Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006237.1 Hibiscus syriacus cultivar Beakdansim tig00014864_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: 77919
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5894 original size:16 final size:16
Alignment explanation
Indices: 5868--5912 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5858 TTTGAATACA
*
5868 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
5885 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
5900 ATTCAATTTATTT
1 ATTCAATTTATTT
5913 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:6854 original size:83 final size:82
Alignment explanation
Indices: 6689--7489 Score: 1183
Period size: 83 Copynumber: 9.7 Consensus size: 82
6679 AATTAAATGA
*
6689 AAGATGAATGTGTTC-ATAGCATCTTTTGGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGAC
1 AAGATGAAT-T-TTCAATAGCATCTTCT-GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-C
*
6752 AGAA-CAATCATTGAGTTTAG
62 AGAACCAATCATTGAATTTAG
*
6772 AAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTT-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
6837 ACCAATCATTGAATTTAG
65 ACCAATCATTGAATTTAG
* *
6855 AAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTT-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
6919 AA-CAATCATTGAGTTTAG
64 AACCAATCATTGAATTTAG
6937 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTT-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
7002 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTAG
7020 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAAT-T-TTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
*
7083 GAA-CAATCATTGAGTTTAG
63 GAACCAATCATTGAATTTAG
7102 AAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATTT-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
7167 ACCAATCATTGAATTTGG
65 ACCAATCATTGAATTTAG
7185 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAAT-T-TTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
7249 AACCAATCATTGAATTTGG
64 AACCAATCATTGAATTTAG
7268 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAAT-T-TTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
7332 AACCAATCAGTGAGTTTAG
64 AACCAATCATTGAATTTAG
* * *
7351 AAGATGAATTTGCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGGTTGGGCAG
1 AAGATGAATTT-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTTGGCAG
**
7416 AACCAATCATTGAATTCGG
64 AACCAATCATTGAATTTAG
*
7435 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTG
1 AAGATGAAT-T-TTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
7490 ATTCAGTAGG
Statistics
Matches: 670, Mismatches: 27, Indels: 42
0.91 0.04 0.06
Matches are distributed among these distances:
80 1 0.00
81 5 0.01
82 189 0.28
83 394 0.59
84 76 0.11
85 4 0.01
86 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (82 bp):
AAGATGAATTTTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAA
CCAATCATTGAATTTAG
Found at i:6989 original size:165 final size:165
Alignment explanation
Indices: 6689--7489 Score: 1279
Period size: 165 Copynumber: 4.8 Consensus size: 165
6679 AATTAAATGA
* *
6689 AAGATGAATGTGTTCATAGCATCTTTTGGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 AAGATGAATGTGTCCATAGCATCTTCT-GGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
**
6754 AACAATCATTGAGTTTAGAAGATGAATTTACCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
65 AACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
6819 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTAG
130 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTAG
* *
6855 AAGATAAATTTG-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
1 AAGATGAATGTGTCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAG
6919 AACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
65 AACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
6984 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTGG
130 CTGATCTGGTTTGGCAGAACCAATCATTGAATTTAG
*
7020 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
1 AAGATGAATGTGTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
7085 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
66 ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
*
7150 TGATCTGGTTTGGCAGAACCAATCATTGAATTTGG
131 TGATCTGGTTTGGCAGAACCAATCATTGAATTTAG
*
7185 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
1 AAGATGAATGTGTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
* * *
7249 AACCAATCATTGAATTTGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTT
65 AA-CAATCATTGAGTTTAGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* *
7313 ATCTGATCTGGTTTGGCAGAACCAATCAGTGAGTTTAG
128 ATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAG
* * *
7351 AAGATGAATTTG-CCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGGTTGGGCA
1 AAGATGAATGTGTCC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GGTTGGACA
* ** *
7415 GAACCAATCATTGAATTCGGAAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGT
64 GAA-CAATCATTGAGTTTAGAAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGT
*
7479 TATTTGATCTG
127 TATCTGATCTG
7490 ATTCAGTAGG
Statistics
Matches: 606, Mismatches: 21, Indels: 15
0.94 0.03 0.02
Matches are distributed among these distances:
165 358 0.59
166 169 0.28
167 79 0.13
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (165 bp):
AAGATGAATGTGTCCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGA
ACAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATC
TGATCTGGTTTGGCAGAACCAATCATTGAATTTAG
Found at i:7175 original size:248 final size:249
