Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005293.1 Hibiscus syriacus cultivar Beakdansim tig00011970_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: 91470
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:166 original size:30 final size:30
Alignment explanation
Indices: 130--200 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
120 ATACATTCCC
130 GAACCATACCCCGAGTTGTAGTTTAAGCCA
1 GAACCATACCCCGAGTTGTAGTTTAAGCCA
*
160 GAACCATACCCCGAGTTGTGGTTTAAGCCA
1 GAACCATACCCCGAGTTGTAGTTTAAGCCA
190 GAACCATACCC
1 GAACCATACCC
201 TGCATCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (30 bp):
GAACCATACCCCGAGTTGTAGTTTAAGCCA
Found at i:732 original size:18 final size:17
Alignment explanation
Indices: 709--750 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
699 AGGAAAAAAA
709 CAACTAATCAAACCGAAG
1 CAACTAATCAAACC-AAG
* *
727 CAACTAAACAAATCAAG
1 CAACTAATCAAACCAAG
744 CAA-TAAT
1 CAACTAAT
751 AACTGAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 6 0.29
18 12 0.57
ACGTcount: A:0.55, C:0.24, G:0.07, T:0.14
Consensus pattern (17 bp):
CAACTAATCAAACCAAG
Found at i:1940 original size:31 final size:31
Alignment explanation
Indices: 1902--1968 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
1892 GTTTCTAATA
*
1902 TTATCAATTCGTTCGATTATGGTACCTAACG
1 TTATCAATTCGTTCGAATATGGTACCTAACG
*
1933 TTATCAATTCGTTCGAATATGGTCCCTAACG
1 TTATCAATTCGTTCGAATATGGTACCTAACG
1964 TTATC
1 TTATC
1969 GATCCATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (31 bp):
TTATCAATTCGTTCGAATATGGTACCTAACG
Found at i:1985 original size:31 final size:31
Alignment explanation
Indices: 1902--1998 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
1892 GTTTCTAATA
* * *
1902 TTATCAATTCGTTCGATTATGGTACCTAACG
1 TTATCAATCCATTCGATTATGGTCCCTAACG
* * *
1933 TTATCAATTCGTTCGAATATGGTCCCTAACG
1 TTATCAATCCATTCGATTATGGTCCCTAACG
* * * *
1964 TTATCGATCCATTTGATTATGGCCCCTAACA
1 TTATCAATCCATTCGATTATGGTCCCTAACG
1995 TTAT
1 TTAT
1999 TTATTCATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (31 bp):
TTATCAATCCATTCGATTATGGTCCCTAACG
Found at i:4867 original size:20 final size:20
Alignment explanation
Indices: 4819--4887 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 20
4809 TATTTTATTA
*
4819 TATTTAATATTTGTATTTAAT
1 TATTTAATA-TAGTATTTAAT
*
4840 T-TTTATTTATTAAGTATTTAAAT
1 TATTTA-ATA-T-AGTATTT-AAT
*
4863 TATTTAATATTGTATTTAAT
1 TATTTAATATAGTATTTAAT
4883 TATTT
1 TATTT
4888 TTTTGCAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 12 0.30
21 11 0.28
22 7 0.17
23 6 0.15
24 4 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
TATTTAATATAGTATTTAAT
Found at i:18796 original size:18 final size:16
Alignment explanation
Indices: 18765--18799 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
18755 CATCTTGTTT
18765 TCGTTCTCATGGTAAA
1 TCGTTCTCATGGTAAA
18781 TCGTATCTCTATGGTAAA
1 TCGT-TCTC-ATGGTAAA
18799 T
1 T
18800 AGGAAGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 4 0.24
18 9 0.53
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (16 bp):
TCGTTCTCATGGTAAA
Found at i:21858 original size:14 final size:14
Alignment explanation
Indices: 21839--21865 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
21829 ATAGCTTAAG
21839 ATCTGAGAGCAAGA
1 ATCTGAGAGCAAGA
21853 ATCTGAGAGCAAG
1 ATCTGAGAGCAAG
21866 TGTCAGGCAT
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:0.41, C:0.15, G:0.30, T:0.15
Consensus pattern (14 bp):
ATCTGAGAGCAAGA
Found at i:30484 original size:23 final size:23
Alignment explanation
Indices: 30458--30511 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
30448 TGTACTTCTG
30458 TGCTGAATCATTCAACACTGTTT
1 TGCTGAATCATTCAACACTGTTT
*
30481 TGCTGAATCATTCAACATTGTTT
1 TGCTGAATCATTCAACACTGTTT
30504 TGCTGAAT
1 TGCTGAAT
30512 TAGTCAGTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (23 bp):
TGCTGAATCATTCAACACTGTTT
Found at i:39585 original size:20 final size:20
Alignment explanation
Indices: 39491--39584 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
39481 AATTGGGAAA
39491 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
39511 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
39532 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
39552 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
*
39572 TTCGCAATGCGAT
1 ATCGCAATGCGAT
39585 TTACATAGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.72
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:40135 original size:19 final size:19
Alignment explanation
Indices: 40093--40169 Score: 91
Period size: 19 Copynumber: 4.0 Consensus size: 19
40083 TAGTTTCGAG
40093 AATAAAAATCGCAACGCGGA
1 AATAAAAATCGCAACGC-GA
**
40113 AATAACTATCGCAACGCGA
1 AATAAAAATCGCAACGCGA
*
40132 AATAAAAATCGCAATGCGA
