Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001080.1 Hibiscus syriacus cultivar Beakdansim tig00002139_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: 201579
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:9234 original size:12 final size:12
Alignment explanation
Indices: 9217--9241 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9207 ATTTTCCTTA
9217 GATAAAGTTCTT
1 GATAAAGTTCTT
9229 GATAAAGTTCTT
1 GATAAAGTTCTT
9241 G
1 G
9242 TTACTTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (12 bp):
GATAAAGTTCTT
Found at i:16935 original size:16 final size:16
Alignment explanation
Indices: 16914--16954 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
16904 CACCGACAAC
16914 ACAATCACCCAAAGAT
1 ACAATCACCCAAAGAT
*
16930 ACAATCACCCAAGGAT
1 ACAATCACCCAAAGAT
16946 ACAATCACC
1 ACAATCACC
16955 GTCACTAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.34, G:0.07, T:0.12
Consensus pattern (16 bp):
ACAATCACCCAAAGAT
Found at i:17900 original size:94 final size:95
Alignment explanation
Indices: 17777--17961 Score: 295
Period size: 95 Copynumber: 2.0 Consensus size: 95
17767 TCGTAGTGTC
* *
17777 AGAGATTCGAAGATACTTCTAAATCTTTT-AAAAGTATG-GA-ATGCAAAAATAATATGGAGAAT
1 AGAGATTCGAAGATACTTCTAAATCTTTTAAAAAATATGAGACA--AAAAAATAATATGGAGAAT
*
17839 CCTTGGCGAGTATACAATCTTAAACTTATATT
64 CCTTGGCGAGTAGACAATCTTAAACTTATATT
*
17871 AGAGATTCGAAGATACTTCTAAATCTTTTAAAAAATATGAGACAAAAAAATAATATGGAGGATCC
1 AGAGATTCGAAGATACTTCTAAATCTTTTAAAAAATATGAGACAAAAAAATAATATGGAGAATCC
17936 TTGGCGAGTAGACAATCTTAAACTTA
66 TTGGCGAGTAGACAATCTTAAACTTA
17962 GATTTTTAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
94 29 0.35
95 52 0.62
96 2 0.02
97 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (95 bp):
AGAGATTCGAAGATACTTCTAAATCTTTTAAAAAATATGAGACAAAAAAATAATATGGAGAATCC
TTGGCGAGTAGACAATCTTAAACTTATATT
Found at i:19068 original size:20 final size:21
Alignment explanation
Indices: 19043--19094 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
19033 GACCAACAAA
19043 TTCGCAACGCGA-TCTCCAAT
1 TTCGCAACGCGAGTCTCCAAT
* *
19063 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGAGTCTCCAAT
*
19083 TTCGCAATGCGA
1 TTCGCAACGCGA
19095 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.27
Consensus pattern (21 bp):
TTCGCAACGCGAGTCTCCAAT
Found at i:19130 original size:21 final size:21
Alignment explanation
Indices: 19104--19149 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
19094 AATATGTAAA
*
19104 TCGCGTTGCGATTTTCCAAAT
1 TCGCGTTGCGATATTCCAAAT
19125 TCGCGTTGCGATATTCCAAAT
1 TCGCGTTGCGATATTCCAAAT
19146 TCGC
1 TCGC
19150 AACGCGATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATATTCCAAAT
Found at i:19166 original size:20 final size:20
Alignment explanation
Indices: 19141--19205 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
19131 TGCGATATTC
*
19141 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
* *
19161 CAAATTCTCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
19181 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
19201 CAAAT
1 CAAAT
19206 ATTTTTAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:19405 original size:22 final size:22
Alignment explanation
Indices: 19333--19402 Score: 104
Period size: 22 Copynumber: 3.2 Consensus size: 22
19323 ATACGGCGAC
19333 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
19355 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
* * * *
19377 ATTCGTCCCCATTTCCGATGAA
1 ATCCATCCCCATCTCCGACGAA
19399 ATCC
1 ATCC
19403 GTCTATCTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.26, C:0.41, G:0.10, T:0.23
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:19637 original size:13 final size:13
Alignment explanation
Indices: 19619--19650 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
19609 AGTATTTGTC
19619 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
19632 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
19645 TTTGTT
1 TTTGTT
19651 GAAGAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:19739 original size:20 final size:20
Alignment explanation
Indices: 19698--19739 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19688 GAAACTAAAA
* * *
19698 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
19718 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
19738 TC
1 TC
19740 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:21907 original size:21 final size:21
Alignment explanation
Indices: 21883--21938 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
21873 TAAGCTCAAT
21883 GCACCTATCATCATTCAAGAG
1 GCACCTATCATCATTCAAGAG
* * *
