Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:169900 original size:19 final size:20
Alignment explanation
Indices: 169846--169912 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
169836 AAGTTTACTT
* *
169846 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
169866 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
169886 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
169905 TCGCAACG
1 TCGCAACG
169913 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:169908 original size:39 final size:34
Alignment explanation
Indices: 169865--169952 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 34
169855 GAAAATGACT
169865 ATCGCAACGCGGAAATGGCTATCGCAATGCGAAATGAAA
1 ATCGCAACGC-GAAAT-G--ATCGCAATGCGAAATG-AA
169904 ATCGCAACGAC-AAA--ATCGCAATGCGAAATGAA
1 ATCGCAACG-CGAAATGATCGCAATGCGAAATGAA
169936 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
169953 AAACCGCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
31 1 0.02
32 14 0.31
33 16 0.36
34 1 0.02
38 3 0.07
39 9 0.20
40 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAATGATCGCAATGCGAAATGAA
Found at i:169966 original size:19 final size:19
Alignment explanation
Indices: 169885--169966 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
169875 GGAAATGGCT
169885 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
169904 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
169918 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
169936 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
169955 ACCGCAATGCGA
1 ATCGCAATGCGA
169967 TTTGTGTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 18 0.35
19 19 0.37
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:170038 original size:20 final size:20
Alignment explanation
Indices: 170013--170078 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
170003 TTATTTCGCA
*
170013 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
170033 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
170053 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTCCGCG
170073 TTGCGA
1 TTGCGA
170079 AAGTAAGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:170089 original size:20 final size:19
Alignment explanation
Indices: 170005--170104 Score: 83
Period size: 20 Copynumber: 5.1 Consensus size: 19
169995 TGCGATTTTT
* * **
170005 ATTTCGCATTGCGATAGCC
1 ATTTCGCGTTGCGAAAGTA
* *
170024 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGAAAGTA
*
170044 ATTTCCGCGTTGCGATAGTCA
1 ATTT-CGCGTTGCGAAAGT-A
*
170065 TTTTCGCGTTGCGAAAGTA
1 ATTTCGCGTTGCGAAAGTA
*
170084 AGTTTCGTGTTGCGAAAGTA
1 A-TTTCGCGTTGCGAAAGTA
170104 A
1 A
170105 ACTATTCTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
19 5 0.07
20 63 0.89
21 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (19 bp):
ATTTCGCGTTGCGAAAGTA
Found at i:170096 original size:40 final size:40
Alignment explanation
Indices: 170005--170098 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
169995 TGCGATTTTT
* * *
170005 ATTT-CGCATTGCGATAGCCATTTCCGCGTTGCGATAGTC
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
* *
170044 ATTTCCGCGTTGCGATAGTCATTTTCGCGTTGCGAAAGTA
1 ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
*
170084 AGTTT-CGTGTTGCGA
1 A-TTTCCGCGTTGCGA
170099 AAGTAAACTA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.09
40 40 0.85
41 3 0.06
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (40 bp):
ATTTCCGCGTTGCGATAGCCATTTCCGCGTTGCGAAAGTA
Found at i:170479 original size:21 final size:20
Alignment explanation
Indices: 170453--170521 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
170443 CTGTCATCCC
170453 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
170474 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
170495 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
170515 TCAAGAG
1 TCAAGAG
170522 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:170533 original size:41 final size:42
Alignment explanation
Indices: 170443--170533 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
170433 CCCGACTCAC
* *
170443 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
170485 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
170526 CTGTCATC
1 CTGTCATC
170534 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:171976 original size:14 final size:14
Alignment explanation
Indices: 171942--171980 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
171932 TTGATTGTTT
171942 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
171956 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
171970 TGTTGATTTGT
1 AATTGATTTGT
171981 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:172041 original size:18 final size:18
Alignment explanation
Indices: 172018--172062 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
172008 TGTGCTTGTT
172018 TAATTGATTGAAATGTAA
1 TAATTGATTGAAATGTAA
*
172036 TAATTGTTTGAAATGTAA
1 TAATTGATTGAAATGTAA
*
172054 TAGTTGATT
1 TAATTGATT
172063 TGTTGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
TAATTGATTGAAATGTAA
Found at i:172156 original size:19 final size:17
Alignment explanation
Indices: 172132--172178 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 17
172122 ACTCAACGAG
172132 AAATCGCAATGCGAAATGA
1 AAATCGCAATGCG-AA-GA
172151 AAATCGCAA--CG-AGA
1 AAATCGCAATGCGAAGA
172165 AAATCGCAATGCGA
1 AAATCGCAATGCGA
172179 TTTCATTCGC
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 2 0.08
17 2 0.08
19 9 0.36
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (17 bp):
AAATCGCAATGCGAAGA
Found at i:172477 original size:20 final size:20
Alignment explanation
Indices: 172454--172550 Score: 167
Period size: 20 Copynumber: 4.8 Consensus size: 20
172444 ATTGCAATTT
*
172454 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
172474 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
172494 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
172514 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
172534 TCAGTATCGCGTTGCGA
1 TCAGAATCGCGTTGCGA
172551 TTTACTTATT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:172786 original size:12 final size:12
Alignment explanation
Indices: 172767--172800 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
172757 TTCTCCGGCG
172767 ACATCCGTTCCT
1 ACATCCGTTCCT
*
172779 ATATCCGTTCCT
1 ACATCCGTTCCT
172791 ACATCC-TTCC
1 ACATCCGTTCC
172801 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:173380 original size:24 final size:24
Alignment explanation
Indices: 173353--173406 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
173343 GTATTCGAAA
*
173353 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
173377 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
173401 TTTGAT
1 TTTGAT
173407 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:175957 original size:33 final size:33
Alignment explanation
Indices: 175915--176041 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
175905 GGAAATTACT
* *
175915 ATCGCAATGCGAAATGAAAATCACAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
175948 ATCGCAATGCGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
175981 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
176014 ATCGCAAAGTGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
176042 CGAATTTAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:175971 original size:19 final size:19
Alignment explanation
Indices: 175915--176006 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
175905 GGAAATTACT
175915 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
175934 ATCACAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
175948 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
175967 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
175981 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
176000 ATCGCAA
1 ATCGCAA
176007 CGAGGGAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.35
15 2 0.04
16 3 0.05
17 3 0.05
18 2 0.04
19 27 0.47
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:176113 original size:31 final size:33
Alignment explanation
Indices: 176078--176154 Score: 106
Period size: 31 Copynumber: 2.4 Consensus size: 33
176068 TTCGCGTTTT
* *
176078 TTTCGCATTGTGATTCTCTAGTTGC-A-TTTCA
1 TTTCGCATTGCGATTATCTAGTTGCGATTTTCA
*
176109 TTTCGCATTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTATCTAGTTGCGATTTTCA
176142 TTTCG-ATTGCGAT
1 TTTCGCATTGCGAT
176155 AGTAATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
31 22 0.54
32 9 0.22
33 10 0.24
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTATCTAGTTGCGATTTTCA
Found at i:176273 original size:14 final size:14
Alignment explanation
Indices: 176254--176287 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
176244 AACTAATTAA
176254 ACAAATCA-ACTTTT
1 ACAAATCACA-TTTT
176268 ACAAATCACATTTT
1 ACAAATCACATTTT
176282 ACAAAT
1 ACAAAT
176288 AATTAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCACATTTT
Found at i:177995 original size:93 final size:88
Alignment explanation
Indices: 177886--178067 Score: 285
Period size: 94 Copynumber: 2.0 Consensus size: 88
177876 ATTTCAAACT
*
177886 TTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAG
1 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAG-TTAG
177950 CAGAATTGGCAGCAACCGAATAAATTTAC
61 CAGAATTGGCAGC-ACCGAATAAATTTAC
*
177979 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTAGCAGTA
1 TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTAGCAGAA
178044 TTGGCAGCACCGAATAAATTTAC
66 TTGGCAGCACCGAATAAATTTAC
178067 T
1 T
178068 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
88 16 0.19
89 16 0.19
90 8 0.09
93 19 0.22
94 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (88 bp):
TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTAGCAGAA
TTGGCAGCACCGAATAAATTTAC
Found at i:179749 original size:20 final size:19
Alignment explanation
Indices: 179722--179777 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 19
179712 TCTTTTGGTT
179722 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
179741 GATAATGAAAATCGCAAACGC
1 GA-AATGAAAATCGC-AACGA
179762 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
179778 TGCGATTTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.12
20 24 0.71
21 6 0.18
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:180381 original size:21 final size:21
Alignment explanation
Indices: 180357--180411 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
180347 ATTCGCATTA
*
180357 CGAATTATGAAAATCGCAACG
1 CGAATTACGAAAATCGCAACG
* *
180378 CGAA-TACGTAAATCGCAATG
1 CGAATTACGAAAATCGCAACG
*
180398 CGAATTAGGAAAAT
1 CGAATTACGAAAAT
180412 TGCATTGCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (21 bp):
CGAATTACGAAAATCGCAACG
Found at i:180420 original size:21 final size:21
Alignment explanation
Indices: 180357--180421 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
180347 ATTCGCATTA
* *
180357 CGAATTATGAAAATCGCAACG
1 CGAATTACGAAAATCGCAATG
*
180378 CGAA-TACGTAAATCGCAATG
1 CGAATTACGAAAATCGCAATG
* * *
180398 CGAATTAGGAAAATTGCATTG
1 CGAATTACGAAAATCGCAATG
180419 CGA
1 CGA
180422 TAGTCAGTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.22
Consensus pattern (21 bp):
CGAATTACGAAAATCGCAATG
Found at i:180475 original size:20 final size:21
Alignment explanation
Indices: 180431--180478 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
180421 ATAGTCAGTA
*
180431 TCGCATTACGATTTTCCAAAT
1 TCGCATTACGATTTTACAAAT
**
180452 TCGCATTACGA-TTTACTTAT
1 TCGCATTACGATTTTACAAAT
180472 TCGCATT
1 TCGCATT
180479 GCGAATTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (21 bp):
TCGCATTACGATTTTACAAAT
Found at i:180927 original size:15 final size:14
Alignment explanation
Indices: 180902--180932 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
180892 AAATATTATT
180902 ATAATGTAATAATA
1 ATAATGTAATAATA
180916 ATAATAGTAATAATA
1 ATAAT-GTAATAATA
180931 AT
1 AT
180933 TTGATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (14 bp):
ATAATGTAATAATA
Found at i:181022 original size:32 final size:31
Alignment explanation
Indices: 180925--181135 Score: 128
Period size: 31 Copynumber: 7.0 Consensus size: 31
180915 AATAATAGTA
180925 ATAATAATTT-GATAAATTTAATGA-TCATTTT
1 ATAATAATTTAG-TAAATTTAATGACT-ATTTT
* * * *
180956 GTAATAGTTTA--AAATTTTTAGTGATTATTTT
1 ATAATAATTTAGTAAA--TTTAATGACTATTTT
*
180987 ATAATAATTTAGTAAGATTTAATGACTATTCT
1 ATAATAATTTAGTAA-ATTTAATGACTATTTT
* * *
181019 ATAATATTTTAATTAATTTTAATGA-TATTTT
1 ATAATAATTT-AGTAAATTTAATGACTATTTT
*
181050 ATAAT-ATTTTGTTAAATTTAATGACTATTTT
1 ATAATAATTTAG-TAAATTTAATGACTATTTT
*
181081 -T-TTAATTT--T--A--TAATGACTATTTT
1 ATAATAATTTAGTAAATTTAATGACTATTTT
* * *
181104 GTAATAATTT-GTTAAATTTAATAATTATTTT
1 ATAATAATTTAG-TAAATTTAATGACTATTTT
181135 A
1 A
181136 CAACTTTTGA
Statistics
Matches: 140, Mismatches: 21, Indels: 38
0.70 0.11 0.19
Matches are distributed among these distances:
23 13 0.09
24 1 0.01
25 7 0.05
27 2 0.01
29 5 0.04
30 19 0.14
31 56 0.40
32 30 0.21
33 6 0.04
34 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (31 bp):
ATAATAATTTAGTAAATTTAATGACTATTTT
Found at i:181024 original size:63 final size:61
Alignment explanation
Indices: 180925--181078 Score: 179
Period size: 63 Copynumber: 2.5 Consensus size: 61
180915 AATAATAGTA
* * *
180925 ATAATAATTTGATAAATTTAATGA-TCATTTTGTAATAGTTTAA-AATTTTTAGTGATTATTTT
1 ATAATAATTTGATAAATTTAATGACT-ATTCTATAATAGTTTAATAA-TTTTAATGA-TATTTT
*
180987 ATAATAATTT-AGTAAGATTTAATGACTATTCTATAATATTTTAATTAATTTTAATGATATTTT
1 ATAATAATTTGA-TAA-ATTTAATGACTATTCTATAATAGTTTAA-TAATTTTAATGATATTTT
* *
181050 ATAATATTTTGTTAAATTTAATGACTATT
1 ATAATAATTTGATAAATTTAATGACTATT
181079 TTTTTAATTT
Statistics
Matches: 80, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
61 1 0.01
62 27 0.34
63 41 0.51
64 9 0.11
65 2 0.03
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (61 bp):
ATAATAATTTGATAAATTTAATGACTATTCTATAATAGTTTAATAATTTTAATGATATTTT
Found at i:181056 original size:10 final size:10
Alignment explanation
Indices: 180981--181059 Score: 52
Period size: 10 Copynumber: 7.6 Consensus size: 10
180971 TTTTAGTGAT
180981 TATTTTATAA
1 TATTTTATAA
*
180991 TAATTTAGTAA
1 TATTTTA-TAA
* * *
181002 GATTTAATGAC
1 TATTTTAT-AA
*
181013 TATTCTATAA
1 TATTTTATAA
181023 TATTTTAATTAA
1 TATTTT-A-TAA
* *
181035 T-TTTAATGA
1 TATTTTATAA
181044 TATTTTATAA
1 TATTTTATAA
181054 TATTTT
1 TATTTT
181060 GTTAAATTTA
Statistics
Matches: 50, Mismatches: 14, Indels: 10
0.68 0.19 0.14
Matches are distributed among these distances:
9 3 0.06
10 26 0.52
11 17 0.34
12 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (10 bp):
TATTTTATAA
Found at i:181078 original size:21 final size:23
Alignment explanation
Indices: 181054--181109 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
181044 TATTTTATAA
181054 TATTTTGTTAA-ATT-TAATGAC
1 TATTTTGTTAATATTATAATGAC
* *
181075 TATTTTTTTAATTTTATAATGAC
1 TATTTTGTTAATATTATAATGAC
181098 TATTTTG-TAATA
1 TATTTTGTTAATA
181110 ATTTGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 10 0.34
22 6 0.21
23 13 0.45
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
TATTTTGTTAATATTATAATGAC
Found at i:181109 original size:54 final size:51
Alignment explanation
Indices: 181031--181134 Score: 145
Period size: 54 Copynumber: 2.0 Consensus size: 51
181021 AATATTTTAA
* *
181031 TTAATTTTAATGATATTTTATAATATTTTGTTAAATTTAATGACTATTTTT
1 TTAATTTTAATGATATTTTATAATAATTTGTTAAATTTAATAACTATTTTT
* *
181082 TTAATTTTATAATGACTATTTTGTAATAATTTGTTAAATTTAATAATTATTTT
1 TTAA-TTT-TAATGA-TATTTTATAATAATTTGTTAAATTTAATAACTATTTT
181135 ACAACTTTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 3 0.07
53 6 0.13
54 33 0.72
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (51 bp):
TTAATTTTAATGATATTTTATAATAATTTGTTAAATTTAATAACTATTTTT
Found at i:186638 original size:14 final size:14
Alignment explanation
Indices: 186619--186645 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
186609 ATCAAGATAA
186619 AATTAAATTTATTT
1 AATTAAATTTATTT
186633 AATTAAATTTATT
1 AATTAAATTTATT
186646 ATTACTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
AATTAAATTTATTT
Found at i:191833 original size:31 final size:32
Alignment explanation
Indices: 191766--191863 Score: 105
Period size: 31 Copynumber: 3.2 Consensus size: 32
191756 TTTTGGTTGC
* * *
191766 TAAATTTTAT-AAAA-ATTATAAAACAGTCAT
1 TAAATTTTATCAAAATGTTATAAAATAATCAT
* * *
191796 T-GATTTTATTAAAATGTTATAAAATGAT-AT
1 TAAATTTTATCAAAATGTTATAAAATAATCAT
*
191826 TAAATTTTATCCAAATGTTATAAAATAATCAT
1 TAAATTTTATCAAAATGTTATAAAATAATCAT
191858 TAAATT
1 TAAATT
191864 CATCAGAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
29 7 0.13
30 8 0.15
31 32 0.58
32 8 0.15
