Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001445.1 Hibiscus syriacus cultivar Beakdansim tig00002794_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: 73735
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7717 original size:21 final size:20
Alignment explanation
Indices: 7668--7720 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
7658 AAATTATCTT
*
7668 TCAGTATTGATATTGAGACC
1 TCAGTATCGATATTGAGACC
*
7688 TCAGTATCGATATTGAGCCAC
1 TCAGTATCGATATTGAGAC-C
*
7709 TCGGTATCGATA
1 TCAGTATCGATA
7721 CCCATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (20 bp):
TCAGTATCGATATTGAGACC
Found at i:11392 original size:19 final size:19
Alignment explanation
Indices: 11365--11403 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
11355 TTTTATATTA
11365 AGGGATGAACTAAAATTCT
1 AGGGATGAACTAAAATTCT
*
11384 AGGGGTGAACTAAAATTCT
1 AGGGATGAACTAAAATTCT
11403 A
1 A
11404 AGGAACGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.23, T:0.26
Consensus pattern (19 bp):
AGGGATGAACTAAAATTCT
Found at i:13396 original size:37 final size:36
Alignment explanation
Indices: 13341--13424 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 36
13331 TGGCAACCAA
13341 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
13378 CTTTGAAAAATGGTTTTTCAAAGTTTGGTATATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
13415 -GTTGAAAAAT
1 CTTTGAAAAAT
13425 TTTAATAGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 15 0.35
37 28 0.65
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:18004 original size:36 final size:36
Alignment explanation
Indices: 17891--18008 Score: 168
Period size: 35 Copynumber: 3.3 Consensus size: 36
17881 TGGCAACCAA
*
17891 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
**
17927 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAACATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
17962 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
*
17999 -GTTGAAAAAT
1 CTTTGAAAAAT
18009 TGTAATGGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
35 32 0.44
36 21 0.29
37 20 0.27
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:19718 original size:27 final size:27
Alignment explanation
Indices: 19678--19770 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 27
19668 TATACAATCA
*
19678 TTAAATAAAATTAAAATATTAATTATAT
1 TTAAA-AAAATTAAAATAATAATTATAT
**
19706 TTAAAAAAATTAATTTAATAATTATAT
1 TTAAAAAAATTAAAATAATAATTATAT
* * * *
19733 ATAAAGAAATTATATAAAAATAAATATAGT
1 TTAAAAAAATTA-A-AATAATAATTATA-T
19763 TTAAAAAA
1 TTAAAAAA
19771 CAAAATTTAA
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
27 29 0.57
28 6 0.12
29 9 0.18
30 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TTAAAAAAATTAAAATAATAATTATAT
Found at i:24238 original size:13 final size:13
Alignment explanation
Indices: 24220--24250 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
24210 CCAGAGATGT
24220 GTCGGATTCGGGA
1 GTCGGATTCGGGA
24233 GTCGGATTCGGGA
1 GTCGGATTCGGGA
24246 GTCGG
1 GTCGG
24251 TTACAGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.48, T:0.23
Consensus pattern (13 bp):
GTCGGATTCGGGA
Found at i:24516 original size:12 final size:11
Alignment explanation
Indices: 24510--24586 Score: 55
Period size: 13 Copynumber: 6.3 Consensus size: 11
24500 AAAAAAGTAA
24510 AAAAAAAAAGAT
1 AAAAAAAAA-AT
*
24522 AAAACAAACAAT
1 AAAA-AAAAAAT
*
24534 AAAAATAAAAT
1 AAAAAAAAAAT
*
24545 AAAATAAGATAAT
1 AAAA-AA-AAAAT
24558 AAACAAATAAAAT
1 AAA-AAA-AAAAT
24571 AAAATAAACAAAT
1 AAAA-AAA-AAAT
24584 AAA
1 AAA
24587 CAAATTAGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
11 9 0.17
12 13 0.25
13 29 0.56
14 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:24545 original size:5 final size:5
Alignment explanation
Indices: 24535--24578 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
24525 ACAAACAATA
*
24535 AAAAT AAAAT AAAAT AAGAT AATAA- ACAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT AAA
24579 CAAATAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 31 0.91
6 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:24556 original size:21 final size:20
Alignment explanation
Indices: 24502--24578 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
