Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012708.1 Corchorus olitorius cultivar O-4 contig12741, 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: 20047
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:1616 original size:9 final size:9
Alignment explanation
Indices: 1602--1629 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
1592 AAAATGGTTG
1602 GTTTGTTTT
1 GTTTGTTTT
1611 GTTTGTTTT
1 GTTTGTTTT
1620 GTTTGTTTT
1 GTTTGTTTT
1629 G
1 G
1630 ATGTTTACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.25, T:0.75
Consensus pattern (9 bp):
GTTTGTTTT
Found at i:5570 original size:18 final size:18
Alignment explanation
Indices: 5547--5584 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
5537 ACACGCTTTC
5547 AAAAAAGGATTTTTCAAAA
1 AAAAAAGG-TTTTTCAAAA
5566 AAAAAAGGTTTTTCAAAA
1 AAAAAAGGTTTTTCAAAA
5584 A
1 A
5585 TGGTTTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.58, C:0.05, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAAAAGGTTTTTCAAAA
Found at i:7215 original size:36 final size:36
Alignment explanation
Indices: 7114--7654 Score: 604
Period size: 36 Copynumber: 15.2 Consensus size: 36
7104 TTCAGATGCT
*
7114 TCAGTTCATTTCAGTTGATCCAGGGTGATCTTTT-A
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* *
7149 TTCGGTTTATTTTAG-TGATCCAGGGTGATCTTTTCA
1 -TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * *
7185 TCAGTTTATTTTAGTTGATCCAGGGAGATCTTTTCT
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * * *
7221 TCAGTTTATTCCAGTTGATCCAGGGCGATCATTTCT
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * * *
7257 TCATTTTACTTCAGTTGATCAAGGGAGATCTTTT-A
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* *
7292 TTCAGTTTATTTCAGTTTATCCAGGGTGATC-TTTCT
1 -TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * * * * *
7328 TCTGTTCATTTTAATTGATCCAAGGCGATCTTTTC-
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
*
7363 TCA-ATTATTTCAGTTGATCCAGGGTGATCTTTT-A
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
7397 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT-A
1 -TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
*
7433 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCT
1 -TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * *
7470 TCAGTTTATTTCAGTTGATCTAGGGCGATC-TTTCC
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * *
7505 TCAG-TTACTTCAGTTGATCTAGTGTGATCTTTT-A
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
*
7539 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCT
1 -TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * *
7576 TCAGTTTATTTCAGTTGAGCCAGGGCGATC-TTTCC
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
* * * *
7611 TCA-ATTACTTCAGTTGATCCAGGGCGATCTTTTCT
1 TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
7646 TCAGTTTAT
1 TCAGTTTAT
7655 CCGGGGCGAT
Statistics
Matches: 431, Mismatches: 59, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
34 69 0.16
35 92 0.21
36 270 0.63
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (36 bp):
TCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCA
Found at i:7282 original size:72 final size:72
Alignment explanation
Indices: 7112--7654 Score: 688
Period size: 72 Copynumber: 7.7 Consensus size: 72
7102 ATTTCAGATG
* * * * *
7112 CTTCAGTTCATTTCAGTTGATCCAGGGTGATCTTTTATTCGGTTTATTTTAG-TGATCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
7176 ATCTTTT
66 ATCTTTT
* * * * *
7183 CATCAGTTTATTTTAGTTGATCCAGGGAGATCTTTTCTTCAGTTTATTCCAGTTGATCCAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
*
7248 ATCATTT
66 ATCTTTT
* * * * * *
7255 CTTCATTTTACTTCAGTTGATCAAGGGAGATCTTTTATTCAGTTTATTTCAGTTTATCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
7320 ATC-TTT
66 ATCTTTT
* * * * * *
7326 CTTCTGTTCATTTTAATTGATCCAAGGCGATCTTTTC-TCA-ATTATTTCAGTTGATCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
7389 ATCTTTT
66 ATCTTTT
* * *
7396 ATTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
7461 ATCTTTT
66 ATCTTTT
* * * * *
7468 CTTCAGTTTATTTCAGTTGATCTAGGGCGATC-TTTCCTCAG-TTACTTCAGTTGATCTAGTGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
7531 ATCTTTT
66 ATCTTTT
* * * *
7538 ATTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGAGCCAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
7603 ATC-TTT
66 ATCTTTT
* * *
7609 CCTCA-ATTACTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTAT
1 CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTAT
7655 CCGGGGCGAT
Statistics
Matches: 404, Mismatches: 62, Indels: 13
0.84 0.13 0.03
Matches are distributed among these distances:
69 24 0.06
70 128 0.32
71 98 0.24
72 154 0.38
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (72 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGTG
