Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002628.1 Hibiscus syriacus cultivar Beakdansim tig00005356_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: 279074
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:202875 original size:14 final size:14
Alignment explanation
Indices: 202856--202882 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
202846 TCCCGTGGTA
202856 TTTTCTTTGGGGAC
1 TTTTCTTTGGGGAC
202870 TTTTCTTTGGGGA
1 TTTTCTTTGGGGA
202883 TTTCTTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.52
Consensus pattern (14 bp):
TTTTCTTTGGGGAC
Found at i:202892 original size:3 final size:3
Alignment explanation
Indices: 202884--202909 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
202874 CTTTGGGGAT
202884 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
202910 TAGTGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:203119 original size:24 final size:24
Alignment explanation
Indices: 203085--203138 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
203075 CTGAAAAATC
203085 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
203109 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
203133 ATCAAA
1 ATCAAA
203139 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:203152 original size:24 final size:24
Alignment explanation
Indices: 203085--203152 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
203075 CTGAAAAATC
* * *
203085 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
203109 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
203133 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
203153 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:204028 original size:20 final size:20
Alignment explanation
Indices: 204005--204072 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
203995 AGAATCTCGT
**
204005 TGCGATTTACTAAATCGCAA
1 TGCGATTTAGAAAATCGCAA
*
204025 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTA-GAAAATCGCAA
* * *
204046 CGCGAATTTGGGAAATCGCAA
1 TGCG-ATTTAGAAAATCGCAA
204067 TGCGAT
1 TGCGAT
204073 AGTTAGAATC
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 10 0.26
21 25 0.66
22 3 0.08
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCGATTTAGAAAATCGCAA
Found at i:204041 original size:21 final size:21
Alignment explanation
Indices: 204016--204071 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
204006 GCGATTTACT
204016 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
204037 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
204058 AAATCGCAATGCGA
1 AAATCGCAATGCGA
204072 TAGTTAGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:218791 original size:19 final size:19
Alignment explanation
Indices: 218770--218805 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
218760 AATATATTTA
218770 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
218788 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
218806 GACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:220201 original size:20 final size:19
Alignment explanation
Indices: 220176--220220 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
220166 ATATTTTTAT
* *
220176 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
220196 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
220215 TATTTA
1 TATTTA
220221 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:220220 original size:29 final size:29
Alignment explanation
Indices: 220161--220226 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
220151 ATTGGGCCTG
* * * *
220161 TAATTATATTTTTATTATTTATTTATTTT
1 TAATAATATTTATATTATTTATATATATT
220190 TAATAATATTTATATGTATTTA-ATATATT
1 TAATAATATTTATAT-TATTTATATATATT
220219 TAATAATA
1 TAATAATA
220227 ATAGTAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (29 bp):
TAATAATATTTATATTATTTATATATATT
Found at i:220227 original size:3 final size:3
Alignment explanation
Indices: 220219--220319 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
220209 TTAATATATT
*
220219 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
220267 TAA TAA TGA TAA TAG TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
220315 TAA TA
1 TAA TA
220320 TGGATAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:220887 original size:113 final size:113
Alignment explanation
Indices: 220636--221080 Score: 687
Period size: 113 Copynumber: 4.0 Consensus size: 113
220626 GAATTATGCC
* * *
220636 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
220700 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
220747 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
220812 TATGAACTTTTTCTGGCAATGTTGATCCATCAAATGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
220860 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
220925 TATGAACTCTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
*
220973 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGGTGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** * * *
