Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001515.1 Hibiscus syriacus cultivar Beakdansim tig00002962_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: 78681
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4794 original size:32 final size:33
Alignment explanation
Indices: 4751--4814 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
4741 GTAATAAAAT
*
4751 AATAATTAATTAATAATTTAT-TTTTTATTAAA
1 AATAATAAATTAATAATTTATATTTTTATTAAA
*
4783 AATAATAAATTAGTAATTTATCATTTTTATTA
1 AATAATAAATTAATAATTTAT-ATTTTTATTA
4815 CCTATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 19 0.68
34 9 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (33 bp):
AATAATAAATTAATAATTTATATTTTTATTAAA
Found at i:7124 original size:48 final size:48
Alignment explanation
Indices: 7015--7234 Score: 298
Period size: 48 Copynumber: 4.6 Consensus size: 48
7005 GAAACAGAAA
* * *
7015 CGGCGGCGACTTCTTCTACCTCGGCCGTCAAT-GGGTTTCAACGGCAG
1 CGGCGACGACTACTTCTACCTCGGCCGTCAATGGGGTTTCAACTGCAG
* *
7062 CAGCGACGAGTACTTCTACCTCGGCCGTCAATGGGGTTTCAACTGCAG
1 CGGCGACGACTACTTCTACCTCGGCCGTCAATGGGGTTTCAACTGCAG
* * *
7110 CGGCGACGGCTACTTCTACCTCGGGCGTCAATGGGGTTTCAACCGCAG
1 CGGCGACGACTACTTCTACCTCGGCCGTCAATGGGGTTTCAACTGCAG
* * * * *
7158 CGACGACGACTACTTCTACGTCGACCGTCAACGGGGTTTCAACTACAG
1 CGGCGACGACTACTTCTACCTCGGCCGTCAATGGGGTTTCAACTGCAG
* *
7206 CGGCGACTACTACTTCTAGCTCGGCCGTC
1 CGGCGACGACTACTTCTACCTCGGCCGTC
7235 GATTTGTCCA
Statistics
Matches: 149, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
47 28 0.19
48 121 0.81
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (48 bp):
CGGCGACGACTACTTCTACCTCGGCCGTCAATGGGGTTTCAACTGCAG
Found at i:7871 original size:19 final size:20
Alignment explanation
Indices: 7826--7872 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
7816 CCACGAATTA
*
7826 TAAATCGAAACACAGTTTCC
1 TAAATCGCAACACAGTTTCC
*
7846 AAAATCGCAACACAGTTT-C
1 TAAATCGCAACACAGTTTCC
7865 TAAATCGC
1 TAAATCGC
7873 GTTGCGATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (20 bp):
TAAATCGCAACACAGTTTCC
Found at i:7935 original size:20 final size:20
Alignment explanation
Indices: 7910--7949 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
7900 GGTAATTAGA
7910 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
*
7930 GTTGCGAATTTGTAAATCGC
1 GTTGCGAATTTGAAAATCGC
7950 AACACAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:7966 original size:20 final size:20
Alignment explanation
Indices: 7943--8006 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
7933 GCGAATTTGT
7943 AAATCGCAACACAGTTTCCA
1 AAATCGCAACACAGTTTCCA
** * **
7963 AAATCGCAACGTGAATTT-GT
1 AAATCGCAAC-ACAGTTTCCA
7983 AAATCGCAACACAGTTTCCA
1 AAATCGCAACACAGTTTCCA
8003 AAAT
1 AAAT
8007 TACGTTGCGA
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 4 0.12
20 24 0.75
21 4 0.12
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (20 bp):
AAATCGCAACACAGTTTCCA
Found at i:8072 original size:20 final size:20
Alignment explanation
Indices: 8047--8093 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
8037 AATAATTAGA
8047 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
*
8067 GTTGCGAATTTGAAAATCGT
1 GTTGCGAATTTGAAAATCGC
8087 GTTGCGA
1 GTTGCGA
8094 TAACAATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:8083 original size:77 final size:77
Alignment explanation
Indices: 8002--8150 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 77
7992 CACAGTTTCC
* ** * *
8002 AAAATTACGTTGCGATAGTACTGTTTATCTATATCAATAATTAGAGTTGCGAATTTGAAAATCGC
1 AAAATCACGTTGCGATAACAATGTTTACCTATATCAATAATTAGAGTTGCGAATTTGAAAATCGC
8067 GTTGCGAATTTG
66 GTTGCGAATTTG
** ** * *
8079 AAAATCGTGTTGCGATAACAATGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGTAAATCGC
1 AAAATCACGTTGCGATAACAATGTTTACCTATATCAATAATTAGAGTTGCGAATTTGAAAATCGC
8144 GTTGCGA
66 GTTGCGA
8151 TAGTACTGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
77 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (77 bp):
AAAATCACGTTGCGATAACAATGTTTACCTATATCAATAATTAGAGTTGCGAATTTGAAAATCGC
GTTGCGAATTTG
Found at i:8166 original size:57 final size:57
Alignment explanation
Indices: 8065--8264 Score: 310
Period size: 57 Copynumber: 3.5 Consensus size: 57
8055 TTTGAAAATC
* * *
8065 GCGTTGCGAATTTGAAAATCGTGTTGCGATAACAATGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTA
* * *
8122 GCGTTGCGAATTTGTAAATCGCGTTGCGATAGTACTGTTAACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTA
* *
8179 GTGTTGTGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTA
* *
8236 GCGTTGCGAATTTGAAATTCTCGTTGCGA
