Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002818.1 Hibiscus syriacus cultivar Beakdansim tig00005798_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: 52327
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:7165 original size:17 final size:18
Alignment explanation
Indices: 7143--7176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7133 TCAGCCGGTC
7143 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
7160 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
7177 CTAGTAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:10766 original size:42 final size:42
Alignment explanation
Indices: 10708--10801 Score: 161
Period size: 42 Copynumber: 2.2 Consensus size: 42
10698 TTAATTTTAT
*
10708 TAATATAATATATTTTCAACATGACATATCAAAACTACGAATA
1 TAAT-TAAAATATTTTCAACATGACATATCAAAACTACGAATA
10751 TAATTAAAATATTTTCAACATGACATATCAAAACTACGAATA
1 TAATTAAAATATTTTCAACATGACATATCAAAACTACGAATA
*
10793 TAATAAAAA
1 TAATTAAAA
10802 ATACACGTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 45 0.92
43 4 0.08
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.31
Consensus pattern (42 bp):
TAATTAAAATATTTTCAACATGACATATCAAAACTACGAATA
Found at i:12023 original size:18 final size:19
Alignment explanation
Indices: 12000--12043 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
11990 CCAGTAATCC
*
12000 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
12018 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
12038 TATTCC
1 TATTCC
12044 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:12031 original size:20 final size:20
Alignment explanation
Indices: 12006--12043 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11996 ATCCTATTCC
*
12006 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
12026 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
12044 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:17808 original size:10 final size:10
Alignment explanation
Indices: 17793--17827 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
17783 TTTATCATAC
17793 CAAATTCTCT
1 CAAATTCTCT
17803 CAAATTCTCT
1 CAAATTCTCT
17813 -AAATTTCTCT
1 CAAA-TTCTCT
17823 CAAAT
1 CAAAT
17828 ATTCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:17832 original size:12 final size:12
Alignment explanation
Indices: 17796--17834 Score: 50
Period size: 10 Copynumber: 3.6 Consensus size: 12
17786 ATCATACCAA
17796 ATTCTCTC-AA-
1 ATTCTCTCAAAT
17806 ATTCTCT-AAAT
1 ATTCTCTCAAAT
17817 -TTCTCTCAAAT
1 ATTCTCTCAAAT
17828 ATTCTCT
1 ATTCTCT
17835 TTTTAAGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 15 0.60
11 4 0.16
12 6 0.24
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTCTCTCAAAT
Found at i:18163 original size:111 final size:111
Alignment explanation
Indices: 17965--18289 Score: 596
Period size: 111 Copynumber: 2.9 Consensus size: 111
17955 ACATATCTCT
*
17965 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATATTTAGT
1 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
18030 TAATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
* *
18076 ACATTTTGCTGATACAATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
18141 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
*
18187 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
18252 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
18290 TTTTTGTAAT
Statistics
Matches: 206, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 206 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (111 bp):
ACACTTTGCTGATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATGCATGATTATTAGATTAAGAATTAAATATATCG
Found at i:19819 original size:18 final size:18
Alignment explanation
Indices: 19796--19835 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
