Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001196.1 Hibiscus syriacus cultivar Beakdansim tig00002369_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: 73408
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:14091 original size:18 final size:19
Alignment explanation
Indices: 14056--14092 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
14046 CACGGAATGT
14056 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
14076 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
14093 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:14960 original size:2 final size:2
Alignment explanation
Indices: 14953--15004 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
14943 ATTTAAATTA
14953 AT AT 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 AT AT
14995 AT AT AT AT AT
1 AT AT AT AT AT
15005 GATAGAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21057 original size:2 final size:2
Alignment explanation
Indices: 21050--21093 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
21040 ATACTCAATA
21050 AT AT 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 AT AT
21092 AT
1 AT
21094 TATTGTAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35942 original size:59 final size:60
Alignment explanation
Indices: 35832--35945 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 60
35822 CTGTTTTGTA
* * *
35832 ACTTTTAATAGTCGAATGACTCAACAAATCAATTTCTTATAGTTGAGGGACCATTTTATG
1 ACTTTTAATAGTCGAATGACTCAACAAAGCAAATTCTTATAGTAGAGGGACCATTTTATG
35892 ACTTTTAATAGTC--ATAGACTCAACAAAGCAACATTC-TATAGTA-AGAGGACCATT
1 ACTTTTAATAGTCGAAT-GACTCAACAAAGCAA-ATTCTTATAGTAGAG-GGACCATT
35946 AATGTACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
58 4 0.08
59 28 0.58
60 16 0.33
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (60 bp):
ACTTTTAATAGTCGAATGACTCAACAAAGCAAATTCTTATAGTAGAGGGACCATTTTATG
Found at i:36297 original size:20 final size:21
Alignment explanation
Indices: 36272--36364 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
36262 TTTTCTCAAT
*
36272 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
36292 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
36313 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
36333 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
36354 TCGCAATGCGA
1 TCGCAATGCGA
36365 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:36317 original size:41 final size:41
Alignment explanation
Indices: 36272--36364 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
36262 TTTTCTCAAT
36272 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
36313 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
36354 TCGCAATGCGA
1 TCGCAATGCGA
36365 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:36377 original size:41 final size:41
Alignment explanation
Indices: 36291--36425 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
36281 GAATAAGTAA
** *
36291 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
36332 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
36373 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
36414 TTCGCAACGCGA
1 ATCGCAACGCGA
36426 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:36378 original size:20 final size:20
Alignment explanation
Indices: 36353--36446 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
36343 AATTGGGAAA
*
36353 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
36373 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
36394 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
36414 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
36434 TTCGCAACGCGAT
1 ATCGCAACGCGAT
36447 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:36662 original size:22 final size:22
Alignment explanation
Indices: 36634--36677 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
36624 CACTCTCTCA
36634 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
36656 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