21904 GCACCTCTTATCGTTCAAGAG
1 GCACCTATCATCATTCAAGAG
* *
21925 TCCCCTATCATCAT
1 GCACCTATCATCAT
21939 CGAAGAAGCC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.32, G:0.12, T:0.29
Consensus pattern (21 bp):
GCACCTATCATCATTCAAGAG
Found at i:23437 original size:61 final size:64
Alignment explanation
Indices: 23354--23495 Score: 157
Period size: 67 Copynumber: 2.2 Consensus size: 64
23344 TTTTACATTG
23354 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-ATTTATTTT-TTGATTAATTGATTTATA
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTTATTTTCTTGATTAATTGATTTATA
* ** * * *
23415 AAAGTTGATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTTGCTTGTTTAATTGATTT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAG-A--ATTTATTTT-CTTGATTAATTGATTT
*
23479 GTA
62 ATA
23482 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
23496 GTTTCTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
61 26 0.39
62 3 0.04
65 8 0.12
67 30 0.45
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (64 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTTATTTTCTTGATTAATTGATTTATA
Found at i:23919 original size:25 final size:24
Alignment explanation
Indices: 23891--23944 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 24
23881 TTGTGATTGA
23891 GATTTTGATTTTGATTGCGATTTTT
1 GATTTTGATTTTGATTGCGA-TTTT
23916 GATTTTGATTTTGATTGCGATTTT
1 GATTTTGATTTTGATTGCGATTTT
23940 GATTT
1 GATTT
23945 CCTTTTGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 9 0.31
25 20 0.69
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (24 bp):
GATTTTGATTTTGATTGCGATTTT
Found at i:23921 original size:7 final size:6
Alignment explanation
Indices: 23891--23944 Score: 63
Period size: 6 Copynumber: 8.8 Consensus size: 6
23881 TTGTGATTGA
** **
23891 GATTTT GATTTT GATTGC GATTTTT GATTTT GATTTT GATTGC GATTTT
1 GATTTT GATTTT GATTTT GA-TTTT GATTTT GATTTT GATTTT GATTTT
23940 GATTT
1 GATTT
23945 CCTTTTGCTT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 35 0.90
7 4 0.10
ACGTcount: A:0.17, C:0.04, G:0.20, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:23944 original size:18 final size:19
Alignment explanation
Indices: 23884--23925 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
23874 AAGCCGGTTG
23884 TGATTGAGA-TTTTGATTT
1 TGATTGAGATTTTTGATTT
*
23902 TGATTGCGATTTTTGATTT
1 TGATTGAGATTTTTGATTT
23921 TGATT
1 TGATT
23926 TTGATTGCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.57
Consensus pattern (19 bp):
TGATTGAGATTTTTGATTT
Found at i:25836 original size:24 final size:24
Alignment explanation
Indices: 25802--25855 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
25792 CCATCACATC
25802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
25826 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
25850 ATCAAA
1 ATCAAA
25856 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:25869 original size:24 final size:24
Alignment explanation
Indices: 25802--25869 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
25792 CCATCACATC
* * *
25802 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
25826 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
25850 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
25870 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:26003 original size:12 final size:12
Alignment explanation
Indices: 25982--26015 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
25972 GGTTGTGGGT
*
25982 TTTGAGATTGTG
1 TTTGATATTGTG
25994 TTTGATATTGTG
1 TTTGATATTGTG
*
26006 TTTGGTATTG
1 TTTGATATTG
26016 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:26798 original size:20 final size:20
Alignment explanation
Indices: 26762--26932 Score: 98
Period size: 20 Copynumber: 8.6 Consensus size: 20
26752 ACTAAAACCT
*
26762 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
26781 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
* ** * *
26800 ATTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGC
*
26820 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
* *
26840 GTTACGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
*** ** *
26861 AACGCGAATTACATATTCGC
1 GTTGCGAATTTGAAATTCGC
* * *
26881 GTTGCGAAATTGGAAACT-GT
1 GTTGCG-AATTTGAAATTCGC
* *
26901 TTTGCGAAATTGAAATTCGC
1 GTTGCGAATTTGAAATTCGC
26921 GTTGCGAATTTG
1 GTTGCGAATTTG
26933 TTGGTCATTT
Statistics
Matches: 107, Mismatches: 38, Indels: 13
0.68 0.24 0.08
Matches are distributed among these distances:
19 33 0.31
20 55 0.51
21 18 0.17
22 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:46896 original size:22 final size:23
Alignment explanation
