Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008081.1 Hibiscus syriacus cultivar Beakdansim tig00110583_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: 45409
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:963 original size:32 final size:33
Alignment explanation
Indices: 922--983 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
912 AAGTTGACAA
922 GTTGGAAA-TTCATCTTGGTTGGTGGCCAACTT
1 GTTGGAAATTTCATCTTGGTTGGTGGCCAACTT
954 GTTGGAAATTTCATCTTGGTTGGTGGCCAA
1 GTTGGAAATTTCATCTTGGTTGGTGGCCAA
984 ACTTTGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.28
33 21 0.72
ACGTcount: A:0.19, C:0.15, G:0.29, T:0.37
Consensus pattern (33 bp):
GTTGGAAATTTCATCTTGGTTGGTGGCCAACTT
Found at i:10420 original size:19 final size:19
Alignment explanation
Indices: 10398--10485 Score: 72
Period size: 21 Copynumber: 4.4 Consensus size: 19
10388 AAAGTTTAAA
10398 AAATTATAAAATATTTATT
1 AAATTATAAAATATTTATT
*
10417 AAATTTATTAAAATA-TTATA
1 AAA-TTA-TAAAATATTTATT
10437 AAATTATTAATAA-ATTTATCT
1 AAATTA-TAA-AATATTTAT-T
*
10458 AAATACTATAAAATAATTATT
1 AAAT--TATAAAATATTTATT
*
10479 ATATTAT
1 AAATTAT
10486 CGAACTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
19 14 0.25
20 16 0.28
21 17 0.30
22 8 0.14
23 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTATAAAATATTTATT
Found at i:10428 original size:31 final size:31
Alignment explanation
Indices: 10393--10479 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
10383 TCAATAAAGT
*
10393 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAATATTATAAAATATTTATTAAATTTA
*
10424 TTAAAATATTATAAAAT-TATTAATAAATTTA
1 TTAAAATATTATAAAATAT-TTATTAAATTTA
* *
10455 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAATATTTATTA
10480 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 46 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
TTAAAATATTATAAAATATTTATTAAATTTA
Found at i:11145 original size:21 final size:21
Alignment explanation
Indices: 11116--11187 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
11106 TTCCAGATTC
*
11116 GCAAAGCGATTTTGGACTATT
1 GCAATGCGATTTTGGACTATT
*
11137 GCAATGCGATTTTGGAATATT
1 GCAATGCGATTTTGGACTATT
** *
11158 GCAATGCGAACTTGGACTATC
1 GCAATGCGATTTTGGACTATT
11179 GCAATGCGA
1 GCAATGCGA
11188 ATATGTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (21 bp):
GCAATGCGATTTTGGACTATT
Found at i:11186 original size:42 final size:42
Alignment explanation
Indices: 11130--11270 Score: 151
Period size: 42 Copynumber: 3.4 Consensus size: 42
11120 AGCGATTTTG
* * * *
11130 GACTATTGCAATGCGATTTTGGAATATTGCAATGCGAACTTG
1 GACTATCGCAATGCGAATTTGGAATATCGCAATGCGAACTTC
* * *
11172 GACTATCGCAATGCGAATATGTAA-ATCGCAATGCGATA-GTC
1 GACTATCGCAATGCGAATTTGGAATATCGCAATGCGA-ACTTC
* * * *
11213 GACTATCGCAATGCGAACTTCGACTATCGCAATACGAACTTC
1 GACTATCGCAATGCGAATTTGGAATATCGCAATGCGAACTTC
*
11255 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
11271 TTTACATATT
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 32 0.40
42 49 0.60
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
GACTATCGCAATGCGAATTTGGAATATCGCAATGCGAACTTC
Found at i:11188 original size:21 final size:21
Alignment explanation
Indices: 11127--11270 Score: 132
Period size: 21 Copynumber: 6.9 Consensus size: 21
11117 CAAAGCGATT
* **
11127 TTGGACTATTGCAATGCGATT
1 TTGGACTATCGCAATGCGAAC
* *
11148 TTGGAATATTGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
11169 TTGGACTATCGCAATGCGAA-
1 TTGGACTATCGCAATGCGAAC
* *
11189 TATGTA-AATCGCAATGCGATA-
1 T-TGGACTATCGCAATGCGA-AC
* *
11210 GTCGACTATCGCAATGCGAAC
1 TTGGACTATCGCAATGCGAAC
* *
11231 TTCGACTATCGCAATACGAAC
1 TTGGACTATCGCAATGCGAAC
* *
11252 TTCGACTATCGCATTGCGA
1 TTGGACTATCGCAATGCGA
11271 TTTACATATT
Statistics
Matches: 104, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
20 16 0.15
21 88 0.85
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (21 bp):
TTGGACTATCGCAATGCGAAC
Found at i:11208 original size:83 final size:83
Alignment explanation
Indices: 11114--11270 Score: 197
Period size: 83 Copynumber: 1.9 Consensus size: 83
11104 GTTTCCAGAT
** * * ** * * * *
11114 TCGCAAAGCGATTTTGGACTATTGCAATGCGATTTTGGAATATTGCAATGCGAACTTGGACTATC
1 TCGCAAAGCGATAGTCGACTATCGCAATGCGAACTTCGAATATCGCAATACGAACTTCGACTATC
11179 GCAATGCGAATATGTAAA
66 GCAATGCGAATATGTAAA
* *
11197 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAATACGAACTTCGACTATC
1 TCGCAAAGCGATAGTCGACTATCGCAATGCGAACTTCGAATATCGCAATACGAACTTCGACTATC
*
11262 GCATTGCGA
66 GCAATGCGA
