Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000140.1 Hibiscus syriacus cultivar Beakdansim tig00000255_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: 127281
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:5405 original size:44 final size:44
Alignment explanation
Indices: 5306--5412 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
5296 ACTTAAAGGG
* * *
5306 AGTATCAATACCAGTATCAGTACACCAGTGTATTTTTACACATT
1 AGTATCAGTACCAGTATCAGTACAACAATGTATTTTTACACATT
* * * * *
5350 AATA-CTGGTACCTGTATCGGTACTACAATGTATTTTTACACATT
1 AGTATC-AGTACCAGTATCAGTACAACAATGTATTTTTACACATT
*
5394 AGTATCAGTACCATTATCA
1 AGTATCAGTACCAGTATCA
5413 ATGCTATGTG
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
43 1 0.02
44 46 0.96
45 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (44 bp):
AGTATCAGTACCAGTATCAGTACAACAATGTATTTTTACACATT
Found at i:5641 original size:24 final size:23
Alignment explanation
Indices: 5614--5659 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
5604 CGAATGGTTG
*
5614 AATTAAATATAAGCTTGAAAATTA
1 AATTAAAAATAAGCTT-AAAATTA
*
5638 AATTAAAAATAATCTTAAAATT
1 AATTAAAAATAAGCTTAAAATT
5660 TCTTTAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAAAATAAGCTTAAAATTA
Found at i:11471 original size:22 final size:23
Alignment explanation
Indices: 11439--11487 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
11429 CGCGTCGTTT
11439 CCGACTCCGGAGGAAAATAGCTG
1 CCGACTCCGGAGGAAAATAGCTG
11462 CCGAC-CCGGAGGAAAATAGCTG
1 CCGACTCCGGAGGAAAATAGCTG
11484 CCGA
1 CCGA
11488 TGATATTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.29, G:0.31, T:0.10
Consensus pattern (23 bp):
CCGACTCCGGAGGAAAATAGCTG
Found at i:16613 original size:29 final size:30
Alignment explanation
Indices: 16557--16641 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
16547 GGACAACAAA
*
16557 TTATCTTAAATT-TTAAA-ATAATCTTTATTT
1 TTATCTTAACTTATTAAATAT-AT-TTTATTT
*
16587 TTATTTTAACTTATTAAATAT-TTTTATTT
1 TTATCTTAACTTATTAAATATATTTTATTT
* *
16616 TTGTCTTAATTTATTAAATATATTTT
1 TTATCTTAACTTATTAAATATATTTT
16642 TTATTTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
29 25 0.53
30 15 0.32
31 5 0.11
32 2 0.04
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (30 bp):
TTATCTTAACTTATTAAATATATTTTATTT
Found at i:16757 original size:18 final size:18
Alignment explanation
Indices: 16724--16770 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 18
16714 CTTGAAATAT
16724 ATTTAAATATTTTATTATTA
1 ATTTAAA-A-TTTATTATTA
*
16744 ATTTAAAATTTATTTTTA
1 ATTTAAAATTTATTATTA
16762 ATTTAAAAT
1 ATTTAAAAT
16771 AAGAATAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 18 0.69
19 1 0.04
20 7 0.27
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTAAAATTTATTATTA
Found at i:16779 original size:29 final size:29
Alignment explanation
Indices: 16747--16877 Score: 111
Period size: 29 Copynumber: 4.3 Consensus size: 29
16737 ATTATTAATT
*
16747 TAAAATTTATTTTTAATTTAAAATAAGAA
1 TAAAATATATTTTTAATTTAAAATAAGAA
*
16776 TAAAGTATATTTTTAAGTAAATATAAAAATAA-AA
1 TAAAATATATTTTTAA-T---T-T-AAAATAAGAA
** *
16810 TATTATATATTTTTAATTTAAAATAAGAG
1 TAAAATATATTTTTAATTTAAAATAAGAA
* * *
16839 TAAAATATATGTTTTTATATTAAATTAATAA
1 TAAAATATAT-TTTTAAT-TTAAAATAAGAA
16870 TAAAATAT
1 TAAAATAT
16878 TTAAATATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
28 7 0.09
29 24 0.30
30 8 0.10
31 17 0.21
33 2 0.02
34 16 0.20
35 7 0.09
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
TAAAATATATTTTTAATTTAAAATAAGAA
Found at i:17018 original size:29 final size:30
Alignment explanation
Indices: 16955--17030 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
16945 TATTTTTTAC
* *
16955 ATTAAAATAAAAATAAAATATATTTAATAA
1 ATTAAAACAAAAATAAAATATAATTAATAA
*
16985 ATTAAGACAAAAATAAAA-ATAATTAA-AA
1 ATTAAAACAAAAATAAAATATAATTAATAA
17013 AGTTAAAACAAAAATAAA
1 A-TTAAAACAAAAATAAA
17031 GAGAAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 22 0.54
30 16 0.39
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (30 bp):
ATTAAAACAAAAATAAAATATAATTAATAA
Found at i:17841 original size:30 final size:30
Alignment explanation
Indices: 17805--17893 Score: 117
Period size: 30 Copynumber: 2.9 Consensus size: 30
17795 AGGACCACTT
*
17805 TCCATATGTTCCGAAGGACATAGGTAACTG
1 TCCATATGTTCCGAAGGACATAGGTAACTA
* *
17835 TCCATATGTCCCTAAGGACATAGGTAAACTA
1 TCCATATGTTCCGAAGGACATAGGT-AACTA
*
17866 TCCATATG-TCTCGAAAGACATAGGTAAC
1 TCCATATGTTC-CGAAGGACATAGGTAAC
17894 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
30 27 0.53
31 24 0.47
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (30 bp):
TCCATATGTTCCGAAGGACATAGGTAACTA
Found at i:17873 original size:31 final size:31
Alignment explanation
Indices: 17805--17892 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
17795 AGGACCACTT
* *
17805 TCCATATGTTCCGAAGGACATAGGT-AACTG
1 TCCATATGTCCCGAAGGACATAGGTAAACTA
*
17835 TCCATATGTCCCTAAGGACATAGGTAAACTA
1 TCCATATGTCCCGAAGGACATAGGTAAACTA
* *
17866 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCCCGAAGGACATAGGTAA
17893 CCCTCGACTC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 23 0.45
31 28 0.55
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAAACTA
Found at i:18134 original size:15 final size:15
Alignment explanation
Indices: 18111--18140 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18101 CACATAAACT
*
18111 CATATCTTCTTATCA
1 CATAGCTTCTTATCA
18126 CATAGCTTCTTATCA
1 CATAGCTTCTTATCA
18141 TATCATTAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (15 bp):
CATAGCTTCTTATCA
Found at i:18310 original size:2 final size:2
Alignment explanation
Indices: 18303--18349 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
18293 ATTTCATACT
18303 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
18345 TA TA T
1 TA TA T
18350 TACTTTGATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19030 original size:34 final size:32
Alignment explanation
Indices: 18977--19046 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
18967 CCTTACAAAC
*
18977 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
19009 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
19043 TCCC
1 TCCC
19047 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:19355 original size:21 final size:21
Alignment explanation
Indices: 19329--19370 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
19319 CCAGAATGGG
*
19329 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
19350 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
19371 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:19557 original size:20 final size:20
Alignment explanation
Indices: 19499--19557 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
19489 ATCTGTACCC
*
19499 GGGGAATC-GATA-CCCCTGA
1 GGGGAATCTG-TACCCCCTGG
*
19518 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
19538 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
19558 ACAATTTGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.26
20 26 0.74
ACGTcount: A:0.17, C:0.29, G:0.34, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:21515 original size:3 final size:3
Alignment explanation
Indices: 21507--21553 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
