Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012115.1 Corchorus olitorius cultivar O-4 contig12148, 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: 134820
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5896 original size:11 final size:11
Alignment explanation
Indices: 5853--5890 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5843 TTCCTATATA
*
5853 AAATAAATTAT
1 AAATTAATTAT
5864 CAAA-TAATTAT
1 -AAATTAATTAT
5875 AAATTAATTAT
1 AAATTAATTAT
5886 AAATT
1 AAATT
5891 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:12985 original size:9 final size:9
Alignment explanation
Indices: 12971--13002 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
12961 TTACCCCAAT
12971 TTATAAATG
1 TTATAAATG
12980 TTATAAATG
1 TTATAAATG
*
12989 TTATACATG
1 TTATAAATG
12998 TTATA
1 TTATA
13003 TAGTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (9 bp):
TTATAAATG
Found at i:15103 original size:36 final size:36
Alignment explanation
Indices: 14994--15120 Score: 164
Period size: 36 Copynumber: 3.5 Consensus size: 36
14984 CTCTCCCTCC
* * *
14994 CCCTCTGAATCTGAGCAGCAGCAGCAACCTCTCTCT
1 CCCTCTGACTCTGAGCAGCAGCAACAGCCTCTCTCT
* * *
15030 CACGCTGACTCTGAGCAGCAGCAACAGCCTCTGTCT
1 CCCTCTGACTCTGAGCAGCAGCAACAGCCTCTCTCT
*
15066 CCCTCTGACTCTGAGCAACAGCAACAGCCTCTCTCT
1 CCCTCTGACTCTGAGCAGCAGCAACAGCCTCTCTCT
* * *
15102 CCCTATAACTCCGAGCAGC
1 CCCTCTGACTCTGAGCAGC
15121 CTCTCTCTCC
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 77 1.00
ACGTcount: A:0.23, C:0.39, G:0.17, T:0.20
Consensus pattern (36 bp):
CCCTCTGACTCTGAGCAGCAGCAACAGCCTCTCTCT
Found at i:15307 original size:18 final size:17
Alignment explanation
Indices: 15254--15307 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
15244 ATTAATCGTA
15254 AATAAACTAATT--AAT
1 AATAAACTAATTAAAAT
* *
15269 TATAAACTAAGTAAAAGT
1 AATAAACTAATTAAAA-T
15287 AATAAACTAATTAGAAAT
1 AATAAACTAATTA-AAAT
15305 AAT
1 AAT
15308 TAATTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 10 0.32
17 2 0.06
18 16 0.52
19 3 0.10
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (17 bp):
AATAAACTAATTAAAAT
Found at i:15739 original size:24 final size:24
Alignment explanation
Indices: 15663--15748 Score: 75
Period size: 24 Copynumber: 3.4 Consensus size: 24
15653 CTTGAAGATT
*
15663 GTTTGACGAAAATGAAGGTTGA-A
1 GTTTGAAGAAAATGAAGGTTGAGA
* * *
15686 GGTTGAAGAAAATGAAATAAAGATTAAGA
1 GTTTGAAGAAAATG-----AAGGTTGAGA
15715 GTTTGAAGAAAATGAAGGTTGAGA
1 GTTTGAAGAAAATGAAGGTTGAGA
*
15739 GTTTTAAGAA
1 GTTTGAAGAA
15749 GTTGTTAGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
23 12 0.24
24 17 0.35
28 6 0.12
29 14 0.29
ACGTcount: A:0.45, C:0.01, G:0.28, T:0.26
Consensus pattern (24 bp):
GTTTGAAGAAAATGAAGGTTGAGA
Found at i:23744 original size:6 final size:6
Alignment explanation
Indices: 23729--23772 Score: 72
Period size: 6 Copynumber: 7.3 Consensus size: 6
23719 AGGATTCGGA
23729 AAAAAG -AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAGAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG AA
23773 GAGTAACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.14
6 25 0.69
7 6 0.17
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:23744 original size:12 final size:12
Alignment explanation
Indices: 23727--23772 Score: 51
Period size: 11 Copynumber: 3.8 Consensus size: 12
23717 TTAGGATTCG
23727 GAAAAAAGAAAA
1 GAAAAAAGAAAA
23739 G-AAAAAGAAAA
1 GAAAAAAGAAAA
23750 -AGAAAAAGAAAAA
1 GA-AAAAAG-AAAA
*
23763 GAAGAAAGAA
1 GAAAAAAGAA
23773 GAGTAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
11 10 0.34
12 9 0.31
13 9 0.31
14 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAAAAGAAAA
Found at i:27993 original size:67 final size:67
Alignment explanation
Indices: 27881--28006 Score: 198
Period size: 67 Copynumber: 1.9 Consensus size: 67
27871 CTGGCACTTA
* *
27881 GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAGGAATTTATTTAATTG
1 GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAAGAACTTATTTAATTG
27946 TT
66 TT
** * *
27948 GTGGGAGAATTTGGGTTTTAGAATGAACCTTTTGTGGTAAGATATTCAAAGAACTTATT
1 GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAAGAACTTATT
28007 ATTTTGGCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (67 bp):
GTGGGAGAATTTGGGTAATAGAATGAACCTTTTGGGGTAAAATATTCAAAGAACTTATTTAATTG
TT
Found at i:29795 original size:22 final size:23
Alignment explanation
Indices: 29770--29830 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
29760 TTGACAGCGC
**
29770 AACAAAAAC-AAAACGAAAACGA
1 AACAAAAACAAAAACGAAAAAAA
29792 AACAAAAACAAAAAC-AAAAAAA
1 AACAAAAACAAAAACGAAAAAAA
* *
29814 AACGAAAACGAAAACGA
1 AACAAAAACAAAAACGA
29831 TGCCAAACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 27 0.82
23 6 0.18
ACGTcount: A:0.75, C:0.16, G:0.08, T:0.00
Consensus pattern (23 bp):
AACAAAAACAAAAACGAAAAAAA
Found at i:29796 original size:16 final size:16
Alignment explanation
Indices: 29775--29826 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
29765 AGCGCAACAA
29775 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
* *
29791 AAACAAAAACAAAAACA
1 AAAC-AAAACGAAAACG
*
29808 AAAAAAAACGAAAACG
1 AAACAAAACGAAAACG
29824 AAA
1 AAA
29827 ACGATGCCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.77, C:0.15, G:0.08, T:0.00
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:29827 original size:16 final size:16
Alignment explanation
Indices: 29774--29827 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
29764 CAGCGCAACA
29774 AAAACAAAACGAAAACG
1 AAAA-AAAACGAAAACG
* *
29791 AAACAAAAACAAAAACA
1 AAA-AAAAACGAAAACG
29808 AAAAAAAACGAAAACG
1 AAAAAAAACGAAAACG
29824 AAAA
1 AAAA
29828 CGATGCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 15 0.47
17 16 0.50
18 1 0.03
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAAAACGAAAACG
Found at i:29829 original size:6 final size:6
Alignment explanation
Indices: 29774--29830 Score: 59
Period size: 6 Copynumber: 10.2 Consensus size: 6
29764 CAGCGCAACA
* * *
29774 AAAAC- AAAACG AAAACG -AAACA AAAACA AAAAC- AAAA-A AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
29818 AAAACG AAAACG A
1 AAAACG AAAACG A
29831 TGCCAAACGA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
5 17 0.37
6 29 0.63
ACGTcount: A:0.75, C:0.16, G:0.09, T:0.00
Consensus pattern (6 bp):
AAAACG
Found at i:32984 original size:5 final size:5
Alignment explanation
Indices: 32932--32999 Score: 57
Period size: 5 Copynumber: 12.8 Consensus size: 5
32922 AATTAAAATT
* * *
32932 AAAGA AAGAGAA AAAGG AAATA AAA-A AAATGAA AAAGA AAAGGA AAAGG
1 AAAGA AA-AG-A AAAGA AAAGA AAAGA AAA-G-A AAAGA AAA-GA AAAGA
32981 AAAGA AAAGA AAAGA AAAG
1 AAAGA AAAGA AAAGA AAAG
33000 CGTGATATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
4 4 0.08
5 31 0.60
6 10 0.19
7 7 0.13
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:38029 original size:36 final size:36
Alignment explanation
Indices: 37982--38054 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
37972 AGCTTTCACG
* **
37982 TGTGTTGCACGTGGCTCAATGTGTTTAAATTAAATA
1 TGTGTTGCACGTGGCCCAACATGTTTAAATTAAATA
38018 TGTGTTGCACGTGGCCCAACATGTTTAAATTAAATA
1 TGTGTTGCACGTGGCCCAACATGTTTAAATTAAATA
38054 T
1 T
38055 TTTTATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (36 bp):
TGTGTTGCACGTGGCCCAACATGTTTAAATTAAATA
Found at i:38124 original size:15 final size:15
Alignment explanation
Indices: 38104--38134 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38094 CTTCATATAA
38104 AATTTTGATAATTAT
1 AATTTTGATAATTAT
38119 AATTTTGATAATTAT
1 AATTTTGATAATTAT
38134 A
1 A
38135 GTAAAGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (15 bp):
AATTTTGATAATTAT
Found at i:38207 original size:22 final size:22
Alignment explanation
Indices: 38182--38255 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
38172 GTTTCATATG
38182 AAATTTTGTTAACTTATCTATA
1 AAATTTTGTTAACTTATCTATA
* * *
38204 AAA--TT-TAAAGTT-TCATATG
1 AAATTTTGTTAACTTATC-TATA
38223 AAATTTTGTTAACTTATCTATA
1 AAATTTTGTTAACTTATCTATA
38245 AAATTTTGTTA
1 AAATTTTGTTA
38256 CACTCCGGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 11 0.27
20 2 0.05
21 2 0.05
22 22 0.54
23 2 0.05
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (22 bp):
AAATTTTGTTAACTTATCTATA
