Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000757.1 Hibiscus syriacus cultivar Beakdansim tig00001464_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: 111592
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4976 original size:13 final size:13
Alignment explanation
Indices: 4960--4997 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
4950 AATATTAAGT
4960 AATAATAAAAATA
1 AATAATAAAAATA
*
4973 AATAATAATAATA
1 AATAATAAAAATA
4986 AATACATAAAAA
1 AATA-ATAAAAA
4998 CAAAAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:6546 original size:5 final size:5
Alignment explanation
Indices: 6538--6666 Score: 258
Period size: 5 Copynumber: 25.8 Consensus size: 5
6528 CCTTTTTATT
6538 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
6588 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA TTTCA
6638 TTTCA TTTCA TTTCA TTTCA TTTCA TTTC
1 TTTCA TTTCA TTTCA TTTCA TTTCA TTTC
6667 CTCTTTTTTT
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 124 1.00
ACGTcount: A:0.19, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCA
Found at i:15290 original size:2 final size:2
Alignment explanation
Indices: 15283--15326 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
15273 TTAAACCAAA
* *
15283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15324 AT A
1 AT A
15327 ATAATGAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16732 original size:9 final size:9
Alignment explanation
Indices: 16708--16783 Score: 61
Period size: 9 Copynumber: 8.7 Consensus size: 9
16698 TTAGGGTTTT
16708 ATAATATT-
1 ATAATATTA
16716 -TAAT-TTA
1 ATAATATTA
16723 ATAATATTA
1 ATAATATTA
*
16732 ATAACATATA
1 ATAATAT-TA
16742 ATAAT-TATA
1 ATAATAT-TA
*
16751 ATAATAATA
1 ATAATATTA
*
16760 ATAATAATA
1 ATAATATTA
*
16769 ATAATTTTA
1 ATAATATTA
*
16778 AAAATA
1 ATAATA
16784 ACAATTTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
6 2 0.04
7 4 0.07
8 4 0.07
9 40 0.71
10 6 0.11
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATATTA
Found at i:16745 original size:3 final size:3
Alignment explanation
Indices: 16721--16773 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
16711 ATATTTAATT
* * *
16721 TAA TAA TAT TAA TAA CATA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
16767 TAA TAA T
1 TAA TAA T
16774 TTTAAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:16783 original size:15 final size:15
Alignment explanation
Indices: 16739--16797 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
16729 TTAATAACAT
*
16739 ATAATAATTATAATA
1 ATAATAATTTTAATA
16754 ATAATAA---TAATA
1 ATAATAATTTTAATA
*
16766 ATAATAATTTTAAAA
1 ATAATAATTTTAATA
* *
16781 ATAACAATTTAAATA
1 ATAATAATTTTAATA
16796 AT
1 AT
16798 TTAAGTAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
12 12 0.32
15 25 0.68
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATAATTTTAATA
Found at i:17081 original size:76 final size:76
Alignment explanation
Indices: 16959--18266 Score: 2190
Period size: 76 Copynumber: 17.3 Consensus size: 76
16949 CTTAAAAAAT
* * ** *
16959 ATCATGCACTGAAGGGCTTACAGATGACCCTAAGATTTTGAAAACATCAAAAAGCTCCCGAAGGT
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
17024 TTTTTGGAAAT
66 TTTTTGGAAAC
* * *
17035 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGAAGGG
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17100 TTTTTGGAAAC
66 TTTTTGGAAAC
*
17111 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCAGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17176 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
17187 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17252 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
17263 ATCATGCACTGTAGAACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
17328 TTTTTGAAAAC
66 TTTTTGGAAAC
17339 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17404 TTTTTGGAAAC