11271 TTTACATATT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
83 61 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (83 bp):
TCGCAAAGCGATAGTCGACTATCGCAATGCGAACTTCGAATATCGCAATACGAACTTCGACTATC
GCAATGCGAATATGTAAA
Found at i:11284 original size:83 final size:84
Alignment explanation
Indices: 11112--11295 Score: 196
Period size: 83 Copynumber: 2.2 Consensus size: 84
11102 CAGTTTCCAG
* ** * * ** * * * *
11112 ATTCGCAAAGCGATTTTGGACTATTGCAATGCGATTTTGGAATATTGCAATGCGAACTTGGACTA
1 ATTCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGAATATCGCAATACGAACTTCGACTA
11177 TCGCAATGCGAATATGTAA
66 TCGCAATGCGAATATGTAA
*
11196 A-TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGACTATCGCAATACGAACTTCGACTA
1 ATTCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGAATATCGCAATACGAACTTCGACTA
*
11260 TCGCATTGCG-AT-T-TACA
66 TCGCAATGCGAATATGTA-A
*
11277 TATTCGCATTGCGATAGTC
1 -ATTCGCAATGCGATAGTC
11296 CAAAATCGCA
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
80 2 0.02
81 2 0.02
82 3 0.04
83 75 0.90
84 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (84 bp):
ATTCGCAATGCGATAGTCGACTATCGCAATGCGAACTTCGAATATCGCAATACGAACTTCGACTA
TCGCAATGCGAATATGTAA
Found at i:11304 original size:83 final size:83
Alignment explanation
Indices: 11158--11311 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 83
11148 TTGGAATATT
* * * **
11158 GCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATCGCA
1 GCAATACGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAAATCGCA
11223 ATGCGAACTTCGACTATC
66 ATGCGAACTTCGACTATC
* *
11241 GCAATACGAACTTCGACTATCGCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCCAAAATC
1 GCAATACGAACTTCGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCCAAAATC
*
11303 GCATTGCGA
63 GCAATGCGA
11312 TAGTCCAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
80 2 0.03
81 2 0.03
82 3 0.05
83 53 0.88
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (83 bp):
GCAATACGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAAATCGCA
ATGCGAACTTCGACTATC
Found at i:11306 original size:21 final size:21
Alignment explanation
Indices: 11280--11324 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
11270 ATTTACATAT
11280 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
11301 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
11322 TCG
1 TCG
11325 TAACGACTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:11420 original size:6 final size:6
Alignment explanation
Indices: 11409--11451 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
11399 AACACGTATT
11409 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
11452 CGAGACGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.30, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:11992 original size:6 final size:6
Alignment explanation
Indices: 11937--11994 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
11927 GTCCGTCTCG
*
11937 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGG GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
11981 GGTCGT GGTCGT GG
1 GGTCGT GGTCGT GG
11995 GAATTATCGA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
5 20 0.39
6 31 0.61
ACGTcount: A:0.00, C:0.17, G:0.57, T:0.26
Consensus pattern (6 bp):
GGTCGT
Found at i:13932 original size:23 final size:23
Alignment explanation
Indices: 13906--13953 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
13896 ATAAAGTACA
*
13906 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
13929 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
13952 AT
1 AT
13954 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:14397 original size:23 final size:23
Alignment explanation
Indices: 14370--14442 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
14360 ACACTTTACA
*
14370 ATATAACCACTACCTATTATATT
1 ATATAACCACTACCTATTACATT
*
14393 ATATAAACGA-TACCTATTACATT
1 ATAT-AACCACTACCTATTACATT
* * *
14416 ATATAAGCGCTACCTATTACATC
1 ATATAACCACTACCTATTACATT
14439 ATAT
1 ATAT
14443 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
22 2 0.05
23 36 0.86
24 4 0.10
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAACCACTACCTATTACATT
Found at i:14916 original size:39 final size:39
Alignment explanation
Indices: 14862--14947 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
14852 CAAGTTGTAG
*
14862 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
14901 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
14940 ATTTTGAT
1 ATTTTGAT