21497 TACATCCTCA
* *
21507 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
21554 CCTTTCTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:22595 original size:34 final size:32
Alignment explanation
Indices: 22542--22611 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
22532 CCTTACAAAC
*
22542 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
22574 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
22608 TCCC
1 TCCC
22612 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:22920 original size:21 final size:21
Alignment explanation
Indices: 22894--22935 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
22884 CCAGAATGGG
*
22894 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
22915 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
22936 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:23090 original size:33 final size:33
Alignment explanation
Indices: 23051--23113 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
23041 CCATGCAGGG
*
23051 GGAATCTGTACCCGGGGAATCGATACCCCTAGA
1 GGAATCTGTACCCGGGGAATCAATACCCCTAGA
* *
23084 GGAATCTGTTCCTGGGGAATCAATACCCCT
1 GGAATCTGTACCCGGGGAATCAATACCCCT
23114 GGGGGGAATC
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:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (33 bp):
GGAATCTGTACCCGGGGAATCAATACCCCTAGA
Found at i:23134 original size:20 final size:21
Alignment explanation
Indices: 23109--23156 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
23099 GGAATCAATA
* *
23109 CCCCTGGGGG-GAATCTTTTC
1 CCCCTGGGGGAGAATCTGTAC
23129 CCCCTGGGGGAGAATCTGTAC
1 CCCCTGGGGGAGAATCTGTAC
23150 CCCCTGG
1 CCCCTGG
23157 ACAATCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.12, C:0.33, G:0.31, T:0.23
Consensus pattern (21 bp):
CCCCTGGGGGAGAATCTGTAC
Found at i:23588 original size:30 final size:30
Alignment explanation
Indices: 23518--23588 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
23508 CCCATAGATC
*
23518 TTATCACATAACTTATCTTTTATACTCATA
1 TTATCACTTAACTTATCTTTTATACTCATA
* ** * *
23548 TAATTTCTTAACTTAT-TTTATATTCTCCTA
1 TTATCACTTAACTTATCTTT-TATACTCATA
23578 TTATCACTTAA
1 TTATCACTTAA
23589 TAGTATTTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.31, C:0.18, G:0.00, T:0.51
Consensus pattern (30 bp):
TTATCACTTAACTTATCTTTTATACTCATA
Found at i:26890 original size:16 final size:16
Alignment explanation
Indices: 26869--26899 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26859 TAATAAATAA
26869 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
26885 ACGAACATAAACGAA
1 ACGAACATAAACGAA
26900 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:26988 original size:16 final size:16
Alignment explanation
Indices: 26967--27021 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
26957 CATTTAATAA
26967 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
26983 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
26999 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
27015 ATAAACG
1 ATAAACG
27022 TTGGAGACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.56, C:0.22, G:0.13, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:28066 original size:10 final size:10
Alignment explanation
Indices: 28051--28084 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
28041 ATAAATGAAT
28051 GAACATAAAC
1 GAACATAAAC
28061 GAACATAAAC
1 GAACATAAAC
*
28071 GAACATAACC
1 GAACATAAAC
28081 GAAC
1 GAAC
28085 GAACATAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.09
Consensus pattern (10 bp):
GAACATAAAC
Found at i:28087 original size:14 final size:14
Alignment explanation
Indices: 28067--28099 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28057 AAACGAACAT
28067 AAACGAACATAACC
1 AAACGAACATAACC
*
28081 GAACGAACATAACC
1 AAACGAACATAACC
28095 AAACG
1 AAACG
28100 TTCACGAGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:28899 original size:24 final size:22
Alignment explanation
Indices: 28851--28910 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
28841 GGCATATGAA
*
28851 ATATGTCCCGAAAGACCTATGC
1 ATATGTCCCGAAAGACCTATCC
*
28873 ATATGTCCCGAAGGACCACTATCC
1 ATATGTCCCGAAAGA-C-CTATCC
*
28897 ATATGTTCC-AAAGA
1 ATATGTCCCGAAAGA
28911 ACATAGGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 14 0.44
23 5 0.16
24 13 0.41
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (22 bp):
ATATGTCCCGAAAGACCTATCC
Found at i:28930 original size:30 final size:29
Alignment explanation
Indices: 28890--28982 Score: 114
Period size: 31 Copynumber: 3.1 Consensus size: 29
28880 CCGAAGGACC
28890 ACTATCCATATGTTCCAAAGAACATAGGTA
1 ACTATCCATATGTTCCAAAG-ACATAGGTA
* * *
28920 ACTGTCCATATGTCCCTAAGGACATAGGTAA
1 ACTATCCATATGTTCC-AAAGACATAGGT-A
*
28951 ACTATCCATATGTCTCGAAAGACATAGGTA
1 ACTATCCATATGT-TCCAAAGACATAGGTA
28981 AC
1 AC
28983 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
30 25 0.47
31 27 0.51
32 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.26
Consensus pattern (29 bp):
ACTATCCATATGTTCCAAAGACATAGGTA
Found at i:28962 original size:31 final size:31
Alignment explanation
Indices: 28890--28981 Score: 116
Period size: 30 Copynumber: 3.0 Consensus size: 31
28880 CCGAAGGACC
* *
28890 ACTATCCATATGTTCCAAAGAACATAGGT-A
1 ACTATCCATATGTCCCAAAGGACATAGGTAA
* *
28920 ACTGTCCATATGTCCCTAAGGACATAGGTAA
1 ACTATCCATATGTCCCAAAGGACATAGGTAA
*
28951 ACTATCCATATGTCTCGAAA-GACATAGGTAA
1 ACTATCCATATGTC-CCAAAGGACATAGGTAA
28982 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 25 0.47
31 25 0.47
32 3 0.06
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (31 bp):
ACTATCCATATGTCCCAAAGGACATAGGTAA
Found at i:29222 original size:15 final size:15
Alignment explanation
Indices: 29199--29228 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29189 CACATAAATC
*
29199 CATATCTTCTTATCA
1 CATAGCTTCTTATCA
29214 CATAGCTTCTTATCA
1 CATAGCTTCTTATCA
29229 TATCATTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.43
Consensus pattern (15 bp):
CATAGCTTCTTATCA
Found at i:29808 original size:30 final size:30
Alignment explanation
Indices: 29738--29808 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 30
29728 CCCATAGATC
*
29738 TTATCACATAACTTATCTTTTATACTCATA
1 TTATCACTTAACTTATCTTTTATACTCATA
* ** * *
29768 TAATTTCTTAACTTAT-TTTATATTCTCTTA
1 TTATCACTTAACTTATCTTT-TATACTCATA
29798 TTATCACTTAA
1 TTATCACTTAA
29809 TAGTAATTTT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.52
Consensus pattern (30 bp):
TTATCACTTAACTTATCTTTTATACTCATA
Found at i:32479 original size:21 final size:21
Alignment explanation
Indices: 32438--32481 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
32428 TGGTTGGGTA
*
32438 TTCTTTCCCAAGAGGGTAATAT
1 TTCTTTCCCAACA-GGTAATAT
32460 TTCTTTCCCAACA-GTAAATAT
1 TTCTTTCCCAACAGGT-AATAT
32481 T
1 T
32482 ATTGGGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 6 0.30
22 12 0.60
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (21 bp):
TTCTTTCCCAACAGGTAATAT
Found at i:35751 original size:20 final size:20
Alignment explanation
Indices: 35728--35768 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
35718 TATTGTATTT
* *
35728 TTATTCTTTTAATTTACTCA
1 TTATACTTTTAAATTACTCA
35748 TTATACTTTTAAATTACTCA
1 TTATACTTTTAAATTACTCA
