Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002689.1 Hibiscus syriacus cultivar Beakdansim tig00005554_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: 76836
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4748 original size:20 final size:20
Alignment explanation
Indices: 4693--4751 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
4683 CCATAAGTTT
* *
4693 TCTTTATCTCAATTTATTTTA
1 TCTTTATATC-ATTTATTTAA
**
4714 T-TTGTATATTGTTTATTTAA
1 TCTT-TATATCATTTATTTAA
4734 TCTTTATATCATTTATTT
1 TCTTTATATCATTTATTT
4752 CTTTAAACAA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.64
Consensus pattern (20 bp):
TCTTTATATCATTTATTTAA
Found at i:4888 original size:19 final size:19
Alignment explanation
Indices: 4852--4901 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
4842 TTTTAAATGA
*
4852 TTTA-TATTTAATTATTAT
1 TTTATTATTTTATTATTAT
*
4870 TTTATTATTTTATTCTTAT
1 TTTATTATTTTATTATTAT
*
4889 CTT-TTATCTTTAT
1 TTTATTAT-TTTAT
4902 CAGAAATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTATTTTATTATTAT
Found at i:12625 original size:29 final size:28
Alignment explanation
Indices: 12567--12626 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
12557 CTTGTTCTAT
*
12567 AAAAAATATTCATTGTTTCGAACATCAAA
1 AAAAAATATTCATTGTTTCGAACA-GAAA
* *
12596 AAAAATTGTTCATTGTTTCGAACAGAAA
1 AAAAAATATTCATTGTTTCGAACAGAAA
12624 AAA
1 AAA
12627 GAAGGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (28 bp):
AAAAAATATTCATTGTTTCGAACAGAAA
Found at i:14529 original size:12 final size:12
Alignment explanation
Indices: 14512--14537 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14502 AAACGATTTA
14512 TATTTAATTATT
1 TATTTAATTATT
14524 TATTTAATTATT
1 TATTTAATTATT
14536 TA
1 TA
14538 ATTATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:16552 original size:13 final size:13
Alignment explanation
Indices: 16536--16560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16526 TAATGCTTCA
16536 AAATAATAATAAT
1 AAATAATAATAAT
16549 AAATAATAATAA
1 AAATAATAATAA
16561 CAATACTATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:16582 original size:24 final size:24
Alignment explanation
Indices: 16555--16613 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
16545 TAATAAATAA
*
16555 TAATAACAATACTATCCTATTTCC
1 TAATAACAATACTATCATATTTCC
16579 TAATAACAATACTATCATATTTCC
1 TAATAACAATACTATCATATTTCC
16603 TAATAACAATA
1 TAATAACAATA
16614 AAATAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (24 bp):
TAATAACAATACTATCATATTTCC
Found at i:18098 original size:20 final size:19
Alignment explanation
Indices: 18073--18126 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
18063 TTTCTATTAT
18073 TTTTTATTATAAATCTAATA
1 TTTTTATTATAAAT-TAATA
*
18093 TTTTTA--ATAAATTATTA
1 TTTTTATTATAAATTAATA
*
18110 ATTTTATT-TAAATTAAT
1 TTTTTATTATAAATTAAT
18127 TTATTATTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 9 0.31
18 14 0.48
20 6 0.21
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTATTATAAATTAATA
Found at i:18174 original size:16 final size:16
Alignment explanation
Indices: 18155--18193 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18145 TAATTTCTGT
18155 TCGGGTTGCTTTCAGA
1 TCGGGTTGCTTTCAGA
* * *
18171 TCGGGTTTCTTTCGGT
1 TCGGGTTGCTTTCAGA
18187 TCGGGTT
1 TCGGGTT
18194 AATTTTGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.05, C:0.18, G:0.33, T:0.44
Consensus pattern (16 bp):
TCGGGTTGCTTTCAGA
Found at i:18225 original size:21 final size:21
Alignment explanation
Indices: 18186--18227 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
18176 TTTCTTTCGG
**
18186 TTCGGGTTAATTTTGGTTTCA
1 TTCGGGTTAATTTCAGTTTCA
*
18207 TTCGGGTTACTTTCAGTTTCA
1 TTCGGGTTAATTTCAGTTTCA
18228 CTAAATTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (21 bp):
TTCGGGTTAATTTCAGTTTCA
Found at i:28600 original size:73 final size:73
Alignment explanation
Indices: 28451--28625 Score: 165
Period size: 73 Copynumber: 2.4 Consensus size: 73
28441 TCATCAAAGA
* * ** * *
28451 AAGTATTGATATTTTAAATTTTGATCTTTTTATCAATGTTTTCAATTTTTAAAAGTATTGATCAT
1 AAGTATTGATATTTTAAATTTTAATCTTTCTATCAATGTTTTCAATACTTAAAAGTATCGATCAC
* *
28516 TGTTGCAT
