Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017476.1 Corchorus olitorius cultivar O-4 contig17509, 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: 32310
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Found at i:463 original size:15 final size:15
Alignment explanation
Indices: 445--483 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
435 AATTATTTTT
445 CCATGAATTATCAAA
1 CCATGAATTATCAAA
*
460 CCATG-ATT-TCCAA
1 CCATGAATTATCAAA
473 CCATGAATTAT
1 CCATGAATTAT
484 TTTTTCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 9 0.43
14 6 0.29
15 6 0.29
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (15 bp):
CCATGAATTATCAAA
Found at i:755 original size:29 final size:29
Alignment explanation
Indices: 713--771 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
703 GCAGACTACA
713 CGCGCAGGCTTAAGGGTTGACATGTGTCC
1 CGCGCAGGCTTAAGGGTTGACATGTGTCC
742 CGCGCAGGCTTAAGGGTTGACATGTGTCC
1 CGCGCAGGCTTAAGGGTTGACATGTGTCC
771 C
1 C
772 CTTAGGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.24
Consensus pattern (29 bp):
CGCGCAGGCTTAAGGGTTGACATGTGTCC
Found at i:1458 original size:16 final size:16
Alignment explanation
Indices: 1433--1463 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1423 TCTACGTATT
1433 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
*
1449 ATAAATATTTAGTAA
1 ATAAAGATTTAGTAA
1464 TATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:2128 original size:48 final size:48
Alignment explanation
Indices: 2076--2177 Score: 204
Period size: 48 Copynumber: 2.1 Consensus size: 48
2066 ATTCATTGTC
2076 TGCATTCTTTTTGGATATTCATTTACTTTGCATCTGGCATAGTCATTT
1 TGCATTCTTTTTGGATATTCATTTACTTTGCATCTGGCATAGTCATTT
2124 TGCATTCTTTTTGGATATTCATTTACTTTGCATCTGGCATAGTCATTT
1 TGCATTCTTTTTGGATATTCATTTACTTTGCATCTGGCATAGTCATTT
2172 TGCATT
1 TGCATT
2178 AATCATGTCA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.50
Consensus pattern (48 bp):
TGCATTCTTTTTGGATATTCATTTACTTTGCATCTGGCATAGTCATTT
Found at i:2145 original size:24 final size:24
Alignment explanation
Indices: 2066--2147 Score: 69
Period size: 24 Copynumber: 3.3 Consensus size: 24
2056 CAGCAAACAC
2066 ATTCATTGTCTGCATTCTTTTTGGAT
1 ATTCATT-T-TGCATTCTTTTTGGAT
* * * *
2092 ATTCA-TTTACTTTGC-ATCTGGCAT
1 ATTCATTTTGCATT-CTTTTTGG-AT
*
2116 AGTCATTTTGCATTCTTTTTGGAT
1 ATTCATTTTGCATTCTTTTTGGAT
2140 ATTCATTT
1 ATTCATTT
2148 ACTTTGCATC
Statistics
Matches: 42, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 8 0.19
24 18 0.43
25 11 0.26
26 5 0.12
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.52
Consensus pattern (24 bp):
ATTCATTTTGCATTCTTTTTGGAT
Found at i:2169 original size:24 final size:24
Alignment explanation
Indices: 2094--2171 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
2084 TTTTGGATAT
2094 TCATTTACTTTGCATCTGGCATAG
1 TCATTTACTTTGCATCTGGCATAG
* * * * *
2118 TCATTTTGCATT-CTTTTTGG-ATAT
1 TCA-TTTACTTTGC-ATCTGGCATAG
2142 TCATTTACTTTGCATCTGGCATAG
1 TCATTTACTTTGCATCTGGCATAG
2166 TCATTT
1 TCATTT
2172 TGCATTAATC
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
23 10 0.25
24 20 0.50
25 10 0.25
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.49
Consensus pattern (24 bp):
TCATTTACTTTGCATCTGGCATAG
Found at i:6598 original size:46 final size:47
Alignment explanation
Indices: 6528--6633 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
6518 TTACTTATTA
*
6528 TTACTTTTTAC-T-TTTTAGCTTAATTAAC-CTTA-CTACTGATTACTC
1 TTAC-TTTTACTTCTTTTAGCTTAATT-ACTCTAATCTACTGATTACTC
*
6573 TTACTTTTACTTCTTTTAGCTTAATTACTCTAATCTTCTGATTACTC
1 TTACTTTTACTTCTTTTAGCTTAATTACTCTAATCTACTGATTACTC
*
6620 TTTCTTTTACTTCT