221038 TATGAACTCGAACTGGAAAAGCTGATCCTTCAAATGATAAATT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATT
221081 TGAATCTTTG
Statistics
Matches: 307, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
111 4 0.01
112 64 0.21
113 239 0.78
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAGGT
Found at i:221863 original size:82 final size:81
Alignment explanation
Indices: 221723--222579 Score: 1435
Period size: 82 Copynumber: 10.5 Consensus size: 81
221713 CCTACTGAAT
*
221723 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
221788 ATTGGTTTTTATCAAAC
66 ATTGG-TTTTATCAAAC
* *
221805 CAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
221870 ATTGGTTTTTATCAAAC
66 ATTGG-TTTTATCAAAC
221887 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
* * *
221952 ATTGGTTCTGTCTAAC
66 ATTGGTTTTATCAAAC
*
221968 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
* * *
222033 ATTGGTTCTGTCTAAC
66 ATTGGTTTTATCAAAC
*
222049 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
222114 ATTGGTTTTTATCAAAC
66 ATTGG-TTTTATCAAAC
*
222131 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
* * *
222196 ATTGGTTCTGTCTAAC
66 ATTGGTTTTATCAAAC
*
222212 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
222277 ATTGGTTTTTATCAAAC
66 ATTGG-TTTTATCAAAC
222294 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
* * *
222359 ATTGGTTATGTCTAAC
66 ATTGGTTTTATCAAAC
*
222375 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
222440 ATTGGTTTTTATCAAAC
66 ATTGG-TTTTATCAAAC
*
222457 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCACATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-A-ACATTCATCTTCCAAATTCAA
* * *
222522 TGATTGGTTCTGTCTAAC
64 TGATTGGTTTTATCAAAC
222540 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
222580 TGAGTCTCTT
Statistics
Matches: 733, Mismatches: 37, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
81 309 0.42
82 349 0.48
83 48 0.07
84 27 0.04
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (81 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
ATTGGTTTTATCAAAC
Found at i:222134 original size:163 final size:163
Alignment explanation
Indices: 221723--222579 Score: 1563
Period size: 163 Copynumber: 5.2 Consensus size: 163
221713 CCTACTGAAT
221723 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
*
221788 ATTGGTTTTTATCAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
66 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
* * *
221853 ATCTTCCAAATTCAATGATTGGTTTTTATCAAAC
131 ATCTTCCAAATTCAATGATTGG-TTCTGTCTAAC
*
221887 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
* * *
221952 ATTGG-TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
66 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
222016 ATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
131 ATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
222049 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
* *
222114 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATTC
66 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
222179 ATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
131 ATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
222212 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
*
222277 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTC
66 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
*
222342 ATCTTCCAAATTCAATGATTGGTTATGTCTAAC
131 ATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
222375 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
222440 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACAT
66 ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-AA-ACAT
*
222505 TCATCTTCCACATTCAATGATTGGTTCTGTCTAAC
129 TCATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
222540 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
222580 TGAGTCTCTT
Statistics
Matches: 671, Mismatches: 19, Indels: 5
0.97 0.03 0.01
Matches are distributed among these distances:
162 77 0.11
163 447 0.67
164 70 0.10
165 77 0.11
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (163 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
ATTGGTTTTTATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATAAACATTC
ATCTTCCAAATTCAATGATTGGTTCTGTCTAAC
Found at i:223730 original size:8 final size:8
Alignment explanation
Indices: 223717--223767 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 8
223707 CTTAACCCCC
223717 TTTTTTCT
1 TTTTTTCT
223725 TTTTTTCT
1 TTTTTTCT
*
223733 TCTTTTC-
1 TTTTTTCT
*
223740 TTTTTTCC
1 TTTTTTCT
*
223748 TTTTCTCT
1 TTTTTTCT
223756 TTTTTT-T
1 TTTTTTCT
223763 TTTTT
1 TTTTT
223768 AAGCATAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
7 12 0.32
8 25 0.68
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTCT
Found at i:223740 original size:16 final size:15
Alignment explanation
Indices: 223716--223767 Score: 70