66 TATTACAT
** *
28524 AAGTATTGATATTTTATCTTTTAATCTTATCT-TCAATTTTTTCAATACTTAAAAGTATCGAT-A
1 AAGTATTGATATTTTAAATTTTAATCTT-TCTATCAATGTTTTCAATACTTAAAAGTATCGATCA
*
28587 CTATTATATT
65 CTATTACA-T
*** * *
28597 AAGTACCAATATTTAAAATTTTGATCTTT
1 AAGTATTGATATTTTAAATTTTAATCTTT
28626 TTACATTTTT
Statistics
Matches: 81, Mismatches: 19, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
72 6 0.07
73 73 0.90
74 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.50
Consensus pattern (73 bp):
AAGTATTGATATTTTAAATTTTAATCTTTCTATCAATGTTTTCAATACTTAAAAGTATCGATCAC
TATTACAT
Found at i:29281 original size:78 final size:78
Alignment explanation
Indices: 29121--29273 Score: 184
Period size: 78 Copynumber: 2.0 Consensus size: 78
29111 GGCGCAATCC
* * * * * * *
29121 ATTTTATTATTAAAAATATTAAGATTCTAGATTGCAACTTGCTTTCTTAGTGAACCATGACATTC
1 ATTTTATTAATAAAAATATTAACATTCTAAATCGCAACCTGATTTCTTAGTGAACCATGACATTA
* **
29186 TTGGGTGCAACAT
66 TTAGGAACAACAT
*
29199 ATTTTATTAATAAAAATATTAACATTAC-AAATCGCAACCT-ATTTCTTAGTGAATCATGACATT
1 ATTTTATTAATAAAAATATTAACATT-CTAAATCGCAACCTGATTTCTTAGTGAACCATGACATT
29262 ATTAGGAACAAC
65 ATTAGGAACAAC
29274 CGTATTTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
77 29 0.46
78 33 0.52
79 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (78 bp):
ATTTTATTAATAAAAATATTAACATTCTAAATCGCAACCTGATTTCTTAGTGAACCATGACATTA
TTAGGAACAACAT
Found at i:36142 original size:26 final size:26
Alignment explanation
Indices: 36113--36195 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
36103 TGTGTTTCTT
36113 TTAGATAAGATTGATTAGTGTTCAAA
1 TTAGATAAGATTGATTAGTGTTCAAA
* * * * **
36139 TTAGTTAATATTTCATT-GTTAATTC-TT
1 TTAGATAAGA-TTGATTAG-T-GTTCAAA
36166 TTAGATAAGATTGATTAGTGTTCAAA
1 TTAGATAAGATTGATTAGTGTTCAAA
36192 TTAG
1 TTAG
36196 TTAATATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
25 3 0.08
26 19 0.47
27 15 0.38
28 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.46
Consensus pattern (26 bp):
TTAGATAAGATTGATTAGTGTTCAAA
Found at i:36188 original size:53 final size:53
Alignment explanation
Indices: 36108--36215 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
36098 TTATATGTGT
36108 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
1 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
36161 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
1 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
36214 TT
1 TT
36216 ACTCTTTGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (53 bp):
TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
Found at i:43889 original size:17 final size:17
Alignment explanation
Indices: 43864--43902 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
43854 GGTCAGGCAC
*
43864 ACTTCAATCCGAGCAGT
1 ACTTGAATCCGAGCAGT
43881 ACTTGAATCCGAGCAGT
1 ACTTGAATCCGAGCAGT
43898 ACTTG
1 ACTTG
43903 CATTAGTGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (17 bp):
ACTTGAATCCGAGCAGT
Found at i:46929 original size:12 final size:12
Alignment explanation
Indices: 46908--46973 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
46898 ATGGAGATAT
*
46908 CAGAAATCAAAA
1 CAGAATTCAAAA
46920 CAGAATTCAAAA
1 CAGAATTCAAAA
*
46932 CAG-ATATCATAA
1 CAGAAT-TCAAAA
* * *
46944 CAGAATCCAGAT
1 CAGAATTCAAAA
* *
46956 CAGAAATCAGAA
1 CAGAATTCAAAA
46968 CAGAAT
1 CAGAAT
46974 CAAGTCAGAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.55, C:0.18, G:0.12, T:0.15
Consensus pattern (12 bp):
CAGAATTCAAAA
Found at i:46940 original size:24 final size:24
Alignment explanation
Indices: 46908--46987 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
46898 ATGGAGATAT
*
46908 CAGAAATCAAAACAGAATTCAAAA
1 CAGAAATCAAAACAGAATCCAAAA
* * * *
46932 CAGATATCATAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATCCAAAA
* **
46956 CAGAAATCAGAACAGAAT-CAAGT
1 CAGAAATCAAAACAGAATCCAAAA
46979 CAGAAATCA
1 CAGAAATCA
46988 GATAAAATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 12 0.26
24 35 0.74
ACGTcount: A:0.54, C:0.19, G:0.12, T:0.15
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATCCAAAA
Found at i:47185 original size:13 final size:13
Alignment explanation