66 TTTTTGGAAAC
* *
17415 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAATATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
17480 TTTTTGAAAAC
66 TTTTTGGAAAC
17491 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17556 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
17567 ATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCTGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17632 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
17643 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATTAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17708 TTTTTGGAAAC
66 TTTTTGGAAAC
*
17719 ATCATGCACTGTATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17784 TTTTTGGAAAC
66 TTTTTGGAAAC
* * *
17795 ATCATGCACTGCAGGACTTAAAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
17860 TTTTTGGAAAC
66 TTTTTGGAAAC
*
17871 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
17936 GTTTTGGAAAC
66 TTTTTGGAAAC
*
17947 ATCATGCACTGTAGGACTTACAGATGACCCTAAGTCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
18012 TTTTTAGAAAC
66 TTTTTGGAAAC
*
18023 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
*
18088 TTTTTGAAAAC
66 TTTTTGGAAAC
*
18099 ATCAGGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
18164 TTTTTGGAAAC
66 TTTTTGGAAAC
18175 ATCATGCAC--T--G-----CAG--GA-CCTAAGGCTTTGAAAACATCAAAAAAGCTCCCGAAGG
1 ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGCTCCCGAAGG
18228 CTTTTTTGGAAAC
65 C-TTTTTGGAAAC
*
18241 ATCATGCACTGTAGGATTTACAGATG
1 ATCATGCACTGTAGGACTTACAGATG
18267 TCGAAAATAG
Statistics
Matches: 1158, Mismatches: 61, Indels: 25
0.93 0.05 0.02
Matches are distributed among these distances:
64 20 0.02
65 19 0.02
66 20 0.02
67 3 0.00
68 1 0.00
70 1 0.00
72 1 0.00
74 1 0.00
75 3 0.00
76 1088 0.94
77 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (76 bp):
ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC
TTTTTGGAAAC
Found at i:18919 original size:22 final size:22
Alignment explanation
Indices: 18894--18970 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
18884 AATAAAGCTT
*
18894 TCATCTTTGAAAAGAGACTCTA
1 TCATCTTTGAAAAGAGAATCTA
*
18916 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
18938 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
18960 TCATCTTTGAA
1 TCATCTTTGAA
18971 GAGTGTAGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:23698 original size:17 final size:18
Alignment explanation
Indices: 23676--23712 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
23666 CTTGATTCAA
23676 TTTCC-TTTTCCTTTTTT
1 TTTCCTTTTTCCTTTTTT
23693 TTTCCTTTTTTCCTTTTTT
1 TTTCC-TTTTTCCTTTTTT
23712 T
1 T
23713 ACCTAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
19 13 0.72
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTCCTTTTTCCTTTTTT
Found at i:23954 original size:2 final size:2
Alignment explanation
Indices: 23947--23976 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23937 ATAACAAAGG
23947 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
23977 TTAAAAGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25626 original size:28 final size:28
Alignment explanation
Indices: 25594--25650 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
25584 GTAATTATGT
25594 AAAAATGAAAATGTAAATACAAACGTAA
1 AAAAATGAAAATGTAAATACAAACGTAA
* * *
25622 AAAAATGCAAATGTAAATGCAAATGTAA
1 AAAAATGAAAATGTAAATACAAACGTAA
25650 A
1 A
25651 TATGTGAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.19
Consensus pattern (28 bp):
AAAAATGAAAATGTAAATACAAACGTAA
Found at i:25639 original size:12 final size:12
Alignment explanation
Indices: 25624--25651 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
25614 AAACGTAAAA
25624 AAATGCAAATGT
1 AAATGCAAATGT
25636 AAATGCAAATGT
1 AAATGCAAATGT
25648 AAAT
1 AAAT