Indices: 46871--46915 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
46861 TCACCACAGC
46871 TCGTATA-AAACGCACCGAAGTG
1 TCGTATAGAAACGCACCGAAGTG
* * *
46893 TCGTGTAGAAATGCACTGAAGTG
1 TCGTATAGAAACGCACCGAAGTG
46916 CCACATAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (23 bp):
TCGTATAGAAACGCACCGAAGTG
Found at i:47013 original size:23 final size:23
Alignment explanation
Indices: 46916--47013 Score: 112
Period size: 23 Copynumber: 4.4 Consensus size: 23
46906 CACTGAAGTG
*
46916 CCACATAGA-ATGTCCCGAAGGA
1 CCACATAGAGTTGTCCCGAAGGA
* *
46938 CCACATATA--TGTTCCGAAGGA
1 CCACATAGAGTTGTCCCGAAGGA
* *
46959 CCACGTAGAGTTATCCCGAAGGA
1 CCACATAGAGTTGTCCCGAAGGA
*
46982 CCACGTAGAGTTGTCCCGAAGGA
1 CCACATAGAGTTGTCCCGAAGGA
*
47005 CCGCATAGA
1 CCACATAGA
47014 ACCCTCGACT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 18 0.28
22 8 0.12
23 39 0.60
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (23 bp):
CCACATAGAGTTGTCCCGAAGGA
Found at i:47269 original size:25 final size:25
Alignment explanation
Indices: 47241--47291 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
47231 AAGACGTATT
*
47241 TACACAATACAAATCATAATCATGC
1 TACACAATACAAATAATAATCATGC
47266 TACACAATACAAATAATAATCATGC
1 TACACAATACAAATAATAATCATGC
47291 T
1 T
47292 TATGCTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.04, T:0.25
Consensus pattern (25 bp):
TACACAATACAAATAATAATCATGC
Found at i:54027 original size:22 final size:23
Alignment explanation
Indices: 53970--54017 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
53960 AGCTCGTATA
*
53970 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
53993 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
54016 AA
1 AA
54018 TGTTCCGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.25, G:0.23, T:0.12
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:54884 original size:20 final size:20
Alignment explanation
Indices: 54836--54885 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
54826 TTGGCTTATG
54836 GTATCGATACTATACAACCA
1 GTATCGATACTATACAACCA
* *
54856 GTTTCGATACTGTACAACCA
1 GTATCGATACTATACAACCA
*
54876 GTATAGATAC
1 GTATCGATAC
54886 CCAAACCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (20 bp):
GTATCGATACTATACAACCA
Found at i:63630 original size:29 final size:30
Alignment explanation
Indices: 63578--63670 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 30
63568 TTCTGTTAAT
*
63578 ATTAATTTTGAGGACTAAAATG-AATTTTA
1 ATTAAGTTTGAGGACTAAAATGAAATTTTA
* **
63607 ATTAAGTTTGGGGACTAAGTTGAAATTTTA
1 ATTAAGTTTGAGGACTAAAATGAAATTTTA
* * * *
63637 GTGAAATTT-ATGGACT-AAATGAAATTATA
1 ATTAAGTTTGA-GGACTAAAATGAAATTTTA
63666 ATTAA
1 ATTAA
63671 AATTGGATTT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
29 31 0.63
30 18 0.37
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (30 bp):
ATTAAGTTTGAGGACTAAAATGAAATTTTA
Found at i:64417 original size:17 final size:16
Alignment explanation
Indices: 64395--64428 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
64385 TGACTGTCGT
*
64395 CGTTGACTGGTGTCTTA
1 CGTTGACCGGTGT-TTA
64412 CGTTGACCGGTGTTTA
1 CGTTGACCGGTGTTTA
64428 C
1 C
64429 CTTTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.21, G:0.29, T:0.38
Consensus pattern (16 bp):
CGTTGACCGGTGTTTA
Found at i:71992 original size:20 final size:20
Alignment explanation
Indices: 71963--72002 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
71953 TATTTAGCCA
* *
71963 CCGATGAACGGTGGCCGGCG
1 CCGATCAACGGCGGCCGGCG
71983 CCGATCAACGGCGGCCGGCG
1 CCGATCAACGGCGGCCGGCG
72003 AGGTGGCCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.35, G:0.42, T:0.07
Consensus pattern (20 bp):
CCGATCAACGGCGGCCGGCG
Found at i:72961 original size:23 final size:23
Alignment explanation
Indices: 72935--72998 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
72925 TTACTTCCCC
72935 TTTTTTTTATTATTTTTGATTAT
1 TTTTTTTTATTATTTTTGATTAT
* * *
72958 TTTTTCTTATCT-TATTTGTTTAT
1 TTTTTTTTAT-TATTTTTGATTAT
72981 TTATTTATTTATTATTTT
1 TT-TTT-TTTATTATTTT
72999 CTTCTCTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 20 0.62
24 5 0.16
25 7 0.22
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (23 bp):
TTTTTTTTATTATTTTTGATTAT
Found at i:84472 original size:105 final size:105
Alignment explanation
Indices: 84260--85075 Score: 1207
Period size: 106 Copynumber: 7.8 Consensus size: 105
84250 GGAGGATATC
* ** * * *
84260 ACTCAAGACAACATAAGTTCAACTTCACAACGAAGGAACGGCTGGTTGTCAAC-A-AA-----CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
* **
84318 ATTTCGGAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