14948 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:15226 original size:18 final size:18
Alignment explanation
Indices: 15203--15239 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
15193 CGAAATATAT
15203 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
15221 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
15239 A
1 A
15240 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:15699 original size:23 final size:23
Alignment explanation
Indices: 15673--15735 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
15663 ATATAACCAC
15673 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
15696 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
15719 TACCTATTACATCATAT
1 TACCTATTACATTATAT
15736 GTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:16138 original size:25 final size:25
Alignment explanation
Indices: 16081--16146 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
16071 CACTCAAAAG
*
16081 ATGTATATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
***
16106 ACAAACATACCTAAATATGTAGTTA
1 ATGTACATACCTAAATATGTAGTTA
*
16131 TTGTACATACCTAAAT
1 ATGTACATACCTAAAT
16147 TTAATGATAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (25 bp):
ATGTACATACCTAAATATGTAGTTA
Found at i:19142 original size:183 final size:183
Alignment explanation
Indices: 18617--19108 Score: 878
Period size: 183 Copynumber: 2.7 Consensus size: 183
18607 TTAAAATTAC
*
18617 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
18682 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCAGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCAGTT
* *
18747 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
* *
18800 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
18865 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCAGTT
18930 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
*
18983 CGACACTTTTTAACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
19047 GATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACC
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACC
19109 GATAGCATTG
Statistics
Matches: 296, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 293 0.99
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCAGTT
ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
Found at i:20615 original size:3 final size:3
Alignment explanation
Indices: 20607--20687 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
20597 ACTTGTTTGG
* * * **
20607 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
20655 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
20688 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:20624 original size:12 final size:12
Alignment explanation
Indices: 20611--20699 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
20601 GTTTGGATCA
* *
20611 TCATCTTCATCA
1 TCATCGTCATCT
* *
20623 TCATCATCATCA
1 TCATCGTCATCT
* *
20635 TCGTCATCATCT
1 TCATCGTCATCT
* *
20647 TCATCGCCAGCT
1 TCATCGTCATCT
*
20659 TCATCGTCATCA
1 TCATCGTCATCT
20671 TCATCGTCATCT
1 TCATCGTCATCT
*
20683 TCATCGTCAGCT
1 TCATCGTCATCT
20695 TCATC
1 TCATC
20700 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:20630 original size:18 final size:18
Alignment explanation
Indices: 20611--20702 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
20601 GTTTGGATCA
* *
20611 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
20629 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
20647 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
20665 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
20683 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
20701 TC
1 TC
20703 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:20663 original size:36 final size:36
Alignment explanation
Indices: 20623--20699 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
20613 ATCTTCATCA
*
20623 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
20659 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
20695 TCATC
1 TCATC
20700 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:20702 original size:6 final size:6
Alignment explanation
Indices: 20611--20702 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
20601 GTTTGGATCA
* * * * * * * *
20611 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
20659 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
20703 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:22398 original size:199 final size:198