Found at i:38219 original size:41 final size:41
Alignment explanation
Indices: 38169--38250 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
38159 AGAATTTCGA
38169 AAAGTTTCATATGAAATTTTGTTAACTTATCTATAAAATTT
1 AAAGTTTCATATGAAATTTTGTTAACTTATCTATAAAATTT
38210 AAAGTTTCATATGAAATTTTGTTAACTTATCTATAAAATTT
1 AAAGTTTCATATGAAATTTTGTTAACTTATCTATAAAATTT
38251 TGTTACACTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (41 bp):
AAAGTTTCATATGAAATTTTGTTAACTTATCTATAAAATTT
Found at i:38342 original size:22 final size:22
Alignment explanation
Indices: 38274--38573 Score: 109
Period size: 22 Copynumber: 13.5 Consensus size: 22
38264 ATCCCTATAA
* *
38274 AAATTTTAATAA-CTGCCTAATG
1 AAATTTTGATAACCT-CCCAATG
* *
38296 AAATTTTGATAATCACCC-ATG
1 AAATTTTGATAACCTCCCAATG
38317 AAATTTTGATAACCTCCCAATG
1 AAATTTTGATAACCTCCCAATG
* * * * **
38339 AAATGTTGGTAAGCGCATATTATG
1 AAATTTTGATAACCTCCCA--ATG
* * * *
38363 ACATTTTGATAACCTTCCGATA
1 AAATTTTGATAACCTCCCAATG
* * * **
38385 AAATATTGGT--CATCATATTATG
1 AAATTTTGATAACCTCCCA--ATG
* *
38407 AAATTTTGATAACCATACC-ATA
1 AAATTTTGATAACC-TCCCAATG
* * *
38429 AAATTGTGAT-ACCTCACTATG
1 AAATTTTGATAACCTCCCAATG
* * * *
38450 AAATTTTTATAAATCTCCCTATA
1 AAATTTTGAT-AACCTCCCAATG
*
38473 AAATTTTGATAACCT-CCATTTG
1 AAATTTTGATAACCTCCCA-ATG
*
38495 TAATTTTGATAACCT--C-ATG
1 AAATTTTGATAACCTCCCAATG
* * *
38514 AAGTTTTGAAAACCACCTCATGACATG
1 AAATTTTGATAACCTCC-C---A-ATG
38541 AAATTTTGATAACC-CCCAATG
1 AAATTTTGATAACCTCCCAATG
38562 AAATTTTGATAA
1 AAATTTTGATAA
38574 TTAATTACAC
Statistics
Matches: 198, Mismatches: 59, Indels: 43
0.66 0.20 0.14
Matches are distributed among these distances:
19 13 0.07
20 4 0.02
21 50 0.25
22 80 0.40
23 18 0.09
24 14 0.07
25 2 0.01
26 2 0.01
27 15 0.08
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCAATG
Found at i:38416 original size:44 final size:45
Alignment explanation
Indices: 38314--38420 Score: 135
Period size: 46 Copynumber: 2.4 Consensus size: 45
38304 ATAATCACCC
* *
38314 ATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCATATT
1 ATGAAATTTTGATAACCTCCCAATAAAATATTGGTAA-CGCATATT
* * * * *
38360 ATGACATTTTGATAACCTTCCGATAAAATATTGGTCA-TCATATT
1 ATGAAATTTTGATAACCTCCCAATAAAATATTGGTAACGCATATT
38404 ATGAAATTTTGATAACC
1 ATGAAATTTTGATAACC
38421 ATACCATAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 22 0.42
46 31 0.58
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (45 bp):
ATGAAATTTTGATAACCTCCCAATAAAATATTGGTAACGCATATT
Found at i:38430 original size:44 final size:45
Alignment explanation
Indices: 38314--38432 Score: 134
Period size: 46 Copynumber: 2.6 Consensus size: 45
38304 ATAATCACCC
* * *
38314 ATGAAATTTTGATAACCTCCCAATGAAATGTTGGTAAGCGCATATT
1 ATGAAATTTTGATAACCTACCAATAAAATATTGGTAA-CGCATATT
* * * * *
38360 ATGACATTTTGATAACCTTCCGATAAAATATTGGTCA-TCATATT
1 ATGAAATTTTGATAACCTACCAATAAAATATTGGTAACGCATATT
38404 ATGAAATTTTGATAACCATACC-ATAAAAT
1 ATGAAATTTTGATAACC-TACCAATAAAAT
38433 TGTGATACCT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 29 0.46
45 3 0.05
46 31 0.49
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (45 bp):
ATGAAATTTTGATAACCTACCAATAAAATATTGGTAACGCATATT
Found at i:38680 original size:21 final size:22
Alignment explanation
Indices: 38293--38703 Score: 101
Period size: 22 Copynumber: 18.5 Consensus size: 22
38283 TAACTGCCTA
* *
38293 ATGAAATTTTGATAATCAC-CC
1 ATGAAATTTTGATAATCTCACT
* * *
38314 ATGAAATTTTGATAACCTCCCA
1 ATGAAATTTTGATAATCTCACT
* * * * *
38336 ATGAAATGTTGGTAAGCGCATATT
1 ATGAAATTTTGATAATCTC--ACT
* * *
38360 ATGACATTTTGATAACCTTC-CG
1 ATGAAATTTTGATAATC-TCACT
* * * * *
38382 ATAAAATATTGGTCATCAT-ATT
1 ATGAAATTTTGATAATC-TCACT
* *
38404 ATGAAATTTTGATAACCAT-ACC
1 ATGAAATTTTGATAATC-TCACT
* * *
38426 ATAAAATTGTGAT-ACCTCACT
1 ATGAAATTTTGATAATCTCACT
* *
38447 ATGAAATTTTTATAAATCTCCCT
1 ATGAAATTTTGAT-AATCTCACT
* *
38470 ATAAAATTTTGATAACCTC-CAT
1 ATGAAATTTTGATAATCTCAC-T
* * *
38492 TTGTAATTTTGATAA-C-CTC-
1 ATGAAATTTTGATAATCTCACT
* * *
38511 ATGAAGTTTTGAAAACCACCTCA-T
1 ATGAAATTTTG-ATA--ATCTCACT
* * *
38535 GACATGAAATTTTGATAA-CCCCCA
1 ---ATGAAATTTTGATAATCTCACT
* *
38559 ATGAAATTTTGATAATTAATTACACC