25652 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (12 bp):
AAATGCAAATGT
Found at i:27273 original size:26 final size:28
Alignment explanation
Indices: 27242--27299 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
27232 ACTTGAAAAT
*
27242 AAAATAAT-A-TACATATAAATATTATG
1 AAAATAATAAGTACATATAAAAATTATG
* *
27268 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAATAAGTACATATAAAAATTATG
27296 AAAA
1 AAAA
27300 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATAAGTACATATAAAAATTATG
Found at i:28834 original size:3 final size:3
Alignment explanation
Indices: 28819--28858 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
28809 ATATTTAATT
*
28819 TAA TAA TAT TAA TAA T-A TATA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
28859 TTTAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:32968 original size:18 final size:18
Alignment explanation
Indices: 32945--32988 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
32935 AATTTTAAAA
32945 TTTAATCTTTTCTT-TTAT
1 TTTAAT-TTTTCTTCTTAT
*
32963 TTTAATTTTTGTTCTTAT
1 TTTAATTTTTCTTCTTAT
32981 TTT-ATTTT
1 TTTAATTTT
32989 GTAAATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTAATTTTTCTTCTTAT
Found at i:33312 original size:21 final size:21
Alignment explanation
Indices: 33287--33328 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
33277 CTTTTTATTC
33287 TCTCTTTCAT-TATTAACTTTT
1 TCTCTTTCATGT-TTAACTTTT
33308 TCTCTTTCATGTTTAACTTTT
1 TCTCTTTCATGTTTAACTTTT
33329 ACTTTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.17, C:0.19, G:0.02, T:0.62
Consensus pattern (21 bp):
TCTCTTTCATGTTTAACTTTT
Found at i:33336 original size:21 final size:21
Alignment explanation
Indices: 33288--33336 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
33278 TTTTTATTCT
*
33288 CTCTTTCATTATTAACTTTTT
1 CTCTTTCATTATTAACTTTTA
33309 CTCTTTCATGT-TTAACTTTTA
1 CTCTTTCAT-TATTAACTTTTA
*
33330 CTTTTTC
1 CTCTTTC
33337 TCTCTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.16, C:0.20, G:0.02, T:0.61
Consensus pattern (21 bp):
CTCTTTCATTATTAACTTTTA
Found at i:42261 original size:90 final size:89
Alignment explanation
Indices: 42109--42281 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
42099 ACACACCCTT
42109 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
42174 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
42198 TTATATCCAAGTTACCCTTATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAACCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
42263 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
42282 TTCAGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (89 bp):
TTATAACCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:49063 original size:24 final size:24
Alignment explanation
Indices: 49036--49142 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
49026 AAACGGAGAT
*
49036 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
49060 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
49084 GTTAGGAATCAGAACAGATTTCAT
1 ATCAGAAATCAAAACAGAATTCAG
** *
49108 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
49132 ATCAGAAATCA
1 ATCAGAAATCA
49143 GATAAAATAT
Statistics
Matches: 62, Mismatches: 21, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:49142 original size:48 final size:48
Alignment explanation
Indices: 49036--49144 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
49026 AAACGGAGAT
* * * *
49036 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
49084 GTTAGGAATCAGAACAGATTTCATATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
49132 ATCAGAAATCAGA
1 ATCAGAAATCAGA
49145 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:51650 original size:30 final size:30
Alignment explanation
Indices: 51615--51714 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
51605 AATTTTACAC
*