Period size: 16 Copynumber: 3.5 Consensus size: 15
223706 CCTTAACCCC
223716 CTTTTTTCTTTTTTT
1 CTTTTTTCTTTTTTT
*
223731 CTTCTTTTCTTTTTTC
1 CTT-TTTTCTTTTTTT
*
223747 CTTTTCTCTTTTTTT
1 CTTTTTTCTTTTTTT
223762 -TTTTTT
1 CTTTTTT
223768 AAGCATAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 5 0.16
15 13 0.41
16 14 0.44
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
CTTTTTTCTTTTTTT
Found at i:223744 original size:23 final size:22
Alignment explanation
Indices: 223716--223767 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
223706 CCTTAACCCC
* *
223716 CTTTTTTCTTTTTTTCTTCTTTT
1 CTTTTTTCCTTTTCTCTT-TTTT
223739 CTTTTTTCCTTTTCTCTTTTTT
1 CTTTTTTCCTTTTCTCTTTTTT
*
223761 TTTTTTT
1 CTTTTTT
223768 AAGCATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
CTTTTTTCCTTTTCTCTTTTTT
Found at i:223751 original size:21 final size:20
Alignment explanation
Indices: 223727--223764 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
223717 TTTTTTCTTT
223727 TTTTCTTCTTTTCTTTTTTCC
1 TTTTC-TCTTTTCTTTTTTCC
223748 TTTTCTCTTTT-TTTTTT
1 TTTTCTCTTTTCTTTTTT
223765 TTTAAGCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTCTCTTTTCTTTTTTCC
Found at i:227313 original size:11 final size:11
Alignment explanation
Indices: 227289--227320 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
227279 TGAAATAAAT
227289 AAATGT-AA-A
1 AAATGTAAAGA
227298 AAATGTAAAGA
1 AAATGTAAAGA
227309 AAATGTAAAGA
1 AAATGTAAAGA
227320 A
1 A
227321 TGATTGCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 6 0.29
10 2 0.10
11 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.19
Consensus pattern (11 bp):
AAATGTAAAGA
Found at i:235198 original size:19 final size:19
Alignment explanation
Indices: 235177--235212 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
235167 AATATATTTA
235177 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
235195 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
235213 GACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:236602 original size:20 final size:19
Alignment explanation
Indices: 236579--236623 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
236569 TATTTTTTAT
* *
236579 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
236599 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
236618 TATTTA
1 TATTTA
236624 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:236613 original size:26 final size:30
Alignment explanation
Indices: 236574--236629 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
236564 AATTATATTT
*
236574 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
236601 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
236630 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:236630 original size:3 final size:3
Alignment explanation
Indices: 236622--236710 Score: 142
Period size: 3 Copynumber: 29.7 Consensus size: 3
236612 TTAATATATT
*
236622 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
236670 TGA TAA TAG TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
236711 TGGATAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:239646 original size:12 final size:12
Alignment explanation
Indices: 239629--239657 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
239619 AATCTAATAT
239629 ATTTATCAACTA
1 ATTTATCAACTA
239641 ATTTATCAACTA
1 ATTTATCAACTA
239653 ATTTA
1 ATTTA
239658 GATCAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTATCAACTA
Found at i:240168 original size:21 final size:19
Alignment explanation
Indices: 240144--240197 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
240134 ATTTGGAATC
240144 AACATGTTATAAAATTATGAA
1 AACATGTTATAAAATTA--AA
* *
240165 AACATTTTAGAAAAATTAAA
1 AACATGTTA-TAAAATTAAA
240185 AACATGTTATAAA
1 AACATGTTATAAA
240198 TCAATCAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 10 0.36
21 8 0.29
22 7 0.25
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (19 bp):
AACATGTTATAAAATTAAA
Found at i:240970 original size:16 final size:16
Alignment explanation
Indices: 240949--241007 Score: 109
Period size: 16 Copynumber: 3.7 Consensus size: 16
240939 CATTTAATAA
240949 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
240965 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
240981 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
240997 ATAAACGAACA
1 ATAAACGAACA
241008 TAAACGTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 41 1.00
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:241799 original size:14 final size:14
Alignment explanation
Indices: 241782--241814 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
241772 GAACGAACAT
241782 AAACGAACATAACC
1 AAACGAACATAACC
241796 AAACGAACATAACC
1 AAACGAACATAACC
*
241810 GAACG
1 AAACG
241815 TTCACGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:241824 original size:24 final size:24
Alignment explanation