1 ATGAAATTTTGATAA-T--CT-CACT
* ** *
38585 ATAAAATTACGATAA-CTTACCT
1 ATGAAATTTTGATAATCTCA-CT
* *
38607 ATGAAATTTTGTTAATCTCCCT
1 ATGAAATTTTGATAATCTCACT
* * *
38629 ATGAAATTTTGAGAACCACACT
1 ATGAAATTTTGATAATCTCACT
* *
38651 ATCAAATTTTGTTAATCTCACT
1 ATGAAATTTTGATAATCTCACT
* *
38673 AT-AAATTTTGATAAACTCATT
1 ATGAAATTTTGATAATCTCACT
*
38694 GTGAAATTTT
1 ATGAAATTTT
38704 AACTACCACA
Statistics
Matches: 275, Mismatches: 87, Indels: 55
0.66 0.21 0.13
Matches are distributed among these distances:
19 8 0.03
20 4 0.01
21 68 0.25
22 131 0.48
23 22 0.08
24 15 0.05
25 1 0.00
26 16 0.06
27 10 0.04
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
ATGAAATTTTGATAATCTCACT
Found at i:38829 original size:23 final size:24
Alignment explanation
Indices: 38777--38831 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
38767 TAACCACACT
38777 ATGAAATTTAGATAATATCCCCTC
1 ATGAAATTTAGATAATATCCCCTC
* * * *
38801 -TAAAATTTCGATTA-ATCTCCTC
1 ATGAAATTTAGATAATATCCCCTC
38823 ATGAAATTT
1 ATGAAATTT
38832 TGTTAACCTC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.38
Consensus pattern (24 bp):
ATGAAATTTAGATAATATCCCCTC
Found at i:38837 original size:22 final size:21
Alignment explanation
Indices: 38803--38850 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
38793 ATCCCCTCTA
*
38803 AAATTTCGATTAATCTCCTCATG
1 AAATTTCGATTAACCT-CT-ATG
*
38826 AAATTTTG-TTAACCTCTATG
1 AAATTTCGATTAACCTCTATG
38846 AAATT
1 AAATT
38851 GTGATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 6 0.26
23 7 0.30
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (21 bp):
AAATTTCGATTAACCTCTATG
Found at i:38954 original size:22 final size:22
Alignment explanation
Indices: 38922--38976 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
38912 TTCACAATGT
*
38922 AATTTTTATAAGCATACTATGA
1 AATTTTAATAAGCATACTATGA
* * * *
38944 AATTTTGATAATCTTCCTATGA
1 AATTTTAATAAGCATACTATGA
38966 AATTTTAATAA
1 AATTTTAATAA
38977 CCTCCATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
AATTTTAATAAGCATACTATGA
Found at i:39020 original size:22 final size:21
Alignment explanation
Indices: 38965--39020 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
38955 TCTTCCTATG
*
38965 AAATTTTAATAA-CCTCCATAT
1 AAATTTTAATAATCCCCCAT-T
*
38986 AAGATTTCAATAATCGCCCCATT
1 AA-ATTTTAATAATC-CCCCATT
*
39009 AAATTTTGATAA
1 AAATTTTAATAA
39021 CTAGAGTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 2 0.07
22 17 0.61
23 4 0.14
24 5 0.18
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (21 bp):
AAATTTTAATAATCCCCCATT
Found at i:39066 original size:22 final size:21
Alignment explanation
Indices: 39027--39243 Score: 120
Period size: 22 Copynumber: 9.9 Consensus size: 21
39017 ATAACTAGAG
39027 TATGAAATTTT-AGTAACCTCC
1 TATGAAATTTTGA-TAACCTCC
* *
39048 TTGTGAAATTTTGACAACCTTCC
1 -TATGAAATTTTGATAACC-TCC
*
39071 CATG-AATTTTGATAACCT-C
1 TATGAAATTTTGATAACCTCC
39090 -ATGAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
39110 ATATGAAAATTTTGATTACATCC
1 -TATG-AAATTTTGATAACCTCC
* *
39133 TTATGAAATTTTATTTTAATAACCTACT
1 -TATG-AA----ATTTTGATAACCT-CC
*
39161 TATGAAATTTTGATAACATCC
1 TATGAAATTTTGATAACCTCC
* * *
39182 CATGGAATTGTGATAA-CTACAC
1 TATGAAATTTTGATAACCT-C-C
* * * *
39204 TATAAAATTTTAACATCCTACC
1 TATGAAATTTTGATAACCT-CC
*
39226 TATGAAATTTTGGTAACC
1 TATGAAATTTTGATAACC
39244 ACAATATAAA
Statistics
Matches: 149, Mismatches: 31, Indels: 30
0.71 0.15 0.14
Matches are distributed among these distances:
18 3 0.02
19 15 0.10
20 3 0.02
21 27 0.18
22 54 0.36
23 30 0.20
26 2 0.01
27 14 0.09
28 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:39099 original size:19 final size:19
Alignment explanation
Indices: 39051--39108 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
39041 AACCTCCTTG
*
39051 TGAAATTTTGACAACCTTCCCA
1 TGAAATTTTGATAACC-T--CA
39073 TG-AATTTTGATAACCTCA
1 TGAAATTTTGATAACCTCA
39091 TGAAATTTTGATAACCTC
1 TGAAATTTTGATAACCTC
39109 CATATGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 4 0.12
19 15 0.44
20 1 0.03
21 12 0.35
22 2 0.06
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (19 bp):
TGAAATTTTGATAACCTCA
