Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008679.1 Hibiscus syriacus cultivar Beakdansim tig00111698_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: 66322
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5941 original size:45 final size:45
Alignment explanation
Indices: 5764--5941 Score: 234
Period size: 45 Copynumber: 3.9 Consensus size: 45
5754 CTTCATACTT
* * *
5764 ATAATGCA-CCATTATGCATTTTCATTTATGGCATTCTTTCATACCA
1 ATAATGCACCCA-TATGCA-TTTCATTTATGGCATCCTTTCATGCCG
* *
5810 ATAATGCACCTATATGCATTTCAATTATGGCA-CCATTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCC-TTTCATGCCG
* * * *
5855 ATAATGCATCCACATGCATTTCATTTATGGAATCATTTCATGCCG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
5900 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATG
1 ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATG
5942 TCCTTTTTAT
Statistics
Matches: 114, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
44 1 0.01
45 96 0.84
46 15 0.13
47 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCATTTATGGCATCCTTTCATGCCG
Found at i:6010 original size:45 final size:45
Alignment explanation
Indices: 5916--6038 Score: 192
Period size: 45 Copynumber: 2.7 Consensus size: 45
5906 CACCCATATG
* *
5916 CATTTCATTTATGGCATCCTTTCATGTCCTTTTTATACACTATTATA
1 CATTTCATTTATGACATACTTTCATG-CC-TTTTATACACTATTATA
5963 CATTTCATTTATGACATACTTTCATGCCTTTTATACACTATTATA
1 CATTTCATTTATGACATACTTTCATGCCTTTTATACACTATTATA
* *
6008 CATTTCATTTGTGACATATTTTCATGCCTTT
1 CATTTCATTTATGACATACTTTCATGCCTTT
6039 CATCTAACTG
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 46 0.64
46 2 0.03
47 24 0.33
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (45 bp):
CATTTCATTTATGACATACTTTCATGCCTTTTATACACTATTATA
Found at i:6142 original size:68 final size:68
Alignment explanation
Indices: 6033--6432 Score: 665
Period size: 68 Copynumber: 5.9 Consensus size: 68
6023 ATATTTTCAT
* *
6033 GCCTTTCATCTAACTGGCATAATTGAAACATTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
6098 TTA
66 TTA
* *
6101 GCCTTTCATCTAGCTGACATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
6166 TTA
66 TTA
*** *
6169 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGATATCAAAGACAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
6234 TTA
66 TTA
*
6237 GCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
6302 TTA
66 TTA
* * *
6305 GTCTTTCATCTAGCTGGCATAATTGCCACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
6370 TTA
66 TTA
* *
6373 GCCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCACAACTAGGCCATCAA
1 GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCC-TCAA
6433 TATTTTATTT
Statistics
Matches: 307, Mismatches: 24, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
68 303 0.99
69 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (68 bp):
GCCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAACTAGGCCTCAAAGGCAC
TTA
Found at i:9298 original size:13 final size:13
Alignment explanation
Indices: 9280--9321 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
9270 TGCGTCATAA
*
9280 ATTTATGACGCGC
1 ATTTATGACGCAC
*
9293 ATTTATGACACAC
1 ATTTATGACGCAC
*
9306 ATTTATGACGCTC
1 ATTTATGACGCAC
9319 ATT
1 ATT
9322 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:15675 original size:75 final size:76
Alignment explanation
Indices: 15515--15744 Score: 390
Period size: 76 Copynumber: 3.0 Consensus size: 76
15505 CTTAACAGTC
* *
15515 AATGGTGAAAAATGTTGATCAAAGGGTCACATTGAGTTTATTTTTTGAATTGGAGAGTCACATTG
1 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
15580 AGAGAAAAAAT
66 AGAGAAAAAAT
*
15591 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTA-TTTTTGAATTGGAGAGTCACGTTG
1 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
*
15655 AGAGAGAAAAT
66 AGAGAAAAAAT
* * *
15666 AATGGTGAAAAACATTGATCAAAGGGCCACATTTGGTTTATTTTTTGAATTGGAGAGTCACATTG