ATCTTTT
Found at i:7518 original size:106 final size:108
Alignment explanation
Indices: 7112--7654 Score: 688
Period size: 106 Copynumber: 5.1 Consensus size: 108
7102 ATTTCAGATG
* * * * *
7112 CTTCAGTTCATTTCAGTTGATCCAGGGTGATCTTTTATTCGGTTTATTTTAG-TGATCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
* * *
7176 ATCTTTTCATCAGTTTATTTTAGTTGATCCAGGGAGATCTTTT
66 ATCTTTTCCTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
* * * * * * *
7219 CTTCAGTTTATTCCAGTTGATCCAGGGCGATCATTTCTTCATTTTACTTCAGTTGATCAAGGGAG
1 CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
** *
7284 ATCTTTTATTCAGTTTATTTCAGTTTATCCAGGGTGATC-TTT
66 ATCTTTTCCTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
* * * * * * * *
7326 CTTCTGTTCATTTTAATTGATCCAAGGCGATCTTTTC-TCA-ATTATTTCAGTTGATCCAGGGTG
1 CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
**
7389 ATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
66 ATCTTTTCCTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
* *
7432 ATTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCTAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
* * *
7497 ATC-TTTCCTCAG-TTACTTCAGTTGATCTAGTGTGATCTTTT
66 ATCTTTTCCTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
* *
7538 ATTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGAGCCAGGGCG
1 CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
* * *
7603 ATC-TTTCCTCA-ATTACTTCAGTTGATCCAGGGCGATCTTTT
66 ATCTTTTCCTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
7644 CTTCAGTTTAT
1 CTTCAGTTTAT
7655 CCGGGGCGAT
Statistics
Matches: 382, Mismatches: 49, Indels: 11
0.86 0.11 0.02
Matches are distributed among these distances:
105 57 0.15
106 172 0.45
107 86 0.23
108 67 0.18
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (108 bp):
CTTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCG
ATCTTTTCCTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTT
Found at i:7647 original size:26 final size:26
Alignment explanation
Indices: 7618--7671 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
7608 TCCTCAATTA
7618 CTTCAGTTGATCCAGGGCGATCTTTT
1 CTTCAGTTGATCCAGGGCGATCTTTT
* *
7644 CTTCAGTTTATCCGGGGCGATCTTTT
1 CTTCAGTTGATCCAGGGCGATCTTTT
7670 CT
1 CT
7672 GCAGCTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (26 bp):
CTTCAGTTGATCCAGGGCGATCTTTT
Found at i:7666 original size:142 final size:144
Alignment explanation
Indices: 7113--7654 Score: 733
Period size: 142 Copynumber: 3.8 Consensus size: 144
7103 TTTCAGATGC
* * *
7113 TTCAGTTCATTTCAGTTGATCCAGGGTGATCTTTTATTCGGTTTATTTTAG-TGATCCAGGGTGA
1 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGA
* * *
7177 TCTTTTCATCAGTTTATTTTAGTTGATCCAGGGAGATCTTTTCTTCAGTTTATTCCAGTTGATCC
66 TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTCCAGTTGATCC
* * *
7242 AGGGCGATCATTTC
131 AGGGTGATCTTTTA
* * * * *
7256 TTCATTTTACTTCAGTTGATCAAGGGAGATCTTTTATTCAGTTTATTTCAGTTTATCCAGGGTGA
1 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGA
* * * * * * *
7321 TC-TTTCTTCTGTTCATTTTAATTGATCCAAGGCGATCTTTTC-TCA-ATTATTTCAGTTGATCC
66 TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTCCAGTTGATCC
7383 AGGGTGATCTTTTA
131 AGGGTGATCTTTTA
7397 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGA
1 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGA
* *
7462 TCTTTTCTTCAGTTTATTTCAGTTGATCTAGGGCGATC-TTTCCTCAG-TTACTT-CAGTTGATC
66 TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTA-TTCCAGTTGATC
* *
7524 TAGTGTGATCTTTTA
130 CAGGGTGATCTTTTA
* * *
7539 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTCTTCAGTTTATTTCAGTTGAGCCAGGGCGA
1 TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGA
* * *
7604 TC-TTTCCTCA-ATTACTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTAT
66 TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTAT
7655 CCGGGGCGAT
Statistics
Matches: 352, Mismatches: 40, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
140 23 0.07
141 108 0.31
142 127 0.36
143 80 0.23
144 14 0.04
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (144 bp):
TTCAGTTTATTTCAGTTGATCCAGGGTGATCTTTTATTCAGTTTATTTCAGTTGATCCAGGGTGA
TCTTTTCTTCAGTTTATTTCAGTTGATCCAGGGCGATCTTTTCTTCAGTTTATTCCAGTTGATCC
AGGGTGATCTTTTA
Found at i:7680 original size:26 final size:26
Alignment explanation
Indices: 7627--7680 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
7617 ACTTCAGTTG
* *
7627 ATCCAGGGCGATCTTTTCTTCAGTTT
1 ATCCAGGGCGATCTTTTCTGCAGCTT
*
7653 ATCCGGGGCGATCTTTTCTGCAGCTT
1 ATCCAGGGCGATCTTTTCTGCAGCTT
7679 AT
1 AT
7681 TTCAGTTGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.15, C:0.24, G:0.22, T:0.39
Consensus pattern (26 bp):
ATCCAGGGCGATCTTTTCTGCAGCTT
Found at i:8146 original size:30 final size:30