35768 T
1 T
35769 GTTTTGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATACTTTTAAATTACTCA
Found at i:37357 original size:33 final size:33
Alignment explanation
Indices: 37320--37383 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
37310 TGCTAAAAGC
* *
37320 TTAAAAATAGACAACAATACTGATATTACTCGA
1 TTAAAAATACACAACAATACCGATATTACTCGA
37353 TTAAAAATACACAACAATACCGATATTACTC
1 TTAAAAATACACAACAATACCGATATTACTC
37384 ATGGTAGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.27
Consensus pattern (33 bp):
TTAAAAATACACAACAATACCGATATTACTCGA
Found at i:45435 original size:2 final size:2
Alignment explanation
Indices: 45428--45455 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45418 ACTATTTACA
45428 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
45456 GTTAATCTTA
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:48683 original size:18 final size:18
Alignment explanation
Indices: 48660--48698 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
48650 TGTCCGTCTA
48660 GGGTTAATTAGACAGGTT
1 GGGTTAATTAGACAGGTT
48678 GGGTTAATTAGACAGGTT
1 GGGTTAATTAGACAGGTT
48696 GGG
1 GGG
48699 CCACTATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.38, T:0.31
Consensus pattern (18 bp):
GGGTTAATTAGACAGGTT
Found at i:50824 original size:12 final size:12
Alignment explanation
Indices: 50796--50829 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
50786 TATCTTTTGT
50796 TTATCTTG-TTC
1 TTATCTTGTTTC
*
50807 TAATCTTGTTTC
1 TTATCTTGTTTC
50819 TTATCTTGTTT
1 TTATCTTGTTT
50830 TCAGCACCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.12, C:0.15, G:0.09, T:0.65
Consensus pattern (12 bp):
TTATCTTGTTTC
Found at i:51145 original size:21 final size:20
Alignment explanation
Indices: 51121--51162 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
51111 AAAATAATAA
*
51121 ATTAATAAATTATTAAAAATT
1 ATTAACAAATTA-TAAAAATT
*
51142 ATTAACCAATTATAAAAATT
1 ATTAACAAATTATAAAAATT
51162 A
1 A
51163 AGACCATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAACAAATTATAAAAATT
Found at i:57793 original size:53 final size:54
Alignment explanation
Indices: 57723--58298 Score: 382
Period size: 54 Copynumber: 10.9 Consensus size: 54
57713 AAAATTTTTT
* * *
57723 TCTACTCCTCCGTAACAAAGGAACGCTAGAGCTTACTTAGTCTTAGAAA-CTGC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
* * * * *
57776 TCCACTCCTCCAAAACAAATGAATGCTAGAGCTTACAT-AGT-TATAGAAATATGT
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTAC-TCAGTCT-TAGAAATCTGC
* * * * * *
57830 TCTACT-CTGCATGACAAATGAATGCTAAAGCTTACTCAGTCTTATAAATTTGC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
* * ** * * * *
57883 TATACTCATTTATAACAAAGGAAAGCTGGAGCTTACTCAATCTTAGAAATCTAC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
* * *
57937 TTTACTCCTCCATGAA-AAAGGAATGCTAGAGCTTACTTTA-TCTTAGAAATTTGC
1 TCTACTCCTCCAT-AACAAAGGAATGCTAGAGCTTAC-TCAGTCTTAGAAATCTGC
** * *
57991 TCTACTCCTCCATAACAAAGGAACACTAGAGCTTACTCAGTCTTAAAAATTTGC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
* * * * ** * * * *
58045 TCTATTCCTCGATGATAAAGGAACACTAGAGTTTACTC-GATCTTAAAAATTTAC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAG-TCTTAGAAATCTGC
* * * * * * * * * *
58099 ACTACTACTCCATTACAATGGAACGCTAGAACTTACTAAGTTTTAAAAATATGC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
* *** * * * *
58153 TCTACTCCTTCATAACAAAGGAACATTAGATCTTACT-AGGTCTTAAAAATTTTC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCA-GTCTTAGAAATCTGC
* * *
58207 TCTACTCCT-C----C-----AATGCTAGAGCTTACTCAGTCTTAAAAATTTAC
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
* * * *
58251 TCTACTCCTCTATGACAAAGGAACGCTAGAACTTACTC-GTCTTA-AAAT
1 TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAAT
58299 TTTACTCTAT
Statistics
Matches: 418, Mismatches: 81, Indels: 49
0.76 0.15 0.09
Matches are distributed among these distances:
44 35 0.08
45 1 0.00
49 2 0.00
52 6 0.01
53 94 0.22
54 275 0.66
55 5 0.01
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (54 bp):
TCTACTCCTCCATAACAAAGGAATGCTAGAGCTTACTCAGTCTTAGAAATCTGC
Found at i:57917 original size:54 final size:54
Alignment explanation
Indices: 57725--58410 Score: 339
Period size: 54 Copynumber: 12.9 Consensus size: 54
57715 AATTTTTTTC
* * * * *
57725 TACTCCTCCGTAACAAAGGAACGCTAGAGCTTACTTAGTCTTAGAAA-CTGCTC
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
* * * * * * *
57778 CACTCCTCCAAAACAAATGAATGCTAGAGCTTACAT-AGT-TATAGAAATATGTTC
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTAC-TCAGTCT-TAGAAATTTGCTA
* * * * * *
57832 TACT-CTGCATGACAAATGAATGCTAAAGCTTACTCAGTCTTATAAATTTGCTA
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
* ** * * * * *
57885 TACTCATTTATAACAAAGGAAAGCTGGAGCTTACTCAATCTTAGAAATCTACTT
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
* * *
57939 TACTCCTCCATGAA-AAAGGAATGCTAGAGCTTACTTTA-TCTTAGAAATTTGCTC
1 TACTCCTCCAT-AACAAAGGAAAGCTAGAGCTTAC-TCAGTCTTAGAAATTTGCTA
* *
57993 TACTCCTCCATAACAAAGGAACA-CTAGAGCTTACTCAGTCTTAAAAATTTGCTC
1 TACTCCTCCATAACAAAGGAA-AGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
* * * * * * *
58047 TATTCCTCGATGATAAAGGAACA-CTAGAGTTTACTC-GATCTTAAAAATTTAC-A
1 TACTCCTCCATAACAAAGGAA-AGCTAGAGCTTACTCAG-TCTTAGAAATTTGCTA
* * * * * * * * * *
58100 CTACTACTCCATTACAATGGAACGCTAGAACTTACTAAGTTTTAAAAATATGCTC
1 -TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
* * * * * *
58155 TACTCCTTCATAACAAAGGAACA-TTAGATCTTACT-AGGTCTTAAAAATTTTCTC
1 TACTCCTCCATAACAAAGGAA-AGCTAGAGCTTACTCA-GTCTTAGAAATTTGCTA
* * * *
58209 TACTCCT-C----C-----AATGCTAGAGCTTACTCAGTCTTAAAAATTTACTC
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
* * * * * *
58253 TACTCCTCTATGACAAAGGAACGCTAGAACTTACTC-GTCTTA-AAATTTTACTC
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAA-TTTGCTA
* * * * * ** *
58306 TATTCCTCTATGTA-AAATGAACA-CTAGAGTTTACTTGGTCTTA-AAAGTTTGCTC
1 TACTCCTCCAT-AACAAAGGAA-AGCTAGAGCTTACTCAGTCTTAGAAA-TTTGCTA
* * * * * *
58360 TACTCCTCTATGACAAGGGAACGCTAGAGATTACT-TGATCTTAGAAATTTG
1 TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAG-TCTTAGAAATTTG
58411 TGTTACTATC
Statistics
Matches: 500, Mismatches: 95, Indels: 75
0.75 0.14 0.11
Matches are distributed among these distances:
44 35 0.07
45 1 0.00
49 2 0.00
52 5 0.01
53 127 0.25
54 322 0.64
55 8 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (54 bp):
TACTCCTCCATAACAAAGGAAAGCTAGAGCTTACTCAGTCTTAGAAATTTGCTA
Found at i:58156 original size:162 final size:161
Alignment explanation
Indices: 57706--58409 Score: 519
Period size: 162 Copynumber: 4.4 Consensus size: 161
57696 AGCGTCGGCC
* ** ** * * * *
57706 CAGTCTTAAAATTTTTTTCTACTCCTCCGTAACAAAGGAACGCTAGAGCTTACT-TAGTCTTAGA
1 CAGTCTTAAAAATTTGCTCTACTCCTCTATGACAAAGGAA-ACTAGAGCTTACTCGA-TCTTAAA
* * * ** * * * * *
57770 AA-CTGCTCCACTCCTCCAAAACAAATGAATGCTAGAGCTTAC-ATAGT-TATAGAAATATGTTC
64 AATTTACTCTACTCCTCCATGACAAAGGAACGCTAGAACTTACTA-AGTCT-TAAAAATATGCTC
* * * ** *
57832 TACT-CTGCATGACAAATGAATGCTAAAGCTTACT
127 TACTCCTCCATAACAAAGGAACACTAGAGCTTACT
* * * * * * * *
57866 CAGTCTTATAAATTTGCTATACTCATTTATAACAAAGGAAAGCTGGAGCTTACTCAATCTTAGAA
1 CAGTCTTAAAAATTTGCTCTACTCCTCTATGACAAAGGAAA-CTAGAGCTTACTCGATCTTAAAA
* * * * * * * *
57931 ATCTACTTTACTCCTCCATGAAAAAGGAATGCTAGAGCTTACTTTA-TCTTAGAAATTTGCTCTA
