Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004489.1 Hibiscus syriacus cultivar Beakdansim tig00009889_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: 58241
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:282 original size:17 final size:17
Alignment explanation
Indices: 260--300 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
250 ACAAAGCATA
*
260 TGGGTATAAATCATGTT
1 TGGGTAGAAATCATGTT
*
277 TGGGTAGAAATCCTGTT
1 TGGGTAGAAATCATGTT
*
294 TCGGTAG
1 TGGGTAG
301 GATTTACTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (17 bp):
TGGGTAGAAATCATGTT
Found at i:636 original size:55 final size:55
Alignment explanation
Indices: 570--673 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
560 TCAAATGATT
* *
570 CATGAAGAAGGATATATGTTGAATCAAGAAATTTGAAACTGATTAAAGAACGATC
1 CATGAAGAAGGACATATGATGAATCAAGAAATTTGAAACTGATTAAAGAACGATC
* * *
625 CATGAAGAAGGACATCTGATGAATCAAGAAATTTGAACCTGATTGAAGA
1 CATGAAGAAGGACATATGATGAATCAAGAAATTTGAAACTGATTAAAGA
674 CTTCTTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (55 bp):
CATGAAGAAGGACATATGATGAATCAAGAAATTTGAAACTGATTAAAGAACGATC
Found at i:1355 original size:9 final size:9
Alignment explanation
Indices: 1333--1361 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1323 AGAGAGAAAT
1333 GAGATAAGG
1 GAGATAAGG
1342 G-GATAAGG
1 GAGATAAGG
1350 GAGATAAGG
1 GAGATAAGG
1359 GAG
1 GAG
1362 CAAATGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.48, T:0.10
Consensus pattern (9 bp):
GAGATAAGG
Found at i:7078 original size:42 final size:41
Alignment explanation
Indices: 7031--7124 Score: 134
Period size: 42 Copynumber: 2.3 Consensus size: 41
7021 TTATAAGTCT
* *
7031 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCC
1 TTCGGGCCATCAGTAAGTCTTTCGAGCAAGATG-ATAAATCC
* * *
7073 TTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCC
1 TTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAATCC
7114 TTCGGGCCATC
1 TTCGGGCCATC
7125 CATAAGACCT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 16 0.35
42 30 0.65
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.31
Consensus pattern (41 bp):
TTCGGGCCATCAGTAAGTCTTTCGAGCAAGATGATAAATCC
Found at i:7833 original size:42 final size:42
Alignment explanation
Indices: 7720--7833 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
7710 TCCAAAATTT
* * *
7720 ATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGC
1 ATAAGTCCTTCAGGCCATCTATAAGCCTTTCGAGCACGATGC
* * * *
7762 TTAAATCCTTC-GGTTCATCTGTAAGCCTTTCGAGCACGATG-
1 ATAAGTCCTTCAGG-CCATCTATAAGCCTTTCGAGCACGATGC
*
7803 ATATGTCCTTCAGGCCATCTATAAGACCTTT
1 ATAAGTCCTTCAGGCCATCTATAAG-CCTTT
7834 GGGCATATTT
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 19 0.33
42 38 0.67
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (42 bp):
ATAAGTCCTTCAGGCCATCTATAAGCCTTTCGAGCACGATGC
Found at i:7894 original size:232 final size:233
Alignment explanation
Indices: 6702--8081 Score: 2093
Period size: 233 Copynumber: 5.9 Consensus size: 233
6692 AAAAAATGAA
*
6702 ATGAGAAAGGTTTCTCATTGAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
*
6767 CTAGTAAAATATTTCCAAAATTTATAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
66 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
* * * * * *
6832 TTAAATCCTTTGGGTCATCTTTAAGTCTTTCGATCAAGATGATAAGTCATTCGGGCTATTCATAA
131 TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
6897 GACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
196 GACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
*
6935 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTCC
1 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* *
7000 CTAGTAAAATATTTTCAAAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
66 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
7065 TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
131 TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
*
7130 GACCTTTGGGCAGGATATTTTCACATGTCTATCAAAAT
196 GACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
*
7168 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGATATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* * *
7233 CTAGTAAAATATTTCCAAATTTTATAATTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGACGC
66 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
* * * *
7298 TTAAATCCTTCGGGTCATCTGTAAGACTTTTGAGCAAGATGATAAGTCCTTTGGGCCGTCCATAA
131 TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
* * * * **
7363 TACCTTCGGGCAAGATGTTTTCACATGTTTATTTAAAT
196 GACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
*