Indices: 47167--47194 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47157 TCATAATATG
47167 ATTTATAGGGATC
1 ATTTATAGGGATC
47180 ATTTATAGGGATC
1 ATTTATAGGGATC
47193 AT
1 AT
47195 CTTACTCGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (13 bp):
ATTTATAGGGATC
Found at i:57572 original size:2 final size:2
Alignment explanation
Indices: 57565--57605 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
57555 GGTGTAAAAC
57565 TA TA TA TA TA 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 TA TA TA TA TA T
57606 TAGGAATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57641 original size:24 final size:22
Alignment explanation
Indices: 57615--57659 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
57605 TTAGGAATTT
57615 TATT-TTTATATTATT-AAAATA
1 TATTATTTA-ATTATTAAAAATA
57636 TATTATTTAATTATTAAAAATA
1 TATTATTTAATTATTAAAAATA
57658 TA
1 TA
57660 AAAATATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATTTAATTATTAAAAATA
Found at i:58831 original size:43 final size:43
Alignment explanation
Indices: 58784--59140 Score: 177
Period size: 43 Copynumber: 8.4 Consensus size: 43
58774 TAGAGACCTT
*
58784 AATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGGCCTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
** * *
58827 AATTAGGAAGTTAGAAAGTGAGATT-AAAAAAATTTAAGGGCCTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAA--TAGGGGCCTC
* * *
58871 AATTATAAAGTTCA-ATAAGTGAGATT--AAAAATTAGAGGCCTC
1 AATTATAAAGGT-AGA-AAGTGAGATTGAAAAAAATAGGGGCCTC
* ** *
58913 AATTATAAAGGTAGAAATTGAGATTGAAAAACTTA-GAG-CTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
* ** *** *
58954 GAGATTGA-AAAGGTAGAAACTGAGATTGAAAAATTTTAAAAGCTTC
1 -A-ATT-ATAAAGGTAGAAAGTGAGATTGAAAAA-AATAGGGGCCTC
* * * * *
59000 AATTATAAA---AAAAAGTGAGATT-ACAAAATTAGGAGTCTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
* * * * *
59039 AATTATATAGGTAAAAAAG-G-GATTGGAAAAAAATAGAGACTTC
1 AATTATAAAGGT-AGAAAGTGAGATT-GAAAAAAATAGGGGCCTC
* * * * ** * *
59082 AATTATAAAGATAAAAAGTTAGAATGAATACTATTA-GGACCTC
1 AATTATAAAGGTAGAAAGTGAGATTGAA-AAAAATAGGGGCCTC
59125 AATTATAAAGGT-GAAA
1 AATTATAAAGGTAGAAA
59141 CATAAGATTT
Statistics
Matches: 245, Mismatches: 46, Indels: 47
0.72 0.14 0.14
Matches are distributed among these distances:
39 15 0.06
40 4 0.02
41 28 0.11
42 39 0.16
43 101 0.41
44 42 0.17
45 14 0.06
46 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (43 bp):
AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
Found at i:58921 original size:42 final size:42
Alignment explanation
Indices: 58766--59045 Score: 193
Period size: 43 Copynumber: 6.6 Consensus size: 42
58756 TATGAAATTG
* * * *
58766 TAAAAAATTAGAGACCTTAATTATAAAGGTAGAAATTGAGAT
1 TAAAAAATTAGAGGCCTCAATTATAAAGTTAGAAAGTGAGAT
* * **
58808 TGAAAAAAATAGGGGCCTCAATTAGGAAGTTAGAAAGTGAGAT
1 T-AAAAAATTAGAGGCCTCAATTATAAAGTTAGAAAGTGAGAT
58851 TAAAAAAATTTA-AGGGCCTCAATTATAAAGTTCA-ATAAGTGAGAT
1 T-AAAAAA-TTAGA-GGCCTCAATTATAAAGTT-AGA-AAGTGAGAT
* *
58896 T-AAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGAT
1 TAAAAAATTAGAGGCCTCAATTATAAAGTTAGAAAGTGAGAT
* * *
58937 TGAAAAACTTAGA-G-CTCGAGATTGA-AAAGGTAGAAACTGAGAT
1 T-AAAAAATTAGAGGCCTC-A-ATT-ATAAAGTTAGAAAGTGAGAT
* * * * *
58980 TGAAAAATTTTAAAAGCTTCAATTATAAA---AAAAAGTGAGAT
1 T-AAAAA-ATTAGAGGCCTCAATTATAAAGTTAGAAAGTGAGAT
* *
59021 TACAAAATTAG-GAGTCTCAATTATA
1 TAAAAAATTAGAG-GCCTCAATTATA
59046 TAGGTAAAAA
Statistics
Matches: 193, Mismatches: 28, Indels: 37
0.75 0.11 0.14
Matches are distributed among these distances:
39 13 0.07
40 4 0.02
41 24 0.12
42 24 0.12
43 83 0.43
44 30 0.16
45 13 0.07
46 2 0.01
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.26
Consensus pattern (42 bp):
TAAAAAATTAGAGGCCTCAATTATAAAGTTAGAAAGTGAGAT
Found at i:58970 original size:21 final size:21
Alignment explanation
Indices: 58923--58985 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
58913 AATTATAAAG
*
58923 GTAGAAATTGAGATTGAAAAAC
1 GTAGAAACTGAGATTG-AAAAC
* * *
58945 TTAG-AGCTCGAGATTGAAAAG
1 GTAGAAACT-GAGATTGAAAAC
58966 GTAGAAACTGAGATTGAAAA
1 GTAGAAACTGAGATTGAAAA
58986 ATTTTAAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.22
Consensus pattern (21 bp):
GTAGAAACTGAGATTGAAAAC