1 TTACTTTTACTTCT
6634 GATTACTCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
44 6 0.11
45 7 0.13
46 16 0.30
47 25 0.46
ACGTcount: A:0.21, C:0.21, G:0.04, T:0.55
Consensus pattern (47 bp):
TTACTTTTACTTCTTTTAGCTTAATTACTCTAATCTACTGATTACTC
Found at i:6633 original size:22 final size:22
Alignment explanation
Indices: 6607--6789 Score: 163
Period size: 22 Copynumber: 8.1 Consensus size: 22
6597 TTACTCTAAT
6607 CTTCTGATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
6629 CTTCTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTA
* *
6651 CTCCTGATTACTCTTTCTTTTG
1 CTTCTGATTACTCTTTCTTTTA
*
6673 CTTTTGCTTTTGATTACT-ATTCTTTTTA
1 C--TT-C---TGATTACTCTTTC-TTTTA
* * *
6701 C-TCTGATTGCTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTA
* *
6722 CTTTTGATTACTCTTCCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
6744 CTCCTGATTACTCTTTGTTTTA
1 CTTCTGATTACTCTTTCTTTTA
* *
6766 CTTTTGATTACTTTTTCTTTTA
1 CTTCTGATTACTCTTTCTTTTA
6788 CT
1 CT
6790 ACTTAGCTTG
Statistics
Matches: 128, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
21 11 0.09
22 97 0.76
24 2 0.02
25 2 0.02
27 3 0.02
28 13 0.10
ACGTcount: A:0.11, C:0.22, G:0.08, T:0.58
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTTTA
Found at i:6853 original size:47 final size:47
Alignment explanation
Indices: 6800--7526 Score: 946
Period size: 47 Copynumber: 15.4 Consensus size: 47
6790 ACTTAGCTTG
6800 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
6847 ATTACCCCGAATTAAACTCTTTTCTTCTTCTCTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
6894 ATCACCCAGAATTAAACTAGCCTCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATT-AA--A--CTCT-TTT-CTTCTTCTCTTGCTCTTTAGTTTA
* * *
6948 ATTACCCAGAATTAAATTGTTTTCTTCTTCTCTCGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
6995 ATTACCCAGAATTAAACTCTTTT-TATCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCT-TCTTCTCTTGCTCTTTAGTTTA
*
7042 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
*
7089 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
** *
7136 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTAATTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * * ** *
7183 ATTACCCATAATTAAAATGTTTTCTTCTTCTCTTAATTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* *
7230 ATTACCCATAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* ** *
7277 ATTACCCGGAATTAAACTCTTTTCTTCTTCTCTTAATTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* * *
7324 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGATTTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* *
7371 ATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* **
7418 ATTACCCGGAATTAAACTCTTTTCTTC-T-TAAT--T-TTTAGTTTA
1 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
* ** * **
7460 ATTACCCAGAATTAAACTGC-TTCCTTCTTCTCTTAATTAATTTTTTTTA
1 ATTACCCAGAATTAAACT-CTTTTCTTCTTCTCTT-GCT-CTTTAGTTTA
7509 ATTACCCAGAATTAAACT
1 ATTACCCAGAATTAAACT
7527 AGCCTCTGTG
Statistics
Matches: 612, Mismatches: 51, Indels: 32
0.88 0.07 0.05
Matches are distributed among these distances:
42 32 0.05
43 3 0.00
44 2 0.00
45 2 0.00
46 2 0.00
47 493 0.81
48 6 0.01
49 27 0.04
50 1 0.00
51 1 0.00
52 4 0.01
53 5 0.01
54 34 0.06
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (47 bp):
ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTA
Found at i:7134 original size:141 final size:141
Alignment explanation
Indices: 6800--7526 Score: 1079
Period size: 141 Copynumber: 5.1 Consensus size: 141
6790 ACTTAGCTTG
* *
6800 ATTACCCAGAATTAAACTCTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCCGAATTAAACT
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
* *
6865 CTTTTCTTCTTCTCTTACTTTTTAGTTTAATCACCCAGAATTAAACTAGCCTCTGTTTACTTCTT
66 CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACT-G----T-TTT-CTTCTT
* *
6930 CTTTTACTCTTTAGTTTA
124 CTCTTAATCTTTAGTTTA
* *
6948 ATTACCCAGAATTAAATTGTTTTCTTCTTCTCTCGCTCTTTAGTTTAATTACCCAGAATTAAACT
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
** * *
7013 CTTTT-TATCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTG
66 CTTTTCT-TCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTA
*
7077 CTCTTTAGTTTA
130 ATCTTTAGTTTA
7089 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
* *
7154 CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCATAATTAAAATGTTTTCTTCTTCTCTTAA
66 CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTAA
*
7219 TTTTTAGTTTA
131 TCTTTAGTTTA
* *
7230 ATTACCCATAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCGGAATTAAACT
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
*
7295 CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGA
66 CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTAA
*
7360 TTTTTAGTTTA
131 TCTTTAGTTTA
* *
7371 ATTACCCAGAATTAAATTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCGGAATTAAACT
1 ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
* *
7436 C--TT-TTC-T-TCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGCTTCCTTCTTCTCTTAA
66 CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTAA
* **
7496 TTAATTTTTTTTA
131 -T-CTTTAGTTTA
7509 ATTACCCAGAATTAAACT
1 ATTACCCAGAATTAAACT
7527 AGCCTCTGTG
Statistics
Matches: 542, Mismatches: 33, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
136 50 0.09
137 2 0.00
138 27 0.05
139 2 0.00
141 351 0.65
142 4 0.01
143 1 0.00
147 2 0.00
148 103 0.19
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (141 bp):
ATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTAATTACCCAGAATTAAACT
CTTTTCTTCTTCTCTTAATTTTTAGTTTAATTACCCAGAATTAAACTGTTTTCTTCTTCTCTTAA
TCTTTAGTTTA
Found at i:14445 original size:16 final size:17
Alignment explanation
Indices: 14420--14461 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
14410 CAAGAAATTC
14420 AAAATCAAAAATAA-AAA
1 AAAATC-AAAATAATAAA
14437 AAAAT-AAAATAATAAA
1 AAAATCAAAATAATAAA
14453 AAAATCAAA
1 AAAATCAAA
14462 TCAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.30
16 8 0.35
17 8 0.35
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATCAAAATAATAAA
Found at i:14453 original size:17 final size:17
Alignment explanation
Indices: 14420--14456 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
14410 CAAGAAATTC
*
14420 AAAATCAAAAATAAAAA
1 AAAATAAAAAATAAAAA
14437 AAAATAAAATAATAAAAA
1 AAAATAAAA-AATAAAAA
14455 AA
1 AA
14457 TCAAATCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAATAAAAAATAAAAA
Found at i:14462 original size:16 final size:15
Alignment explanation
Indices: 14427--14473 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
14417 TTCAAAATCA
14427 AAAATAAAAAAAAAT
1 AAAATAAAAAAAAAT
14442 AAAATAATAAAAAAAT
1 AAAATAA-AAAAAAAT
*
14458 CAAATCAAAATAAAAA
1 AAAAT-AAAA-AAAAA
14474 GAGAATTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAATAAAAAAAAAT
Found at i:14787 original size:14 final size:15
Alignment explanation
Indices: 14763--14797 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
14753 TCAAGTGCAC
*
14763 AAAAAATGGAAAATG
1 AAAAAATGGAAAAAG
14778 AAAAAA-GGAAAAAG
1 AAAAAATGGAAAAAG
14792 AAAAAA
1 AAAAAA
14798 AAGGAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (15 bp):
AAAAAATGGAAAAAG
Found at i:16490 original size:168 final size:168
Alignment explanation
Indices: 16212--16840 Score: 988