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (32 bp):
TAAATTTTATCAAAATGTTATAAAATAATCAT
Found at i:194445 original size:15 final size:16
Alignment explanation
Indices: 194409--194480 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 16
194399 TTAAAATAGT
*
194409 TATTATTTTTATATAA
1 TATTATTTATATATAA
*
194425 TA-TATTTATGTA-AA
1 TATTATTTATATATAA
*
194439 TATTATTTATTATTAAAA
1 TATTATTTA-TA-TATAA
* *
194457 TAATATTTATA-A-AT
1 TATTATTTATATATAA
194471 TATTATTTAT
1 TATTATTTAT
194481 TTAGAATTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
14 14 0.30
15 15 0.33
16 3 0.07
17 4 0.09
18 10 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (16 bp):
TATTATTTATATATAA
Found at i:194478 original size:32 final size:31
Alignment explanation
Indices: 194408--194481 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 31
194398 TTTAAAATAG
*
194408 TTATTATTT-TTATATAATATATTTATGTAAA
1 TTATTATTTATTATAAAATATATTTA-GTAAA
194439 -TATTATTTATTATTAAAATAATATTTA-TAAA
1 TTATTATTTATTA-TAAAAT-ATATTTAGTAAA
194470 TTATTATTTATT
1 TTATTATTTATT
194482 TAGAATTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 8 0.21
31 7 0.18
32 16 0.42
33 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (31 bp):
TTATTATTTATTATAAAATATATTTAGTAAA
Found at i:196205 original size:21 final size:21
Alignment explanation
Indices: 196175--196222 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
196165 GCGCGGGGTA
* *
196175 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
196196 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
196217 ATGCCA
1 ATGCCA
196223 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:196751 original size:28 final size:28
Alignment explanation
Indices: 196710--196802 Score: 89
Period size: 30 Copynumber: 3.2 Consensus size: 28
196700 GATAAATGTT
* *
196710 TTTAAAATACAAAT-TATATTATTCGAAA
1 TTTAAAATAAAAATAAATATTATTC-AAA
196738 TTTAAAATAAAAATAAAATATTATTCAAA
1 TTTAAAATAAAAAT-AAATATTATTCAAA
* * *
196767 TTTAAATTTAAAAATAATTATAGTATTCGAA
1 TTTAAA-ATAAAAATAA--ATATTATTCAAA
196798 TTTAA
1 TTTAA
196803 CATTAAATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 13 0.24
29 11 0.20
30 16 0.29
31 15 0.27
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTAAAATAAAAATAAATATTATTCAAA
Found at i:196761 original size:30 final size:32
Alignment explanation
Indices: 196725--196802 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 32
196715 AATACAAATT
196725 ATATTATTCGAAATTTAAA-ATAAAAATAA-A
1 ATATTATTCGAAATTTAAATATAAAAATAATA
* *
196755 ATATTATTC-AAATTTAAATTTAAAAATAATT
1 ATATTATTCGAAATTTAAATATAAAAATAATA
*
196786 ATAGTATTCG-AATTTAA
1 ATATTATTCGAAATTTAA
196803 CATTAAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 9 0.21
30 18 0.43
31 15 0.36
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (32 bp):
ATATTATTCGAAATTTAAATATAAAAATAATA
Found at i:197679 original size:126 final size:126
Alignment explanation
Indices: 197182--197658 Score: 922
Period size: 126 Copynumber: 3.8 Consensus size: 126
197172 TTTAAGTTAT
*
197182 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
197247 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
197308 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
197373 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
197434 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
197499 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
197560 TCCCCGA-GGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
197624 GCG-CCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
197659 CCGATATAGA
Statistics
Matches: 349, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
124 32 0.09
125 60 0.17
126 257 0.74
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.22
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:197732 original size:8 final size:8
Alignment explanation
Indices: 197719--197759 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
197709 AGTTCATCTT
197719 TCAAATTC
1 TCAAATTC
197727 TCAAATTC
1 TCAAATTC
* *
197735 CCAAACTC
1 TCAAATTC
197743 T-AAATTC
1 TCAAATTC
197750 TCAAATTC
1 TCAAATTC
197758 TC
1 TC
197760 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:200738 original size:12 final size:12
Alignment explanation
Indices: 200721--200759 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
200711 AAATACATAA
200721 TATTTAATATAT
1 TATTTAATATAT
*
200733 TATTTAATATAA
1 TATTTAATATAT
200745 TATTTAATATTAT
1 TATTTAATA-TAT
200758 TA
1 TA
200760 GTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
TATTTAATATAT
Found at i:200806 original size:23 final size:23
Alignment explanation
Indices: 200768--200825 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
200758 TAGTTATAAT
200768 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
200789 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
200812 TTTTACATAATATA
1 TTTTACATAATATA
200826 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:202482 original size:60 final size:59
Alignment explanation
Indices: 202389--202557 Score: 214
Period size: 60 Copynumber: 2.8 Consensus size: 59
202379 GATAAATTTG
* ** *
202389 GGGATGAAATTGGAATATGAAAAAGTTTAAGGACCAATTTAGAAA-GAGGGTCATAGTTT
1 GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTA-AAATGAGAGTCATAGTTT
* *
202448 AGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAGTTTAAAATGAGAGTCATAGTTT
1 -GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGTTT
* ** *
202508 GAGGATGAAATTAAAATATTCAAAAGCCTAAGGATCAATTTAAAATGAGA
1 G-GGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGA
202558 ATTATAATTT
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
59 4 0.04
60 91 0.96
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (59 bp):
GGGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAAAATGAGAGTCATAGTTT
Found at i:208394 original size:164 final size:164
Alignment explanation
Indices: 208121--208448 Score: 608
Period size: 164 Copynumber: 2.0 Consensus size: 164
208111 AATAACCCAC
208121 ACCTTCCTTGTAGAATCATCGATGAAGGTGACATAATATAATGAGCCTGCAAGAGATGGAACTGG
1 ACCTTCCTTGTAGAATCATCGATGAAGGTGACATAATATAATGAGCCTGCAAGAGATGGAACTGG
208186 GAGATGGTCCCCATACATCAGTATGAACCAACTCTAACTTTTAGCCTT-GGTGTCTTACCAATCT
66 GAGATGGTCCCCATACATCAGTATGAACCAACTCTAACTTTTAGCCTTGGGTGTCTTACCAATCT
208250 TTGT-AAGCTGACTTTCTTTATTTGCCAAAGATGCA
131 TTGTAAAGCTGACTTTC-TT-TTTGCCAAAGATGCA
208285 ACCTTCCTTGTAGAATCATCGATGAAGGTGACATAATATAATGAGCCTGCAAGAGATGGAACT-G
1 ACCTTCCTTGTAGAATCATCGATGAAGGTGACATAATATAATGAGCCTGCAAGAGATGGAACTGG
208349 GAGATGGTCCCCATACATCAGTATGAACCAACTCTAACTTTTTAGCCTTGGGTGTCTTACCAATC
66 GAGATGGTCCCCATACATCAGTATGAACCAACTCTAAC-TTTTAGCCTTGGGTGTCTTACCAATC
208414 TTTGTAAAGCTGACTTTCTTTTTGCCAAAGATGCA
130 TTTGTAAAGCTGACTTTCTTTTTGCCAAAGATGCA
208449 TCCTCTTCAT
Statistics
Matches: 161, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
163 39 0.24
164 88 0.55
165 22 0.14
166 12 0.07
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (164 bp):
ACCTTCCTTGTAGAATCATCGATGAAGGTGACATAATATAATGAGCCTGCAAGAGATGGAACTGG
GAGATGGTCCCCATACATCAGTATGAACCAACTCTAACTTTTAGCCTTGGGTGTCTTACCAATCT
TTGTAAAGCTGACTTTCTTTTTGCCAAAGATGCA
Found at i:221728 original size:37 final size:36
Alignment explanation
Indices: 221682--221820 Score: 145
Period size: 37 Copynumber: 3.6 Consensus size: 36
221672 TGAACATAAT
221682 AACATTAGATTAAATTATAAAATTTTAAAATTTTAA
1 AACATTAGATTAAATTATAAAATTTTAAAATTTTAA
** **
221718 AACATTTAGATTAAATTATAAAAAATATCGTGTTTGAA-CATAA
1 AACA-TTAGATTAAATTAT---AAA-AT--T-TTAAAATTTTAA
221761 TAACATTAGATTAAATTATAAAATTTTAAAATTTTAA
1 -AACATTAGATTAAATTATAAAATTTTAAAATTTTAA
221798 AACATTTAGATTAAATTATAAAA
1 AACA-TTAGATTAAATTATAAAA
221821 AAATATCGTG
Statistics
Matches: 84, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
36 12 0.14
37 36 0.43
39 2 0.02
40 6 0.07
41 2 0.02
43 18 0.21
44 8 0.10
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (36 bp):
AACATTAGATTAAATTATAAAATTTTAAAATTTTAA
Found at i:221743 original size:80 final size:80
Alignment explanation
Indices: 221654--221853 Score: 373
Period size: 80 Copynumber: 2.5 Consensus size: 80
221644 TGATTCTCAA
*
221654 TATAAAAAATATCGTTTTTGAACATAATAACATTAGATTAAATTATAAAATTTTAAAATTTTAAA
1 TATAAAAAATATCGTGTTTGAACATAATAACATTAGATTAAATTATAAAATTTTAAAATTTTAAA
221719 ACATTTAGATTAAAT
66 ACATTTAGATTAAAT
221734 TATAAAAAATATCGTGTTTGAACATAATAACATTAGATTAAATTATAAAATTTTAAAATTTTAAA
