Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000876.1 Hibiscus syriacus cultivar Beakdansim tig00001695_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: 362593
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:217896 original size:18 final size:18
Alignment explanation
Indices: 217875--217943 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
217865 CTCTAACCTT
* *
217875 AACCTTAACTCGAACCAA
1 AACCTAAACTCAAACCAA
* *
217893 AACCCAAACTCAAACCCA
1 AACCTAAACTCAAACCAA
* *
217911 AACCTAAGCCTGAAACC-A
1 AACCTAA-ACTCAAACCAA
*
217929 AACCTAAACCCAAAC
1 AACCTAAACTCAAAC
217944 TCGAACTTGA
Statistics
Matches: 40, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
17 5 0.12
18 28 0.70
19 7 0.17
ACGTcount: A:0.48, C:0.38, G:0.04, T:0.10
Consensus pattern (18 bp):
AACCTAAACTCAAACCAA
Found at i:217913 original size:6 final size:6
Alignment explanation
Indices: 217887--218044 Score: 59
Period size: 6 Copynumber: 26.2 Consensus size: 6
217877 CCTTAACTCG
* * * * * *
217887 AACCAA AACCCA AACTCA AACCCA AACCTA AGCCTGA AA-CCA AACCTA
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACC-CA AACCCA AACCCA
* * *** * * ** *
217935 AACCCA AACTCG AACTTG AACCTA AAACCA AACCCA AACCTG AACCCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * ** * * *
217983 AACCTGA TA-CCA AACCCA AACCCAA AACCTG AACCCG AACCCG AATCCA
1 AACC-CA AACCCA AACCCA AACCC-A AACCCA AACCCA AACCCA AACCCA
*
218032 AACCCG AACCCA A
1 AACCCA AACCCA A
218045 TCTAAACCCG
Statistics
Matches: 113, Mismatches: 34, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
5 5 0.04
6 100 0.88
7 8 0.07
ACGTcount: A:0.46, C:0.39, G:0.07, T:0.08
Consensus pattern (6 bp):
AACCCA
Found at i:217968 original size:30 final size:30
Alignment explanation
Indices: 217898--218004 Score: 96
Period size: 30 Copynumber: 3.5 Consensus size: 30
217888 ACCAAAACCC
*
217898 AAACTCAAACCCAAACCT-AAGCCTGAAACC--
1 AAAC-CAAACCCAAACCTGAA-CCCG-AACCTA
**
217928 AAACCTAAACCCAAA-CTCGAACTTGAACCTA
1 AAACC-AAACCCAAACCT-GAACCCGAACCTA
*
217959 AAACCAAACCCAAACCTGAACCCGAACCTG
1 AAACCAAACCCAAACCTGAACCCGAACCTA
*
217989 ATACCAAACCCAAACC
1 AAACCAAACCCAAACC
218005 CAAAACCTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.11
30 50 0.76
31 9 0.14
ACGTcount: A:0.46, C:0.37, G:0.07, T:0.10
Consensus pattern (30 bp):
AAACCAAACCCAAACCTGAACCCGAACCTA
Found at i:217974 original size:36 final size:36
Alignment explanation
Indices: 217887--218023 Score: 125
Period size: 36 Copynumber: 3.8 Consensus size: 36
217877 CCTTAACTCG
* * *
217887 AACCAAAACCCAAACTCAAACCCAAACCT-AAGCCTGA
1 AACC-AAACCCAAACCCAAACCCGAACCTGAA-CCTAA
* * *
217924 AACCAAACCTAAACCCAAACTCGAACTTGAACCTAA
1 AACCAAACCCAAACCCAAACCCGAACCTGAACCTAA
**
217960 AACCAAACCCAAACCTGAACCCGAACCTGATACC-AA
1 AACCAAACCCAAACCCAAACCCGAACCTGA-ACCTAA
* **
217996 ACCCAAACCCAAAACCTGAACCCGAACC
1 AACCAAACCC-AAACCCAAACCCGAACC
218024 CGAATCCAAA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
36 59 0.69
37 26 0.31
ACGTcount: A:0.46, C:0.39, G:0.07, T:0.09
Consensus pattern (36 bp):
AACCAAACCCAAACCCAAACCCGAACCTGAACCTAA
Found at i:217978 original size:24 final size:24
Alignment explanation
Indices: 217929--217980 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
217919 CCTGAAACCA
* * * *
217929 AACCTAAACCCAAACTCGAACTTG
1 AACCTAAAACCAAACCCAAACCTG
217953 AACCTAAAACCAAACCCAAACCTG
1 AACCTAAAACCAAACCCAAACCTG
217977 AACC
1 AACC
217981 CGAACCTGAT
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:0.46, C:0.37, G:0.06, T:0.12
Consensus pattern (24 bp):
AACCTAAAACCAAACCCAAACCTG
Found at i:218020 original size:37 final size:36
Alignment explanation
Indices: 217945--218044 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 36
217935 AACCCAAACT
* *
217945 CGAACTTGAACCTAAAACCAAACCC-AAACCTGAACC
1 CGAACCTGAACC-AAACCCAAACCCAAAACCTGAACC
217981 CGAACCTGATACCAAACCCAAACCCAAAACCTGAACC
1 CGAACCTGA-ACCAAACCCAAACCCAAAACCTGAACC
* *
218018 CGAACCCGAATCCAAACCCGAACCCAA
1 CGAACCTGAA-CCAAACCCAAACCCAA
218045 TCTAAACCCG
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
36 20 0.35
37 37 0.65
ACGTcount: A:0.43, C:0.40, G:0.09, T:0.08
Consensus pattern (36 bp):
CGAACCTGAACCAAACCCAAACCCAAAACCTGAACC
Found at i:218035 original size:12 final size:12
Alignment explanation
Indices: 217965--218044 Score: 72
Period size: 12 Copynumber: 6.6 Consensus size: 12
