Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004745.1 Hibiscus syriacus cultivar Beakdansim tig00010711_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: 166578
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2629 original size:18 final size:18
Alignment explanation
Indices: 2603--2640 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2593 AGAAGTGCTC
2603 CCTTCATCTCCTACCAAT
1 CCTTCATCTCCTACCAAT
*
2621 CCTTTATCTCCTACCAAT
1 CCTTCATCTCCTACCAAT
2639 CC
1 CC
2641 AAAGGAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (18 bp):
CCTTCATCTCCTACCAAT
Found at i:7081 original size:3 final size:3
Alignment explanation
Indices: 7075--7141 Score: 109
Period size: 3 Copynumber: 22.7 Consensus size: 3
7065 TATTATTCTT
* *
7075 ATA ATA ATA ATA AGA ATA ACA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7122 ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA AT
7142 CAAAGGGCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:9768 original size:2 final size:2
Alignment explanation
Indices: 9761--9786 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9751 AATTGCATGA
9761 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9787 CGCACGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14015 original size:88 final size:88
Alignment explanation
Indices: 13853--14027 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 88
13843 TAAACTGTAA
* *
13853 CAACAAAGTGAAAAGTCACCACCAAGCTTTGAAGAACCCATCTCTCGCCATTCCATATTTTGCCA
1 CAACAAAGAGAAAAGTCACCACCAAGCTTTGAAGAACCCATCTCTCGCCATTCCATACTTTGCCA
* *
13918 GTGTAACTGCCATCGAAGAGCTG
66 ATGAAACTGCCATCGAAGAGCTG
* ** ** * * * *
13941 CAACAAAGAGAAATGTCACCGGCAAGCTTTGAAGAGTCCATCTCTCGCCCTTCCGTCCTTTGTCA
1 CAACAAAGAGAAAAGTCACCACCAAGCTTTGAAGAACCCATCTCTCGCCATTCCATACTTTGCCA
14006 AT-AAGACTGCCATCGAAGAGCT
66 ATGAA-ACTGCCATCGAAGAGCT
14028 ACACCAAGGC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
87 1 0.01
88 72 0.99
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (88 bp):
CAACAAAGAGAAAAGTCACCACCAAGCTTTGAAGAACCCATCTCTCGCCATTCCATACTTTGCCA
ATGAAACTGCCATCGAAGAGCTG
Found at i:17699 original size:2 final size:2
Alignment explanation
Indices: 17692--17724 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17682 ATATGATTTA
17692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17725 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22031 original size:23 final size:23
Alignment explanation
Indices: 22005--22048 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21995 CGGGGAGTAA
22005 TTGAAA-AAGAAGAGGAAGGAGAC
1 TTGAAAGAAGAAGAGG-AGGAGAC
*
22028 TTGAAAGAATAAGAGGAGGAG
1 TTGAAAGAAGAAGAGGAGGAG
22049 GGAAACAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.50, C:0.02, G:0.36, T:0.11
Consensus pattern (23 bp):
TTGAAAGAAGAAGAGGAGGAGAC
Found at i:23920 original size:36 final size:36
Alignment explanation
Indices: 23856--23997 Score: 250
Period size: 36 Copynumber: 4.0 Consensus size: 36
23846 TTCGTTCTAG
*
23856 TTGAATCGGAAGTG-CGATGCTTCTTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
23891 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
*
23927 TTAAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
*
23963 TTGAATCGGAAGTGCCGATGCTTCCTTCCATTCGA
1 TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGA
23998 CTAGAAACGC
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 14 0.14
36 88 0.86
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (36 bp):
TTGAATCGGAAGTGCCGATGCTTCCTTCCGTTCGAT
Found at i:26428 original size:59 final size:60
Alignment explanation
Indices: 26260--26435 Score: 167
Period size: 59 Copynumber: 3.0 Consensus size: 60
26250 CATGTCTCCT
* * * * * * *** *
26260 AACTATGATCTTCGTTTTAAATTGATCATTAAACTTTTAAATATTTTGATTTCATCATCA
1 AACTATGACCCTCATTTTAAATTGATCCTTAAACTTTTGAATCTTCCAATTTCATCCTCA
* * * * **
26320 AATTATGACTCTCATTCTAAATTAATCCTTAAACTTTTGAA-CAGCCCAATTTCATCCTC-
1 AACTATGACCCTCATTTTAAATTGATCCTTAAACTTTTGAATC-TTCCAATTTCATCCTCA
* *
26379 AACTATGACCCTTATTTTAAATTGATCCTAAAACTTTTGAATCTTCCAATTTCATCC
1 AACTATGACCCTCATTTTAAATTGATCCTTAAACTTTTGAATCTTCCAATTTCATCC
26436 AAATATATAA
Statistics
Matches: 90, Mismatches: 24, Indels: 5
0.76 0.20 0.04
Matches are distributed among these distances:
59 47 0.52
60 43 0.48
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.41
Consensus pattern (60 bp):
AACTATGACCCTCATTTTAAATTGATCCTTAAACTTTTGAATCTTCCAATTTCATCCTCA
Found at i:26613 original size:29 final size:29
Alignment explanation
Indices: 26562--26673 Score: 84
Period size: 29 Copynumber: 3.8 Consensus size: 29
26552 TGTAAGTCAT
* *
26562 AGTTTGGGGATGAATTT-GAAATGTTTAAA
1 AGTTTGAGGATTAATTTAG-AATGTTTAAA
* * * *
26591 ATTTTGAGGATTAATTTAGAATGATCGTCAT
1 AGTTTGAGGATTAATTTAGAATG-T-TTAAA
* * *
26622 AGTTTAAAGATTAAATTAGAATGTTTAAA
1 AGTTTGAGGATTAATTTAGAATGTTTAAA
*
26651 AGTTT-AGAGACTAATTTAGAATG
1 AGTTTGAG-GATTAATTTAGAATG
26674 CGAATCAAAA
Statistics
Matches: 63, Mismatches: 16, Indels: 8
0.72 0.18 0.09
Matches are distributed among these distances:
28 1 0.02
29 38 0.60
30 3 0.05
31 21 0.33
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (29 bp):
AGTTTGAGGATTAATTTAGAATGTTTAAA
Found at i:30442 original size:28 final size:28
Alignment explanation
Indices: 30401--30455 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
30391 TTATAAGAAT
30401 TCCTTCGTTTATTGAA-CTCTCCGAAGGC
1 TCCTTCGTTTATTGAATC-CTCCGAAGGC
30429 TCCTTC-TTTGATTGAATCCTCCGAAGG
1 TCCTTCGTTT-ATTGAATCCTCCGAAGG
30456 TTCATATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 3 0.12
28 21 0.84
29 1 0.04
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (28 bp):
TCCTTCGTTTATTGAATCCTCCGAAGGC
Found at i:40472 original size:104 final size:104
Alignment explanation
Indices: 40299--40498 Score: 319
Period size: 104 Copynumber: 1.9 Consensus size: 104
40289 AATTATAAAC
* * * *
40299 AGATGATCAAGCTTAAGAGCTTATGAAATAAATGGCAATTATATTGGTACGAAATTATATACATT
1 AGATGATCAAACTTAAGAGCTTATGAAATAAATGACAAGTATATTGGTAAGAAATTATATACATT