19786 CCAGCAGCCA
19796 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
19814 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
19832 CCGC
1 CCGC
19836 CATCGCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.23, T:0.20
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:20184 original size:9 final size:9
Alignment explanation
Indices: 20172--20203 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
20162 ACCTGCTTAG
*
20172 GACGACGAC
1 GACGACGAT
20181 GACGACGAT
1 GACGACGAT
20190 GACGACGAT
1 GACGACGAT
20199 GACGA
1 GACGA
20204 TGGTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.25, G:0.34, T:0.06
Consensus pattern (9 bp):
GACGACGAT
Found at i:20282 original size:35 final size:35
Alignment explanation
Indices: 20243--20320 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
20233 ATATTTCAGT
20243 TAATTTTGTT-T-A-TTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATCATTTACCATTTAAT-TC--TTATTG
*
20278 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTATCATTTACCATTTAATTCTTATTG
*
20313 TAAGTTTG
1 TAATTTTG
20321 CTGTATTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
35 21 0.57
36 1 0.03
37 3 0.08
38 12 0.32
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (35 bp):
TAATTTTGTTATCATTTACCATTTAATTCTTATTG
Found at i:35245 original size:70 final size:70
Alignment explanation
Indices: 35122--35257 Score: 236
Period size: 70 Copynumber: 1.9 Consensus size: 70
35112 TTATGTAATA
*
35122 TTTCAAGTTTGAATCTCGACGTAAACACTAACAAGTAACACTATTTTAAACATTTGAAGCCATGT
1 TTTCAAGTTTGAATCACGACGTAAACACTAACAAGTAACACTATTTTAAACATTTGAAGCCATGT
35187 TCTTG
66 TCTTG
* * *
35192 TTTCGAGTTTGAATCACGTCGTAAACACTAACAAGTAACACTATTTTATACATTTGAAGCCATGT
1 TTTCAAGTTTGAATCACGACGTAAACACTAACAAGTAACACTATTTTAAACATTTGAAGCCATGT
35257 T
66 T
35258 ATGTCTTTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (70 bp):
TTTCAAGTTTGAATCACGACGTAAACACTAACAAGTAACACTATTTTAAACATTTGAAGCCATGT
TCTTG
Found at i:38373 original size:18 final size:18
Alignment explanation
Indices: 38347--38381 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38337 ATTAATATAA
*
38347 TTATAAAAATATTATTTT
1 TTATAAAAATAATATTTT
*
38365 TTATTAAAATAATATTT
1 TTATAAAAATAATATTT
38382 ATATAATTAT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTATAAAAATAATATTTT
Found at i:38570 original size:24 final size:25
Alignment explanation
Indices: 38520--38577 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
38510 AGCGATATGG
*
38520 TAATATTT-TTTTTATAATTAATGT
1 TAATATTTATTGTTATAATTAATGT
**
38544 TAATATTTATTGTTATGTTTAAT-T
1 TAATATTTATTGTTATAATTAATGT
38568 TAA-ATTTATT
1 TAATATTTATT
38578 ATGAATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 12 0.40
25 11 0.37
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (25 bp):
TAATATTTATTGTTATAATTAATGT
Found at i:40201 original size:42 final size:42
Alignment explanation
Indices: 40125--40224 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
40115 ATGCCACAAT
* * *
40125 GGTACATGCCTAGCCCTCCACTTCAGATGCCATCTCCTCAGG
1 GGTACATGCCAAGCCCACCACTTCAGATGCCATCTCCGCAGG
* * * *
40167 GGTATATGCCAAGCCCACCAGTTCATATGTCATCTCCGCAGG
1 GGTACATGCCAAGCCCACCACTTCAGATGCCATCTCCGCAGG
* * *
40209 GTTACATTCCTAGCCC
1 GGTACATGCCAAGCCC
40225 GCCAGGTTAC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (42 bp):
GGTACATGCCAAGCCCACCACTTCAGATGCCATCTCCGCAGG
Found at i:40253 original size:21 final size:21
Alignment explanation
Indices: 40202--40253 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
40192 TATGTCATCT
*
40202 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
40223 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
40244 CCGCAGGGTT
1 CCGCAGGGTT
40254 TTATACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:40829 original size:32 final size:32