Found at i:59002 original size:129 final size:125
Alignment explanation
Indices: 58768--59091 Score: 318
Period size: 129 Copynumber: 2.6 Consensus size: 125
58758 TGAAATTGTA
* * *
58768 AAAAATTAGAGACCTTAATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGGCCTCAATTAG
1 AAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGAGCCTCAATTAG
* * * ** *
58833 GAAGTTAGAAAGTGAGATTAAAAAAATTTAAGGGCCTCAATTATAAAGTTCAATAAGTGAGATT
66 AAAGGTAGAAACTGAGATTAAAAAAATTTAAAAGCCTCAATTATAAA----AAAAAGTGAGATT
**
58897 AAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAACTTA-GAG-CTCGAGATT
1 AAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGAGCCTC-A-ATT
* * *
58960 -GAAAAGGTAGAAACTGAGATTGAAAAATTTTAAAAGCTTCAATTATAAAAAAAAGTGAGATT
64 AG-AAAGGTAGAAACTGAGATTAAAAAAATTTAAAAGCCTCAATTATAAAAAAAAGTGAGATT
* * ** * *
59022 ACAAAATTAG-GAGTCTCAATTATATAGGTA-AAAAAGGGATTGGAAAAAAATA-GAGACTTCAA
1 A-AAAATTAGAG-GCCTCAATTATAAAGGTAGAAATTGAGATT-GAAAAAAATAGGAG-CCTCAA
*
59084 TTATAAAG
62 TTAGAAAG
59092 ATAAAAAGTT
Statistics
Matches: 163, Mismatches: 23, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
125 22 0.13
126 42 0.26
127 4 0.02
128 6 0.04
129 89 0.55
ACGTcount: A:0.48, C:0.07, G:0.19, T:0.26
Consensus pattern (125 bp):
AAAAATTAGAGGCCTCAATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGAGCCTCAATTAG
AAAGGTAGAAACTGAGATTAAAAAAATTTAAAAGCCTCAATTATAAAAAAAAGTGAGATT
Found at i:61474 original size:23 final size:23
Alignment explanation
Indices: 61447--61492 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
61437 CTGATTGGAT
*
61447 CTTCTAGAAGCTGTTGACTGGGC
1 CTTCTAGAAGCTGCTGACTGGGC
*
61470 CTTCTAGAAGTTGCTGACTGGGC
1 CTTCTAGAAGCTGCTGACTGGGC
61493 ACCATGTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.30
Consensus pattern (23 bp):
CTTCTAGAAGCTGCTGACTGGGC
Found at i:64180 original size:29 final size:29
Alignment explanation
Indices: 64140--64309 Score: 245
Period size: 29 Copynumber: 5.9 Consensus size: 29
64130 CAACCAGCAT
*
64140 AGGTCGCTATGCACGCCCGGCGTCCT-TA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
64168 TAGGTCGCCATGCACGCCCGGCGTCCT-TA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
* **
64197 TAGGTCGCCATGCATGCCTAGCGTCCTATA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
*
64227 AGGTTGCCATGCACGCCCGGCGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
* *
64256 AGGTTGCCATGCACGCCTGGCGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
64285 AGGTCGCCATGCACGCCCGGCGTCC
1 AGGTCGCCATGCACGCCCGGCGTCC
64310 AACGTTCTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
29 127 0.98
30 2 0.02
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGTCCTATA
Found at i:64355 original size:28 final size:28
Alignment explanation
Indices: 64313--64370 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
64303 GGCGTCCAAC
*
64313 GTTCTTTGCCCGCTGCTGCTCTGCTTTG
1 GTTCTTTGCCCGCTGATGCTCTGCTTTG
*
64341 GTTCTTTGCCTGCTGATGCTCTGCTTTG
1 GTTCTTTGCCCGCTGATGCTCTGCTTTG
64369 GT
1 GT
64371 GCTATGCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.02, C:0.28, G:0.26, T:0.45
Consensus pattern (28 bp):
GTTCTTTGCCCGCTGATGCTCTGCTTTG
Found at i:64955 original size:35 final size:31
Alignment explanation
Indices: 64892--64984 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 31
64882 TGAATTTATA
64892 TTATATAAAAAAATTAGTTAATTAGTTTAAG
1 TTATATAAAAAAATTAGTTAATTAGTTTAAG
*
64923 TTATATAAAAGAATAATTATTTAAATTAGTTT-A-
1 TTATAT-AAA-AA-AATTAGTT-AATTAGTTTAAG
* **
64956 TTGT-TATAAATTATTAGTTAATTAGTTTA
1 TTATATA-AAAAAATTAGTTAATTAGTTTA
64985 TTATTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 9 0.18
30 6 0.12
31 8 0.16
32 6 0.12
33 5 0.10
34 8 0.16
35 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATATAAAAAAATTAGTTAATTAGTTTAAG
Found at i:64967 original size:18 final size:18
Alignment explanation
Indices: 64944--64998 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
64934 AATAATTATT
64944 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
64962 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
64974 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
64991 TAAATTAG
1 TAAATTAG