51615 AAATAGCACC-CAAACAGAATTTAATTCCCA
1 AAATAGCACCAAAAACAGAA-TTAATTCCCA
*
51645 AAATAGCACCAAAAACCGAATTAATTCCCA
1 AAATAGCACCAAAAACAGAATTAATTCCCA
* * *
51675 AAATAGCACCAAAATC-GAATTATTTACCA
1 AAATAGCACCAAAAACAGAATTAATTCCCA
*
51704 AAATATCACCA
1 AAATAGCACCA
51715 GTTTCGAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
29 21 0.33
30 35 0.56
31 7 0.11
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.20
Consensus pattern (30 bp):
AAATAGCACCAAAAACAGAATTAATTCCCA
Found at i:51721 original size:29 final size:29
Alignment explanation
Indices: 51615--51728 Score: 104
Period size: 29 Copynumber: 3.9 Consensus size: 29
51605 AATTTTACAC
* * *
51615 AAATAGCACCCAAA-CAGAATTTAATTCCCA
1 AAATAGCACCAAAATC-GAA-TTATTTACCA
* * *
51645 AAATAGCACCAAAAACCGAATTAATTCCCA
1 AAATAGCACC-AAAATCGAATTATTTACCA
51675 AAATAGCACCAAAATCGAATTATTTACCA
1 AAATAGCACCAAAATCGAATTATTTACCA
* ***
51704 AAATATCACCAGTTTCGAATTATTT
1 AAATAGCACCAAAATCGAATTATTT
51729 CCGTGCGACG
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 37 0.50
30 30 0.41
31 6 0.08
32 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.25
Consensus pattern (29 bp):
AAATAGCACCAAAATCGAATTATTTACCA
Found at i:53246 original size:90 final size:89
Alignment explanation
Indices: 53094--53266 Score: 292
Period size: 90 Copynumber: 1.9 Consensus size: 89
53084 ACATACCCTT
53094 TTATAACCAAATTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATATTTA
1 TTATAACCAAATTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATATTTA
* *
53159 ATTAATTGGAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* * *
53183 TTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAACCAAATTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATCAAATCTATATTT
53248 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
53267 TTCAGGATTA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 29 0.37
90 49 0.63
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (89 bp):
TTATAACCAAATTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:56331 original size:18 final size:18
Alignment explanation
Indices: 56308--56377 Score: 113
Period size: 18 Copynumber: 3.9 Consensus size: 18
56298 TATGTGATAT
*
56308 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCAGGACATA
56326 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACATA
56344 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCAGGACATA
* *
56362 ATGGTCCTTCGGGACA
1 GTGGTCCTTCAGGACA
56378 AATTCTAAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 49 1.00
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:59268 original size:29 final size:30
Alignment explanation
Indices: 59216--59274 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
59206 AAATTTAAGG
**
59216 CAAAATGTTTTTGGGTTTGAATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
59246 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
59275 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:59380 original size:21 final size:21
Alignment explanation
Indices: 59354--59431 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
59344 AGGGGGTCAA
*
59354 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCATAC
**
59375 AGTGCATCCATGCACCTGTAC
1 AGTGCATCCATGCACCCATAC
* * *
59396 TAGTGCATCGATGCA-TCATGC
1 -AGTGCATCCATGCACCCATAC
59417 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
59432 TCAAACACCG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 13 0.28
21 21 0.45
22 13 0.28
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCATAC
Found at i:59422 original size:20 final size:19
Alignment explanation
Indices: 59397--59507 Score: 70
Period size: 20 Copynumber: 5.8 Consensus size: 19
59387 CACCTGTACT
59397 AGTGCATCGATGCATCATGC
1 AGTGCATCGATGCATCAT-C
*
59417 AGTGCATCCATGCA-C-TC
1 AGTGCATCGATGCATCATC
** *
59434 A-AACACCGAATGCA--ATC
1 AGTGCATCG-ATGCATCATC
