Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005016.1 Hibiscus syriacus cultivar Beakdansim tig00011260_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: 68469
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:8731 original size:64 final size:66
Alignment explanation
Indices: 8575--8734 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 66
8565 GAATAAATTG
* * *
8575 AACATCGAATGCATTTCATGCACCGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATACATCGATGCACTCAGAGTTTTATGA
8639 A
66 A
* *
8640 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATACATCGATGCACTCAG-GCTATTT-T
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATACATCGATGCACTCAGAG-T-TTTAT
8702 G-A
64 GAA
*
8704 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
8735 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
64 32 0.37
65 49 0.57
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (66 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATACATCGATGCACTCAGAGTTTTATGA
A
Found at i:12723 original size:17 final size:17
Alignment explanation
Indices: 12678--12728 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
12668 ATAATGTTAA
12678 AATTTGTTTAAATTATG
1 AATTTGTTTAAATTATG
*
12695 AATTAAGTTTAAATTGAT-
1 AATT-TGTTTAAATT-ATG
*
12713 AATTTGTTTAAGTTAT
1 AATTTGTTTAAATTAT
12729 CCTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 2 0.07
17 12 0.41
18 13 0.45
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (17 bp):
AATTTGTTTAAATTATG
Found at i:21746 original size:201 final size:198
Alignment explanation
Indices: 21368--21820 Score: 500
Period size: 201 Copynumber: 2.3 Consensus size: 198
21358 TTACACTGCT
* * * * * *
21368 TCTAATCTTATAAATTATTAAAATTTTCATATTAACTTCCCAACAATACTCCCTGAACATGCCTA
1 TCTAATCTTATAAATTA-CAAAATTTTCAAATTAAC-TACCAAAAATACCCCCTAAACATGCCTA
* * *
21433 TCAAGCCATTTTAGTTTTTCTTCATGCACAAAACCAAGCTTTGGAACCATTTTGAACGCGATTTT
64 TCAAACCATTTTAGTTTTTCTTCATGCACAAAACCAAGCTTTGGAACCATTTTCAACACGATTTT
* * * * ** * * * *
21498 TACCCCGCTTAGAATGTCTTGTATGTGCTGATATTACCCTCAATTGAAAGATAAGTTACAATATT
129 TAACCCGCTTACAATATATCATATGTGCTCATATTACCATCAATTGAAAGATAAATTACAATACT
21563 ACACC
194 ACACC
* * *
21568 TCTAATCTTATAAATTACAAAACTTTTCAAATTAACTACCTGAAAATACCCCCTCAAATATGTCT
1 TCTAATCTTATAAATTACAAAA-TTTTCAAATTAACTACC-AAAAATACCCCCT-AAACATGCCT
* * * *
21633 ATCAAACCATTTTAGTTTTTTTTTCATGCGCAAAA-CAAGCTTTGGAATCATTTTCAACATGATT
63 ATCAAACCATTTTAG-TTTTTCTTCATGCACAAAACCAAGCTTTGGAACCATTTTCAACACGATT
* **
21697 TTTAACCCGCTTACAATATATCATATGTG-TCA-A-TACTGGATCAAATTGAAAGATAAATTTTA
127 TTTAACCCGCTTACAATATATCATATGTGCTCATATTAC--CATC-AATTGAAAGATAAATTACA
21759 ATACTACACC
189 ATACTACACC
* *
21769 TCTAATCTTATAAATTACAAATATTTTTAGATTAACTACCCAAAAATACCCC
1 TCTAATCTTATAAATTACAAA-ATTTTCAAATTAACTA-CCAAAAATACCCC
21821 TCGAACGTGC
Statistics
Matches: 212, Mismatches: 32, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
198 3 0.01
199 8 0.04
200 43 0.20
201 138 0.65
202 20 0.09
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (198 bp):
TCTAATCTTATAAATTACAAAATTTTCAAATTAACTACCAAAAATACCCCCTAAACATGCCTATC
AAACCATTTTAGTTTTTCTTCATGCACAAAACCAAGCTTTGGAACCATTTTCAACACGATTTTTA