217955 CCTAAAACCA
*
217965 AACCCAAACCTG
1 AACCCAAACCCG
* *
217977 AACCCGAACCTG
1 AACCCAAACCCG
*
217989 ATA-CCAAACCCA
1 A-ACCCAAACCCG
*
218001 AACCCAAAACCTG
1 AACCC-AAACCCG
*
218014 AACCCGAACCCG
1 AACCCAAACCCG
*
218026 AATCCAAACCCG
1 AACCCAAACCCG
218038 AACCCAA
1 AACCCAA
218045 TCTAAACCCG
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
11 1 0.02
12 42 0.78
13 11 0.20
ACGTcount: A:0.42, C:0.42, G:0.09, T:0.06
Consensus pattern (12 bp):
AACCCAAACCCG
Found at i:218081 original size:12 final size:12
Alignment explanation
Indices: 218001--218083 Score: 51
Period size: 12 Copynumber: 6.9 Consensus size: 12
217991 ACCAAACCCA
*
218001 AACCCAAAACCTG
1 AACCCAAATCC-G
* *
218014 AACCCGAACCCG
1 AACCCAAATCCG
* *
218026 AATCCAAACCCG
1 AACCCAAATCCG
**
218038 AACCC-AATCTA
1 AACCCAAATCCG
* **
218049 AACCCGAATTTG
1 AACCCAAATCCG
*
218061 AATCCAAATCCG
1 AACCCAAATCCG
218073 AACCCAAATCC
1 AACCCAAATCC
218084 AAATCTGAAT
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
11 8 0.15
12 37 0.69
13 9 0.17
ACGTcount: A:0.41, C:0.39, G:0.08, T:0.12
Consensus pattern (12 bp):
AACCCAAATCCG
Found at i:218088 original size:18 final size:18
Alignment explanation
Indices: 217977--218086 Score: 89
Period size: 18 Copynumber: 6.1 Consensus size: 18
217967 CCCAAACCTG
*
217977 AACCCGAACCTG-ATACCA
1 AACCCGAACCCGAAT-CCA
* * * *
217995 AACCCAAACCCAAAACCTG
1 AACCCGAACCCGAATCC-A
218014 AACCCGAACCCGAATCCA
1 AACCCGAACCCGAATCCA
*
218032 AACCCGAACCC-AATCTA
1 AACCCGAACCCGAATCCA
***
218049 AACCCGAATTTGAATCCA
1 AACCCGAACCCGAATCCA
* *
218067 AATCCGAACCCAAATCCA
1 AACCCGAACCCGAATCCA
218085 AA
1 AA
218087 TCTGAATCTA
Statistics
Matches: 70, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
17 13 0.19
18 42 0.60
19 15 0.21
ACGTcount: A:0.43, C:0.38, G:0.08, T:0.11
Consensus pattern (18 bp):
AACCCGAACCCGAATCCA
Found at i:218308 original size:2 final size:2
Alignment explanation
Indices: 218303--218369 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
218293 GTACATGCTT
218303 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
218345 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 T
218370 TTAAAAAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:220727 original size:20 final size:20
Alignment explanation
Indices: 220702--220782 Score: 99
Period size: 20 Copynumber: 4.0 Consensus size: 20
220692 CAATAGTTGG
220702 TGCTTGATTCTGCTTGATAT
1 TGCTTGATTCTGCTTGATAT
* * *
220722 TGCTTGATTATGTTTTATAT
1 TGCTTGATTCTGCTTGATAT
* * *
220742 TGTTTGCTTCTGTTTGATAT
1 TGCTTGATTCTGCTTGATAT
*
220762 TGCTTGATTCTACTTGATAT
1 TGCTTGATTCTGCTTGATAT
220782 T
1 T
220783 TGTAAGGGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.16, C:0.11, G:0.17, T:0.56
Consensus pattern (20 bp):
TGCTTGATTCTGCTTGATAT
Found at i:220905 original size:23 final size:23
Alignment explanation
Indices: 220875--220929 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
220865 CTGAATGCAG
*
220875 GATGCTTGCTGAATTGATGCAAT
1 GATGCTTGCTGAATTGATACAAT
*
220898 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATACAAT
220921 GATGCTTGC
1 GATGCTTGC
220930 CAGTTGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATACAAT
Found at i:221486 original size:13 final size:13
Alignment explanation
Indices: 221467--221504 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
221457 TAATTTAATG
221467 ATTATAAATAA-A
1 ATTATAAATAAGA
221479 ATTTATAATATAAGA
1 A-TTATAA-ATAAGA
221494 ATTATAAATAA
1 ATTATAAATAA
221505 TGTAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATTATAAATAAGA
Found at i:226906 original size:29 final size:29
Alignment explanation
Indices: 226863--226945 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
226853 CTCACCTAAC
*
226863 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
226893 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
226922 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
226946 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:231673 original size:29 final size:29
Alignment explanation
Indices: 231630--231712 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
231620 CTCACCTAAC
*
231630 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
231660 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
231689 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