65 ATTTACTCTACTCCTCCATGACAAAGGAACGCTAGAACTTAC-TAAGTCTTAAAAATATGCTCTA
57995 CTCCTCCATAACAAAGGAACACTAGAGCTTACT
129 CTCCTCCATAACAAAGGAACACTAGAGCTTACT
* * * *
58028 CAGTCTTAAAAATTTGCTCTATTCCTCGATGATAAAGGAACACTAGAGTTTACTCGATCTTAAAA
1 CAGTCTTAAAAATTTGCTCTACTCCTCTATGACAAAGGAA-ACTAGAGCTTACTCGATCTTAAAA
* * * * *
58093 ATTTACACTACTACTCCATTACAATGGAACGCTAGAACTTACTAAGTTTTAAAAATATGCTCTAC
65 ATTTACTCTACTCCTCCATGACAAAGGAACGCTAGAACTTACTAAGTCTTAAAAATATGCTCTAC
* * *
58158 TCCTTCATAACAAAGGAACATTAGATCTTACT
130 TCCTCCATAACAAAGGAACACTAGAGCTTACT
* *
58190 -AGGTCTTAAAAATTTTCTCTACTCCTC-----C-AATG---CTAGAGCTTACTC-AGTCTTAAA
1 CA-GTCTTAAAAATTTGCTCTACTCCTCTATGACAAAGGAAACTAGAGCTTACTCGA-TCTTAAA
* * * * *
58244 AATTTACTCTACTCCTCTATGACAAAGGAACGCTAGAACTTACT-CGTCTTAAAATTTTACTCTA
64 AATTTACTCTACTCCTCCATGACAAAGGAACGCTAGAACTTACTAAGTCTTAAAAATATGCTCTA
* * * * *
58308 TTCCTCTATGTA-AAATGAACACTAGAGTTTACT
129 CTCCTCCAT-AACAAAGGAACACTAGAGCTTACT
** * * * * * *
58341 TGGTCTTAAAAGTTTGCTCTACTCCTCTATGACAAGGGAACGCTAGAGATTACTTGATCTTAGAA
1 CAGTCTTAAAAATTTGCTCTACTCCTCTATGACAAAGGAA-ACTAGAGCTTACTCGATCTTAAAA
58406 ATTT
65 ATTT
58410 GTGTTACTAT
Statistics
Matches: 433, Mismatches: 87, Indels: 47
0.76 0.15 0.08
Matches are distributed among these distances:
151 62 0.14
152 59 0.14
156 4 0.01
157 2 0.00
160 51 0.12
161 75 0.17
162 179 0.41
163 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (161 bp):
CAGTCTTAAAAATTTGCTCTACTCCTCTATGACAAAGGAAACTAGAGCTTACTCGATCTTAAAAA
TTTACTCTACTCCTCCATGACAAAGGAACGCTAGAACTTACTAAGTCTTAAAAATATGCTCTACT
CCTCCATAACAAAGGAACACTAGAGCTTACT
Found at i:60909 original size:17 final size:16
Alignment explanation
Indices: 60877--60916 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
60867 AAATTATCAA
* *
60877 TTTTATTTAAATTAAT
1 TTTTATTCAAAATAAT
60893 TTATTATTCAAAATAAT
1 TT-TTATTCAAAATAAT
60910 TTTTATT
1 TTTTATT
60917 ATTTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTCAAAATAAT
Found at i:61299 original size:18 final size:18
Alignment explanation
Indices: 61276--61310 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
61266 AATTGATATT
*
61276 AAATCATTAAATTATTAG
1 AAATCATTAAACTATTAG
61294 AAATCATTAAACTATTA
1 AAATCATTAAACTATTA
61311 TCAGAGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATCATTAAACTATTAG
Found at i:67375 original size:21 final size:21
Alignment explanation
Indices: 67346--67398 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
67336 ATTCTGACTA
67346 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
67367 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
67388 TCGCAATGCGA
1 TCGCATTGCGA
67399 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:67413 original size:20 final size:20
Alignment explanation
Indices: 67388--67480 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
67378 TTTTCCTAAT
*
67388 TCGCAATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
67408 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
*
67428 TCGTAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
67448 TCGCGATGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
67468 TCGCAACGCGAAT
1 TCGCAACGCGAAT
67481 CTGACTATCG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:67706 original size:22 final size:22
Alignment explanation
Indices: 67678--67743 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
67668 GGTGACATCC
*
67678 GTCCCCATCTCCGATGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
67700 GTCCCCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
67722 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
67744 TTCACGGTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:68158 original size:20 final size:20
Alignment explanation
Indices: 68115--68182 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
68105 CGATTCTTGC
** **
68115 GTTGCGATAGTCAAATTCAC
1 GTTGCGATAGTCATTTTCGT
68135 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
68155 GTTGCGATTTTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
*
68175 GTTACGAT
1 GTTGCGAT
68183 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.43
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:68192 original size:20 final size:20
Alignment explanation
Indices: 68149--68192 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
68139 CGATAGTCAT
* * *
68149 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
68169 TTTCGTGTTACGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
68189 TTTC
1 TTTC
68193 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:70094 original size:20 final size:20
Alignment explanation
Indices: 70069--70119 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
70059 AGAATAGTTT
*
70069 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
70089 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
70109 ACTATCGCAAC
1 ACTATCGCAAC
70120 AAGAGAATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:70346 original size:20 final size:20
Alignment explanation
Indices: 70266--70358 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
70256 AATAATCAAA
**
70266 TTCGCATTGCGATAGTCAAA
1 TTCGCATTGCGATAGTCATT
70286 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
* *
70306 TTCGCGTTGCGATAGCCATT
1 TTCGCATTGCGATAGTCATT
*
70326 TTCGCATTGCGATAGTTATT
1 TTCGCATTGCGATAGTCATT
*
70346 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
70359 TTTAAGTTTC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCATT
Found at i:70933 original size:21 final size:20
Alignment explanation
Indices: 70842--70946 Score: 68
Period size: 21 Copynumber: 5.0 Consensus size: 20
70832 GACTCACCTG
70842 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
70862 CCTATCGTTCAAGAGGCCCCTA
1 TC-ATCGTTCAAGAGG-CCCTC
** *
70884 TCATCCCTCAAGAGTCCCATC
1 TCATCGTTCAAGAGGCCC-TC
* * *
70905 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
70926 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
70947 CCAACATTCT
Statistics
Matches: 62, Mismatches: 17, Indels: 11
0.69 0.19 0.12
Matches are distributed among these distances:
20 4 0.06
21 51 0.82
22 4 0.06
23 3 0.05
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:70939 original size:42 final size:42
Alignment explanation
Indices: 70867--70949 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
70857 CCTCCCCTAT
*
70867 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCATCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCC-TCCCAC
* ** *
70909 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
70950 ACATTCTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 30 0.86
43 5 0.14
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:72523 original size:33 final size:33
Alignment explanation
Indices: 72484--72568 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
72474 TCGCAACGCG
** *
72484 GAAATGACTAGCGCAATGAGAGAATCGCAATAC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAATAC
* *
72517 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAATAC
*
72550 GAAAATGAAAATCGCAACG
1 G-AAATGAAAAGCGCAACG
72569 CGAAACTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.63
34 17 0.37
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAATAC
Found at i:72561 original size:34 final size:33
Alignment explanation
Indices: 72495--72568 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
72485 AAATGACTAG
*
72495 CGCAATGAGAGAATCGCAATACGAAATGAAAAT
1 CGCAACGAGAGAATCGCAATACGAAATGAAAAT
*
72528 CGCAACGAGAGAATCGCAATGCGAAAATGAAAAT
1 CGCAACGAGAGAATCGCAATACG-AAATGAAAAT
72562 CGCAACG
1 CGCAACG
72569 CGAAACTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 21 0.55
34 17 0.45
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
CGCAACGAGAGAATCGCAATACGAAATGAAAAT
Found at i:72642 original size:20 final size:20
Alignment explanation
Indices: 72617--72685 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
72607 GCGATTCTCT
*
72617 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
72637 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
72657 CGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
72677 CGTTGCGAT
1 CGTTGCGAT
72686 TTCCGCGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.23, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:72695 original size:34 final size:33
Alignment explanation
Indices: 72581--72704 Score: 106
Period size: 34 Copynumber: 3.5 Consensus size: 33
72571 AAACTAAATT
** *
72581 CGCGTTGCGATTTTCATTTTCGCATTGCGA-TTC
1 CGCGTTGCGATAGTCA-TTTCGCGTTGCGATTTC
* *
72614 TCTCGTTGCAATAGTCATTTCCGCGTTGCGATAGTCAATTC
1 -CGCGTTGCGATAGTCATTT-CGCGTTGCG--A-T---TTC
72655 CGCGTTGCGATAGTCATATTCGCGTTGCGATTTC
1 CGCGTTGCGATAGTCAT-TTCGCGTTGCGATTTC
72689 CGCGTTGCGATAGTCA
1 CGCGTTGCGATAGTCA
72705 AATGAATGTC
Statistics
Matches: 74, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
33 3 0.04
34 39 0.53
36 1 0.01
37 1 0.01
38 1 0.01
40 24 0.32
41 5 0.07
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.36
Consensus pattern (33 bp):
CGCGTTGCGATAGTCATTTCGCGTTGCGATTTC
Found at i:73297 original size:3 final size:3
Alignment explanation
Indices: 73283--73317 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
73273 AGAGATATTC
*
73283 TCT TCA TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
73318 ATGTACGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:75066 original size:31 final size:32
Alignment explanation
Indices: 74993--75100 Score: 132
Period size: 31 Copynumber: 3.4 Consensus size: 32
74983 AGAGTCGAGG
74993 GTATACCTATGTTCTAC-AGAACATATGGACA
1 GTATACCTATGTTCTACGAGAACATATGGACA
* * *
75024 GAATTACCTATGTTTTTCGAG-ACATATGGACA
1 GTA-TACCTATGTTCTACGAGAACATATGGACA
*
75056 GTATACCTATGTTCTAAG-GAACATATGGACA
1 GTATACCTATGTTCTACGAGAACATATGGACA
* *
75087 GTTTACCTAGGTTC
1 GTATACCTATGTTC
75101 ATCGGAACCT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
30 1 0.02
31 37 0.57
32 25 0.38
33 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (32 bp):
GTATACCTATGTTCTACGAGAACATATGGACA
Found at i:75108 original size:31 final size:30
Alignment explanation
Indices: 74996--75120 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 30
74986 GTCGAGGGTA
* *
74996 TACCTATGTTCTACAGAACATATGGACAGAAT
1 TACCTATGTTCT-CGGAACATATGGACAG-TT
* *
75028 TACCTATGTTTTTC-GAGACATATGGACAGTA
1 TACCTATG-TTCTCGGA-ACATATGGACAGTT
*
75059 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCT-CGGAACATATGGACAGTT
* * *
75090 TACCTAGGTTCATCGGAACCTATAGACAGTT
1 TACCTATGTTC-TCGGAACATATGGACAGTT
75121 ATCGAGGATC
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
30 3 0.04
31 48 0.62
32 24 0.31
33 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (30 bp):
TACCTATGTTCTCGGAACATATGGACAGTT
Found at i:77848 original size:24 final size:24
Alignment explanation
Indices: 77821--77867 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
77811 CAAAATCCGA
77821 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
77845 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
77868 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:77876 original size:24 final size:24
Alignment explanation
Indices: 77825--77876 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
77815 ATCCGAGTAT
** *
77825 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
77849 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
77873 TGAC
1 TGAC
77877 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:78730 original size:20 final size:20
Alignment explanation
Indices: 78705--78771 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
78695 AAATTCAGTA
78705 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
78725 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
* *
78745 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCTCG
78765 TTGCGAT
1 TTGCGAT
78772 TTACGTATCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:78788 original size:20 final size:20
Alignment explanation
Indices: 78758--78850 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
78748 CGATAGTCAG
*
78758 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
78778 ATCCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
78798 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
78818 ATTCGTATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
78838 ATTCGCATTGCGA
1 ATTCGCATTGCGA
78851 ATTAGGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:78871 original size:21 final size:21
Alignment explanation
Indices: 78847--78892 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
78837 TATTCGCATT
78847 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
78868 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
78889 GCGA
1 GCGA
78893 TAATCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:79053 original size:15 final size:15
Alignment explanation
Indices: 79029--79075 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
79019 TTAAAAAATC
79029 TAAATTTTAAATT-T
1 TAAATTTTAAATTAT
79043 TAAATTTTTAAATTAT
1 TAAA-TTTTAAATTAT
*
79059 T-AA-TTAAAATTAT
1 TAAATTTTAAATTAT
79072 TAAA
1 TAAA
79076 ATAAAAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 10 0.34
14 6 0.21
15 11 0.38
16 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAATTTTAAATTAT
Found at i:79225 original size:29 final size:28
Alignment explanation
Indices: 79193--79278 Score: 70
Period size: 30 Copynumber: 2.9 Consensus size: 28
79183 ATAAAATCTG
79193 AAAATTTAATATCTATTTTATAATTTTTA
1 AAAATTTAATA-CTATTTTATAATTTTTA
* *
79222 AAAATTCAATAAC-ATATTA-AATCATTTTA
1 AAAATTTAAT-ACTATTTTATAAT--TTTTA
79251 ACAAATTTAATGACTA-TTTATGAATTTT
1 A-AAATTTAAT-ACTATTTTAT-AATTTT
79279 ACCAAATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
27 3 0.07
28 5 0.11
29 16 0.36
30 17 0.38
31 1 0.02
32 3 0.07
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (28 bp):
AAAATTTAATACTATTTTATAATTTTTA
Found at i:80683 original size:16 final size:16
Alignment explanation
Indices: 80662--80693 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
80652 AAAAAGGGTA
80662 AACTACGTTATGTGTC
1 AACTACGTTATGTGTC
80678 AACTACGTTATGTGTC
1 AACTACGTTATGTGTC
80694 CTCCTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
AACTACGTTATGTGTC
Found at i:80844 original size:3 final size:3
Alignment explanation
Indices: 80838--80901 Score: 65
Period size: 3 Copynumber: 20.0 Consensus size: 3
80828 TTGTTTATAC
* * *
80838 ATT ATT ATAT ATAT ATAT ATAT ATT ATA ACT ATT ATT ATT ATT ATT ACT