40364 GTTTATTTCATGTTAATATGTGTAAAATGAAATATAAGA
66 GTTTATTTCATGTTAATATGTGTAAAATGAAATATAAGA
* * *
40403 AGATGATTAAACTTATGAGCTTATGGAATAAATGACAAGTATATTGGTAAGAAATTATATACATT
1 AGATGATCAAACTTAAGAGCTTATGAAATAAATGACAAGTATATTGGTAAGAAATTATATACATT
* *
40468 GTTTATTTCATGTTGATATGTGTAACATGAA
66 GTTTATTTCATGTTAATATGTGTAAAATGAA
40499 GATAATACAT
Statistics
Matches: 87, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (104 bp):
AGATGATCAAACTTAAGAGCTTATGAAATAAATGACAAGTATATTGGTAAGAAATTATATACATT
GTTTATTTCATGTTAATATGTGTAAAATGAAATATAAGA
Found at i:47831 original size:36 final size:36
Alignment explanation
Indices: 47784--47852 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
47774 ATAGGTTTGT
*
47784 AAGGGTGAATAGACCATACTGTTAATAAATCATTGC
1 AAGGGTGAATAGACCATACTATTAATAAATCATTGC
47820 AAGGGTGAATAGACCATACTATTAATAAATCAT
1 AAGGGTGAATAGACCATACTATTAATAAATCAT
47853 ATGGGCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (36 bp):
AAGGGTGAATAGACCATACTATTAATAAATCATTGC
Found at i:49804 original size:2 final size:2
Alignment explanation
Indices: 49797--49822 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
49787 CCTACACCTG
49797 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
49823 CCTGAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51017 original size:11 final size:11
Alignment explanation
Indices: 51001--51029 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
50991 GTAATACAAT
51001 AAATATTTAAA
1 AAATATTTAAA
51012 AAATATTTAAA
1 AAATATTTAAA
51023 AAATATT
1 AAATATT
51030 CTTGTTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATATTTAAA
Found at i:54936 original size:23 final size:23
Alignment explanation
Indices: 54879--54936 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
54869 CTAACACTAA
*
54879 ACGAACACTAAACAAATATGTTC
1 ACGAACAATAAACAAATATGTTC
* *
54902 ACGAA-AATTAAACGAATATGTTT
1 ACGAACAA-TAAACAAATATGTTC
*
54925 GCGAACAATAAA
1 ACGAACAATAAA
54937 TAAACAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.03
23 26 0.90
24 2 0.07
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.22
Consensus pattern (23 bp):
ACGAACAATAAACAAATATGTTC
Found at i:59431 original size:2 final size:2
Alignment explanation
Indices: 59424--59449 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59414 CTTAAACCAA
59424 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59450 GTAGACCCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61856 original size:28 final size:25
Alignment explanation
Indices: 61812--61862 Score: 66
Period size: 28 Copynumber: 1.9 Consensus size: 25
61802 TATCTCACTA
61812 TTTTTTTTTTCTCATTTCATTTTCC
1 TTTTTTTTTTCTCATTTCATTTTCC
*
61837 TTTTTTTTATTACTCTATTTTATTTT
1 TTTTTTTT-TT-CTC-ATTTCATTTT
61863 TTATCATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 2 0.09
27 3 0.14
28 9 0.41
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTTTTTTCTCATTTCATTTTCC
Found at i:64923 original size:32 final size:32
Alignment explanation
Indices: 64887--64960 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
64877 GCATCTTTAA
* * *
64887 AGATTAAACAGTAAATGTTGGGGCATATTTGG
1 AGATTCAACAGTAAATATTAGGGCATATTTGG
* * *
64919 AGATTCAACATTGAATATTATGGCATATTTGG
1 AGATTCAACAGTAAATATTAGGGCATATTTGG
*
64951 GGATTCAACA
1 AGATTCAACA
64961 TCCTGATGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (32 bp):
AGATTCAACAGTAAATATTAGGGCATATTTGG
Found at i:65307 original size:64 final size:64
Alignment explanation
Indices: 65219--65349 Score: 208
Period size: 64 Copynumber: 2.0 Consensus size: 64
65209 GGAGCGTCTG
* *
65219 TCAACAAATAACTTTACAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGTAC
1 TCAACAAACAACTTTACAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAC
* * * *
65283 TCAACAAACAATTTTCCAGTTTCATTCAGAGTCATTTTCAACTTCACAGCGAAGGATATTGAAC
1 TCAACAAACAACTTTACAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAC
65347 TCA
1 TCA
65350 CAATTTGCTC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.36, C:0.21, G:0.11, T:0.31
Consensus pattern (64 bp):
TCAACAAACAACTTTACAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAAC
Found at i:65475 original size:43 final size:43
Alignment explanation
Indices: 65426--65541 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
65416 ACGAAGGGGT
* *
65426 CATCCACGATTTCAACTCCACGATGGAGGATATCGTACCAATA
1 CATCCACGATTTCAACTCCACAACGGAGGATATCGTACCAATA
* * * * *
65469 GATCCACTATTTCAACTCCACAACGGAGTATATCGTGCCCATA
1 CATCCACGATTTCAACTCCACAACGGAGGATATCGTACCAATA
* * * *
65512 CATTCACGGTTTCAACTTCACAACGAAGGA
1 CATCCACGATTTCAACTCCACAACGGAGGA
65542 AAATCGTATA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACAACGGAGGATATCGTACCAATA
Found at i:65822 original size:44 final size:44
Alignment explanation
Indices: 65730--65852 Score: 169
Period size: 44 Copynumber: 2.8 Consensus size: 44
65720 ACGAAAGGGC
* *
65730 CATCCACGATTTTAACTCCACGACA-AAGGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGACAGAAGGATATCGTACCAACA
* * *
65773 GATCCACGATTTCAACTCCACGACAGAAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACAGAAGGATATCGTACCAACA
* *
65817 CATCCATGATTTCAACTTCACGAC-GAAGGATATCGT
1 CATCCACGATTTCAACTCCACGACAGAAGGATATCGT
65853 CTCCACCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 35 0.49
44 36 0.51
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (44 bp):
CATCCACGATTTCAACTCCACGACAGAAGGATATCGTACCAACA
Found at i:72545 original size:3 final size:3
Alignment explanation
Indices: 72531--72564 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
72521 AGAAAGTTTG
72531 TAA TACA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
72565 ATATATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:74205 original size:3 final size:3
Alignment explanation
Indices: 74199--74294 Score: 147
Period size: 3 Copynumber: 31.7 Consensus size: 3
74189 TTTTTATCCA
* * *
74199 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
74247 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
74293 TA
1 TA
74295 AAAATAATAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 81 0.96