Alignment explanation
Indices: 6689--7489 Score: 1332
Period size: 248 Copynumber: 3.2 Consensus size: 249
6679 AATTAAATGA
*
6689 AAGATGAATGTGTTCATAGCATCTTTTGGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACA
1 AAGATGAATGTGTTCATAGCATCTTCT-GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
* * *
6753 GAA-CAATCATTGAGTTTAGAAGATGAAT-T-TACCAATAGCATCTTCTGGAAGTGTTCTTTGAG
64 GAACCAATCATTGAATTTGGAAGATGAATGTGT-TC-ATAGCATCTTCTGGAAGTGTTCTTTGAG
* *
6815 TTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATAAATTTGCCAATAGCATCTT
127 TTATCTGATCTGGTTTGGCAGAACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTT
* *
6880 CTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAA-CAATCATTGAGTTTAG
192 CTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAATTTGG
*
6937 AAGATGAATTTG-TCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 AAGATGAATGTGTTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
7001 AACCAATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
65 AACCAATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
7066 TCTGATCTGG-TTGGACAGAA-CAATCATTGAGTTTAGAAGATGAATTTGTCAATAGCATCTTCT
130 TCTGATCTGGTTTGG-CAGAACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCT
7129 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGG
194 GGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGG
7185 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
7250 ACCAATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 ACCAATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
7315 CTGATCTGGTTTGGCAGAACCAATCAGTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTAG
131 CTGATCTGGTTTGGCAGAACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGG
* *
7380 AAGTGTTCTTTGAGTTATCTGATCTGGGTTGGGCAGAACCAATCATTGAATTCGG
196 AAGTGTTCTTTGAGTTATCTGATCT-GGTTTGGCAGAACCAATCATTGAATTTGG
*
7435 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTG
1 AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
7490 ATTCAGTAGG
Statistics
Matches: 524, Mismatches: 17, Indels: 22
0.93 0.03 0.04
Matches are distributed among these distances:
247 114 0.22
248 253 0.48
249 75 0.14
250 82 0.16
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (249 bp):
AAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTGGAAGATGAATGTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTTGGCAGAACCAATCATTGAGTTTAGAAGATGAATTTGCCAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTGG
Found at i:8543 original size:116 final size:116
Alignment explanation
Indices: 8125--8766 Score: 882
Period size: 116 Copynumber: 5.6 Consensus size: 116
8115 TCGAATCCAC
* *
8125 TTGATGGATCAGTC-TTTCCAGAGAAG-GTTCATAATGAGAAGAACTCG---TCTGAAGAAGGAA
1 TTGATGGATCA-TCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
* * * ** *
8185 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCCGAATCCATCAT
64 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
* * *
8238 TTGATGGATCAGTCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACT--T-ATCTGAAGAAGGAA
1 TTGATGGATCA-TCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
* * * *
8299 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT-TTCTGAATTCATCAAA
64 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCT-TGAATTCATC-AT
* * *
8353 TTGACGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
8418 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
66 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
*
8469 TTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
8534 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
66 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
*
8585 TTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
1 TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
*
8650 AGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTGCTTGAATTCATCAT
66 AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
** * *
8701 TTGATGGATCATCATCCCCAGCAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAG-A
1 TTGATGGATCATCATTGCCAG--GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
8761 GAAGAA
64 GAAGAA
8767 TTTATTCAAT
Statistics
Matches: 494, Mismatches: 23, Indels: 24
0.91 0.04 0.04
Matches are distributed among these distances:
113 24 0.05
114 131 0.27
115 11 0.02
116 247 0.50
117 79 0.16
118 2 0.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (116 bp):
TTGATGGATCATCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGA
AGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
Found at i:8917 original size:3 final size:3
Alignment explanation
Indices: 8900--8957 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
8890 TTTTTATCCA
* *
8900 TAT TTT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8947 TAT TAT TAT TA
1 TAT TAT TAT TA
8958 AATATATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:8984 original size:14 final size:15
Alignment explanation
Indices: 8956--8990 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
8946 TTATTATTAT
8956 TAAATATATATTAAA
1 TAAATATATATTAAA
8971 TAAATATATA-TAAA
1 TAAATATATATTAAA
8985 TAAATA
1 TAAATA
8991 ATTACAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATATATATTAAA
Found at i:9442 original size:17 final size:16
Alignment explanation
Indices: 9419--9466 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
9409 CACCGGAGAC
9419 AGAGACAGAAAAAAAG
1 AGAGACAGAAAAAAAG
* *
9435 AGGAGACAGATAACACAG
1 A-GAGACAGA-AAAAAAG
9453 AGAGACA-AAAAAAA
1 AGAGACAGAAAAAAA
9467 AACAGAGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
15 4 0.15
16 2 0.08
17 14 0.54