24492 ATGACTTAAA
*
24502 AAAAGTAAAA-AAAAAAAGAT
1 AAAA-TAAAATAAAAAAAAAT
*
24522 AAAACAAACAATAAAAATAAAAT
1 AAAA-TAA-AATAAAAA-AAAAT
* *
24545 AAAATAAGATAATAAACAAAT
1 AAAATAAAATAA-AAAAAAAT
24566 AAAATAAAATAAA
1 AAAATAAAATAAA
24579 CAAATAAACA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
20 7 0.15
21 21 0.46
22 10 0.22
23 8 0.17
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (20 bp):
AAAATAAAATAAAAAAAAAT
Found at i:24565 original size:26 final size:26
Alignment explanation
Indices: 24520--24591 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
24510 AAAAAAAAAG
*
24520 ATAAAACAAAC-AAT-AA-AAATAAA
1 ATAAAATAAACAAATAAACAAATAAA
*
24543 ATAAAATAAGA-TAATAAACAAATAAA
1 ATAAAATAA-ACAAATAAACAAATAAA
24569 ATAAAATAAACAAATAAACAAAT
1 ATAAAATAAACAAATAAACAAAT
24592 TAGAAAAACC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 8 0.19
24 4 0.10
25 3 0.07
26 27 0.64
ACGTcount: A:0.75, C:0.07, G:0.01, T:0.17
Consensus pattern (26 bp):
ATAAAATAAACAAATAAACAAATAAA
Found at i:24576 original size:18 final size:18
Alignment explanation
Indices: 24498--24586 Score: 66
Period size: 18 Copynumber: 5.2 Consensus size: 18
24488 ATAAATGACT
* *
24498 TAAAA-AAAGTAAAAAAA
1 TAAAATAAAATAAACAAA
* *
24515 AAAAGATAAAACAAAC-AA
1 TAAA-ATAAAATAAACAAA
24533 TAAAAATAAAAT--A-AAA
1 T-AAAATAAAATAAACAAA
*
24549 TAAGAT--AATAAACAAA
1 TAAAATAAAATAAACAAA
24565 TAAAATAAAATAAACAAA
1 TAAAATAAAATAAACAAA
24583 TAAA
1 TAAA
24587 CAAATTAGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 17
0.69 0.10 0.21
Matches are distributed among these distances:
13 3 0.05
15 5 0.09
16 12 0.22
17 3 0.05
18 23 0.42
19 9 0.16
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.15
Consensus pattern (18 bp):
TAAAATAAAATAAACAAA
Found at i:25085 original size:24 final size:21
Alignment explanation
Indices: 25058--25104 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
25048 AATAAGTAAA
*
25058 AAAGATAGTAGTAATAGAAATAAT
1 AAAGATAATA-TAA-AG-AATAAT
25082 AAAGATAATATAAAGAATAAT
1 AAAGATAATATAAAGAATAAT
25103 AA
1 AA
25105 TAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 3 0.14
24 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (21 bp):
AAAGATAATATAAAGAATAAT
Found at i:25110 original size:21 final size:21
Alignment explanation
Indices: 25076--25116 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25066 TAGTAATAGA
*
25076 AATAATAAAGATAATATAAAG
1 AATAATAAAGATAAAATAAAG
25097 AATAATAATA-ATAAAATAAA
1 AATAATAA-AGATAAAATAAA
25117 AATGGTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (21 bp):
AATAATAAAGATAAAATAAAG
Found at i:25181 original size:30 final size:29
Alignment explanation
Indices: 25129--25185 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
25119 TGGTAAAGAG
25129 TATAAAAAAAATAAGTATATATATATATA
1 TATAAAAAAAATAAGTATATATATATATA
*
25158 TATATAAAATAATAACGTA-ATATATATA
1 TATA-AAAAAAATAA-GTATATATATATA
25186 AAAAAAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 18 0.72
31 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (29 bp):
TATAAAAAAAATAAGTATATATATATATA
Found at i:26727 original size:105 final size:105
Alignment explanation
Indices: 26561--27643 Score: 1743
Period size: 105 Copynumber: 10.3 Consensus size: 105
26551 CGAGCACGAA
* * ** * *
26561 ATCCCTCGTCGTGAAGTTGAAAACGAGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGT
1 ATCCTTCGTTGTGAAGTTGAAATTG-GCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGT
*
26626 CCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAAT
64 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* ** * * *
26668 ATCCTTTGTTGTGAAGCAGAAATTGGTTCTGAAATTGAGAAATTTTTGCTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
*
26733 CTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* ** * *
26773 ATCCTTTGTTGTGAAGCAGAAATTGGTTCTGAAATTGAGAAATGTTTGCTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
*
26838 CTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* ** * *
26878 ATCCTTTGTTGTGAAGCAGAAATTGGTTCTGAAATTGAGAAATGTTTGCTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
26943 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
26983 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAATGTTTGTTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