1 AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
15731 AGAGAAAAAAT
66 AGAGAAAAAAT
15742 AAT
1 AAT
15745 ACGATAACCA
Statistics
Matches: 144, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
75 70 0.49
76 74 0.51
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.30
Consensus pattern (76 bp):
AATGGTGAAAAACGTTGATCAAAGGGTCACATTGGGTTTATTTTTTGAATTGGAGAGTCACATTG
AGAGAAAAAAT
Found at i:18912 original size:11 final size:11
Alignment explanation
Indices: 18896--18920 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18886 GAGGTGGTGC
18896 ATGTGAAGATG
1 ATGTGAAGATG
18907 ATGTGAAGATG
1 ATGTGAAGATG
18918 ATG
1 ATG
18921 AAAAGAGACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (11 bp):
ATGTGAAGATG
Found at i:19522 original size:41 final size:40
Alignment explanation
Indices: 19456--19575 Score: 109
Period size: 41 Copynumber: 2.9 Consensus size: 40
19446 TTTTTAGTAA
*
19456 AAATGCCGCAATAGAGTAG-ACATTTAGCGGCGTTTTAGGC-C
1 AAATGCCGCAATAGAGT-GTA-ATTTAGCGGCGTTTTA-CCAC
* *
19497 AAATGCCGCAATATAGTGTTAATTTAGCTGCGTTTATACCAC
1 AAATGCCGCAATAGAGTG-TAATTTAGCGGCGTTT-TACCAC
* * *
19539 AAACGCCGTAATAGAGTGGTAAATTAGCGGCAGTTTT
1 AAATGCCGCAATAGAGT-GTAATTTAGCGGC-GTTTT
19576 GTCTAAAACG
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
40 1 0.02
41 30 0.46
42 29 0.45
43 5 0.08
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (40 bp):
AAATGCCGCAATAGAGTGTAATTTAGCGGCGTTTTACCAC
Found at i:21680 original size:81 final size:81
Alignment explanation
Indices: 21545--21711 Score: 262
Period size: 81 Copynumber: 2.1 Consensus size: 81
21535 CGAAGCCGTC
* ** * *
21545 ATCACCTACACCGTCGCTGCTTGGTACTCAACTGTTGCTGGTCGCCGCCGCTTGAAGCCGTCGTT
1 ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCACCGCCGCTTGAAGCCGTCGTT
*
21610 CCTGCTGCTGCTCGTT
66 CCTGCTGCTGCTCGTG
* *
21626 ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCATCGCCGCTTGAAGCTGTCGTT
1 ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCACCGCCGCTTGAAGCCGTCGTT
21691 CCTGCTGCTGCTCGTG
66 CCTGCTGCTGCTCGTG
21707 ATCAC
1 ATCAC
21712 CGCCATCGTT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.13, C:0.35, G:0.24, T:0.28
Consensus pattern (81 bp):
ATCACATACACCGTCGCTGCCCGGTACTCAACTGCTGCTGGTCACCGCCGCTTGAAGCCGTCGTT
CCTGCTGCTGCTCGTG
Found at i:29408 original size:21 final size:21
Alignment explanation
Indices: 29366--29408 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29356 TTTATGGGTT
* * *
29366 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
29387 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
29408 A
1 A
29409 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:29474 original size:67 final size:68
Alignment explanation
Indices: 29388--29539 Score: 234
Period size: 68 Copynumber: 2.2 Consensus size: 68
29378 ACCCATTCAA
* *
29388 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
29452 GGG
66 GGG
* * * *
29455 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
29520 GGG
66 GGG
*
29523 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
29540 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
67 22 0.29
68 55 0.71
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:29876 original size:29 final size:29
Alignment explanation
Indices: 29842--29913 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
29832 TATATTATGA
**
29842 TACATGACATGAATTTGTATTA-ATTGTAT
1 TACATGACATGAATTCATATTATA-TGTAT
29871 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
29900 TACATGACATGAAT
1 TACATGACATGAAT
29914 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:29970 original size:30 final size:31
Alignment explanation
Indices: 29928--29987 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
29918 AGAAAAAGTT
*
29928 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
29959 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