Alignment explanation
Indices: 8109--8800 Score: 892
Period size: 30 Copynumber: 23.1 Consensus size: 30
8099 ACTTTGTCAA
*
8109 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8139 ATTATTTTAATCCTGATTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8169 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8199 TTTATTTTAATCCTTGTTGAGGAT-AGCTGC
1 TTTATTTTAATCCTGGTTGAGGATCA-TTGC
* * *
8229 TTTATTTTAATCCTGATTAAGGATCACTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8259 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8289 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8319 TTTATTTTAATCCTGGTCGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
** **
8349 TTTATTTTAATCCTGAATGAGGATCGCTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8379 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
8409 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* **
8439 TTTATTTTAATCCTGATTGAGGATCGCTGCC
1 TTTATTTTAATCCTGGTTGAGGATCATTG-C
* * * **
8470 TTTATTCTAATCATGATTGAGGATCGCTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
8500 TTTATTCTAATCCTGGTGGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8530 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
8560 TTTGTTTTAATCCTGTTTAAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
8590 TTTGTTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * *
8620 TTTGTTTTAATCCTGTTTGATGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
8650 TTTATTTTAATCCTGGTTAAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
8680 -TTATTCTAA-CCTTGGTTTAGGATCATTGC
1 TTTATTTTAATCC-TGGTTGAGGATCATTGC
*
8709 -TTATTTTAATCCTGGTTGAGGATCATTCC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
8738 TTCATTTCAATCCTGG-TGTAGGATCGTTG-
1 TTTATTTTAATCCTGGTTG-AGGATCATTGC
* *
8767 TTTATTTTTCAATCCTGGTTTAGGATCATCGC
1 TTTA-TTTT-AATCCTGGTTGAGGATCATTGC
8799 TT
1 TT
8801 CATCAGTTAA
Statistics
Matches: 591, Mismatches: 60, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
28 2 0.00
29 53 0.09
30 488 0.83
31 45 0.08
32 3 0.01
ACGTcount: A:0.20, C:0.15, G:0.19, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:14060 original size:21 final size:20
Alignment explanation
Indices: 14036--14078 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
14026 AAAATATTTC
*
14036 ATTAGAAATTAATTTCTAATA
1 ATTACAAATT-ATTTCTAATA
* *
14057 ATTACATATTATTTTTAATA
1 ATTACAAATTATTTCTAATA
14077 AT
1 AT
14079 ATTTACTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTACAAATTATTTCTAATA
Found at i:14109 original size:33 final size:30
Alignment explanation
Indices: 14066--14153 Score: 74
Period size: 30 Copynumber: 2.8 Consensus size: 30
14056 AATTACATAT
*
14066 TATTTTTAATAATATTTACTGTATATTAAATAAA
1 TATTTCTAATAATATTTAC---ATATT-AATAAA
*
14100 TA-TTCTAAT-ATTTATTACATATTAATAAA
1 TATTTCTAATAATAT-TTACATATTAATAAA
*
14129 TATTTCTAATAAAATTTGA-ATATTA
1 TATTTCTAATAATATTT-ACATATTA
14154 TTTAAAATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
29 8 0.17
30 20 0.43
31 3 0.07
32 3 0.07
33 10 0.22
34 2 0.04
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (30 bp):
TATTTCTAATAATATTTACATATTAATAAA
Found at i:14111 original size:30 final size:30
Alignment explanation
Indices: 14075--14139 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
14065 TTATTTTTAA
**
14075 TAATATTTACTGTATATTAAATAAATA-TTC
1 TAATATTTACTACATATT-AATAAATATTTC
*
14105 TAATATTTATTACATATTAATAAATATTTC
1 TAATATTTACTACATATTAATAAATATTTC
14135 TAATA
1 TAATA
14140 AAATTTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 8 0.26
30 23 0.74
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.48
Consensus pattern (30 bp):
TAATATTTACTACATATTAATAAATATTTC
Found at i:14230 original size:22 final size:21
Alignment explanation
Indices: 14204--14266 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
14194 AATCTTAATT
*
14204 AACGAACATAAACGAGCTATTA
1 AACGAACATAAACGAGC-ACTA
*
14226 AACGAACAATAAACGAACACTA
1 AACGAAC-ATAAACGAGCACTA
*
14248 AACGAACATGAATCGAGCA
1 AACGAACAT-AAACGAGCA
14267 TGTTCGTGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 24 0.69
23 9 0.26
ACGTcount: A:0.52, C:0.21, G:0.14, T:0.13
Consensus pattern (21 bp):
AACGAACATAAACGAGCACTA
Found at i:14240 original size:11 final size:11
Alignment explanation
Indices: 14204--14255 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
14194 AATCTTAATT
14204 AACGAAC-ATA
1 AACGAACAATA
* *
14214 AACGAGCTATTA
1 AACGAAC-AATA
14226 AACGAACAATA
1 AACGAACAATA
*
14237 AACGAACACTA
1 AACGAACAATA
14248 AACGAACA
1 AACGAACA
14256 TGAATCGAGC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 6 0.17
11 21 0.60
12 8 0.23
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (11 bp):
AACGAACAATA
Done.