36678 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:36907 original size:19 final size:19
Alignment explanation
Indices: 36883--36933 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
36873 ATCAACCAAG
36883 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
36902 AATCGCAACGCGAAATGCA
1 AATCGCAACGCGAAATGCA
36921 AATCGCAACGCGA
1 AATCGCAACGCGA
36934 TTTTAGTTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGCA
Found at i:36984 original size:20 final size:20
Alignment explanation
Indices: 36959--36996 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36949 CGATTCTCTC
36959 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
36979 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
36997 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:38336 original size:18 final size:18
Alignment explanation
Indices: 38315--38359 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
38305 TCCACTTCGG
* * *
38315 GAGCCATTACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
38333 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
38351 GAGCCATCA
1 GAGCCATCA
38360 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:38866 original size:20 final size:19
Alignment explanation
Indices: 38832--38896 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
38822 TAGTTTACTT
38832 TCGCAACACGAAATGACTA
1 TCGCAACACGAAATGACTA
* *
38851 TCGCAACGCGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
* **
38871 TCGCAATACGAAATGAAAA
1 TCGCAACACGAAATGACTA
38890 TCGCAAC
1 TCGCAAC
38897 GACAAAATCG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 21 0.57
20 16 0.43
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:38905 original size:14 final size:14
Alignment explanation
Indices: 38886--38925 Score: 80
Period size: 14 Copynumber: 2.9 Consensus size: 14
38876 ATACGAAATG
38886 AAAATCGCAACGAC
1 AAAATCGCAACGAC
38900 AAAATCGCAACGAC
1 AAAATCGCAACGAC
38914 AAAATCGCAACG
1 AAAATCGCAACG
38926 CGAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.50, C:0.28, G:0.15, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:38978 original size:14 final size:14
Alignment explanation
Indices: 38959--39016 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
38949 TTGTGTTTCG
38959 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
38973 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38989 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
39005 CGTTGCGATTTT
1 CGTTGCGATTTT
39017 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:38993 original size:32 final size:33
Alignment explanation
Indices: 38954--39032 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
38944 GCGATTTGTG
38954 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
38986 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
39019 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
39033 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:39031 original size:19 final size:19
Alignment explanation
Indices: 38973--39088 Score: 91
Period size: 20 Copynumber: 6.3 Consensus size: 19
38963 GCGATTTTGT
38973 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
38991 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
39005 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
39024 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
39044 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
39063 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
39083 TGTTGC
1 CGTTGC
39089 AAAAGTAAAC
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 11 0.14
19 26 0.33
20 27 0.34
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:41086 original size:19 final size:19
Alignment explanation
Indices: 41062--41199 Score: 116
Period size: 19 Copynumber: 7.7 Consensus size: 19
41052 AAAACCGACT
41062 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
41081 ATCGCAA--CG--A-GAAA
1 ATCGCAACGCGAAATGAAA
*
41095 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