29988 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:30267 original size:23 final size:22
Alignment explanation
Indices: 30207--30274 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
30197 TTATGGACAT
30207 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
30229 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
30251 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
30274 A
1 A
30275 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:36411 original size:66 final size:67
Alignment explanation
Indices: 36305--36476 Score: 215
Period size: 67 Copynumber: 2.6 Consensus size: 67
36295 TTTATGGGTT
* * *
36305 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATA-CCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
36367 CTAG
64 CTAG
* * *
36371 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
36436 TG
66 AG
* *
36438 AGGGGAATCGATACCCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
36477 ATGAGAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
64 2 0.02
65 12 0.13
66 25 0.27
67 36 0.39
68 18 0.19
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:36813 original size:29 final size:29
Alignment explanation
Indices: 36779--36850 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
36769 TATATTATGA
**
36779 TACATGACATGAATTTGTATTA-ATTGTAT
1 TACATGACATGAATTCATATTATA-TGTAT
36808 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTATATGTAT
36837 TACATGACATGAAT
1 TACATGACATGAAT
36851 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 39 0.98
30 1 0.03
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATATGTAT
Found at i:36907 original size:30 final size:31
Alignment explanation
Indices: 36865--36924 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
36855 AGAAAAAGTT
*
36865 ATATGCACTATGTGATAAAGGTATGTAAATG
1 ATATGCACTATGTGATAAAGGTATGGAAATG
*
36896 ATATGC-CTATGTGTTAAAGGTATGGAAAT
1 ATATGCACTATGTGATAAAGGTATGGAAAT
36925 ACTATGTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (31 bp):
ATATGCACTATGTGATAAAGGTATGGAAATG
Found at i:37204 original size:23 final size:22
Alignment explanation
Indices: 37144--37211 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
37134 TTATGGACAT
37144 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
37166 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
37188 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
37211 A
1 A
37212 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:37985 original size:21 final size:21
Alignment explanation
Indices: 37909--38010 Score: 84
Period size: 21 Copynumber: 4.9 Consensus size: 21
37899 TGAAGCAAGG
* * *
37909 GAAGCAAAGAGAGCAGTAGCG
1 GAAGCACAGAGAGAAGTAGCA
* *
37930 GAAGCAGAGAGAGCAA-CAGCA
1 GAAGCACAGAGAG-AAGTAGCA
*
37951 GAAGCAGAGAGAGAAGTAGC-
1 GAAGCACAGAGAGAAGTAGCA
* *
37971 GACAGCACAGAGAGAAGCAG-T
1 GA-AGCACAGAGAGAAGTAGCA
37992 GATAGCACAGAGAGAAGTA
1 GA-AGCACAGAGAGAAGTA
38011 ACATATCAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
20 4 0.06
21 63 0.93
22 1 0.01
ACGTcount: A:0.45, C:0.15, G:0.35, T:0.05
Consensus pattern (21 bp):
GAAGCACAGAGAGAAGTAGCA
Found at i:38004 original size:42 final size:42
Alignment explanation
Indices: 37909--38010 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 42
37899 TGAAGCAAGG
* *
37909 GAAGCAAAGAGAGCAGTAGCGGAAGCAGAGAGAGCAACAGCA
1 GAAGCAAAGAGAGAAGTAGCGGAAGCACAGAGAGCAACAGCA
* *
37951 GAAGCAGAGAGAGAAGTAGC-GACAGCACAGAGAG-AAGCAG-T
1 GAAGCAAAGAGAGAAGTAGCGGA-AGCACAGAGAGCAA-CAGCA
*
37992 GATAGCACAGAGAGAAGTA
1 GA-AGCAAAGAGAGAAGTA
38011 ACATATCAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
41 6 0.12
42 46 0.88
ACGTcount: A:0.45, C:0.15, G:0.35, T:0.05
Consensus pattern (42 bp):
GAAGCAAAGAGAGAAGTAGCGGAAGCACAGAGAGCAACAGCA
Found at i:38472 original size:44 final size:44
Alignment explanation