ACCCGCTTACAATATATCATATGTGCTCATATTACCATCAATTGAAAGATAAATTACAATACTAC
ACC
Found at i:23419 original size:10 final size:10
Alignment explanation
Indices: 23396--23424 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
23386 TACAATTAGG
23396 TATTTTTAAA
1 TATTTTTAAA
23406 -ATTTTTAAA
1 TATTTTTAAA
23415 TATTTTTAAA
1 TATTTTTAAA
23425 ACCAAAGTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TATTTTTAAA
Found at i:27768 original size:4 final size:4
Alignment explanation
Indices: 27759--27786 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
27749 TATCAAAAAC
27759 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
27787 AATAAACGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:32368 original size:16 final size:17
Alignment explanation
Indices: 32349--32380 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
32339 TGCTACCATA
32349 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
32365 ATATTATATTTTATAT
1 ATATTATATTTTATAT
32381 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:41182 original size:24 final size:25
Alignment explanation
Indices: 41141--41189 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
41131 AAAATACGTA
41141 TGAACAACAATCTGCTACAGTACCG
1 TGAACAACAATCTGCTACAGTACCG
* *
41166 TGAACAATAA-CTGCTACATTACCG
1 TGAACAACAATCTGCTACAGTACCG
41190 ATTACACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (25 bp):
TGAACAACAATCTGCTACAGTACCG
Found at i:41244 original size:21 final size:22
Alignment explanation
Indices: 41218--41262 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
41208 GAATGCAAAT
41218 AGGGAATCG-GTACCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
* *
41239 AGGGAATCGATTCCCCTGCTAC
1 AGGGAATCGAGTACCCTGCTAC
41261 AG
1 AG
41263 TACTGCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (22 bp):
AGGGAATCGAGTACCCTGCTAC
Found at i:41897 original size:23 final size:23
Alignment explanation
Indices: 41832--41916 Score: 57
Period size: 23 Copynumber: 3.7 Consensus size: 23
41822 CATATAAATT
**
41832 TGCACCGAAGTGCCACGTAGAATT
1 TGCACCGAAGTGCCACGTA-AAGA
**
41856 TGTC-CCGAAG-GACTGCGTAAAGA
1 TG-CACCGAAGTG-CCACGTAAAGA
* * *
41879 TGCATCGAAGTGCCACGTAGAGT
1 TGCACCGAAGTGCCACGTAAAGA
*
41902 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
41917 TATAATATGT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 1 0.02
23 30 0.65
24 14 0.30
25 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAAAGA
Found at i:43696 original size:22 final size:22
Alignment explanation
Indices: 43670--43726 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
43660 CGTTGAAAAC
*
43670 CAGAAAATCAAGAACCGAGGAT
1 CAGAATATCAAGAACCGAGGAT
43692 CAGAATATCAAGAACCGAGGAT
1 CAGAATATCAAGAACCGAGGAT
43714 CAGAATATCAAGA
1 CAGAATATCAAGA
43727 TTGGCAAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.12
Consensus pattern (22 bp):
CAGAATATCAAGAACCGAGGAT
Found at i:44820 original size:67 final size:67
Alignment explanation
Indices: 44759--44892 Score: 153
Period size: 67 Copynumber: 2.0 Consensus size: 67
44749 ATATATAATA
* *
44759 AAGTTCTT-AAAACATATGGTATAGTTTTTGAAAACATATTATATAGTTTTAAAAAACATATAAT
1 AAGTTCTTGAAAACATATAGTATAG-TTTT-AAAACATATGATATAGTTTTAAAAAACATATAAT