7401 ATGAGAAAGATTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* * * * * *
7466 CTAGTAAAATATTTCTAAAATTTATAAGTCATTCGGGCCATAATTAAGTC-TTAGAGCATGATGA
66 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
* * * * *
7530 TTAAATCATTCGGGTTATCTGTAAGAT-TTT-GAGTAAGATGATAAGTCCTTTGAGCCATCCATA
131 TTAAATCCTTCGGGTCATCTGTAAG-TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATA
* * * *
7593 AGACCTTCGGGTAGGATGTTCTCACATGTCTATCGAAAT
195 AGACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
* * ** * *
7632 ATGAGAAAGATTTCTCATTGAAAAATGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* * *
7697 CTAGTAAATTATTTCCAAAATTTATAAGTCCTTCAGGCCATCAATAAGTCTTTCGAGCATGATGC
66 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
* * * * * *
7762 TTAAATCCTTCGGTTCATCTGTAAGCCTTTCGAGCACGATGATATGTCCTTCAGGCCATCTATAA
131 TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
* * *
7827 GACCTTTGGGCA-TATTTTTTCACATGTCTATCGAAAT
196 GACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
* * *
7864 ATGAGAAAGGTTTCTCATTTAAATATGAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTAC
1 ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
* * *
7929 CTAGTAAACTATTTCAAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATAATGC
66 CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
* * * *
7994 CTAAATCCTTCTGGTCATCTGTAAGTCTTTCTAGCAAGATGATAAGTCCTTCGAGCCATCCATAA
131 TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
8059 GACCTTTGGGCAGGATGTTTTCA
196 GACCTTTGGGCAGGATGTTTTCA
8082 AAGGTCCCTC
Statistics
Matches: 1040, Mismatches: 102, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
231 166 0.16
232 285 0.27
233 589 0.57
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (233 bp):
ATGAGAAAGGTTTCTCATTTAAATCTTAAATTTGAGATTTTTGAAAAGTAAGAAAGGTTTCTTAC
CTAGTAAAATATTTCCAAAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGC
TTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
GACCTTTGGGCAGGATGTTTTCACATGTCTATCAAAAT
Found at i:8326 original size:3 final size:3
Alignment explanation
Indices: 8318--8390 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
8308 ATATTACCAC
8318 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8366 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
8391 GTAGGATCCC
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:14657 original size:46 final size:47
Alignment explanation
Indices: 14590--14683 Score: 129
Period size: 46 Copynumber: 2.0 Consensus size: 47
14580 TTTTGTTTAT
* *
14590 CCTAACCTCATGTCATCTAGTTCGCATTC-TTATTCAAAAAATTAAA
1 CCTAACCGCATGTCATCTAGTTCGCATACATTATTCAAAAAATTAAA
*
14636 CCTAACCGCATGATC-TCTAGTTCGCATACATTTATTCAAGAAATTAAA
1 CCTAACCGCATG-TCATCTAGTTCGCATACA-TTATTCAAAAAATTAAA
14684 ATTACACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
46 24 0.57
47 2 0.05
48 16 0.38
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (47 bp):
CCTAACCGCATGTCATCTAGTTCGCATACATTATTCAAAAAATTAAA
Found at i:18060 original size:16 final size:16
Alignment explanation
Indices: 18039--18074 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
18029 AATCATAGTG
18039 TTTTTTTTCTTTTTGC
1 TTTTTTTTCTTTTTGC
*
18055 TTTTTTTTCTTTTTTC
1 TTTTTTTTCTTTTTGC
18071 TTTT
1 TTTT
18075 ACTTTGAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (16 bp):
TTTTTTTTCTTTTTGC
Found at i:18736 original size:6 final size:6
Alignment explanation
Indices: 18712--18774 Score: 63
Period size: 7 Copynumber: 9.5 Consensus size: 6
18702 TCATTGTATT
18712 TTTTTAC TTTTTGC TTTTTC TTTTTTTC TTTTTC TTTTTC TTTTTTC TTTTTTC
1 TTTTT-C TTTTT-C TTTTTC --TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC
*
18766 TTTTAC TTT
1 TTTTTC TTT
18775 GAAACACAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
6 21 0.41
7 24 0.47
8 6 0.12
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:18763 original size:20 final size:20
Alignment explanation
Indices: 18711--18774 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 20
18701 ATCATTGTAT
*
18711 TTTTTTACTTTTTGCTTTTTC
1 TTTTTT-CTTTTTTCTTTTTC
18732 TTTTTT-TCTTTTTCTTTTTC
1 TTTTTTCT-TTTTTCTTTTTC
*
18752 TTTTTTCTTTTTTCTTTTAC
1 TTTTTTCTTTTTTCTTTTTC
18772 TTT
1 TTT
18775 GAAACACAAC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.03
20 31 0.79
21 7 0.18
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTTCTTTTTTCTTTTTC
Found at i:18991 original size:3 final size:3
Alignment explanation
Indices: 18983--19021 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
18973 TGGATCGTGC
*
18983 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19022 GGTAATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20002 original size:233 final size:233