* *
27048 CTTCGTCGTGAGGTTGAACTTGTGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
** * * *
27088 ATCCTTCGTTGTGAAGCAGAAATTGGCTTTGAAATTGAGAAATGTTCGTTGACAACCAGTGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
27153 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* * *
27193 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
27258 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* * *
27298 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
27363 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
* * * *
27403 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGTTTATTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
27468 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
*
27508 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCC
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
*
27573 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGTCCAAT
66 CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
27613 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 ATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
27644 GGTAAAACCT
Statistics
Matches: 931, Mismatches: 45, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
105 899 0.97
106 14 0.02
107 18 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
ATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCC
CTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAAT
Found at i:37918 original size:10 final size:10
Alignment explanation
Indices: 37893--37926 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
37883 AAGGTTAGTA
*
37893 AAATAGAAAT
1 AAATAAAAAT
*
37903 AGATAAAAAT
1 AAATAAAAAT
37913 AAATAAAAAT
1 AAATAAAAAT
37923 AAAT
1 AAAT
37927 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:38939 original size:12 final size:11
Alignment explanation
Indices: 38924--39000 Score: 55
Period size: 13 Copynumber: 6.3 Consensus size: 11
38914 AAAAAGTATA
38924 AAAAAAAAAGAT
1 AAAAAAAAA-AT
*
38936 AAAACAAACAAT
1 AAAA-AAAAAAT
*
38948 AAAAATAAAAT
1 AAAAAAAAAAT
*
38959 AAAATAAGATAAT
1 AAAA-AA-AAAAT
38972 AAACAAATAAAAT
1 AAA-AAA-AAAAT
38985 AAAATAAACAAAT
1 AAAA-AAA-AAAT
38998 AAA
1 AAA
39001 CAAATTAGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
11 9 0.17
12 13 0.25
13 29 0.56
14 1 0.02
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:38959 original size:5 final size:5
Alignment explanation
Indices: 38949--38992 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
38939 ACAAACAATA
*
38949 AAAAT AAAAT AAAAT AAGAT AATAA- ACAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT AAA
38993 CAAATAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 31 0.91
6 3 0.09
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:38970 original size:21 final size:20
Alignment explanation
Indices: 38925--38992 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 20
38915 AAAAGTATAA
*
38925 AAAAAAAAGATAAAACAAACAAT
1 AAAAAAAA-ATAAAA-TAA-AAT
*
38948 AAAAATAAAATAAAATAAGAT
1 AAAAA-AAAATAAAATAAAAT
*
38969 AATAAACAAATAAAATAAAAT
1 AA-AAAAAAATAAAATAAAAT
38990 AAA
1 AAA
38993 CAAATAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 19 0.49
22 5 0.13
23 11 0.28
24 3 0.08
ACGTcount: A:0.78, C:0.04, G:0.03, T:0.15
Consensus pattern (20 bp):
AAAAAAAAATAAAATAAAAT
Found at i:38979 original size:26 final size:26
Alignment explanation
Indices: 38921--39005 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
38911 TAAAAAAAGT
* *
38921 ATAAA-AAAAAAAGATAAAACAAAC-A
1 ATAAACAAATAAA-ATAAAATAAACAA
*
38946 AT-AA-AAATAAAATAAAATAAGA-TA
1 ATAAACAAATAAAATAAAATAA-ACAA
38970 ATAAACAAATAAAATAAAATAAACAA
1 ATAAACAAATAAAATAAAATAAACAA
38996 ATAAACAAAT
1 ATAAACAAAT
39006 TAGAAAAACC
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
23 8 0.15
24 12 0.23
25 5 0.10
26 27 0.52
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.15
Consensus pattern (26 bp):
ATAAACAAATAAAATAAAATAAACAA
Found at i:38990 original size:18 final size:18
Alignment explanation
Indices: 38921--39000 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
38911 TAAAAAAAGT
*
38921 ATAAA-AAAAAAAGATAAA
1 ATAAACAAATAAA-ATAAA
*
38939 ACAAAC-AATAAAAATAAA