4 3 0.04
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:74805 original size:15 final size:16
Alignment explanation
Indices: 74780--74816 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
74770 GAGAACGACA
74780 AGAAA-AAAAAAACAG
1 AGAAAGAAAAAAACAG
74795 A-AAAGAAAAAAACAG
1 AGAAAGAAAAAAACAG
74810 AGAAAGA
1 AGAAAGA
74817 GAACACAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 12 0.60
16 5 0.25
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAAAAACAG
Found at i:74819 original size:18 final size:18
Alignment explanation
Indices: 74779--74819 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
74769 AGAGAACGAC
74779 AAGA-AAAAAAAAACAGA
1 AAGAGAAAAAAAAACAGA
* *
74796 AA-AGAAAAAAACAGAGA
1 AAGAGAAAAAAAAACAGA
74813 AAGAGAA
1 AAGAGAA
74820 CACAGCAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 1 0.05
17 15 0.75
18 4 0.20
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (18 bp):
AAGAGAAAAAAAAACAGA
Found at i:78316 original size:14 final size:14
Alignment explanation
Indices: 78296--78348 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
78286 ATTTTAAATA
*
78296 ATTTACATTTATAT
1 ATTTACATTTACAT
* *
78310 TTTTACATTTGCAT
1 ATTTACATTTACAT
*
78324 ATTTACATTTGGCAT
1 ATTTACATTT-ACAT
*
78339 CTTTACATTT
1 ATTTACATTT
78349 GTATTGCACA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (14 bp):
ATTTACATTTACAT
Found at i:78343 original size:15 final size:15
Alignment explanation
Indices: 78311--78349 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
78301 CATTTATATT
78311 TTTACATTT-GCATA
1 TTTACATTTGGCATA
*
78325 TTTACATTTGGCATC
1 TTTACATTTGGCATA
78340 TTTACATTTG
1 TTTACATTTG
78350 TATTGCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.51
Consensus pattern (15 bp):
TTTACATTTGGCATA
Found at i:83971 original size:83 final size:83
Alignment explanation
Indices: 83827--84435 Score: 981
Period size: 83 Copynumber: 7.4 Consensus size: 83
83817 ATATCCCAGT
* *
83827 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
83892 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
* *
83910 TCAATCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
83975 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
*
83993 TCAAGCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
84058 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
*
84076 TCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
84141 TGATCTGATTGGACAGAA
66 TGATCTGATTGGACAGAA
* *
84159 TCAATCATTGAATTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * **
84224 TGACCTGGTTTAACAGAA
66 TGATCTGATTGGACAGAA
* *
84242 CCAAGCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* * *
84307 TGACCTGGTT-TAGCAGAA
66 TGATCTGATTGGA-CAGAA
* *
84325 -CAATCATCGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
1 TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
* *
84389 TGATTTGTTTGGACAGAA
66 TGATCTGATTGGACAGAA
* *
84407 -CAATCATTGAATTTGGAAGATGAATTTGC
1 TCAAGCATTGAATTTAGAAGATGAATTTGC
84436 TCATAGTAAA
Statistics
Matches: 496, Mismatches: 28, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
82 101 0.20
83 395 0.80
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (83 bp):
TCAAGCATTGAATTTAGAAGATGAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGATTGGACAGAA
Found at i:85238 original size:113 final size:113
Alignment explanation
Indices: 85075--86724 Score: 2952
Period size: 113 Copynumber: 14.6 Consensus size: 113
85065 ATGGAGCAGC
*
85075 TTTT-CCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85138 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
*
85186 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85251 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
*
85299 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85364 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
85412 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85477 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
85525 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
*
85590 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
*
85638 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85703 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
*
85751 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85816 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
85864 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
85929 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
85977 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
*
86042 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
*
86090 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
*
86155 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
86203 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
*
86268 GAAGAATTTGTTCAACCTTTTACTTGAATTCATCACTTGATGGATTAT
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
86316 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
* *
86381 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATCAA
66 GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
** *
86429 CATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
1 TTTTGCCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
86493 AGAAGAATTTGTTCAACCTTTTACTTGAATTCATCATTTGATGGATCAA
65 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
** * *
86542 CATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 TTTTGCCAGAG-AAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * * *
86606 AGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATCAA
65 AGAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
** *
86655 CATTGCCAGAGAA-GTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAA-AAAGTTCATAATG
1 TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAA-TTCATAATG
86718 AGAAGAA
65 AGAAGAA
86725 CTCATCAAGA
Statistics
Matches: 1512, Mismatches: 22, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
111 6 0.00
112 61 0.04
113 1444 0.96