1 AATAAAAATCGCAACGCGA
** *
40151 AACCAAAATCGCAATGCGA
1 AATAAAAATCGCAACGCGA
40170 TTTTGGTTTC
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 35 0.70
20 15 0.30
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (19 bp):
AATAAAAATCGCAACGCGA
Found at i:40198 original size:19 final size:19
Alignment explanation
Indices: 40165--40361 Score: 171
Period size: 19 Copynumber: 10.8 Consensus size: 19
40155 AAAATCGCAA
**
40165 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
40184 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
40203 TGTGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
40222 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
40241 TGCGCTTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
40260 TGCGA--TTC---TCTCAT
1 TGCGATTTTCATTTCGCGT
* **
40274 CGCGATAGTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
* *
40293 TGCGA--TTC---TCTCAT
1 TGCGATTTTCATTTCGCGT
**
40307 TGCGATAGTCATTTTCGCGT
1 TGCGATTTTCA-TTTCGCGT
* *
40327 TGCGATTCTCATTATCTCGT
1 TGCGATTTTCATT-TCGCGT
40347 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
40362 AACCAAAAGA
Statistics
Matches: 143, Mismatches: 23, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
14 17 0.12
16 4 0.03
17 5 0.03
19 87 0.61
20 30 0.21
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:40291 original size:33 final size:33
Alignment explanation
Indices: 40249--40336 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
40239 GTTGCGCTTT
40249 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
40282 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
40315 TCATTTTCGCGTTGCGATTCTC
1 TCA-TTTCGCGTTGCGATTCTC
40337 ATTATCTCGT
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 35 0.66
34 18 0.34
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:40353 original size:20 final size:20
Alignment explanation
Indices: 40301--40359 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
40291 GTTGCGATTC
* ** *
40301 TCTCATTGCGATAGTCATTT
1 TCTCGTTGCGATTCTCATTA
*
40321 TCGCGTTGCGATTCTCATTA
1 TCTCGTTGCGATTCTCATTA
*
40341 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTCTCATT
40360 TCAACCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (20 bp):
TCTCGTTGCGATTCTCATTA
Found at i:42499 original size:42 final size:42
Alignment explanation
Indices: 42453--42586 Score: 169
Period size: 42 Copynumber: 3.2 Consensus size: 42
42443 CCTATCATTG
42453 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
** * * * ** * * *
42495 AAGAGGCCATTGTCATCCCTCAAGAGTCTACTCCTATCGTTG
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
*
42537 AAGAGGCTCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
42579 AAGAGGCC
1 AAGAGGCC
42587 ACTGTCATCG
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
Found at i:42583 original size:21 final size:21
Alignment explanation
Indices: 42559--42623 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 21
42549 TCATTCCTCG
42559 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
42580 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
42601 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
42622 AG
1 AG
42624 TGCCCGATTC
Statistics
Matches: 30, Mismatches: 13, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
21 29 0.97
22 1 0.03
ACGTcount: A:0.23, C:0.37, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:42604 original size:84 final size:84
Alignment explanation
Indices: 42431--42595 Score: 294
Period size: 84 Copynumber: 2.0 Consensus size: 84
42421 GAAGACACCG
42431 CAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1 CAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
*
42496 AGAGGCCATTGTCATCCCT
66 AGAGGCCACTGTCATCCCT
* * *
42515 CAAGAGTCTACTCCTATCGTTGAAGAGGCTCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
1 CAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
42580 AGAGGCCACTGTCATC
66 AGAGGCCACTGTCATC
42596 GTTGAAGAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (84 bp):
CAAGAGTCCACTCCTATCATTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCA
AGAGGCCACTGTCATCCCT
Found at i:42611 original size:42 final size:41
Alignment explanation
Indices: 42453--42623 Score: 132
Period size: 42 Copynumber: 4.1 Consensus size: 41
42443 CCTATCATTG
* * *
42453 AAGAGGCCCCTATCATTCCTCG-AGAGTCCCCTCCCACCGTTC
1 AAGAGGCCACTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTC
* * * * * * *
42495 AAGAGGCCATTGTCATCCCTCAAGAGTCTACTCCTATCGTTG
1 AAGAGGCCACTGTCATCCTTGAAGAGTC-CCTCCCACCGTTC
* *
42537 AAGAGGCTC-CTATCATTCCTCG-AGAGTCCCCTCCCACCGTTC
1 AAGAGGC-CACTGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTC
* *
42579 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTGTCATCCTTGAAGA-GTCCCTCCCACCGTTC