1 ATAAACAAAT-AAAATAAA
*
38957 AT--A-AAATAAGAT--A
1 ATAAACAAATAAAATAAA
38970 ATAAACAAATAAAATAAA
1 ATAAACAAATAAAATAAA
38988 ATAAACAAATAAA
1 ATAAACAAATAAA
39001 CAAATTAGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
13 3 0.06
15 5 0.10
16 12 0.24
18 26 0.53
19 3 0.06
ACGTcount: A:0.78, C:0.05, G:0.03, T:0.15
Consensus pattern (18 bp):
ATAAACAAATAAAATAAA
Found at i:39303 original size:2 final size:2
Alignment explanation
Indices: 39296--39333 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
39286 AAACATGTAA
39296 AT AT AT AT AT 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 AT AT AT AT AT
39334 TAGTTAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39505 original size:24 final size:21
Alignment explanation
Indices: 39478--39524 Score: 58
Period size: 24 Copynumber: 2.1 Consensus size: 21
39468 AATAAGTAAA
*
39478 AAAGATAGTAGTAATAGAAATAAT
1 AAAGATAATA-TAA-AG-AATAAT
39502 AAAGATAATATAAAGAATAAT
1 AAAGATAATATAAAGAATAAT
39523 AA
1 AA
39525 TAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 3 0.14
24 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (21 bp):
AAAGATAATATAAAGAATAAT
Found at i:39535 original size:9 final size:9
Alignment explanation
Indices: 39489--39536 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
39479 AAGATAGTAG
*
39489 TAATAGAAA
1 TAATAAAAA
*
39498 TAATAAAGA
1 TAATAAAAA
*
39507 TAATATAAA
1 TAATAAAAA
* *
39516 GAATAATAA
1 TAATAAAAA
39525 TAATAAAAA
1 TAATAAAAA
39534 TAA
1 TAA
39537 AAATGGTAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (9 bp):
TAATAAAAA
Found at i:39587 original size:12 final size:11
Alignment explanation
Indices: 39562--39615 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 11
39552 ATAAAAAGAA
39562 ATAAGTATATAT
1 ATAA-TATATAT
*
39574 ATATATATACAT
1 ATA-ATATATAT
39586 ATAATA-ATA-
1 ATAATATATAT
39595 ATAATA-ATA-
1 ATAATATATAT
39604 ATAATATATAT
1 ATAATATATAT
39615 A
1 A
39616 ATAAAACGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
9 15 0.41
10 5 0.14
11 4 0.11
12 12 0.32
13 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (11 bp):
ATAATATATAT
Found at i:39594 original size:3 final size:3
Alignment explanation
Indices: 39586--39619 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
39576 ATATATACAT
39586 ATA ATA ATA ATA ATA ATA ATA AT- ATA TATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA A
39620 AACGTAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:39616 original size:12 final size:12
Alignment explanation
Indices: 39570--39619 Score: 59
Period size: 12 Copynumber: 4.1 Consensus size: 12
39560 AAATAAGTAT
39570 ATATATATATATA
1 ATATATATA-ATA
39583 CATATA-ATAATA
1 -ATATATATAATA
39595 ATA-ATAATAATA
1 ATATAT-ATAATA
39607 ATATATATAATA
1 ATATATATAATA
39619 A
1 A
39620 AACGTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.03
11 3 0.09
12 19 0.58
13 5 0.15
14 5 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATATAATA
Found at i:54221 original size:195 final size:193
Alignment explanation
Indices: 53836--54225 Score: 762
Period size: 195 Copynumber: 2.0 Consensus size: 193
53826 GGTATGATTT
53836 TTAAAATTACTGAAAATTTAGATACTAAAACAGACTAAAAGTGATAGTTTAGGTACTAACACATA
1 TTAAAATTACTGAAAATTTAGATACTAAAACAGACTAAAAGTGATAGTTTAGGTACTAACACATA
53901 ATTTATCCATAATTTTAATACAATAAAAAGGGCTTAATGCATTTTATACACCCTAACGTTACCTG
66 ATTTATCCATAATTTTAATACAATAAAAAGGGCTTAATGCATTTTATACACCCTAACGTTACCTG
53966 CTTTCCAATTTGGTATGTAGTGTTTTTTCCTCAGTAGTGCCTAACATTTATAAAAGTTACTTA
131 CTTTCCAATTTGGTATGTAGTGTTTTTTCCTCAGTAGTGCCTAACATTTATAAAAGTTACTTA
54029 TTAAAATTACTGAAAATTTAGATACTAAAACAGACTAAAAGTGATAGTTTAGGTACTAAACACAT
1 TTAAAATTACTGAAAATTTAGATACTAAAACAGACTAAAAGTGATAGTTTAGGTACT-AACACAT
54094 AATTTATCCATAATTTTAATACAATAAAAAGGGCTTAATGCATTTTATACACCCTAACGTTTACC
65 AATTTATCCATAATTTTAATACAATAAAAAGGGCTTAATGCATTTTATACACCCTAACG-TTACC
54159 TGCTTTCCAATTTGGTATGTAGTGTTTTTTCCTCAGTAGTGCCTAACATTTATAAAAGTTACTTA
129 TGCTTTCCAATTTGGTATGTAGTGTTTTTTCCTCAGTAGTGCCTAACATTTATAAAAGTTACTTA
54224 TT
1 TT
54226 TATAAAAAAT
Statistics
Matches: 195, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
193 57 0.29
194 66 0.34
195 72 0.37
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (193 bp):