*
59451 AGTGCATCGATGCATCCTTC
1 AGTGCATCGATGCAT-CATC
* *
59471 TGTGCATCGATGCATCAAGGC
1 AGTGCATCGATGCATC-A-TC
*
59492 TGTGCATCGATGCATC
1 AGTGCATCGATGCATC
59508 TTGTTGTGCA
Statistics
Matches: 71, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
16 3 0.04
17 15 0.21
18 5 0.07
19 2 0.03
20 29 0.41
21 17 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (19 bp):
AGTGCATCGATGCATCATC
Found at i:59496 original size:21 final size:20
Alignment explanation
Indices: 59452--59507 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 20
59442 AATGCAATCA
***
59452 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCAGGCT
59472 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-AGGCT
59493 GTGCATCGATGCATC
1 GTGCATCGATGCATC
59508 TTGTTGTGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCAGGCT
Found at i:59499 original size:41 final size:41
Alignment explanation
Indices: 59452--59534 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
59442 AATGCAATCA
*
59452 GTGCATCGATGCATCCTT-CTGTGCATCGATGCATC-AAGGCT
1 GTGCATCGATGCAT-CTTGCTGTGCATCCATGCA-CGAAGGCT
*
59493 GTGCATCGATGCATCTTGTTGTGCATCCATGCACGAAGGCT
1 GTGCATCGATGCATCTTGCTGTGCATCCATGCACGAAGGCT
59534 G
1 G
59535 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
40 4 0.11
41 34 0.89
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (41 bp):
GTGCATCGATGCATCTTGCTGTGCATCCATGCACGAAGGCT
Found at i:59517 original size:20 final size:20
Alignment explanation
Indices: 59452--59525 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
59442 AATGCAATCA
59452 GTGCATCGATGCATCCTT-CT
1 GTGCATCGATGCAT-CTTGCT
**
59472 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-TTGCT
*
59493 GTGCATCGATGCATCTTGTT
1 GTGCATCGATGCATCTTGCT
*
59513 GTGCATCCATGCA
1 GTGCATCGATGCA
59526 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 28 0.61
21 17 0.37
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCTTGCT
Found at i:62854 original size:29 final size:30
Alignment explanation
Indices: 62783--62842 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
62773 AAATTTAAGG
62783 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
62814 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
62843 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:62948 original size:21 final size:21
Alignment explanation
Indices: 62922--62979 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
62912 AGGGTGTCAA
*
62922 AGTGCATCCATGTACCCCTAC
1 AGTGCATCCATGCACCCCTAC
* *
62943 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTAC
*
62964 AGTGCATTCATGCACC
1 AGTGCATCCATGCACC
62980 TGCACTAGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTAC
Found at i:63071 original size:20 final size:20
Alignment explanation
Indices: 63048--63114 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
63038 TTAGTGCAAT
63048 GATGCATCCTTCTGTGCATC
1 GATGCATCCTTCTGTGCATC
***
63068 GATGCATCAAGGCTGTGCATC
1 GATGCATC-CTTCTGTGCATC
63089 GATGCATCCTGT-TGTGCATC
1 GATGCATCCT-TCTGTGCATC
*
63109 CATGCA
1 GATGCA
63115 CGAAGGCTGC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (20 bp):
GATGCATCCTTCTGTGCATC
Found at i:70018 original size:15 final size:15
Alignment explanation
Indices: 69998--70028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
69988 AAATCGTTAT
*
69998 AACAAAGTTTATATA
1 AACAAAATTTATATA
70013 AACAAAATTTATATA
1 AACAAAATTTATATA
70028 A
1 A
70029 TTCACAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (15 bp):
AACAAAATTTATATA
Found at i:70623 original size:24 final size:24
Alignment explanation
Indices: 70551--70615 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
70541 TGTCACATAG
* * * *
70551 ATTTGTCTCGAAGGATCGCGCAGA
1 ATTTGTCTCGAATGACCACACAGA
70575 ATTTGTCTCGAATGACCACACAGA
1 ATTTGTCTCGAATGACCACACAGA
70599 ATTTGT-TCCGAATGACC
1 ATTTGTCT-CGAATGACC