Found at i:39116 original size:40 final size:44
Alignment explanation
Indices: 39051--39144 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 44
39041 AACCTCCTTG
39051 TGAAATTTTGACAACCTTCCCATG-AATTTTGA-TA-A-CCTCA
1 TGAAATTTTGACAACCTTCCCATGAAATTTTGATTACATCCTCA
* * *
39091 TGAAATTTTGATAACC-TCCATATGAAAATTTTGATTACATCCTTA
1 TGAAATTTTGACAACCTTCC-CATG-AAATTTTGATTACATCCTCA
39136 TGAAATTTT
1 TGAAATTTT
39145 ATTTTAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
39 3 0.07
40 18 0.40
42 8 0.18
43 2 0.04
44 1 0.02
45 13 0.29
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (44 bp):
TGAAATTTTGACAACCTTCCCATGAAATTTTGATTACATCCTCA
Found at i:39255 original size:44 final size:44
Alignment explanation
Indices: 39195--39290 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
39185 GGAATTGTGA
* * * * *
39195 TAACTACACTATAAAATTTTAACATCCTAC-CTATGAAATTTTGG
1 TAACCACAATATAAAATTTTAACA-ACTACACTATAAAATTTTAG
* *
39239 TAACCACAATATAAAATTTTGAGAACTACACTATAAAATTTTAG
1 TAACCACAATATAAAATTTTAACAACTACACTATAAAATTTTAG
39283 TAACCACA
1 TAACCACA
39291 CAATGAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 4 0.09
44 40 0.91
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (44 bp):
TAACCACAATATAAAATTTTAACAACTACACTATAAAATTTTAG
Found at i:39291 original size:22 final size:22
Alignment explanation
Indices: 39195--39291 Score: 90
Period size: 22 Copynumber: 4.4 Consensus size: 22
39185 GGAATTGTGA
* *
39195 TAACTACACTATAAAATTTTAA
1 TAACCACACTATAAAATTTTAG
* * * *
39217 CATCCTAC-CTATGAAATTTTGG
1 TAACC-ACACTATAAAATTTTAG
*
39239 TAACCACAATATAAAATTTTGAG
1 TAACCACACTATAAAATTTT-AG
*
39262 -AACTACACTATAAAATTTTAG
1 TAACCACACTATAAAATTTTAG
39283 TAACCACAC
1 TAACCACAC
39292 AATGAATTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
21 4 0.07
22 50 0.88
23 3 0.05
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (22 bp):
TAACCACACTATAAAATTTTAG
Found at i:39307 original size:21 final size:22
Alignment explanation
Indices: 39230--39307 Score: 72
Period size: 22 Copynumber: 3.6 Consensus size: 22
39220 CCTACCTATG
*
39230 AAATTTTGGTAACCACA-ATATA
1 AAATTTTGATAACCACACA-ATA
* * *
39252 AAATTTTGAGAACTACACTATA
1 AAATTTTGATAACCACACAATA
39274 AAATTTT-AGTAACCACACAAT-
1 AAATTTTGA-TAACCACACAATA
*
39295 GAATTTTGATAAC
1 AAATTTTGATAAC
39308 TTCCAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
21 11 0.24
22 34 0.76
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (22 bp):
AAATTTTGATAACCACACAATA
Found at i:41659 original size:27 final size:26
Alignment explanation
Indices: 41609--41661 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
41599 ATTTCCATTA
41609 TTTTAATAATGAAATAATTAAAATATT
1 TTTTAATAATGAAAT-ATTAAAATATT
41636 TTTTAATAATGACAAT-TTAGAAATAT
1 TTTTAATAATGA-AATATTA-AAATAT
41662 ATTTGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 18 0.75
28 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (26 bp):
TTTTAATAATGAAATATTAAAATATT
Found at i:41810 original size:21 final size:21
Alignment explanation
Indices: 41782--41925 Score: 98
Period size: 21 Copynumber: 6.8 Consensus size: 21
41772 TGAATATTTT
41782 TATGAAATTTTGATAACTACC
1 TATGAAATTTTGATAACTACC
* *
41803 TATTAAATTTTGATAATTACC
1 TATGAAATTTTGATAACTACC
* *
41824 TATAAAATTGTGATAAACT-CC
1 TATGAAATTTTGAT-AACTACC
* * *
41845 ATAAGAAACTTTGATAACCTAAC
1 -TATGAAATTTTGATAA-CTACC
* * *
41868 TATGAAATTTTAATAAATTTTCC
1 TATGAAATTTTGAT-AA-CTACC
*
41891 TATG-AATTTTG-TAACATTCC
1 TATGAAATTTTGATAAC-TACC
*
41911 TATG-ATTTTTGATAA
1 TATGAAATTTTGATAA
41926 TCACTCTGTG
Statistics
Matches: 96, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
20 16 0.17
21 39 0.41
22 32 0.33
23 9 0.09
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAACTACC
Found at i:43027 original size:28 final size:28
Alignment explanation
Indices: 42996--43068 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
42986 GTCATCTAGG
* *
42996 GGGCATTTTGGTCATTCT-TCATGTCCAA
1 GGGCATTTTGGTCATT-TGGCATATCCAA
*
43024 GGGCATTTTGGTCATTTGGCATATCCAG
1 GGGCATTTTGGTCATTTGGCATATCCAA
*
43052 GGGTATTTTGGTCATTT
1 GGGCATTTTGGTCATTT
43069 CGAGTGCACT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.41