TTAAAATTACTGAAAATTTAGATACTAAAACAGACTAAAAGTGATAGTTTAGGTACTAACACATA
ATTTATCCATAATTTTAATACAATAAAAAGGGCTTAATGCATTTTATACACCCTAACGTTACCTG
CTTTCCAATTTGGTATGTAGTGTTTTTTCCTCAGTAGTGCCTAACATTTATAAAAGTTACTTA
Found at i:57015 original size:22 final size:23
Alignment explanation
Indices: 56990--57042 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
56980 AAGAGCAAAG
56990 AAATTAAA-AGCAT-AATGAAAAT
1 AAATTAAATAGCATAAAT-AAAAT
*
57012 AAA-TAAATAGTATAAATAAAAT
1 AAATTAAATAGCATAAATAAAAT
57034 AAA-TAAATA
1 AAATTAAATA
57043 AATAAAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 4 0.14
22 21 0.75
23 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.06, T:0.25
Consensus pattern (23 bp):
AAATTAAATAGCATAAATAAAAT
Found at i:57017 original size:4 final size:4
Alignment explanation
Indices: 57008--57048 Score: 55
Period size: 4 Copynumber: 9.8 Consensus size: 4
56998 AGCATAATGA
*
57008 AAAT AAAT AAAT AGTAT AAAT AAAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT A-AAT AAAT -AAAT AAAT AAAT AAAT AAA
57049 AATGTATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:57026 original size:13 final size:12
Alignment explanation
Indices: 57008--57048 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
56998 AGCATAATGA
57008 AAATAAATAAAT
1 AAATAAATAAAT
*
57020 AGTATAAATAAAAT
1 A-AATAAAT-AAAT
57034 AAATAAATAAAT
1 AAATAAATAAAT
57046 AAA
1 AAA
57049 AATGTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:57042 original size:30 final size:30
Alignment explanation
Indices: 57008--57110 Score: 88
Period size: 30 Copynumber: 3.4 Consensus size: 30
56998 AGCATAATGA
57008 AAATAAATAAATAGTATAAATAAAATAAAT
1 AAATAAATAAATAGTATAAATAAAATAAAT
* ** *
57038 AAATAAATAAAAATGTATGTATAATAT-AAT
1 AAATAAATAAATA-GTATAAATAAAATAAAT
*
57068 AAA-ATACTAAATAGTA-ACAATAATAATAAAT
1 AAATA-AATAAATAGTATA-AATAA-AATAAAT
*
57099 AAATGAA-AAATA
1 AAATAAATAAATA
57111 AATATACATA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
29 8 0.14
30 31 0.55
31 17 0.30
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATAAATAAATAGTATAAATAAAATAAAT
Found at i:57049 original size:17 final size:18
Alignment explanation
Indices: 57008--57049 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
56998 AGCATAATGA
*
57008 AAAT-AAATAAATAGTAT
1 AAATAAAATAAATAGAAT
57025 AAATAAAATAAATA-AAT
1 AAATAAAATAAATAGAAT
57042 AAATAAAA
1 AAATAAAA
57050 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AAATAAAATAAATAGAAT
Found at i:57181 original size:2 final size:2
Alignment explanation
Indices: 57174--57204 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57164 AATGATAAGA
57174 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 A
57205 ACGTTAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57833 original size:37 final size:36
Alignment explanation
Indices: 57787--57874 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 36
57777 CTTGTGGATC
* * *
57787 CTATCTTTAGGAGTTTAAATAATAGTAGAACTCTATT
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTA-T
* ** *
57824 CTATTTTTAGGAGTTTGAATCCTAGCAAAATTCTAT
1 CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTAT
57860 CATATTTTTAGGAGT
1 C-TATTTTTAGGAGT
57875 CTGAATCCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
36 2 0.05
37 41 0.95
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (36 bp):
CTATTTTTAGGAGTTTAAATAATAGCAAAACTCTAT
Found at i:58805 original size:106 final size:106
Alignment explanation
Indices: 58621--59987 Score: 1987
Period size: 106 Copynumber: 13.0 Consensus size: 106
58611 GCATTGTTCC
* * * **
58621 GAGTCCAATATCCTCCG-TCGTAAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * * *
58685 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
58727 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * *
58792 CCAGCCGTCCCTTCGTTTGTGAAGTTGAACTTGTGCTGTCTC
66 CCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
58834 GATTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *** * *
58893 TCAGCCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * *
58935 G-GTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
*
58999 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
59040 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