42621 AAG
1 AAG
42624 TGCCCGATTC
Statistics
Matches: 98, Mismatches: 23, Indels: 16
0.72 0.17 0.12
Matches are distributed among these distances:
41 9 0.09
42 82 0.84
43 7 0.07
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (41 bp):
AAGAGGCCACTGTCATCCTTGAAGAGTCCCTCCCACCGTTC
Found at i:43904 original size:14 final size:14
Alignment explanation
Indices: 43885--43918 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
43875 ATTATTGCTT
43885 ATTTGTAAAAGGTG
1 ATTTGTAAAAGGTG
*
43899 ATTTGTAAAAGTTG
1 ATTTGTAAAAGGTG
43913 ATTTGT
1 ATTTGT
43919 TTTAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (14 bp):
ATTTGTAAAAGGTG
Found at i:44050 original size:19 final size:19
Alignment explanation
Indices: 44026--44072 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
44016 AAAAAGTACT
*
44026 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
44045 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
44064 ATCGCAACG
1 ATCGCAACG
44073 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:44144 original size:33 final size:31
Alignment explanation
Indices: 44102--44222 Score: 158
Period size: 33 Copynumber: 3.9 Consensus size: 31
44092 TTAAATTCGT
44102 GTTGCGATTTTCATTTCGCATTGCGATTCCCTC
1 GTTGCGATTTTCATTTCGCATTGCGATT--CTC
**
44135 GTTGCGATTTTCATTTCGCATTGCGAAATTAGC
1 GTTGCGATTTTCATTTCGCATTGCG--ATTCTC
*
44168 GTTGCGATTTTCATTTCGCATAGC---TCTC
1 GTTGCGATTTTCATTTCGCATTGCGATTCTC
44196 GTTGCGATTTTCATTTCGCATTGCGAT
1 GTTGCGATTTTCATTTCGCATTGCGAT
44223 AGTAATTTCC
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
28 25 0.32
33 49 0.64
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (31 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCTC
Found at i:44160 original size:19 final size:19
Alignment explanation
Indices: 44103--44160 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
44093 TAAATTCGTG
44103 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
**
44122 TTGCGA--TTC-CCTCG--
1 TTGCGATTTTCATTTCGCA
44136 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
44155 TTGCGA
1 TTGCGA
44161 AATTAGCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 6 0.20
16 6 0.20
17 6 0.20
19 12 0.40
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:44218 original size:61 final size:63
Alignment explanation
Indices: 44102--44221 Score: 190
Period size: 61 Copynumber: 1.9 Consensus size: 63
44092 TTAAATTCGT
*
44102 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTCATTTCGCATAGC-A-T-CCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
44167 C
63 C
44168 GTTGCGATTTTCATTTCGCATAGC-T-CTCGTTGCGATTTTCATTTCGCATTGCGA
1 GTTGCGATTTTCATTTCGCATAGCATCCTCGTTGCGATTTTCATTTCGCATTGCGA
44222 TAGTAATTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
61 29 0.55
63 1 0.02
66 23 0.43
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (63 bp):
GTTGCGATTTTCATTTCGCATAGCATCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAGC
Found at i:46534 original size:12 final size:12
Alignment explanation
Indices: 46517--46549 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
46507 CGGGGACTTG
46517 TTCTTCTTCTTT
1 TTCTTCTTCTTT
46529 TTCTTCTTCTTT
1 TTCTTCTTCTTT
46541 TTCTTCTTC
1 TTCTTCTTC
46550 AGGATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:46758 original size:24 final size:24
Alignment explanation
Indices: 46724--46777 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
46714 CTGAAACATC
*
46724 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
46748 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
46772 ATCAAA
1 ATCAAA
46778 TTTCGAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:47605 original size:21 final size:20
Alignment explanation
Indices: 47562--47613 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
47552 TTTTCCTAAT
*
47562 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
47582 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
47603 TCGTAATGCGA
1 TCGCAATGCGA
47614 TACTGACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:47635 original size:20 final size:20
Alignment explanation
Indices: 47612--47680 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
47602 ATCGTAATGC
47612 GATACTGACTATCGCAACGA
1 GATACTGACTATCGCAACGA
* *
47632 GATAAT-ACAAAATCGCAACGA
1 GATACTGAC--TATCGCAACGA
* *
47653 GATTCTGACTTTCGCAACGA
1 GATACTGACTATCGCAACGA
*
47673 GATTCTGA
1 GATACTGA
47681 AAATCGCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (20 bp):
GATACTGACTATCGCAACGA
Found at i:47687 original size:20 final size:20
Alignment explanation
Indices: 47640--47689 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
47630 GAGATAATAC
47640 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