Indices: 241752--241813 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
241742 ATAAATGAAT
* *
241752 GAACATAAACGCACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
241776 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCGAAC
*
241800 GAACATAACCGAAC
1 GAACATAAACGAAC
241814 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.53, C:0.26, G:0.11, T:0.10
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:245773 original size:44 final size:44
Alignment explanation
Indices: 245706--245791 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
245696 TGCAGTAGTG
* *
245706 AAAACCAATAATAATGTTAATTTATTATGCAGTAGAAAAATCTA
1 AAAAACAATAATAATGTTAATTTATTATGCAATAGAAAAATCTA
* * *
245750 AAAAACAATAATAAT-TATTATTTATTCTGCAATAGGAAAATC
1 AAAAACAATAATAATGT-TAATTTATTATGCAATAGAAAAATC
245792 CATTAATAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 1 0.03
44 35 0.97
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.33
Consensus pattern (44 bp):
AAAAACAATAATAATGTTAATTTATTATGCAATAGAAAAATCTA
Found at i:249140 original size:12 final size:11
Alignment explanation
Indices: 249074--249141 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 11
249064 AAAATTACAT
249074 TATTAAAAATA
1 TATTAAAAATA
249085 TATTAAAAATA
1 TATTAAAAATA
* * ***
249096 CACTATTGATA
1 TATTAAAAATA
249107 -ATT-AAAATA
1 TATTAAAAATA
*
249116 TTTTAAAAATA
1 TATTAAAAATA
249127 TATTAAAAATTA
1 TATTAAAAA-TA
249139 TAT
1 TAT
249142 AATACAACAA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
9 3 0.07
10 4 0.09
11 31 0.72
12 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:249204 original size:14 final size:14
Alignment explanation
Indices: 249182--249218 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
249172 TATTACAATG
*
249182 AACCTTAAACCTTA
1 AACCCTAAACCTTA
*
249196 AACCCTAAACTTTA
1 AACCCTAAACCTTA
249210 AACCCTAAA
1 AACCCTAAA
249219 TTATACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (14 bp):
AACCCTAAACCTTA
Found at i:250341 original size:20 final size:20
Alignment explanation
Indices: 250313--250352 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
250303 ACACGTTAAC
*
250313 AATGCATATTCTAGAATGCA
1 AATGCATATTCCAGAATGCA
*
250333 AATGTATATTCCAGAATGCA
1 AATGCATATTCCAGAATGCA
250353 TATTTCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGCATATTCCAGAATGCA
Found at i:250573 original size:35 final size:35
Alignment explanation
Indices: 250462--250575 Score: 167
Period size: 35 Copynumber: 3.3 Consensus size: 35
250452 TAGTAAATCA
*
250462 TCCGTTCTAGTTGAATCGAAAGTGCGATGCTTCCT
1 TCCGTTCTAATTGAATCGAAAGTGCGATGCTTCCT
*
250497 TCCATTCTAATTGAATCGAAAGTGCGATGCTTCCT
1 TCCGTTCTAATTGAATCGAAAGTGCGATGCTTCCT
** *
250532 TCCGTTCTTCTTGAATCGAAAGTGCGATGCCTCCCT
1 TCCGTTCTAATTGAATCGAAAGTGCGATG-CTTCCT
250568 T-CGTTCTA
1 TCCGTTCTA
250576 CTATAGACGA
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
35 65 0.92
36 6 0.08
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (35 bp):
TCCGTTCTAATTGAATCGAAAGTGCGATGCTTCCT
Found at i:252237 original size:20 final size:20
Alignment explanation
Indices: 252209--252248 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
252199 ACACGTTAAC
*
252209 AATGCATATTCTAGAATGCA
1 AATGCATATTCCAGAATGCA
*
252229 AATGTATATTCCAGAATGCA
1 AATGCATATTCCAGAATGCA
252249 TATTCCAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (20 bp):
AATGCATATTCCAGAATGCA
Found at i:255344 original size:3 final size:3
Alignment explanation
Indices: 255336--255385 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
255326 TTCTCACCTT
* *
255336 TTC TTC TTC TTC TTC TTC TT- TT- TGTC TTC ATC TCTC TTC ATC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC T-TC TTC TTC T-TC TTC TTC TTC
255381 TTC TT
1 TTC TT
255386 TAAAATCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.08
3 33 0.82
4 4 0.10
ACGTcount: A:0.04, C:0.30, G:0.02, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:261723 original size:21 final size:21
Alignment explanation
Indices: 261698--261737 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
261688 CATCATGCTC
* *
261698 CTCTCTTGACTTTGCATACTT
1 CTCTCTTGAATTTGAATACTT
261719 CTCTCTTGAATTTGAATAC
1 CTCTCTTGAATTTGAATAC
261738 ACCAAAAAAT
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:0.20, C:0.25, G:0.10, T:0.45
Consensus pattern (21 bp):
CTCTCTTGAATTTGAATACTT
Found at i:264490 original size:18 final size:18
Alignment explanation
Indices: 264467--264517 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
264457 GTTCTTAAGG
*
264467 AGTGGTACTTCGAGACAT
1 AGTGGTCCTTCGAGACAT
*
264485 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGAGACAT
*
264503 AGTGATCCTTCGAGA
1 AGTGGTCCTTCGAGA
264518 ATTTTCTACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:270410 original size:21 final size:21
Alignment explanation
Indices: 270359--270411 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
270349 ATTATGACTA
270359 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