59105 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
59146 GAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
59211 TCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
59252 GAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
59317 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC---GT-T-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
59353 --GT-CAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
59415 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
59456 GAGTCCAATATCATTCGCTGTGAAGTTGTAATTGGCTCTGGAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
59521 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
59562 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
59627 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
59668 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
59733 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
**
59774 GAGTCCAATATCCTTCATTGTG-AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
59838 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
59879 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * *
59943 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
59984 GAGT
1 GAGT
59988 GGCACGATAT
Statistics
Matches: 1150, Mismatches: 92, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
98 89 0.08
99 2 0.00
100 54 0.05
101 28 0.02
102 4 0.00
103 5 0.00
104 3 0.00
105 158 0.14
106 746 0.65
107 61 0.05
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:59503 original size:416 final size:417
Alignment explanation
Indices: 58621--59987 Score: 1962
Period size: 416 Copynumber: 3.3 Consensus size: 417
58611 GCATTGTTCC
* * * **
58621 GAGTCCAATATCCTCCG-TCGTAAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
* * * * *
58685 ACTAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTATGA
65 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGA
* * * *
58750 AGTTGAAATTGGCTTTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTTGTGAA
130 AGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTC-ATCGTGAA
* * * * * *
58815 GTTGAACTTGTGCTGTCTCGATTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T-
194 GTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTG
* * * * *** * *
58877 -GAAAT-TTTGTTGATAATCAGCCACCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTGGGTCC
259 GGAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC-T-TG-CG--TT-GGTCC
* * *
58940 AAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCG
318 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCG
*
59005 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
383 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
59040 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * *
59105 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAA
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
* *
59170 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAATCAGCGGTCCCTTCATCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGT
* *
59235 TGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGG
196 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
59300 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTT-GT-CAATATCC
261 AA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGGTCCAATATCC
* *
59363 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAACGGTCCCTT
325 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTT
59428 CGTCGTGAAGTTGAACTTGCGTTGTCTA
390 CGTCGTGAAGTTGAACTTGCGTTGTCTA
* * * *
59456 GAGTCCAATATCATTCGCTGTGAAGTTGTAATTGGCTCTGGAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* *
59521 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTTGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
* *
59586 GTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGT
*
59651 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG
196 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
59716 AAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
261 -AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC---GT-T-G-GTCCA
**
59781 ATATCCTTCATTGTG-AGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
319 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGG
*
59845 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
384 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
* * * *
59879 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGTCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * *
59943 CCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTTGAGT
66 CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGT
59988 GGCACGATAT
Statistics
Matches: 857, Mismatches: 75, Indels: 29
0.89 0.08 0.03
Matches are distributed among these distances:
416 387 0.45
417 4 0.00
418 57 0.07
419 172 0.20
420 3 0.00
421 1 0.00
422 54 0.06
423 131 0.15
424 48 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (417 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
CCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCATCGTGAAGT
TGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGG
AATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGGTCCAATATCCT
TCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTC
GTCGTGAAGTTGAACTTGCGTTGTCTA
Found at i:61481 original size:13 final size:11
Alignment explanation
Indices: 61465--61529 Score: 58
Period size: 13 Copynumber: 5.4 Consensus size: 11
61455 TTCTTTTTGA
*
61465 TTTTTGTTCTT
1 TTTTTTTTCTT
61476 TCTTTTTGTTCTT
1 T-TTTTT-TTCTT
61489 TTGTTTTTTCCTT
1 TT-TTTTTT-CTT
*
61502 TTTTTCTTTTTT
1 TTTTT-TTTCTT
61514 TCTTTTTTTCTT
1 T-TTTTTTTCTT
61526 TTTT
1 TTTT
61530 CCCTTTTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 4 0.09
12 19 0.42
13 22 0.49
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:61487 original size:29 final size:29
Alignment explanation
Indices: 61452--61520 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
61442 TTTTTGTCCC
61452 TTTTTCTTTTTGATTTTT-GTTCTTTCTT
1 TTTTTCTTTTTGATTTTTCGTTCTTTCTT
* * *
61480 TTTGTTC-TTTTGTTTTTTCCTTTTTTTCTT
1 TTT-TTCTTTTTGATTTTT-CGTTCTTTCTT
61510 TTTTTCTTTTT
1 TTTTTCTTTTT
61521 TTCTTTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
28 13 0.38
29 6 0.18
30 15 0.44
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (29 bp):
TTTTTCTTTTTGATTTTTCGTTCTTTCTT
Found at i:61490 original size:21 final size:21
Alignment explanation
Indices: 61454--61522 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
61444 TTTGTCCCTT
*
61454 TTTCTTTTTGAT-TTTTGTTC
1 TTTCTTTTTGTTCTTTTGTTC
*
61474 TTTCTTTTTGTTCTTTTGTTT
1 TTTCTTTTTGTTCTTTTGTTC
*
61495 TTTCCTTTTT-TTCTTTTTTTC
1 TTT-CTTTTTGTTCTTTTGTTC
61516 TTT-TTTT
1 TTTCTTTT
61523 CTTTTTTCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
19 4 0.09
20 11 0.26
21 22 0.51
22 6 0.14
ACGTcount: A:0.01, C:0.12, G:0.06, T:0.81
Consensus pattern (21 bp):
TTTCTTTTTGTTCTTTTGTTC
Found at i:61506 original size:16 final size:16
Alignment explanation
Indices: 61487--61542 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
61477 CTTTTTGTTC
*
61487 TTTTGTTTTTTCCTTT
1 TTTTCTTTTTTCCTTT
*
61503 TTTTCTTTTTTTCTTT
1 TTTTCTTTTTTCCTTT
61519 TTTTCTTTTTTCCCTTT
1 TTTTCTTTTTT-CCTTT
61536 TTGTTCT
1 TT-TTCT
61543 GATTGAATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
16 25 0.71
17 6 0.17
18 4 0.11
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTCTTTTTTCCTTT
Found at i:61537 original size:9 final size:8
Alignment explanation
Indices: 61452--61529 Score: 70
Period size: 8 Copynumber: 9.5 Consensus size: 8
61442 TTTTTGTCCC
61452 TTTTTCTT
1 TTTTTCTT
*
61460 TTTGAT-TT
1 TTT-TTCTT
*
61468 TTGTTCTT
1 TTTTTCTT
61476 TCTTTT-TGT
1 T-TTTTCT-T
*
61485 TCTTTTGTT
1 T-TTTTCTT
*
61494 TTTTCCTT
1 TTTTTCTT
61502 TTTTTCTT
1 TTTTTCTT
61510 TTTTTCTT
1 TTTTTCTT
61518 TTTTTCTT
1 TTTTTCTT
61526 TTTT
1 TTTT
61530 CCCTTTTTGT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
7 1 0.02
8 43 0.74
9 13 0.22
10 1 0.02
ACGTcount: A:0.01, C:0.12, G:0.05, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:67370 original size:20 final size:20
Alignment explanation
Indices: 67347--67389 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
67337 AATCCACCAC
*
67347 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTCCTAA
* *
67367 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
67387 ATG
1 ATG
67390 AGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Done.