47660 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
47680 AAAATCGCAA
1 AAAATCGCAA
47690 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:47998 original size:20 final size:20
Alignment explanation
Indices: 47903--47990 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
47893 CAACGGGGAA
47903 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
47923 ATCACAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
47943 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
47963 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
47983 ATCGCAAC
1 ATCGCAAC
47991 TAGAAAATTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 5 0.09
20 44 0.81
21 5 0.09
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:48041 original size:14 final size:14
Alignment explanation
Indices: 48022--48075 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
48012 GAAAATCGCA
48022 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
*
48036 TTGCGATTTTAATTTCG
1 TTGCGA-TTT--TCTCG
48053 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
48069 TTGCGAT
1 TTGCGAT
48076 AGTCAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 6 0.18
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:48041 original size:33 final size:33
Alignment explanation
Indices: 48004--48074 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
47994 AAAATTGCAA
48004 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** * **
48037 TGCGATTTTAATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
48070 TGCGA
1 TGCGA
48075 TAGTCAGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:48221 original size:14 final size:14
Alignment explanation
Indices: 48202--48238 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48192 CATCAATTAA
48202 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
48216 ACAAATCATCTTTT
1 ACAAATCAACATTT
48230 ACAAATCAA
1 ACAAATCAA
48239 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:50123 original size:20 final size:20
Alignment explanation
Indices: 50100--50153 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
50090 GAAACTTAAA
50100 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* * *
50120 ATCGCAACGCGGAAATGGCT
1 ATCGCAATGCGAAAATGACT
*
50140 ATCGCAATACGAAA
1 ATCGCAATGCGAAA
50154 TGAAAATCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:50175 original size:14 final size:14
Alignment explanation
Indices: 50156--50246 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
50146 ATACGAAATG
50156 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
50170 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
50189 AAAATCGCAATGAC
1 AAAATCGCAACGAC
*
50203 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
50219 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
50235 AAAATCGCAACG
1 AAAATCGCAACG
50247 CGAAACACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 30 0.50
15 1 0.02
16 8 0.13
17 1 0.02
18 10 0.17
19 10 0.17
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:50231 original size:32 final size:33
Alignment explanation
Indices: 50140--50251 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
50130 GGAAATGGCT
* *
50140 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
50173 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
50206 ATCGCAATGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
50238 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
50252 CACAAATCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 29 0.38
33 47 0.62
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:50259 original size:65 final size:66
Alignment explanation
Indices: 50140--50262 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
50130 GGAAATGGCT
* *
50140 ATCGCAATACGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAATGACAA
1 ATCGCAATACGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAATGACAA
50205 A
66 A
* *
50206 ATCGCAATGCGAAATG-AAATCGCAATGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATACGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
50263 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 36 0.69
66 15 0.29
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (66 bp):
ATCGCAATACGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAATGACAA
A
Found at i:50299 original size:14 final size:14
Alignment explanation
Indices: 50280--50337 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
50270 TTTCATTTCG
50280 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
50294 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
50310 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
50326 CGTTGCGATTTT
1 CGTTGCGATTTT
50338 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:50344 original size:33 final size:33