84358 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAAGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
84423 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
84463 ACTCAAGACAACGCAAATTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCC
84528 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
84569 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGAGACCGCTGGTTGTGAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCC
*
84634 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
84675 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCC
* * *
84740 AATTTCAAAGCCAATTTCAACTTCACAGCAAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
84781 ACTCCAGACAACGCAAGTTCGACTTCACGACGAAGGGACCGCTAGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
84846 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
84886 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
*
84951 ATTTCAGAGCCAATTTCAACTTCACAGA-GAAGGATATTAG
66 ATTTCAGAGCCAATTTCAACTTCACA-ACGAAGGATATTGG
* **
84991 ACTCCAGACAACGCAAGTTCAACTTCACGACGATGGGACCGCTGGTTGTCAACGAACATTTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCC
*
85056 AATTTCAGAGACAATTTCAA
65 AATTTCAGAGCCAATTTCAA
85076 AGGATATTAG
Statistics
Matches: 658, Mismatches: 50, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
98 45 0.07
99 1 0.00
100 2 0.00
105 287 0.44
106 323 0.49
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:87065 original size:5 final size:5
Alignment explanation
Indices: 87055--87080 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
87045 TATATATATA
87055 TGTTT TGTTT TGTTT TGTTT TGTTT T
1 TGTTT TGTTT TGTTT TGTTT TGTTT T
87081 ATATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TGTTT
Found at i:87504 original size:10 final size:10
Alignment explanation
Indices: 87474--87498 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
87464 ACTTCCCTTT
87474 TTTTTGATTA
1 TTTTTGATTA
87484 TTTTTGATTA
1 TTTTTGATTA
87494 TTTTT
1 TTTTT
87499 TCTTATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (10 bp):
TTTTTGATTA
Found at i:105308 original size:325 final size:326
Alignment explanation
Indices: 104657--105312 Score: 1188
Period size: 326 Copynumber: 2.0 Consensus size: 326
104647 AACCTGTACA
*
104657 AACATCACAAAGAATTTCACATGGTTTGTTCAAGCATAAAATCAGAGGGAGTATCCAAAGATCAT
1 AACATCACAAAGAATTTCACATGGTTTGTTCAAGCATAAAATCAGAGGAAGTATCCAAAGATCAT
* * * *
104722 ATTAAACTTCGTGTTTTCCCTTTTTCCTTAGATGATTTAGCTAAGGATTGGTTTTTTTATTTACT
66 ATTAAACTTCGTGTTTTCCCTTTTTCCTTAGATGATTTAGCTAACGATTAGTTGTTTTATTTACC
104787 GCCTAATTTCGTTACTACATAGGTTTAACCTATTTTATTAAAAAAATATTAATATTAAATATCGC
131 GCCTAATTTCGTTACTACATAGGTTTAACCTATTTTATTAAAAAAATATTAATATTAAATATCGC
*
104852 AACCTATTTCTTAGTGAGCCATGACATTCTTGGGCGCAACCATATTTCTTATAATCGTTCATAAC
196 AACCTATTTCTTAGTGAGCCATGACATTCTTCGGCGCAACCATATTTCTTATAATCGTTCATAAC
*
104917 ATTTTCAACTTTTAACTTATTTTCCTATCATGGAAAATTTAAGGCTCCATCAACTAAAATTCTGA
261 ATTTTCAACTCTTAACTTATTTTCCTATCATGGAAAATTTAAGGCTCCATCAACTAAAATTCTGA
104982 T
326 T
* *
104983 AACATCACACAGAATTTCACATGGTTTGTTCAAGCATAAAATTAGAGGAAGTATCCAAAGATCAT
1 AACATCACAAAGAATTTCACATGGTTTGTTCAAGCATAAAATCAGAGGAAGTATCCAAAGATCAT
*
105048 ATTAAACTTCGTGTTTTCCCTTTTTCCTTAGCTGATTTAGCTAACGATTAGTTGTTTTATTTACC
66 ATTAAACTTCGTGTTTTCCCTTTTTCCTTAGATGATTTAGCTAACGATTAGTTGTTTTATTTACC
* *
105113 GTCTAATTTCGTTACTACATAGGTTTAACCTATTTTATT-AAAAAATATTAATATTAAATATCTC
131 GCCTAATTTCGTTACTACATAGGTTTAACCTATTTTATTAAAAAAATATTAATATTAAATATCGC
105177 AACCTATTTCTTAGTGAGCCATGACATTCTTCGGCGCAACCATATTTCTTATAATCGTTCATAAC
196 AACCTATTTCTTAGTGAGCCATGACATTCTTCGGCGCAACCATATTTCTTATAATCGTTCATAAC
*
105242 ATTTTCAACTCTTAACTTATTTTCCTATCATGGAAAATTTAAGGCTCCATCAACTAAACTTCTGA
261 ATTTTCAACTCTTAACTTATTTTCCTATCATGGAAAATTTAAGGCTCCATCAACTAAAATTCTGA
105307 T
326 T
105308 AACAT
1 AACAT
105313 TTTAGGCGCA
Statistics
Matches: 317, Mismatches: 13, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
325 157 0.50
326 160 0.50
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (326 bp):
AACATCACAAAGAATTTCACATGGTTTGTTCAAGCATAAAATCAGAGGAAGTATCCAAAGATCAT
ATTAAACTTCGTGTTTTCCCTTTTTCCTTAGATGATTTAGCTAACGATTAGTTGTTTTATTTACC
GCCTAATTTCGTTACTACATAGGTTTAACCTATTTTATTAAAAAAATATTAATATTAAATATCGC
AACCTATTTCTTAGTGAGCCATGACATTCTTCGGCGCAACCATATTTCTTATAATCGTTCATAAC
ATTTTCAACTCTTAACTTATTTTCCTATCATGGAAAATTTAAGGCTCCATCAACTAAAATTCTGA
T
Found at i:108052 original size:483 final size:483
Alignment explanation
Indices: 107146--108112 Score: 1659
Period size: 483 Copynumber: 2.0 Consensus size: 483
107136 CTTCGCAGCA
*
107146 ATCAACATATCATCAACATACAATAACAGAAAAATAAAAGAACCATCATCAAGGCTCTTAACATA
1 ATCAACATATCATCAACATAAAATAACAGAAAAATAAAAGAACCATCATCAAGGCTCTTAACATA
