCG-TTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCT
* *
310720 GTTATATTGTTATGTATTGATACATGTTTATAAAGTATCGATACTTTATAGGCGCCATTATTACT
260 GTTATATTGTTATGTATTGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTATT
310785 TTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGG
325 TTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGG
* *
310850 TAGCGCTTTACCGATTTTGTCATATTGAACCCGATTTTGTCATATTTTTAC-ATGATA-TGTTAT
390 TAGCGCTTTACCG-TTTTGTCATATTGAA-ACG-TTTTGTCATATTTTTACGATTATATTGTTAT
310913 GTATCGATACTT
452 GTATCGATACTT
310925 ATTTGAATGG
Statistics
Matches: 878, Mismatches: 99, Indels: 31
0.87 0.10 0.03
Matches are distributed among these distances:
524 18 0.02
525 108 0.12
526 162 0.18
527 362 0.41
528 2 0.00
529 206 0.23
530 2 0.00
531 4 0.00
532 13 0.01
533 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (523 bp):
TATCGATACCTTCAACATATCCGGTAGCGCTTTACCGATTTTTTCATAATGAAACTGATTTTGTC
ATATTTTTACCTGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
GCTATTATTGTTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTT
CAACATATCTGGTAGCGCTTTACCGTTTTGTCATAATGAAACCGGTTTTGTCATATTTTTACCTG
TTATATTGTTATGTATTGATACATGTTTATAAAGTATCGATACTTTATAGGCGCTATTATTATTT
TTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCGATACCTTCAACATATCCGGT
AGCGCTTTACCGTTTTGTCATATTGAAACGTTTTGTCATATTTTTACGATTATATTGTTATGTAT
CGATACTTTAAAAGCGCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAA
TGA
Found at i:317345 original size:11 final size:11
Alignment explanation
Indices: 317329--317361 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
317319 TAAAGAGAAC
317329 TAAACTAAATA
1 TAAACTAAATA
*
317340 TAAACTAAAAA
1 TAAACTAAATA
317351 TAAACTAAATA
1 TAAACTAAATA
317362 CCATGCAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (11 bp):
TAAACTAAATA
Found at i:330038 original size:16 final size:16
Alignment explanation
Indices: 330017--330049 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
330007 TTTAATAAAT
330017 AAACGAACATAAACGA
1 AAACGAACATAAACGA
330033 AAACGAACATAAACGA
1 AAACGAACATAAACGA
330049 A
1 A
330050 CAATTTTTTT
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:0.64, C:0.18, G:0.12, T:0.06
Consensus pattern (16 bp):
AAACGAACATAAACGA
Found at i:330822 original size:15 final size:15
Alignment explanation
Indices: 330798--330828 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
330788 TCTCTTTCAA
330798 AAAATGTAAAAGTTT
1 AAAATGTAAAAGTTT
*
330813 AAAATTTAAAAGTTT
1 AAAATGTAAAAGTTT
330828 A
1 A
330829 CTCCTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (15 bp):
AAAATGTAAAAGTTT
Found at i:336166 original size:19 final size:19
Alignment explanation
Indices: 336142--336188 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
336132 ACTAAAGGAC
*
336142 TTGTATATAGCGGCGTTTT
1 TTGTATATAGCGGCGTTTG
336161 TTGTATATAGCGGCGTTTG
1 TTGTATATAGCGGCGTTTG
*
336180 TTGGATATA
1 TTGTATATA
336189 AACACCGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.19, C:0.09, G:0.28, T:0.45
Consensus pattern (19 bp):
TTGTATATAGCGGCGTTTG
Found at i:336167 original size:44 final size:43
Alignment explanation
Indices: 335974--336169 Score: 160
Period size: 44 Copynumber: 4.5 Consensus size: 43
335964 TTAAGATATT
* * * * *
335974 TAGCGGCGTTTTTTGGATACAAACGCCGTAATAGGTCTGGTATA
1 TAGCGGCGTTTTTTGTATATAAACGCCCTAA-AGGACTTGTATA
* * * * * * *
336018 TAGCAGCATTTTTT-TATACAAATGCCTCAAAAGGTCTCGTATA
1 TAGCGGCGTTTTTTGTATATAAACGCC-CTAAAGGACTTGTATA
* * * * * *
336061 TAGCGGCGTTTGTCGGATATAAATGCCGCTAAAGAACTTGTGTA
1 TAGCGGCGTTTTTTGTATATAAACGCC-CTAAAGGACTTGTATA
* * *
336105 TAGCGGCGCTTGTCGTATATAAACGCCACTAAAGGACTTGTATA
1 TAGCGGCGTTTTTTGTATATAAACGCC-CTAAAGGACTTGTATA
336149 TAGCGGCGTTTTTTGTATATA
1 TAGCGGCGTTTTTTGTATATA
336170 GCGGCGTTTG
Statistics
Matches: 122, Mismatches: 28, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
43 31 0.25
44 91 0.75
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (43 bp):
TAGCGGCGTTTTTTGTATATAAACGCCCTAAAGGACTTGTATA
Found at i:336171 original size:63 final size:63
Alignment explanation
Indices: 336098--336225 Score: 184
Period size: 63 Copynumber: 2.0 Consensus size: 63
336088 GCTAAAGAAC
* * *