Consensus pattern (28 bp):
GGGCATTTTGGTCATTTGGCATATCCAA
Found at i:49240 original size:2 final size:2
Alignment explanation
Indices: 49233--49259 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49223 TAGTATAATA
49233 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 A
49260 ACATAAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51546 original size:11 final size:10
Alignment explanation
Indices: 51530--51582 Score: 56
Period size: 11 Copynumber: 5.2 Consensus size: 10
51520 AAGTCCATGT
51530 TTGAAGATTTA
1 TTGAAGA-TTA
*
51541 TTGAAGATAA
1 TTGAAGATTA
51551 TTTGAAGA-T-
1 -TTGAAGATTA
51560 TTGAAGATTA
1 TTGAAGATTA
51570 TTGAAGAATTA
1 TTGAAG-ATTA
51581 TT
1 TT
51583 TCAAGAGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 1 0.03
10 8 0.22
11 20 0.56
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
TTGAAGATTA
Found at i:51565 original size:19 final size:18
Alignment explanation
Indices: 51541--51576 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51531 TGAAGATTTA
51541 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
51560 TTGAAGATTATTGAAGA
1 TTGAAGATAATTGAAGA
51577 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:61502 original size:2 final size:2
Alignment explanation
Indices: 61497--61524 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61487 TAATATATGA
61497 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
61525 CAGACTAATC
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:61798 original size:37 final size:37
Alignment explanation
Indices: 61748--61830 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
61738 GGATTAAATG
*
61748 TTAAGTCGTCGCTTGTAAATACCTAATTTCCTTGAAA
1 TTAAGTCTTCGCTTGTAAATACCTAATTTCCTTGAAA
***
61785 TTAAGTCTTCGCTTGTTCTTACCTAATTTCCTTGAAA
1 TTAAGTCTTCGCTTGTAAATACCTAATTTCCTTGAAA
61822 TTAAGTCTT
1 TTAAGTCTT
61831 TGACTGATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.43
Consensus pattern (37 bp):
TTAAGTCTTCGCTTGTAAATACCTAATTTCCTTGAAA
Found at i:61851 original size:36 final size:36
Alignment explanation
Indices: 61771--62247 Score: 439
Period size: 36 Copynumber: 13.1 Consensus size: 36
61761 TGTAAATACC
* * *
61771 TAATTTCCTTGAAATTAAGTCTTCG-CTTGT-TCTTACC
1 TAATTTCCCTG-AATTAAGTCTTTGAC-TGTAT-TTACT
* *
61808 TAATTTCCTTGAAATTAAGTCTTTGACTG-ATTTACC
1 TAATTTCCCTG-AATTAAGTCTTTGACTGTATTTACT
* * * * *
61844 TAGTTTCCTTGAAACTAAATCTCTGACTG-ATTTACT
1 TAATTTCCCTG-AATTAAGTCTTTGACTGTATTTACT
* * * *
61880 TAATTACACTGAATTAAATCTGTG-CTTGTATTTACT
1 TAATTTCCCTGAATTAAGTCTTTGAC-TGTATTTACT
* * *
61916 TAATTTCCCTGAATTAAGCCTTTGTCTGCT-TTCACT
1 TAATTTCCCTGAATTAAGTCTTTGACTG-TATTTACT
* * * * *
61952 TAATTACCCTCAATTAAGGCTTTGAGTGTGTTTACT
1 TAATTTCCCTGAATTAAGTCTTTGACTGTATTTACT
*
61988 TAATTACCCTGAATTAAGTCTTTGACTGCT-TTTACT
1 TAATTTCCCTGAATTAAGTCTTTGACTG-TATTTACT
*
62024 TAATTTCCCTGAATTAAGTCTTTGACAGTGTTTTTACT
1 TAATTTCCCTGAATTAAGTCTTTGAC--TGTATTTACT
* *
62062 TAATTACCCTGAATTAAGTCTTTGGCTGCT-TTTACT
1 TAATTTCCCTGAATTAAGTCTTTGACTG-TATTTACT
* *
62098 TAATTTCCCTGAATTAAGTCTTTGATTGTGTTTACT
1 TAATTTCCCTGAATTAAGTCTTTGACTGTATTTACT
** * * *
62134 TAATCACCCTGAATTAAATCTTTGGCTGCATTTACT
1 TAATTTCCCTGAATTAAGTCTTTGACTGTATTTACT
* *
62170 TAATTTCCCTGAATTAAGTCTTTGACTGTGTTTTTACC
1 TAATTTCCCTGAATTAAGTCTTTGAC--TGTATTTACT
* * *
62208 AAATTACCCTGAATTAAGTCTTTGATTGTATTTACT
1 TAATTTCCCTGAATTAAGTCTTTGACTGTATTTACT
62244 TAAT
1 TAAT
62248 GCATGGATGC
Statistics
Matches: 372, Mismatches: 53, Indels: 31
0.82 0.12 0.07
Matches are distributed among these distances:
34 1 0.00
35 15 0.04
36 261 0.70
37 32 0.09
38 63 0.17
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (36 bp):
TAATTTCCCTGAATTAAGTCTTTGACTGTATTTACT
Found at i:62242 original size:146 final size:145
Alignment explanation
Indices: 61783--62247 Score: 537
Period size: 146 Copynumber: 3.2 Consensus size: 145
61773 ATTTCCTTGA
* * * * *
61783 AATTAAGTCTTCGCTTG-TTCTTACCTAATTTCCTTGAAATTAAGTCTTTGACTG-ATTTACCTA
1 AATTAAGTCTTTG-TTGCTT-TTACTTAATTTCCCTG-AATTAAGTCTTTGACTGTGTTTACTTA
* * * * * * * * *
61846 GTTTCCTTGAAACTAAATCTCTGACTG-ATTTACTTAATTACACTGAATTAAATCTGTG-CT-TG