Alignment explanation
Indices: 19256--20002 Score: 1088
Period size: 233 Copynumber: 3.2 Consensus size: 233
19246 GAGGGACCTT
* *
19256 TGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTAATCATCTTGCTCGAAAGACT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATAGCCCGAAGGACTTATCATCTTGCTCGAAAGACT
*
19321 TACAGATGACCCGAAGGATTTAGGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT
66 TACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT
* * *
19386 AAATTTTGGAAATAGTTTACTAGGTAAAAAAACATTTCTTACTTTTCAGAAATTTCAAATTTCAG
131 AAATTTTGGAAATAGTTTACTAGGT-AAGAAACCTTTCTTACTTTTCAAAAATTTCAAATTTCAG
19451 ATTTAAATGAGAAA-CATTTCTCT-TATTTCGATAGACATG
195 ATTTAAATGAGAAATC-TTTCT-TATATTTCGATAGACATG
** * * * * *
19490 TGAAAACATTATGTCCAAAGGTCTTATGGATAACTCGAATGACTTATCATCTTGCTCGAAAGGCT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATAGCCCGAAGGACTTATCATCTTGCTCGAAAGACT
* * * * *
19555 TACAAATGACCCGAACGATTTAAGCATCATCCTCGAAAGACTTACTAATGGACCGAAGGACTTAT
66 TACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT
19620 AAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAATTTCAGA
131 AAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAATTTCAGA
* * *
19685 CTTAAATGAGAAATATTTCTCATATTTCGATAGACATG
196 TTTAAATGAGAAATCTTTCTTATATTTCGATAGACATG
* * * *
19723 TAAAAACATCCT-ACCAGAAGGTCTTATGGATAGCCC-AAGTGACTTATCATCTTGCTCAAAAGT
1 TGAAAACATCCTGCCCA-AAGGTCTTATGGATAGCCCGAAG-GACTTATCATCTTGCTCGAAAGA
* *
19786 CTTACAGATGACCCGAAGGATTTAAGCGTCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTT
64 CTTACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* * * *
19851 ATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTATTTTTCAAAAATCTCAAATTTAA
129 ATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAATTTCA
* *
19916 GATTTAAATGAGAAATCTTTCTTATATTTTGAAAGACATG
194 GATTTAAATGAGAAATCTTTCTTATATTTCGATAGACATG
* * * *
19956 TGAAAACATCCTGCCCGAAGGTCTTATTGATGGCCCAAAGGACTTAT
1 TGAAAACATCCTGCCCAAAGGTCTTATGGATAGCCCGAAGGACTTAT
20003 AAAATTTGGA
Statistics
Matches: 456, Mismatches: 51, Indels: 13
0.88 0.10 0.03
Matches are distributed among these distances:
232 5 0.01
233 306 0.67
234 145 0.32
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (233 bp):
TGAAAACATCCTGCCCAAAGGTCTTATGGATAGCCCGAAGGACTTATCATCTTGCTCGAAAGACT
TACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAT
AAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAATTTCAGA
TTTAAATGAGAAATCTTTCTTATATTTCGATAGACATG
Found at i:20056 original size:150 final size:150
Alignment explanation
Indices: 19828--20152 Score: 519
Period size: 150 Copynumber: 2.2 Consensus size: 150
19818 GCTCGAAAGA
* * * *
19828 CTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
1 CTTATTGATGGCCCAAAGGACTTATAAAATTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
* *
19893 TTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAATC-TTTCTTATATTTTGAAAGACATGT
66 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAA-CATTTCTCATATTTTGAAAGACATGT
*
19957 GAAAACATCCTGCCCGAAGGT
130 GAAAACATCCTGCCCAAAGGT
19978 CTTATTGATGGCCCAAAGGACTTATAAAATTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
1 CTTATTGATGGCCCAAAGGACTTATAAAATTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
* *
20043 CTTTTCAAAAATCTCAAATTTAAGATTTGAATGAGAAACATTTCTCATATTTTGATAGACATGTG
66 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACATTTCTCATATTTTGAAAGACATGTG
20108 AAAACATCCTGCCCAAAGGT
131 AAAACATCCTGCCCAAAGGT
* *
20128 CTTATGGATGGCTCGAAA-GACTTAT
1 CTTATTGATGGC-CCAAAGGACTTAT
20153 TATCTTGCTC
Statistics
Matches: 162, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
149 1 0.01
150 157 0.97
151 4 0.02
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (150 bp):
CTTATTGATGGCCCAAAGGACTTATAAAATTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACATTTCTCATATTTTGAAAGACATGTG
AAAACATCCTGCCCAAAGGT
Found at i:20328 original size:383 final size:383
Alignment explanation
Indices: 19610--20385 Score: 1250
Period size: 383 Copynumber: 2.0 Consensus size: 383
19600 TAATGGACCG
* *
19610 AAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC
1 AAGGACTTATAAAATTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTC
* *
19675 AAATTTCAGACTTAAATGAGAAATATTTCTCATATTTCGATAGACATGTAAAAACATCCTACCAG
66 AAATTTAAGACTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTAAAAACATCCTACCAG
* *
19740 AAGGTCTTATGGATAGCCCAAGTGACTTATCATCTTGCTCAAAAGTCTTACAGATGACCCGAAGG
131 AAGGTCTTATGGATAGCCCAAGAGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGG
* *
19805 ATTTAAGCGTCATGCTCGAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAATATTT
196 ATTTAAGCATCATGCTCAAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAATATTT
* *
19870 TACTAGGTAAGAAACCTTTCTTATTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAATCTT
261 TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTT
* * * * * *
19935 TCTTATATTTTGAAAGACATGTGAAAACATCCTGCCCGAAGGTCTTATTGATGGCCCA
326 TCTCATATTTTGAAAGACATATGAAAACATCCTACCCAAAGGTCTTATGGATAGCCCA
*
19993 AAGGACTTATAAAATTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTC
1 AAGGACTTATAAAATTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTC
* * * * *
20058 AAATTTAAGATTTGAATGAGAAACATTTCTCATATTTTGATAGACATGTGAAAACATCCTGCCCA
66 AAATTTAAGACTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTAAAAACATCCT-ACCA
* * * *
20123 -AAGGTCTTATGGATGGCTCGAA-AGACTTATTATCTTGCTCGAAAGACTTACAGATGACCCGAA
130 GAAGGTCTTATGGATAGC-CCAAGAGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAA
* *
20186 GGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAATGACTTATAAATTTTGGAAATAT
194 GGATTTAAGCATCATGCTCAAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAATAT
20251 TTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACC
259 TTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACC
* *
20316 TTTCTCATATTTTGATAGACATATGAAAACATCCTACCCAAAGGTCTTATGGATAGCCCG
324 TTTCTCATATTTTGAAAGACATATGAAAACATCCTACCCAAAGGTCTTATGGATAGCCCA
20376 AAGGACTTAT
1 AAGGACTTAT
20386 CATCTTGCTC
Statistics
Matches: 361, Mismatches: 30, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
383 355 0.98
384 6 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (383 bp):
AAGGACTTATAAAATTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTC
AAATTTAAGACTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTAAAAACATCCTACCAG
AAGGTCTTATGGATAGCCCAAGAGACTTATCATCTTGCTCAAAAGACTTACAGATGACCCGAAGG
ATTTAAGCATCATGCTCAAAAGACTTACTGATAGCCCGAAGGACTTATAAATTTTGGAAATATTT
TACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTT
TCTCATATTTTGAAAGACATATGAAAACATCCTACCCAAAGGTCTTATGGATAGCCCA
Found at i:20393 original size:233 final size:233
Alignment explanation
Indices: 19978--20556 Score: 1014
Period size: 233 Copynumber: 2.5 Consensus size: 233
19968 GCCCGAAGGT
* * * *
19978 CTTATTGATGGCCCAAAGGACTTATAAAATTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
1 CTTACTGATGGCCCGAATGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
* * *
20043 CTTTTCAAAAATCTCAAATTTAAGATTTGAATGAGAAACATTTCTCATATTTTGATAGACATGTG
66 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTTTCTCATATTTTGATAGACATATG
* * * *
20108 AAAACATCCTGCCCAAAGGTCTTATGGATGGCTCGAAAGACTTATTATCTTGCTCGAAAGACTTA
131 AAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTTA
20173 CAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
196 CAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
20211 CTTACTGATGGCCCGAATGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
1 CTTACTGATGGCCCGAATGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
20276 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTTTCTCATATTTTGATAGACATATG
66 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTTTCTCATATTTTGATAGACATATG
*
20341 AAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTA
131 AAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTTA
20406 CAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
196 CAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
* * * *
20444 CTTACTAATGGCCCGAATGATTTATAAATTTTGGAAATATTTTTCTAGCTAAGAAACCTTTCTTA
1 CTTACTGATGGCCCGAATGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
20509 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTTTCTCAT
66 CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTTTCTCAT
20557 TTCATTTTTT
Statistics
Matches: 330, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
233 330 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (233 bp):
CTTACTGATGGCCCGAATGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTA
CTTTTCAAAAATCTCAAATTTAAGATTTAAATGAGAAACCTTTCTCATATTTTGATAGACATATG
AAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCAAAAGA
Found at i:20443 original size:42 final size:42
Alignment explanation
Indices: 20372--20467 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
20362 TTATGGATAG
* * * *
20372 CCCGAAGGACTT-ATCATCTTGCTCGAAAGACTTAC-AGATGA
1 CCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTA-ATGA
*
20413 CCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTAATGG
1 CCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTAATGA
*
20455 CCCGAATGATTTA
1 CCCGAAGGATTTA