64999 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:65279 original size:22 final size:22
Alignment explanation
Indices: 65253--65300 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
65243 ATAGTTTATT
*
65253 AGTTAACGTTATATTAAAGAAC
1 AGTTAAAGTTATATTAAAGAAC
*
65275 AGTTAAAGTTATATTAAAGAAT
1 AGTTAAAGTTATATTAAAGAAC
65297 AGTT
1 AGTT
65301 TATTAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (22 bp):
AGTTAAAGTTATATTAAAGAAC
Found at i:66615 original size:23 final size:23
Alignment explanation
Indices: 66587--66631 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
66577 TTTAATTATT
*
66587 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
66610 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
66632 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:66631 original size:18 final size:20
Alignment explanation
Indices: 66581--66631 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
66571 GTTATTTTTA
66581 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
66602 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
66622 TTTATTATTT
1 ATTATTATTT
66632 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:67589 original size:60 final size:60
Alignment explanation
Indices: 67520--67633 Score: 210
Period size: 60 Copynumber: 1.9 Consensus size: 60
67510 AATCATTACT
67520 AATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTAATATCA
1 AATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTAATATCA
* *
67580 AATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATTAAATCATTA
1 AATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTA
67634 TTATAATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.46, C:0.11, G:0.01, T:0.42
Consensus pattern (60 bp):
AATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTAATATCA
Found at i:67622 original size:13 final size:12
Alignment explanation
Indices: 67604--67640 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
67594 AATAATAATT
67604 TCATTATTACTAA
1 TCATTATTA-TAA
67617 TCATTATTA-AA
1 TCATTATTATAA
67628 TCATTATTATAA
1 TCATTATTATAA
67640 T
1 T
67641 TTCGTAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (12 bp):
TCATTATTATAA
Found at i:67633 original size:21 final size:21
Alignment explanation
Indices: 67554--67633 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 21
67544 TCATTAGTAC
*
67554 TAATCATTACTAAATCATTAA
1 TAATCATTATTAAATCATTAA
*
67575 T-ATCAAATCATTAAAT-ATTAA
1 TAATC--ATTATTAAATCATTAA
** * *
67596 TAAT-A--ATTTCATTATTAC
1 TAATCATTATTAAATCATTAA
67614 TAATCATTATTAAATCATTA
1 TAATCATTATTAAATCATTA
67634 TTATAATTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
17 5 0.11
18 8 0.18
19 2 0.05
20 3 0.07
21 16 0.36
22 10 0.23
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATCATTATTAAATCATTAA
Found at i:67899 original size:59 final size:60
Alignment explanation
Indices: 67786--67910 Score: 218
Period size: 60 Copynumber: 2.1 Consensus size: 60
67776 TAATTTCATT
*
67786 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATATTATTATTACTAATC
*
67845 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA-ATTATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATATTATTATTACTAATC
67904 ATTACTA
1 ATTACTA
67911 TCAAATATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 28 0.44
60 35 0.56
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (60 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATATTATTATTACTAATC
Found at i:67939 original size:59 final size:59
Alignment explanation
Indices: 67786--67939 Score: 201
Period size: 60 Copynumber: 2.6 Consensus size: 59
67776 TAATTTCATT
*
67786 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTAATAT-AAATCATTAAATATTAATAATAATATTATTATTACTAATC
*
67845 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA-ATTATTATTACTAATC
1 ATTACTAAATCATTAATAT-AAATCATTAAATATTAATAATAATATTATTATTACTAATC
67904 ATTACTATCAAAT-ATTAATAT-AAT-ATTAAATTATTA
1 ATTAC--T-AAATCATTAATATAAATCATTAAA-TATTA
67940 TTACTAATCA
Statistics
Matches: 87, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
58 6 0.07
59 34 0.39
60 35 0.40
61 8 0.09
62 4 0.05
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (59 bp):