1 TATAAAAAATATCGTGTTTGAACATAATAACATTAGATTAAATTATAAAATTTTAAAATTTTAAA
221799 ACATTTAGATTAAAT
66 ACATTTAGATTAAAT
*
221814 TATAAAAAAATATCGTGTTTGAACATAATAAAATTAGATT
1 TAT-AAAAAATATCGTGTTTGAACATAATAACATTAGATT
221854 GAACAAATAA
Statistics
Matches: 117, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
80 82 0.70
81 35 0.30
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (80 bp):
TATAAAAAATATCGTGTTTGAACATAATAACATTAGATTAAATTATAAAATTTTAAAATTTTAAA
ACATTTAGATTAAAT
Found at i:224068 original size:2 final size:2
Alignment explanation
Indices: 224061--224089 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
224051 TCAGTAAAAT
224061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
224090 GGTTATTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:224453 original size:21 final size:21
Alignment explanation
Indices: 224429--224489 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
224419 AACTTTGAAA
224429 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
224450 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
*
224464 AAATGATTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
224485 AAATG
1 AAATG
224490 TTTCTTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 3 0.10
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.33
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:224535 original size:36 final size:36
Alignment explanation
Indices: 224421--224542 Score: 167
Period size: 35 Copynumber: 3.4 Consensus size: 36
224411 TGGAAACCAA
*
224421 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
224458 CTTTG-AAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* * *
224493 CTTTGAAAAATAGTTTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
224530 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
224543 AATGGGATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 27 0.35
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:225743 original size:15 final size:16
Alignment explanation
Indices: 225725--225754 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
225715 ATGGCAGATC
225725 AAAATCCAG-ACGGGG
1 AAAATCCAGAACGGGG
225740 AAAATCCAGAACGGG
1 AAAATCCAGAACGGG
225755 AAAGAAAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.20, G:0.30, T:0.07
Consensus pattern (16 bp):
AAAATCCAGAACGGGG
Found at i:228983 original size:37 final size:38
Alignment explanation
Indices: 228937--229019 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 38
228927 TGGCAACCAA
** *
228937 CTTTGAAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATAAATTTTCAAAGTTTGATAAATGTTT
*
228974 CTTTG-AAAAATAAATTTTCAAAGTTTGATAGATGTTT
1 CTTTGAAAAAATAAATTTTCAAAGTTTGATAAATGTTT
*
229011 -GTTGAAAAA
1 CTTTGAAAAA
229020 TGATAATGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
36 9 0.23
37 30 0.77
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (38 bp):
CTTTGAAAAAATAAATTTTCAAAGTTTGATAAATGTTT
Found at i:229016 original size:36 final size:37
Alignment explanation
Indices: 228951--229020 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
228941 GAAAAAATGG
* *
228951 TTTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATAAA
1 TTTTCAAAGTTTGATAAATGTTTCGTTGAAAAATAAA
*
228988 TTTTCAAAGTTTGATAGATGTTT-GTTGAAAAAT
1 TTTTCAAAGTTTGATAAATGTTTCGTTGAAAAAT
229021 GATAATGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.36, C:0.04, G:0.16, T:0.44
Consensus pattern (37 bp):
TTTTCAAAGTTTGATAAATGTTTCGTTGAAAAATAAA
Found at i:230916 original size:25 final size:26
Alignment explanation
Indices: 230863--230916 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
230853 GAGTGCTATG
** **
230863 TTTGTAATTTTTTTAAAAATGTTATT
1 TTTGTAATTTTTGAAAAAATGACATT
230889 TTTGTAATTTTTGAAAAAATGACATT
1 TTTGTAATTTTTGAAAAAATGACATT
230915 TT
1 TT
230917 AATAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (26 bp):
TTTGTAATTTTTGAAAAAATGACATT
Found at i:230980 original size:29 final size:28
Alignment explanation
Indices: 230923--230988 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
230913 TTTTAATAAA
*
230923 TATTTTGAAAATGGTGCTATATTAGTAAT
1 TATTTT-AAAATGGTGATATATTAGTAAT
*
230952 TAATTTTAAAATGGTGATATTTTCA-TAAT
1 T-ATTTTAAAATGGTGATATATT-AGTAAT
230981 T-TTTTAAA
1 TATTTTAAA
230989 TAATTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 7 0.21
29 20 0.61
30 6 0.18
ACGTcount: A:0.36, C:0.03, G:0.12, T:0.48
Consensus pattern (28 bp):
TATTTTAAAATGGTGATATATTAGTAAT
Found at i:238192 original size:29 final size:29
Alignment explanation
Indices: 238137--238192 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
238127 CCGTTAATCG
* * * *
238137 GGTGACATTTTAGTAATTATTTTGAAACT
1 GGTGACATATTAGGAATTAATTCGAAACT
*
238166 GGTGACATATTGGGAATTAATTCGAAA
1 GGTGACATATTAGGAATTAATTCGAAA
238193 AAGGGTGCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (29 bp):
GGTGACATATTAGGAATTAATTCGAAACT
Found at i:240671 original size:11 final size:10
Alignment explanation
Indices: 240648--240779 Score: 53
Period size: 11 Copynumber: 13.2 Consensus size: 10
240638 ATAAATTTTG
240648 ATAA-ATTTA
1 ATAATATTTA
*
240657 ATAATCATTTT
1 ATAAT-ATTTA
240668 ATAATATTTCA
1 ATAATATTT-A
* *
240679 A-AAAATCTA
1 ATAATATTTA
* * *
240688 ATGACTGTTTT
1 AT-AATATTTA
240699 ATAATAATTTA
1 ATAAT-ATTTA
240710 ATAA-ATTTA
1 ATAATATTTA
* *
240719 ATGATAATTTT
1 ATAAT-ATTTA
240730 ATAATTATTTA
1 ATAA-TATTTA
*
240741 A-AA-ATTCTC
1 ATAATATT-TA
*
240750 ATAATATTTT
1 ATAATATTTA
*
240760 ATAATAATTA
1 ATAATATTTA
240770 A-AAT-TTTA
1 ATAATATTTA
240778 AT
1 AT
240780 GATTAAAAAA
Statistics
Matches: 89, Mismatches: 21, Indels: 26
0.65 0.15 0.19
Matches are distributed among these distances:
8 7 0.08
9 19 0.21
10 25 0.28
11 37 0.42
12 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (10 bp):
ATAATATTTA
Found at i:240699 original size:31 final size:30
Alignment explanation
Indices: 240663--240772 Score: 107
Period size: 31 Copynumber: 3.6 Consensus size: 30
240653 TTTAATAATC
240663 ATTTTATAATATTTCAAAAAATCTAATGACT-
1 ATTTTATAATATTT-AAAAAATCTAATGA-TA
* * *
240694 GTTTTATAATAATTTAATAAATTTAATGATA
1 ATTTTATAAT-ATTTAAAAAATCTAATGATA
* * *
240725 ATTTTATAATTATTTAAAAATTCTCATAAT-
1 ATTTTATAA-TATTTAAAAAATCTAATGATA
*
240755 ATTTTATAATAATTAAAA
1 ATTTTATAATATTTAAAA
240773 TTTTAATGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
29 8 0.12
30 10 0.15
31 43 0.65
32 5 0.08
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTTTATAATATTTAAAAAATCTAATGATA
Found at i:240742 original size:28 final size:27
Alignment explanation
Indices: 240649--240782 Score: 72
Period size: 31 Copynumber: 4.5 Consensus size: 27
240639 TAAATTTTGA
*
240649 TAAATTTAATAATCATTTTATAAT-ATT
1 TAAATTTAATGAT-ATTTTATAATAATT
* *
240676 TCAAAAAATCTAATGACTGTTTTATAATAATTT
1 T----AAATTTAATGA-TATTTTATAATAA-TT
*
240709 AATAAATTTAATGATAATTTTATAATTATT
1 --TAAATTTAATGAT-ATTTTATAATAATT
* *
240739 TAAAAATTCTCATAATATTTTATAATAATT
1 T--AAATT-TAATGATATTTTATAATAATT
*
240769 AAAATTTTAATGAT
1 TAAA-TTTAATGAT
240783 TAAAAAATCA
Statistics
Matches: 81, Mismatches: 12, Indels: 27
0.68 0.10 0.22
Matches are distributed among these distances:
27 1 0.01
28 9 0.11
29 2 0.02
30 21 0.26
31 43 0.53
32 2 0.02
33 2 0.02
35 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (27 bp):
TAAATTTAATGATATTTTATAATAATT
Found at i:240744 original size:62 final size:60
Alignment explanation
Indices: 240648--240782 Score: 166
Period size: 62 Copynumber: 2.2 Consensus size: 60
240638 ATAAATTTTG
* * * *
240648 ATAAATTTAATAATCATTTTATAATATTTCAAAAAATCTAATGACTGTTTTATAATAATTTA
1 ATAAATTTAATGATAATTTTATAATATTTCAAAAAATCTAAT-AATATTTTATAATAA-TTA
* *
240710 ATAAATTTAATGATAATTTTATAATTATTT-AAAAATTCTCATAATATTTTATAATAATTA
1 ATAAATTTAATGATAATTTTATAA-TATTTCAAAAAATCTAATAATATTTTATAATAATTA
*
240770 A-AATTTTAATGAT
1 ATAAATTTAATGAT
240783 TAAAAAATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
59 11 0.17
60 4 0.06
61 13 0.20
62 32 0.49
63 5 0.08
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (60 bp):
ATAAATTTAATGATAATTTTATAATATTTCAAAAAATCTAATAATATTTTATAATAATTA
Found at i:267365 original size:19 final size:19
Alignment explanation
Indices: 267341--267401 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
267331 TTTATATTAT
267341 AAAATTTCATTATAAGAAA
1 AAAATTTCATTATAAGAAA
** *
267360 AAAATTT-AAGATGAGCAAA
1 AAAATTTCATTATAAG-AAA
* *
267379 ATAGTTTCATTATAAGAAA