63 ATTACCCTG-AATTAAATCTTTGACTGCATTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTG
* *
61908 TATTTACTTAATTTCCCTG
127 TTTTTACTTAATTACCCTG
* * * * * *
61927 AATTAAGCCTTTGTCTGCTTTCACTTAATTACCCTCAATTAAGGCTTTGAGTGTGTTTACTTAAT
1 AATTAAGTCTTTGT-TGCTTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTTACTTAAT
* * *
61992 TACCCTGAATTAAGTCTTTGACTGCTTTTACTTAATTTCCCTGAATTAAGTCTTTGACAGTGTTT
65 TACCCTGAATTAAATCTTTGACTGCATTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTT
62057 TTACTTAATTACCCTG
130 TTACTTAATTACCCTG
* *
62073 AATTAAGTCTTTGGCTGCTTTTACTTAATTTCCCTGAATTAAGTCTTTGATTGTGTTTACTTAAT
1 AATTAAGTCTTT-GTTGCTTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTTACTTAAT
* *
62138 CACCCTGAATTAAATCTTTGGCTGCATTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTT
65 TACCCTGAATTAAATCTTTGACTGCATTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTT
**
62203 TTACCAAATTACCCTG
130 TTACTTAATTACCCTG
62219 AATTAAGTCTTTGATTG-TATTTACTTAAT
1 AATTAAGTCTTTG-TTGCT-TTTACTTAAT
62248 GCATGGATGC
Statistics
Matches: 272, Mismatches: 40, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
143 30 0.11
144 63 0.23
145 5 0.02
146 173 0.64
147 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (145 bp):
AATTAAGTCTTTGTTGCTTTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTTACTTAATT
ACCCTGAATTAAATCTTTGACTGCATTTACTTAATTTCCCTGAATTAAGTCTTTGACTGTGTTTT
TACTTAATTACCCTG
Found at i:70264 original size:16 final size:16
Alignment explanation
Indices: 70240--70270 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
70230 CAACTTGTTA
70240 AAAAAAAAATAATAAT
1 AAAAAAAAATAATAAT
*
70256 AAAATAAAATAATAA
1 AAAAAAAAATAATAA
70271 AAGAAATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAAAAAAATAATAAT
Found at i:91152 original size:76 final size:76
Alignment explanation
Indices: 91015--91159 Score: 179
Period size: 76 Copynumber: 1.9 Consensus size: 76
91005 ACAAGGACCC
* * *
91015 CGACTTCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
91080 GGGCAATGTCA
66 GGGCAATGTCA
* * **
91091 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGTGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
91153 GATGGGC
63 GATGGGC
91160 TGTCTCATAG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.07
76 49 0.83
77 6 0.10
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (76 bp):
CGACTCCACCTGGGTGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAATGTCA
Found at i:97554 original size:21 final size:20
Alignment explanation
Indices: 97530--97571 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
97520 TTGGCCGGGT
97530 ATGGCCGGGCAAATGGCGCGG
1 ATGGCC-GGCAAATGGCGCGG
**
97551 ATGGCCGGCACGTGGCGCGG
1 ATGGCCGGCAAATGGCGCGG
97571 A
1 A
97572 GGATAGCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.17, C:0.26, G:0.48, T:0.10
Consensus pattern (20 bp):
ATGGCCGGCAAATGGCGCGG
Found at i:100498 original size:21 final size:19
Alignment explanation
Indices: 100465--100508 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
100455 AACGCAGAAA
100465 AAAAAATTGTTTTTATGACGC
1 AAAAAATTGTTTTTAT--CGC
* *
100486 AAAAACTTTTTTTTATCGC
1 AAAAAATTGTTTTTATCGC
100505 AAAA
1 AAAA
100509 CCGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
21 14 0.67
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (19 bp):
AAAAAATTGTTTTTATCGC
Found at i:102167 original size:16 final size:16
Alignment explanation
Indices: 102146--102178 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
102136 TCCAATTATG
102146 GGCTTATATGGGCTGA
1 GGCTTATATGGGCTGA
102162 GGCTTATATGGGCTGA
1 GGCTTATATGGGCTGA
102178 G
1 G
102179 TATTATCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.39, T:0.30
Consensus pattern (16 bp):
GGCTTATATGGGCTGA
Found at i:102184 original size:16 final size:16
Alignment explanation
Indices: 102149--102184 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
102139 AATTATGGGC
*
102149 TTATATGGGCTGAGGC
1 TTATATGGGCTGAGGA
*
102165 TTATATGGGCTGAGTA
1 TTATATGGGCTGAGGA
102181 TTAT
1 TTAT
102185 CCCATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (16 bp):
TTATATGGGCTGAGGA