336098 TTGTGTATAGCGGCGCTTGTCGTATATAAACGCCACTAAAGGACTTGTATATAGCGGCGTTTT
1 TTGTATATAGCGGCGCTTGTCGGATATAAACACCACTAAAGGACTTGTATATAGCGGCGTTTT
* * * * *
336161 TTGTATATAGCGGCGTTTGTTGGATATAAACACCGCTAAAGGACTTGTATATAGTGGCTTTTT
1 TTGTATATAGCGGCGCTTGTCGGATATAAACACCACTAAAGGACTTGTATATAGCGGCGTTTT
336224 TT
1 TT
336226 ACAAACGCCG
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (63 bp):
TTGTATATAGCGGCGCTTGTCGGATATAAACACCACTAAAGGACTTGTATATAGCGGCGTTTT
Found at i:336593 original size:20 final size:22
Alignment explanation
Indices: 336552--336593 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
336542 TCTACTGATA
336552 TGCTGCTTCTCTCTGTGCTTCCG
1 TGCTGCTTCTCTCTGT-CTTCCG
336575 TGCTGC-TCTCTCTGT-TTCC
1 TGCTGCTTCTCTCTGTCTTCC
336594 CTTGCTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.00, C:0.36, G:0.19, T:0.45
Consensus pattern (22 bp):
TGCTGCTTCTCTCTGTCTTCCG
Found at i:344956 original size:219 final size:219
Alignment explanation
Indices: 344577--345015 Score: 745
Period size: 219 Copynumber: 2.0 Consensus size: 219
344567 ATTACACCTA
344577 TTGTAACATCCCGAAATCCGGGTCAGTGATTAAAATGAGAATTTTTGAAATTTGGAGATAAAAGT
1 TTGTAACATCCCGAAATCCGGGTCAGTGATTAAAATGAGAATTTTTGAAATTTGGAGATAAAAGT
* * * *
344642 ATAATAGTTAAATAGTTTAATGACTTATTGGAAATATAGTTGAAGGTTGGTTGATAATTATTCAA
66 AGAATAATCAAATAGTTTAATGACTTATTGGAAATATAGTTGAAGATTGGTTGATAATTATTCAA
* * *
344707 TGAATTAAAGGGTAAAATGGTCAATTGACAAGTAAGATTTTTATTTTCCTTTATAAGATAAGGGG
131 TGAATTAAAGGGTAAAATAGTCAATTGACAAGTAAGATTTTTATTTCCCTTTATAAGATAAGGGA
*
344772 ACCACGTGGAAGAGGAGAGATTTC
196 ACCACGTGAAAGAGGAGAGATTTC
* *
344796 TTGTAACATCCCGAAATCTGGGTCAGTGATTAAAATGAGAATTTTTGAAATTTGGTGATAAAAGT
1 TTGTAACATCCCGAAATCCGGGTCAGTGATTAAAATGAGAATTTTTGAAATTTGGAGATAAAAGT
* *
344861 AGAATAATCAAATAGTTTAATGACTTATTGGAAATATAGTTGAAGATTGTTTCG-TAATTATTGA
66 AGAATAATCAAATAGTTTAATGACTTATTGGAAATATAGTTGAAGATTGGTT-GATAATTATTCA
344925 ATGAATTAAAGGGTAAAATAGTCAATTGACAAGTAAGATTTTTATTTCCCTTTATAAGATAAGGG
130 ATGAATTAAAGGGTAAAATAGTCAATTGACAAGTAAGATTTTTATTTCCCTTTATAAGATAAGGG
*
344990 AACCGCGTGAAAGAGGAGAGATTTC
195 AACCACGTGAAAGAGGAGAGATTTC
345015 T
1 T
345016 CCAGAGTTCT
Statistics
Matches: 206, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
219 205 1.00
220 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.33
Consensus pattern (219 bp):
TTGTAACATCCCGAAATCCGGGTCAGTGATTAAAATGAGAATTTTTGAAATTTGGAGATAAAAGT
AGAATAATCAAATAGTTTAATGACTTATTGGAAATATAGTTGAAGATTGGTTGATAATTATTCAA
TGAATTAAAGGGTAAAATAGTCAATTGACAAGTAAGATTTTTATTTCCCTTTATAAGATAAGGGA
ACCACGTGAAAGAGGAGAGATTTC
Found at i:346817 original size:2 final size:2
Alignment explanation
Indices: 346810--346849 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
346800 AGGTAAAATG
346810 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
346850 GACTATGAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:350381 original size:64 final size:64
Alignment explanation
Indices: 350244--350401 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 64
350234 AATTGTTCAG
* * * * * *
350244 TGTGTATCGATGCACAGAAAGTGCATCGATGCACCCCTTAAAAATGAAAATATCGAATGCAATT
1 TGTGTATCGATGCATAGGAAGTGCATCGATACACCCCTTAAAAATGAAAACATCAAAGGCAATT
* * * * * * *
350308 AGTGCATCGATGTATAGGAAGTGCATCGATACACCCCCTT-AAGATTAAAACATCAAAGGTACTT
1 TGTGTATCGATGCATAGGAAGTGCATCGATACA-CCCCTTAAAAATGAAAACATCAAAGGCAATT
* *
350372 TGTGTATCGATGCATGGGTAGTGCATCGAT
1 TGTGTATCGATGCATAGGAAGTGCATCGAT
350402 GCACATGTTA
Statistics
Matches: 75, Mismatches: 18, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
64 69 0.92
65 6 0.08
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (64 bp):
TGTGTATCGATGCATAGGAAGTGCATCGATACACCCCTTAAAAATGAAAACATCAAAGGCAATT
Found at i:351336 original size:2 final size:2
Alignment explanation
Indices: 351329--351373 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
351319 GATTAGATTA
351329 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
351371 AT A
1 AT A
351374 AGTGAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:351554 original size:2 final size:2
Alignment explanation
Indices: 351547--351584 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
351537 AGGTAAAATG
351547 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