Alignment explanation
Indices: 40775--40875 Score: 132
Period size: 32 Copynumber: 3.1 Consensus size: 32
40765 AATGTTTTTA
* *
40775 AAATATAAATTATAATATTCGAAATTTAAAATT
1 AAATA-AAAATATATTATTCGAAATTTAAAATT
*
40808 AAATAAAAATATATTATTCGAAATTTAAATTT
1 AAATAAAAATATATTATTCGAAATTTAAAATT
* *
40840 AAATATAAAT-TATATATTCGAAATTTAACATT
1 AAATAAAAATATAT-TATTCGAAATTTAAAATT
40872 AAAT
1 AAAT
40876 TCAAGTTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
31 3 0.05
32 53 0.87
33 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (32 bp):
AAATAAAAATATATTATTCGAAATTTAAAATT
Found at i:41178 original size:30 final size:31
Alignment explanation
Indices: 41120--41196 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
41110 AAAACTGAAT
*
41120 TAAACGGGGACGGGGAAAAAATCGTTTATGC
1 TAAACGGGGACGGGGAAAAAATCATTTATGC
* * * *
41151 TAAACAGGGATGGGGAAAAACT-ATTTATGT
1 TAAACGGGGACGGGGAAAAAATCATTTATGC
41181 TAAACGGGGACGGGGA
1 TAAACGGGGACGGGGA
41197 CGGGTTTAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 20 0.51
31 19 0.49
ACGTcount: A:0.36, C:0.10, G:0.34, T:0.19
Consensus pattern (31 bp):
TAAACGGGGACGGGGAAAAAATCATTTATGC
Found at i:41485 original size:19 final size:18
Alignment explanation
Indices: 41461--41497 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
41451 ATTCCAACGA
*
41461 TTTTTTAAGCGGGGACGGG
1 TTTTTTAAAC-GGGACGGG
41480 TTTTTTAAACGGGACGGG
1 TTTTTTAAACGGGACGGG
41498 GGACCAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.32
Consensus pattern (18 bp):
TTTTTTAAACGGGACGGG
Found at i:42231 original size:124 final size:126
Alignment explanation
Indices: 41754--42255 Score: 791
Period size: 124 Copynumber: 4.0 Consensus size: 126
41744 GCGCTTTAAA
41754 GTCCCCTAAGGAATAATAGGTATTGACATG-ATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATA-GTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
41818 CAATGATAACATATTCTCTGACAAAATAATGAAAGGCGC-CCCCCGGGAACGCGCCTTCACG
65 CAATGATAACATATTCTCTGACAAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
41879 GTCCCCTAAGGAATAATATTATTGACATAAATAGTTCCC-GGGGACATAATAAGTGACATAATAG
1 GTCCCCTAAGGAATAATAGTATTGACATGAATAGTTCCCGGGGGAC---ATAAGTGACATAATAG
* * * * *
41943 GGTAATGATATCATATTCTCTGACAAAATAATGGAAGGCACGCCCCCGGGAACGCACCTTCACG
63 GGCAATGATAACATATTCTCTGACAAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
42007 GTCCCCTAAGGAATAATAGGTATTGACACGAATAGTTCCCGGGGGACATAAGTGACATAATA-GG
1 GTCCCCTAAGGAATAATA-GTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* * *
42071 CAATGATAACATATTCTCGGACAAAATAATGGAAGGCGCTCCCCCGGGAACGCGCCTTCACG
65 CAATGATAACATATTCTCTGACAAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
42133 GTCCCCTAAGGAATAAT-GTATTGATATGAATAGTTCCC-GGGGACATAAGTGACATAATAGGGC
1 GTCCCCTAAGGAATAATAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGGC
* *
42196 AATGATAACATATTTTCTGACAAAATAATGAAAGGCGCGCCCCCGAGAACGCGCCTTCAC
66 AATGATAACATATTCTCTGACAAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCAC
42256 ATGAATAGTA
Statistics
Matches: 346, Mismatches: 23, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
123 21 0.06
124 92 0.27
125 27 0.08
126 75 0.22
127 68 0.20
128 39 0.11
129 18 0.05
130 6 0.02
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (126 bp):
GTCCCCTAAGGAATAATAGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGGC
AATGATAACATATTCTCTGACAAAATAATGAAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:44114 original size:139 final size:139
Alignment explanation
Indices: 43864--44141 Score: 529
Period size: 139 Copynumber: 2.0 Consensus size: 139
43854 TTGAGTTCGA
43864 AACTCAACATCATTACGTGAATGATCGAGTGGTTCGTGATCGCTGCCAATTCTACCGTGTCTTTT
1 AACTCAACATCATTACGTGAATGATCGAGTGGTTCGTGATCGCTGCCAATTCTACCGTGTCTTTT