1 GCGTTGCGAATTTGAAAATCGCGTTGCGA
8265 ATTTAAAAAT
Statistics
Matches: 128, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 128 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (57 bp):
GCGTTGCGAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTA
Found at i:8260 original size:20 final size:20
Alignment explanation
Indices: 8236--8284 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
8226 TCGGTAATTA
* *
8236 GCGTTGCGAATTTGAAATTC
1 GCGTTGCGAATTTAAAAATC
*
8256 TCGTTGCGAATTTAAAAATC
1 GCGTTGCGAATTTAAAAATC
8276 GCGTTGCGA
1 GCGTTGCGA
8285 TAGTACTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTAAAAATC
Found at i:8340 original size:77 final size:77
Alignment explanation
Indices: 8186--8345 Score: 225
Period size: 77 Copynumber: 2.1 Consensus size: 77
8176 TTAGTGTTGT
* * *
8186 GAATTTGAAAATCGCGTTGCGATAATACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTGA
1 GAATTTAAAAATCGCGTTGCGATAATACTGTTTACCTACATCGGTAATTAACGTTGCGAATTTGA
* *
8251 AATTCTCGTTGC
66 AATTCGCATTGC
* *
8263 GAATTTAAAAATCGCGTTGCGATAGTACTGTTTACCTACATCGGTAATTAATGTTGCG-ATTT-A
1 GAATTTAAAAATCGCGTTGCGATAATACTGTTTACCTACATCGGTAATTAACGTTGCGAATTTGA
8326 CATATTCGCATTGC
66 -A-ATTCGCATTGC
8340 GAATTT
1 GAATTT
8346 GGAAAACCGT
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
75 1 0.01
76 5 0.07
77 68 0.92
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (77 bp):
GAATTTAAAAATCGCGTTGCGATAATACTGTTTACCTACATCGGTAATTAACGTTGCGAATTTGA
AATTCGCATTGC
Found at i:8380 original size:21 final size:21
Alignment explanation
Indices: 8336--8432 Score: 81
Period size: 21 Copynumber: 4.7 Consensus size: 21
8326 CATATTCGCA
* * *
8336 TTGCGAATTTGGAAAACCGTG
1 TTGCGAATTTAGAAAATCGAG
*
8357 TTGCGAATTTAGAAAATCAAG
1 TTGCGAATTTAGAAAATCGAG
* * * *
8378 TTGCG-ATTTACATATTCGCG
1 TTGCGAATTTAGAAAATCGAG
*
8398 TTGCGAATTTGGAAAATCGCA-
1 TTGCGAATTTAGAAAATCG-AG
*
8419 TTGCGATTTTAGAA
1 TTGCGAATTTAGAA
8433 CCTGTGTTAC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.26
21 43 0.74
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGCGAATTTAGAAAATCGAG
Found at i:8390 original size:62 final size:62
Alignment explanation
Indices: 8315--8432 Score: 191
Period size: 62 Copynumber: 1.9 Consensus size: 62
8305 GGTAATTAAT
**
8315 GTTGCGATTTACATATTCGCATTGCGAATTTGGAAAACCGTGTTGCGAATTTAGAAAATCAA
1 GTTGCGATTTACATATTCGCATTGCGAATTTGGAAAACCGCATTGCGAATTTAGAAAATCAA
* * *
8377 GTTGCGATTTACATATTCGCGTTGCGAATTTGGAAAATCGCATTGCGATTTTAGAA
1 GTTGCGATTTACATATTCGCATTGCGAATTTGGAAAACCGCATTGCGAATTTAGAA
8433 CCTGTGTTAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (62 bp):
GTTGCGATTTACATATTCGCATTGCGAATTTGGAAAACCGCATTGCGAATTTAGAAAATCAA
Found at i:8662 original size:60 final size:57
Alignment explanation
Indices: 8569--8685 Score: 180
Period size: 60 Copynumber: 2.0 Consensus size: 57
8559 AAAATAAGAA
*
8569 ATGACCATTTCTTGAATTCTCCTATGCAGCTACGCAAATTGACACTTTTGCATATTC
1 ATGACCATTTCTTGAATTCTCCTATGCAACTACGCAAATTGACACTTTTGCATATTC
* *
8626 ATGACCATTTCTCTTGGAATTCTCCTCTGCAACTACGTAAATTGACACTTTTGCATATTC
1 ATGACCA-TT-TCTT-GAATTCTCCTATGCAACTACGCAAATTGACACTTTTGCATATTC
8686 TGCATATTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 7 0.13
58 2 0.04
59 4 0.07
60 41 0.76
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.38
Consensus pattern (57 bp):
ATGACCATTTCTTGAATTCTCCTATGCAACTACGCAAATTGACACTTTTGCATATTC
Found at i:9273 original size:120 final size:119
Alignment explanation
Indices: 9045--9284 Score: 354
Period size: 120 Copynumber: 2.0 Consensus size: 119
9035 GGGAGCTTTT
* * *
9045 CTTCAACACATTGAGTCAGTTCTAATCTGAACACTAATTTTTAAGGAAAAAACTAAATTGTTCAT
1 CTTCAACACATTGAGTCAGTTCCAATCCGAACACCAATTTTTAAGGAAAAAACTAAATTGTTCAT
** * *
9110 GTCATTTAGATAATGAACAACAATAATAAAATATGAAGTGTTCTTAGTATGTTA
66 ACCATTAAGACAATGAACAACAATAATAAAATATGAAGTGTTCTTAGTATGTTA
* * * *
9164 CTTCAACACATTGAGTTCAGTTCCAATCCGAACACCAGTTTTTAAGGTAGAAATTAAATTGTTCA
1 CTTCAACACATTGAG-TCAGTTCCAATCCGAACACCAATTTTTAAGGAAAAAACTAAATTGTTCA
* *
9229 TACCATTAAGACAATGAACAATAATAATAAAATATTAAGTGTTCTTAGTATGTTA
65 TACCATTAAGACAATGAACAACAATAATAAAATATGAAGTGTTCTTAGTATGTTA
9284 C
1 C
9285 AGTCAATTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
119 15 0.14
120 92 0.86
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (119 bp):
CTTCAACACATTGAGTCAGTTCCAATCCGAACACCAATTTTTAAGGAAAAAACTAAATTGTTCAT
ACCATTAAGACAATGAACAACAATAATAAAATATGAAGTGTTCTTAGTATGTTA
Found at i:9826 original size:17 final size:17
Alignment explanation
Indices: 9804--9836 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9794 CAAAATTATT