Indices: 38358--38475 Score: 164
Period size: 44 Copynumber: 2.7 Consensus size: 44
38348 AAATGATGCA
* * *
38358 ATATACCATACATGTAGCGGCGTTTGTATCCTAAAAACGCCGCT
1 ATATACCAGACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCT
* *
38402 ATATACCAGACCTTTAGCGGCTTTTGTATCCTAAAAACGCCGCT
1 ATATACCAGACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCT
* **
38446 ATATACCAGATCTATAGTTGCGTTTGTATC
1 ATATACCAGACCTATAGCGGCGTTTGTATC
38476 AAAAAATTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 65 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
ATATACCAGACCTATAGCGGCGTTTGTATCCTAAAAACGCCGCT
Found at i:38537 original size:43 final size:43
Alignment explanation
Indices: 38489--38661 Score: 217
Period size: 43 Copynumber: 4.0 Consensus size: 43
38479 AAATTCCACG
* **
38489 AAATCTCAACACCTATTGTGGCGTTTTTGAGAAAAACACCGCT
1 AAATCTCAACACATATTGTGGCGTTTTTGAGAAAAATGCCGCT
* * *
38532 AAATCTCAAAACTTATTGTGGCGTTTGTGAGAAAAATGCCGCT
1 AAATCTCAACACATATTGTGGCGTTTTTGAGAAAAATGCCGCT
*
38575 AAATCTCAACACATATTGTGGC-TTTTGTGGGAAAAATGCCGCT
1 AAATCTCAACACATATTGTGGCGTTTT-TGAGAAAAATGCCGCT
* *
38618 AAA-CATCAACACATATTGTGGCGTTTGT-ATGACAAATGCCGCT
1 AAATC-TCAACACATATTGTGGCGTTTTTGA-GAAAAATGCCGCT
38661 A
1 A
38662 TATATCGTCA
Statistics
Matches: 114, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
42 4 0.04
43 107 0.94
44 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (43 bp):
AAATCTCAACACATATTGTGGCGTTTTTGAGAAAAATGCCGCT
Found at i:41464 original size:26 final size:25
Alignment explanation
Indices: 41420--41471 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
41410 TTAATTAAGA
* *
41420 TTTAGGATATTATTTTAAATATTTT
1 TTTAGGATATTAGTTTAAATAGTTT
*
41445 TTTAGGTATTTTAGTTTAAATAGTTT
1 TTTAGG-ATATTAGTTTAAATAGTTT
41471 T
1 T
41472 AAGTGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (25 bp):
TTTAGGATATTAGTTTAAATAGTTT
Found at i:41471 original size:24 final size:25
Alignment explanation
Indices: 41420--41481 Score: 56
Period size: 26 Copynumber: 2.5 Consensus size: 25
41410 TTAATTAAGA
* * *
41420 TTTAGG-ATATTATTTTAAATATTTT
1 TTTAGGTATTTTAGTTTAAATA-TGT
41445 TTTAGGTATTTTAGTTTAAATA-GT
1 TTTAGGTATTTTAGTTTAAATATGT
* *
41469 TTTAAGTGTTTTA
1 TTTAGGTATTTTA
41482 ATTAGGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 12 0.39
25 6 0.19
26 13 0.42
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (25 bp):
TTTAGGTATTTTAGTTTAAATATGT
Found at i:42719 original size:23 final size:23
Alignment explanation
Indices: 42681--42734 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
42671 TTCCTAGTGG
*
42681 CGGGACTACGTTTCAATTAAAGA
1 CGGGACTCCGTTTCAATTAAAGA
*
42704 CGGTACTCCGTTTCAATTAAAGA
1 CGGGACTCCGTTTCAATTAAAGA
42727 CGGGACTC
1 CGGGACTC
42735 ATTCATCTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
CGGGACTCCGTTTCAATTAAAGA
Found at i:44498 original size:2 final size:2
Alignment explanation
Indices: 44493--44527 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
44483 TTTTTAACTT
44493 TA TA TA 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 TA TA TA T
44528 TATTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46426 original size:19 final size:20
Alignment explanation
Indices: 46381--46426 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
46371 AATAATAATA
*
46381 TTAATTTTTTTGTAATTTTT
1 TTAAATTTTTTGTAATTTTT
* *
46401 CT-GATTTTTTGT-ATTTTT
1 TTAAATTTTTTGTAATTTTT
46419 TTAAATTT
1 TTAAATTT
46427 GTAAAATTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
18 7 0.35
19 12 0.60
20 1 0.05
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (20 bp):
TTAAATTTTTTGTAATTTTT
Found at i:48522 original size:22 final size:22
Alignment explanation
Indices: 48497--48547 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
48487 ACTAGTTCGA
48497 ATAGTGGTGTTTGAGTGGGATT
1 ATAGTGGTGTTTGAGTGGGATT