270380 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
270401 TCGCAATGCGA
1 TCGCAATGCGA
270412 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:270444 original size:21 final size:21
Alignment explanation
Indices: 270401--270555 Score: 79
Period size: 21 Copynumber: 7.5 Consensus size: 21
270391 TTTTCCCAAT
** *
270401 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTCGAAAA
*
270421 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTCGAAAA
* **
270442 TCGCAATGCG-A-TACTGACTA
1 TCGCAATGCGAATTTC-GAAAA
** *
270462 TCGCAATGC-AATTTTCTTAAT
1 TCGCAATGCGAA-TTTCGAAAA
* * *
270483 TCGCATTGCGATTTTC-ATAAT
1 TCGCAATGCGAATTTCGA-AAA
**
270504 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATTTCGAAAA
* * *
270525 TCGCAATGTGAA-TACGTAAA
1 TCGCAATGCGAATTTCGAAAA
270545 TCGCAATGCGA
1 TCGCAATGCGA
270556 TTTACATAGC
Statistics
Matches: 102, Mismatches: 25, Indels: 16
0.71 0.17 0.11
Matches are distributed among these distances:
19 1 0.01
20 42 0.41
21 55 0.54
22 4 0.04
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGAATTTCGAAAA
Found at i:270446 original size:41 final size:41
Alignment explanation
Indices: 270401--270555 Score: 120
Period size: 41 Copynumber: 3.8 Consensus size: 41
270391 TTTTCCCAAT
270401 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
* * *** *
270442 TCGCAATGCG-AT-ACTGACTATCGCAATGC-AATTTTCTTAAT
1 TCGCAATGCGAATAAGT-A-AATCGCAATGCGAA-TTTGGAAAA
* * * * *
270483 TCGCATTGCGATTTTCA-TAATTCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGA--ATAAGTAAATCGCAATGCGAATTTGGAAAA
* *
270525 TCGCAATGTGAATACGTAAATCGCAATGCGA
1 TCGCAATGCGAATAAGTAAATCGCAATGCGA
270556 TTTACATAGC
Statistics
Matches: 84, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
39 2 0.02
40 6 0.07
41 48 0.57
42 22 0.26
43 3 0.04
44 2 0.02
45 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAA
Found at i:270462 original size:103 final size:102
Alignment explanation
Indices: 270339--270556 Score: 278
Period size: 103 Copynumber: 2.1 Consensus size: 102
270329 GTTTCCAGAT
* * * *
270339 TCGCAACGCGATTATGACTATCGCAATGCGATTTTC-CAATTTCGCGTTGCGATTTTCCCAATTC
1 TCGCAATGCGA-TATGACTATCGCAATGCAATTTTCTCAA-TTCGCATTGCGATTTTCACAATTC
* **
270403 GCAATGCGAA-TAAGTAAATCGCAATGCGAATTTGGAAAA
64 GCAATGCGAATTAAGAAAATCGCAATGCGAA-TACGAAAA
* *
270442 TCGCAATGCGATACTGACTATCGCAATGCAATTTTCTTAATTCGCATTGCGATTTTCATAATTCG
1 TCGCAATGCGATA-TGACTATCGCAATGCAATTTTCTCAATTCGCATTGCGATTTTCACAATTCG
* * *
270507 CAATGCGAATTAGGAAAATCGCAATGTGAATACGTAAA
65 CAATGCGAATTAAGAAAATCGCAATGCGAATACGAAAA
270545 TCGCAATGCGAT
1 TCGCAATGCGAT
270557 TTACATAGCG
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
102 2 0.02
103 79 0.79
104 19 0.19
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (102 bp):
TCGCAATGCGATATGACTATCGCAATGCAATTTTCTCAATTCGCATTGCGATTTTCACAATTCGC
AATGCGAATTAAGAAAATCGCAATGCGAATACGAAAA
Found at i:271134 original size:19 final size:19
Alignment explanation
Indices: 271110--271154 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
271100 GCAACGAGAG
*
271110 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
271129 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
271148 AATCGCA
1 AATCGCA
271155 TTGCAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:271191 original size:14 final size:14
Alignment explanation
Indices: 271172--271227 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
271162 TTTCATTTCG
271172 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
271186 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
271205 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
271219 CGTTGCGAT
1 CGTTGCGAT
271228 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:271206 original size:33 final size:33
Alignment explanation
Indices: 271164--271251 Score: 167
Period size: 33 Copynumber: 2.6 Consensus size: 33
271154 ATTGCAATTT
271164 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
271197 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
271230 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
271252 ATTATCTCGT
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 39 0.72
34 15 0.28
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:271253 original size:20 final size:20
Alignment explanation
Indices: 271219--271276 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
271209 GCGATTCTCT
**
271219 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
271239 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
271259 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
271277 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:273445 original size:21 final size:21
Alignment explanation
Indices: 273421--273487 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
273411 TCATTCCTCG
273421 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
273442 AGAGGCCACTTTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