351585 GACTATGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:351834 original size:14 final size:14
Alignment explanation
Indices: 351814--351877 Score: 78
Period size: 14 Copynumber: 4.6 Consensus size: 14
351804 GATTATATGT
351814 ATATGTGATCC-AAG
1 ATATGTGA-CCTAAG
*
351828 TTATGTGACCTAAG
1 ATATGTGACCTAAG
351842 ATATGTGATCC-AAG
1 ATATGTGA-CCTAAG
*
351856 TTATGTGACCTAAG
1 ATATGTGACCTAAG
351870 ATATGTGA
1 ATATGTGA
351878 AAGGTGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.09
14 37 0.86
15 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (14 bp):
ATATGTGACCTAAG
Found at i:351847 original size:28 final size:28
Alignment explanation
Indices: 351814--351877 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
351804 GATTATATGT
351814 ATATGTGATCCAAGTTATGTGACCTAAG
1 ATATGTGATCCAAGTTATGTGACCTAAG
351842 ATATGTGATCCAAGTTATGTGACCTAAG
1 ATATGTGATCCAAGTTATGTGACCTAAG
351870 ATATGTGA
1 ATATGTGA
351878 AAGGTGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (28 bp):
ATATGTGATCCAAGTTATGTGACCTAAG
Found at i:352582 original size:83 final size:83
Alignment explanation
Indices: 352461--352613 Score: 200
Period size: 83 Copynumber: 1.8 Consensus size: 83
352451 GCGTTTGTAC
* ** * * *
352461 AAAAACGCCGCTAAAGTATTAATATTTTGCGGCATTTGTTGA-AAAAGCGCCACTATAGATTACA
1 AAAAACGCCGCTAAAGGACAAATATTTTGCGACATTTGTTGAGAAAA-CGCCACTATAGATCAAA
352525 CCTATTAAGGCATTTATAT
65 CCTATTAAGGCATTTATAT
* * * *
352544 AAAAACGCCGGTAAAGGACAAATATTTTGTGACGTTTGTTGAGAAAACGCCATTATAGATCAAAC
1 AAAAACGCCGCTAAAGGACAAATATTTTGCGACATTTGTTGAGAAAACGCCACTATAGATCAAAC
352609 CTATT
66 CTATT
352614 GCGAAATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
83 55 0.93
84 4 0.07
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.29
Consensus pattern (83 bp):
AAAAACGCCGCTAAAGGACAAATATTTTGCGACATTTGTTGAGAAAACGCCACTATAGATCAAAC
CTATTAAGGCATTTATAT
Found at i:353651 original size:22 final size:22
Alignment explanation
Indices: 353621--353669 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
353611 CACGTTTTCA
353621 AAAGCTATTATTTTTATATTCG
1 AAAGCTATTATTTTTATATTCG
* *
353643 AAAGTTATTATTTTTCTATTCG
1 AAAGCTATTATTTTTATATTCG
353665 AAAGC
1 AAAGC
353670 AGAAAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (22 bp):
AAAGCTATTATTTTTATATTCG
Found at i:354320 original size:42 final size:42
Alignment explanation
Indices: 354254--354394 Score: 144
Period size: 42 Copynumber: 3.4 Consensus size: 42
354244 ACGTTTGTAT
* *
354254 AAAAACGCCGCTAAATTACTACTCTATTGCGGCGTTTGTTGGA
1 AAAAACGCCACTAAATTAC-ACTCTATTGCGACGTTTGTTGGA
* * * **
354297 AAAAATGCCACTATATATA-ACTCTATTTCGACGTTT-TTGCT
1 AAAAACGCCACTAAAT-TACACTCTATTGCGACGTTTGTTGGA
* *
354338 ACAAACGCCACTAAATTACCACTCTATTGCAACGTTTGTTGG-
1 AAAAACGCCACTAAATTA-CACTCTATTGCGACGTTTGTTGGA
*
354380 AAAAACGCCGCTAAA
1 AAAAACGCCACTAAA
354395 GTATCATTTT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
40 2 0.03
41 16 0.20
42 43 0.54
43 16 0.20
44 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
AAAAACGCCACTAAATTACACTCTATTGCGACGTTTGTTGGA
Found at i:356089 original size:18 final size:18
Alignment explanation
Indices: 356068--356106 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
356058 ATATACATGT
356068 TCAATGATATGTATATTC
1 TCAATGATATGTATATTC
356086 TCAATGATATGTATATTC
1 TCAATGATATGTATATTC
356104 TCA
1 TCA
356107 TCAAATATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (18 bp):
TCAATGATATGTATATTC
Found at i:357203 original size:18 final size:16
Alignment explanation
Indices: 357164--357195 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
357154 TTTTCTTTAT
357164 TTAATTTTTAAAAATA
1 TTAATTTTTAAAAATA
357180 TATAATTTTTAAAAAT
1 T-TAATTTTTAAAAAT
357196 TAATTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATTTTTAAAAATA
Found at i:361914 original size:34 final size:34
Alignment explanation
Indices: 361871--361939 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
361861 AGAAATTGTT
361871 TAGTTATGCAAAGTGTATGTTTAATCAGTTATGA
1 TAGTTATGCAAAGTGTATGTTTAATCAGTTATGA
361905 TAGTTATGCAAAGTGTATGTTTAATCAGTTATGA
1 TAGTTATGCAAAGTGTATGTTTAATCAGTTATGA
361939 T
1 T