9804 TTAAATATTT-TAAAAAA
1 TTAAAT-TTTATAAAAAA
9821 TTAAATTTTATAAAAA
1 TTAAATTTTATAAAAA
9837 TACATATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTAAATTTTATAAAAAA
Found at i:13196 original size:26 final size:26
Alignment explanation
Indices: 13167--13219 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
13157 ACAAGGTAAG
13167 AAAATGAGTTATAATTGGTAAATGTT
1 AAAATGAGTTATAATTGGTAAATGTT
13193 AAAATGAGTTATAATTGGTAAATGTT
1 AAAATGAGTTATAATTGGTAAATGTT
13219 A
1 A
13220 TAGATACTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (26 bp):
AAAATGAGTTATAATTGGTAAATGTT
Found at i:13519 original size:13 final size:12
Alignment explanation
Indices: 13498--13544 Score: 55
Period size: 11 Copynumber: 4.0 Consensus size: 12
13488 AATGTTATGA
13498 ATTTAG-ATTTG
1 ATTTAGTATTTG
13509 ATTTAGTGATTTG
1 ATTTAGT-ATTTG
13522 A-TTA-TATGTTG
1 ATTTAGTAT-TTG
13533 ATTTAGTATTTG
1 ATTTAGTATTTG
13545 TAAATTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
10 2 0.06
11 11 0.35
12 9 0.29
13 9 0.29
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (12 bp):
ATTTAGTATTTG
Found at i:14192 original size:16 final size:16
Alignment explanation
Indices: 14171--14210 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
14161 TTTTGGTTGA
14171 TGTTTTGGCTTAATTC
1 TGTTTTGGCTTAATTC
14187 TGTTTTGGCTTAATTC
1 TGTTTTGGCTTAATTC
14203 TGTTTTGG
1 TGTTTTGG
14211 AATGGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.10, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTTTGGCTTAATTC
Found at i:17809 original size:54 final size:55
Alignment explanation
Indices: 17730--18420 Score: 647
Period size: 54 Copynumber: 12.8 Consensus size: 55
17720 ACCAAATAGG
*
17730 CACTAAGTGTGC-AATCCATGAAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* * * * * * *
17784 TACTATGTGTGCAAAT-CATGGAATTCATCATATGTTGATGAACAACCGTTTAGG
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* *
17838 CACTAAGTGTGC-AATCCACGAAATTCATCATATGTTGATGAACAACAGTTTC-A
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* * *
17891 GTACTAAGTGTGCAAAT-CACGAAATTCATCATATATTGATGAATAACCATTTC-A
1 -CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* * * *
17945 GCACT--GTGTGTAAAT-CATGGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 -CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* *
17998 CACTAAGTGTGC-AATCCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGA
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTC-GA
** * * *
18053 -ACTATTTGTGCAAAT-CACGGAATTCATCATATGTTGATGAATAACCGTTGCGG
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* * *
18106 CACTAAGTGTGC-AATCCACGGAATTCATCATATGTTGATGAACAACCGTTTCGG
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
* * * * * * *
18160 CACTAAGTGTGC-AATTCACAAAATTCATCATATATTGATGGACAATCATTTC-A
1 CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
** * * *
18213 GCACTATCTGTGCAAACCCACGAAATTCATCACGA-GTTGATGAATAACCG-TAC-A
1 -CACTAAGTGTGCAAATCCACGAAATTCATCA-TATGTTGATGAATAACCGTTTCGA
* * * * *
18267 TGCACTATGTGTGTAAATCCACGGAATTCATCATGA-GTTGATGAATAACCG-TACAA
1 --CACTAAGTGTGCAAATCCACGAAATTCATCAT-ATGTTGATGAATAACCGTTTCGA
* * * *
18323 GCACTATGTGTGCAAATCCACGAAATTCATCAT-TAGTTGATGAATAACCGTATAGG
1 -CACTAAGTGTGCAAATCCACGAAATTCATCATAT-GTTGATGAATAACCGTTTCGA
* * *
18379 CACGATGTGTGC-AACCCAC-ATAATTCATCATGA-GTTGATGAA
1 CACTAAGTGTGCAAATCCACGA-AATTCATCAT-ATGTTGATGAA
18421 CTACCGTATA
Statistics
Matches: 541, Mismatches: 72, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
52 45 0.08
53 11 0.02
54 344 0.64
55 139 0.26
56 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
CACTAAGTGTGCAAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
Found at i:17917 original size:108 final size:109
Alignment explanation
Indices: 17726--18420 Score: 729
Period size: 108 Copynumber: 6.4 Consensus size: 109
17716 GATTACCAAA
* * *
17726 TAGGCACTAAGTGTGCAATCCATGAAATTCATCATATGTTGATGAATAACCGTTTC-GATACTAT
1 TAGGCACTAAGTGTGCAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCAG-CACTAA
* *
17790 GTGTGCAAAT-CATGGAATTCATCATATGTTGATGAACAACCGTT
65 GTGTGCAAATCCACGAAATTCATCATATGTTGATGAACAACCGTT
* * *
17834 TAGGCACTAAGTGTGCAATCCACGAAATTCATCATATGTTGATGAACAACAGTTTCAGTACTAAG
1 TAGGCACTAAGTGTGCAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCAGCACTAAG
* * *
17899 TGTGCAAAT-CACGAAATTCATCATATATTGATGAATAACCATT
66 TGTGCAAATCCACGAAATTCATCATATGTTGATGAACAACCGTT
* * * *
17942 TCA-GCACT--GTGTGTAAAT-CATGGAATTCATCATATGTTGATGAATAACCGTTTCGGCACTA
1 T-AGGCACTAAGTGTG-CAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCAGCACTA
*
18003 AGTGTGC-AATCCACGGAATTCATCATATGTTGATGAACAACCGTT
64 AGTGTGCAAATCCACGAAATTCATCATATGTTGATGAACAACCGTT
* * ** * * *
18048 TCGGAACTATTTGTGCAAAT-CACGGAATTCATCATATGTTGATGAATAACCGTTGCGGCACTAA
1 TAGGCACTAAGTGTGC-AATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCAGCACTAA
*
18112 GTGTGC-AATCCACGGAATTCATCATATGTTGATGAACAACCGTT
65 GTGTGCAAATCCACGAAATTCATCATATGTTGATGAACAACCGTT
* * * * * * * * **
18156 TCGGCACTAAGTGTGCAATTCACAAAATTCATCATATATTGATGGACAATCATTTCAGCACTATC
1 TAGGCACTAAGTGTGCAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCAGCACTAAG
* * * *
18221 TGTGCAAACCCACGAAATTCATCACGA-GTTGATGAATAACCGTA
66 TGTGCAAATCCACGAAATTCATCA-TATGTTGATGAACAACCGTT
* * * * * *
18265 CATGCACTATGTGTGTAAATCCACGGAATTCATCATGA-GTTGATGAATAACCG-TACAAGCACT
1 TAGGCACTAAGTGTG-CAATCCACGAAATTCATCAT-ATGTTGATGAATAACCGTTTC-AGCACT
* * *
18328 ATGTGTGCAAATCCACGAAATTCATCAT-TAGTTGATGAATAACCGTA
63 AAGTGTGCAAATCCACGAAATTCATCATAT-GTTGATGAACAACCGTT
* * *
18375 TAGGCACGATGTGTGCAACCCAC-ATAATTCATCATGA-GTTGATGAA
1 TAGGCACTAAGTGTGCAATCCACGA-AATTCATCAT-ATGTTGATGAA
18421 CTACCGTATA
Statistics
Matches: 502, Mismatches: 68, Indels: 33
0.83 0.11 0.05
Matches are distributed among these distances:
105 3 0.01
106 84 0.17
107 6 0.01
108 248 0.49
109 73 0.15
110 87 0.17
111 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (109 bp):
TAGGCACTAAGTGTGCAATCCACGAAATTCATCATATGTTGATGAATAACCGTTTCAGCACTAAG
TGTGCAAATCCACGAAATTCATCATATGTTGATGAACAACCGTT
Found at i:18212 original size:268 final size:268
Alignment explanation
Indices: 17727--18427 Score: 898
Period size: 268 Copynumber: 2.6 Consensus size: 268
17717 ATTACCAAAT
* *
17727 AGGCACTAAGTGTGCAATCCATGAAATTCATCATATGTTGATGAATAACCGTTTCGATACTATGT
1 AGGCACTAAGTGTGCAATCCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA-ACTATGT
* *
17792 GTGCAAATCATGGAATTCATCATATGTTGATGAACAACCGTTTAGGCACTAAGTGTGCAATCCAC
65 GTGCAAATCACGGAATTCATCATATGTTGATGAATAACCG-TTAGGCACTAAGTGTGCAATCCAC
* * *
17857 GAAATTCATCATATGTTGATGAACAACAGTTTCAGTACTAAGTGTGCAAATCACGAAATTCATCA
129 GAAATTCATCATATGTTGATGAACAACCGTTTCAGCACTAAGTGTGCAAATCACAAAATTCATCA
* * * * * * *
17922 TATATTGATGAATAACCATTTCAGCAC-TGTGTGTAAA-TCATGGAATTCATCA-TATGTTGATG
194 TATATTGATGAACAACCATTTCAGCACATCTGTGCAAACCCACGAAATTCATCACGA-GTTGATG
*
17984 AATAACCGTTTC
258 AATAACCG-TAC
* *
17996 -GGCACTAAGTGTGCAATCCACGGAATTCATCATATGTTGATGAACAACCGTTTCGGAACTATTT
1 AGGCACTAAGTGTGCAATCCACGGAATTCATCATATGTTGATGAATAACCGTTTC-GAACTATGT
*
18060 GTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTGCGGCACTAAGTGTGCAATCCAC
65 GTGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTT-AGGCACTAAGTGTGCAATCCAC
* * *
18125 GGAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTGTGCAATTCACAAAATTCATCA
129 GAAATTCATCATATGTTGATGAACAACCGTTTCAGCACTAAGTGTGCAAATCACAAAATTCATCA
* *
18190 TATATTGATGGACAATCATTTCAGCACTATCTGTGCAAACCCACGAAATTCATCACGAGTTGATG
194 TATATTGATGAACAACCATTTCAGCAC-ATCTGTGCAAACCCACGAAATTCATCACGAGTTGATG
18255 AATAACCGTAC
258 AATAACCGTAC
* * * * *
18266 ATGCACTATGTGTGTAAATCCACGGAATTCATCATGA-GTTGATGAATAACCG-TACAAGCACTA
1 AGGCACTAAGTGTG-CAATCCACGGAATTCATCAT-ATGTTGATGAATAACCGTTTC--GAACTA
* * *
18329 TGTGTGCAAATCCACGAAATTCATCAT-TAGTTGATGAATAACCGTATAGGCACGATGTGTGCAA
62 TGTGTGCAAAT-CACGGAATTCATCATAT-GTTGATGAATAACCGT-TAGGCACTAAGTGTGCAA
* *
18393 CCCAC-ATAATTCATCATGA-GTTGATGAACTACCGT
124 TCCACGA-AATTCATCAT-ATGTTGATGAACAACCGT
18428 ATAGGCATTA
Statistics
Matches: 379, Mismatches: 38, Indels: 26
0.86 0.09 0.06
Matches are distributed among these distances:
267 2 0.01
268 199 0.53
269 2 0.01
270 10 0.03
271 40 0.11
272 50 0.13
273 74 0.20
274 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (268 bp):
AGGCACTAAGTGTGCAATCCACGGAATTCATCATATGTTGATGAATAACCGTTTCGAACTATGTG
TGCAAATCACGGAATTCATCATATGTTGATGAATAACCGTTAGGCACTAAGTGTGCAATCCACGA
AATTCATCATATGTTGATGAACAACCGTTTCAGCACTAAGTGTGCAAATCACAAAATTCATCATA
TATTGATGAACAACCATTTCAGCACATCTGTGCAAACCCACGAAATTCATCACGAGTTGATGAAT
AACCGTAC
Found at i:18749 original size:81 final size:81
Alignment explanation
Indices: 18584--18751 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 81
18574 TATTCCAAAA
* * * *
18584 TAAAAGATTAATGGCCTAGTTGTGCATTTGATAGAAAGGTGACAATTATGCCAGTTATATGAAAG
1 TAAAAGATTAATAGCCTAGCTGTACATTTGACAGAAAGGTGACAATTATGCCAGTTATATGAAAG
*
18649 GTTAAATACCTTTGAG
66 GCTAAATACCTTTGAG
* * *
18665 TAAAAGATTAATAGCCTAGCTGTACATTTGACAGAAATGTGTCAATTGTGCCAGTTAGT-TGAAA
1 TAAAAGATTAATAGCCTAGCTGTACATTTGACAGAAAGGTGACAATTATGCCAGTTA-TATGAAA
* *
18729 GGCTATATA-CTTTTAGG
65 GGCTAAATACCTTTGA-G
18746 TAAAAG