1 AAAATTTCATTATAAGAAA
267398 AAAA
1 AAAA
267402 ATAAGATGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
18 5 0.17
19 20 0.67
20 5 0.17
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (19 bp):
AAAATTTCATTATAAGAAA
Found at i:267408 original size:37 final size:38
Alignment explanation
Indices: 267345--267419 Score: 125
Period size: 38 Copynumber: 2.0 Consensus size: 38
267335 TATTATAAAA
* *
267345 TTTCATTATAAGAAAAAAATTTAAGATGAGCAAAATAG
1 TTTCATTATAAGAAAAAAATATAAGATGAACAAAATAG
267383 TTTCATTATAAGAAAAAAA-ATAAGATGAACAAAATAG
1 TTTCATTATAAGAAAAAAATATAAGATGAACAAAATAG
267420 ATTTTTCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
37 16 0.46
38 19 0.54
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (38 bp):
TTTCATTATAAGAAAAAAATATAAGATGAACAAAATAG
Found at i:272059 original size:26 final size:25
Alignment explanation
Indices: 272030--272081 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
272020 ATTTGGTCTC
*
272030 TTAATTATTTATATT-TTATTTTTATT
1 TTAATTA-TTAAATTATTA-TTTTATT
272056 TTAATTATTAAATTATTATTTTATT
1 TTAATTATTAAATTATTATTTTATT
272081 T
1 T
272082 GATAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (25 bp):
TTAATTATTAAATTATTATTTTATT
Found at i:274818 original size:18 final size:21
Alignment explanation
Indices: 274789--274840 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 21
274779 AATGATCACT
274789 ATTATGTTTATAATAATT-ATA
1 ATTAT-TTTATAATAATTAATA
*
274810 A-T-TTTTAT-ATATTTAATA
1 ATTATTTTATAATAATTAATA
274828 ATTATTTTATAAT
1 ATTATTTTATAAT
274841 TTTTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 5 0.19
18 9 0.35
19 2 0.08
20 7 0.27
21 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATTTTATAATAATTAATA
Found at i:274838 original size:29 final size:29
Alignment explanation
Indices: 274805--274860 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
274795 TTTATAATAA
* *
274805 TTATAATTTTTATATATTTAATAATTATT
1 TTATAATTTTTAAAAATTTAATAATTATT
274834 TTATAATTTTTAAAAATTTAATAATTA
1 TTATAATTTTTAAAAATTTAATAATTA
274861 AAATAATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATAATTTTTAAAAATTTAATAATTATT
Found at i:274845 original size:21 final size:20
Alignment explanation
Indices: 274812--274851 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
274802 TAATTATAAT
*
274812 TTTTATATATTTAATAATTA
1 TTTTATATATTTAAAAATTA
*
274832 TTTTATAATTTTTAAAAATT
1 TTTTAT-ATATTTAAAAATT
274852 TAATAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATATTTAAAAATTA
Found at i:276427 original size:20 final size:19
Alignment explanation
Indices: 276380--276439 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
276370 TTTATATAAA
*
276380 AATTAAATATTTTATAATT
1 AATTAAATAATTTATAATT
** *
276399 CAAAAAAATAGTTTATAATT
1 -AATTAAATAATTTATAATT
*
276419 AATTTAAATAATATATAATT
1 AA-TTAAATAATTTATAATT
276439 A
1 A
276440 TAAAATAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTAAATAATTTATAATT
Found at i:276681 original size:184 final size:185
Alignment explanation
Indices: 276372--276767 Score: 670
Period size: 184 Copynumber: 2.1 Consensus size: 185
276362 TTTTCTAATT
* * * *
276372 TATATAA-AAATTAAATATTTTATAATTCAAAAAAATAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAAT-TTTTATAATTCAAAAAAACAATTTATAATTAATTTAAATAATATATA
276436 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
276501 TTAAATCTTAAATTATTAATTGA-TTTTAAATGGTTTGGGCTGAGCCCATATGTTA
130 TTAAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
276556 TATATAATATATTTAATTTTTTTAATTCAGAAAAACAATTTATAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATTTTTATAATTCAAAAAAACAATTTATAATTAATTTAAATAATATATAA
*
276621 TTATAAAATGAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
* *
276686 TAGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TAAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* *
276741 TATATAATATATTTAAATTTTAAAATT
1 TATATAATATATTTAATTTTTATAATT
276768 TTATTTCGGT
Statistics
Matches: 198, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
184 136 0.69
185 62 0.31
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (185 bp):
TATATAATATATTTAATTTTTATAATTCAAAAAAACAATTTATAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TAAATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:277904 original size:18 final size:18
Alignment explanation
Indices: 277881--277919 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
277871 GTGTAATTAA
277881 ATCTTAATTTAATTGTTT
1 ATCTTAATTTAATTGTTT
277899 ATCTTAATTTAATTGTTT
1 ATCTTAATTTAATTGTTT
277917 ATC
1 ATC
277920 AAGGCTTGGC
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:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (18 bp):
ATCTTAATTTAATTGTTT
Found at i:280336 original size:26 final size:24
Alignment explanation
Indices: 280307--280357 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 24
280297 TAGTTCTAAT
280307 ATGGTGTTCTTTTTTTTATAAAAAAA
1 ATGGTG-T-TTTTTTTTATAAAAAAA
280333 ATGGTGTTTTTTTTTATAAAAAAA
1 ATGGTGTTTTTTTTTATAAAAAAA
280357 A
1 A
280358 AGTTCATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.72
25 1 0.04
26 6 0.24
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (24 bp):
ATGGTGTTTTTTTTTATAAAAAAA
Found at i:280358 original size:26 final size:26
Alignment explanation
Indices: 280307--280358 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
280297 TAGTTCTAAT
*
280307 ATGGTGTTCTTTTTTTTATAAAAAAA
1 ATGGTGTTCTTTTTTTTAAAAAAAAA
280333 ATGGTGTT-TTTTTTTATAAAAAAAAA
1 ATGGTGTTCTTTTTTT-TAAAAAAAAA
280359 GTTCATCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (26 bp):
ATGGTGTTCTTTTTTTTAAAAAAAAA
Found at i:282124 original size:19 final size:19
Alignment explanation
Indices: 282100--282145 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
282090 TTAATTTTCT
* *
282100 TTATTTTTTAAATTATT-TG
1 TTATTTTTCAAA-TATTATA
282119 TTATTTTTCAAATATTATA
1 TTATTTTTCAAATATTATA
282138 TTATTTTT
1 TTATTTTT
282146 ATGTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTTTTCAAATATTATA
Found at i:287644 original size:56 final size:57
Alignment explanation
Indices: 287542--287677 Score: 195
Period size: 56 Copynumber: 2.4 Consensus size: 57
287532 GTTCACATTC
*
287542 AAAAATTCCCAAAATATCACCTTTTTCAAAATAATTCACAGAATATCA-C-TTTTCA
1 AAAAATTCCCAAAATGTCACCTTTTTCAAAATAATTCACAGAATATCACCATTTTCA
* * *
287597 AAAAATTCTCAAAATGTCACCTTTTTTTAAAATAATTCCCAGAATATCACCATTTTTCA
1 AAAAATTCCCAAAATGTCACC-TTTTTCAAAATAATTCACAGAATATCACCA-TTTTCA
287656 AAATAATTCCCAAAATGTCACC
1 AAA-AATTCCCAAAATGTCACC
287678 GGGTCGGGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
55 19 0.27
56 25 0.35
57 1 0.01
59 9 0.13
60 17 0.24
ACGTcount: A:0.42, C:0.22, G:0.03, T:0.33
Consensus pattern (57 bp):
AAAAATTCCCAAAATGTCACCTTTTTCAAAATAATTCACAGAATATCACCATTTTCA
Found at i:287647 original size:30 final size:29
Alignment explanation
Indices: 287545--287677 Score: 164
Period size: 30 Copynumber: 4.6 Consensus size: 29
287535 CACATTCAAA
287545 AATTCCCAAAATATCACCTTTTTCAAAAT
1 AATTCCCAAAATATCACCTTTTTCAAAAT
* *
287574 AATTCACAGAATATCA-C-TTTTCAAAA-
1 AATTCCCAAAATATCACCTTTTTCAAAAT
* * *
287600 AATTCTCAAAATGTCACCTTTTTTTAAAAT
1 AATTCCCAAAATATCACC-TTTTTCAAAAT
*
287630 AATTCCCAGAATATCACCATTTTTCAAAAT
1 AATTCCCAAAATATCACC-TTTTTCAAAAT
*
287660 AATTCCCAAAATGTCACC
1 AATTCCCAAAATATCACC
287678 GGGTCGGGTC
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
26 13 0.15
27 10 0.11
28 1 0.01
29 22 0.25
30 41 0.47
ACGTcount: A:0.41, C:0.23, G:0.03, T:0.34
Consensus pattern (29 bp):
AATTCCCAAAATATCACCTTTTTCAAAAT
Found at i:291750 original size:20 final size:20
Alignment explanation
Indices: 291703--291743 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
291693 TATTATCAGT
*
291703 GTTCTCGATCGAAATCTGAA
1 GTTCTCGATCGAAATCTAAA
291723 GTTCTCGATCGAAATCTAAA
1 GTTCTCGATCGAAATCTAAA
291743 G
1 G
291744 GTTTCGAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
GTTCTCGATCGAAATCTAAA
Found at i:293992 original size:32 final size:31
Alignment explanation
Indices: 293897--294029 Score: 97
Period size: 31 Copynumber: 4.2 Consensus size: 31
293887 AAAGAGTTAC
*
293897 CCTAAGAGAACATCTTAGGGCCTG-AGAGCCTA
1 CCTAAGA-AACATCTCAGGGCC-GCAGAGCCTA
* * * * * * *
293929 CCCAAGATAGATTTCGGGGCCGTAGAACCTA
1 CCTAAGAAACATCTCAGGGCCGCAGAGCCTA
** *
293960 CCTAAGAACACATCTTTGGGCCGCAGGGCCTA
1 CCTAAGAA-ACATCTCAGGGCCGCAGAGCCTA