361940 GAAGATTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (34 bp):
TAGTTATGCAAAGTGTATGTTTAATCAGTTATGA
Found at i:364234 original size:103 final size:103
Alignment explanation
Indices: 364009--364226 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
363999 GTCAAGGGTC
364009 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
364074 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
364112 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
364177 TTGATCCCTAGTATATGTATATTATTCTTAAGAAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
364215 TATGTGGTCCTT
1 TATGTGGTCCTT
364227 ATGGACATTA
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGAAATGA
Found at i:364309 original size:23 final size:23
Alignment explanation
Indices: 364233--364310 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
364223 CCTTATGGAC
*
364233 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
364257 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
364280 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
364303 ATTATATG
1 ATTATATG
364311 AGCTGTGATG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:369623 original size:103 final size:103
Alignment explanation
Indices: 369439--369652 Score: 392
Period size: 103 Copynumber: 2.1 Consensus size: 103
369429 GTCGAGGGTC
369439 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
369504 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
369542 TATGTGGTTCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
369607 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
369645 TATGTGGT
1 TATGTGGT
369653 CCTTATGGAC
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:369739 original size:23 final size:23
Alignment explanation
Indices: 369663--369740 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
369653 CCTTATGGAC
*
369663 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
369687 ATTCTACGCGGCACTCCGGTACA
1 ATTATATGTGGCACTACGGTGCA
*
369710 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
369733 ATTATATG
1 ATTATATG
369741 AGCTATGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:379196 original size:18 final size:18
Alignment explanation
Indices: 379169--379203 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
379159 CATTAGAAAG
*
379169 TGAGCTTCTTATTGATCT
1 TGAGCATCTTATTGATCT
*
379187 TGAGCATCTTCTTGATC
1 TGAGCATCTTATTGATC
379204 AAGAGGAGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (18 bp):
TGAGCATCTTATTGATCT
Found at i:380304 original size:31 final size:31
Alignment explanation
Indices: 380266--380376 Score: 89
Period size: 31 Copynumber: 3.4 Consensus size: 31
380256 TTAGGTCCAT
380266 AAGGAATTACCAGTAGGTGCTGAACCTATAC
1 AAGGAATTACCAGTAGGTGCTGAACCTATAC
* * *
380297 AAGGAATTACCAGCA-GTAACTGAACCTACCATAGAT
1 AAGGAATTACCAGTAGGT-GCTGAACCT---AT--AC
* * * * *
380333 AAGGAATTATCAATCGGTGTTGAACATATAC
1 AAGGAATTACCAGTAGGTGCTGAACCTATAC
380364 AAGGAATTACCAG
1 AAGGAATTACCAG
380377 CAGCAACTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
30 2 0.03
31 34 0.57
33 2 0.03
34 2 0.03
36 18 0.30
37 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (31 bp):
AAGGAATTACCAGTAGGTGCTGAACCTATAC
Found at i:380372 original size:67 final size:67
Alignment explanation
Indices: 380264--380390 Score: 200
Period size: 67 Copynumber: 1.9 Consensus size: 67
380254 CTTTAGGTCC
* * *
380264 ATAAGGAATTACCAGTAGGTGCTGAACCTATACAAGGAATTACCAGCAGTAACTGAACCTACCAT
1 ATAAGGAATTACCAATAGGTGCTGAACATATACAAGGAATTACCAGCAGCAACTGAACCTACCAT
380329 AG
66 AG
* * *
380331 ATAAGGAATTATCAATCGGTGTTGAACATATACAAGGAATTACCAGCAGCAACTGAACCT
1 ATAAGGAATTACCAATAGGTGCTGAACATATACAAGGAATTACCAGCAGCAACTGAACCT
380391 GCTAGAGTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (67 bp):
ATAAGGAATTACCAATAGGTGCTGAACATATACAAGGAATTACCAGCAGCAACTGAACCTACCAT
AG
Found at i:381837 original size:22 final size:22
Alignment explanation
Indices: 381811--381859 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
381801 GGCTTTTTCG
*
381811 GTCAAAATCAACAGTCTGACCA
1 GTCAAAATCAACAGTCAGACCA
* * *
381833 GTCAAAGTCTACGGTCAGACCA
1 GTCAAAATCAACAGTCAGACCA
381855 GTCAA
1 GTCAA
381860 CGATCAACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (22 bp):