273463 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
273484 AGAG
1 AGAG
273488 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:273445 original size:42 final size:42
Alignment explanation
Indices: 273369--273487 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
273359 GACTCGCCTG
* * * * * * *
273369 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
273411 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTT
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
273453 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
273488 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:274864 original size:14 final size:14
Alignment explanation
Indices: 274845--274880 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
274835 ATTGTTTAAT
274845 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
274859 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
274873 TGATTTGT
1 TGATTTGT
274881 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:275062 original size:19 final size:19
Alignment explanation
Indices: 274987--275053 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
274977 AAAAAGTACT
*
274987 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
275006 ATCGCAA--CG--A-GATA
1 ATCGCAACGCGAAATGAAA
275020 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
275039 ATCGCAACGCGAAAT
1 ATCGCAACGCGAAAT
275054 TAAATTCGCG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:275099 original size:33 final size:32
Alignment explanation
Indices: 275062--275185 Score: 169
Period size: 33 Copynumber: 3.8 Consensus size: 32
275052 ATTAAATTCG
275062 CGTTGCGATTTTCATTTCGCATTGCAATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCAATT-CCT
**
275095 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGC--AATTCCT
**
275128 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCAATTC-CT
275161 CGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGC
275186 GATAGTAATT
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 73 0.91
35 4 0.05
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCAATTCCT
Found at i:275140 original size:66 final size:66
Alignment explanation
Indices: 275055--275187 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
275045 ACGCGAAATT
*
275055 AAATTCGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
275120 G
66 G
** *
275121 AAATTAGCGTTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
275186 G
66 G
275187 A
1 A
275188 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:277704 original size:24 final size:24
Alignment explanation
Indices: 277670--277723 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
277660 CTGAAACATC
* *
277670 ATCAAAATCCGAGTATTGGCCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
277694 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
277718 ATCAAA
1 ATCAAA
277724 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:278531 original size:20 final size:21
Alignment explanation
Indices: 278506--278557 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
278496 TTTTCCTAAT
*
278506 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
278526 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
278547 TCGCAATGCGA
1 TCGCAATGCGA
278558 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:278571 original size:20 final size:20
Alignment explanation
Indices: 278546--278603 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
278536 AATTTGGAAA
* *
278546 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
*
278566 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
278586 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
278604 AAATCGCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:278610 original size:20 final size:20
Alignment explanation
Indices: 278542--278612 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
278532 TGCGAATTTG
* * *
278542 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATTCT
**
278562 GACTATCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
***
278582 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATTCT
278602 GAAAATCGCAA
1 GAAAATCGCAA
278613 TCATCTTCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAATCGCAACGAGATTCT
Found at i:278939 original size:20 final size:20
Alignment explanation
Indices: 278824--278931 Score: 128
Period size: 20 Copynumber: 5.4 Consensus size: 20
278814 ACACCGGGAA
* *
278824 ATCGCAACACGAAAATGGTT
1 ATCGCAACGCGAAAATGGCT
278844 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
278864 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
278884 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
278904 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
278924 ATCGCAAC
1 ATCGCAAC
278932 TAGAAAATCG
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.07
20 62 0.86
21 5 0.07
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Done.