1 ATT ATT AT-T AT-T AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
80887 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
80902 TTTTACTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 39 0.72
4 15 0.28
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:86358 original size:124 final size:124
Alignment explanation
Indices: 86178--86603 Score: 615
Period size: 124 Copynumber: 3.5 Consensus size: 124
86168 GAAATAATAC
* * * * * * *
86178 TTGGATTTCAACTTCACGGCAAATGATATCCAATTC--ATCACAACTTCACAAAGAAGGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGACAT
* * * *
86241 CCATGATTTCAATTTCACGACGAATGATATCGTGCCCACCAGCAACATTCATTTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGA
* *
86300 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGACAT
* *
86365 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGTAATATTCATCTTTAGA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGA
*
86424 TTGGATTTCAACTTCACGACGAATGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGACAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGACAT
* * * * * *
86489 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCATACAACTCTAAA
66 CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGA
* *
86548 TTGGATTT-AACTTCACGACGAAGGATATACAATTCAAAGCTCAACTTCACAGCGAA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAA
86604 AGAGCTTTCC
Statistics
Matches: 274, Mismatches: 28, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
122 33 0.12
123 45 0.16
124 196 0.72
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGGGACAT
CCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGA
Found at i:87202 original size:23 final size:23
Alignment explanation
Indices: 87175--87220 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
87165 CCTTTTTATC
*
87175 TTACAATT-ATAATATTTATATAT
1 TTAC-ATTAATAATATATATATAT
*
87198 TTACATTAATTATATATATATAT
1 TTACATTAATAATATATATATAT
87221 ACTATCTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (23 bp):
TTACATTAATAATATATATATAT
Found at i:87938 original size:20 final size:21
Alignment explanation
Indices: 87913--87955 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
87903 CAACTTTGTT
87913 TTCG-AAAGGAGGAAAAGATA
1 TTCGAAAAGGAGGAAAAGATA
* *
87933 TTCGAAAAGGTGTAAAAGATA
1 TTCGAAAAGGAGGAAAAGATA
87954 TT
1 TT
87956 TTGGGCCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.23
Consensus pattern (21 bp):
TTCGAAAAGGAGGAAAAGATA
Found at i:88352 original size:12 final size:12
Alignment explanation
Indices: 88320--88353 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
88310 TATTATTTAG
88320 TATTTGTTTATTT
1 TATTT-TTTATTT
88333 TA-TTTTTATTT
1 TATTTTTTATTT
88344 TATTTTTTAT
1 TATTTTTTAT
88354 CTACTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 9 0.45
13 2 0.10
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (12 bp):
TATTTTTTATTT
Found at i:88565 original size:28 final size:29
Alignment explanation
Indices: 88507--88576 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
88497 TTATTTTATT
* *
88507 TTTATTTTATTTTTTATCTTTGTTGTATTTA
1 TTTA-TTTA-TTTTTATCTTTCTAGTATTTA
*
88538 TTTATTTATTTTT-TCTTTCTAGTTTTTA
1 TTTATTTATTTTTATCTTTCTAGTATTTA
* *
88566 TGTATCTATTT
1 TTTATTTATTT
88577 AGTATATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 21 0.62
29 5 0.15
30 4 0.12
31 4 0.12
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.73
Consensus pattern (29 bp):
TTTATTTATTTTTATCTTTCTAGTATTTA
Found at i:88702 original size:20 final size:20
Alignment explanation
Indices: 88650--88702 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
88640 TTTATTAAAT
* * *
88650 TTATCTTATTTATCTTTATT
1 TTATCTTATTTGTATTTATC
*
88670 TTATTTTGA-TTGTATTTATC
1 TTATCTT-ATTTGTATTTATC
88690 TTATCTTATTTGT
1 TTATCTTATTTGT
88703 TTCATTTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.68
Consensus pattern (20 bp):
TTATCTTATTTGTATTTATC
Found at i:90561 original size:2 final size:2
Alignment explanation
Indices: 90556--90586 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
90546 TCTCTCTCTC
90556 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
90587 TGGAGAGCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110225 original size:23 final size:23
Alignment explanation
Indices: 110199--110243 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
110189 TATTAGGTAA
**
110199 CGCTTATATAATGTAATAGATAG
1 CGCTTATATAATAAAATAGATAG
110222 CGCTTATATAATAAAATAGATA
1 CGCTTATATAATAAAATAGATA
110244 TTTAACGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.33
Consensus pattern (23 bp):
CGCTTATATAATAAAATAGATAG
Found at i:110301 original size:87 final size:87
Alignment explanation
Indices: 110165--110330 Score: 305
Period size: 87 Copynumber: 1.9 Consensus size: 87
110155 TATTTAATCA
*
110165 GAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATAGCGCTTATA
1 GAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAGCGCTTATA
110230 TAATAAAATAGATATTTAACGG
66 TAATAAAATAGATATTTAACGG
110252 GAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAGCGCTTATA
1 GAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAGCGCTTATA
**
110317 TAATGTAATAGATA
66 TAATAAAATAGATA
110331 GCGCTTATAT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.33
Consensus pattern (87 bp):
GAAATATTATCAAGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAGCGCTTATA
TAATAAAATAGATATTTAACGG
Found at i:110327 original size:110 final size:110
Alignment explanation
Indices: 110199--110452 Score: 438
Period size: 110 Copynumber: 2.3 Consensus size: 110
110189 TATTAGGTAA
110199 CGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGATATTTAACGGGAAATATTATCA
1 CGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGATATTTAACGGGAAATATTATCA
110264 AGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAG
66 AGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAG
*
110309 CGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGGTATTTAACGGGAAATATTATCA
1 CGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGATATTTAACGGGAAATATTATCA
* * *
110374 AGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAG
66 AGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAG
110419 CGCTTATATATAATGTAATATG-TAGCGCTTATAT
1 CGC-T-TATATAATGTAATA-GATAGCGCTTATAT
110453 TGACCTATTT
Statistics
Matches: 137, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
110 109 0.80
111 1 0.01
112 26 0.19
113 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (110 bp):
CGCTTATATAATGTAATAGATAGCGCTTATATAATAAAATAGATATTTAACGGGAAATATTATCA
AGTACAATAACATATTAGATAACGCTTATATAATGTAATAGATAG
Found at i:110350 original size:23 final size:23
Alignment explanation
Indices: 110279--110343 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
110269 AATAACATAT
*
110279 TAGATAACGCTTATATAATGTAA
1 TAGATAGCGCTTATATAATGTAA
110302 TAGATAGCGCTTATATAATGTAA
1 TAGATAGCGCTTATATAATGTAA
110325 TAGATAGCGCTTATATAAT
1 TAGATAGCGCTTATATAAT
110344 AAAATAGGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (23 bp):
TAGATAGCGCTTATATAATGTAA
Found at i:110434 original size:25 final size:25
Alignment explanation
Indices: 110389--110452 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