44823 ATAT
64 ATAT
** * * * ** *
44827 ATTTTTTTGAAAATATATAGTATAGTTTTAAAACATATGGTATAGTTTTTGAAAACATATTATAT
1 AAGTTCTTGAAAACATATAGTATAGTTTTAAAACATATGATATAGTTTTAAAAAACATATAATAT
44892 A
66 A
44893 GTTTAAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
67 32 0.58
68 9 0.16
69 14 0.25
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (67 bp):
AAGTTCTTGAAAACATATAGTATAGTTTTAAAACATATGATATAGTTTTAAAAAACATATAATAT
AT
Found at i:44839 original size:25 final size:23
Alignment explanation
Indices: 44709--45057 Score: 212
Period size: 22 Copynumber: 15.3 Consensus size: 23
44699 ATAATATTTA
* *
44709 ATATATAGTTTTGTCAAAAAATA-
1 ATATATAGTTTT-TGAAAACATAT
*
44732 ATATATTA-TTTTTGAAAATATAT
1 ATATA-TAGTTTTTGAAAACATAT
* *
44755 A-ATAAAGTTCTT-AAAACATAT
1 ATATATAGTTTTTGAAAACATAT
**
44776 -GGTATAGTTTTTGAAAACATAT
1 ATATATAGTTTTTGAAAACATAT
**
44798 -TATATAGTTTTAAAAAACATAT
1 ATATATAGTTTTTGAAAACATAT
*
44820 AATATATATTTTTTTG-AAA-ATAT
1 -ATATATA-GTTTTTGAAAACATAT
44843 ATAGTATAG-TTTT-AAAACATAT
1 ATA-TATAGTTTTTGAAAACATAT
**
44865 -GGTATAGTTTTTGAAAACATAT
1 ATATATAGTTTTTGAAAACATAT
**
44887 -TATATAG-TTTAAAAAACATAT
1 ATATATAGTTTTTGAAAACATAT
**
44908 AATATATAGTTTTTTTTAAA-ATAT
1 -ATATATAG-TTTTTGAAAACATAT
* *
44932 ATAGTATAGTTTCTAAAAACATATTT
1 ATA-TATAGTTTTTGAAAACATA--T
*
44958 TTATATAG-TTTTGAAAACATACAAT
1 ATATATAGTTTTTGAAAACAT---AT
44983 ATATATAGTTTTTGAAAAACATAT
1 ATATATAGTTTTTG-AAAACATAT
* **
45007 GTAATATTTTTTTTTGAAAACATAT
1 AT-ATA-TAGTTTTTGAAAACATAT
* *
45032 -TATAT-GATTTTGAAAATATA-
1 ATATATAGTTTTTGAAAACATAT
45052 ATATAT
1 ATATAT
45058 TATATAGTTT
Statistics
Matches: 259, Mismatches: 38, Indels: 60
0.73 0.11 0.17
Matches are distributed among these distances:
20 5 0.02
21 57 0.22
22 64 0.25
23 38 0.15
24 37 0.14
25 35 0.14
26 15 0.06
27 8 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (23 bp):
ATATATAGTTTTTGAAAACATAT
Found at i:44844 original size:42 final size:42
Alignment explanation
Indices: 44798--44936 Score: 120
Period size: 45 Copynumber: 3.2 Consensus size: 42
44788 GAAAACATAT
*
44798 TATATAGTTTTAAAAAACATATAATATATATTTTTTTGAAAA
1 TATATAGTTTTAAAAAACATATAATATATATTTTTTTAAAAA
** ** * **
44840 TATATAGTATAGTTTTAAAACATATGGTATA-GTTTTTGAAAACATA
1 TATATAGT-T--TTAAAAAACATATAATATATATTTTTTTAAA-A-A
*
44886 TTATATAG-TTTAAAAAACATATAATATATAGTTTTTTTTAAAA
1 -TATATAGTTTTAAAAAACATATAATATATA-TTTTTTTAAAAA
44929 TATATAGT
1 TATATAGT
44937 ATAGTTTCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
42 15 0.21
43 17 0.24
44 8 0.11
45 24 0.33
46 1 0.01
47 7 0.10
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (42 bp):
TATATAGTTTTAAAAAACATATAATATATATTTTTTTAAAAA
Found at i:44862 original size:89 final size:89
Alignment explanation
Indices: 44732--45031 Score: 374
Period size: 89 Copynumber: 3.2 Consensus size: 89
44722 TCAAAAAATA
* *
44732 ATATATTATTTTTGAAAATATATAATAAAGTTCTTAAAACATATGGTATAGTTTTTGAAAACATA
1 ATATATT-TTTTTGAAAATATATAGTATAGTT-TTAAAACATATGGTATAGTTTTTGAAAACATA
44797 TTATATAGTTTTAAAAAACATATAAT
64 TTATATAGTTTTAAAAAACATATAAT
44823 ATATATTTTTTTGAAAATATATAGTATAGTTTTAAAACATATGGTATAGTTTTTGAAAACATATT
1 ATATATTTTTTTGAAAATATATAGTATAGTTTTAAAACATATGGTATAGTTTTTGAAAACATATT