* *
107211 GACACAACAATCATACTCACAACGGTTGTAGCCAATCTTGATCATATAGGAGTCAAACCGTTTAT
66 GACACAACAATCATACTCACAACGCTTGTAGCCAATCTTGATCATATAGGAGTCAAACCATTTAT
*
107276 ACCACTGTCTCGGAGACTGTTTCAACCCATACAAAGATTTCATCAATCTACAAACTAAATGCTCA
131 ACCACTGTCTCAGAGACTGTTTCAACCCATACAAAGATTTCATCAATCTACAAACTAAATGCTCA
* * * *
107341 TTTCCAGGTTGAGTGAAACCTTCAGGTTGCTGCATATAGATCTGATCCTCTAAATCACCATGTAA
196 TTTCCAGGTTGAGTGAAACCTTCACGATGCTGCATATAGATCTGATCATCTAAATCACCATGCAA
* *
107406 AAAAGGAGTTTTAACATCCATCTTCTCTAAATGCAAATCCCAACTAGCCACCAATGCAAGTACTA
261 AAAAGGAGTTTTAACATCCATCTGCTCTAAATGAAAATCCCAACTAGCCACCAATGCAAGTACTA
* *
107471 CTCGGATTGAAGTGTGCCTGACCATAGGAGAAAATATTTCATCATAATCAACTCCTTTCTGCTGT
326 CTCGGATTGAAGTGTGCCTGACCACAGGAGAAAAAATTTCATCATAATCAACTCCTTTCTGCTGT
*
107536 GAAAAACCCTTTGCTACCAAACGAGCCTTGAACTTCTCCCCCTCTTTTTCTGTTACTGCTGGTTT
391 GAAAAACCCTTTGCTACCAAACGAGCCTTGAACTTCTCCCCCTCTTTTTCTGTTACTGCTCGTTT
* *
107601 CTTTTTATACACCCATTTGCAACCAATC
456 CTTCTTATACACCCATTTACAACCAATC
*
107629 ATCAACATATCATCAACATAAAATAACAGAAAAATAAAATAACCATCATCAAGGCTCTTAACATA
1 ATCAACATATCATCAACATAAAATAACAGAAAAATAAAAGAACCATCATCAAGGCTCTTAACATA
* *
107694 GACACAACAATCATACTCACATCGCTTGTAGCCAATCTTGATCATATAGGAGTCAAACCATTTGT
66 GACACAACAATCATACTCACAACGCTTGTAGCCAATCTTGATCATATAGGAGTCAAACCATTTAT
* *
107759 ACCATTGTCTCAGAGACTGTTTCAACCCGTACAAAGATTT-ATTCAATCTACAAACTAAATGCTC
131 ACCACTGTCTCAGAGACTGTTTCAACCCATACAAAGATTTCA-TCAATCTACAAACTAAATGCTC
* * *
107823 ATTTCCAGGTTGA-TGAAACCTTCACGATGTTGCATGTAGATCTGCTCATCTAAATCACCATGCA
195 ATTTCCAGGTTGAGTGAAACCTTCACGATGCTGCATATAGATCTGATCATCTAAATCACCATGCA
* *
107887 AAAAAGTAGTTTTAACATCCATCTGCTCTAAATGAAAAATCCCAACTAGCCATCAATGCAAGTAC
260 AAAAAGGAGTTTTAACATCCATCTGCTCTAAATG-AAAATCCCAACTAGCCACCAATGCAAGTAC
*
107952 TACTCGGATTGAAGTGTGTCTGACCACAGGAGAAAAAATTTCATCATAATCAACTCCTTTCTGCT
324 TACTCGGATTGAAGTGTGCCTGACCACAGGAGAAAAAATTTCATCATAATCAACTCCTTTCTGCT
*
108017 GTGAAAAACCCTTTGCTACCAAACGAGCCTTGAACTTCTCCCCCTCTTTTTCTGTTACTGTTCGT
389 GTGAAAAACCCTTTGCTACCAAACGAGCCTTGAACTTCTCCCCCTCTTTTTCTGTTACTGCTCGT
108082 TTCTTCTTATACACCCATTTACAACCAATC
454 TTCTTCTTATACACCCATTTACAACCAATC
108112 A
1 A
108113 ACTTCTTACT
Statistics
Matches: 455, Mismatches: 27, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
482 77 0.17
483 378 0.83
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (483 bp):
ATCAACATATCATCAACATAAAATAACAGAAAAATAAAAGAACCATCATCAAGGCTCTTAACATA
GACACAACAATCATACTCACAACGCTTGTAGCCAATCTTGATCATATAGGAGTCAAACCATTTAT
ACCACTGTCTCAGAGACTGTTTCAACCCATACAAAGATTTCATCAATCTACAAACTAAATGCTCA
TTTCCAGGTTGAGTGAAACCTTCACGATGCTGCATATAGATCTGATCATCTAAATCACCATGCAA
AAAAGGAGTTTTAACATCCATCTGCTCTAAATGAAAATCCCAACTAGCCACCAATGCAAGTACTA
CTCGGATTGAAGTGTGCCTGACCACAGGAGAAAAAATTTCATCATAATCAACTCCTTTCTGCTGT
GAAAAACCCTTTGCTACCAAACGAGCCTTGAACTTCTCCCCCTCTTTTTCTGTTACTGCTCGTTT
CTTCTTATACACCCATTTACAACCAATC
Found at i:111930 original size:20 final size:19
Alignment explanation
Indices: 111900--111977 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 19
111890 CATTTTCTCC
*
111900 AAGGAATCGATCCTTTTGAA
1 AAGG-ATCGATCCTTTTAAA
**
111920 AAGAGATCGATCCTTTCTCCCA
1 AAG-GATCGATCCTTT-T-AAA
*
111942 ATGGATCGATCCTTTTAAA
1 AAGGATCGATCCTTTTAAA
*
111961 AAGCGATTGATCCTTTT
1 AAG-GATCGATCCTTTT
111978 TCTAGATAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 3 0.06
20 27 0.57
21 14 0.30
22 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (19 bp):
AAGGATCGATCCTTTTAAA
Found at i:111952 original size:41 final size:40
Alignment explanation
Indices: 111893--111976 Score: 116
Period size: 41 Copynumber: 2.1 Consensus size: 40
111883 GATTAATCAT
*
111893 TTTCTCCAAGGAATCGATCCTTTTGAAAAGAGATCGATCC
1 TTTCTCCAAGGAATCGATCCTTTTAAAAAGAGATCGATCC
* *
111933 TTTCTCCCAATGG-ATCGATCCTTTTAAAAAGCGATTGATCC
1 TTTCT-CCAA-GGAATCGATCCTTTTAAAAAGAGATCGATCC
111974 TTT
1 TTT
111977 TTCTAGATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 5 0.13
41 32 0.82
42 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (40 bp):
TTTCTCCAAGGAATCGATCCTTTTAAAAAGAGATCGATCC
Found at i:114594 original size:21 final size:21
Alignment explanation
Indices: 114568--114609 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
114558 GACTCCACTT
114568 TCCTCTACTCTCGTGGACCTC
1 TCCTCTACTCTCGTGGACCTC
114589 TCCTCTACTCTCGTGGACCTC
1 TCCTCTACTCTCGTGGACCTC
114610 ATCTCCTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.43, G:0.14, T:0.33
Consensus pattern (21 bp):
TCCTCTACTCTCGTGGACCTC
Found at i:124212 original size:22 final size:21
Alignment explanation
Indices: 124170--124209 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
124160 GAGTTTGTTT
*