***
41114 ATCGCAACGCGAAAATGGTT
1 ATCGCAACGCG-AAATGAAA
*
41134 ATCACAA--CG--A-GAAA
1 ATCGCAACGCGAAATGAAA
*
41148 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
41167 ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
41186 ATCGCAACGAGAAA
1 ATCGCAACGCGAAA
41200 ATCACAATGC
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
14 18 0.19
15 2 0.02
16 4 0.04
17 2 0.02
18 4 0.04
19 54 0.57
20 11 0.12
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:41096 original size:14 final size:14
Alignment explanation
Indices: 41077--41129 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 14
41067 AACGCGAAAT
41077 GAAAATCGCAACGA
1 GAAAATCGCAACGA
41091 GAAAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
*
41109 TGAAAATCGCAACGC
1 -GAAAATCGCAACGA
41124 GAAAAT
1 GAAAAT
41130 GGTTATCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
14 17 0.52
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.33
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:41107 original size:33 final size:33
Alignment explanation
Indices: 41062--41211 Score: 142
Period size: 33 Copynumber: 4.4 Consensus size: 33
41052 AAAACCGACT
*
41062 ATCGCAACGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
41095 ATCGCAATGCGAAATGAAAATCGCAACGCGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
* ** *
41128 ATGGTTAT-C-ACAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGA-AA--TGAAAATCGCAA--CG--A-GAAA
*
41167 ATCGTAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
41200 ATCACAATGCGA
1 ATCGCAATGCGA
41212 TTTTCATTTC
Statistics
Matches: 95, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
31 1 0.01
32 3 0.03
33 50 0.53
34 12 0.13
36 4 0.04
38 11 0.12
39 10 0.11
40 3 0.03
41 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:41283 original size:20 final size:20
Alignment explanation
Indices: 41230--41287 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
41220 TCGCATTGCG
* * *
41230 ATTTTCTCGTTGCAATAACC
1 ATTTTCGCGTTGCGATAGCC
41250 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
41270 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
41288 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:42372 original size:24 final size:24
Alignment explanation
Indices: 42345--42398 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
42335 GTATTCGAAA
* *
42345 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
42369 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
42393 TTTGAT
1 TTTGAT
42399 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:44893 original size:19 final size:19
Alignment explanation
Indices: 44871--45001 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
44861 GGAAATTACT
44871 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
44890 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
44904 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
44923 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
44937 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
44956 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
44970 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
44989 ATCGCAACGCGAA
1 ATCGCAATGCGAA
45002 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:44913 original size:33 final size:33
Alignment explanation
Indices: 44871--44997 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
44861 GGAAATTACT
44871 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
44904 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
44936 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
44970 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
44998 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:44978 original size:66 final size:66
Alignment explanation
Indices: 44872--45004 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
44862 GAAATTACTA
*
44872 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
44937 T
66 T
*
44938 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