Alignment explanation
Indices: 50263--50353 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
50253 ACAAATCGCA
*
50263 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
50296 TTGCGA-TTTCATTTCGCATTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
50328 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
50354 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:50372 original size:20 final size:19
Alignment explanation
Indices: 50338--50392 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
50328 TTGCGATTTT
*
50338 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
50357 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
50377 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
50393 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:50894 original size:18 final size:18
Alignment explanation
Indices: 50871--50918 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
50861 CGGGTCGATC
*
50871 AGATGATGGCTCTGGGTG
1 AGATGATGGCTCTGGGCG
*
50889 AGATGATAGCTCTGGGCG
1 AGATGATGGCTCTGGGCG
*
50907 AGGTGATGGCTC
1 AGATGATGGCTC
50919 CCGAAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.42, T:0.25
Consensus pattern (18 bp):
AGATGATGGCTCTGGGCG
Found at i:52286 original size:20 final size:20
Alignment explanation
Indices: 52238--52296 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
52228 AATAGTTTCT
** *
52238 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
52258 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
52278 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
52297 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:52586 original size:22 final size:22
Alignment explanation
Indices: 52559--52602 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
52549 GATGGAGATA
52559 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
52581 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
52603 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:52876 original size:61 final size:61
Alignment explanation
Indices: 52770--52907 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
52760 CACTTTGAAA
* * * *
52770 ATCGCATTGCGATTATGTATTATCGCGTTGCAAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * * *
52831 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
52892 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
52908 CCCAATTCGT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:52904 original size:20 final size:20
Alignment explanation
Indices: 52770--52904 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
52760 CACTTTGAAA
*
52770 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * * *
52791 ATCGCGTTGCAAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
52811 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
52831 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
52852 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
52872 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
52892 ATCGCATTGCGAT
1 ATCGCATTGCGAT
52905 TTTCCCAATT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.05
20 65 0.69
21 22 0.23
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:53015 original size:21 final size:21
Alignment explanation
Indices: 52975--53015 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
52965 ACTGTAGACC
**
52975 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
52996 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
53016 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:66166 original size:12 final size:11
Alignment explanation
Indices: 66101--66167 Score: 50
Period size: 11 Copynumber: 6.3 Consensus size: 11
66091 AAAATTACAT
66101 TATTAAAAATA
1 TATTAAAAATA
66112 TATTAAAAATA
1 TATTAAAAATA
* ***
66123 CATTATTGATA
1 TATTAAAAATA
**
66134 -ATTATGAA-A
1 TATTAAAAATA
66143 T-TTAAAAATA
1 TATTAAAAATA
66153 TATTAAAAATTA
1 TATTAAAAA-TA
66165 TAT
1 TAT
66168 AATACAACTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
9 6 0.14
10 8 0.18
11 25 0.57
12 5 0.11
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:66200 original size:19 final size:19
Alignment explanation
Indices: 66176--66214 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
66166 ATAATACAAC
66176 TAAACCATATTGTAATGCA
1 TAAACCATATTGTAATGCA
66195 TAAACCATATTGTAATGCA
1 TAAACCATATTGTAATGCA
66214 T
1 T
66215 TTAATATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (19 bp):
TAAACCATATTGTAATGCA
Found at i:67148 original size:22 final size:22
Alignment explanation
Indices: 67120--67193 Score: 121
Period size: 22 Copynumber: 3.4 Consensus size: 22
67110 GGACTATTAT
*
67120 GTCCCGAAAGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
67142 GTCCCGAATGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