GTCAAAATCAACAGTCAGACCA
Found at i:388534 original size:23 final size:23
Alignment explanation
Indices: 388497--388556 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
388487 AGCTCATATA
*
388497 AATTGCGCCGAAGTGCCA-CGTAG
1 AATTGCACCGAAGTG-CAGCGTAG
*
388520 AATTGCACCGTAGTGCAGCGTAG
1 AATTGCACCGAAGTGCAGCGTAG
*
388543 AAATGCACCGAAGT
1 AATTGCACCGAAGT
388557 TCCATATAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCAGCGTAG
Found at i:390320 original size:21 final size:21
Alignment explanation
Indices: 390283--390337 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
390273 TCGGTTGAGG
*
390283 GGGTATCGATT-CCATTGAAT
1 GGGTACCGATTCCCATTGAAT
*
390303 GGGTACTGATTCCCATTGAAT
1 GGGTACCGATTCCCATTGAAT
390324 GGGTACCGATTCCC
1 GGGTACCGATTCCC
390338 CTAGCCCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (21 bp):
GGGTACCGATTCCCATTGAAT
Found at i:395386 original size:21 final size:21
Alignment explanation
Indices: 395362--395417 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
395352 TCGGTTGAGG
*
395362 GGGTATCGATTCCCATTGAAT
1 GGGTATCGATTCCCATTAAAT
*
395383 GGGTACCGATTCCCATTAAAT
1 GGGTATCGATTCCCATTAAAT
395404 GGGTAAT-GATTCCC
1 GGGT-ATCGATTCCC
395418 CTAGCCCAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (21 bp):
GGGTATCGATTCCCATTAAAT
Found at i:400263 original size:21 final size:21
Alignment explanation
Indices: 400237--400291 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
400227 GATTTACATA
400237 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
400258 TTCGCATTGCAATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
400279 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
400292 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:400378 original size:21 final size:21
Alignment explanation
Indices: 400352--400394 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
400342 TACATATTCA
400352 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
400373 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
400394 C
1 C
400395 GTTGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:400391 original size:111 final size:111
Alignment explanation
Indices: 400197--400398 Score: 377
Period size: 111 Copynumber: 1.8 Consensus size: 111
400187 GTTTCCAGAT
*
400197 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCG
400262 CATTGCAATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
66 CATTGCAATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
*
400308 TCGCAACGCGACCTTCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCG
1 TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCG
*
400373 CATTGCGATAGTCGAAGTTCGCGTTG
66 CATTGCAATAGTCGAAGTTCGCGTTG
400399 TTTTTTAAGA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 88 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (111 bp):
TCGCAACGCGAACTTCGACTATCGCATTGCGATTTACATATTCACATTGCGATAGTCCAAGTTCG
CATTGCAATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGACTA
Found at i:434568 original size:29 final size:29
Alignment explanation
Indices: 434526--434582 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
434516 AGTGTTGGTC
434526 GTAGGTCACCATGCACTCCGGGAGACCTT
1 GTAGGTCACCATGCACTCCGGGAGACCTT
* *
434555 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCACCATGCACTCCGGGAGACCT
434583 ACCCTTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.18, C:0.33, G:0.30, T:0.19
Consensus pattern (29 bp):
GTAGGTCACCATGCACTCCGGGAGACCTT
Found at i:434617 original size:12 final size:12
Alignment explanation
Indices: 434600--434624 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
434590 CTCAAACAGA
434600 GAGAATGAACGT
1 GAGAATGAACGT
434612 GAGAATGAACGT
1 GAGAATGAACGT
434624 G
1 G
434625 TTGCATGGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:434686 original size:29 final size:29
Alignment explanation
Indices: 434653--434737 Score: 152
Period size: 29 Copynumber: 2.9 Consensus size: 29
434643 TCCCAACACA
434653 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
434682 TAGGTCGCCATGCCCTCCGGACGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACCTTG
*
434711 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCGACCT
434738 ACCCTCGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.13, C:0.38, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACCTTG
Found at i:434782 original size:33 final size:33
Alignment explanation
Indices: 434741--434825 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
434731 GCGACCTACC
*
434741 CTCGCTCGGCTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCGG-TTGCCCTCGGATGCCCTCGCATAG
434774 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * * *
434807 CACGTTCGGATGGCCTCGG
1 CTCGCTCGGTTGCCCTCGG
434826 TCGGATGGCC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 2 0.04
33 44 0.96
ACGTcount: A:0.09, C:0.39, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:434797 original size:10 final size:10
Alignment explanation
Indices: 434753--434868 Score: 54
Period size: 10 Copynumber: 10.7 Consensus size: 10
434743 CGCTCGGCTT
*
434753 CCCTCGGATT
1 CCCTCGGATG
*
434763 CCCTCGCATAG
1 CCCTCGGAT-G
*
434774 CTCGCTCGGTTG
1 C-C-CTCGGATG
434786 CCCTCGGATG
1 CCCTCGGATG
*
434796 CCCTCGCATAG
1 CCCTCGGAT-G
*
434807 CACGTTCGGATGG
1 C-C-CTCGGAT-G
434820 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
434833 GCCTCGGATG
1 CCCTCGGATG
*
434843 GCCTCGGATG
1 CCCTCGGATG
*
434853 CTCTC-GATG
1 CCCTCGGATG
*
434862 GCCTCGG
1 CCCTCGG
434869 TCGGATGGCC
Statistics
Matches: 81, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
9 7 0.09
10 44 0.54
11 4 0.05
12 6 0.07
13 14 0.17
14 6 0.07
ACGTcount: A:0.10, C:0.35, G:0.31, T:0.23
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:434831 original size:14 final size:14
Alignment explanation
Indices: 434812--434896 Score: 88
Period size: 14 Copynumber: 6.0 Consensus size: 14
434802 CATAGCACGT
434812 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
434826 TCGGATGG-C-C--
1 TCGGATGGCCTCGG
434836 TCGGATGGCCTCGGATG
1 TCGGATGGCCTC-G--G
*
434853 CTCTCGATGGCCTCGG
1 -TC-GGATGGCCTCGG
434869 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
434883 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
434897 ATGCCCAGCG
Statistics
Matches: 60, Mismatches: 2, Indels: 18
0.75 0.03 0.22
Matches are distributed among these distances:
10 8 0.13
11 1 0.02
12 2 0.03
13 1 0.02
14 33 0.55
15 2 0.03
16 1 0.02
18 3 0.05
19 9 0.15
ACGTcount: A:0.08, C:0.29, G:0.40, T:0.22
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:434839 original size:57 final size:57
Alignment explanation
Indices: 434778--434902 Score: 180
Period size: 57 Copynumber: 2.2 Consensus size: 57
434768 GCATAGCTCG
* *
434778 CTCGGTTGCCCTCGGATGCCCTCGCATAG-CACGTTCGGATGGCCTCGGTCGGATGGC
1 CTCGGATGCCCTCGGATGCCCTCG-ATAGCCACGGTCGGATGGCCTCGGTCGGATGGC
* * * *
434835 CTCGGATGGCCTCGGATGCTCTCGATGGCCTCGGTCGGATGGCCTCGGTCGGATGGC
1 CTCGGATGCCCTCGGATGCCCTCGATAGCCACGGTCGGATGGCCTCGGTCGGATGGC
434892 CTCGGATGCCC
1 CTCGGATGCCC
434903 AGCGTGTTGG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 3 0.05
57 57 0.95
ACGTcount: A:0.10, C:0.33, G:0.35, T:0.22
Consensus pattern (57 bp):
CTCGGATGCCCTCGGATGCCCTCGATAGCCACGGTCGGATGGCCTCGGTCGGATGGC
Found at i:434863 original size:19 final size:20
Alignment explanation
Indices: 434826--434868 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
434816 ATGGCCTCGG
434826 TCGGATGGCCTCGGATGGCC
1 TCGGATGGCCTCGGATGGCC
434846 TCGGAT-GCTCTC-GATGGCC
1 TCGGATGGC-CTCGGATGGCC
434865 TCGG
1 TCGG
434869 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.23
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGGCC
Found at i:434899 original size:10 final size:10
Alignment explanation
Indices: 434826--434868 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
434816 ATGGCCTCGG
434826 TCGGATGGCC
1 TCGGATGGCC
434836 TCGGATGGCC
1 TCGGATGGCC
434846 TCGGAT-GCTC
1 TCGGATGGC-C
434856 TC-GATGGCC
1 TCGGATGGCC
434865 TCGG
1 TCGG
434869 TCGGATGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.27
10 22 0.73
ACGTcount: A:0.09, C:0.30, G:0.37, T:0.23
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:435796 original size:39 final size:39
Alignment explanation
Indices: 435742--435820 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
435732 GAATATGTAT