48519 ATAGTGGTGTTTGAGTGGGATT
1 ATAGTGGTGTTTGAGTGGGATT
48541 ATAGTGG
1 ATAGTGG
48548 AGTAGGTTCA
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:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (22 bp):
ATAGTGGTGTTTGAGTGGGATT
Found at i:48982 original size:14 final size:17
Alignment explanation
Indices: 48951--48987 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
48941 AAATATATTA
48951 ATAATAATCATAATAAT
1 ATAATAATCATAATAAT
48968 ATAATAAT-AT-A-AAT
1 ATAATAATCATAATAAT
48982 ATAATA
1 ATAATA
48988 TTTTTATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 2 0.10
17 8 0.40
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATCATAATAAT
Found at i:49524 original size:42 final size:42
Alignment explanation
Indices: 49450--49544 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
49440 ATGAATGGCC
* * *
49450 CGAAGGACTT-ATCATCTTGCTCGAAAGGCTTACAGATGACA
1 CGAAGGACTTAAGCATCATGCTCGAAAGACTTACAGATGACA
* * * *
49491 CGAAGGATTTAAGCATCATGCTTGAAAGACTTACTGATGACC
1 CGAAGGACTTAAGCATCATGCTCGAAAGACTTACAGATGACA
49533 CGAAGGACTTAA
1 CGAAGGACTTAA
49545 AAATCAAGAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 9 0.20
42 36 0.80
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (42 bp):
CGAAGGACTTAAGCATCATGCTCGAAAGACTTACAGATGACA
Found at i:49777 original size:90 final size:90
Alignment explanation
Indices: 49624--50189 Score: 911
Period size: 90 Copynumber: 6.3 Consensus size: 90
49614 TGGATGTCCC
* *
49624 ATGGATGTCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
1 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
49689 GAAAACATCCTGCACTGAAGGTCTT
66 GAAAACATCCTGCACTGAAGGTCTT
* *
49714 ATGGATGTCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
1 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
49779 GAAAACATCCTGCACTGAAGGTCTT
66 GAAAACATCCTGCACTGAAGGTCTT
**
49804 ATGGATGACCAAAAGGACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTT
1 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
* *
49868 GAAAACATCATGTACTGAAGGTCTT
66 GAAAACATCCTGCACTGAAGGTCTT
* * *
49893 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTACTTTTTTAAATCTCATTT
1 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
* *
49958 GAAATCATCCTGCACTGAAGGTATT
66 GAAAACATCCTGCACTGAAGGTCTT
* * *
49983 ATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAAATCTCATTT
1 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
* *
50048 GAAATCATCTTGCACTGAAGGTCTT
66 GAAAACATCCTGCACTGAAGGTCTT
* *
50073 ATGGATGA-CCGAAGGACTTACAAACCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTT
1 ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
*
50137 GAAATCATCCTGCACTGAAGGTCTT
66 GAAAACATCCTGCACTGAAGGTCTT
* *
50162 ATGGATGGCCCGAAGGACTTACACATCA
1 ATGGATGACCCGAAGGACTTACAAATCA
50190 TGCTCGAAAG
Statistics
Matches: 448, Mismatches: 26, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
89 170 0.38
90 278 0.62
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (90 bp):
ATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
GAAAACATCCTGCACTGAAGGTCTT
Found at i:49925 original size:179 final size:179
Alignment explanation
Indices: 49624--50189 Score: 936
Period size: 179 Copynumber: 3.2 Consensus size: 179
49614 TGGATGTCCC
*
49624 ATGGATGTCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTT
1 ATGGATGGCCCAAAGGACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTT
* * *
49689 GAAAACATCCTGCACTGAAGGTCTTATGGATGTCCCAAAGGACTTACAAATCAAGAAACCCCCGA
65 GAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGA
* *
49754 AGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTT
130 AGGCTTAGTTTCTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTCTT
* *
49804 ATGGATGACCAAAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
1 ATGGATGGCCCAAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
*