110379 AATAACATAT
110389 TAGGTAGCGC-T-TATATAATGTAA
1 TAGGTAGCGCTTATATATAATGTAA
110412 TAGGTAGCGCTTATATATAATGTAA
1 TAGGTAGCGCTTATATATAATGTAA
*
110437 TATGTAGCGCTTATAT
1 TAGGTAGCGCTTATAT
110453 TGACCTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 10 0.26
24 1 0.03
25 27 0.71
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (25 bp):
TAGGTAGCGCTTATATATAATGTAA
Found at i:114184 original size:120 final size:120
Alignment explanation
Indices: 113971--114209 Score: 408
Period size: 120 Copynumber: 2.0 Consensus size: 120
113961 TCTTCCATTC
* *
113971 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
1 TGGACATAAAGTACCGACAAAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
114036 AAACCGGTATTCTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTA
66 AAACCGGTATTCTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTA
* *
114091 TGGACATAAAGTACCGACAAAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACAAAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
* *
114156 AAACTGGTATAT-TTATACCGGTTATATTACAAAATTATCTATTACATTATAATT
66 AAACCGGTAT-TCTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATT
114210 CTGGGTTCCG
Statistics
Matches: 112, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
120 111 0.99
121 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.33
Consensus pattern (120 bp):
TGGACATAAAGTACCGACAAAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
AAACCGGTATTCTTATACCGGTTATATTACAAAATTATCTAGTACATTATAATTA
Found at i:114358 original size:303 final size:303
Alignment explanation
Indices: 113802--114392 Score: 1076
Period size: 303 Copynumber: 2.0 Consensus size: 303
113792 TTAAAATTAG
* *
113802 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACAAAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
113867 ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
* *
113932 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTCTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACAGACACAATATT
113997 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATTCTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATTCTTATACCGGTTATA
114062 TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
*
114105 CGACAAAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATATTT
1 CGACAAAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
114170 ATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
114235 CACTTTCTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACAGACACAATATT
131 CACTTTCTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACAGACACAATATT
* * *
114300 AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACTGGTATAT-TTATACCGGTTAT
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTAT-TCTTATACCGGTTAT
*
114364 ATTACAAAATTATCTATTACATTATAATT
260 ATTACAAAATTATCTAGTACATTATAATT
114393 CTGGGTTCTG
Statistics
Matches: 277, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
303 276 1.00
304 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (303 bp):
CGACAAAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGATTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
CACTTTCTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACAGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATTCTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
Found at i:114399 original size:183 final size:183
Alignment explanation
Indices: 114091--114675 Score: 967
Period size: 183 Copynumber: 3.2 Consensus size: 183
114081 ATTATAATTA
* *
114091 TGGACATAAAGTACCGACAAAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
114156 AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA
66 AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA
*
114221 TGTGTAAATGTCGACACTTTCTGACAAGGTATCGACACATTTTTCTTCCATTC
131 TGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTC
*
114274 TGGACATAAAGTACAGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
*
114339 AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCTGA
66 AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA
* *
114404 TGTGTAAATGTCAACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTA
131 TGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTC
*
114457 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTATAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
* * * *
114522 AAACCGGTATATTTATACCGATTATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGA
66 AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA
* * * * * *
114587 TGTTTTTTCAA--TCGACACTTTTTGAAAAGATATCCACACATTTTTCTTTCATTC
131 TG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTC
114641 TGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGT
114676 GAAAACTTTG
Statistics
Matches: 377, Mismatches: 22, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
183 301 0.80
184 72 0.19
186 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
AAACTGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA
TGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTC
Found at i:115893 original size:3 final size:3
Alignment explanation
Indices: 115885--115935 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
115875 ACTTGTTTGG
* * * *
115885 ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
115933 ATC
1 ATC
115936 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:115936 original size:12 final size:12
Alignment explanation
Indices: 115889--115952 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
115879 GTTTGGATCA
* *
115889 TCATCATCATCA
1 TCATCTTCATCG
*
115901 TCATCATCATCG
1 TCATCTTCATCG
115913 TCATCTTCATCG
1 TCATCTTCATCG
115925 TCATCTTCATCG
1 TCATCTTCATCG
* *
115937 TCAGCTTCATCT
1 TCATCTTCATCG
115949 TCAT
1 TCAT
115953 TGACCGCTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 47 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:115950 original size:6 final size:6
Alignment explanation
Indices: 115889--115952 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
115879 GTTTGGATCA
* * * * * *
115889 TCATCA TCATCA TCATCA TCATCG TCATCT TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
115937 TCAGCT TCATCT TCAT
1 TCATCT TCATCT TCAT
115953 TGACCGCTTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 50 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:117722 original size:200 final size:200
Alignment explanation
Indices: 117398--118147 Score: 1206
Period size: 200 Copynumber: 3.8 Consensus size: 200
117388 AACATTAAAC
* * * *
117398 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
117462 AAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
*
117527 GGATCGACACTTTATGGTTGCACCTTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
117592 TACAAA
195 TACAAA
* *
117598 AGTGTCGATACATTATTTAGACCTATTCTCTTATAAAATCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
117663 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
117728 AATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
117793 ACAAA
196 ACAAA
117798 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
117863 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
** * * *
117928 GATCGACACTTTATTATTGCACCCTGTTTGCCATTCGTTATGGACAAAAAATATCGACACAAACT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