Period size: 168 Copynumber: 3.7 Consensus size: 168
16202 TCCATGAAAG
*
16212 TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGTATTGGTAAGTCCTCCGGGCACAAATTCA
1 TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCA
* * *
16277 GAAACCTCCAGGTAATAATTCTGATAAGTCTTCCGGGCAATTGATAAAACCTCCGGGTACCATTT
66 GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTACCATTT
*
16342 GATTTCATCAAGTTTTTCAACAAAATCCATGTTTAAGT
131 GATTTCATCAAGTTTTTCATCAAAATCCATGTTTAAGT
*
16380 TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCAGGCACAAATTCA
1 TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCA
*
16445 GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACTTCCGGGTACCATTT
66 GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTACCATTT
*
16510 GATTTCATCGAGTTTTTCATCAAAATCCATGTTTAAGT
131 GATTTCATCAAGTTTTTCATCAAAATCCATGTTTAAGT
*
16548 TTAAAATCCTTGTTTAAGATCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCA
1 TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCA
16613 GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTACCATTT
66 GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTACCATTT
* *
16678 GATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAAGC
131 GATTTCATCAAGTTTTTCATC-AAAATCCATGTTT-AAGT
* * * * * * * * * * **
16718 TTAAAATCCTTGGTCAAGGTCTCAATTTAGAGTTTGCGTTGATAAGACTTCCGAGCACATTTTTC
1 TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACA-AATTC
* * * *
16783 AGAAACCTCCGGGTATTAATTGTGATAAGTCCTCCGGGCATTTGATAAGACATCCGGG
65 AGAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGG
16841 CATTGCATAT
Statistics
Matches: 427, Mismatches: 31, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
168 307 0.72
169 12 0.03
170 51 0.12
171 57 0.13
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (168 bp):
TTAAAATCCTTGTTTAAGGTCTCTATTCAGAGTTCGCATTGGTAAGTCCTCCGGGCACAAATTCA
GAAACCTCCGGGTATTAATTCTGATAAGTCCTCCGGGCAATTGATAAAACCTCCGGGTACCATTT
GATTTCATCAAGTTTTTCATCAAAATCCATGTTTAAGT
Found at i:16830 original size:20 final size:20
Alignment explanation
Indices: 16805--16844 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16795 GTATTAATTG
* *
16805 TGATAAGTCCTCCGGGCATT
1 TGATAAGACATCCGGGCATT
16825 TGATAAGACATCCGGGCATT
1 TGATAAGACATCCGGGCATT
16845 GCATATTTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.28
Consensus pattern (20 bp):
TGATAAGACATCCGGGCATT
Found at i:16930 original size:30 final size:30
Alignment explanation
Indices: 16880--17394 Score: 789
Period size: 30 Copynumber: 17.2 Consensus size: 30
16870 ACTTTGTCAG
*
16880 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
16910 TTCATTCTAATCATGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
16940 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
16970 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
17000 TTCATTTTAATCCTGTTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
17030 TTTATTTTAATCCTGGTTGAGGAACATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
17060 TTTATTTTAATCTTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
17090 TTCATTTTAATCCTGTTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
17120 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
17150 TTCATTTTAATCCT-GTCGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
17179 TTTATTTTAATCCTGGTTGAAGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
17209 TTCATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
17239 TTTATTTTAATCCTGTTTGAGGATCATTGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
17269 TTTATTTTAATCCTGGTTAAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