45003 T
66 T
45004 T
1 T
45005 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:45180 original size:14 final size:14
Alignment explanation
Indices: 45161--45197 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
45151 CATCAATTAA
45161 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
45175 ACAAATCACCTTTT
1 ACAAATCAACTTTT
45189 ACAAATCAA
1 ACAAATCAA
45198 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:46650 original size:21 final size:21
Alignment explanation
Indices: 46584--46650 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
46574 GTGAATCGGG
*
46584 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
46604 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
46626 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
46647 CTCT
1 CTCT
46651 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:46669 original size:42 final size:41
Alignment explanation
Indices: 46584--46706 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
46574 GTGAATCGGG
* * * * *
46584 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
46626 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
46668 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
46707 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:48768 original size:33 final size:33
Alignment explanation
Indices: 48724--48813 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
48714 TCGCAACGAG
* *
48724 AACGCGGAAATGACTATCGCAACGAGAGAATCGC
1 AACGC-GAAATGACTATCGCAACCAGACAATCGC
*
48758 AACGCGAAATGACTATCGCGACCAGACAATCGC
1 AACGCGAAATGACTATCGCAACCAGACAATCGC
**
48791 AACGCGAAATGAAAATCGCAACC
1 AACGCGAAATGACTATCGCAACC
48814 GCGAAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.90
34 5 0.10
ACGTcount: A:0.40, C:0.27, G:0.22, T:0.11
Consensus pattern (33 bp):
AACGCGAAATGACTATCGCAACCAGACAATCGC
Found at i:48807 original size:19 final size:19
Alignment explanation
Indices: 48785--48893 Score: 191
Period size: 19 Copynumber: 5.7 Consensus size: 19
48775 GCGACCAGAC
48785 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
48804 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
48824 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
48843 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
48862 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
48881 AATCGCAATGCGA
1 AATCGCAACGCGA
48894 TTTTGGTTTC
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
19 68 0.79
20 18 0.21
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:48922 original size:19 final size:19
Alignment explanation
Indices: 48889--48931 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
48879 AAAATCGCAA
*
48889 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
48908 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
48927 TGCGA
1 TGCGA
48932 CTATCTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:49517 original size:20 final size:20
Alignment explanation
Indices: 49492--49539 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
49482 ATGTAAATCA
*
49492 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTAAGTATCG
*
49512 CGTTGCGAAAGTAAGTATCT
1 CGTTGCGAAAGTAAGTATCG
49532 CGTTGCGA
1 CGTTGCGA
49540 TTTTGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (20 bp):
CGTTGCGAAAGTAAGTATCG
Found at i:49594 original size:20 final size:20
Alignment explanation
Indices: 49550--49642 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
49540 TTTTGTATTA
* **
49550 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
49571 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* *
49591 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-TAT
*
49612 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
49632 TCGCATTGCGA
1 TCGCATTGCGA
49643 ATTGGGAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:49595 original size:41 final size:41
Alignment explanation
Indices: 49550--49642 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
49540 TTTTGTATTA