124170 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
124191 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
124210 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:127058 original size:21 final size:22
Alignment explanation
Indices: 127012--127069 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
127002 CAAAAAAGAT
* *
127012 AAGGGATCAATCC-TTTCTTTC
1 AAGGGATCGATCCTTTTCTTCC
*
127033 GAGGGATCGATCCTTTTC-TCC
1 AAGGGATCGATCCTTTTCTTCC
*
127054 AAGGGATAGATCCTTT
1 AAGGGATCGATCCTTT
127070 GCTGGACAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (22 bp):
AAGGGATCGATCCTTTTCTTCC
Found at i:129002 original size:26 final size:24
Alignment explanation
Indices: 128940--129002 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
128930 CATTTTAATC
128940 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
128964 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
128987 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
129003 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:129004 original size:22 final size:23
Alignment explanation
Indices: 128957--129020 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
128947 TAATTATTAA
* *
128957 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
128978 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
129001 -ATATTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
129021 AAATAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 11 0.30
22 22 0.59
23 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:129093 original size:47 final size:52
Alignment explanation
Indices: 128983--129110 Score: 130
Period size: 53 Copynumber: 2.5 Consensus size: 52
128973 TTATTAATAT
*
128983 TTATAATAATAT-AATATTATATTTTTAATATTATAATAAAATAATCAATTATA
1 TTAT-ATAATATAAATATTATATTTTT-ATATTATAATAAAATAATCAATTAAA
*
129036 TTATAATAATATAAGATATTATATTTTTA-ATT-TAATAATAT-AT-AA-TAAA
1 TTAT-ATAATATAA-ATATTATATTTTTATATTATAATAAAATAATCAATTAAA
129085 TTAT-TAATA-AAAT-TTATATTATTTAT
1 TTATATAATATAAATATTATATT-TTTAT
129111 TAATTTCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
44 7 0.10
45 6 0.09
46 2 0.03
47 5 0.07
49 7 0.10
50 2 0.03
51 2 0.03
52 8 0.12
53 15 0.22
54 2 0.03
55 13 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TTATATAATATAAATATTATATTTTTATATTATAATAAAATAATCAATTAAA
Found at i:131807 original size:7 final size:7
Alignment explanation
Indices: 131795--131834 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
131785 TAATTATAAA
131795 AAAATAT
1 AAAATAT
131802 AAAATATT
1 AAAATA-T
* *
131810 TAAATTT
1 AAAATAT
131817 AAAATAT
1 AAAATAT
131824 AAAATAT
1 AAAATAT
131831 AAAA
1 AAAA
131835 AATTATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 23 0.82
8 5 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AAAATAT
Found at i:136239 original size:42 final size:42
Alignment explanation
Indices: 136180--136262 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
136170 CTACAAGGAA
* *
136180 CATATTATAATAACATAGAATATCAAAGCAGACATTTAGATG
1 CATATTACAATAACATAGAAGATCAAAGCAGACATTTAGATG
* ** *
136222 CATATTACAATAGCATAGAAGATCGGATCAGACATTTAGAT
1 CATATTACAATAACATAGAAGATCAAAGCAGACATTTAGAT
136263 ATAAAAGTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (42 bp):
CATATTACAATAACATAGAAGATCAAAGCAGACATTTAGATG
Found at i:144077 original size:23 final size:23
Alignment explanation
Indices: 144047--144121 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
144037 GTTCGTGTTC
144047 GTTCGTGTAGCTTTCACGAACAT
1 GTTCGTGTAGCTTTCACGAACAT
144070 GTTCGTGTAGCTTTCACGAACAT
1 GTTCGTGTAGCTTTCACGAACAT
* * *
144093 GTTCGTTTAACTTTTGA-GAACAT
1 GTTCGTGTAGC-TTTCACGAACAT
144116 GTTCGT
1 GTTCGT
144122 TTATTGTTCG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
23 44 0.92
24 4 0.08
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (23 bp):
GTTCGTGTAGCTTTCACGAACAT
Found at i:144277 original size:29 final size:29
Alignment explanation
Indices: 144245--144303 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
144235 ATGTGTCATT
144245 TTAGTTCATATTCATCAATATTTAAAATG
1 TTAGTTCATATTCATCAATATTTAAAATG
144274 TTAGTTCATATTCATCAATATTTAAAATG
1 TTAGTTCATATTCATCAATATTTAAAATG
144303 T
1 T
144304 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (29 bp):
TTAGTTCATATTCATCAATATTTAAAATG
Found at i:146480 original size:18 final size:18
Alignment explanation
Indices: 146457--146491 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
146447 CCGATTCTTC
*
146457 TGACCGATTAAATCAATT
1 TGACCGATTAAAACAATT
146475 TGACCGATTAAAACAAT
1 TGACCGATTAAAACAAT
146492 GAACTAATAG
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:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (18 bp):