435742 ACATTATCGATAAATTAAGAAAGTTTTAAACATACTAAA
1 ACATTATCGATAAATTAAGAAAGTTTTAAACATACTAAA
*
435781 ACATTATTGATAAATTAAGAAAGTTTTAAACATACTAAA
1 ACATTATCGATAAATTAAGAAAGTTTTAAACATACTAAA
435820 A
1 A
435821 TCCTTTAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.32
Consensus pattern (39 bp):
ACATTATCGATAAATTAAGAAAGTTTTAAACATACTAAA
Found at i:437878 original size:17 final size:17
Alignment explanation
Indices: 437856--437892 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
437846 TAAATAATTA
437856 TTTTAGACTCTATTATT
1 TTTTAGACTCTATTATT
*
437873 TTTTAGTCTCTATTATT
1 TTTTAGACTCTATTATT
437890 TTT
1 TTT
437893 AAAAGTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (17 bp):
TTTTAGACTCTATTATT
Found at i:440664 original size:188 final size:190
Alignment explanation
Indices: 440347--440733 Score: 679
Period size: 188 Copynumber: 2.0 Consensus size: 190
440337 CATAACTTCA
*
440347 TTTTCTTGCATCTGAATCCATAAAAAGTGAACCTATTTTTTCATTTAGATTGGCTGATGGTTGTG
1 TTTTCTTGCATCTGAATCCATAAAAAGTGAACCTATTTTTTCATTTAGATTGGCTGATGGTTATG
*
440412 GAAACTGCAAAGATAAGACTTTAAACAGGAAACAAGCAGGATAACGGGAGTGAAATGTGTTCACT
66 GAAACTGCAAAGATAAGACTTTAAACAGGAAACAAGCAGCATAACGGGAGTGAAATGTGTTCACT
440477 TCTC-TATGATACAGTATTTAGGATAGTATGCATTGTTAATGGAGTGAAACTAC-AGTCT
131 TCTCTTATGATACAGTATTTAGGATAGTATGCATTGTTAATGGAGTGAAACTACAAGTCT
* *
440535 TTTTCTTGCATCTGAATCCATAAAAAGTGAACTTATTTTTTCATTTGGATTGGCTGATGGTTATG
1 TTTTCTTGCATCTGAATCCATAAAAAGTGAACCTATTTTTTCATTTAGATTGGCTGATGGTTATG
* *
440600 GAAACTGCGAAGATAAGACTTTAAACAGGAAACAAGCAGCATAGCGGGAGTGAAATGTGTTCACT
66 GAAACTGCAAAGATAAGACTTTAAACAGGAAACAAGCAGCATAACGGGAGTGAAATGTGTTCACT
*
440665 TCTCTTTGTGATACAGTATTTAGGATAGTATGCATTGTTAATGGAGTGAAACTACATAGTCT
131 TCTC-TTATGATACAGTATTTAGGATAGTATGCATTGTTAATGGAGTGAAACTACA-AGTCT
440727 TTTTCTT
1 TTTTCTT
440734 CTTCTCTTTT
Statistics
Matches: 188, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
188 128 0.68
190 48 0.26
192 12 0.06
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (190 bp):
TTTTCTTGCATCTGAATCCATAAAAAGTGAACCTATTTTTTCATTTAGATTGGCTGATGGTTATG
GAAACTGCAAAGATAAGACTTTAAACAGGAAACAAGCAGCATAACGGGAGTGAAATGTGTTCACT
TCTCTTATGATACAGTATTTAGGATAGTATGCATTGTTAATGGAGTGAAACTACAAGTCT
Found at i:450364 original size:118 final size:118
Alignment explanation
Indices: 450223--450438 Score: 269
Period size: 118 Copynumber: 1.8 Consensus size: 118
450213 AATCCAATTT
* * * *
450223 TATTGGGTTAGTTTTTTTATAAAAAAATCGGGTTC-ATGTCGGGTCT-CATTTTTTGGATTAT-A
1 TATTGAGTTAGTTTTTTTATAAAAAAATCAGGTTCGA-GTCGGAT-TGAATTTTTTGGATTATGA
* * * *
450285 ATTCGGTTCGGGTCAGATTAGGTTTAGGGTGAAAAATATCAGACTCGATACAACTC
64 ATTCGGGTCGGATCAGA-TAGGTTTAAGGTAAAAAATATCAGACTCGATACAACTC
* *
450341 TATTGAGTTAGATTTTTTT-TAAAAAAATTAGGTTCGAGTCGGATTGAATTTTTTGGATTATGAG
1 TATTGAGTTAG-TTTTTTTATAAAAAAATCAGGTTCGAGTCGGATTGAATTTTTTGGATTATGAA
*
450405 TTCGGGTCGGATCAGATCGGTTTAAGGTAAAAAA
65 TTCGGGTCGGATCAGATAGGTTTAAGGTAAAAAA
450439 ATATTTGACC
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
117 1 0.01
118 59 0.71
119 23 0.28
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (118 bp):
TATTGAGTTAGTTTTTTTATAAAAAAATCAGGTTCGAGTCGGATTGAATTTTTTGGATTATGAAT
TCGGGTCGGATCAGATAGGTTTAAGGTAAAAAATATCAGACTCGATACAACTC
Found at i:450807 original size:97 final size:97
Alignment explanation
Indices: 450685--450874 Score: 263
Period size: 97 Copynumber: 2.0 Consensus size: 97
450675 AAGTTGAGTC
* ** **
450685 GAGTTTCAAGTGGAAGTTGTATTTTTATTGGATCAAGTAAAGTCACCCTAAACTTAGGTTGAGTC
1 GAGTTTCAAGTGGAAGTTATATTTTTATTGGATCAAGTAAAGTCACCCTAAACCCAAATTGAGTC
*
450750 AAGCTTCAAGTGGAAGTTATATTTTTATGGCT
66 AAGCTTCAAGTGAAAGTTATATTTTTATGGCT
* ** * *
450782 GAGTTTCAAGTGGAAGTTATATTTTTATTGGGTCGGGTAAAGTCGCCCTAAACCCAAATTGGGTC
1 GAGTTTCAAGTGGAAGTTATATTTTTATTGGATCAAGTAAAGTCACCCTAAACCCAAATTGAGTC
* *
450847 AAGTTTCAAGTGAAAGTTGTATTTTTAT
66 AAGCTTCAAGTGAAAGTTATATTTTTAT
450875 TGAATCGGGT
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 80 1.00
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (97 bp):
GAGTTTCAAGTGGAAGTTATATTTTTATTGGATCAAGTAAAGTCACCCTAAACCCAAATTGAGTC
AAGCTTCAAGTGAAAGTTATATTTTTATGGCT
Found at i:450917 original size:65 final size:65
Alignment explanation