49550 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
49591 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
49632 TCGCATTGCGA
1 TCGCATTGCGA
49643 ATTGGGAAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:49654 original size:41 final size:41
Alignment explanation
Indices: 49550--49656 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 41
49540 TTTTGTATTA
* * **
49550 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTGCGAAATTCGCGTTGCGATTTACTTAT
* * **
49591 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTGCGAAATTCGCGTTGCGATTTACTTAT
*
49632 TCGCATTGCGAATTGGGAAATTCGC
1 TCGCATTGCGAATTGCGAAATTCGC
49657 AACGATACTG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGAATTGCGAAATTCGCGTTGCGATTTACTTAT
Found at i:51047 original size:69 final size:70
Alignment explanation
Indices: 50946--51107 Score: 220
Period size: 69 Copynumber: 2.3 Consensus size: 70
50936 TGCAAGTATA
* *
50946 AATACTTTCGAA-TTAAAAAGATATGAAAAATGATAAGACCGCAAAATATCAATATTTTTCTACA
1 AATACTTTCGAATTTAAAAA-ATATGAAAAATGAGAAGACCGCAAAATATCAATATTTCTCTACA
51010 AATATC
65 AATATC
* * * * * *
51016 GATACTTTCAAATTTAAAAAA-ATGAAAAATGAGAATACCGTAAAGTTTCAATATTTCTCTACAA
1 AATACTTTCGAATTTAAAAAATATGAAAAATGAGAAGACCGCAAAATATCAATATTTCTCTACAA
51080 ATATC
66 ATATC
*
51085 AATATTTTCGAATTTAAAAAATA
1 AATACTTTCGAATTTAAAAAATA
51108 GATAGAAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 60 0.76
70 12 0.15
71 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (70 bp):
AATACTTTCGAATTTAAAAAATATGAAAAATGAGAAGACCGCAAAATATCAATATTTCTCTACAA
ATATC
Found at i:51504 original size:76 final size:75
Alignment explanation
Indices: 51397--51631 Score: 337
Period size: 76 Copynumber: 3.1 Consensus size: 75
51387 CATAACCTGT
* * *
51397 TAAATTAAAATAAGCGCAACCTATTACGTTAAACTAACTA-CTAGTTTGTTTAAAGGTATAATAA
1 TAAAATAAAATAGGC-CAACCTATTACGTTAAACTAACTACCGA-TTTGTTTAAAGGTATAATAA
51461 TAATGTAAACGG
64 TAATGTAAACGG
*
51473 TGAAATAAAATAGGCTCAACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGC-CAACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAAT
51538 AATGTAAACGG
65 AATGTAAACGG
* * * **
51549 TAAAATAAAATAGACGATATCTATTACGTTAAACTAGTTACCGATTTGTTTAAAGGTATAATAAT
1 TAAAATAAAATAGGCCA-ACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAAT
*
51614 AATGTAAACGT
65 AATGTAAACGG
51625 TAAAATA
1 TAAAATA
51632 TTTACAATTT
Statistics
Matches: 145, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
75 1 0.01
76 142 0.98
77 2 0.01
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (75 bp):
TAAAATAAAATAGGCCAACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAATA
ATGTAAACGG
Found at i:51775 original size:176 final size:176
Alignment explanation
Indices: 51475--52164 Score: 460
Period size: 176 Copynumber: 3.9 Consensus size: 176
51465 GTAAACGGTG
* * * *
51475 AAATAAAATAGGCTCAACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTATAATAATAA
1 AAATAAAATAAGCGCAACCTATTACGTTAAACTAACTACCAATTTATTTAAAGGTATAATAATAA
* *
51540 TGTAAACGGTAAAATAAAATAGACGATATCTATTACGTTAAACTAGTTACCGATTTGTTTAAAGG
66 TGTAAACGGTAAAATAAAATAGACGATATCTATTAAGTTAAACTAGCTACCGATTTGTTTAAAGG
51605 TATAATAATAATGTAAACGTTAAAATATTTACAATTTAACCGGTTA
131 TATAATAATAATGTAAACGTTAAAATATTTACAATTTAACCGGTTA
* * ** * * *
51651 AAATAAAATAAGCGCAACTTATTACGTTAAACTAGCTATTAATTTATTTAAAGTTATAATTATAT
1 AAATAAAATAAGCGCAACCTATTACGTTAAACTAACTACCAATTTATTTAAAGGTATAATAATAA
*
51716 TGTAAACGGTGAAATAAAATA-AGCGCA-A-CATATTAAGTTAAACTAGCTACCTG-TTTGTTTA
66 TGTAAACGGTAAAATAAAATAGA-CG-ATATC-TATTAAGTTAAACTAGCTACC-GATTTGTTTA
* * ** * *** **
51777 AATGTATAATAATAATAATGTAACCGGTTAAAATAAAATAGACGCT-ACCTATTA
127 AA-G-GT-ATAATAATAATGTAAAC-GTTAAAAT-ATTTACAATTTAACCGGTTA
*** * * * ** * * * * *
51831 CGTTAAACT-A-C-CTATCGGTT-TGTTGAAA-TGTA-TA--ATATTAATGTAACCGGTGA-AAT
1 AAATAAAATAAGCGCAACCTATTACGTT-AAACT-AACTACCA-ATTTATTTAA-AGGT-ATAAT
* * * * * * *
51887 ATTCACAACT-TAACCGGTTAAAATAAAATAAACGCTA-CATATTATGTTAAACTACCTACCGGT
61 A---ATAA-TGTAAACGG-TAAAATAAAATAGACGATATC-TATTAAGTTAAACTAGCTACCGAT