49869 AAAACATCATGTACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAA
66 AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAA
* * *
49934 GGCTTACTTTTTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTATT
131 GGCTTAGTTTCTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTCTT
* *
49983 ATGGATGGCCCGAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAAATCTCATTT
1 ATGGATGGCCCAAAGGACTTACAAATCAAGAAACCC-CGAAGGCTTAGTTTCTAAAATCTCATTT
* * *
50048 GAAATCATCTTGCACTGAAGGTCTTATGGATGA-CCGAAGGACTTACAAACCAAGAAACCCCCGA
65 GAAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGA
50112 AGGCTTAGTTTCTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTCTT
130 AGGCTTAGTTTCTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTCTT
* *
50162 ATGGATGGCCCGAAGGACTTACACATCA
1 ATGGATGGCCCAAAGGACTTACAAATCA
50190 TGCTCGAAAG
Statistics
Matches: 362, Mismatches: 23, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
179 274 0.76
180 88 0.24
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (179 bp):
ATGGATGGCCCAAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTG
AAAACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAA
GGCTTAGTTTCTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTCTT
Found at i:50050 original size:269 final size:268
Alignment explanation
Indices: 49526--50189 Score: 986
Period size: 269 Copynumber: 2.4 Consensus size: 268
49516 AAGACTTACT
* *
49526 GATGACCCGAAGGACTTAAAAATCAAGAAACCTTCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGA-CCGAAGGACTTACAAATCAAGAAACC-CCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
* *
49591 AACATCATGCATTGAAGGTCTTATGGATGTCCCATGGATGTCCCAAAGGACTTACAAATCAAGAA
64 AACATCATGCACTGAAGGTCTTAT-G--G----AT-GA---CCCGAAGGACTTACAAATCAAGAA
* *
49656 ACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATG
118 ACCCCCGAAGGCTTACTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTATTATGGATG
*
49721 TCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACA
183 GCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACA
49786 TCCTGCACTGAAGGTCTTATG
248 TCCTGCACTGAAGGTCTTATG
*
49807 GATGACCAAAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAA
1 GATGACC-GAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAA
*
49872 ACATCATGTACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
65 ACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGC
* * * *
49937 TTACTTTTTTAAATCTCATTTGAAATCATCCTGCACTGAAGGTATTATGGATGGCCCGAAGGACT
130 TTACTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTATTATGGATGGCCCAAAGGACT
* * * *
50002 TACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAAATCTCATTTGAAATCATCTTGCACTGAA
195 TACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAA
50067 GGTCTTATG
260 GGTCTTATG
* *
50076 GATGACCGAAGGACTTACAAACCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAAA
1 GATGACCGAAGGACTTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAA
* * * *
50141 TCATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTACACATCA
65 ACATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCA
50190 TGCTCGAAAG
Statistics
Matches: 356, Mismatches: 25, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
268 20 0.06
269 248 0.70
272 2 0.01
273 2 0.01
277 1 0.00
279 1 0.00
280 55 0.15
281 27 0.08
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (268 bp):
GATGACCGAAGGACTTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAA
CATCATGCACTGAAGGTCTTATGGATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCT
TACTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTATTATGGATGGCCCAAAGGACTT
ACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAG
GTCTTATG
Found at i:50222 original size:20 final size:20
Alignment explanation
Indices: 50165--50226 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
50155 AGGTCTTATG
50165 GATGGCCCGAAGGACTTACACAT