70616 GCTTAGAACC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
ATTTGTCTCGAATGACCACACAGA
Found at i:75989 original size:50 final size:50
Alignment explanation
Indices: 75926--76037 Score: 206
Period size: 50 Copynumber: 2.2 Consensus size: 50
75916 CTTTACATGA
*
75926 GGGGAAAAGATTTGGCATTGAATGTGGGATATTTGATTGGACGTAAAGTT
1 GGGGAAAATATTTGGCATTGAATGTGGGATATTTGATTGGACGTAAAGTT
*
75976 GGGGAAAATATTTGGCATTGAATGTGTGATATTTGATTGGACGTAAAGTT
1 GGGGAAAATATTTGGCATTGAATGTGGGATATTTGATTGGACGTAAAGTT
76026 GGGGAAAATATT
1 GGGGAAAATATT
76038 ACTTTCCCTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.33
Consensus pattern (50 bp):
GGGGAAAATATTTGGCATTGAATGTGGGATATTTGATTGGACGTAAAGTT
Found at i:83678 original size:10 final size:10
Alignment explanation
Indices: 83665--83689 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
83655 CTAATATAAC
83665 CTAAATGCAA
1 CTAAATGCAA
83675 CTAAATGCAA
1 CTAAATGCAA
83685 CTAAA
1 CTAAA
83690 ATATTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:84521 original size:2 final size:2
Alignment explanation
Indices: 84514--84541 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84504 ACTTTGGTGC
84514 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
84542 CTGATTATTT
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:85392 original size:259 final size:256
Alignment explanation
Indices: 84886--85671 Score: 945
Period size: 259 Copynumber: 3.1 Consensus size: 256
84876 AATCATCATA
* ** * * *
84886 CCCGAAAGACTTACTGATTTTTGAAATAGTTTACTAGGTAGGAAACTTTGGAAATTGCTTTCTTA
1 CCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGCTTTCTTA
* * * * * * *
84951 CTTTTCAAAAATTTCATTTTTTTTAAATACTAAATGATAAACTTTGAAAATCGCTTTCCCATTTT
66 CTTTTCAAAAATTTCA-TTTTCTAAAAAAATTAATGAGAAACTTTGAAAATCGCTTTCTCATTTT
* * * *
85016 TTGAAAATCATGTGAAAATATCCTGCCTGAAGGCCTTATGGATGGCCCCAAGGACTTATCATCTT
130 TTGAAAATGATGTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAA-GACTTATCATCTT
** **
85081 GCTCGAAAGAT-TGACAGATGACTTAAATAATTTAATCATCATGCTCAAAAGACTTATTGATGG
194 GCTCGAAAG-TCTGACAGATGACTCGAAGGATTTAATCATCATGCTCAAAAGACTTATTGATGG
*
85144 CCCAAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGCTTTCTTA
1 CCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGCTTTCTTA
* * *
85209 CTTTTCAAAATTTTCATTTTCTAAAAAAATTAGATGAGAAAC-TTGCAAAATCGGTTTTTCATTT
66 CTTTTCAAAAATTTCATTTTCTAAAAAAATTA-ATGAGAAACTTTG-AAAATCGCTTTCTCATTT
* *
85273 TTTCGAAAATGATGTGAAAACATCCTGCCCGAAGGCCTTATGGACGGCTCGAAGAACTTATCATC
129 TTT-GAAAATGATGTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAAG-ACTTATCATC
** * *
85338 TCACTCGAAAGTCTGATAGATGACTCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGG
192 TTGCTCGAAAGTCTGACAGATGACTCGAAGGATTTAATCATCATGCTCAAAAGACTTATTGATGG
* * * * * * * *
85403 ACTGAAGGACTTACCAATTTTGGAAATAATTTTCTAGGTTAGAAACTTCGAAAATCGTTTTCTTA
1 CCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGCTTTCTTA
* * * *
85468 CTTTTCAAAAATTTCATTTTCTGAAAACATTAATTAAGAAACTTTGGAAATCGCTTTCTCATTTT
66 CTTTTCAAAAATTTCATTTTCTAAAAAAATTAA-TGAGAAACTTTGAAAATCGCTTTCTCATTTT
* * * *
85533 TTGAAAATGATGT--AAACATCCTGCCCGAAAGACTTATAGATGTCCCGAATGACTTATCATCTT
130 TTGAAAATGATGTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAA-GACTTATCATCTT
* * * * ** * *
85596 GCTCGAAAGACTGACAAATTAC-CTGAAGGA-ATAATCATCATGCTTGAAAGATTTGTTGATGG
194 GCTCGAAAGTCTGACAGATGACTC-GAAGGATTTAATCATCATGCTCAAAAGACTTATTGATGG
85658 CCCGAAGGACTTAC
1 CCCGAAGGACTTAC
85672 TAAGTAAGAA
Statistics
Matches: 452, Mismatches: 67, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
255 39 0.09
256 64 0.14
257 15 0.03
258 113 0.25
259 218 0.48
260 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (256 bp):
CCCGAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGCTTTCTTA
CTTTTCAAAAATTTCATTTTCTAAAAAAATTAATGAGAAACTTTGAAAATCGCTTTCTCATTTTT