1 TAAAAG
18752 TCTAAATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
80 5 0.07
81 69 0.92
82 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TAAAAGATTAATAGCCTAGCTGTACATTTGACAGAAAGGTGACAATTATGCCAGTTATATGAAAG
GCTAAATACCTTTGAG
Found at i:20211 original size:2 final size:2
Alignment explanation
Indices: 20204--20236 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
20194 CTTTGATTTA
20204 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20237 TATGTTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20278 original size:21 final size:21
Alignment explanation
Indices: 20222--20278 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
20212 ATATATATAT
20222 ATATATATAATATATTATGTTTG
1 ATATATATAA-AT-TTATGTTTG
*
20245 ATATTTATAAATTTATGTTTG
1 ATATATATAAATTTATGTTTG
* *
20266 GTATATATTAATT
1 ATATATATAAATT
20279 AATTCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 19 0.63
22 2 0.07
23 9 0.30
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (21 bp):
ATATATATAAATTTATGTTTG
Found at i:21534 original size:22 final size:23
Alignment explanation
Indices: 21483--21541 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 23
21473 TTTTTTAAAT
21483 TAAGTTAATAATAAAATATATTTAA
1 TAAGTTAAT-ATAAAATATATTT-A
21508 TAAGTTAATATAAAA-ATATTT-
1 TAAGTTAATATAAAATATATTTA
21529 TCAAGTTAATATA
1 T-AAGTTAATATA
21542 TATAAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.03
22 11 0.33
23 6 0.18
24 6 0.18
25 9 0.27
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (23 bp):
TAAGTTAATATAAAATATATTTA
Found at i:21548 original size:25 final size:24
Alignment explanation
Indices: 21483--21558 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 24
21473 TTTTTTAAAT
21483 TAAGTTAATA-ATAAAATATATTTAA
1 TAAGTTAATATATAAAA-ATATTT-A
21508 TAAGTT-A-ATATAAAAATATTT-
1 TAAGTTAATATATAAAAATATTTA
21529 TCAAGTTAATATATATAAAATTATATTA
1 T-AAGTTAATATATA-AAAA-TAT-TTA
21557 TA
1 TA
21559 TATAATCCGG
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
21 1 0.02
22 5 0.12
23 8 0.19
24 12 0.28
25 10 0.23
26 3 0.07
27 3 0.07
28 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (24 bp):
TAAGTTAATATATAAAAATATTTA
Found at i:22312 original size:31 final size:31
Alignment explanation
Indices: 22277--22363 Score: 131
Period size: 31 Copynumber: 2.8 Consensus size: 31
22267 TAACTCCGGA
*
22277 TGATCATGTCTTAATTAAATGAAAAA-GAAAG
1 TGATCATATCTTAATTAAAT-AAAAACGAAAG
*
22308 TGATCATATCTTAATTATATAAAAACGAAAG
1 TGATCATATCTTAATTAAATAAAAACGAAAG
*
22339 TGACCATATCTTAATTAAATAAAAA
1 TGATCATATCTTAATTAAATAAAAA
22364 TAAAAACGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.10
31 46 0.90
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (31 bp):
TGATCATATCTTAATTAAATAAAAACGAAAG
Found at i:23214 original size:48 final size:47
Alignment explanation
Indices: 23162--23334 Score: 215
Period size: 48 Copynumber: 3.6 Consensus size: 47
23152 GAAACAGAAA
* * *
23162 CGGCGGCGACTTCTTCTACCTCAGCCGTCAATAGGGTTTCAACTGCAG
1 CGGCGACGACTACTTCTACCTC-GCCGTCAATGGGGTTTCAACTGCAG
*
23210 CGGCGACGACTACTTCTACCTCGGCCGTCAATGGGGTTTCAACCGCAG
1 CGGCGACGACTACTTCTACCTC-GCCGTCAATGGGGTTTCAACTGCAG
*
23258 CGGCGACGACTACTTCAACCTCGACCGTC-ATCGGGGTTTCAACTGCAG
1 CGGCGACGACTACTTCTACCTCG-CCGTCAAT-GGGGTTTCAACTGCAG
* *
23306 CGGCGA-GTACTACGTCTAGCTCGGCCGTC
1 CGGCGACG-ACTACTTCTACCTC-GCCGTC
23335 GATTTGTCCA
Statistics
Matches: 111, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
47 4 0.04
48 106 0.95
49 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (47 bp):
CGGCGACGACTACTTCTACCTCGCCGTCAATGGGGTTTCAACTGCAG
Found at i:27439 original size:6 final size:6
Alignment explanation
Indices: 27428--27459 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
27418 GTGTTTGGTT
*
27428 TCGGAA TCGGAA TCGGAA TCGGAA TCGAAA TC
1 TCGGAA TCGGAA TCGGAA TCGGAA TCGGAA TC
27460 TTTTACATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (6 bp):
TCGGAA
Found at i:33511 original size:72 final size:71
Alignment explanation
Indices: 33405--33554 Score: 171
Period size: 72 Copynumber: 2.1 Consensus size: 71
33395 TAAGTGTTGG
* ** * *
33405 AAAAAATAAATTTTAAGGGTAGCCTCATGGTAATAAGTAT-TGAAAAAATGAGACC-CTAATAAA
1 AAAAAATAAATTTTAAGAGTAGCCTCATAATAATAAATATCT-AAAAAATGA-ACCTCCAATAAA
33468 AAATATTA
64 AAATATTA
* *
33476 AAAAAAGTATATTTTAAGAGTATG-CTCATAATAATAAATATCTAAAAATTGAACCTCCAATAAA
1 AAAAAA-TAAATTTTAAGAGTA-GCCTCATAATAATAAATATCTAAAAAATGAACCTCCAATAAA
*
33540 AAATATTG
64 AAATATTA
33548 AAAAAAT
1 AAAAAAT
33555 CAGATTCATA
Statistics
Matches: 67, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