231713 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:233811 original size:35 final size:34
Alignment explanation
Indices: 233761--233835 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
233751 TTAGTAAAAT
*
233761 AATTTAATGTATTAACGTTCTATAGAATGTGCTTA
1 AATTTAATGTATTAACGTTATATAGAATGTG-TTA
* *
233796 AATTTAATGTGTTAACGTTATATAGAATGTGTTT
1 AATTTAATGTATTAACGTTATATAGAATGTGTTA
233830 AATTTA
1 AATTTA
233836 GTAAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 8 0.22
35 29 0.78
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (34 bp):
AATTTAATGTATTAACGTTATATAGAATGTGTTA
Found at i:240907 original size:34 final size:37
Alignment explanation
Indices: 240837--240910 Score: 100
Period size: 34 Copynumber: 2.1 Consensus size: 37
240827 ACAACATCTT
* **
240837 CATGAGGTATCGATACCGAAAGGGGTAGTATCGATAC
1 CATGAGGTATCGATACAGAAAGGCATAGTATCGATAC
240874 CATG-GGTATCGATACAG-AAGGCAT-GTATCGATAC
1 CATGAGGTATCGATACAGAAAGGCATAGTATCGATAC
240908 CAT
1 CAT
240911 TTTTGGACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 13 0.38
35 5 0.15
36 12 0.35
37 4 0.12
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (37 bp):
CATGAGGTATCGATACAGAAAGGCATAGTATCGATAC
Found at i:241580 original size:19 final size:19
Alignment explanation
Indices: 241558--241614 Score: 51
Period size: 21 Copynumber: 2.9 Consensus size: 19
241548 TATATAATCC
*
241558 TTTGGAACATATGTGGTCA
1 TTTGGAACATATATGGTCA
* * *
241577 TTTGAGACGCATATTTGGTCC
1 TTTG-GA-ACATATATGGTCA
*
241598 TTTGGAATATATATGGT
1 TTTGGAACATATATGGT
241615 TCTTAAGGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 12 0.40
20 4 0.13
21 14 0.47
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.40
Consensus pattern (19 bp):
TTTGGAACATATATGGTCA
Found at i:241686 original size:23 final size:23
Alignment explanation
Indices: 241659--241706 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
241649 TTTTGTATGA
*
241659 CACTTCGGTGCATTTCTACGCGG
1 CACTTCGGTGCAATTCTACGCGG
*
241682 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTCTACGCGG
241705 CA
1 CA
241707 TTTTCGATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.29, G:0.25, T:0.29
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGG
Found at i:247042 original size:30 final size:30
Alignment explanation
Indices: 247008--247069 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
246998 AGGTCTTGCA
247008 GTTGGTGTTGAAGACCTTGTTGTGGACCTT
1 GTTGGTGTTGAAGACCTTGTTGTGGACCTT
247038 GTTGGTGTTGAAGACCTTGTTGTGGACCTT
1 GTTGGTGTTGAAGACCTTGTTGTGGACCTT
247068 GT
1 GT
247070 CAGCGTGGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.13, G:0.34, T:0.40
Consensus pattern (30 bp):
GTTGGTGTTGAAGACCTTGTTGTGGACCTT
Found at i:247046 original size:18 final size:18
Alignment explanation
Indices: 247008--247059 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
246998 AGGTCTTGCA
247008 GTTGGTGTTGAAGACCTT
1 GTTGGTGTTGAAGACCTT
247026 G-T--TG-TG--GACCTT
1 GTTGGTGTTGAAGACCTT
247038 GTTGGTGTTGAAGACCTT
1 GTTGGTGTTGAAGACCTT
247056 GTTG
1 GTTG
247060 TGGACCTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 7 0.25
13 1 0.04
14 2 0.07
15 4 0.14
16 2 0.07
17 1 0.04
18 11 0.39
ACGTcount: A:0.13, C:0.12, G:0.35, T:0.40
Consensus pattern (18 bp):
GTTGGTGTTGAAGACCTT
Found at i:259221 original size:18 final size:18
Alignment explanation
Indices: 259198--259235 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
259188 TGATCTTTTA
*
259198 ATATAATATATTCTAATT
1 ATATAATATAGTCTAATT
259216 ATATAATATAGTCTAATT
1 ATATAATATAGTCTAATT
259234 AT
1 AT
259236 TTTCATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (18 bp):
ATATAATATAGTCTAATT
Found at i:259455 original size:20 final size:20
Alignment explanation
Indices: 259412--259456 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
259402 CTTCAAAAGT
*
259412 TTAAAAATTATTATTATTAA
1 TTAAAAATTAATATTATTAA
*
259432 TTAAAAATTAAATATT-TTAG
1 TTAAAAATT-AATATTATTAA
259452 TTAAA
1 TTAAA
259457 CTCTCTTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
TTAAAAATTAATATTATTAA
Found at i:262491 original size:25 final size:25
Alignment explanation
Indices: 262442--262491 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
262432 ACAAGTTGAA
* **
262442 AAACGAACTCATAAACGAGTTTTAT
1 AAACAAACTCATAAACGAGACTTAT
*
262467 AAACAAACTCATAAACTAGACTTAT