ATTACTAAATCATTAATATAAATCATTAAATATTAATAATAATATTATTATTACTAATC
Found at i:67943 original size:45 final size:48
Alignment explanation
Indices: 67845--68153 Score: 256
Period size: 45 Copynumber: 6.6 Consensus size: 48
67835 ATTACTAATC
67845 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
*
67894 ATTACTAATCATTACTATCAAAT-ATT-AATA-TAATATTAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* *
67939 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
* *
67988 ATTACTAATCATTAC--T-AAATCATT-AATATCAAATCATTAAA-TATT
1 ATTACTAATCATTACTATCAAATCATTAAATAT-TAAT-AATAAATTATT
* * * * * *
68033 AATAATAATTTCATTATTA-CTAATCATT-ACTATT-A-AAT-TATTATT
1 ATTACTAA--TCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* * * *
68078 ATTA--AATCATTATTAT-AATGATTATTATAATGATTATTATTAAATTATT
1 ATTACTAATCATTACTATCAA--ATCATTA-AAT-ATTAATAATAAATTATT
* *
68127 ATTA-TAATGATTATTATCAAATCATTA
1 ATTACTAATCATTACTATCAAATCATTA
68154 CTAAATCATC
Statistics
Matches: 212, Mismatches: 25, Indels: 46
0.75 0.09 0.16
Matches are distributed among these distances:
41 10 0.05
43 7 0.03
44 1 0.00
45 61 0.29
46 22 0.10
47 18 0.08
48 29 0.14
49 51 0.24
50 11 0.05
51 2 0.01
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:68004 original size:153 final size:155
Alignment explanation
Indices: 67694--68082 Score: 640
Period size: 153 Copynumber: 2.5 Consensus size: 155
67684 GTTCAAGTCG
67694 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATC-A
1 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
* *
67758 ATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAATATCAAATCATTAAATATTAAT
66 AT-ATT-AATATTAATAATAAATTCATTATTACTAATCATTAATATCAAATCATTAAAAATTAAT
*
67823 AATAATTTTATTATTACTAATCATTAC
129 AATAATTTCATTATTACTAATCATTAC
67850 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
1 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
* *
67915 ATATTAATA-TAATATTAAATT-ATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAA
66 ATATTAATATTAATAATAAATTCATTATTACTAATCATTAATATCAAATCATTAAAAATTAATAA
67978 TAATTTCATTATTACTAATCATTAC
131 TAATTTCATTATTACTAATCATTAC
* * *
68003 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATTA
1 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACTATCA
*
68068 AATTATTATTATTAA
65 AA-TATTAATATTAA
68083 ATCATTATTA
Statistics
Matches: 220, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
153 103 0.47
154 34 0.15
155 11 0.05
156 69 0.31
157 3 0.01
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (155 bp):
TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
ATATTAATATTAATAATAAATTCATTATTACTAATCATTAATATCAAATCATTAAAAATTAATAA
TAATTTCATTATTACTAATCATTAC
Found at i:68068 original size:41 final size:40
Alignment explanation
Indices: 68023--68153 Score: 106
Period size: 38 Copynumber: 3.3 Consensus size: 40
68013 ATATCAAATC
*
68023 ATTAAA-TATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTAAATTATTAATAATAA-ATCATTATTA-TAATCATTACT
* * * *
68064 ATTAAATTATTATTATTAAATCATTATTATAATGATTATT
1 ATTAAATTATTAATAATAAATCATTATTATAATCATTACT
* * * * * *
68104 A-T-AATGATTATTATTAAATTATTATTATAATGATTATT
1 ATTAAATTATTAATAATAAATCATTATTATAATCATTACT
* *
68142 ATCAAATCATTA
1 ATTAAATTATTA
68154 CTAAATCATC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
38 35 0.45
39 1 0.01
40 17 0.22
41 15 0.19
42 10 0.13
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (40 bp):
ATTAAATTATTAATAATAAATCATTATTATAATCATTACT
Found at i:68077 original size:3 final size:3
Alignment explanation
Indices: 68069--68143 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
68059 TTACTATTAA
* * * * * *
68069 ATT ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
68116 ATT A-A ATT ATT ATT ATA ATG ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
68144 CAAATCATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (3 bp):
ATT
Found at i:68089 original size:63 final size:60
Alignment explanation
Indices: 67939--68064 Score: 227
Period size: 60 Copynumber: 2.1 Consensus size: 60
67929 TTAAATTATT
*
67939 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
67998 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
68058 ATTACTA