114 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (113 bp):
TTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGA
GAAGAATTTGTTCAACCTTTTACCTGAATTCATCACTTGATGGATTAT
Found at i:86982 original size:3 final size:3
Alignment explanation
Indices: 86976--87067 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
86966 TTTTTATCCA
* *
86976 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
87024 TAT CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
87068 AATATATTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:87587 original size:15 final size:16
Alignment explanation
Indices: 87567--87598 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
87557 ACGACAAGAA
87567 AAAAAAACAGA-AAAG
1 AAAAAAACAGAGAAAG
87582 AAAAAAACAGAGAAAG
1 AAAAAAACAGAGAAAG
87598 A
1 A
87599 GAACACAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAACAGAGAAAG
Found at i:90296 original size:20 final size:21
Alignment explanation
Indices: 90273--90354 Score: 98
Period size: 22 Copynumber: 4.0 Consensus size: 21
90263 AATAAAAAGT
90273 TAAATAA-ATATTTTAAAAAA
1 TAAATAATATATTTTAAAAAA
*
90293 TAAATAATATTATTTCAAAAAA
1 TAAATAATA-TATTTTAAAAAA
*
90315 TAAATAATATAATTTT-AAAAT
1 TAAATAATAT-ATTTTAAAAAA
*
90336 TAAATAA-ATATTTTTAAAA
1 TAAATAATATATTTTAAAAA
90355 TATTATAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
19 5 0.09
20 13 0.24
21 13 0.24
22 24 0.44
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATAATATATTTTAAAAAA
Found at i:90355 original size:20 final size:20
Alignment explanation
Indices: 90267--90355 Score: 90
Period size: 20 Copynumber: 4.2 Consensus size: 20
90257 TAGTATAATA
*
90267 AAAAGTTAAATAAATATTTTA
1 AAAA-TTAAATAAATATTTTT
*
90288 AAAAATAAAT-AATATTATTT
1 AAAATTAAATAAATATT-TTT
* *
90308 CAAAAAATAAATAATATAATTTT
1 --AAAATTAAATAA-ATATTTTT
90331 AAAATTAAATAAATATTTTT
1 AAAATTAAATAAATATTTTT
90351 AAAAT
1 AAAAT
90356 ATTATAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
19 6 0.10
20 19 0.33
21 15 0.26
22 10 0.17
23 4 0.07
24 4 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (20 bp):
AAAATTAAATAAATATTTTT
Found at i:90359 original size:22 final size:21
Alignment explanation
Indices: 90265--90366 Score: 97
Period size: 21 Copynumber: 4.9 Consensus size: 21
90255 TTTAGTATAA
90265 TAAAAAGTTAAATAAATA-TTT
1 TAAAAA-TTAAATAAATATTTT
*
90286 TAAAAAATAAAT-AATATTATT
1 TAAAAATTAAATAAATATT-TT
* *
90307 TCAAAAAATAAATAATATAATTT
1 T-AAAAATTAAATAA-ATATTTT
90330 T-AAAATTAAATAAATATTTT
1 TAAAAATTAAATAAATATTTT
90350 TAAAATATT--ATAAATAT
1 TAAAA-ATTAAATAAATAT
90367 AATTTTCAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 15
0.79 0.04 0.17
Matches are distributed among these distances:
19 4 0.06
20 21 0.30
21 23 0.33
22 14 0.20
23 4 0.06
24 4 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
TAAAAATTAAATAAATATTTT
Found at i:90372 original size:22 final size:22
Alignment explanation
Indices: 90267--90372 Score: 82
Period size: 22 Copynumber: 5.0 Consensus size: 22
90257 TAGTATAATA
*
90267 AAAAGTTAAATAAATAT--TTTA
1 AAAA-TTAAATAAATATAATTTT
* * *
90288 AAAAATAAAT-AATATTATTTCA
1 AAAATTAAATAAATATAATTT-T
*
90310 AAAAATAAAT-AATATAATTTT
1 AAAATTAAATAAATATAATTTT
90331 AAAATTAAATAAATAT--TTTT
1 AAAATTAAATAAATATAATTTT
*
90351 AAAA-TATTATAAATATAATTTT
1 AAAATTA-AATAAATATAATTTT
90373 CAGAATGATT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
19 7 0.10
20 21 0.29
21 16 0.22
22 29 0.40
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
AAAATTAAATAAATATAATTTT
Found at i:99796 original size:2 final size:2
Alignment explanation
Indices: 99789--99816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
99779 AAAATAATTA
99789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
99817 TGTACATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:107359 original size:14 final size:15
Alignment explanation
Indices: 107248--107365 Score: 148
Period size: 15 Copynumber: 7.5 Consensus size: 15
107238 TAATAAGGTT
107248 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
107263 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
107278 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
107293 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
107308 ATTTATTATAAAAAATGGA
1 ATTTATT-T-TAAAAT--A
107327 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
107345 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
107359 ATTTATT
1 ATTTATT
107366 AGTATGGATT
Statistics
Matches: 92, Mismatches: 4, Indels: 15
0.83 0.04 0.14
Matches are distributed among these distances:
14 12 0.13
15 59 0.64
16 1 0.01
17 5 0.05
18 1 0.01
19 1 0.01
20 5 0.05
21 1 0.01
22 7 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:107383 original size:32 final size:32
Alignment explanation
Indices: 107345--107496 Score: 155
Period size: 32 Copynumber: 5.4 Consensus size: 32
107335 TTTTAAAATA
107345 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
107377 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
107399 ATTTATTTTAAATAATTTATTAGCATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
107431 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
107453 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
107485 ATTTATTTTAAA
1 ATTTATTTTAAA
107497 ATATGGATTG
Statistics
Matches: 98, Mismatches: 2, Indels: 40
0.70 0.01 0.29
Matches are distributed among these distances:
22 27 0.28
23 8 0.08
25 2 0.02
26 6 0.06
28 6 0.06
29 2 0.02
31 8 0.08
32 39 0.40
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.52
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:107384 original size:22 final size:22
Alignment explanation
Indices: 107368--107410 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
107358 AATTTATTAG
107368 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
107390 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
107411 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:107411 original size:54 final size:54
Alignment explanation
Indices: 107345--107781 Score: 443