** **
293992 CCCGAGAATGATCTCAGGGCCGCAGAGCCTA
1 CCTAAGAAACATCTCAGGGCCGCAGAGCCTA
294023 CCTAAGA
1 CCTAAGA
294030 GTCATATTAG
Statistics
Matches: 74, Mismatches: 25, Indels: 5
0.71 0.24 0.05
Matches are distributed among these distances:
30 1 0.01
31 45 0.61
32 28 0.38
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.17
Consensus pattern (31 bp):
CCTAAGAAACATCTCAGGGCCGCAGAGCCTA
Found at i:294012 original size:63 final size:63
Alignment explanation
Indices: 293897--294030 Score: 157
Period size: 63 Copynumber: 2.1 Consensus size: 63
293887 AAAGAGTTAC
* * *
293897 CCTAAGAGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTAGAACCTA
1 CCTAAGAGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAACCTA
* * * *
293960 CCTAAGA-ACACATCTTTGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCT
1 CCTAAGAGA-ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAACCT
294022 A
63 A
294023 CCTAAGAG
1 CCTAAGAG
294031 TCATATTAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
62 3 0.05
63 57 0.95
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (63 bp):
CCTAAGAGAACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAACCTA
Found at i:295049 original size:29 final size:28
Alignment explanation
Indices: 294945--295070 Score: 135
Period size: 29 Copynumber: 4.4 Consensus size: 28
294935 CTTTTTTTAA
* ** *
294945 AAAATAATTCCCAGAATGTCATTTTTTT
1 AAAATAATTCTCAGAATGTCACATTTTC
*
294973 AAAATAATTCTCAGAATGTCACTTTTTC
1 AAAATAATTCTCAGAATGTCACATTTTC
* * *
295001 AAAAAAAAATTCTGAAAATGTCACCATTTTC
1 --AAAATAATTCTCAGAATGTCA-CATTTTC
*
295032 AAAATAATTCTCATAATGTCACCATTTTC
1 AAAATAATTCTCAGAATGTCA-CATTTTC
295061 AAAATAATTC
1 AAAATAATTC
295071 ACAAAATATC
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
28 25 0.29
29 36 0.42
30 18 0.21
31 6 0.07
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.37
Consensus pattern (28 bp):
AAAATAATTCTCAGAATGTCACATTTTC
Found at i:295082 original size:29 final size:29
Alignment explanation
Indices: 294918--295083 Score: 120
Period size: 29 Copynumber: 5.6 Consensus size: 29
294908 CACATTCGAA
* * *
294918 AATTCCCAAAATGTCACCTTTTTTTAAAAAAT
1 AATTCACAAAATGTCACC--ATTTT-CAAAAT
* * ** *
294950 AATTCCCAGAATGTCA-TTTTTTTAAAAT
1 AATTCACAAAATGTCACCATTTTCAAAAT
* * * *
294978 AATTCTCAGAATGTCA-CTTTTTCAAAAAAA
1 AATTCACAAAATGTCACCATTTTC--AAAAT
**
295008 AATTCTGAAAATGTCACCATTTTCAAAAT
1 AATTCACAAAATGTCACCATTTTCAAAAT
* *
295037 AATTCTCATAATGTCACCATTTTCAAAAT
1 AATTCACAAAATGTCACCATTTTCAAAAT
*
295066 AATTCACAAAATATCACC
1 AATTCACAAAATGTCACC
295084 GGGTCGGGTC
Statistics
Matches: 115, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
28 25 0.22
29 51 0.44
30 18 0.16
31 6 0.05
32 15 0.13
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.36
Consensus pattern (29 bp):
AATTCACAAAATGTCACCATTTTCAAAAT
Found at i:295120 original size:19 final size:19
Alignment explanation
Indices: 295092--295128 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
295082 CCGGGTCGGG
295092 TCAGACCGATTCGGACCGA
1 TCAGACCGATTCGGACCGA
* *
295111 TCAGATCGATTTGGACCG
1 TCAGACCGATTCGGACCG
295129 GTCAAGCCGG
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (19 bp):
TCAGACCGATTCGGACCGA
Found at i:297120 original size:35 final size:35
Alignment explanation
Indices: 297081--297149 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
297071 AAAGTCGCTT
*
297081 GTAAATATTGGATGATACAAGAAACTAAAATTATC
1 GTAAATATTGGATGACACAAGAAACTAAAATTATC
297116 GTAAATATTGGATGACACAAGAAACTAAAATTAT
1 GTAAATATTGGATGACACAAGAAACTAAAATTAT
297150 AAAATAGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (35 bp):
GTAAATATTGGATGACACAAGAAACTAAAATTATC
Found at i:301336 original size:3 final size:3
Alignment explanation
Indices: 301324--301403 Score: 126
Period size: 3 Copynumber: 27.0 Consensus size: 3
301314 TTTCATTTTG
* * *
301324 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT ATA AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
301371 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
301404 TAATTATAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:302703 original size:21 final size:22
Alignment explanation
Indices: 302664--302704 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
302654 TAGTTTAATA
*
302664 ATTTTTATTTAATATATTTTGC
1 ATTTTAATTTAATATATTTTGC
*
302686 ATTTTAATTTTATA-ATTTT
1 ATTTTAATTTAATATATTTT
302705 AATTTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTTAATTTAATATATTTTGC
Found at i:303667 original size:18 final size:18
Alignment explanation
Indices: 303626--303660 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
303616 ATTTCATTCA
*
303626 ATTATTTTTTTATCCTTT
1 ATTATTTTTATATCCTTT
303644 ATTATTTTTATATCCTT
1 ATTATTTTTATATCCTT
303661 ATATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTATTTTTATATCCTTT
Found at i:306054 original size:21 final size:20
Alignment explanation
Indices: 306030--306088 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
306020 TTTTTCATTA
306030 CATTTTCATTTTT-TATGTTT
1 CATTTTCATTTTTATAT-TTT
*
306050 GCATTTGCATTTTTATATTTT
1 -CATTTTCATTTTTATATTTT
*
306071 CATCTTCA-TTTTATATTT
1 CATTTTCATTTTTATATTT
306089 GCATCTTTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.29
20 6 0.18
21 15 0.44
22 3 0.09
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (20 bp):
CATTTTCATTTTTATATTTT
Found at i:306062 original size:20 final size:20
Alignment explanation
Indices: 306034--306095 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
306024 TCATTACATT
*
306034 TTCATTTTTTATGTTTGCAT-
1 TTCA-TTTTTATATTTGCATC
*
306054 TTGCATTTTTATATTTTCATC
1 TT-CATTTTTATATTTGCATC
306075 TTCA-TTTTATATTTGCATC
1 TTCATTTTTATATTTGCATC
306094 TT
1 TT
306096 TGCATTGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 16 0.43
20 17 0.46
21 4 0.11
ACGTcount: A:0.18, C:0.13, G:0.06, T:0.63
Consensus pattern (20 bp):
TTCATTTTTATATTTGCATC
Found at i:310921 original size:54 final size:54
Alignment explanation
Indices: 310844--310951 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 54
310834 CTGACCAGAA
310844 ATCTGAGCAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
1 ATCTGAGCAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
* * *
310898 ATCTGTGCAGAAA-CCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGAGCA-AAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
310952 CAATGATTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 47 0.94
55 3 0.06
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (54 bp):
ATCTGAGCAAAAGCCACAGGAAAGGATGAATGTGTTGTCAAATATTTTACGAAC
Found at i:312210 original size:45 final size:45
Alignment explanation
Indices: 312116--312228 Score: 118
Period size: 45 Copynumber: 2.5 Consensus size: 45
312106 GGAGCTTTTT
* * ** * * *
312116 GATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGCAT
1 GATGTTTTAAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAG
* * *
312161 GATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCCG
1 GATGTTTTAAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAG
312206 GATGTTTTCAAAAAGCCTTCGGG
1 GATGTTTT-AAAAA-CCTTCGGG
312229 AACTTTTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 44 0.79
46 4 0.07
47 8 0.14
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (45 bp):
GATGTTTTAAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAG
Found at i:312235 original size:121 final size:121
Alignment explanation
Indices: 312017--312577 Score: 783
Period size: 121 Copynumber: 4.7 Consensus size: 121
312007 CTATTTCCCA
* *
312017 CATCTGTAAGACCTTCAGTGCATAATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
*
312082 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGCTTTCAAAACCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
* *
312138 CATCTGTAAGCCCTTCAATGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
* * *
312203 CCGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATATTTTCAAAACCTTCGGGAT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGG-T
* * * * * **
312260 -ATTTGTAAGCCCTTCAGTGCATGATGGTTTCAAAACCATCGGGTTGTCCATAAGACCTGCAGTG
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
*
312324 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
* * * ** *
312380 CATCTATAAGACCTACAATGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGATTTGTAGTG
1 CATCTGTAAGACCTTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