1 GATGGCCCGAAGGACTT--AC-T
* * *
50188 CAT-GCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTTACT
50207 GATGGCCCGAAGGACTTACT
1 GATGGCCCGAAGGACTTACT
50227 CATCAAGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.09
20 16 0.50
22 11 0.34
23 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.21
Consensus pattern (20 bp):
GATGGCCCGAAGGACTTACT
Found at i:50379 original size:43 final size:43
Alignment explanation
Indices: 50265--50412 Score: 210
Period size: 43 Copynumber: 3.5 Consensus size: 43
50255 AGTTTCTTAG
*
50265 TTGTCACCAAGGAACCCCTACATATCACGTTGGTCCCTCAAG-
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
* * *
50307 -TGTTCATTAATGAACCCCTACATATCACGTTGATCCCTCAAGC
1 TTG-TCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
** *
50350 TTGTCATCAAGGAACCCCTACATATCACGTTGGTATCTAAAGC
1 TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
50393 TTGTCATCAAGGAACCCCTA
1 TTGTCATCAAGGAACCCCTA
50413 AAAATTAGGC
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 2 0.02
42 35 0.38
43 54 0.58
44 2 0.02
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (43 bp):
TTGTCATCAAGGAACCCCTACATATCACGTTGGTCCCTCAAGC
Found at i:52563 original size:9 final size:9
Alignment explanation
Indices: 52549--52688 Score: 94
Period size: 9 Copynumber: 16.8 Consensus size: 9
52539 TTGATTCATT
52549 TTCTTTTTC
1 TTCTTTTTC
*
52558 TTCTTTTCTT
1 TTCTTTT-TC
*
52568 TTCTTTTTT
1 TTCTTTTTC
*
52577 TTCTCTTT-
1 TTCTTTTTC
*
52585 TTC-TCTT-
1 TTCTTTTTC
52592 TT-TTTTTC
1 TTCTTTTTC
52600 -TCTTTTTTC
1 TTC-TTTTTC
52609 TT-TTTTT-
1 TTCTTTTTC
52616 TTCTTTTTCC
1 TTCTTTTT-C
52626 TT-TTTTTCC
1 TTCTTTTT-C
52635 TT-TTTTTC
1 TTCTTTTTC
52643 TT-TTTTT-
1 TTCTTTTTC
52650 TTC-TTTTC
1 TTCTTTTTC
52658 -TCTTTTTC
1 TTCTTTTTC
*
52666 TTCTTTCTC
1 TTCTTTTTC
52675 TT-TTTTTC
1 TTCTTTTTC
52683 TT-TTTT
1 TTCTTTT
52689 CTCGAAGAAC
Statistics
Matches: 111, Mismatches: 7, Indels: 27
0.77 0.05 0.19
Matches are distributed among these distances:
7 18 0.16
8 37 0.33
9 45 0.41
10 11 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (9 bp):
TTCTTTTTC
Found at i:52566 original size:8 final size:7
Alignment explanation
Indices: 52547--52690 Score: 105
Period size: 8 Copynumber: 18.9 Consensus size: 7
52537 TCTTGATTCA
52547 TTTTC-T
1 TTTTCTT
52553 TTTTCTT
1 TTTTCTT
52560 CTTTTCTT
1 -TTTTCTT
52568 TTCTT-TT
1 TT-TTCTT
52575 TTTTCTCT
1 TTTTCT-T
52583 TTTTCTCT
1 TTTTCT-T
52591 TTTT-TT
1 TTTTCTT
*
52597 TTCTCTT
1 TTTTCTT
52604 TTTTCTTTTT
1 TTTTC---TT
52614 TTTTCTT
1 TTTTCTT
*
52621 TTTCCTTT
1 TTTTC-TT
52629 TTTTCCTTT
1 TTTT-C-TT
52638 TTTTCTT
1 TTTTCTT
*
52645 TTTTTTT
1 TTTTCTT
52652 CTTTTCTCT
1 -TTTTCT-T
52661 TTTTCTT
1 TTTTCTT
52668 CTTTCTCTTT
1 -TTT-TC-TT
52678 TTTTCTT
1 TTTTCTT
52685 TTTTCT
1 TTTTCT
52691 CGAAGAACTC
Statistics
Matches: 116, Mismatches: 6, Indels: 31
0.76 0.04 0.20
Matches are distributed among these distances:
6 11 0.09
7 38 0.33
8 44 0.38
9 14 0.12
10 9 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:52575 original size:1 final size:1
Alignment explanation
Indices: 52547--52688 Score: 50
Period size: 1 Copynumber: 142.0 Consensus size: 1
52537 TCTTGATTCA
* * * * * * * * * * * *
52547 TTTTCTTTTTCTTCTTTTCTTTTCTTTTTTTTCTCTTTTTCTCTTTTTTTTTCTCTTTTTTCTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** ** * * * * * * * *
52612 TTTTTTCTTTTTCCTTTTTTTCCTTTTTTTCTTTTTTTTTCTTTTCTCTTTTTCTTCTTTCTCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
52677 TTTTTCTTTTTT
1 TTTTTTTTTTTT
52689 CTCGAAGAAC
Statistics
Matches: 93, Mismatches: 48, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
1 93 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (1 bp):
T
Found at i:52674 original size:73 final size:74
Alignment explanation
Indices: 52547--52688 Score: 204
Period size: 74 Copynumber: 1.9 Consensus size: 74
52537 TCTTGATTCA