Period size: 54 Copynumber: 8.1 Consensus size: 54
107335 TTTTAAAATA
107345 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
107399 ATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
107453 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* **
107507 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * **
107556 CATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * * * * * ***
107610 TATGGA-TTGAATTATTTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
107667 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAGAAA-ATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
*
107721 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
107775 ATTTATT
1 ATTTATT
107782 ATTATAGTTG
Statistics
Matches: 335, Mismatches: 30, Indels: 36
0.84 0.07 0.09
Matches are distributed among these distances:
47 4 0.01
48 27 0.08
49 3 0.01
50 5 0.01
51 1 0.00
52 2 0.01
53 4 0.01
54 241 0.72
55 7 0.02
56 7 0.02
57 13 0.04
58 20 0.06
59 1 0.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:107448 original size:22 final size:22
Alignment explanation
Indices: 107423--107464 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
107413 ATTTATTAGC
107423 ATGGATTGATTTATTTTAAAAT
1 ATGGATTGATTTATTTTAAAAT
107445 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
107465 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAT
Found at i:107539 original size:134 final size:134
Alignment explanation
Indices: 107390--107876 Score: 895
Period size: 134 Copynumber: 3.6 Consensus size: 134
107380 TATTTTAAAA
107390 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
107455 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
107520 GTTG
131 GTTG
107524 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
*
107589 TTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
107654 GTTG
131 GTTG
*
107658 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAGAAA-ATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTA-AAATATGGATTGA
* *
107722 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTAT
65 TTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
107787 AGTTG
130 AGTTG
* * *
107792 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
107857 TTATTTTAAATAATTTATTA
66 TTATTTTAAATAATTTATTA
107877 TTGTAGTTGT
Statistics
Matches: 344, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
133 3 0.01
134 338 0.98
135 3 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
GTTG
Found at i:107539 original size:188 final size:187
Alignment explanation
Indices: 107345--107781 Score: 636
Period size: 188 Copynumber: 2.3 Consensus size: 187
107335 TTTTAAAATA
107345 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
107410 ATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TT
66 ATAATTTATTAGCATGGATTGAATTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT
* * ***
107474 AGTATGGATTGATTTATTTT-AA-AA-TA-T-GGATTGATTTA-TTATTGTAGTTGTATGGATTG
125 -GTATGGATTGATTTATTTTAAATAATTATTAGGATGGATTGATTTATTGTAG-AAAATGGATTG
*
107533 ATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
107598 ATAATTTATTAGTATGGATTGAATTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
66 ATAATTTATTAGCATGGATTGAATTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
* *
107663 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAGAAAATGGATTG
131 ATTGATTTATTTTAAATAA-TTATTAGGATGGATTGATTTATTGTAGAAAATGGATTG
*
107721 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
107782 ATTATAGTTG
Statistics
Matches: 228, Mismatches: 13, Indels: 16
0.89 0.05 0.06
Matches are distributed among these distances:
182 22 0.10
183 4 0.02
184 4 0.02
186 4 0.02
187 1 0.00
188 185 0.81
189 8 0.04
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (187 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGCATGGATTGAATTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGG
ATTGATTTATTTTAAATAATTATTAGGATGGATTGATTTATTGTAGAAAATGGATTG
Found at i:107544 original size:80 final size:80
Alignment explanation
Indices: 107444--107593 Score: 291
Period size: 80 Copynumber: 1.9 Consensus size: 80
107434 TATTTTAAAA
*
107444 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
107509 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
107524 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
107589 TTATT
66 TTATT
107594 TTAAATAATT
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:107566 original size:32 final size:31
Alignment explanation
Indices: 107525--107630 Score: 122
Period size: 32 Copynumber: 3.6 Consensus size: 31
107515 TTGTAGTTGT
107525 ATGGATTGATTTATTTTAAATAATTTATTAG
1 ATGGATTGATTTATTTTAAATAATTTATTAG
107556 CATGGATTGATTTATTTT--A-AA---A-T--
1 -ATGGATTGATTTATTTTAAATAATTTATTAG
107579 ATGGATTGATTTATTTTAAATAATTTATTAG
1 ATGGATTGATTTATTTTAAATAATTTATTAG
*
107610 TATGGATTGAATTATTTTAAA
1 -ATGGATTGATTTATTTTAAA
107631 ATATGGATTG
Statistics
Matches: 63, Mismatches: 1, Indels: 20
0.75 0.01 0.24
Matches are distributed among these distances:
22 17 0.27
24 1 0.02
25 3 0.05
26 1 0.02
28 1 0.02
29 3 0.05
30 1 0.02
32 36 0.57
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (31 bp):
ATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:107582 original size:22 final size:22
Alignment explanation
Indices: 107557--107598 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
107547 ATTTATTAGC
107557 ATGGATTGATTTATTTTAAAAT
1 ATGGATTGATTTATTTTAAAAT
107579 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
107599 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAT
Found at i:107626 original size:22 final size:22
Alignment explanation
Indices: 107601--107674 Score: 53
Period size: 22 Copynumber: 3.2 Consensus size: 22
107591 ATTTTAAATA
107601 ATTTATTAGTATGGATTGAATT
1 ATTTATTAGTATGGATTGAATT
* *
107623 ATTT-TAAAATATGGATTGATTTATT
1 ATTTAT-TAGTATGGATTGA---ATT
*
107648 ATTGTAGTT-GTATGGATTGATTT
1 ATT-TA-TTAGTATGGATTGAATT
107671 ATTT
1 ATTT
107675 TAAATAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 14