TGAAAATGATGTGAAAACATCCTGCCCGAAGGCCTTATGGATGGCCCGAAGACTTATCATCTTGC
TCGAAAGTCTGACAGATGACTCGAAGGATTTAATCATCATGCTCAAAAGACTTATTGATGG
Found at i:87839 original size:15 final size:16
Alignment explanation
Indices: 87819--87852 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
87809 ACTTGATTTA
87819 TTCTTTTTCT-TCTTT
1 TTCTTTTTCTCTCTTT
87834 TTCTTTTTCTCTCTTT
1 TTCTTTTTCTCTCTTT
87850 TTC
1 TTC
87853 GAATATGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTTTTCTCTCTTT
Found at i:88592 original size:33 final size:33
Alignment explanation
Indices: 88555--88617 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
88545 GACTTTATTT
* *
88555 CCTCAAAGATAGGTAAAGGTATGATTTTGGGTG
1 CCTCAAAGAGAGGTAAAGGTATGACTTTGGGTG
*
88588 CCTCAAAGAGAGGTAATGGTATGACTTTGG
1 CCTCAAAGAGAGGTAAAGGTATGACTTTGG
88618 TGACTCAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.29
Consensus pattern (33 bp):
CCTCAAAGAGAGGTAAAGGTATGACTTTGGGTG
Found at i:92842 original size:4 final size:4
Alignment explanation
Indices: 92833--92864 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
92823 CTTTTTTGCA
*
92833 AAAT AAAT AAAT AACT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
92865 CTTAGGGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:94229 original size:2 final size:2
Alignment explanation
Indices: 94224--94248 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
94214 ACACACACAC
94224 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 A
94249 AATAAAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95260 original size:2 final size:2
Alignment explanation
Indices: 95253--95278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
95243 GTAATTGGAT
95253 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
95279 ATGATAACTT
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):
TA
Found at i:97881 original size:19 final size:19
Alignment explanation
Indices: 97842--97887 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
97832 ATACATTTTC
97842 ATGAACAGTACTATACGGT
1 ATGAACAGTACTATACGGT
* **
97861 ATGAATAGTACTATATTGT
1 ATGAACAGTACTATACGGT
97880 ATGAACAG
1 ATGAACAG
97888 CACCGTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (19 bp):
ATGAACAGTACTATACGGT
Found at i:97959 original size:21 final size:21
Alignment explanation
Indices: 97929--97968 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
97919 CAGTGTTACT
97929 GTGTACCGATGCACTGCTATA
1 GTGTACCGATGCACTGCTATA
*
97950 GTGTATCGATGCACTGCTA
1 GTGTACCGATGCACTGCTA
97969 CAGTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTATA
Found at i:98812 original size:22 final size:22
Alignment explanation
Indices: 98782--98842 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
98772 GGCATCTGAA
* * * *
98782 ATTTTTCCCAAAGGACTTATGT
1 ATTTGTCCCGAAGGACCTATGC
*
98804 ATTTGTCCCGAATGACCTATGC
1 ATTTGTCCCGAAGGACCTATGC
98826 ATTTGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
98843 GCGTAGAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGC
Found at i:100635 original size:55 final size:56
Alignment explanation
Indices: 100533--100638 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 56
100523 TCGAAATAGG
* **
100533 TGCTATTTTGGTAATTTTTTTCAAAAAAATGTGATATTTTGGGAATTAATTCATGA
1 TGCTATTTTGGGAATTTAATTCAAAAAAATGTGATATTTTGGGAATTAATTCATGA
* * *
100589 TGCTATTTTGGGAA-TTAATTC-AAAAAAGGTGTTATTTTTGGTAATTAATT
1 TGCTATTTTGGGAATTTAATTCAAAAAAATGTGATA-TTTTGGGAATTAATT
100639 TGAAAAGTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
54 11 0.26
55 19 0.44
56 13 0.30
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.46
Consensus pattern (56 bp):
TGCTATTTTGGGAATTTAATTCAAAAAAATGTGATATTTTGGGAATTAATTCATGA
Found at i:100673 original size:29 final size:30
Alignment explanation
Indices: 100589--100683 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 30
100579 TAATTCATGA
* * * *