117993 ACAAA
196 ACAAA
* *
117998 AGTGTCGATACATTATTTAG----A----C-C-T--AACCGGTATACTTGTATCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
118051 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACAC-TTTT-TATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
118114 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
118148 ATTGTAAATT
Statistics
Matches: 524, Mismatches: 25, Indels: 16
0.93 0.04 0.03
Matches are distributed among these distances:
186 38 0.07
187 4 0.01
188 78 0.15
190 1 0.00
191 1 0.00
192 1 0.00
196 1 0.00
200 396 0.76
201 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:120229 original size:33 final size:33
Alignment explanation
Indices: 120192--120257 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
120182 CATCTTAATA
*
120192 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
120225 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
120258 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:120332 original size:21 final size:21
Alignment explanation
Indices: 120302--120354 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
120292 TCTCAGTGTA
*
120302 TCTTCGACTCTCTCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
*
120323 TCTTCTACTCTATCAAGTTTC
1 TCTTCGACTCTATCAAGTTTC
120344 TCTTCGACTCT
1 TCTTCGACTCT
120355 TGATTGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.15, C:0.32, G:0.08, T:0.45
Consensus pattern (21 bp):
TCTTCGACTCTATCAAGTTTC
Found at i:122599 original size:22 final size:19
Alignment explanation
Indices: 122552--122599 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
122542 ATCCGTATCG
122552 TTTACCGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
122571 TGATACCGGTTTTTTATCATATT
1 T-TTACCGG--TTTTATCAT-TT
122594 TTTACC
1 TTTACC
122600 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 6 0.26
22 13 0.57
23 3 0.13
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:122990 original size:178 final size:180
Alignment explanation
Indices: 122520--122988 Score: 671
Period size: 178 Copynumber: 2.6 Consensus size: 180
122510 CGTACTTACG
*
122520 AAAGTATCGACACTTTCAATATATCC-GTATCGTTTACCGGTTTTATCATTTTGATACCGGTTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTACCGGTTTTATCATTTTGATACCGG--TT
* * *
122584 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTA
64 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
*
122649 TAGGCACTAAAAACTGCTTCTTTTTTAAATTCACAAAGTGTCGATCCTTATAT
129 TAGGCACTAAAAACTGCTTCTCTTTTAAATTCACAAAG-GTCGATCCTTATAT
*
122702 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACC-GTTTTATCATTTTGATACCAGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACG-TTTACCGGTTTTATCATTTTGATACCGGTTT
*
122766 TATCATATTTTTACATG-TATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACAC-TTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* * *
122829 AGG-ATTTAAAACTGCTTCTCTTTTAAATTCACGAA-GTCGATCCTTATATT
130 AGGCACTAAAAACTGCTTCTCTTTTAAATTCACAAAGGTCGATCCTTATA-T
* * * * **
122879 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACG-TTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
122944 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
122989 AATTTGGATT
Statistics
Matches: 260, Mismatches: 22, Indels: 13
0.88 0.07 0.04
Matches are distributed among these distances:
176 13 0.05
177 36 0.14
178 63 0.24
179 33 0.13
180 39 0.15
181 19 0.07
182 26 0.10
183 25 0.10
184 6 0.02
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTACCGGTTTTATCATTTTGATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGCACTAAAAACTGCTTCTCTTTTAAATTCACAAAGGTCGATCCTTATAT
Found at i:123840 original size:27 final size:25
Alignment explanation
Indices: 123796--123854 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
123786 GAGAAAAGAA
* **
123796 TAATAAAAAATTTTAATATAATAATAT
1 TAATAAAAAAATGAAATA-AATAA-AT
123823 TAATAAAAAAATGAAATAAATAAAT
1 TAATAAAAAAATGAAATAAATAAAT
*
123848 AAATAAA
1 TAATAAA
123855 TATATAAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.29
26 5 0.18
27 15 0.54
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
TAATAAAAAAATGAAATAAATAAAT
Found at i:123845 original size:4 final size:4
Alignment explanation
Indices: 123810--123862 Score: 52
Period size: 4 Copynumber: 12.5 Consensus size: 4
123800 AAAAAATTTT
* * *
123810 AATA TAATA ATATT AATA AAAA AATGA AATA AATA AATA AATA AATA TATA
1 AATA -AATA A-ATA AATA AATA AAT-A AATA AATA AATA AATA AATA AATA
123861 AA
1 AA
123863 ACAATGTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
4 29 0.73
5 11 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:124292 original size:32 final size:33
Alignment explanation
Indices: 124211--124295 Score: 120
Period size: 33 Copynumber: 2.6 Consensus size: 33
124201 GTCCTACTTG
124211 GACTCAAAATAC-TTCGGTTTTAGTGTTTCAATAA
1 GACTC-AAATACGTT-GGTTTTAGTGTTTCAATAA
* *
124245 GATTCAAATACGTTGGTTTTAGTGTTTCAATAT
1 GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
124278 GACTC-AATACGTTGGTTT
1 GACTCAAATACGTTGGTTT
124296 ATTTCTGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 13 0.28
33 28 0.60
34 6 0.13
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (33 bp):
GACTCAAATACGTTGGTTTTAGTGTTTCAATAA
Found at i:124352 original size:3 final size:3
Alignment explanation
Indices: 124344--124400 Score: 55
Period size: 3 Copynumber: 18.3 Consensus size: 3
124334 GGCTTGCAAA
*
124344 AAT AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAAT AAAT AAAT AAT -AT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT -AAT -AAT AAT AAT
124392 AAT AA- AAT A
1 AAT AAT AAT A
124401 TTTTTATAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 30 0.62
4 14 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:124364 original size:13 final size:12
Alignment explanation
Indices: 124345--124400 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
124335 GCTTGCAAAA
124345 ATAATAATAAAT
1 ATAATAATAAAT
124357 ATTAATAAT-AAT
1 A-TAATAATAAAT
124369 AATAATAAATAAAT
1 -ATAAT-AATAAAT
124383 A-AATAATATAAT
1 ATAATAATA-AAT
*
124395 AAAATA
1 ATAATA
124401 TTTTTATAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
11 4 0.11
12 15 0.39
13 16 0.42
14 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:124397 original size:16 final size:15
Alignment explanation
Indices: 124345--124396 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
124335 GCTTGCAAAA
*
124345 ATAATAATAAATATT
1 ATAATAATAAATAAT
124360 AATAATAAT-AATAAT
1 -ATAATAATAAATAAT
124375 A-AATAAATAAATAAT
1 ATAAT-AATAAATAAT
124390 ATAATAA
1 ATAATAA
124397 AATATTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.09
14 4 0.12
15 14 0.44
16 11 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:125843 original size:18 final size:19
Alignment explanation
Indices: 125812--125858 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
125802 GTAATGAGCT
*
125812 ATTTAAAT-AATAAAAATG
1 ATTTAAATAAATAAAAATA
*
125830 A-TTAAATAAATAAAAGTA
1 ATTTAAATAAATAAAAATA
125848 ATTTAAATAAA
1 ATTTAAATAAA
125859 AATAAGAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 10 0.40
19 9 0.36
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
ATTTAAATAAATAAAAATA
Done.