44888 ATATAG-TTTAAAAAACATATAAT
66 ATATAGTTTTAAAAAACATATAAT
* **
44911 ATATAGTTTTTTTTAAAATATATAGTATAGTTTCTAAAAACATATTTTTATA-TAGTTTTGAAAA
1 ATATA-TTTTTTTGAAAATATATAGTATAGTTT-T-AAAACATA-TGGTATAGT--TTTTGAAAA
*
44975 CATACAATATATATAGTTTTTGAAAAACATATGTAAT
60 CAT---AT-TATATAG-TTTTAAAAAACATA--TAAT
*
45012 AT-T-TTTTTTTGAAAACATAT
1 ATATATTTTTTTGAAAATATAT
45032 TATATGATTT
Statistics
Matches: 187, Mismatches: 8, Indels: 21
0.87 0.04 0.10
Matches are distributed among these distances:
88 22 0.12
89 66 0.35
90 23 0.12
91 16 0.09
92 5 0.03
93 12 0.06
96 2 0.01
97 7 0.04
98 15 0.08
99 12 0.06
100 1 0.01
101 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (89 bp):
ATATATTTTTTTGAAAATATATAGTATAGTTTTAAAACATATGGTATAGTTTTTGAAAACATATT
ATATAGTTTTAAAAAACATATAAT
Found at i:44995 original size:72 final size:69
Alignment explanation
Indices: 44838--45006 Score: 178
Period size: 72 Copynumber: 2.4 Consensus size: 69
44828 TTTTTTTGAA
* * * * *
44838 AATATATAGTATAGTTTTAAAACATATGGTATAGTTTTTGAAAACATATTATATAGTTTAAAAAA
1 AATATATAGTGT-TTTTTAAAACATATAGTATAGTTTCTAAAAACATATTATATAGTTTAAAAAA
*
44903 CATAT
65 CATAC
* * **
44908 AATATATAGTTTTTTTTAAAATATATAGTATAGTTTCTAAAAACATATTTTTATATAGTTTTGAA
1 AATATATAGTGTTTTTTAAAACATATAGTATAGTTTCTAAAAACATA---TTATATAGTTTAAAA
44973 AACATAC
63 AACATAC
*
44980 AATATATA-TAGTTTTTGAAAAACATAT
1 AATATATAGT-GTTTTT-TAAAACATAT
45007 GTAATATTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
69 30 0.37
70 11 0.13
71 1 0.01
72 32 0.39
73 8 0.10
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (69 bp):
AATATATAGTGTTTTTTAAAACATATAGTATAGTTTCTAAAAACATATTATATAGTTTAAAAAAC
ATAC
Found at i:45043 original size:21 final size:21
Alignment explanation
Indices: 45018--45057 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45008 TAATATTTTT
*
45018 TTTTGAAAACATATTATATGA
1 TTTTGAAAACATAATATATGA
*
45039 TTTTGAAAATATAATATAT
1 TTTTGAAAACATAATATAT
45058 TATATAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (21 bp):
TTTTGAAAACATAATATATGA
Found at i:45057 original size:26 final size:27
Alignment explanation
Indices: 45028--45091 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
45018 TTTTGAAAAC
45028 ATATTATAT-GATTTTGAAAATATA-AT
1 ATATTATATAG-TTTTGAAAATATAGAT
* *
45054 ATATTATATAGTTTTTAATATATAGAT
1 ATATTATATAGTTTTGAAAATATAGAT
45081 ATATATATATA
1 ATAT-TATATA
45092 TATTAAGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 20 0.61
27 7 0.21
28 6 0.18
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (27 bp):
ATATTATATAGTTTTGAAAATATAGAT
Found at i:45108 original size:3 final size:3
Alignment explanation
Indices: 45100--45137 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
45090 TATATTAAGC
45100 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
45138 TTCTTTTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:53561 original size:30 final size:30
Alignment explanation
Indices: 53527--53591 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
53517 CTTAAATTTC
53527 TATTTTTGATATTTT-AGTCCTTTA-ACCTTT
1 TATTTTTGATATTTTGA-TCCTTTACA-CTTT
*
53557 TATTTTTGCTATTTTGATCCTTTACACTTT
1 TATTTTTGATATTTTGATCCTTTACACTTT