20468 TAAATTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 11 0.23
42 35 0.74
43 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (42 bp):
CCCGAAGGATTTAAGCATCATGCTCAAAAGACTTACTAATGA
Found at i:28665 original size:3 final size:3
Alignment explanation
Indices: 28657--28710 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
28647 TTGGATCCTG
* *
28657 TAA TAA TAA TAA AAA AAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
28703 TAA TAA TA
1 TAA TAA TA
28711 GTGATAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 46 0.96
4 2 0.04
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:30250 original size:47 final size:47
Alignment explanation
Indices: 30181--30288 Score: 198
Period size: 47 Copynumber: 2.3 Consensus size: 47
30171 CTATCGGATA
30181 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
1 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
* *
30228 TCTCGGCGTCTTCTATATATGTTCGTTCAAAAGATGTTTATGGGAGC
1 TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
30275 TCTCGGCGTCTTCT
1 TCTCGGCGTCTTCT
30289 TCAGCCTTGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 59 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (47 bp):
TCTCGGCGTCTTCTATATATGTTAGTTCAAAAGATGTTCATGGGAGC
Found at i:30315 original size:32 final size:32
Alignment explanation
Indices: 30270--30355 Score: 136
Period size: 32 Copynumber: 2.7 Consensus size: 32
30260 GATGTTTATG
* *
30270 GGAGCTCTCGGCGTCTTCTTCAGCCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAACCTTGGGGT
*
30302 GGAGTTCTTGGCGTCTTCTTCAACCTTGGGGT
1 GGAGTTCTCGGCGTCTTCTTCAACCTTGGGGT
*
30334 GGAGTTCTCGGTGTCTTCTTCA
1 GGAGTTCTCGGCGTCTTCTTCA
30356 TCAGCATCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.08, C:0.24, G:0.31, T:0.36
Consensus pattern (32 bp):
GGAGTTCTCGGCGTCTTCTTCAACCTTGGGGT
Found at i:30554 original size:47 final size:49
Alignment explanation
Indices: 30485--30592 Score: 148
Period size: 51 Copynumber: 2.2 Consensus size: 49
30475 ATAATGTTGC
*
30485 AAAAGTATTGGGCCCTAGCAATAAAC-AA-AATCACATGTTTTATAAAAG
1 AAAAGT-TTGGGCCCTAGCAATAAACAAACAAGCACATGTTTTATAAAAG
* *
30533 AAAAGTTTGGTCCCTCGCAATAAACGAAAGCAAGCACATGTTTTATAAAAG
1 AAAAGTTTGGGCCCTAGCAATAAAC-AAA-CAAGCACATGTTTTATAAAAG
30584 AAAAGTTTG
1 AAAAGTTTG
30593 TTGTTATTAG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
47 17 0.32
48 6 0.11
49 2 0.04
51 28 0.53
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (49 bp):
AAAAGTTTGGGCCCTAGCAATAAACAAACAAGCACATGTTTTATAAAAG
Found at i:33539 original size:14 final size:14
Alignment explanation
Indices: 33522--33853 Score: 223
Period size: 14 Copynumber: 25.2 Consensus size: 14
33512 TTTCAATTAC
33522 GATTTAACTTTAAT
1 GATTTAACTTTAAT
*
33536 GATTTAA---TAGT
1 GATTTAACTTTAAT
*
33547 -AATT-ACTTTAAT
1 GATTTAACTTTAAT
*
33559 GATTTAATTTTAAT
1 GATTTAACTTTAAT
33573 GATTTAA---TAAT
1 GATTTAACTTTAAT
*
33584 -AATT-ACTTTAAT
1 GATTTAACTTTAAT
*
33596 GATTTAA-TAATAAT
1 GATTTAACT-TTAAT
* *
33610 TACTTAACTTTAAT
1 GATTTAACTTTAAT
33624 GATTTAA---TAAT
1 GATTTAACTTTAAT
*
33635 -AATT-ACTTTAAT
1 GATTTAACTTTAAT
*
33647 GATTTAATTTTAAT
1 GATTTAACTTTAAT
*
33661 GATTTAA-TAATAAT
1 GATTTAACT-TTAAT
*
33675 TATTTAACTTTAAT
1 GATTTAACTTTAAT
*
33689 GATTTAATTTTAAT
1 GATTTAACTTTAAT
33703 GATTTAA---TAAT
1 GATTTAACTTTAAT
*
33714 -AATT-ACTTTAAT
1 GATTTAACTTTAAT
33726 GATTTAACTTTAAT
1 GATTTAACTTTAAT
*
33740 GATTTAA-TAATAAT
1 GATTTAACT-TTAAT
*
33754 TATTTAACTTTAAT
1 GATTTAACTTTAAT
*
33768 GATTTAA-TAATAAT
1 GATTTAACT-TTAAT
* *
33782 TACTTAACTTTAAT
1 GATTTAACTTTAAT
33796 GATTT-ACTTTAAT
1 GATTTAACTTTAAT
*
33809 GATTTAA-TAATAAT
1 GATTTAACT-TTAAT
* * *
33823 TACTTGACTTTAAT
1 GATTTAACTTTAAT
33837 GATTTATA-TTTAAT
1 GATTTA-ACTTTAAT
33851 GAT
1 GAT
33854 ATAATAATAG
Statistics
Matches: 245, Mismatches: 41, Indels: 64
0.70 0.12 0.18
Matches are distributed among these distances:
9 4 0.02
10 12 0.05
11 15 0.06
12 15 0.06
13 30 0.12
14 163 0.67
15 6 0.02
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.50
Consensus pattern (14 bp):
GATTTAACTTTAAT
Found at i:33554 original size:23 final size:22
Alignment explanation
Indices: 33528--33698 Score: 108
Period size: 23 Copynumber: 7.8 Consensus size: 22
33518 TTACGATTTA
*
33528 ACTTTAATGATTTAATAGTAATT
1 ACTTTAATGATTTAAT-TTAATT
*
33551 ACTTTAATGATTTAATTTTAATG
1 ACTTTAATGATTTAA-TTTAATT
* * *
33574 A-TTTAATAATAATTACTTTAATG
1 ACTTTAATGAT--TTAATTTAATT
* *
33597 A-TTTAAT-A-ATAA-TTACTT
1 ACTTTAATGATTTAATTTAATT
*
33615 AACTTTAATGATTTAATAATAATT
1 -ACTTTAATGATTTAAT-TTAATT
*
33639 ACTTTAATGATTTAATTTTAATG
1 ACTTTAATGATTTAA-TTTAATT
* *
33662 A-TTTAAT-A-ATAA-TTATTT