0.68 0.08 0.24
Matches are distributed among these distances:
21 1 0.03
22 16 0.40
23 5 0.12
25 6 0.15
26 11 0.28
28 1 0.03
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.53
Consensus pattern (22 bp):
ATTTATTAGTATGGATTGAATT
Found at i:107662 original size:80 final size:80
Alignment explanation
Indices: 107578--107727 Score: 275
Period size: 80 Copynumber: 1.9 Consensus size: 80
107568 TATTTTAAAA
107578 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTA-AAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAGAAA-ATGGATTGA
107642 TTTATTATTGTAGTTG
65 TTTATTATTGTAGTTG
*
107658 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAGAAAATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAGAAAATGGATTGAT
107723 TTATT
66 TTATT
107728 TTAAATAATT
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
80 65 0.96
81 3 0.04
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAATTATTTTAGAAAATGGATTGAT
TTATTATTGTAGTTG
Found at i:107698 original size:32 final size:32
Alignment explanation
Indices: 107657--107764 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
107647 TATTGTAGTT
107657 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
107689 GTATGGATTGATTTATTTT--A-GA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
107713 --ATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
107743 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
107765 ATATAGATTG
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
22 17 0.27
24 2 0.03
25 1 0.02
26 1 0.02
28 1 0.02
29 1 0.02
30 2 0.03
32 39 0.61
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:107797 original size:80 final size:80
Alignment explanation
Indices: 107713--107861 Score: 289
Period size: 80 Copynumber: 1.9 Consensus size: 80
107703 ATTTTAGAAA
*
107713 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATT
1 ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATT
107778 TATTATTATAGTTGT
66 TATTATTATAGTTGT
107793 ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATT
1 ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATT
107858 TATT
66 TATT
107862 TTAAATAATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (80 bp):
ATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATAGATTGATT
TATTATTATAGTTGT
Found at i:110136 original size:13 final size:13
Alignment explanation
Indices: 110120--110151 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
110110 GATATAACTG
*
110120 TATATTATATGTA
1 TATATTATATATA
110133 TATATTATATATA
1 TATATTATATATA
110146 TATATT
1 TATATT
110152 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TATATTATATATA
Found at i:110319 original size:7 final size:7
Alignment explanation
Indices: 110246--110331 Score: 63
Period size: 7 Copynumber: 12.0 Consensus size: 7
110236 TTAATGTATA
110246 TATATTT
1 TATATTT
* *
110253 AATAATT
1 TATATTT
110260 TA-ATTT
1 TATATTT
110266 T-TACTTT
1 TATA-TTT
*
110273 TAGTTTTT
1 TA-TATTT
110281 TATA-TT
1 TATATTT
110287 TAT-TTT
1 TATATTT
110293 TAAATATTTT
1 T--ATA-TTT
110303 TAATATTT
1 T-ATATTT
110311 TATATTT
1 TATATTT
110318 TATATTT
1 TATATTT
110325 TATATTT
1 TATATTT
110332 AAAATAATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
6 13 0.20
7 31 0.48
8 11 0.17
9 5 0.08
10 4 0.06
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (7 bp):
TATATTT
Found at i:110740 original size:11 final size:10
Alignment explanation
Indices: 110724--110750 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
110714 TTAATTATTT
110724 AAAAAAATAA
1 AAAAAAATAA
110734 AAAAAAATAA
1 AAAAAAATAA
110744 AAAAAAA
1 AAAAAAA
110751 CATTTGATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:112501 original size:27 final size:27
Alignment explanation
Indices: 112427--112507 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
112417 TAATATTTTT
*
112427 ATATATATTATTTAATTGT-ATGATATG
1 ATATACATTATTTAATT-TAATGATATG
**
112454 -TATCACATTATTTAAAATAATGATATG
1 ATAT-ACATTATTTAATTTAATGATATG
112481 ATATA-ATTATTTATATTTAATTGATAT
1 ATATACATTATTTA-ATTTAA-TGATAT
112508 AATAATATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
26 12 0.27
27 23 0.52
28 9 0.20
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (27 bp):
ATATACATTATTTAATTTAATGATATG
Found at i:116673 original size:30 final size:29
Alignment explanation
Indices: 116637--116705 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
116627 ATTTTTTAAC
116637 ATAAAATGATAAATTTAAAACATATAAATA
1 ATAAAATGATAAATTTAAAACAT-TAAATA
* * * * *
116667 ATAAAATTATCATTTTATAACATTTAATA
1 ATAAAATGATAAATTTAAAACATTAAATA
*
116696 ATTAAATGAT
1 ATAAAATGAT
116706 TTAACAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (29 bp):
ATAAAATGATAAATTTAAAACATTAAATA
Found at i:118940 original size:17 final size:17
Alignment explanation
Indices: 118913--118951 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
118903 AATTTATAAT
118913 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
118929 TAATTATAAATAATATC
1 TAATTATAAATAATATC
118946 TAATTA
1 TAATTA
118952 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:119083 original size:9 final size:9
Alignment explanation
Indices: 119069--119094 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
119059 TATATTTAAA
119069 GGTTAATTC
1 GGTTAATTC
119078 GGTTAATTC
1 GGTTAATTC
119087 GGTTAATT
1 GGTTAATT
119095 AATCGATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (9 bp):
GGTTAATTC
Found at i:120556 original size:19 final size:19
Alignment explanation
Indices: 120532--120569 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
120522 AAAATTCAAC
120532 AAAATAAAATTTTATAATT
1 AAAATAAAATTTTATAATT
**
120551 AAAATATTATTTTATAATT
1 AAAATAAAATTTTATAATT
120570 TTTAATAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAAATAAAATTTTATAATT
Found at i:125907 original size:26 final size:25
Alignment explanation
Indices: 125878--125930 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
125868 AAATATCTAC
*
125878 AATTAAATTT-AAACATAAACTTAAAT
1 AATTAAATTTGAAAAATAAA--TAAAT