18 6 0.23
ACGTcount: A:0.65, C:0.10, G:0.23, T:0.02
Consensus pattern (16 bp):
AGAGACAGAAAAAAAG
Found at i:14320 original size:58 final size:59
Alignment explanation
Indices: 14228--14349 Score: 165
Period size: 60 Copynumber: 2.1 Consensus size: 59
14218 AATTTAAAAA
* *
14228 AATTGTAACACCCTTACCTGTATTTCATTCCC-AAATACGAGTCAAAATGTCACAAGCT
1 AATTGTAACACCCTTACCTGTATTTAATTCCCAAAATACGAGTCAAAATGTCACAAACT
** * * *
14286 AATTGTAACAGTCTTACCTGTATTTAATTTCCAAAAATATGAGTCAGAATGTCACAAACT
1 AATTGTAACACCCTTACCTGTATTTAA-TTCCCAAAATACGAGTCAAAATGTCACAAACT
14346 AATT
1 AATT
14350 TTATAGTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 24 0.44
59 4 0.07
60 27 0.49
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (59 bp):
AATTGTAACACCCTTACCTGTATTTAATTCCCAAAATACGAGTCAAAATGTCACAAACT
Found at i:17518 original size:31 final size:31
Alignment explanation
Indices: 17480--17543 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
17470 TATACTTGGA
* * *
17480 GGCTCCTCAGCTTTGTGCTCGGGGTCTTACT
1 GGCTCCTCAGCTCTGTGCTCAGGGTCCTACT
*
17511 GGCTCCTCGGCTCTGTGCTCAGGGTCCTACT
1 GGCTCCTCAGCTCTGTGCTCAGGGTCCTACT
17542 GG
1 GG
17544 ACTTGACGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.06, C:0.31, G:0.31, T:0.31
Consensus pattern (31 bp):
GGCTCCTCAGCTCTGTGCTCAGGGTCCTACT
Found at i:19176 original size:17 final size:17
Alignment explanation
Indices: 19151--19190 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
19141 AAATTTCTTG
*
19151 AATTTTCGATTCGATCT
1 AATTATCGATTCGATCT
19168 AATTATCGATTCGATCT
1 AATTATCGATTCGATCT
*
19185 GATTAT
1 AATTAT
19191 TTGAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
AATTATCGATTCGATCT
Found at i:19844 original size:5 final size:5
Alignment explanation
Indices: 19833--19865 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
19823 TCAATTTGAT
*
19833 TTTAA TTCAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTT
19866 TTAAGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:19853 original size:15 final size:15
Alignment explanation
Indices: 19821--19865 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
19811 GAACACAGAT
*
19821 ATTCAATTTGATTTTA
1 ATTCAATTT-AATTTA
19837 ATTCAATTTAATTTA
1 ATTCAATTTAATTTA
*
19852 ATTTAATTTAATTT
1 ATTCAATTTAATTT
19866 TTAAGAAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (15 bp):
ATTCAATTTAATTTA
Found at i:23781 original size:34 final size:34
Alignment explanation
Indices: 23735--23802 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
23725 ATATATACAT
23735 GATTACAAGAGATCAATTAGACTACAATTAAGGA
1 GATTACAAGAGATCAATTAGACTACAATTAAGGA
* *
23769 GATTACAGGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGACTACAATTAAGGA
23803 AACAAAGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.24
Consensus pattern (34 bp):
GATTACAAGAGATCAATTAGACTACAATTAAGGA
Found at i:28396 original size:34 final size:34
Alignment explanation
Indices: 28350--28416 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
28340 ATATATACAT
28350 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
1 GATTACAAGAGATCAATTAGGCTACAATTAAGGA
*
28384 GATTACAGGAGATCAATTAGGCTACAATTAAGG
1 GATTACAAGAGATCAATTAGGCTACAATTAAGG
28417 GAACAAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (34 bp):
GATTACAAGAGATCAATTAGGCTACAATTAAGGA
Found at i:31085 original size:20 final size:21
Alignment explanation
Indices: 31044--31089 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31034 TATTAAGGAC
*
31044 AAATATATAATTATGCCAATT
1 AAATATAAAATTATGCCAATT
*
31065 AAATATAAAATTAT-TCAATT
1 AAATATAAAATTATGCCAATT
31085 AAATA
1 AAATA
31090 ATTGAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (21 bp):
AAATATAAAATTATGCCAATT
Found at i:44807 original size:18 final size:18
Alignment explanation
Indices: 44784--44818 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44774 TTCCATCCGG
*
44784 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
44802 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
44819 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:54447 original size:26 final size:26
Alignment explanation
Indices: 54418--54469 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
54408 ACATGGAGGT
54418 TTGAATAATCAGCTGGTTTACCAGTC
1 TTGAATAATCAGCTGGTTTACCAGTC
*
54444 TTGATTAATCAGCTGGTTTACCAGTC
1 TTGAATAATCAGCTGGTTTACCAGTC
54470 CACATCTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
TTGAATAATCAGCTGGTTTACCAGTC
Found at i:56820 original size:16 final size:16
Alignment explanation
Indices: 56799--56831 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56789 GTTGGATCAT
56799 ATAAGCATCCATGAGA
1 ATAAGCATCCATGAGA
56815 ATAAGCATCCATGAGA
1 ATAAGCATCCATGAGA
56831 A
1 A
56832 GTAGCGTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (16 bp):
ATAAGCATCCATGAGA
Found at i:67405 original size:19 final size:19
Alignment explanation
Indices: 67381--67426 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
67371 TTTTGGGTAC
67381 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
67400 CGATGCACATACCATGCAT
1 CGATGCACATACCATGCAT
*
67419 CGTTGCAC
1 CGATGCAC
67427 TCCATGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (19 bp):
CGATGCACATACCATGCAT
Found at i:76975 original size:13 final size:13
Alignment explanation
Indices: 76957--76986 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
76947 GAGATGAAAG
76957 AAAGTAAAAGTGA
1 AAAGTAAAAGTGA
76970 AAAGTAAAAGTGA
1 AAAGTAAAAGTGA
76983 AAAG
1 AAAG
76987 AAGATAAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.13
Consensus pattern (13 bp):
AAAGTAAAAGTGA
Done.