TGACCGATTAAAACAATT
Found at i:149362 original size:18 final size:18
Alignment explanation
Indices: 149339--149376 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
149329 AACCGACCTA
149339 ACCCGACCCAAAC-CGTTG
1 ACCCGACCC-AACTCGTTG
*
149357 ACCCGATCCAACTCGTTG
1 ACCCGACCCAACTCGTTG
149375 AC
1 AC
149377 TTTGACCCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.26, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
ACCCGACCCAACTCGTTG
Found at i:154121 original size:195 final size:195
Alignment explanation
Indices: 153789--154178 Score: 771
Period size: 195 Copynumber: 2.0 Consensus size: 195
153779 ATTAGAAGTA
153789 TATGGGTTCCTAAAGAACTCATTAATACTAAATATAAGGATATCCTACACAAATGGATACCTAAG
1 TATGGGTTCCTAAAGAACTCATTAATACTAAATATAAGGATATCCTACACAAATGGATACCTAAG
153854 GGGACTAGGATTTTGGAAACTAATGAATATGGACCCAAAAGAATTTGGGTACCAAAAATAAAAAA
66 GGGACTAGGATTTTGGAAACTAATGAATATGGACCCAAAAGAATTTGGGTACCAAAAATAAAAAA
153919 ATTAATCTATGTTTGTAGGAAAAGGAGGATTGCTACAAGGCACGAGAAACGAATTCAAACTCATG
131 ATTAATCTATGTTTGTAGGAAAAGGAGGATTGCTACAAGGCACGAGAAACGAATTCAAACTCATG
153984 TATGGGTTCCTAAAGAACTCATTAATACTAAATATAAGGATATCCTACACAAATGGATACCTAAG
1 TATGGGTTCCTAAAGAACTCATTAATACTAAATATAAGGATATCCTACACAAATGGATACCTAAG
154049 GGGACTAGGATTTTGGAAACTAATGAATATGGACCCAAAAGAATTTGGGTACCAAAAATAAAAAA
66 GGGACTAGGATTTTGGAAACTAATGAATATGGACCCAAAAGAATTTGGGTACCAAAAATAAAAAA
*
154114 ATTAATCTATGTTTGTAGGAAAAGGAGGATTGCTACAAGGCACGAGAAATGAATTCAAACTCATG
131 ATTAATCTATGTTTGTAGGAAAAGGAGGATTGCTACAAGGCACGAGAAACGAATTCAAACTCATG
154179 GTACCTTGAT
Statistics
Matches: 194, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 194 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (195 bp):
TATGGGTTCCTAAAGAACTCATTAATACTAAATATAAGGATATCCTACACAAATGGATACCTAAG
GGGACTAGGATTTTGGAAACTAATGAATATGGACCCAAAAGAATTTGGGTACCAAAAATAAAAAA
ATTAATCTATGTTTGTAGGAAAAGGAGGATTGCTACAAGGCACGAGAAACGAATTCAAACTCATG
Found at i:157533 original size:20 final size:22
Alignment explanation
Indices: 157478--157534 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
157468 TTGTGCATGA
157478 GGAATCGATACCCCCTTGAAGG
1 GGAATCGATACCCCCTTGAAGG
* *
157500 GGAACCGATTCCCCCTTG-A-G
1 GGAATCGATACCCCCTTGAAGG
*
157520 GGAATCAATACCCCC
1 GGAATCGATACCCCC
157535 ACGAGGTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 13 0.43
21 1 0.03
22 16 0.53
ACGTcount: A:0.26, C:0.33, G:0.23, T:0.18
Consensus pattern (22 bp):
GGAATCGATACCCCCTTGAAGG
Found at i:160941 original size:19 final size:19
Alignment explanation
Indices: 160917--160954 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
160907 AGATTATGAA
160917 GGGGGTATAGATTCCCCCT
1 GGGGGTATAGATTCCCCCT
*
160936 GGGGGTATCGATTCCCCCT
1 GGGGGTATAGATTCCCCCT
160955 AAATGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.29, G:0.32, T:0.26
Consensus pattern (19 bp):
GGGGGTATAGATTCCCCCT
Found at i:162024 original size:23 final size:24
Alignment explanation
Indices: 161992--162049 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
161982 ATCTTATATA
* *
161992 GCACTACGGTGC-ATTTCTACGCG
1 GCACTTCGGTGCAAATTCTACGCG
*
162015 GCACTTCGGTGCAAATTCTACGTG
1 GCACTTCGGTGCAAATTCTACGCG
162039 GCACTTCGGTG
1 GCACTTCGGTG
162050 TAATTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (24 bp):
GCACTTCGGTGCAAATTCTACGCG
Found at i:162924 original size:18 final size:18
Alignment explanation
Indices: 162896--162960 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
162886 GTTCATACGA
* *
162896 TACTTTTCATATGTATTT
1 TACTGTTCATACGTATTT
*
162914 TATTGTTCATACGTATTT
1 TACTGTTCATACGTATTT
*
162932 TACTGTTCATACATATTT
1 TACTGTTCATACGTATTT
162950 TACTGTTCATA
1 TACTGTTCATA
162961 AACATGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.25, C:0.14, G:0.08, T:0.54
Consensus pattern (18 bp):
TACTGTTCATACGTATTT
Found at i:166891 original size:11 final size:11
Alignment explanation
Indices: 166875--166908 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
166865 AAACATTTCA
166875 TTTCTTCTTCC
1 TTTCTTCTTCC
166886 TTTCTTCTTCC
1 TTTCTTCTTCC
166897 TTTCTTCTTCC
1 TTTCTTCTTCC
166908 T
1 T
166909 CCTCCCGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTCTTCTTCC
Found at i:176995 original size:20 final size:20
Alignment explanation
Indices: 176970--177018 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
176960 GAAAACATTT
176970 CCAACGGCTCCAAATCACTC
1 CCAACGGCTCCAAATCACTC
176990 CCAACGGCTCCAAATCACTC
1 CCAACGGCTCCAAATCACTC
*
177010 ACAACGGCT
1 CCAACGGCT
177019 AGAAACAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.43, G:0.12, T:0.14
Consensus pattern (20 bp):
CCAACGGCTCCAAATCACTC