1 ACTTTAATGATTTAATTTAATT
33680 AACTTTAATGATTTAATTT
1 -ACTTTAATGATTTAATTT
33699 TAATGATTTA
Statistics
Matches: 116, Mismatches: 17, Indels: 30
0.71 0.10 0.18
Matches are distributed among these distances:
18 8 0.07
19 4 0.03
20 15 0.13
21 3 0.03
22 21 0.18
23 56 0.48
24 9 0.08
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (22 bp):
ACTTTAATGATTTAATTTAATT
Found at i:33572 original size:37 final size:37
Alignment explanation
Indices: 33522--33603 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
33512 TTTCAATTAC
* *
33522 GATTTAACTTTAATGATTTAATAGTAATTACTTTAAT
1 GATTTAATTTTAATGATTTAATAATAATTACTTTAAT
33559 GATTTAATTTTAATGATTTAATAATAATTACTTTAAT
1 GATTTAATTTTAATGATTTAATAATAATTACTTTAAT
33596 GATTTAAT
1 GATTTAAT
33604 AATAATTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (37 bp):
GATTTAATTTTAATGATTTAATAATAATTACTTTAAT
Found at i:33621 original size:20 final size:22
Alignment explanation
Indices: 33567--33827 Score: 112
Period size: 23 Copynumber: 12.1 Consensus size: 22
33557 ATGATTTAAT
33567 TTTAATGATTTAATAATAATTAC
1 TTTAA-GATTTAATAATAATTAC
33590 TTTAATGATTTAATAATAATTAC
1 TTTAA-GATTTAATAATAATTAC
* * *
33613 -TTAA-CTTTAATGAT--TTAA
1 TTTAAGATTTAATAATAATTAC
* * * *
33631 TAATAATTACTTTAATGAT--TTAAT
1 T-TTAA-GA-TTTAATAATAATT-AC
33655 TTTAATGATTTAATAATAATTA-
1 TTTAA-GATTTAATAATAATTAC
* * *
33677 TTTAA-CTTTAATGAT--TTAAT
1 TTTAAGATTTAATAATAATT-AC
33697 TTTAATGATTTAATAATAATTAC
1 TTTAA-GATTTAATAATAATTAC
* *
33720 TTTAATGATTTAACT-TTAATGA-
1 TTTAA-GATTTAA-TAATAATTAC
*
33742 TTT-A-A--TAATAATTATTTAAC
1 TTTAAGATTTAATAA-TAATT-AC
33762 TTTAATGATTTAATAATAATTAC
1 TTTAA-GATTTAATAATAATTAC
* *
33785 -TTAA-CTTTAATGAT--TTAC
1 TTTAAGATTTAATAATAATTAC
33803 TTTAATGATTTAATAATAATTAC
1 TTTAA-GATTTAATAATAATTAC
33826 TT
1 TT
33828 GACTTTAATG
Statistics
Matches: 185, Mismatches: 24, Indels: 58
0.69 0.09 0.22
Matches are distributed among these distances:
16 1 0.01
17 3 0.02
18 12 0.06
19 7 0.04
20 35 0.19
21 10 0.05
22 32 0.17
23 68 0.37
24 11 0.06
25 6 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTAAGATTTAATAATAATTAC
Found at i:33622 original size:51 final size:50
Alignment explanation
Indices: 33562--33721 Score: 176
Period size: 51 Copynumber: 3.0 Consensus size: 50
33552 CTTTAATGAT
33562 TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAATAATAATTAC
1 TTAA-TTTAATGATTTAATAATAATTACTTTAATGATTTAATAATAATTAC
** * *
33613 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGAT
1 TTAA-TTTAATGATTTAATAATAATTACTTTAATGATTTAATAATAATTAC
* * * *
33664 TTAATAATAATTATTTAACTTTAATGATTTAATTTTAATGATTTAATAATAATTAC
1 TTAAT-TTAATGATTTAA---TAAT-AATT-ACTTTAATGATTTAATAATAATTAC
33720 TT
1 TT
33722 TAATGATTTA
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.01
51 60 0.67
54 4 0.04
55 3 0.03
56 22 0.24
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (50 bp):
TTAATTTAATGATTTAATAATAATTACTTTAATGATTTAATAATAATTAC
Found at i:33704 original size:79 final size:79
Alignment explanation
Indices: 33613--33816 Score: 309
Period size: 79 Copynumber: 2.5 Consensus size: 79
33603 TAATAATTAC
*
33613 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAT
1 TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAT
33678 TTAACTTTAATGAT
66 TTAACTTTAATGAT
*
33692 TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTAT
1 TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAT
33757 TTAACTTTAATGAT
66 TTAACTTTAATGAT
** * * *
33771 TTAATAATAATTACTTAACTTTAATGATTTACTTTAATGATTTAAT
1 TTAATTTTAATGATTTAA---TAAT-AATTACTTTAATGATTTAAT
33817 AATAATTACT
Statistics
Matches: 113, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
79 91 0.81
82 4 0.04
83 18 0.16
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.50
Consensus pattern (79 bp):
TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAATTTTAATGATTTAATAATAATTAT
TTAACTTTAATGAT
Found at i:33724 original size:65 final size:65
Alignment explanation
Indices: 33528--33786 Score: 311
Period size: 65 Copynumber: 4.1 Consensus size: 65
33518 TTACGATTTA
*
33528 ACTTTAATGATTTAATAGT-A--A-TT-ACTTTAATGATTTAATTTTAATGATTTAATAATAATT
1 ACTTTAATGATTTAATAATAATTATTTAACTTTAATGATTTAATTTTAATGATTTAATAATAATT
* ** * *
33588 ACTTTAATGATTTAATAATAATTACTTAACTTTAATGATTTAATAATAATTACTTTAATGAT--T
1 ACTTTAATGATTTAATAATAATTATTTAACTTTAATGATTTAATTTTAATGA-TTTAATAATAAT
33651 T
65 T
*
33652 AATTTTAATGATTTAATAATAATTATTTAACTTTAATGATTTAATTTTAATGATTTAATAATAAT
1 -ACTTTAATGATTTAATAATAATTATTTAACTTTAATGATTTAATTTTAATGATTTAATAATAAT
33717 T
65 T
* * * * *
33718 ACTTTAATGATTTAACT-TTAATGATTTAA-TAATAATTATTTAACTTTAATGATTTAATAATAA