*
67164 GACCCGAATGACCACTGGATAC
1 GTCCCGAATGACCACTGGATAC
*
67186 ATCCCGAA
1 GTCCCGAA
67194 GGACTAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.31, C:0.32, G:0.22, T:0.15
Consensus pattern (22 bp):
GTCCCGAATGACCACTGGATAC
Found at i:67906 original size:2 final size:2
Alignment explanation
Indices: 67899--67943 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
67889 TACCAATTCC
67899 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
67941 TA T
1 TA T
67944 CTAACTCATG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70635 original size:15 final size:15
Alignment explanation
Indices: 70605--70661 Score: 96
Period size: 15 Copynumber: 3.7 Consensus size: 15
70595 TGTGCAAATC
70605 CGGGTACCCGGATTTT
1 CGGGTACCC-GATTTT
70621 CGGGTACCCGATTTT
1 CGGGTACCCGATTTT
*
70636 CGGGTACCCAATTTT
1 CGGGTACCCGATTTT
70651 CGGGTACCCGA
1 CGGGTACCCGA
70662 AACTTCCGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
15 30 0.77
16 9 0.23
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (15 bp):
CGGGTACCCGATTTT
Found at i:70720 original size:17 final size:16
Alignment explanation
Indices: 70698--70766 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
70688 CCGTGTCCCG
*
70698 ACCCGGATGTTACGGGT
1 ACCCGGATATT-CGGGT
* *
70715 ACCCGG-TAATCGAGT
1 ACCCGGATATTCGGGT
*
70730 ACCCGGATTTTGCGGGT
1 ACCCGGATATT-CGGGT
*
70747 ACCCGG-TAATCGGGT
1 ACCCGGATATTCGGGT
70762 ACCCG
1 ACCCG
70767 ATACTCGGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
15 20 0.48
16 6 0.14
17 16 0.38
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (16 bp):
ACCCGGATATTCGGGT
Found at i:70733 original size:15 final size:15
Alignment explanation
Indices: 70710--70766 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
70700 CCGGATGTTA
70710 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
70725 CGAGTACCCGGATTTT
1 CGGGTACCCGG-TAAT
70741 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
70757 CGGGTACCCG
1 CGGGTACCCG
70767 ATACTCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:70735 original size:32 final size:32
Alignment explanation
Indices: 70698--70766 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
70688 CCGTGTCCCG
70698 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
* * *
70730 ACCCGGATTTTGCGGGTACCCGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGGTAATCGAGT
70762 ACCCG
1 ACCCG
70767 ATACTCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.28, G:0.32, T:0.22
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGGTAATCGAGT
Found at i:70774 original size:15 final size:15
Alignment explanation
Indices: 70710--70774 Score: 58
Period size: 15 Copynumber: 4.2 Consensus size: 15
70700 CCGGATGTTA
*
70710 CGGGTACCCGGTAAT
1 CGGGTACCCGATAAT
* **
70725 CGAGTACCCGGATTTT
1 CGGGTACCC-GATAAT
*
70741 GCGGGTACCCGGTAAT
1 -CGGGTACCCGATAAT
*
70757 CGGGTACCCGATACT
1 CGGGTACCCGATAAT
70772 CGG
1 CGG
70775 TTTTTAATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
15 24 0.63
16 6 0.16
17 8 0.21
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (15 bp):
CGGGTACCCGATAAT
Found at i:72826 original size:22 final size:22
Alignment explanation
Indices: 72798--72848 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
72788 GACTATTATA
72798 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
72820 TCCCGAAGGACCACTGGATACG
1 TCCCGAAGGACCACTGGATACG
72842 TCCCGAA
1 TCCCGAA
72849 TGACTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.25, T:0.14
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATACG
Found at i:77203 original size:11 final size:11
Alignment explanation
Indices: 77189--77302 Score: 165
Period size: 11 Copynumber: 10.3 Consensus size: 11
77179 TTAAAATCCG
77189 TCGAGCTTGAA
1 TCGAGCTTGAA
*
77200 TCGAGTTTGAA
1 TCGAGCTTGAA
77211 TCGAGCTTGAA
1 TCGAGCTTGAA
*
77222 TCGAGTTTGAA
1 TCGAGCTTGAA
77233 TCGAGCTTGAA
1 TCGAGCTTGAA
77244 TCGAGCTTGAA
1 TCGAGCTTGAA
77255 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
77266 TCGAGTTTAAAA
1 TCGAGCTT-GAA
*
77278 TTGAGCTTGAA
1 TCGAGCTTGAA
*
77289 TTGAGCTTGAA
1 TCGAGCTTGAA
77300 TCG
1 TCG
77303 GGTTTAAAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
11 84 0.91
12 8 0.09
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:77490 original size:32 final size:32
Alignment explanation
Indices: 77453--77529 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
77443 CTTGCGAGTT
*
77453 TTCGAGTCGAGCTTGTTCATATAATTTTCGAG
1 TTCGAGTCGAGCTTGTTCATATAATTTTAGAG
*
77485 TTCGAGTCGAGCTTGTTCATATAGTTTTAGAG
1 TTCGAGTCGAGCTTGTTCATATAATTTTAGAG
*
77517 TTCGAGCCGAGCT
1 TTCGAGTCGAGCT
77530 CAGCAATACT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (32 bp):
TTCGAGTCGAGCTTGTTCATATAATTTTAGAG
Done.