1 AAACAAACTCATAAACGAGACTTAT
262492 CATGGTCTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (25 bp):
AAACAAACTCATAAACGAGACTTAT
Found at i:262575 original size:14 final size:15
Alignment explanation
Indices: 262550--262579 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
262540 TTAGTATCGT
262550 ACTAACATAATATAA
1 ACTAACATAATATAA
262565 ACTAA-ATAATATAA
1 ACTAACATAATATAA
262579 A
1 A
262580 AGTCTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
ACTAACATAATATAA
Found at i:264059 original size:29 final size:30
Alignment explanation
Indices: 264020--264081 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
264010 ATATATAACT
* *
264020 TTTTAAAAA-TTATATTCTTAG-TCCTAAAC
1 TTTTAAAAATTTATACT-TTAGCTACTAAAC
*
264049 TTTTACAAATTTATACTTTAGCTACTAAAC
1 TTTTAAAAATTTATACTTTAGCTACTAAAC
264079 TTT
1 TTT
264082 CAAAGCTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTAAAAATTTATACTTTAGCTACTAAAC
Found at i:264156 original size:15 final size:15
Alignment explanation
Indices: 264136--264166 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
264126 TACCCCAAAG
264136 TTTTTCTTTCATAAT
1 TTTTTCTTTCATAAT
*
264151 TTTTTCTTTTATAAT
1 TTTTTCTTTCATAAT
264166 T
1 T
264167 GTATTCACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTCTTTCATAAT
Found at i:265375 original size:5 final size:5
Alignment explanation
Indices: 265365--265389 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
265355 AACGAAATAC
265365 CAAAA CAAAA CAAAA CAAAA CAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA
265390 TGTTATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
CAAAA
Found at i:267155 original size:29 final size:30
Alignment explanation
Indices: 267122--267181 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
267112 CTTTACACTC
*
267122 TTTTTTATTTTACTC-ATTAAC-TTTTAATT
1 TTTTTTA-TTTACTCAATGAACTTTTTAATT
267151 TTTTTTATTTACTCAATGAACTTTTTAATT
1 TTTTTTATTTACTCAATGAACTTTTTAATT
267181 T
1 T
267182 CTCCTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 7 0.25
29 12 0.43
30 9 0.32
ACGTcount: A:0.25, C:0.10, G:0.02, T:0.63
Consensus pattern (30 bp):
TTTTTTATTTACTCAATGAACTTTTTAATT
Found at i:267190 original size:30 final size:28
Alignment explanation
Indices: 267130--267190 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 28
267120 TCTTTTTTAT
* * **
267130 TTTACTCATTAACTTTTAATTTTTTTTA
1 TTTACTCATGAACTTTTAATTTCTCCTA
267158 TTTACTCAATGAACTTTTTAATTTCTCCTA
1 TTTACTC-ATGAAC-TTTTAATTTCTCCTA
267188 TTT
1 TTT
267191 TGATAACTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.26
29 5 0.19
30 15 0.56
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTACTCATGAACTTTTAATTTCTCCTA
Found at i:273252 original size:22 final size:22
Alignment explanation
Indices: 273211--273277 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
273201 CTCGTATAAA
273211 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
273234 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
273256 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
273278 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:274978 original size:21 final size:21
Alignment explanation
Indices: 274954--274998 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
274944 TCTTGTTCGT
* *
274954 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
274975 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
274996 TTG
1 TTG
274999 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:278167 original size:22 final size:22
Alignment explanation
Indices: 278126--278192 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
278116 CTCGTATAAA
278126 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
278149 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
278171 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
278193 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 31 0.72
23 12 0.28
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:279902 original size:21 final size:21
Alignment explanation
Indices: 279878--279918 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
279868 TCTTGTTCGT
* *
279878 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
279899 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
279919 TTGCCCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:280850 original size:93 final size:94