Alignment explanation
Indices: 22149--23313 Score: 2115
Period size: 199 Copynumber: 5.9 Consensus size: 198
22139 TTTAAATTAG
*
22149 TATCGACACAAACTATATTAGTGTCGACACATTATTTAAACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
22214 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
22279 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGGAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAA
22344 AAAA
195 AAAA
22348 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
22413 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
22478 CGACAC-TTTT-TATATGGATCGACATTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
22541 AAA
196 AAA
22544 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
22609 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
22674 CGACACTTTTTATATATGGATCGACACTATATGTGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
22739 AAA
196 AAA
* *
22742 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACTGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
22807 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
22871 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
22934 AAA
196 AAA
*
22937 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
23002 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
23067 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACACTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
23132 AAAA
195 AAAA
* *
23136 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTAGA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* * *
23201 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGA
* *
23266 TTGACACTTTTTTATATATGGATCGACACTTTATGGGTACACCCTGTT
130 TCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
23314 GGCCATATTG
Statistics
Matches: 937, Mismatches: 21, Indels: 14
0.96 0.02 0.01
Matches are distributed among these distances:
195 174 0.19
196 162 0.17
197 68 0.07
198 224 0.24
199 250 0.27
200 21 0.02
201 38 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (198 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:23002 original size:393 final size:393
Alignment explanation
Indices: 22149--23313 Score: 2107
Period size: 393 Copynumber: 2.9 Consensus size: 393
22139 TTTAAATTAG
22149 TATCGACACAAACTATATTAGTGTCGACACATTATTTAAACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAAACATATTCTCTCATAAAACCGGTATA
22214 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
22279 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGGGAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GGAAA
*
22344 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGG
22409 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTG
260 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTG
*
22474 GGATCGACACTTTTTATATGGATCGACATTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
324 GGATCGACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAA
22539 AAAAA
389 AAAAA
*
22544 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAAACATATTCTCTCATAAAACCGGTATA
22609 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
22674 CGACACTTTTTATATATGGATCGACACTATATGTGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
*
22739 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACTGGT
196 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGT
22804 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGG
261 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGG
22869 ATCGACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
326 ATCGACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
22934 AAA
391 AAA
*
22937 TATCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAAACATATTCTCTCATAAAACCGGTATA
23002 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
23067 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACACTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAA
23132 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-TCG
195 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACT-G
* * * *
23196 GTAGACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTT
259 GTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATG-ATT
* *
23261 TGGGATTGACACTTTTTTATATATGGATCGACACTTTATGGGTACACCCTGTT
322 TGGGATCGACAC--TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTT
23314 GGCCATATTG
Statistics
Matches: 745, Mismatches: 18, Indels: 10
0.96 0.02 0.01
Matches are distributed among these distances:
393 261 0.35
394 241 0.32