1 ACTTTAATGATTTAA-TAATAATTATTTAACT-TTAATGATTTAATTTTAATGATTTAATAATAA
33781 TT
64 TT
33783 ACTT
1 ACTT
33787 AACTTTAATG
Statistics
Matches: 171, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
60 18 0.11
61 1 0.01
63 1 0.01
64 13 0.08
65 127 0.74
66 11 0.06
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (65 bp):
ACTTTAATGATTTAATAATAATTATTTAACTTTAATGATTTAATTTTAATGATTTAATAATAATT
Found at i:33833 original size:69 final size:65
Alignment explanation
Indices: 33562--33842 Score: 227
Period size: 65 Copynumber: 4.3 Consensus size: 65
33552 CTTTAATGAT
* * * * * *
33562 TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAA-TAATAATTACTTAACT-TTAATG
1 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAACT-TTAATGATTTAA-TAATAATT
*
33625 AT
64 AC
* * * * * * *
33627 TTAA-TAATAATTACTTTAATGAT--TTAATTTTAATGATTTAA-TAATAATTATTTAACT-TTA
1 TTAACT-TTAATGA-TTTAATAATAATT-ACTTTAATGATTTAACT-TTAATGATTTAA-TAATA
* *
33687 ATGAT
61 ATTAC
* *
33692 TTAATTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTAT
1 TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTAC
33757 TTAACTTTAATGATTTAATAATAATTACTTAACTTTAATGATTT-ACTTTAATGATTTAATAATA
1 TTAACTTTAATGATTTAATAAT-A--A-TT-ACTTTAATGATTTAACTTTAATGATTTAATAATA
33821 ATTAC
61 ATTAC
*
33826 TTGACTTTAATGATTTA
1 TTAACTTTAATGATTTA
33843 TATTTAATGA
Statistics
Matches: 187, Mismatches: 16, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
64 12 0.06
65 106 0.57
66 13 0.07
68 1 0.01
69 42 0.22
70 13 0.07
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (65 bp):
TTAACTTTAATGATTTAATAATAATTACTTTAATGATTTAACTTTAATGATTTAATAATAATTAC
Found at i:36661 original size:33 final size:30
Alignment explanation
Indices: 36621--36697 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 30
36611 CTCCCATGTG
*
36621 AAGAAAACGCCGAGCATTCCACCCCAAATTGTA
1 AAGAAAACGCCGAGCAATCCA-CCCAAA--GTA
* *
36654 AAGAAAACGCCGAGTAATCCACCCAAAGTG
1 AAGAAAACGCCGAGCAATCCACCCAAAGTA
*
36684 AAGAAGACGCCGAG
1 AAGAAAACGCCGAG
36698 ACATCCTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 15 0.38
32 6 0.15
33 19 0.47
ACGTcount: A:0.42, C:0.27, G:0.21, T:0.10
Consensus pattern (30 bp):
AAGAAAACGCCGAGCAATCCACCCAAAGTA
Found at i:36694 original size:30 final size:29
Alignment explanation
Indices: 36588--36703 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 29
36578 TGCATTATTA
* * * *
36588 TGAAGAAGACGCCGAGACATCCCCTCCCATG
1 TGAAGAAAACGCCGAGA-ATCCAC-CCAAAG
*
36619 TGAAGAAAACGCCGAGCATTCCACCCCAAATTG
1 TGAAGAAAACGCCGAG-AATCCA-CCCAAA--G
*
36652 TAAAGAAAACGCCGAGTAATCCACCCAAAG
1 TGAAGAAAACGCCGAG-AATCCACCCAAAG
*
36682 TGAAGAAGACGCCGAGACATCC
1 TGAAGAAAACGCCGAGA-ATCC
36704 TCTACTTAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
29 1 0.01
30 19 0.27
31 21 0.30
32 8 0.11
33 21 0.30
ACGTcount: A:0.37, C:0.30, G:0.21, T:0.12
Consensus pattern (29 bp):
TGAAGAAAACGCCGAGAATCCACCCAAAG
Found at i:36762 original size:20 final size:20
Alignment explanation
Indices: 36737--36775 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36727 CTATTATCAA
*
36737 CTCACCCCGTGAATTCCCTG
1 CTCACCACGTGAATTCCCTG
36757 CTCACCACGTGAATTCCCT
1 CTCACCACGTGAATTCCCT
36776 TTTGCGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.44, G:0.13, T:0.26
Consensus pattern (20 bp):
CTCACCACGTGAATTCCCTG
Found at i:40725 original size:45 final size:46
Alignment explanation
Indices: 40675--40779 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 46
40665 TGCATGGATT
* * *
40675 GTGCATCGATGCATCAAATGGATTTGATGTTTTAATTAAATCA-GA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
* ** * *
40720 GTGCATCGATACATGGAATGCATTCGATGTTTCAATTTATTCATTGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCA-TGA
40767 -TGCATCGATGCAT
1 GTGCATCGATGCAT
40780 GGTATTGATG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 35 0.71
46 12 0.24
47 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (46 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAAATCATGA
Found at i:40786 original size:21 final size:21
Alignment explanation
Indices: 40762--40801 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40752 CAATTTATTC
40762 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
40783 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
40802 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:43400 original size:21 final size:22
Alignment explanation
Indices: 43345--43403 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
43335 CATGGTCTTG
*
43345 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATGC-AGGCA
43368 TGCATC-AGTGCATCATGC-GG-A
1 TGCATCGA-TGCA-CATGCAGGCA