53587 TATTT
1 TATTT
53592 ATTTATTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 30 0.94
31 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.06, T:0.62
Consensus pattern (30 bp):
TATTTTTGATATTTTGATCCTTTACACTTT
Found at i:53629 original size:25 final size:23
Alignment explanation
Indices: 53601--53675 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 23
53591 TATTTATTTA
53601 TTTATTTCTTTTCTTTTCTTTTAAT
1 TTTATTT-TTTT-TTTTCTTTTAAT
*
53626 TTTAATATTTTTTATTTCTTTTAAT
1 TTT-AT-TTTTTTTTTTCTTTTAAT
53651 TTAATATTTTTTTTATTTCTTTTAA
1 TT--TATTTTTTTT-TTTCTTTTAA
53676 CATTGTTATA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
25 22 0.51
26 18 0.42
27 3 0.07
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTATTTTTTTTTTTCTTTTAAT
Found at i:53662 original size:26 final size:25
Alignment explanation
Indices: 53615--53675 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 25
53605 TTTCTTTTCT
53615 TTTCTTTTAATTTTAATATTTTTTA
1 TTTCTTTTAATTTTAATATTTTTTA
53640 TTTCTTTTAA-TTTAATATTTTTTTTA
1 TTTCTTTTAATTTTAATA--TTTTTTA
53666 TTTCTTTTAA
1 TTTCTTTTAA
53676 CATTGTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.21
25 10 0.29
26 17 0.50
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTCTTTTAATTTTAATATTTTTTA
Found at i:55241 original size:21 final size:21
Alignment explanation
Indices: 55217--55265 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
55207 CATAAAATAA
55217 TATTTATAAAAGTACA-ATATT
1 TATTTATAAAAGTA-AGATATT
*
55238 TATTTATAAATGTAAGATATT
1 TATTTATAAAAGTAAGATATT
55259 TATTTAT
1 TATTTAT
55266 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (21 bp):
TATTTATAAAAGTAAGATATT
Found at i:56185 original size:29 final size:29
Alignment explanation
Indices: 56141--56264 Score: 187
Period size: 29 Copynumber: 4.3 Consensus size: 29
56131 TTTCTTTGGG
*
56141 TTCTCTTTCTAACGAGAGAACCCTCTCTC
1 TTCTCTCTCTAACGAGAGAACCCTCTCTC
* *
56170 TTTTCTCTCTAACGAGAGAACCCTCTCCC
1 TTCTCTCTCTAACGAGAGAACCCTCTCTC
56199 TTCTCTCTCTAACGAGAGAACCCTCT-TCC
1 TTCTCTCTCTAACGAGAGAACCCTCTCT-C
* *
56228 TTCTCTCTCTAACGAGATAACCCTCTCAC
1 TTCTCTCTCTAACGAGAGAACCCTCTCTC
56257 TTCTCTCT
1 TTCTCTCT
56265 AAAAGGATCT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
29 86 1.00
ACGTcount: A:0.20, C:0.37, G:0.09, T:0.34
Consensus pattern (29 bp):
TTCTCTCTCTAACGAGAGAACCCTCTCTC
Found at i:57083 original size:3 final size:3
Alignment explanation
Indices: 57075--57143 Score: 61
Period size: 3 Copynumber: 22.3 Consensus size: 3
57065 ATTCTTTATT
* *
57075 TAA TAA TAA TAA T-A TATA TAA T-A TATA TAA TAGA TAT TAT TAAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TA-A TAA TAA T-AA TAA
*
57122 TAA TAA TAA TAA TAA AAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
57144 TAAAGTAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
2 4 0.07
3 41 0.73
4 11 0.20
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:57463 original size:45 final size:45
Alignment explanation
Indices: 57399--58043 Score: 1029
Period size: 45 Copynumber: 14.2 Consensus size: 45
57389 TAAAATCTCA
* * ** *
57399 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGGAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