395 193 0.26
396 13 0.02
398 4 0.01
399 33 0.04
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (393 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAAACATATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACTGGT
ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGG
ATCGACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:23477 original size:19 final size:19
Alignment explanation
Indices: 23431--23479 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
23421 TTATATTCAC
*
23431 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
23450 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
*
23469 TTACAAAATTA
1 ATACAAAATTA
23480 ACCCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:25316 original size:32 final size:32
Alignment explanation
Indices: 25274--25334 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
25264 TTAATATCAC
*
25274 CCCTTAACACCCCAACTTCTTTCACCACTTCA
1 CCCTCAACACCCCAACTTCTTTCACCACTTCA
* *
25306 CCCTCAACACCTCTACTTCTTTCACCACT
1 CCCTCAACACCCCAACTTCTTTCACCACT
25335 CCATCTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.30
Consensus pattern (32 bp):
CCCTCAACACCCCAACTTCTTTCACCACTTCA
Found at i:25393 original size:21 final size:21
Alignment explanation
Indices: 25368--25432 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
25358 CCCCTTATGC
* *
25368 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
25389 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
25410 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
25431 CT
1 CT
25433 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:27711 original size:21 final size:19
Alignment explanation
Indices: 27664--27711 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
27654 TCCGGTATCA
27664 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
27683 TTGATACCGGTTTTTATCATAT
1 TT-TTACCGG-TTTTATCAT-T
27705 TTTTACC
1 TTTTACC
27712 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 6 0.25
21 13 0.54
22 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:27863 original size:17 final size:18
Alignment explanation
Indices: 27841--27883 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
27831 ATATATCCGG
27841 TATCATT-TTACCGGTTT
1 TATCATTGTTACCGGTTT
27858 TATCATTTTGTTACCGGTTT
1 TATCA--TTGTTACCGGTTT
27878 TATCAT
1 TATCAT
27884 ATTTTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 5 0.22
18 1 0.04
19 2 0.09
20 15 0.65
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (18 bp):
TATCATTGTTACCGGTTT
Found at i:27891 original size:20 final size:19
Alignment explanation
Indices: 27846--27891 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
27836 TCCGGTATCA
27846 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
27865 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
27886 TTTTAC
1 TTTTAC
27892 ATGGTATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.17, C:0.15, G:0.11, T:0.57
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:27958 original size:181 final size:182
Alignment explanation
Indices: 27631--28104 Score: 700
Period size: 182 Copynumber: 2.6 Consensus size: 182
27621 CGTACTTACG
*
27631 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGG-TT
* * *
27696 TTATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTA
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTA
* *
27761 TAGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
27813 AAAGTATCGACACTTTTAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
27878 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
27943 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * ** * *
27995 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGATTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
28059 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
28105 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
181 107 0.41
182 155 0.59
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:28566 original size:227 final size:227
Alignment explanation
Indices: 28171--28655 Score: 855
Period size: 227 Copynumber: 2.1 Consensus size: 227
28161 ACCTACTTTT
*
28171 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
28236 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
28301 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* *
28366 CAAATATAATAAT-ATATGTTTTCAACAGTGAA
196 CAAAGATAATAATAATATATTTTC-ACAGTGAA
28398 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
* *