71 10 0.15
72 55 0.82
73 2 0.03
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (71 bp):
AAAAAATAAATTTTAAGAGTAGCCTCATAATAATAAATATCTAAAAAATGAACCTCCAATAAAAA
ATATTA
Found at i:34047 original size:21 final size:21
Alignment explanation
Indices: 34021--34130 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
34011 CTTTCAATAA
34021 AATAATATAATCATTTAAAAT
1 AATAATATAATCATTTAAAAT
34042 AATAATATAAT-ATTTAAACATTT
1 AATAATATAATCATTTAAA-A--T
* *
34065 GAATCAATATCAGTTTCCTTTCAATAA-
1 -AAT-AATAT-A--ATCATTT-AA-AAT
34092 AATAATATAATCATTTAAAAT
1 AATAATATAATCATTTAAAAT
34113 AATAATATAAT-ATTTAAA
1 AATAATATAATCATTTAAA
34131 CATTTGAATT
Statistics
Matches: 73, Mismatches: 4, Indels: 25
0.72 0.04 0.25
Matches are distributed among these distances:
20 16 0.22
21 25 0.34
22 5 0.07
23 1 0.01
24 4 0.05
25 10 0.14
26 4 0.05
28 1 0.01
29 3 0.04
30 3 0.04
31 1 0.01
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (21 bp):
AATAATATAATCATTTAAAAT
Found at i:34091 original size:71 final size:71
Alignment explanation
Indices: 34009--34152 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 71
33999 ACTCATTCAA
34009 TCCTTTCAATAAAATAATATAATCATTTAAAATAATAATATAATATTTAAACATTTGAATCAATA
1 TCCTTTCAATAAAATAATATAATCATTTAAAATAATAATATAATATTTAAACATTTGAATCAATA
34074 TCAGTT
66 TCAGTT
*
34080 TCCTTTCAATAAAATAATATAATCATTTAAAATAATAATATAATATTTAAACATTTGAATTAATA
1 TCCTTTCAATAAAATAATATAATCATTTAAAATAATAATATAATATTTAAACATTTGAATCAATA
34145 TCAGTT
66 TCAGTT
34151 TC
1 TC
34153 AGGCAGCAAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (71 bp):
TCCTTTCAATAAAATAATATAATCATTTAAAATAATAATATAATATTTAAACATTTGAATCAATA
TCAGTT
Found at i:34257 original size:23 final size:24
Alignment explanation
Indices: 34213--34257 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
34203 CTAAAAACTA
**
34213 TCTAACTTAAAAATATTTCTTTAT
1 TCTAACTTAAAAATATAACTTTAT
34237 TCTAA-TTAAAAATATAACTTT
1 TCTAACTTAAAAATATAACTTT
34258 TTTTATCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (24 bp):
TCTAACTTAAAAATATAACTTTAT
Found at i:36620 original size:508 final size:508
Alignment explanation
Indices: 35665--36666 Score: 1986
Period size: 508 Copynumber: 2.0 Consensus size: 508
35655 GTTCTCATTC
35665 ATTCATTTCCCCCAATTCTCCTTCGATACTCATCTCTCGTCCTCCTTCTTCTCCCTCTCGTCTTC
1 ATTCATTTCCCCCAATTCTCCTTCGATACTCATCTCTCGTCCTCCTTCTTCTCCCTCTCGTCTTC
35730 CCTCTCCCACCGTGACAATACCCACCCCATCAGATGATCCTTGTCCCCAAGGATCAAACGATGGA
66 CCTCTCCCACCGTGACAATACCCACCCCATCAGATGATCCTTGTCCCCAAGGATCAAACGATGGA
35795 AAACTGCCCTCACAGCACTGAATAGTCTTCCCAAGTGTCGTGCATCTCGTCCAGGTTAGTCCATC
131 AAACTGCCCTCACAGCACTGAATAGTCTTCCCAAGTGTCGTGCATCTCGTCCAGGTTAGTCCATC
35860 GAACCAACAACTGTGTAATCGGTTTATTGTGTCGATTAACAATTCTTCTGCCTAATATTTTTTTG
196 GAACCAACAACTGTGTAATCGGTTTATTGTGTCGATTAACAATTCTTCTGCCTAATATTTTTTTG
35925 GGTTCTATCCGAAACTGACCCTCATCATCAATCGTAGGAGGATCTGTGGAAGTTGCTGCATCAGG
261 GGTTCTATCCGAAACTGACCCTCATCATCAATCGTAGGAGGATCTGTGGAAGTTGCTGCATCAGG
35990 CCCAACATGCTTCTTCAATAAACTGACATGAAAGACTGGGTGCAACCGCGAAGAATCTGGTAAGT
326 CCCAACATGCTTCTTCAATAAACTGACATGAAAGACTGGGTGCAACCGCGAAGAATCTGGTAAGT
36055 CAAGTTTGTAGGCTACTTCCCCAATTTTTTCAATAATCTTGTAAGGGCCATAAAACCTTGTTGCT
391 CAAGTTTGTAGGCTACTTCCCCAATTTTTTCAATAATCTTGTAAGGGCCATAAAACCTTGTTGCT
36120 AATTTCAAATTTTTCCTCAGGGCGATAGAAGTCTGTCGAATTGCTAATTTCAA
456 AATTTCAAATTTTTCCTCAGGGCGATAGAAGTCTGTCGAATTGCTAATTTCAA
36173 ATTCATTTCCCCCAATTCTCCTTCGATACTCATCTCTCGTCCTCCTTCTTCTCCCTCTCGTCTTC
1 ATTCATTTCCCCCAATTCTCCTTCGATACTCATCTCTCGTCCTCCTTCTTCTCCCTCTCGTCTTC
36238 CCTCTCCCACCGTGACAATACCCACCCCATCAGATGATCCTTGTCCCCAAGGATCAAACGATGGA
66 CCTCTCCCACCGTGACAATACCCACCCCATCAGATGATCCTTGTCCCCAAGGATCAAACGATGGA
* *
36303 AAACTGCCCTCGCAGTACTGAATAGTCTTCCCAAGTGTCGTGCATCTCGTCCAGGTTAGTCCATC
131 AAACTGCCCTCACAGCACTGAATAGTCTTCCCAAGTGTCGTGCATCTCGTCCAGGTTAGTCCATC
36368 GAACCAACAACTGTGTAATCGGTTTATTGTGTCGATTAACAATTCTTCTGCCTAATATTTTTTTG
196 GAACCAACAACTGTGTAATCGGTTTATTGTGTCGATTAACAATTCTTCTGCCTAATATTTTTTTG
36433 GGTTCTATCCGAAACTGACCCTCATCATCAATCGTAGGAGGATCTGTGGAAGTTGCTGCATCAGG
261 GGTTCTATCCGAAACTGACCCTCATCATCAATCGTAGGAGGATCTGTGGAAGTTGCTGCATCAGG
36498 CCCAACATGCTTCTTCAATAAACTGACATGAAAGACTGGGTGCAACCGCGAAGAATCTGGTAAGT
326 CCCAACATGCTTCTTCAATAAACTGACATGAAAGACTGGGTGCAACCGCGAAGAATCTGGTAAGT
36563 CAAGTTTGTAGGCTACTTCCCCAATTTTTTCAATAATCTTGTAAGGGCCATAAAACCTTGTTGCT
391 CAAGTTTGTAGGCTACTTCCCCAATTTTTTCAATAATCTTGTAAGGGCCATAAAACCTTGTTGCT
36628 AATTTCAAATTTTTCCTCAGGGCGATAGAAGTCTGTCGA
456 AATTTCAAATTTTTCCTCAGGGCGATAGAAGTCTGTCGA
36667 TATGGCTGCA
Statistics