* * *
312445 CAGGATGTTTTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTTAAAGCC-TCAGGGT
66 CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTC-GGGT
* * * * *
312501 CATCTGTAA-AACTTACAGTGCAAGATG---ATAAAACCTTTGGGTCATCCATAAGACCTCCAGT
1 CATCTGTAAGACCTT-CAGTGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGT
312562 GCAGGATGTTTTCAAA
65 GCAGGATGTTTTCAAA
312578 TGAGATTTTA
Statistics
Matches: 391, Mismatches: 45, Indels: 11
0.87 0.10 0.02
Matches are distributed among these distances:
118 44 0.11
120 6 0.02
121 340 0.87
122 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (121 bp):
CATCTGTAAGACCTTCAGTGCATGATGTTTTTAAAACCTTCGGGTCATCCATAAGACCTGCAGTG
CAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
Found at i:312361 original size:76 final size:74
Alignment explanation
Indices: 312281--312423 Score: 178
Period size: 76 Copynumber: 1.9 Consensus size: 74
312271 CTTCAGTGCA
** * *
312281 TGATGGTTTCAAAACCATCGGGTTGTCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGGTTTCAAAACCATCGGGTCATCCATAAGACCTACAATGCAGGATGTTTT-AAAAA-CCTT
312346 CGGGAGCTTTT
64 CGGGAGCTTTT
* * * * * *
312357 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGACCTACAATGCATGATGTTTTTAAAACCTTCG
1 TGATGGTTTCAAAACCATCGGGTCATCCATAAGACCTACAATGCAGGATGTTTTAAAAACCTTCG
312422 GG
66 GG
312424 TCATCCATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 8 0.14
75 4 0.07
76 45 0.79
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (74 bp):
TGATGGTTTCAAAACCATCGGGTCATCCATAAGACCTACAATGCAGGATGTTTTAAAAACCTTCG
GGAGCTTTT
Found at i:312452 original size:45 final size:45
Alignment explanation
Indices: 312358--312470 Score: 118
Period size: 45 Copynumber: 2.5 Consensus size: 45
312348 GGAGCTTTTT
* * * *
312358 GATGTTTTCAAAGCCTTCGGGTCATCTATAAGACCTACAATGCAT
1 GATGTTTTAAAAACCTTCGGGTCATCCATAAGACCTACAATGCAG
* ** ** *
312403 GATGTTTTTAAAACCTTCGGGTCATCCATAAGATTTGTAGTGCAG
1 GATGTTTTAAAAACCTTCGGGTCATCCATAAGACCTACAATGCAG
312448 GATGTTTTCAAAAAGCCTTCGGG
1 GATGTTTT-AAAAA-CCTTCGGG
312471 AGTTTTTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 44 0.79
46 4 0.07
47 8 0.14
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (45 bp):
GATGTTTTAAAAACCTTCGGGTCATCCATAAGACCTACAATGCAG
Found at i:312847 original size:3 final size:3
Alignment explanation
Indices: 312833--312901 Score: 95
Period size: 3 Copynumber: 23.3 Consensus size: 3
312823 TTTCATTTTG
* * *
312833 ATT ATT -TT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
312880 ATT ATT ACT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
312902 AATTATAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:314218 original size:21 final size:22
Alignment explanation
Indices: 314179--314219 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
314169 TAGTTTAATA
*
314179 ATTTTTATTTAATATATTTTGC
1 ATTTTAATTTAATATATTTTGC
*
314201 ATTTTAATTTTATA-ATTTT
1 ATTTTAATTTAATATATTTT
314220 AATTTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTTTAATTTAATATATTTTGC
Found at i:314288 original size:23 final size:23
Alignment explanation
Indices: 314262--314319 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
314252 AATTTTATTT
314262 TGTTTTTATTATTACTTTCGA-TA
1 TGTTTTTATTATTACTTTC-ATTA
**
314285 TGTTTAAATTATTACTTTCATTA
1 TGTTTTTATTATTACTTTCATTA
314308 T-TATTTTATTAT
1 TGT-TTTTATTAT
314320 CTTAGTCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 27 0.93
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (23 bp):
TGTTTTTATTATTACTTTCATTA
Found at i:321003 original size:24 final size:24
Alignment explanation
Indices: 320971--321020 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
320961 GATTAAAATC
*
320971 GACTCATTCATTTAAGATAATTTT
1 GACTCATTCATTTAAGATAATCTT
320995 GACTCATTCATTTAAGATAATCTT
1 GACTCATTCATTTAAGATAATCTT
321019 GA
1 GA
321021 TTAATTCGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (24 bp):
GACTCATTCATTTAAGATAATCTT
Found at i:321027 original size:24 final size:24
Alignment explanation
Indices: 320971--321027 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
320961 GATTAAAATC
* *
320971 GACTCATTCATTTAAGATAATTTT
1 GACTAATTCATTTAAGATAATCTT
*
320995 GACTCATTCATTTAAGATAATCTT
1 GACTAATTCATTTAAGATAATCTT
*
321019 GATTAATTC
1 GACTAATTC
321028 GAGATCTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (24 bp):
GACTAATTCATTTAAGATAATCTT
Found at i:322924 original size:22 final size:22
Alignment explanation
Indices: 322899--322945 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
322889 ATAATGTTAT
*
322899 AATTAAATGTAAAATTTTGATA
1 AATTAAATATAAAATTTTGATA
* * *
322921 AATTTATTATAATATTTTGATA
1 AATTAAATATAAAATTTTGATA
322943 AAT
1 AAT
322946 GATCATTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (22 bp):
AATTAAATATAAAATTTTGATA
Found at i:323053 original size:21 final size:21
Alignment explanation
Indices: 323012--323055 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
323002 TTATTTATAG
*
323012 TTTTTTATATTTGATGTAAAT
1 TTTTTTATATTTGATGAAAAT
*
323033 TTTTTTATAGTTT-TTGAAAAT
1 TTTTTTATA-TTTGATGAAAAT
323054 TT
1 TT
323056 AATGATCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTTATATTTGATGAAAAT
Found at i:324970 original size:27 final size:28
Alignment explanation
Indices: 324910--324970 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
324900 ATCATAACTA
* *
324910 TATTTATGGTGTCTATGTACTTATTTCG
1 TATTTAAGGTGTCTATGTACTTATATCG
* *
324938 TATTTAAGGTGTTTATG-ACTTGTATCG
1 TATTTAAGGTGTCTATGTACTTATATCG
*
324965 TGTTTA
1 TATTTA
324971 TGAATCATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 13 0.46
28 15 0.54
ACGTcount: A:0.20, C:0.08, G:0.20, T:0.52
Consensus pattern (28 bp):
TATTTAAGGTGTCTATGTACTTATATCG
Found at i:325585 original size:2 final size:2
Alignment explanation
Indices: 325580--325605 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
325570 CTGTTTTATT
325580 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
325606 ATTAAAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:342306 original size:34 final size:32
Alignment explanation
Indices: 342244--342313 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
342234 ACCTTACAAC
* *
342244 TCCCTAGTTTTTCCGAGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGAGATAAACTAGAACCTT
*
342276 TCCCTAGCTTTTACACGAGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGAGATAAACTAGAACCTT
342310 TCCC
1 TCCC
342314 CAGGATAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGAGATAAACTAGAACCTT
Found at i:342320 original size:23 final size:23
Alignment explanation
Indices: 342294--342337 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
342284 TTTTACACGA
342294 GATAAGCTAGAACCTTTCCCCAG
1 GATAAGCTAGAACCTTTCCCCAG
342317 GATAAGCTAGAACCTTTCCCC
1 GATAAGCTAGAACCTTTCCCC
342338 TTTACAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.32, G:0.16, T:0.23
Consensus pattern (23 bp):
GATAAGCTAGAACCTTTCCCCAG
Found at i:342822 original size:22 final size:23
Alignment explanation
Indices: 342789--342831 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
342779 ATGGATGCAC
342789 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
342812 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
342832 GCATGGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:342846 original size:21 final size:20
Alignment explanation
Indices: 342775--342873 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
342765 CGGTGTTTGA
342775 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCATG
*
342795 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCATG
342817 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCATG
* *
342837 GATACATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-TG
342859 GTGCATGGATGCACT
1 GTGCATGGATGCACT
342874 TTGACACCCT
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.06
20 15 0.22
21 29 0.43
22 16 0.24
23 4 0.06
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCATG
Found at i:342974 original size:29 final size:28
Alignment explanation
Indices: 342942--343006 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 28
342932 AAAACCTTTT
342942 AAAACTTTGAATAAATTCAATT-AAGTCCA
1 AAAACTTTG--TAAATTCAATTCAAGTCCA
342971 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAAC--TTTGTAAATTCAATTCAAGTCCA
343001 AAAACT
1 AAAACT
343007 ATTTTGCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 1 0.03