28463 ATTTTTTTAATATTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
*
28528 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
*
28593 TAAAGATAATAATAAATATATTTTCACAGTGAA
196 CAAAGATAATAAT-AATATATTTTCACAGTGAA
* *
28626 ATAAGTATAGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
28656 GATAATTTAC
Statistics
Matches: 246, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
227 201 0.82
228 36 0.15
229 9 0.04
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (227 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTAATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAAGATAATAATAATATATTTTCACAGTGAA
Found at i:30038 original size:28 final size:28
Alignment explanation
Indices: 29985--30039 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
29975 ATTTATCATT
* * *
29985 GGATTGAATTATAATTTTACACTTTTAA
1 GGATTGAATAAAAATTATACACTTTTAA
30013 GGATTGAATAAAAATTATATCA-TTTTA
1 GGATTGAATAAAAATTATA-CACTTTTA
30040 GAGGGGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (28 bp):
GGATTGAATAAAAATTATACACTTTTAA
Found at i:30749 original size:23 final size:24
Alignment explanation
Indices: 30702--30755 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
30692 CATTTTAATA
30702 AAAATATTAATTATTAACATATTT
1 AAAATATTAATTATTAACATATTT
* * *
30726 AAAATA-TATTTATTAATATTTTT
1 AAAATATTAATTATTAACATATTT
30749 AATAATA
1 AA-AATA
30756 ATATAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATTAATTATTAACATATTT
Found at i:31204 original size:23 final size:22
Alignment explanation
Indices: 31177--31234 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 22
31167 TAGTCTAATA
31177 ATATTATAA-AAATTCTTTAAAAT
1 ATATTATAATAAA-T-TTTAAAAT
31200 ATATTTATTAATAAATTTTAAAAT
1 ATA-TTA-TAATAAATTTTAAAAT
*
31224 ATAATATAATA
1 ATATTATAATA
31235 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 5 0.16
23 5 0.16
24 14 0.45
25 4 0.13
26 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTATAATAAATTTTAAAAT
Found at i:31412 original size:21 final size:21
Alignment explanation
Indices: 31373--31414 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31363 TAAATTATTC
31373 TAATATTTTTAAAATAATAAT
1 TAATATTTTTAAAATAATAAT
*
31394 TAAT-TTTTTATAATAAATAAT
1 TAATATTTTTAAAAT-AATAAT
31415 ATTATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTTAAAATAATAAT
Found at i:38430 original size:4 final size:4
Alignment explanation
Indices: 38421--38446 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
38411 TCGATACCGT
38421 AGGA AGGA AGGA AGGA AGGA AGGA AG
1 AGGA AGGA AGGA AGGA AGGA AGGA AG
38447 AAGAACCTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (4 bp):
AGGA
Found at i:40036 original size:19 final size:19
Alignment explanation
Indices: 40012--40052 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
40002 AAATTAATAA
40012 AACCCTCAAATTCCGATTC
1 AACCCTCAAATTCCGATTC
* **
40031 AACCCTTATTTTCCGATTC
1 AACCCTCAAATTCCGATTC
40050 AAC
1 AAC
40053 GATTTGATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (19 bp):
AACCCTCAAATTCCGATTC
Found at i:42984 original size:21 final size:21
Alignment explanation
Indices: 42954--43008 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
42944 CGGTTCAACC
42954 TAAATATTTTTAAT-TTTTTAT
1 TAAAT-TTTTTAATATTTTTAT
**
42975 TAAATGTTTTTGGTATTTTTAT
1 TAAAT-TTTTTAATATTTTTAT
*
42997 TTAATTTTTTAA
1 TAAATTTTTTAA
43009 ATAATTATCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (21 bp):
TAAATTTTTTAATATTTTTAT
Found at i:43428 original size:53 final size:54
Alignment explanation
Indices: 43340--43447 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 54
43330 CATAATCACC
* * *
43340 TTTAGAAATTATCAGTTTCCTGTCAATCGATACTTTGA-ATAAATTTCTTCGTT
1 TTTAAAAATTATCAGTTTCCTGTCAATCGAGACTTTGAGATAAACTTCTTCGTT
* * * *
43393 TTTAAAAATTATCAG-TTCTTTGTCAATTGAGACTTTTAGATAGACTTCTTCGTT
1 TTTAAAAATTATCAGTTTC-CTGTCAATCGAGACTTTGAGATAAACTTCTTCGTT
43447 T
1 T
43448 GCTGAAGTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
52 3 0.07
53 29 0.63
54 14 0.30
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (54 bp):
TTTAAAAATTATCAGTTTCCTGTCAATCGAGACTTTGAGATAAACTTCTTCGTT
Found at i:44222 original size:15 final size:15
Alignment explanation
Indices: 44202--44231 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
44192 AACCCTACAA
44202 AGGTTAACATAGTTG
1 AGGTTAACATAGTTG
44217 AGGTTAACATAGTTG
1 AGGTTAACATAGTTG
44232 CAAACACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.27, T:0.33
Consensus pattern (15 bp):
AGGTTAACATAGTTG
Done.