Alignment explanation
Indices: 280691--280923 Score: 423
Period size: 93 Copynumber: 2.5 Consensus size: 94
280681 TCAGTTATGG
280691 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
280756 CTCAGTTATGG-AAAATAATATTGACCAT
66 CTCAGTTATGGAAAAATAATATTGACCAT
*
280784 AAAAACCAACCCCAAGTTGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
280849 CTCAGTTATGGAAAAATAATATTGACCAT
66 CTCAGTTATGGAAAAATAATATTGACCAT
* * *
280878 AAAAACCAACCCCAAGTAGACTCATCTAACTAAAGCATGGACCCAT
1 AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCAT
280924 GAAAATCGTA
Statistics
Matches: 134, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
93 75 0.56
94 59 0.44
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (94 bp):
AAAAACCAACCCCAAGTAGACTCATCTAATTAAACCAGGGACCCATATGAATTGTAGCCGCATGA
CTCAGTTATGGAAAAATAATATTGACCAT
Found at i:284481 original size:7 final size:7
Alignment explanation
Indices: 284469--284495 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
284459 ATAAAATCAA
284469 TGGTATC
1 TGGTATC
284476 TGGTATC
1 TGGTATC
284483 TGGTATC
1 TGGTATC
284490 TGGTAT
1 TGGTAT
284496 TTGCAGGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.44
Consensus pattern (7 bp):
TGGTATC
Found at i:286204 original size:2 final size:2
Alignment explanation
Indices: 286199--286250 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
286189 TATACTAAAC
286199 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
286241 TA TA TA TA TA
1 TA TA TA TA TA
286251 GCCATGTTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:290341 original size:39 final size:37
Alignment explanation
Indices: 290271--290343 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 37
290261 GGACCGATAT
**
290271 AAATAGTAGCCACGACTTTCAAAGTTGGGAAACTTGA
1 AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
* *
290308 AAATCGTAGCCACAGGACTTTCAAGGTCAGGAAACT
1 AAATAGTAGCCAC--GACTTTCAAAGTCAGGAAACT
290344 ATATAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 12 0.40
39 18 0.60
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (37 bp):
AAATAGTAGCCACGACTTTCAAAGTCAGGAAACTTGA
Found at i:295256 original size:39 final size:39
Alignment explanation
Indices: 295210--295284 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
295200 TTCATTTCCA
295210 ATCGATAAAGTTTG-TTCTAGAGATTCTCAACCATTTCTG
1 ATCGATAAAGTTTGTTTC-AGAGATTCTCAACCATTTCTG
* *
295249 ATCGATAATGTTTGTTTCAGAGATTCTCAATCATTT
1 ATCGATAAAGTTTGTTTCAGAGATTCTCAACCATTT
295285 GACAATAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 30 0.91
40 3 0.09
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (39 bp):
ATCGATAAAGTTTGTTTCAGAGATTCTCAACCATTTCTG
Found at i:295966 original size:2 final size:2
Alignment explanation
Indices: 295961--295991 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
295951 TATATATATT
295961 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
295992 CTTACCTCTT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:298408 original size:173 final size:174
Alignment explanation
Indices: 298011--298409 Score: 755
Period size: 173 Copynumber: 2.3 Consensus size: 174
298001 GGAGGAATAG
*
298011 TTCTCAAGTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
1 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
298076 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
66 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
*
298141 TTCCTGTTCCTCTATAGTCATATCAATAATGTCAACGGGCATGA
131 TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
298185 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
1 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
298250 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATC-AAACCAGAGCATCCTTCAGA
66 CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
298314 TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
131 TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
* *
298358 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAAAATCAGAGGAAACCAC
1 TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCAC
298410 TACTTTTGTA
Statistics
Matches: 221, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
173 113 0.51
174 108 0.49
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (174 bp):
TTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAACATCAGATGAAACCACCGCAATTGAGGTG