* * * * * *
51950 TTGTTTAAAGGTATAATATTAATGTAACCGGTAAAATATCTACTACTTAACCGGTTA
120 TTGTTTAAAGGTATAATAATAATGTAAACGTTAAAATATTTACAATTTAACCGGTTA
* * * ** **
52007 AAATAAAATAGGTG-ATACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGTATAATAATA
1 AAATAAAATAAGCGCA-ACCTATTACGTTAAACTAACTACCAATTTATTTAAAGGTATAATAATA
* * * * * * * * * *
52071 ATGTAAACTGTGAAATAAAATAGGCGCTACCTATTACGTTAAACTACCCACTGGTTTGTTTAAAG
65 ATGTAAACGGTAAAATAAAATAGACGATATCTATTAAGTTAAACTAGCTACCGATTTGTTTAAAG
52136 GTATAATAATAATGTAACACGTTAAAATA
130 GTATAATAATAATGTAA-ACGTTAAAATA
52165 AAATAAGCGC
Statistics
Matches: 387, Mismatches: 91, Indels: 71
0.70 0.17 0.13
Matches are distributed among these distances:
174 1 0.00
175 14 0.04
176 199 0.51
177 45 0.12
178 3 0.01
179 35 0.09
180 78 0.20
181 12 0.03
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (176 bp):
AAATAAAATAAGCGCAACCTATTACGTTAAACTAACTACCAATTTATTTAAAGGTATAATAATAA
TGTAAACGGTAAAATAAAATAGACGATATCTATTAAGTTAAACTAGCTACCGATTTGTTTAAAGG
TATAATAATAATGTAAACGTTAAAATATTTACAATTTAACCGGTTA
Found at i:51840 original size:80 final size:78
Alignment explanation
Indices: 51641--51881 Score: 262
Period size: 80 Copynumber: 3.1 Consensus size: 78
51631 ATTTACAATT
* * * *
51641 TAACCGGTTAAAATAAAATAAGCGCAACTTATTACGTTAAACTAGCTATTAATTTATTTAAA-GT
1 TAACCGGTTAAAATAAAATAAGCGCAACATATTACGTTAAACTAGCTACT-GTTTGTTTAAATGT
*
51705 -T-ATAATTATATTG
65 ATAATAA-TATAATG
* * *
51718 TAAACGG-TGAAATAAAATAAGCGCAACATATTAAGTTAAACTAGCTACCTGTTTGTTTAAATGT
1 TAACCGGTTAAAATAAAATAAGCGCAACATATTACGTTAAACTAGCTA-CTGTTTGTTTAAATGT
51782 ATAATAATAATAATG
65 ATAATAAT-ATAATG
* * * * *
51797 TAACCGGTTAAAATAAAAT-AGACGCTACCTATTACGTTAAACTACCTATCGGTTTGTTGAAATG
1 TAACCGGTTAAAATAAAATAAG-CGCAACATATTACGTTAAACTAGCTA-CTGTTTGTTTAAATG
51861 TATAAT-AT-TAATG
64 TATAATAATATAATG
51874 TAACCGGT
1 TAACCGGT
51882 GAAATATTCA
Statistics
Matches: 140, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
76 46 0.33
77 22 0.16
78 2 0.01
79 19 0.14
80 51 0.36
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (78 bp):
TAACCGGTTAAAATAAAATAAGCGCAACATATTACGTTAAACTAGCTACTGTTTGTTTAAATGTA
TAATAATATAATG
Found at i:51970 original size:100 final size:100
Alignment explanation
Indices: 51797--52087 Score: 431
Period size: 100 Copynumber: 2.9 Consensus size: 100
51787 AATAATAATG
* * *
51797 TAACCGGTTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTATCGGTTTGTTGAAATGT
1 TAACCGGTTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGT
51862 ATAATATTAATGTAACCGGTGAAATAT-TCACAACT
66 ATAATATTAATGTAACCGGTGAAATATCT-ACAACT
* * *
51897 TAACCGGTTAAAATAAAATAAACGCTACATATTATGTTAAACTACCTACCGGTTTGTTTAAAGGT
1 TAACCGGTTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGT
* *
51962 ATAATATTAATGTAACCGGTAAAATATCTACTACT
66 ATAATATTAATGTAACCGGTGAAATATCTACAACT
** * *
51997 TAACCGGTTAAAATAAAATAGGTGATACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGT
1 TAACCGGTTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGT
* * *
52062 ATAATAATAATGTAAACTGTGAAATA
66 ATAATATTAATGTAACCGGTGAAATA
52088 AAATAGGCGC
Statistics
Matches: 171, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
100 170 0.99
101 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.32
Consensus pattern (100 bp):
TAACCGGTTAAAATAAAATAGACGCTACCTATTACGTTAAACTACCTACCGGTTTGTTTAAAGGT
ATAATATTAATGTAACCGGTGAAATATCTACAACT
Found at i:52102 original size:76 final size:77
Alignment explanation
Indices: 52003--52197 Score: 295
Period size: 76 Copynumber: 2.5 Consensus size: 77
51993 TACTTAACCG
* *
52003 GTTAAAATAAAATAGGTGATACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGTATAATA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGTATAATA
52068 ATAATGTAA-AC
66 ATAATGTAACAC
* * * *
52079 -TGTGAAATAAAATAGGCGCTACCTATTACGTTAAACTACCCACTGGTTTGTTTAAAGGTATAAT
1 GT-TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGTATAAT
52143 AATAATGTAACAC
65 AATAATGTAACAC
* *
52156 GTTAAAATAAAATAAGCGCTACCTATTACGGTAAACTACCTA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTA
52198 TCATTTATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
75 1 0.01
76 66 0.62
77 38 0.36
78 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (77 bp):
GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGTATAATA
ATAATGTAACAC
Found at i:52209 original size:76 final size:76
Alignment explanation
Indices: 52003--52239 Score: 275
Period size: 76 Copynumber: 3.1 Consensus size: 76
51993 TACTTAACCG
* * * *
52003 GTTAAAATAAAATAGGTGATACCTATTACGTTAAACTACCTACCGGTTCGTTTAAAGGTATAATA
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATC-GTTTGTTTAAAGGTATAATA
52068 ATAATGTAA-AC
65 ATAATGTAACAC
* * *
52079 -TGTGAAATAAAATAGGCGCTACCTATTACGTTAAACTACCCACTGGTTTGTTTAAAGGTATAAT
1 GT-TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTA-TCGTTTGTTTAAAGGTATAAT
52143 AATAATGTAACAC
64 AATAATGTAACAC
* * * * ** * *
52156 GTTAAAATAAAATAAGCGCTACCTATTACGGTAAACTACCTATCATTTATTTAATTGTACAATAT
1 GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATCGTTTGTTTAAAGGTATAATAA
52221 TAATGTGAACA-
66 TAATGT-AACAC
52232 G-TAAAATA
1 GTTAAAATA
52240 TTTACAATTT
Statistics
Matches: 138, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
75 8 0.06
76 87 0.63
77 42 0.30
78 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (76 bp):
GTTAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTATCGTTTGTTTAAAGGTATAATAA
TAATGTAACAC
Found at i:52280 original size:99 final size:100
Alignment explanation
Indices: 52156--52352 Score: 254
Period size: 100 Copynumber: 2.0 Consensus size: 100
52146 AATGTAACAC
* * **
52156 GTTAAAATAAAATAAGCGCTACCTATTACGGTAAACTACCTATC-ATTTATTTAATTGTACAATA
1 GTTAAAATAAAATAAGCGCTACCTATTACGCTAAACTACCTACCGATTTATTTAAAGGTACAATA
* * *
52220 TTAATGTGAACAGTAAAATATTTACAATTTAACCG
66 ATAATGTAAACAGTAAAATATTTACAACTTAACCG
* * * * *
52255 GTTAAAATAAAATAA-CTGTTACCTATTACGCTAAACTACTTACCGGTTTGTTTAAAGGTATAAT
1 GTTAAAATAAAATAAGC-GCTACCTATTACGCTAAACTACCTACCGATTTATTTAAAGGTACAAT
*
52319 AATAATGTAAACGGTAAAATATTTACAACTTAAC
65 AATAATGTAAACAGTAAAATATTTACAACTTAAC
52353 TGTTTGAAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
98 1 0.01
99 38 0.46
100 44 0.53
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (100 bp):
GTTAAAATAAAATAAGCGCTACCTATTACGCTAAACTACCTACCGATTTATTTAAAGGTACAATA
ATAATGTAAACAGTAAAATATTTACAACTTAACCG
Found at i:52809 original size:21 final size:20
Alignment explanation
Indices: 52783--52849 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
52773 TCATGAATAC
52783 GTATCGATACATATACACTAA
1 GTATCGATACAT-TACACTAA
*
52804 GTATCGGT--ATTA-A-TAA
1 GTATCGATACATTACACTAA
* *
52820 -TTTCCATACATCTACACTAA
1 GTATCGATACAT-TACACTAA
52840 GTATCGATAC
1 GTATCGATAC
52850 GGAGTTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 3 0.09
18 4 0.12
19 3 0.09
20 3 0.09
21 14 0.41
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.33
Consensus pattern (20 bp):
GTATCGATACATTACACTAA
Found at i:53213 original size:108 final size:108
Alignment explanation
Indices: 53090--53343 Score: 321
Period size: 108 Copynumber: 2.4 Consensus size: 108
53080 GTATGTTATT
* * * * *
53090 TATTTATAACAAAATAAGTATTTAACATATTTTGTTGTCGTGAGATTTCGAATGCCCTATCAGCT
1 TATTTATAACAAAATAAGTAATTAACATATTTTGTTATAGTGAGATTTCGAAGGCCCTATCAACT
* * *
53155 TAAAGTTTGGTAGCATATTAAGCACAACCTAATATGTTGATAA
66 TAAAGTTTAGTAACATATTAAGCACAACATAATATGTTGATAA
* *
53198 TATTTATAACAAAATAAGTAATTAACTTATTTTGTTATAGTGAGATTTCTAAGGCCCTATCAACT
1 TATTTATAACAAAATAAGTAATTAACATATTTTGTTATAGTGAGATTTCGAAGGCCCTATCAACT
* * * ***
53263 TAAATTTTAGTAACATTTTAGGCGTTACATAATATGTTGATAA
66 TAAAGTTTAGTAACATATTAAGCACAACATAATATGTTGATAA
* * *
53306 TATTAATAATAAAATAAGTAATTAA-ACTATTTAGTTAT
1 TATTTATAACAAAATAAGTAATTAACA-TATTTTGTTAT
53344 TTTCATATTT
Statistics
Matches: 125, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
108 125 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.39
Consensus pattern (108 bp):
TATTTATAACAAAATAAGTAATTAACATATTTTGTTATAGTGAGATTTCGAAGGCCCTATCAACT
TAAAGTTTAGTAACATATTAAGCACAACATAATATGTTGATAA
Done.