Matches: 492, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
508 492 1.00
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (508 bp):
ATTCATTTCCCCCAATTCTCCTTCGATACTCATCTCTCGTCCTCCTTCTTCTCCCTCTCGTCTTC
CCTCTCCCACCGTGACAATACCCACCCCATCAGATGATCCTTGTCCCCAAGGATCAAACGATGGA
AAACTGCCCTCACAGCACTGAATAGTCTTCCCAAGTGTCGTGCATCTCGTCCAGGTTAGTCCATC
GAACCAACAACTGTGTAATCGGTTTATTGTGTCGATTAACAATTCTTCTGCCTAATATTTTTTTG
GGTTCTATCCGAAACTGACCCTCATCATCAATCGTAGGAGGATCTGTGGAAGTTGCTGCATCAGG
CCCAACATGCTTCTTCAATAAACTGACATGAAAGACTGGGTGCAACCGCGAAGAATCTGGTAAGT
CAAGTTTGTAGGCTACTTCCCCAATTTTTTCAATAATCTTGTAAGGGCCATAAAACCTTGTTGCT
AATTTCAAATTTTTCCTCAGGGCGATAGAAGTCTGTCGAATTGCTAATTTCAA
Found at i:44309 original size:19 final size:19
Alignment explanation
Indices: 44285--44333 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
44275 TATGTGTAGA
*
44285 GGTTTCGAAACTTTTAGGG
1 GGTTTCGAAACCTTTAGGG
44304 GGTTTCGAAACCTTTAGGG
1 GGTTTCGAAACCTTTAGGG
*
44323 AGTTTCGAAAC
1 GGTTTCGAAAC
44334 ATTCATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (19 bp):
GGTTTCGAAACCTTTAGGG
Found at i:44652 original size:19 final size:19
Alignment explanation
Indices: 44589--44652 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
44579 TGGTTCCACA
*
44589 AATAGCTTAATTTCATTTT
1 AATAGCTTAATTTCATATT
* * * *
44608 CATAACATAATTTCAAATT
1 AATAGCTTAATTTCATATT
*
44627 CAA-AGCTTAATTTTATATT
1 -AATAGCTTAATTTCATATT
44646 AATAGCT
1 AATAGCT
44653 CAATGCATAT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
18 2 0.06
19 30 0.91
20 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (19 bp):
AATAGCTTAATTTCATATT
Found at i:51668 original size:14 final size:14
Alignment explanation
Indices: 51639--51684 Score: 74
Period size: 14 Copynumber: 3.1 Consensus size: 14
51629 CATTCGTGAA
51639 CGTTCGATTATATGTT
1 CGTTC-ATT-TATGTT
51655 CGTTCATTTATGTT
1 CGTTCATTTATGTT
51669 CGTTCATTTATGTT
1 CGTTCATTTATGTT
51683 CG
1 CG
51685 AACAAATGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 22 0.73
15 3 0.10
16 5 0.17
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.52
Consensus pattern (14 bp):
CGTTCATTTATGTT
Found at i:52435 original size:3 final size:3
Alignment explanation
Indices: 52427--52540 Score: 156
Period size: 3 Copynumber: 38.0 Consensus size: 3
52417 CCATATTGAT
* * * *
52427 TTA TTA TTA TTA TTA TTA TAA TTA TTA TAA TTA TTA TTA TTA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
52475 TTA TTA TTA TTA TAA TAA TAA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
52523 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
52541 AATATATTAA
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:53007 original size:14 final size:14
Alignment explanation
Indices: 52988--53022 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
52978 AGAGACGGAG
52988 AGAGAACCAGAAAC
1 AGAGAACCAGAAAC
53002 AGAGAACCAGAAAC
1 AGAGAACCAGAAAC
53016 AGAGAAC
1 AGAGAAC
53023 AAAGAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.57, C:0.20, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAGAACCAGAAAC
Found at i:53028 original size:21 final size:21
Alignment explanation
Indices: 52990--53051 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
52980 AGACGGAGAG
* *
52990 AGAACCAGA-AACAGAGAACC
1 AGAAACAGAGAACAAAGAACC
*
53010 AGAAACAGAGAACAAAGAAAC
1 AGAAACAGAGAACAAAGAACC
* * *
53031 AAAAACAAAGAACAAATAACC
1 AGAAACAGAGAACAAAGAACC
53052 CACCACCAGC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.65, C:0.19, G:0.15, T:0.02
Consensus pattern (21 bp):
AGAAACAGAGAACAAAGAACC
Found at i:58712 original size:18 final size:18
Alignment explanation
Indices: 58686--58731 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
58676 AAATTTGTAA
* *
58686 TTTAACATTCGTAGAATT
1 TTTATCATTCGTAGAATG
58704 TTTATCATTCGTAGAATG
1 TTTATCATTCGTAGAATG
*
58722 TTTATTATTC
1 TTTATCATTC
58732 AATGATAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TTTATCATTCGTAGAATG
Found at i:59128 original size:3 final size:3
Alignment explanation
Indices: 59120--59190 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
59110 AATTGAACTT
59120 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59168 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
59191 TTACGAATAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63580 original size:65 final size:61
Alignment explanation
Indices: 63421--63604 Score: 199
Period size: 65 Copynumber: 2.9 Consensus size: 61
63411 TGATCGTTGG
* * * *
63421 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCAATGTTTCAAA
1 ATCCTCAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAA
* * * *
63483 ATAGCTAGAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATA
1 AT-CCT-CAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATG-TTTC--A
63548 AA
60 AA
*
63550 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCGATG
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATG
63605 ATCAATTTAA
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 41 0.40
65 48 0.47
66 2 0.02
67 5 0.05
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (61 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAA
Found at i:63645 original size:65 final size:64
Alignment explanation
Indices: 63447--63646 Score: 194
Period size: 65 Copynumber: 3.1 Consensus size: 64
63437 TGCACTAAGA
* * * * * *
63447 GTGCATCGATGCATCAAGTGCATTCAATGTTTCA-AAATAGC-TAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTATCATAAA-ATCAT-CAGTGCATCGATGCATGGTT
63510 G
64 G
* * *
63511 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TATCATAAAATCATCAGTGCATCGATGCATGGT-T
63576 -
64 G
* * *
63576 GTGCATCGATGCATGAAATGCATTCGATG-ATCAATTTAATTCAT-AGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTATC-A-TAAAATCATCAGTGCATCGATGCATGG-T
63639 TG
63 TG
63641 GTGCAT
1 GTGCAT
63647 TGGTGTATCA
Statistics
Matches: 116, Mismatches: 12, Indels: 15
0.81 0.08 0.10
Matches are distributed among these distances:
63 2 0.02
64 45 0.39
65 64 0.55
66 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTATCATAAAATCATCAGTGCATCGATGCATGGTTG
Found at i:63974 original size:12 final size:12
Alignment explanation
Indices: 63952--63984 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
63942 TAAGATTTTC
63952 TTTGAAAATAAAT
1 TTTG-AAATAAAT
63965 TTTGAAATAAAT
1 TTTGAAATAAAT
63977 TTTGAAAT
1 TTTGAAAT
63985 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (12 bp):
TTTGAAATAAAT
Found at i:72178 original size:18 final size:17
Alignment explanation
Indices: 72124--72172 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
72114 TTGGATCCTT
* *
72124 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
72142 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
72160 AGTGCATTCGATG
1 AGTGCA-TCGATG
72173 TTTCAAAATA
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:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:72277 original size:65 final size:64
Alignment explanation
Indices: 72118--72303 Score: 234
Period size: 65 Copynumber: 2.9 Consensus size: 64
72108 TGACCGTTGG
* * *
72118 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAA
1 ATCCTCAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
72181 T
64 T
* ** *
72182 AGCCAGAGTGCATCGATGCATGGCTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA
1 ATCCTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
72247 -
64 T
*
72247 ATCCTCAGTGCATCGGTGCATGGTACGTGCATCGATGCATGAAATGCATTCGATGTT
1 ATCCTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
72304 CAATTTAATT
Statistics
Matches: 106, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 47 0.44
65 54 0.51
66 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (64 bp):
ATCCTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:72342 original size:65 final size:64
Alignment explanation
Indices: 72143--72353 Score: 216
Period size: 65 Copynumber: 3.3 Consensus size: 64
72133 GTGCACTAAG
* * ** *
72143 AGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTT
* *
72207 AGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGG
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGG
72270 -T
63 TT
* * *
72271 ACGTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATAGA
1 A-GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCAT-GG
72335 TT
63 TT
* *
72337 GGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
72354 CTCTGAAAAT
Statistics
Matches: 123, Mismatches: 14, Indels: 19
0.79 0.09 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 51 0.41
65 63 0.51
66 1 0.01
67 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTT
Found at i:75369 original size:33 final size:34
Alignment explanation
Indices: 75327--75397 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
75317 GAGCTTTCCA
75327 ATAATTTTTCATGGTGAATATTCTA-TTAAACCAT
1 ATAATTTTTCATGGTGAATA-TCTATTTAAACCAT
75361 ATAA-TTTTCATGGTGAATATCTATTTAAACCAT
1 ATAATTTTTCATGGTGAATATCTATTTAAACCAT
75394 ATAA
1 ATAA
75398 ACCTACAAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 4 0.11
33 28 0.78
34 4 0.11
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (34 bp):
ATAATTTTTCATGGTGAATATCTATTTAAACCAT
Done.