CCATTTTTCATATCTTGAGGTTCCTGAGCCTGCAAGTTCGAATCAAAACCAGAGCATCCTTCAGA
TTCCTGTTCCTCTATACTCATATCAATAATGTCAACGGGCATGA
Found at i:298705 original size:141 final size:140
Alignment explanation
Indices: 298351--298707 Score: 365
Period size: 141 Copynumber: 2.5 Consensus size: 140
298341 AATGTCAACG
* * * * *
298351 GGCATGATTCTCAATTCTGAAGTCATCCTGTTACCCCCATCAAAATCAGAGGAAACCACTACTTT
1 GGCATGCTTCTCAATT-TGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTT
* * * * * * * *
298416 TGTAGCATCTTTTTTTATACATTGTGAATCACAACCAGATTTCTGTTCCTCTGCACTCAAAACGC
65 TGTAGTATCATCTATTATACATTGTGAACCACAACCAGATTCCTGTTCCTCTGCACCCAAAACAC
298481 CAGTCCCAGCA
130 CAGTCCCAGCA
* * ** * * * *
298492 GGCATGCTTCTCAAGTCTGAGGTCATCCTATTACAACCATCAACCTCAGATAAAACAACTTCGTT
1 GGCATGCTTCTCAA-TTTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTT
* * * * * *
298557 TGAAGTATCATCTATTATGTC-TTGTGAACCATAACCAGATTCCTGTTTCTCTGTACCCAAATCA
65 TGTAGTATCATCTATTAT-ACATTGTGAACCACAACCAGATTCCTGTTCCTCTGCACCCAAAACA
* *
298621 TCAGTCTCAGCA
129 CCAGTCCCAGCA
* * * * *
298633 GGTATGCTTCTCAACTTTGAAGTCATCCCATTACCCCCACCAACATCGGATGAAACCATTTCTTT
1 GGCATGCTTCTCAA-TTTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTT
298698 TGTAGTATCA
65 TGTAGTATCA
298708 ATTTTTATAT
Statistics
Matches: 170, Mismatches: 44, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
141 168 0.99
142 2 0.01
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (140 bp):
GGCATGCTTCTCAATTTGAAGTCATCCTATTACCCCCATCAACATCAGATGAAACCACTTCTTTT
GTAGTATCATCTATTATACATTGTGAACCACAACCAGATTCCTGTTCCTCTGCACCCAAAACACC
AGTCCCAGCA
Found at i:307269 original size:20 final size:21
Alignment explanation
Indices: 307244--307282 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
307234 GGGCTTTCTT
*
307244 TTGACTTG-GATTTTGGGTGG
1 TTGACTTGAGATTTAGGGTGG
307264 TTGACTTGAGATTTAGGGT
1 TTGACTTGAGATTTAGGGT
307283 TTGTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.05, G:0.36, T:0.44
Consensus pattern (21 bp):
TTGACTTGAGATTTAGGGTGG
Found at i:307375 original size:28 final size:28
Alignment explanation
Indices: 307344--307402 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
307334 TATATATTAA
* *
307344 TAAAATATGTTATGTCATAACAAAATAT
1 TAAAATATGTCAAGTCATAACAAAATAT
307372 TAAAATATGTCAAGTCATAACAAAATAT
1 TAAAATATGTCAAGTCATAACAAAATAT
307400 TAA
1 TAA
307403 TAAAAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (28 bp):
TAAAATATGTCAAGTCATAACAAAATAT
Found at i:308695 original size:29 final size:29
Alignment explanation
Indices: 308658--308720 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
308648 AAAATCTATT
* *
308658 TTCGCCCCCTAAAATTTTATAAGTTTAAG
1 TTCGTCCCCTAAAATTTTATAAGTTTAAA
*
308687 TTCGTCCCCTAAAATTTTATTAGTTTAAA
1 TTCGTCCCCTAAAATTTTATAAGTTTAAA
308716 TTCGT
1 TTCGT
308721 TCCATAGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.43
Consensus pattern (29 bp):
TTCGTCCCCTAAAATTTTATAAGTTTAAA
Found at i:309454 original size:29 final size:31
Alignment explanation
Indices: 309400--309467 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
309390 AACGGTTTAG
309400 TGATATAATTGAGATAAAAATCAAAGTTCAA
1 TGATATAATTGAGATAAAAATCAAAGTTCAA
* * * *
309431 TGCTATAATT-AG-TAAAACTGAAAGTTCAG
1 TGATATAATTGAGATAAAAATCAAAGTTCAA
309460 TGATATAA
1 TGATATAA
309468 ACGATACAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 21 0.66
30 2 0.06
31 9 0.28
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.31
Consensus pattern (31 bp):
TGATATAATTGAGATAAAAATCAAAGTTCAA
Found at i:312460 original size:109 final size:107
Alignment explanation
Indices: 312283--312523 Score: 258
Period size: 109 Copynumber: 2.2 Consensus size: 107
312273 ACTCTTGCAC
* * * *
312283 GTTTTTGCATGTTAGTTATCTGTAGGGACCAAATCTGCTATTTACTCGTTTCTTATGTATGTTAT
1 GTTTTTGCATGTTGGTCATCTGTAGGGACCAAATCTGCTATTTACTCGTTTCTTATGCATATTAT
*
312348 ATATATTT-GGTATAATTATTGTTTAGTCCCCCATAGTTTAG-CGT
66 ATATATTTGGGT-TAATTATTGTTTAGT-CCCC-TA-TTTAGACAT
* * *
312392 GTTTTTGCATGTTGGTCA-CTTGTAGGGACTGAAAT-TGTTGTTTAC-CTGTTTCTTATGCATAT
1 GTTTTTGCATGTTGGTCATC-TGTAGGGAC-CAAATCTGCTATTTACTC-GTTTCTTATGCATAT
* * *
312454 TGTATATTTTTGGGTTATTTATTGTTTAGTCCCCTATTTAGACAT
63 TATATATATTTGGGTTAATTATTGTTTAGTCCCCTATTTAGACAT
* * *
312499 GTTTTTACATTTTGGTCATGTGTAG
1 GTTTTTGCATGTTGGTCATCTGTAG
312524 TGATGATTTA
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