Indices: 450782--450939 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
450772 TTTTATGGCT
* ** * ***
450782 GAGTTTCAAGTGGAAGTTATATTTTTATTGGGTCGGGTAAAGTCGCCCTAAACCCAAATTGGGTC
1 GAGTTTCAAGTGAAAGTTATATTTTTATTGAATCGGGTAAAGTCACCCTAAACCCAAATTAAATC
* * * **
450847 AAGTTTCAAGTGAAAGTTGTATTTTTATTGAATCGGGTGAAGTCACCCTAAACCCACGTTAAATC
1 GAGTTTCAAGTGAAAGTTATATTTTTATTGAATCGGGTAAAGTCACCCTAAACCCAAATTAAATC
450912 GAGTTTCAAGTAGAAA-TTATATTTTTAT
1 GAGTTTCAAGT-GAAAGTTATATTTTTAT
450940 CTGGTCATGT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 74 0.95
66 4 0.05
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (65 bp):
GAGTTTCAAGTGAAAGTTATATTTTTATTGAATCGGGTAAAGTCACCCTAAACCCAAATTAAATC
Found at i:450922 original size:162 final size:162
Alignment explanation
Indices: 450647--450939 Score: 399
Period size: 162 Copynumber: 1.8 Consensus size: 162
450637 GAATTAGGTT
* * * *
450647 TTGGGTCAGGTGAAGTGACCCTAAACCCAAGTTGAGTCGAGTTTCAAGTGGAAGTTGTATTTTTA
1 TTGGGTCAGGTAAAGTGACCCTAAACCCAAATTGAGTCAAGTTTCAAGTGAAAGTTGTATTTTTA
* ** * * * * *
450712 TTGGATCAAGTAAAGTCACCCTAAACTTAGGTTGAGTCAAGCTTCAAGTGGAAGTTATATTTTTA
66 TTGAATCAAGTAAAGTCACCCTAAACCCACGTTAAATCAAGCTTCAAGTAGAAATTATATTTTTA
450777 TGGCTGAGTTTCAAGTGGAAGTTATATTTTTA
131 TGGCTGAGTTTCAAGTGGAAGTTATATTTTTA
* *
450809 TTGGGTCGGGTAAAGTCG-CCCTAAACCCAAATTGGGTCAAGTTTCAAGTGAAAGTTGTATTTTT
1 TTGGGTCAGGTAAAGT-GACCCTAAACCCAAATTGAGTCAAGTTTCAAGTGAAAGTTGTATTTTT
** * * *
450873 ATTGAATCGGGTGAAGTCACCCTAAACCCACGTTAAATCGAGTTTCAAGTAGAAATTATATTTTT
65 ATTGAATCAAGTAAAGTCACCCTAAACCCACGTTAAATCAAGCTTCAAGTAGAAATTATATTTTT
450938 AT
130 AT
450940 CTGGTCATGT
Statistics
Matches: 111, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
162 110 0.99
163 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (162 bp):
TTGGGTCAGGTAAAGTGACCCTAAACCCAAATTGAGTCAAGTTTCAAGTGAAAGTTGTATTTTTA
TTGAATCAAGTAAAGTCACCCTAAACCCACGTTAAATCAAGCTTCAAGTAGAAATTATATTTTTA
TGGCTGAGTTTCAAGTGGAAGTTATATTTTTA
Found at i:451907 original size:43 final size:44
Alignment explanation
Indices: 451860--451974 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 44
451850 TTACAACATA
451860 TAGCGGCGATTGT-TCA-ACAAACGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATT-TATCATACAAACGCCGCAAAAGGTATTGATATT
* *
451903 TAGCGGCG-TTTATCATTA-AAACGCCGCAATAGGTTTTGATATT
1 TAGCGGCGATTTATCA-TACAAACGCCGCAAAAGGTATTGATATT
* ** *
451946 TAACGGC-ATTTGGCAGACAAACGCCGCAA
1 TAGCGGCGATTTATCATACAAACGCCGCAA
451975 TAGTCGTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
41 1 0.02
42 6 0.10
43 53 0.87
44 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
TAGCGGCGATTTATCATACAAACGCCGCAAAAGGTATTGATATT
Found at i:451975 original size:43 final size:44
Alignment explanation
Indices: 451876--451977 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 44
451866 CGATTGTTCA
* * * * *
451876 ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATT
1 ACAAACGCCGCAATAGGTATTGATATTTAACGGCATTTAGCATG
* *
451920 A-AAACGCCGCAATAGGTTTTGATATTTAACGGCATTTGGCA-G
1 ACAAACGCCGCAATAGGTATTGATATTTAACGGCATTTAGCATG
451962 ACAAACGCCGCAATAG
1 ACAAACGCCGCAATAG
451978 TCGTTGATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.02
43 48 0.96
44 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (44 bp):
ACAAACGCCGCAATAGGTATTGATATTTAACGGCATTTAGCATG
Found at i:452465 original size:21 final size:21
Alignment explanation
Indices: 452441--452481 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
452431 ATATATTACT
*
452441 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
452462 TCTCTCTGTGCTGCCGCTGC
1 TCTCTCTGTGCTGCCGCTGC
452482 TTCCGCTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:452494 original size:21 final size:21
Alignment explanation
Indices: 452451--452515 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
452441 TCTCTCTGTT
* *
452451 CTGCCGCTGCCTCTCTCTG-TG
1 CTGCCGCTGCTTC-CGCTGCTG
452472 CTGCCGCTGCTTCCGCTGCTG
1 CTGCCGCTGCTTCCGCTGCTG
*
452493 CT-CTAGCTGCTTCCGCTGCTG
1 CTGC-CGCTGCTTCCGCTGCTG
452514 CT
1 CT
452516 CTCTCTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
20 5 0.13
21 34 0.87
ACGTcount: A:0.02, C:0.42, G:0.25, T:0.32
Consensus pattern (21 bp):
CTGCCGCTGCTTCCGCTGCTG
Done.