29 16 0.48
30 12 0.36
31 4 0.12
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (28 bp):
AAAACTTTGTAAATTCAATTCAAGTCCA
Found at i:343000 original size:30 final size:30
Alignment explanation
Indices: 342953--343012 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
342943 AAACTTTGAA
342953 TAAATTCAATTAAGTCCAAAAAC-ATTTTG
1 TAAATTCAATTAAGTCCAAAAACTATTTTG
342982 TAAATTCAATTCAAGTCCAAAAACTATTTTG
1 TAAATTCAATT-AAGTCCAAAAACTATTTTG
343013 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACTATTTTG
Found at i:344284 original size:22 final size:22
Alignment explanation
Indices: 344228--344285 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 22
344218 TTTTAAATCA
344228 AATTTTTTTTCTTCAAAACTTTC
1 AATTTTTTTT-TTCAAAACTTTC
*
344251 AATTTTTTTTTTCAAAACTTTT
1 AATTTTTTTTTTCAAAACTTTC
344273 AATTTTTATTTTT
1 AATTTTT-TTTTT
344286 GAAAGCTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 18 0.55
23 15 0.45
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (22 bp):
AATTTTTTTTTTCAAAACTTTC
Found at i:344327 original size:19 final size:19
Alignment explanation
Indices: 344303--344348 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
344293 CTAAATCCTT
344303 TTTCAAAAT-TCATTTTGGC
1 TTTCAAAATCT-ATTTTGGC
* *
344322 TTTCAAAATCTATTTTTGT
1 TTTCAAAATCTATTTTGGC
344341 TTTCAAAA
1 TTTCAAAA
344349 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 23 0.96
20 1 0.04
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTCAAAATCTATTTTGGC
Found at i:345582 original size:21 final size:21
Alignment explanation
Indices: 345548--345610 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
345538 TAAAAAAGAC
*
345548 TGCACATAACATGGTGCATCGG
1 TGCAC-TATCATGGTGCATCGG
345570 TGCACTATCATGGTGCATCGG
1 TGCACTATCATGGTGCATCGG
*
345591 TGCACTATCATTGTGCATCG
1 TGCACTATCATGGTGCATCG
345611 ATATCCCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 34 0.87
22 5 0.13
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (21 bp):
TGCACTATCATGGTGCATCGG
Found at i:345695 original size:20 final size:20
Alignment explanation
Indices: 345666--345739 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
345656 GCAGCCTTCG
* *
345666 TGCATGGATGCACAGCATGA
1 TGCATCGATGCACACCATGA
*
345686 TGCATCGATGCACAACCTTGA
1 TGCATCGATGCAC-ACCATGA
* **
345707 TGTATCGATGCACATAATGA
1 TGCATCGATGCACACCATGA
345727 TGCATCGATGCAC
1 TGCATCGATGCAC
345740 TAATTGCATT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 28 0.62
21 17 0.38
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (20 bp):
TGCATCGATGCACACCATGA
Found at i:345938 original size:29 final size:29
Alignment explanation
Indices: 345917--345974 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
345907 AAACTTTGAA
345917 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
345946 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
345975 TGTCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:345964 original size:30 final size:30
Alignment explanation
Indices: 345917--345977 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 30
345907 AAACTTTGAA
345917 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
345946 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
345977 T
1 T
345978 CTTAAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.37
30 11 0.37
31 8 0.27
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:346254 original size:18 final size:18
Alignment explanation
Indices: 346231--346282 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
346221 TAAAATGATC
346231 ATTAAATTTTATAAAATT
1 ATTAAATTTTATAAAATT
** *
346249 ATTAAAAATTATTAAATTT
1 ATTAAATTTTA-TAAAATT
*
346268 ATCAAACTTTTATAA
1 ATTAAA-TTTTATAA
346283 TTATTATAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 9 0.35
19 14 0.54
20 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTAAATTTTATAAAATT
Found at i:348855 original size:14 final size:14
Alignment explanation
Indices: 348832--348870 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
348822 GTCAATCTCG
348832 ATGT-TTTTTAAAA
1 ATGTATTTTTAAAA
348845 ATGTATTTTTAAAA
1 ATGTATTTTTAAAA
348859 ATG-A-TTTTAAAA
1 ATGTATTTTTAAAA
348871 GCATCCTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.32
13 5 0.20
14 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (14 bp):
ATGTATTTTTAAAA
Found at i:355656 original size:24 final size:25
Alignment explanation
Indices: 355636--355684 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
355626 ATTAATTATT
355636 TAATTTCACA-CTCCTAAAATTTTA
1 TAATTTCACACCTCCTAAAATTTTA
* *
355660 TAATTTCGCACCTTCTAAAATTTTA
1 TAATTTCACACCTCCTAAAATTTTA
355685 ATATAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATTTCACACCTCCTAAAATTTTA
Found at i:357474 original size:32 final size:32
Alignment explanation
Indices: 357401--357474 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
357391 GCCTGACAGA
* *
357401 CTATCCAAGAGAGTACCTTAGGGCCTAAAAGC
1 CTATCCAAGGGAGTACATTAGGGCCTAAAAGC
* * * *
357433 CTACCCAAGGGAGTACATTGGGGCCTTAGAGC
1 CTATCCAAGGGAGTACATTAGGGCCTAAAAGC
357465 CTATCCAAGG
1 CTATCCAAGG
357475 AAATGCCTTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (32 bp):
CTATCCAAGGGAGTACATTAGGGCCTAAAAGC
Found at i:358206 original size:24 final size:24
Alignment explanation
Indices: 358179--358224 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
358169 AATGCCGCGT
*
358179 AGAATTTGCACAGAAGTGCCACGA
1 AGAATATGCACAGAAGTGCCACGA
*
358203 AGAATATGCACCGAAGTGCCAC
1 AGAATATGCACAGAAGTGCCAC
358225 ATAGATTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (24 bp):
AGAATATGCACAGAAGTGCCACGA
Found at i:358349 original size:15 final size:16
Alignment explanation
Indices: 358331--358364 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
358321 TAATTATTTC
358331 AATTAACA-TTATTCA
1 AATTAACATTTATTCA
*
358346 AATTATCATTTATTCA
1 AATTAACATTTATTCA
358362 AAT
1 AAT
358365 AGAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (16 bp):
AATTAACATTTATTCA
Found at i:359890 original size:15 final size:16
Alignment explanation
Indices: 359872--359902 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
359862 GCCATAGTTC
359872 ATAAAT-AGTAATTCA
1 ATAAATCAGTAATTCA
359887 ATAAATCAGTAATTCA
1 ATAAATCAGTAATTCA
359903 GAATATTGAA
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:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (16 bp):
ATAAATCAGTAATTCA
Found at i:363017 original size:19 final size:19
Alignment explanation
Indices: 362993--363029 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
362983 ATGACCAACA
362993 AAATCGCAA-TGCGATCTCT
1 AAATCGCAACT-CGATCTCT
363012 AAATCGCAACTCGATCTC
1 AAATCGCAACTCGATCTC
363030 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATCGCAACTCGATCTCT
Found at i:363127 original size:21 final size:21
Alignment explanation
Indices: 363103--363156 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
363093 AATTCGCGTT
* *
363103 GCGATTTTAGAAAATCGCAAC
1 GCGATTTTACAAAATAGCAAC
** *
363124 GCGATAATACAAAATAGCAAT
1 GCGATTTTACAAAATAGCAAC
363145 GCGATTTT-CAAA
1 GCGATTTTACAAA
363157 GCGCCATTAG
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (21 bp):
GCGATTTTACAAAATAGCAAC
Found at i:363324 original size:22 final size:22
Alignment explanation
Indices: 363299--363340 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
363289 GTGACATCCG
363299 TCCCCATCTCCGACGAAATCAA
1 TCCCCATCTCCGACGAAATCAA
*
363321 TCCCCATCTCCGGCGAAATC
1 TCCCCATCTCCGACGAAATC
363341 CATCTATCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.43, G:0.12, T:0.19
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAA
Found at i:363753 original size:20 final size:20
Alignment explanation
Indices: 363730--363841 Score: 109
Period size: 20 Copynumber: 5.7 Consensus size: 20
363720 GATAGTTTAA
*
363730 TTCGCCTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
* **
363750 TTCGTGTTGCGATTTTCA-T
1 TTCGCGTTGCGATAGTCATT
* **
363769 TTCGCGTTACGATAGTCAAA
1 TTCGCGTTGCGATAGTCATT
363789 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCATT
* * **
363809 TTTGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATAGTCATT
*
363829 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
363842 TTTAAGTTTC
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 15 0.20
20 59 0.80
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCATT
Done.