*
43929 GGACTTACCCTTAATGTATTAATGCAGTCAAGTACTGTAAACCAGTTGTCCAAATTGATGGTACT
66 GGACTTACCCTCAATGTATTAATGCAGTCAAGTACTGTAAACCAGTTGTCCAAATTGATGGTACT
43994 TTCTTGTAT
131 TTCTTGTAT
*
44003 AACTCAACATCATTACGTGAATGATCGAGTGGTTCGTGATCGCTGCTAATTCTACCGTGTCTTTT
1 AACTCAACATCATTACGTGAATGATCGAGTGGTTCGTGATCGCTGCCAATTCTACCGTGTCTTTT
*
44068 GGACTTACCCTCAGTGTATTAATGCAGTCAAGTACTGTAAACCAGTTGTCCAAATTGATGGTACT
66 GGACTTACCCTCAATGTATTAATGCAGTCAAGTACTGTAAACCAGTTGTCCAAATTGATGGTACT
44133 TTCTTGTAT
131 TTCTTGTAT
44142 GAGAATTCAA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 136 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (139 bp):
AACTCAACATCATTACGTGAATGATCGAGTGGTTCGTGATCGCTGCCAATTCTACCGTGTCTTTT
GGACTTACCCTCAATGTATTAATGCAGTCAAGTACTGTAAACCAGTTGTCCAAATTGATGGTACT
TTCTTGTAT
Found at i:46337 original size:51 final size:51
Alignment explanation
Indices: 46258--46385 Score: 143
Period size: 51 Copynumber: 2.5 Consensus size: 51
46248 TAGCAGTAAA
* **
46258 GCGCCCCCTTGAACCGCGCTATATGCTGATTTGGCG-T-CACGTGGGGTATAGC
1 GCGCCCCC-TGAACCGCGCTATACGCTGACATGG-GTTACACGT-GGGTATAGC
* *
46310 GCGCCCCCTGTACCGCGCTATACGCTGACATGGGTTACACGTGTGTATAGC
1 GCGCCCCCTGAACCGCGCTATACGCTGACATGGGTTACACGTGGGTATAGC
* **
46361 GCGCCCCCTGATCCGTTCTATACGC
1 GCGCCCCCTGAACCGCGCTATACGC
46386 CACGTAGGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
50 1 0.02
51 51 0.78
52 13 0.20
ACGTcount: A:0.16, C:0.33, G:0.27, T:0.24
Consensus pattern (51 bp):
GCGCCCCCTGAACCGCGCTATACGCTGACATGGGTTACACGTGGGTATAGC
Found at i:49545 original size:65 final size:65
Alignment explanation
Indices: 49413--49572 Score: 232
Period size: 65 Copynumber: 2.5 Consensus size: 65
49403 GCACCAAGTG
* ***
49413 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGCTTA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* **
49477 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* *
49542 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
49573 CAATTAATTC
Statistics
Matches: 85, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
64 27 0.32
65 58 0.68
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:49561 original size:17 final size:19
Alignment explanation
Indices: 49523--49569 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
49513 ATATTCAGAG
49523 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
49542 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
49559 TGCATTCGATG
1 TGCA-TCGATG
49570 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:49592 original size:65 final size:62
Alignment explanation
Indices: 49413--49619 Score: 211
Period size: 65 Copynumber: 3.2 Consensus size: 62
49403 GCACCAAGTG
* **
49413 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCTTA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG-AGA
* *
49477 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
49541 A
62 A
* * * * *
49542 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
49607 TGCATCGGTGCAT
1 TGCATCGATGCAT
49620 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
63 2 0.02
64 35 0.29
65 78 0.64
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:49810 original size:20 final size:21
Alignment explanation
Indices: 49787--49826 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
49777 GAATCGAATA
49787 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
49807 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
49827 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:50067 original size:2 final size:2
Alignment explanation
Indices: 50060--50101 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
50050 TAGCCAATTG
50060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50102 TAGGCTGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.