57444 TTTGAGAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
57489 TTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
57535 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
57580 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
57625 TTTTAAGAACATCATGAACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAA-AACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
57671 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
*
57717 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGATCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
57762 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
57808 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
57853 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAAGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG-AAGGT
* *
57899 TTTGAGAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
57944 TTTGAAAACATCATGCACTAAAGGGCTTACAAATGACCCGGAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
* * *
57990 TTTGAAAACATCATGCACTAAAGGGATTACAGATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
58035 TTTGAAAAC
1 TTTGAAAAC
58044 CAAAAAGCTC
Statistics
Matches: 558, Mismatches: 36, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
45 302 0.54
46 256 0.46
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:57570 original size:91 final size:91
Alignment explanation
Indices: 57399--58043 Score: 1069
Period size: 91 Copynumber: 7.1 Consensus size: 91
57389 TAAAATCTCA
* * ** * *
57399 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGGAGG-TTTTGAGAACATCATGCACT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
*
57463 GAAGGGCTTACAGATGACCCAAAGGT
66 GAAGGGCTTACAGATGACCCGAAGGT
*
57489 TTTGAAAACATCATGTACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
57554 GAAGGGCTTACAGATGACCCGAAGGT
66 GAAGGGCTTACAGATGACCCGAAGGT
* *
57580 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGGTTTTT-AAGAACATCATGAAC
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAA-AACATCATGCAC
57644 TGAAGGGCTTACAGATGACCCGAAGGT
65 TGAAGGGCTTACAGATGACCCGAAGGT
57671 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
*
57736 GAAGGGCTTACAGATGATCCGAAGGT
66 GAAGGGCTTACAGATGACCCGAAGGT
*
57762 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGGTTTTTGAAAACATCATGCACT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
57827 GAAGGGCTTACAGATGACCCGAAGGT
66 GAAGGGCTTACAGATGACCCGAAGGT
* * *
57853 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAAGTTTTTGAGAACATCATGCACT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
*
57918 GAAGGGCTTACAGATAACCCGAAGGT
66 GAAGGGCTTACAGATGACCCGAAGGT
* * *
57944 TTTGAAAACATCATGCACTAAAGGGCTTACAAATGACCCGGAGGTTTTTGAAAACATCATGCACT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
* * *
58009 AAAGGGATTACAGATGACCCAAAGGT
66 GAAGGGCTTACAGATGACCCGAAGGT
58035 TTTGAAAAC
1 TTTGAAAAC
58044 CAAAAAGCTC
Statistics
Matches: 523, Mismatches: 29, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
90 40 0.08
91 481 0.92
92 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (91 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACT
GAAGGGCTTACAGATGACCCGAAGGT
Found at i:58749 original size:22 final size:20
Alignment explanation
Indices: 58724--58779 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
58714 AATAAAGCTT
58724 TCATCTTTAAAATGAGAATCTA
1 TCATCTTT-AAA-GAGAATCTA
*
58746 TCATCTTTGAAGAGAATCTA
1 TCATCTTTAAAGAGAATCTA
*
58766 TCATCTTTGAAGAG
1 TCATCTTTAAAGAG
58780 TGTAGATGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
20 23 0.70
21 2 0.06
22 8 0.24
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (20 bp):
TCATCTTTAAAGAGAATCTA
Found at i:58762 original size:20 final size:20
Alignment explanation
Indices: 58737--58779 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
58727 TCTTTAAAAT
58737 GAGAATCTATCATCTTTGAA
1 GAGAATCTATCATCTTTGAA
58757 GAGAATCTATCATCTTTGAA
1 GAGAATCTATCATCTTTGAA
58777 GAG
1 GAG
58780 TGTAGATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
GAGAATCTATCATCTTTGAA
Found at i:60012 original size:2 final size:2
Alignment explanation
Indices: 59999--60049 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
59989 TTTTAAGAAA
59999 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
60039 AT AT AT TT AT A
1 AT AT AT AT AT A
60050 AATAAGATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:60178 original size:21 final size:21
Alignment explanation
Indices: 60154--60202 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
60144 CATAAAATAA
60154 TATTTATAAAAGTACA-ATATT
1 TATTTATAAAAGTA-AGATATT
*
60175 TATTTATAAAATTAAGATATT
1 TATTTATAAAAGTAAGATATT
60196 TATTTAT
1 TATTTAT
60203 TTAAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
TATTTATAAAAGTAAGATATT
Found at i:60191 original size:135 final size:132
Alignment explanation
Indices: 60037--60280 Score: 339
Period size: 135 Copynumber: 1.8 Consensus size: 132
60027 ATATATATAT
* * *
60037 ATATATATTTATAAATAAGATATTTATTTACTTAGAAATATCAGAAAAT-GACTTCTAGGTGCTT
1 ATATATATTTATAAATAAGATATTTATTTACTTAAAAATATCAGAAAATGGACATCCAGGTGCTT
60101 TAAGACAACCCATTTCTTAATATT-AAGAAATAAATAAATAAAACATAAAATAATATTTATAAAA
66 TAAGACAACCC-TTTCTTAATATTGAA-AAATAAAT-AATAAAACATAAAATAATATTTATAAAA
60165 GTACA
128 GTACA
* * *
60170 ATATTTATTTATAAAATTAAGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGC
1 ATATATATTTAT-AAA-TAAGATATTTATTTACTTAAAAATATCAGAAAATGGACATCCAGGTGC
*** *
60235 TTTAAGATTTCCCTTTCTTAATATTGAAAAATAAATATTAAAACAT
64 TTTAAGACAACCCTTTCTTAATATTGAAAAATAAATAATAAAACAT
60281 GATTTATATT
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
133 11 0.11
134 12 0.12
135 52 0.54
136 22 0.23
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.37
Consensus pattern (132 bp):
ATATATATTTATAAATAAGATATTTATTTACTTAAAAATATCAGAAAATGGACATCCAGGTGCTT
TAAGACAACCCTTTCTTAATATTGAAAAATAAATAATAAAACATAAAATAATATTTATAAAAGTA
CA
Found at i:67211 original size:21 final size:22
Alignment explanation
Indices: 67185--67233 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
67175 CCTCACATAG
*
67185 CCGACATCTATA-TCTTTAGAT
1 CCGACATCTACATTCTTTAGAT
67206 CCGACATCTACATTCTTTAGAT
1 CCGACATCTACATTCTTTAGAT
67228 CCGACA
1 CCGACA
67234 ACTTTCCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (22 bp):
CCGACATCTACATTCTTTAGAT
Done.