1 ATTACTA
68065 TTAAATTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 6 0.09
60 58 0.91
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:68105 original size:26 final size:25
Alignment explanation
Indices: 68023--68334 Score: 124
Period size: 26 Copynumber: 12.5 Consensus size: 25
68013 ATATCAAATC
*
68023 ATTAAAT-ATTAATAATAAT-TTCATT
1 ATTAAATCATT-ATTATAATATT-ATT
*
68048 ATTACTAATCATTACTATTAAATTATTATT
1 ATTA--AATCATTATTA-T-AA-TATTATT
68078 ATTAAATCATTATTATAATGATTATT
1 ATTAAATCATTATTATAAT-ATTATT
*
68104 A-T-AATGATTATTATTAA-ATTATT
1 ATTAAATCATTATTA-TAATATTATT
* *
68127 ATTATAATGATTATTATCAA-ATCATT
1 ATTA-AATCATTATTAT-AATATTATT
* * *
68153 ACTAAATC---ATCA-AATCATTAAT
1 ATTAAATCATTATTATAAT-ATTATT
68175 -TTAAATCATTATTA-AATCATTATT
1 ATTAAATCATTATTATAAT-ATTATT
* *
68199 A-T-AATGATTATTACTAA-ATCATT
1 ATTAAATCATTATTA-TAATATTATT
*
68222 ATTATAATGATTATTATCAA-ATTATT
1 ATTA-AATCATTATTAT-AATATTATT
* * *
68248 ATTATAATGATTATTATCATATCATT
1 ATTA-AATCATTATTATAATATTATT
* * * * * *
68274 ACTAAATCATCA-AATCAT-TAAAT
1 ATTAAATCATTATTATAATATTATT
68297 ATTAAATTCATTATTA-AAT-TTATT
1 ATTAAA-TCATTATTATAATATTATT
*
68321 AATTCAATCATTAT
1 -ATTAAATCATTAT
68335 AATCATTATT
Statistics
Matches: 227, Mismatches: 31, Indels: 59
0.72 0.10 0.19
Matches are distributed among these distances:
20 2 0.01
21 6 0.03
22 7 0.03
23 31 0.14
24 47 0.21
25 29 0.13
26 73 0.32
27 6 0.03
28 14 0.06
29 2 0.01
30 8 0.04
31 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (25 bp):
ATTAAATCATTATTATAATATTATT
Found at i:68120 original size:153 final size:152
Alignment explanation
Indices: 67810--68264 Score: 478
Period size: 153 Copynumber: 3.0 Consensus size: 152
67800 ATATCAAATC
* *
67810 ATTAAATATTAATAATAATTTTATTATTACTAATCATTACTAAATCATTACTATCAAATCATTAA
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAA
* * *
67875 ATATTAATAATAAATT-ATTATTACTAATCATTACTATCAAATATTAATATAATATTAAATTATT
66 ATATTAATAAT-AATTCATTATTACTAATCATTACTAT-TAA-ATT-AT-TATTATTAAATCATT
* *
67939 ATTACTAATCATTACTATCAA--ATCATT
126 ATTA-TAATCATTATTAT-AATGATTATT
67966 A--AAA-ATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAA
1 ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAA
68028 ATATTAATAATAATTTCATTATTACTAATCATTACTATTAAATTATTATTATTAAATCATTATTA
66 ATATTAATAATAA-TTCATTATTACTAATCATTACTATTAAATTATTATTATTAAATCATTATTA
*
68093 TAATGATTATTATAATGATTATT
130 TAATCATTATTATAATGATTATT
* * * *
68116 ATTAAATTATT-ATTATAA--TGATTATTATCAAATCATTACTAAATCATCAA-ATCATTAAT--
1 ATTAAA-TATTAATAATAATTTCATTATTA-CTAATCATTACTAAATCATTAATATCA--AATCA
* * * * * *
68175 TTAAATCATT-AT--TAAATCATTATTA-TAATGATTATTACTAAATCATTATTA-T-AATGATT
62 TTAAAT-ATTAATAATAATTCATTATTACTAATCATTACTATTAAATTATTATTATTAAATCATT
*
68234 ATTATCAAATTATTATTATAATGATTATT
126 ATTAT--AATCATTATTATAATGATTATT
68263 AT
1 AT
68265 CATATCATTA
Statistics
Matches: 266, Mismatches: 19, Indels: 37
0.83 0.06 0.11
Matches are distributed among these distances:
145 11 0.04
146 1 0.00
147 45 0.17
148 11 0.04
149 14 0.05
150 23 0.09
151 22 0.08
152 31 0.12
153 80 0.30
154 27 0.10
156 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (152 bp):
ATTAAATATTAATAATAATTTCATTATTACTAATCATTACTAAATCATTAATATCAAATCATTAA
ATATTAATAATAATTCATTATTACTAATCATTACTATTAAATTATTATTATTAAATCATTATTAT
AATCATTATTATAATGATTATT
Found at i:68225 original size:121 final size:124
Alignment explanation
Indices: 68063--68358 Score: 427
Period size: 121 Copynumber: 2.5 Consensus size: 124
68053 TAATCATTAC
* * *
68063 TATTAAATTATTATTATTAAATCATTATTATAATGATTATTATAATGATTATTATTAAATTATTA
1 TATTAAATCATTATTATTAAATCATTATTATAATCATTATTATAATGATTATTATCAAATTATTA
68128 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATT-AAT-TTAAA-TCAT
66 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
*
68184 TATTAAATCATTATTA-T-AATGATTATTACTAAATCATTATTATAATGATTATTATCAAATTAT
1 TATTAAATCATTATTATTAAATCATTATTA-T-AATCATTATTATAATGATTATTATCAAATTAT
*
68247 TATTATAATGATTATTATCATATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
64 TATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
*
68308 TATTAAAT--TTATTAATTCAATC---ATTATAATCATTA-T-TAATGATTATTATCA
1 TATTAAATCATTATT-ATTAAATCATTATTATAATCATTATTATAATGATTATTATCA