106 5 0.04
107 25 0.22
108 6 0.05
109 69 0.62
110 7 0.06
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (107 bp):
GTTTTTGCATGTTGGTCATCTGTAGGGACCAAATCTGCTATTTACTCGTTTCTTATGCATATTAT
ATATATTTGGGTTAATTATTGTTTAGTCCCCTATTTAGACAT
Found at i:315787 original size:15 final size:16
Alignment explanation
Indices: 315749--315789 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
315739 ACAGAGCCTC
*
315749 TGAATCATTCAGCATT
1 TGAATCATTCAGCACT
*
315765 TGAATCATTCAGCGCT
1 TGAATCATTCAGCACT
315781 T-AATCATTC
1 TGAATCATTC
315790 TGAAGCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCACT
Found at i:316948 original size:24 final size:24
Alignment explanation
Indices: 316921--316969 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
316911 AGAGGCAAAG
*
316921 GCACCAACTTCGTCTCTGAAAGAA
1 GCACCAACTTCGTCACTGAAAGAA
*
316945 GCACCAACTTCGTCACTGAACGAA
1 GCACCAACTTCGTCACTGAAAGAA
316969 G
1 G
316970 AACAAGCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (24 bp):
GCACCAACTTCGTCACTGAAAGAA
Found at i:319220 original size:35 final size:35
Alignment explanation
Indices: 319181--319255 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
319171 TAAATACTTT
319181 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
* * *
319216 AATTTGGGGTTTAGAATGTAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
319251 AATTT
1 AATTT
319256 TGAACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
Found at i:322799 original size:31 final size:32
Alignment explanation
Indices: 322764--322826 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
322754 GAAAAAGAAG
*
322764 AAAAGAACAAAGATGATGAAAACGG-TAAAAA
1 AAAAGAACAAAGATGATGAAAAAGGCTAAAAA
* ** *
322795 AAAAGTACAGTGATGATTAAAAAGGCTAAAAA
1 AAAAGAACAAAGATGATGAAAAAGGCTAAAAA
322827 GAGAAAGACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.60, C:0.06, G:0.19, T:0.14
Consensus pattern (32 bp):
AAAAGAACAAAGATGATGAAAAAGGCTAAAAA
Found at i:324048 original size:22 final size:22
Alignment explanation
Indices: 324023--324080 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
324013 AGTCAAAGTG
* *
324023 TTGACTTTTACCAGAGA-TGACT
1 TTGACTTTGACCA-ACATTGACT
*
324045 TTGACTTTGACCAACATTGAGT
1 TTGACTTTGACCAACATTGACT
324067 TTGACTTTGACCAA
1 TTGACTTTGACCAA
324081 AAAGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (22 bp):
TTGACTTTGACCAACATTGACT
Found at i:327595 original size:27 final size:29
Alignment explanation
Indices: 327538--327595 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
327528 CATGACAAAT
* ** *
327538 GGCTAAATTATTTTTTTATTTTGTTTGAA
1 GGCTAAATTAGTTTTTTATTAAGTTTCAA
327567 GGCTAAATTAGTTTTTT-TTAAG-TTCAA
1 GGCTAAATTAGTTTTTTATTAAGTTTCAA
327594 GG
1 GG
327596 GTTTATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 6 0.24
28 3 0.12
29 16 0.64
ACGTcount: A:0.26, C:0.05, G:0.17, T:0.52
Consensus pattern (29 bp):
GGCTAAATTAGTTTTTTATTAAGTTTCAA
Found at i:329475 original size:21 final size:21
Alignment explanation
Indices: 329445--329492 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
329435 AATCATAAGT
329445 ATTTTTTAT-TT-T-TTGTTTA
1 ATTTTTTATATTATATT-TTTA
329464 ATTTTTTATATTATATTTTTA
1 ATTTTTTATATTATATTTTTA
*
329485 TTTTTTTA
1 ATTTTTTA
329493 ATTCTTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 9 0.36
20 2 0.08
21 12 0.48
22 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (21 bp):
ATTTTTTATATTATATTTTTA
Found at i:339950 original size:15 final size:15
Alignment explanation
Indices: 339926--339959 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
339916 ATACCAAAGG
339926 AAGGGCATCAATACT
1 AAGGGCATCAATACT
*
339941 AAGGGTATCAATACT
1 AAGGGCATCAATACT
339956 AAGG
1 AAGG
339960 TATAAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (15 bp):
AAGGGCATCAATACT
Found at i:340034 original size:19 final size:19
Alignment explanation
Indices: 340010--340095 Score: 136
Period size: 19 Copynumber: 4.5 Consensus size: 19
340000 TCGAGAATGG
340010 GTATCGATACTGACGTATA
1 GTATCGATACTGACGTATA
*
340029 GTATCGATACTGACATATA
1 GTATCGATACTGACGTATA
*
340048 ATATCGATACTGACGTATA
1 GTATCGATACTGACGTATA
*
340067 GTATTGATACTGACGTATA
1 GTATCGATACTGACGTATA
*
340086 ATATCGATAC
1 GTATCGATAC
340096 CATAATGTAG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (19 bp):
GTATCGATACTGACGTATA
Found at i:340062 original size:38 final size:38