*
125904 AATTAGATTTGAAAAATAAATAAAT
1 AATTAAATTTGAAAAATAAATAAAT
125929 AA
1 AA
125931 AATTTGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 9 0.38
27 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
AATTAAATTTGAAAAATAAATAAAT
Found at i:138944 original size:15 final size:15
Alignment explanation
Indices: 138924--138957 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
138914 TTTAATTCAC
138924 ATTTCAAATATAAAT
1 ATTTCAAATATAAAT
138939 ATTTCAAATATAAAT
1 ATTTCAAATATAAAT
138954 ATTT
1 ATTT
138958 TAATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTTCAAATATAAAT
Found at i:147810 original size:28 final size:28
Alignment explanation
Indices: 147745--147812 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
147735 CCTAAACCCG
* *
147745 AACCCGACCCAAATATCACACTTAAAAA
1 AACCCAACCCGAATATCACACTTAAAAA
*
147773 AA-TCAGACCCGAATATCACACTTAAAAA
1 AACCCA-ACCCGAATATCACACTTAAAAA
147801 AACCCAACCCGA
1 AACCCAACCCGA
147813 CCCGACTCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 31 0.91
29 2 0.06
ACGTcount: A:0.49, C:0.32, G:0.06, T:0.13
Consensus pattern (28 bp):
AACCCAACCCGAATATCACACTTAAAAA
Found at i:147935 original size:27 final size:28
Alignment explanation
Indices: 147812--147939 Score: 125
Period size: 28 Copynumber: 4.4 Consensus size: 28
147802 ACCCAACCCG
*
147812 ACCCGACTCGAATATCAAACTTAAAAAA
1 ACCCGACCCGAATATCAAACTTAAAAAA
* * ** *
147840 ATCCGATCCG-ATCCCAAATTTTTTAAAAAA
1 ACCCGACCCGAATATCAAA---CTTAAAAAA
147870 ACCCGACCGACCCGAATATCAAACTTAAAAAA
1 A--C--CCGACCCGAATATCAAACTTAAAAAA
147902 ACCCGACCCGAATATCAAACTT-AAAAA
1 ACCCGACCCGAATATCAAACTTAAAAAA
147929 ACCCGACCCGA
1 ACCCGACCCGA
147940 CCCAAATCCG
Statistics
Matches: 81, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
27 22 0.27
28 27 0.33
30 10 0.12
32 9 0.11
34 7 0.09
35 6 0.07
ACGTcount: A:0.45, C:0.30, G:0.09, T:0.17
Consensus pattern (28 bp):
ACCCGACCCGAATATCAAACTTAAAAAA
Found at i:148002 original size:31 final size:33
Alignment explanation
Indices: 147957--148022 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 33
147947 CCGAACCCGT
*
147957 AATTTTTTTAAAAAAATCCGACCCG-ATCCCAA
1 AATTTTTTTAAAAAAATCCGACCCGAATACCAA
147989 AATTTTTTT-AAAAAATCCGACCCGAATACCAA
1 AATTTTTTTAAAAAAATCCGACCCGAATACCAA
148021 AA
1 AA
148023 GATTGATGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (33 bp):
AATTTTTTTAAAAAAATCCGACCCGAATACCAA
Found at i:149393 original size:44 final size:41
Alignment explanation
Indices: 149316--149397 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
149306 GCAACGCGAT
* *
149316 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
149357 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
149398 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 25 0.69
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:149407 original size:19 final size:20
Alignment explanation
Indices: 149318--149408 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
149308 AACGCGATTT
149318 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
149338 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
149357 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
149382 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
149401 TGAAAAAT
1 TGAAAAAT
149409 CCAAAATAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 34 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:149843 original size:21 final size:21
Alignment explanation
Indices: 149817--149907 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
149807 ATTTTAGAAA
149817 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
149838 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
* **
149857 ATCGCAACTCGAACTTAAACT
1 ATCGCAACGCGAACTTGGACT
*
149878 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
149899 ATCGCAACG
1 ATCGCAACG
149908 AATTTGAACT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
19 16 0.29
21 40 0.71
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:149870 original size:40 final size:40
Alignment explanation
Indices: 149787--149958 Score: 167
Period size: 40 Copynumber: 4.3 Consensus size: 40
149777 ACTAGTCGCA
* *
149787 AACTTGGACTATGGCAACGAATTTTAGAAAATCGCAACGCG
1 AACTTGGACTATCGCAACGAA-TTTGGAAAATCGCAACGCG
*
149828 AACTTGGACTATCGCAACGAATTTGGAAAATCGCAACTCG
1 AACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCG
** * **
149868 AACTTAAACTATCGCAACGTGAACTTGGACTATCGCAA--CG
1 AACTTGGACTATCGCAAC--GAATTTGGAAAATCGCAACGCG
* * *
149908 AATTTGAACTA--ACATA--AATTTGGAAAATCGCAACGCG
1 AACTTGGACTATCGCA-ACGAATTTGGAAAATCGCAACGCG
149945 AACTTGGACTATCG
1 AACTTGGACTATCG
149959 TAAAATCGCG
Statistics
Matches: 107, Mismatches: 17, Indels: 16
0.76 0.12 0.11
Matches are distributed among these distances:
35 14 0.13
37 11 0.10
38 2 0.02
39 1 0.01
40 44 0.41
41 20 0.19
42 15 0.14
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (40 bp):
AACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCG
Found at i:151119 original size:28 final size:29
Alignment explanation
Indices: 151088--151142 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
151078 TTAAGGATTA
*
151088 AATTAATA-TTTTATATAAACTTAAAGTC
1 AATTAATATTTTTATATAAAATTAAAGTC
* *
151116 AATTGATATTTTTATTTAAAATTAAAG
1 AATTAATATTTTTATATAAAATTAAAG
151143 GATTAAGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 7 0.30
29 16 0.70
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.45
Consensus pattern (29 bp):
AATTAATATTTTTATATAAAATTAAAGTC
Found at i:152215 original size:16 final size:16
Alignment explanation
Indices: 152189--152226 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
152179 CATACTTATT
152189 TTTTATATTTTGACCAC
1 TTTT-TATTTTGACCAC
152206 TTTTTATTTTGACCAC
1 TTTTTATTTTGACCAC
152222 TTTTT
1 TTTTT
152227 TTTCTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.18, C:0.16, G:0.05, T:0.61
Consensus pattern (16 bp):
TTTTTATTTTGACCAC
Found at i:152806 original size:33 final size:32
Alignment explanation