Found at i:108313 original size:15 final size:15
Alignment explanation
Indices: 108293--108331 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
108283 ATTGTTAAGT
*
108293 AACTTTCTTAAGAGA
1 AACTTTCTTAAGAAA
*
108308 AACTTTCATAAGAAA
1 AACTTTCTTAAGAAA
*
108323 AATTTTCTT
1 AACTTTCTT
108332 GGGAAAGACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (15 bp):
AACTTTCTTAAGAAA
Found at i:111705 original size:36 final size:35
Alignment explanation
Indices: 111641--111729 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 35
111631 TTTTAATTTT
* * *
111641 AAATATATTATATATATGTTATAAATTAAAAATCTGA
1 AAATATA-TAAATATAT-ATATAAATTAAAAATCAGA
*
111678 AAATATATAAATATATATATAACATTAATAATCAGA
1 AAATATATAAATATATATATAA-ATTAAAAATCAGA
*
111714 AAAT-CA-AAATATATAT
1 AAATATATAAATATATAT
111730 TTTTAATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.22
35 6 0.13
36 23 0.50
37 7 0.15
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.36
Consensus pattern (35 bp):
AAATATATAAATATATATATAAATTAAAAATCAGA
Found at i:111922 original size:9 final size:9
Alignment explanation
Indices: 111908--111936 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
111898 ATAAATATGT
111908 GTCGGTTAA
1 GTCGGTTAA
111917 GTCGGTTAA
1 GTCGGTTAA
111926 GTCGGTTAA
1 GTCGGTTAA
111935 GT
1 GT
111937 TTGAAAACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.10, G:0.34, T:0.34
Consensus pattern (9 bp):
GTCGGTTAA
Found at i:113450 original size:19 final size:20
Alignment explanation
Indices: 113422--113466 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
113412 AAGATTTTTA
*
113422 ATAATAATTATTCAA-TAAT
1 ATAATTATTATTCAATTAAT
*
113441 ATAATTATTATTTAATTAAT
1 ATAATTATTATTCAATTAAT
113461 -TAATTA
1 ATAATTA
113467 ATTTCAGCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
ATAATTATTATTCAATTAAT
Found at i:113837 original size:13 final size:13
Alignment explanation
Indices: 113819--113844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
113809 AAGGTAACAA
113819 CAAAAATCATCAC
1 CAAAAATCATCAC
113832 CAAAAATCATCAC
1 CAAAAATCATCAC
113845 TCATGCCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAATCATCAC
Found at i:115406 original size:22 final size:22
Alignment explanation
Indices: 115357--115407 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
115347 AAATATTACC
* **
115357 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
115379 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
115402 A-AATTA
1 ATAATTA
115408 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:119822 original size:19 final size:18
Alignment explanation
Indices: 119793--119834 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
119783 GGAGTCATTC
*
119793 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
119811 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
119830 TTAAA
1 TTAAA
119835 ATAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:119838 original size:19 final size:19
Alignment explanation
Indices: 119798--119834 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
119788 CATTCTTAAG
119798 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
119817 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
119835 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:132381 original size:60 final size:60
Alignment explanation
Indices: 132288--132449 Score: 188
Period size: 60 Copynumber: 2.7 Consensus size: 60
132278 CTAAGTCCTT
*
132288 AAATAAGGACCT-AA-TATTCGCTAAAATGCTCAAATAAGTGTG-T-GATCTTTTAATTTGGCC
1 AAATAAGGACCTAAAGT-TTC-CCAAAATGCTCAAATAAG-G-GCTCGATCTTTTAATTTGGCC
** * ** *
132348 AAATAAGGGTCTAACGTTTGTCAAAATGCTCAAATAAGGGCTCGATTTTTTAATTTGGCC
1 AAATAAGGACCTAAAGTTTCCCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGCC
*
132408 AAATAAGGACCTAAAGTTTCCCAAAATGTTCAAATAAGGGCT
1 AAATAAGGACCTAAAGTTTCCCAAAATGCTCAAATAAGGGCT
132450 TGGCATCGAA
Statistics
Matches: 85, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
58 1 0.01
59 2 0.02
60 78 0.92
61 3 0.04
62 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (60 bp):
AAATAAGGACCTAAAGTTTCCCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGCC
Done.