Found at i:179415 original size:37 final size:38
Alignment explanation
Indices: 179370--179448 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
179360 ATATTTTGTT
179370 ATATCAAAAA-GGGGAGATTCTTGAACCATGTTTTATA
1 ATATCAAAAAGGGGGAGATTCTTGAACCATGTTTTATA
*
179407 ATATCAAAAAGGGGGAGATTGTTGAACCATGTTTTATA
1 ATATCAAAAAGGGGGAGATTCTTGAACCATGTTTTATA
179445 ATAT
1 ATAT
179449 TTTGATATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 10 0.25
38 30 0.75
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (38 bp):
ATATCAAAAAGGGGGAGATTCTTGAACCATGTTTTATA
Found at i:179684 original size:20 final size:20
Alignment explanation
Indices: 179656--179708 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
179646 AGGTAAGAGA
*
179656 AGTATCGATACTATCTAGGT
1 AGTACCGATACTATCTAGGT
*
179676 AGTACCGATACTATCTATGT
1 AGTACCGATACTATCTAGGT
179696 AGTACCGATACTA
1 AGTACCGATACTA
179709 ACAAATTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (20 bp):
AGTACCGATACTATCTAGGT
Found at i:183893 original size:44 final size:44
Alignment explanation
Indices: 183834--183931 Score: 187
Period size: 44 Copynumber: 2.2 Consensus size: 44
183824 CAAAGAAAAA
*
183834 TTAAAATAATAATTGGTGACTAAATATGTAATTTACCAAATTAT
1 TTAAGATAATAATTGGTGACTAAATATGTAATTTACCAAATTAT
183878 TTAAGATAATAATTGGTGACTAAATATGTAATTTACCAAATTAT
1 TTAAGATAATAATTGGTGACTAAATATGTAATTTACCAAATTAT
183922 TTAAGATAAT
1 TTAAGATAAT
183932 GTACGGACAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (44 bp):
TTAAGATAATAATTGGTGACTAAATATGTAATTTACCAAATTAT
Found at i:184263 original size:25 final size:25
Alignment explanation
Indices: 184229--184278 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
184219 GGAAATGACT
184229 GTAACTGGACATATATATCAATACC
1 GTAACTGGACATATATATCAATACC
184254 GTAACTGGACATATATATCAATACC
1 GTAACTGGACATATATATCAATACC
184279 AACACTACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (25 bp):
GTAACTGGACATATATATCAATACC
Found at i:185601 original size:14 final size:14
Alignment explanation
Indices: 185582--185637 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
185572 CGTTCGTGAA
185582 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
185596 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
185609 --TT-GTTTATGTT
1 CGTTCGATTATGTT
185620 CGTTCGATTATGTT
1 CGTTCGATTATGTT
185634 CGTT
1 CGTT
185638 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:185616 original size:24 final size:24
Alignment explanation
Indices: 185589--185658 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
185579 GAACGTTCGA
*
185589 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
185613 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
185637 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
185659 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:186397 original size:10 final size:10
Alignment explanation
Indices: 186382--186456 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
186372 GGGTCTCCAA
186382 CGTTTATGTT
1 CGTTTATGTT
186392 CGTTTATGTT
1 CGTTTATGTT
186402 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
186413 ATGTTCGTGTT
1 -CGTTTATGTT
186424 CGTTTATGTT
1 CGTTTATGTT
186434 CG----TGTT
1 CGTTTATGTT
186440 CGTTTATGTT
1 CGTTTATGTT
186450 CGTTTAT
1 CGTTTAT
186457 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:186413 original size:16 final size:16
Alignment explanation
Indices: 186388--186452 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
186378 CCAACGTTTA
186388 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
186404 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
186420 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
186436 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
186452 T
1 T
186453 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:191093 original size:71 final size:70
Alignment explanation
Indices: 190932--191083 Score: 169
Period size: 71 Copynumber: 2.1 Consensus size: 70
190922 ACGAATATAG
* * ** *
190932 ATATTTTAATATTAATTTTTTATAGATAGATATAAATAAAATTCTAGAATTAATATTTTTAGAAT
1 ATATATTAATA-TAATTTTTTATAAATAGATATAAATAAAATTCTAGAAGGAATATTTTTAAAAT
*
190997 GAATAT
65 AAATAT
* *
191003 ATATATTAATATTATTTTTTTATAAATAGATATAAATAAAATTTTAGAAGGAATATTATTAATAA
1 ATATATTAATA-TAATTTTTTATAAATAGATATAAATAAAATTCTAGAAGGAATATT-TT--TAA
191068 AATAAACTAT
62 AATAAA-TAT
*
191078 TTATAT
1 ATATAT
191084 AAAAATTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 51 0.75
72 2 0.03
74 7 0.10
75 8 0.12
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.45
Consensus pattern (70 bp):
ATATATTAATATAATTTTTTATAAATAGATATAAATAAAATTCTAGAAGGAATATTTTTAAAATA
AATAT
Done.