Indices: 152769--152842 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
152759 TGAATATCTA
*
152769 AAAATTTTAGAAGGGTC-AAATTGATTTTTTTTT
1 AAAATTTTAGAA-GGTCAAAATT-AATTTTTTTT
152802 AAAATATTTA-AAGGTCAAAATTAATTTTTTTT
1 AAAAT-TTTAGAAGGTCAAAATTAATTTTTTTT
152834 -AAATTTTAG
1 AAAATTTTAG
152843 GGAGGCCATG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
30 4 0.11
31 4 0.11
32 13 0.35
33 12 0.32
34 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (32 bp):
AAAATTTTAGAAGGTCAAAATTAATTTTTTTT
Found at i:152818 original size:32 final size:34
Alignment explanation
Indices: 152769--152842 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
152759 TGAATATCTA
*
152769 AAAATTTTAGAAGGGTC-AAATTGATTTTTTTTT
1 AAAATTTTAGAAGGGTCAAAATTAATTTTTTTTT
152802 AAAATATTTA-AA-GGTCAAAATTAA-TTTTTTTT
1 AAAAT-TTTAGAAGGGTCAAAATTAATTTTTTTTT
152834 -AAATTTTAG
1 AAAATTTTAG
152843 GGAGGCCATG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
30 4 0.11
31 4 0.11
32 12 0.32
33 13 0.35
34 4 0.11
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (34 bp):
AAAATTTTAGAAGGGTCAAAATTAATTTTTTTTT
Found at i:155003 original size:24 final size:24
Alignment explanation
Indices: 154971--155037 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
154961 TTGGGGTAAC
*
154971 TTGGTGGCTTCGGTGGAAG-ATATG
1 TTGGTGGCTTCGGTGG-AGCATAAG
* *
154995 TTGGTGGCTTGGGTGGAGCGTAAG
1 TTGGTGGCTTCGGTGGAGCATAAG
155019 TTGGTGGCTT-GGTTGGAGC
1 TTGGTGGCTTCGG-TGGAGC
155038 CTTGGGTGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 4 0.11
24 34 0.89
ACGTcount: A:0.12, C:0.09, G:0.46, T:0.33
Consensus pattern (24 bp):
TTGGTGGCTTCGGTGGAGCATAAG
Found at i:155063 original size:39 final size:39
Alignment explanation
Indices: 155020--155147 Score: 184
Period size: 39 Copynumber: 3.3 Consensus size: 39
155010 GAGCGTAAGT
155020 TGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGGGTAAAC
1 TGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGGGTAAAC
* * * * *
155059 TGGTGGCTTGGGTAGTGTCTTGGGTGGAGGAGAGTAAAC
1 TGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGGGTAAAC
* * *
155098 TGGTGGCTTGGTTGGCGCCTTGGGTGGAGCAGGGTAAAG
1 TGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGGGTAAAC
155137 TGGTGGCTTGG
1 TGGTGGCTTGG
155148 GTGGTGGAGG
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.14, C:0.10, G:0.48, T:0.27
Consensus pattern (39 bp):
TGGTGGCTTGGTTGGAGCCTTGGGTGGAGGAGGGTAAAC
Found at i:155158 original size:27 final size:27
Alignment explanation
Indices: 155116--155174 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
155106 TGGTTGGCGC
*
155116 CTTGGGTGGAGCAGGGTAAAGTGGTGG
1 CTTGGGTGGAGCAGGGTAAACTGGTGG
* *
155143 CTTGGGTGGTGGAGGGTAAACTGGTGG
1 CTTGGGTGGAGCAGGGTAAACTGGTGG
155170 CTTGG
1 CTTGG
155175 TTGGCGCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.15, C:0.08, G:0.51, T:0.25
Consensus pattern (27 bp):
CTTGGGTGGAGCAGGGTAAACTGGTGG
Found at i:155207 original size:66 final size:66
Alignment explanation
Indices: 155077--155218 Score: 187
Period size: 66 Copynumber: 2.2 Consensus size: 66
155067 TGGGTAGTGT
* * **
155077 CTTGGGTGGAGGAGAGTAAACTGGTGGCTTGGTTGGCGCCTTGGGTGGAGCAGGGTAAAGTGGTG
1 CTTGGGTGGTGGAGAGTAAACTGGTGGCTTGGTTGGCGCCTTGGGCGGAGCAGCATAAAGTGGTG
155142 G
66 G
* * * *
155143 CTTGGGTGGTGGAGGGTAAACTGGTGGCTTGGTTGGCGCTTTTGGCGGAGGAGCAT-AAGTTGGT
1 CTTGGGTGGTGGAGAGTAAACTGGTGGCTTGGTTGGCGCCTTGGGCGGAGCAGCATAAAG-TGGT
155207 GG
65 GG
*
155209 CTTGGTTGGT
1 CTTGGGTGGT
155219 ACTGTGGGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
65 3 0.05
66 63 0.95
ACGTcount: A:0.14, C:0.11, G:0.47, T:0.28
Consensus pattern (66 bp):
CTTGGGTGGTGGAGAGTAAACTGGTGGCTTGGTTGGCGCCTTGGGCGGAGCAGCATAAAGTGGTG
G
Found at i:158986 original size:22 final size:21
Alignment explanation
Indices: 158961--159002 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
158951 GAATTCTACC
158961 TAAAAATCAC-AAAATATATATA
1 TAAAAAT-ACTAAAATA-ATATA
158983 TAAAAATACTAAAATAATAT
1 TAAAAATACTAAAATAATAT
159003 CATTTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATACTAAAATAATATA
Found at i:164323 original size:29 final size:29
Alignment explanation
Indices: 164273--164376 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
164263 GCCAATGGAG
* * **
164273 AGGTCGCCATGCAATCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
*
164302 AGGTCGCAATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
**
164331 AGGTCGCCATGTAGTCCCGGCGACCAAGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
164360 AGGTCGCCATGTAGTCC
1 AGGTCGCCATGTAGTCC
164377 TAGCTCACGA
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:165022 original size:44 final size:43
Alignment explanation
Indices: 164936--165033 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 43
164926 ATATGTTTGA
* *
164936 TAGTTATAGTTAAAAATAATTAATTAGTTTGTTTTGTTAATAGT
1 TAGTTATA-TAAAAAATAATTAATTAGTTTGTTTAGTTAATAGT
* *
164980 TAGTTATATAAAAAATTATT-TTTAGTTTGTGTTAGTTAAATAGT
1 TAGTTATATAAAAAATAATTAATTAGTTTGT-TTAGTT-AATAGT
165024 TAAGTTATAT
1 T-AGTTATAT
165034 TTGTTTGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 9 0.19
43 15 0.32
44 15 0.32
45 8 0.17
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (43 bp):
TAGTTATATAAAAAATAATTAATTAGTTTGTTTAGTTAATAGT
Found at i:165220 original size:16 final size:16
Alignment explanation
Indices: 165188--165234 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
165178 TTTTAAAAGT
*
165188 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
165204 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
165220 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
165235 ATTTTAGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:166467 original size:22 final size:23
Alignment explanation
Indices: 166425--166468 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
166415 TTTAATTATT
*
166425 ATTTAAATTAACTATATTATTTG
1 ATTTAAATCAACTATATTATTTG
*
166448 ATTTAAATCAA-TTTATTATTT
1 ATTTAAATCAACTATATTATTT
166469 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTTAAATCAACTATATTATTTG
Done.