100589 TGCTATTTTGGGAATTAATTCAAAAA-AGG
1 TGCTATCTTGGTAATTAATTTAAAAAGGGG
* * * *
100618 TGTTATTTTTGGTAATTAATTTGAAAA-GTG
1 TGCTA-TCTTGGTAATTAATTTAAAAAGGGG
* *
100648 TGCTATCTTGGTTATTATTTTAAAAAGGGG
1 TGCTATCTTGGTAATTAATTTAAAAAGGGG
100678 TGCTAT
1 TGCTAT
100684 TTATGTAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
29 21 0.40
30 31 0.60
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (30 bp):
TGCTATCTTGGTAATTAATTTAAAAAGGGG
Found at i:101423 original size:24 final size:24
Alignment explanation
Indices: 101396--101456 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
101386 TACCTGATTG
101396 TTGACCTGGATTCAAATATGATAC
1 TTGACCTGGATTCAAATATGATAC
* ***
101420 TTGACCTGAATTTTTATATGATAC
1 TTGACCTGGATTCAAATATGATAC
*
101444 TTGACATGGATTC
1 TTGACCTGGATTC
101457 TGATTTGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (24 bp):
TTGACCTGGATTCAAATATGATAC
Found at i:107240 original size:22 final size:21
Alignment explanation
Indices: 107214--107261 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
107204 TTTGACCGGT
107214 CCGACCCGACCCGACCATTGA
1 CCGACCCGACCCGACCATTGA
*
107235 CTCGACCCGACCCGACCGTTGA
1 C-CGACCCGACCCGACCATTGA
107257 CCGAC
1 CCGAC
107262 TATATTCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (21 bp):
CCGACCCGACCCGACCATTGA
Found at i:107323 original size:28 final size:29
Alignment explanation
Indices: 107263--107373 Score: 93
Period size: 28 Copynumber: 3.8 Consensus size: 29
107253 TTGACCGACT
* **
107263 ATATTCTGGGAATTAATTCG-ATTTGGTG
1 ATATTCTGGGAATTAATTCGAAATAAGTG
107291 ATATTCTGGGAATTAATT-GAAATAAGTG
1 ATATTCTGGGAATTAATTCGAAATAAGTG
* ** *
107319 TTATT-TGGGTAATTGTTTCGAAAAAAGGGTG
1 ATATTCTGGG-AATTAATTCGAAATAA--GTG
* *
107350 ATATTATGGGAATTAATTTGAAAT
1 ATATTCTGGGAATTAATTCGAAAT
107374 GATGCTATTT
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.08
28 33 0.51
29 6 0.09
31 17 0.26
32 4 0.06
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (29 bp):
ATATTCTGGGAATTAATTCGAAATAAGTG
Found at i:107419 original size:28 final size:28
Alignment explanation
Indices: 107388--107460 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 28
107378 CTATTTTAAG
*
107388 AATTAATTCAAAAAGGTGGTATTTTGGT
1 AATTAATTCAAAAAGGTGCTATTTTGGT
* *
107416 AATTAATTTGAAAAGGGTGCTATTTTGGT
1 AATTAA-TTCAAAAAGGTGCTATTTTGGT
* * *
107445 TATTATTTTAAAAAGG
1 AATTAATTCAAAAAGG
107461 GGTGTTATTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (28 bp):
AATTAATTCAAAAAGGTGCTATTTTGGT
Found at i:107470 original size:30 final size:29
Alignment explanation
Indices: 107340--107470 Score: 106
Period size: 28 Copynumber: 4.6 Consensus size: 29
107330 ATTGTTTCGA
* * *
107340 AAAAAGGGTGATATTATGGGAATTAATTT
1 AAAAAGGGTGCTATTTTGGTAATTAATTT
* * * * *
107369 -GAAATGATGCTATTTTAAG-AATTAATTC
1 AAAAAGGGTGCTATTTT-GGTAATTAATTT
*
107397 AAAAA-GGTGGTATTTTGGTAATTAATTT
1 AAAAAGGGTGCTATTTTGGTAATTAATTT
* * *
107425 GAAAAGGGTGCTATTTTGGTTATTATTTT
1 AAAAAGGGTGCTATTTTGGTAATTAATTT
*
107454 AAAAAGGGGTGTTATTT
1 AAAAA-GGGTGCTATTT
107471 ATGTAAAATG
Statistics
Matches: 79, Mismatches: 18, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
27 1 0.01
28 40 0.51
29 28 0.35
30 10 0.13
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.40
Consensus pattern (29 bp):
AAAAAGGGTGCTATTTTGGTAATTAATTT
Found at i:108194 original size:23 final size:24
Alignment explanation
Indices: 108168--108226 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
108158 TACCTGATTG
108168 TTGACCTGGATTCAAATATGATA-
1 TTGACCTGGATTCAAATATGATAC
***
108191 TTGACCT-GATTTTTATATGATAC
1 TTGACCTGGATTCAAATATGATAC
*
108214 TTGACATGGATTC
1 TTGACCTGGATTC
108227 TGATTTGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 12 0.41
23 13 0.45
24 4 0.14
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.41
Consensus pattern (24 bp):
TTGACCTGGATTCAAATATGATAC
Done.