*
52547 TTTTCTTTTTCTTCTTTTCTTTTCTTTTTTTTCTCTTTTTCTCTTTTTTTTTCTC-TTTTTTCTT
1 TTTTCTTTTTCTTCCTTTCTTTTCTTTTTTTTCTCTTTTTCTCTTTTTTTTTCTCTTTTTTTCTT
52611 TTTTTTTCT
66 TTTTTTTCT
52620 TTTTCCTTTTT-TTCCTTT-TTTTCTTTTTTTT-TC-TTTTCTCTTTTTCTTCTTTCTCTTTTTT
1 TTTT-CTTTTTCTTCCTTTCTTTTCTTTTTTTTCTCTTTTTCTC-TTTT-TT-TTTCTCTTTTTT
52681 TCTTTTTT
62 TCTTTTTT
52689 CTCGAAGAAC
Statistics
Matches: 63, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
70 7 0.11
71 6 0.10
72 15 0.24
73 16 0.25
74 19 0.30
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (74 bp):
TTTTCTTTTTCTTCCTTTCTTTTCTTTTTTTTCTCTTTTTCTCTTTTTTTTTCTCTTTTTTTCTT
TTTTTTTCT
Found at i:52679 original size:64 final size:66
Alignment explanation
Indices: 52547--52687 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 66
52537 TCTTGATTCA
* * *
52547 TTTTCTTTTTCTTCTTTTCTTTTCTTTTTTTTCTCTTTTTCTCTTTTTTTTTCTCTTTTTTCTTT
1 TTTTCTTTTTC-TCTTTTCTTTTCCTTTTTTTCTCTTTTTCTCTTTTTTTTTCTCTTCTTTCTCT
52612 TT
65 TT
* *
52614 TTTTCTTTTTC-C-TTT-TTTTCCTTTTTTTCTTTTTTTTTCTTTTCTCTTTT-TCTTCTTTCTC
1 TTTTCTTTTTCTCTTTTCTTTTCCTTTTTTTCTCTTTTTCTCTTTT-T-TTTTCTCTTCTTTCTC
52675 TTT
64 TTT
52678 TTTTCTTTTT
1 TTTTCTTTTT
52688 TCTCGAAGAA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
63 25 0.37
64 26 0.39
65 5 0.07
67 11 0.16
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (66 bp):
TTTTCTTTTTCTCTTTTCTTTTCCTTTTTTTCTCTTTTTCTCTTTTTTTTTCTCTTCTTTCTCTT
T
Found at i:52691 original size:17 final size:17
Alignment explanation
Indices: 52550--52691 Score: 125
Period size: 17 Copynumber: 8.1 Consensus size: 17
52540 TGATTCATTT
*
52550 TCTTTTTCTTCTTTTCTTT
1 TCTTTTT-TTCTTTT-TTC
52569 TCTTTTTTTTCTCTTTTTC
1 TC-TTTTTTTCT-TTTTTC
52588 TCTTTTTTTTTCTCTTTTT-
1 TC--TTTTTTTCT-TTTTTC
*
52607 TCTTTTTTTTTCTTTTTC
1 TCTTTTTTTCT-TTTTTC
52625 -CTTTTTTTCCTTTTTT-
1 TCTTTTTTT-CTTTTTTC
52641 TCTTTTTTT-TTCTTTTC
1 TCTTTTTTTCTT-TTTTC
*
52658 TC--TTTTTCTTCTTTC
1 TCTTTTTTTCTTTTTTC
52673 TCTTTTTTTCTTTTTTC
1 TCTTTTTTTCTTTTTTC
52690 TC
1 TC
52692 GAAGAACTCT
Statistics
Matches: 107, Mismatches: 5, Indels: 24
0.79 0.04 0.18
Matches are distributed among these distances:
15 13 0.12
16 6 0.06
17 51 0.48
18 1 0.01
19 12 0.11
20 24 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTTTTTTTCTTTTTTC
Found at i:55405 original size:12 final size:12
Alignment explanation
Indices: 55384--55421 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
55374 AATTATGCAA
*
55384 ATATGTAAATGC
1 ATATGCAAATGC
55396 ATATGCAAATGC
1 ATATGCAAATGC
55408 ATATGCAAAATGC
1 ATATGC-AAATGC
55421 A
1 A
55422 AAGATGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
ATATGCAAATGC
Found at i:58604 original size:22 final size:22
Alignment explanation
Indices: 58576--58618 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
58566 TCTAGTTCGA
*
58576 ATAGTGGTGTTTGAGTGGGATT
1 ATAGTGGGGTTTGAGTGGGATT
*
58598 ATAGTGGGGTTTGATTGGGAT
1 ATAGTGGGGTTTGAGTGGGAT
58619 AGTGGGGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.40
Consensus pattern (22 bp):
ATAGTGGGGTTTGAGTGGGATT
Found at i:59630 original size:3 final size:3
Alignment explanation
Indices: 59622--59658 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
59612 CCTGCAAAAT
* *
59622 ATA ATA ATA ATA ACA TTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
59659 ATATAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:59664 original size:15 final size:15
Alignment explanation
Indices: 59618--59669 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
59608 ATGGCCTGCA
59618 AAATATAATAATAAT
1 AAATATAATAATAAT
59633 AACAT-TAATAATAAT
1 AA-ATATAATAATAAT
59648 -AATAATAATAA-ATAT
1 AAAT-ATAATAATA-AT
59663 AAATATA
1 AAATATA
59670 GTATTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 2 0.06
15 23 0.72
16 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATATAATAATAAT
Done.