43389 TGCATCGATGCACAT
1 TGCATCGATGCACAT
43404 TCAAAGGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 4 0.12
23 10 0.31
24 4 0.12
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (22 bp):
TGCATCGATGCACATGCAGGCA
Found at i:49261 original size:18 final size:17
Alignment explanation
Indices: 49207--49255 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
49197 TTGGACTCCT
* *
49207 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
49225 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
49243 AGTGCATTCGATG
1 AGTGCA-TCGATG
49256 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:49276 original size:64 final size:60
Alignment explanation
Indices: 49207--49386 Score: 175
Period size: 64 Copynumber: 2.8 Consensus size: 60
49197 TTGGACTCCT
49207 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGGTGCA-T-AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * * *
49268 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATC
1 ---AGTGCATCGGTGCATAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATC
49333 AG
59 AG
*
49335 AGTGCATCGGTGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGGTGCAT--AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
49387 CAATTTATTC
Statistics
Matches: 97, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 84 0.87
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (60 bp):
AGTGCATCGGTGCATAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:49357 original size:19 final size:19
Alignment explanation
Indices: 49333--49371 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
49323 TAATTAAATC
49333 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGGTGCATGG
49352 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGGTGCATGG
49371 A
1 A
49372 ATGCATTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.41, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGGTGCATGG
Found at i:49421 original size:21 final size:21
Alignment explanation
Indices: 49397--49436 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
49387 CAATTTATTC
49397 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
49418 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
49437 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:51590 original size:169 final size:169
Alignment explanation
Indices: 51309--51642 Score: 445
Period size: 169 Copynumber: 2.0 Consensus size: 169
51299 GCCGCCATGA
* * *
51309 TCAAAGCCCCCAAAACAATTCATGGATAGTCGTCGCTGTTCGCTGGAATTGAGCCCTTGAACTTT
1 TCAAAGCCCCCAAAACAATTCATGCATAGTCGTCGCTGTTCGCTAGAATCGAGCCCTTGAACTTT
* * * * ** *
51374 CGTCGAAAACCCACCCTGACGCCTCGGATTTTGGACGATTTCGACCGCCTTGGACCTCCGTTCCC
66 CGTCGAAAACCCACCCCGACACCTCAGATTTTGGACGATTCCGACCGCCTCAGACCACCGTTCCC
* *
51439 CTCATCGCAACCATAGTTAGCTTCCTAGTCGCCGTCATC
131 CTCAACACAACCATAGTTAGCTTCCTAGTCGCCGTCATC
* * * *
51478 TCAAAGCTCCCAAAACAATTCGTGCATA-TCTGTCGTTGTTCGCTAGAATCGAGCCCTTGAAGTT
1 TCAAAGCCCCCAAAACAATTCATGCATAGTC-GTCGCTGTTCGCTAGAATCGAGCCCTTGAACTT
* * *
51542 TCGTCGAAAATCCACCCCGACACCTCAGATTTTGGACGATTCCGACCGCCTCAGATCACCGTTCG
65 TCGTCGAAAACCCACCCCGACACCTCAGATTTTGGACGATTCCGACCGCCTCAGACCACCGTTCC
* * * *
51607 CCTCAACACCACCATATTTAGCTTCCTCGTTGCCGT
130 CCTCAACACAACCATAGTTAGCTTCCTAGTCGCCGT
51643 TCGCTCAACA
Statistics
Matches: 141, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
168 2 0.01
169 139 0.99
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.26
Consensus pattern (169 bp):
TCAAAGCCCCCAAAACAATTCATGCATAGTCGTCGCTGTTCGCTAGAATCGAGCCCTTGAACTTT
CGTCGAAAACCCACCCCGACACCTCAGATTTTGGACGATTCCGACCGCCTCAGACCACCGTTCCC
CTCAACACAACCATAGTTAGCTTCCTAGTCGCCGTCATC
Found at i:54982 original size:36 final size:36
Alignment explanation
Indices: 54942--55021 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
54932 TTAACGGTTG
54942 GGAATTTAATCAACATTCTACTGCTGCTGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGCTGTTCAAGT
*
54978 GGAATTTAATTAACATTCTACTGCTGCTGTTCAAGT
1 GGAATTTAATCAACATTCTACTGCTGCTGTTCAAGT
*
55014 AGAATTTA
1 GGAATTTA
55022 GTTACATTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (36 bp):
GGAATTTAATCAACATTCTACTGCTGCTGTTCAAGT
Found at i:57965 original size:31 final size:32
Alignment explanation
Indices: 57915--57977 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
57905 TTTATGTTTG
* *
57915 ATTGAATTTTTACACTTAACTTTGAT-TTTTT
1 ATTGAATTTTGACACTTAACTTTAATATTTTT
* *
57946 ATTGAATTTTGCCAGTTAACTTTAATATTTTT
1 ATTGAATTTTGACACTTAACTTTAATATTTTT
57978 TTGGACAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.56
Consensus pattern (32 bp):
ATTGAATTTTGACACTTAACTTTAATATTTTT
Done.