68359 TTTTTATGGT
Statistics
Matches: 161, Mismatches: 6, Indels: 19
0.87 0.03 0.10
Matches are distributed among these distances:
118 15 0.09
119 11 0.07
120 10 0.06
121 91 0.57
122 12 0.07
123 6 0.04
124 13 0.08
125 3 0.02
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (124 bp):
TATTAAATCATTATTATTAAATCATTATTATAATCATTATTATAATGATTATTATCAAATTATTA
TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
Found at i:68555 original size:17 final size:18
Alignment explanation
Indices: 68535--68569 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
68525 TATTAGTAAA
68535 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
68552 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
68570 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:72816 original size:21 final size:21
Alignment explanation
Indices: 72791--72863 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
72781 ACGCTGCAAT
72791 CATGCAGCTATGGATGCAACG
1 CATGCAGCTATGGATGCAACG
* * *
72812 CATGCAGCTACGAATGCATGAATCC
1 CATGCAGCTATGGATGC---AA-CG
72837 CA-GCTAGCTATGGATGCAACG
1 CATGC-AGCTATGGATGCAACG
72858 CATGCA
1 CATGCA
72864 TGAGTGATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
21 19 0.47
22 4 0.10
24 4 0.10
25 13 0.32
ACGTcount: A:0.30, C:0.26, G:0.25, T:0.19
Consensus pattern (21 bp):
CATGCAGCTATGGATGCAACG
Found at i:72943 original size:17 final size:17
Alignment explanation
Indices: 72921--72954 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
72911 ATGGATGCAT
72921 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
72938 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
72955 AAGTTTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (17 bp):
GATGAGGGATAGGGTTA
Found at i:73096 original size:34 final size:35
Alignment explanation
Indices: 73053--73122 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
73043 CCCCAATCTC
73053 CCCATGCATGAA-CGATCCTTGGTCGCCCCGAGTG
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
73087 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
73122 C
1 C
73123 ATGGCACGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 12 0.34
35 23 0.66
ACGTcount: A:0.17, C:0.37, G:0.26, T:0.20
Consensus pattern (35 bp):
CCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
Found at i:73125 original size:29 final size:29
Alignment explanation
Indices: 73057--73183 Score: 91
Period size: 29 Copynumber: 4.2 Consensus size: 29
73047 AATCTCCCCA
73057 TGCATGAA-CGATCCTTGGTCGCCCCGAGTG
1 TGCATGAACCGATCCTTGGTCGCCCCGA--G
73087 CCCATGCATGAACCGATCCTTGGTCGCCCCGAG
1 ----TGCATGAACCGATCCTTGGTCGCCCCGAG
* **** *
73120 TGCATG-GCACGATCTCCCCAATCTCCCC-A-
1 TGCATGAAC-CGA--TCCTTGGTCGCCCCGAG
73149 TGCATGAACCGATCCTTGGTCGCCCCGAG
1 TGCATGAACCGATCCTTGGTCGCCCCGAG
73178 TGCATG
1 TGCATG
73184 GCGACCTCCT
Statistics
Matches: 74, Mismatches: 12, Indels: 19
0.70 0.11 0.18
Matches are distributed among these distances:
27 9 0.12
28 2 0.03
29 24 0.32
30 2 0.03
31 9 0.12
33 1 0.01
34 8 0.11
35 19 0.26
ACGTcount: A:0.18, C:0.36, G:0.24, T:0.21
Consensus pattern (29 bp):
TGCATGAACCGATCCTTGGTCGCCCCGAG
Found at i:73209 original size:29 final size:29
Alignment explanation
Indices: 73177--73256 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
73167 GTCGCCCCGA
*
73177 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTACTTGGTCGTTGGGC
*
73206 GTGCATGGCGACCTATTTGGTCGTTGGGC
1 GTGCATGGCGACCTACTTGGTCGTTGGGC
*
73235 GTGCATGGCGACCTATTTGGTC
1 GTGCATGGCGACCTACTTGGTC
73257 ACTGTACAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.10, C:0.24, G:0.36, T:0.30
Consensus pattern (29 bp):
GTGCATGGCGACCTACTTGGTCGTTGGGC
Found at i:74873 original size:17 final size:17
Alignment explanation
Indices: 74828--74877 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
74818 AGGTACCTAC
* * *
74828 AAAAATCAAATTAAAGA
1 AAAAATAAAAATAAACA
*
74845 AAAAATGTAAAATAAACA
1 AAAAAT-AAAAATAAACA
74863 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
74878 AACTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 14 0.50
18 14 0.50
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAATAAAAATAAACA
Done.