Alignment explanation
Indices: 340011--340095 Score: 152
Period size: 38 Copynumber: 2.2 Consensus size: 38
340001 CGAGAATGGG
340011 TATCGATACTGACGTATAGTATCGATACTGACATATAA
1 TATCGATACTGACGTATAGTATCGATACTGACATATAA
* *
340049 TATCGATACTGACGTATAGTATTGATACTGACGTATAA
1 TATCGATACTGACGTATAGTATCGATACTGACATATAA
340087 TATCGATAC
1 TATCGATAC
340096 CATAATGTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (38 bp):
TATCGATACTGACGTATAGTATCGATACTGACATATAA
Found at i:340848 original size:23 final size:23
Alignment explanation
Indices: 340781--340852 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
340771 AGTTATACAC
* *
340781 GGTCCTTCGGGACAATTTCTACGT
1 GGTCCTTAGGGAC-ATTTCTATGT
* * *
340805 GGTCCTTCA-GGATAATACTATGT
1 GGTCCTT-AGGGACATTTCTATGT
340828 GGTCCTTAGGGACATTTCTATGT
1 GGTCCTTAGGGACATTTCTATGT
340851 GG
1 GG
340853 CACTTTGGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
22 1 0.03
23 27 0.71
24 10 0.26
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (23 bp):
GGTCCTTAGGGACATTTCTATGT
Found at i:341206 original size:27 final size:27
Alignment explanation
Indices: 341168--341220 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
341158 TATGCTTAAG
341168 TATTTTTAAATGTTTGATTTTTGTATA
1 TATTTTTAAATGTTTGATTTTTGTATA
341195 TATTTTTAAATGTTTGATTTTTGTAT
1 TATTTTTAAATGTTTGATTTTTGTAT
341221 TTTATATGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (27 bp):
TATTTTTAAATGTTTGATTTTTGTATA
Found at i:351677 original size:17 final size:20
Alignment explanation
Indices: 351636--351678 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
351626 GTATAATTAA
351636 AAATAAATAAATTTATTATT
1 AAATAAATAAATTTATTATT
*
351656 TAATAAA-AAA-TTA-TATT
1 AAATAAATAAATTTATTATT
351673 AAATAA
1 AAATAA
351679 TTTAGGATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 3 0.14
19 3 0.14
20 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATAAATAAATTTATTATT
Found at i:351679 original size:20 final size:20
Alignment explanation
Indices: 351631--351679 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
351621 TATTTGTATA
351631 ATTAAA-AATAAATAAATTT
1 ATTAAATAATAAATAAATTT
**
351650 ATTATTTAATAAA-AAATTAT
1 ATTAAATAATAAATAAATT-T
351670 ATTAAATAAT
1 ATTAAATAAT
351680 TTAGGATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTAAATAATAAATAAATTT
Found at i:357567 original size:29 final size:30
Alignment explanation
Indices: 357521--357577 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
357511 TCTCTCCTAT
* * *
357521 TTTACTCACTGTACTTTC-AATTTTTCTAA
1 TTTACTCACTGAAATTTCGAATTGTTCTAA
*
357550 TTTACTCATTGAAATTTCGAATTGTTCT
1 TTTACTCACTGAAATTTCGAATTGTTCT
357578 TGTTTTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 15 0.65
30 8 0.35
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (30 bp):
TTTACTCACTGAAATTTCGAATTGTTCTAA
Found at i:359014 original size:60 final size:60
Alignment explanation
Indices: 358930--359045 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
358920 AATGGTCCCC
* * *
358930 TGATTATAGAACGCTACTCCGTCGATTCATTC-GACTATTAAATGTTACAAAATAGTCTCG
1 TGATTATAGAACGATACTCCGTCGAGTC-TTCGGACTATTAAAAGTTACAAAATAGTCTCG
* ** *
358990 TGATTATAGGACGATACTTTGTCGAGTCTTCGGATTATTAAAAGTTACAAAATAGT
1 TGATTATAGAACGATACTCCGTCGAGTCTTCGGACTATTAAAAGTTACAAAATAGT
359046 TGTTCGACTA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 3 0.06
60 45 0.94
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (60 bp):
TGATTATAGAACGATACTCCGTCGAGTCTTCGGACTATTAAAAGTTACAAAATAGTCTCG
Found at i:360521 original size:20 final size:20
Alignment explanation
Indices: 360496--360542 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
360486 CGATATACCA
*
360496 GTAAAAATATGATAAAACCG
1 GTAAAAAAATGATAAAACCG
360516 GTAAAAAAATGATAAAACCG
1 GTAAAAAAATGATAAAACCG
360536 GTAAAAA
1 GTAAAAA
360543 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.60, C:0.09, G:0.15, T:0.17
Consensus pattern (20 bp):
GTAAAAAAATGATAAAACCG
Found at i:360720 original size:17 final size:19
Alignment explanation
Indices: 360681--360723 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
360671 AGGTGAAAAT
360681 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
360701 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
360718 ATGATA
1 ATGATA
360724 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Done.