17299 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
17329 TTTATTTTAATCCTGGTTTAGGATCATTGT
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
17359 TTTATTTTGAATCCTGGTTTAGGATCATTGT
1 TTTATTTT-AATCCTGGTTGAGGATCATTGC
17390 TTTAT
1 TTTAT
17395 CAGTTAACCC
Statistics
Matches: 442, Mismatches: 41, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
29 27 0.06
30 388 0.88
31 27 0.06
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:19720 original size:18 final size:20
Alignment explanation
Indices: 19698--19745 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
19688 CCCTCTCTTC
19698 CCTCACACACCTCCAT-CAA
1 CCTCACACACCTCCATACAA
* *
19717 -CTCACACATCTCCTTACAA
1 CCTCACACACCTCCATACAA
19736 CCTCACACAC
1 CCTCACACAC
19746 TACACCGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 8 0.33
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (20 bp):
CCTCACACACCTCCATACAA
Found at i:23841 original size:28 final size:28
Alignment explanation
Indices: 23801--23870 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
23791 CTTTTAAGGA
23801 TAAAACGGTAATTTAGTCACTCTTAGGG
1 TAAAACGGTAATTTAGTCACTCTTAGGG
23829 TAAAACGGTAATTTAGTCACTCTTAGGG
1 TAAAACGGTAATTTAGTCACTCTTAGGG
23857 TAAAACGGTAATTT
1 TAAAACGGTAATTT
23871 TATGCCCATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (28 bp):
TAAAACGGTAATTTAGTCACTCTTAGGG
Found at i:24607 original size:3 final size:3
Alignment explanation
Indices: 24599--24651 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
24589 CCCTTTTTCC
24599 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
24646 -TT CTT C
1 CTT CTT C
24652 CGGCAGCCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:25675 original size:19 final size:20
Alignment explanation
Indices: 25624--25677 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
25614 CTAAAAAAGT
*
25624 TTAATAAAGTTACTACAATA
1 TTAATAACGTTACTACAATA
*
25644 TTAATAACATTACTACAA-A
1 TTAATAACGTTACTACAATA
* *
25663 TTATTAAGGTTACTA
1 TTAATAACGTTACTA
25678 AAAACCTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (20 bp):
TTAATAACGTTACTACAATA
Found at i:25770 original size:21 final size:21
Alignment explanation
Indices: 25717--25772 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
25707 AAAGTTATTA
* *
25717 AAAAG-CTTAATAAGGCTTCT
1 AAAAGTCTTAATAAGACTACT
25737 AAAA-T-TTACAATAAGACTACT
1 AAAAGTCTT--AATAAGACTACT
25758 AAAAGTCTTAATAAG
1 AAAAGTCTTAATAAG
25773 GTTAGGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
19 2 0.07
20 4 0.14
21 20 0.69
22 1 0.03
23 2 0.07
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAAGTCTTAATAAGACTACT
Found at i:26324 original size:16 final size:16
Alignment explanation
Indices: 26303--26333 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
26293 TCTACAAATT
26303 ATAAAGATTTAGTAAA
1 ATAAAGATTTAGTAAA
26319 ATAAAGATTTAGTAA
1 ATAAAGATTTAGTAA
26334 TATTTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
ATAAAGATTTAGTAAA
Found at i:29060 original size:27 final size:27
Alignment explanation
Indices: 29030--29084 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
29020 CTTGTATCAC
29030 CCTAACAAGGGTAAAAAGGTAATTTTA
1 CCTAACAAGGGTAAAAAGGTAATTTTA
* * ** *
29057 CCTATCGAGGGTATTACGGTAATTTTA
1 CCTAACAAGGGTAAAAAGGTAATTTTA
29084 C
1 C
29085 TCTCTTTGAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (27 bp):
CCTAACAAGGGTAAAAAGGTAATTTTA
Found at i:29617 original size:49 final size:49
Alignment explanation
Indices: 29541--29634 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 49
29531 ATAATATATA
* *
29541 TTTTTTCTTTCTCCCTTTTCAAATTGGGCCCAAG-CCGTTTGGGCCCCTT
1 TTTTTTCTCTCTCCCTTTTCAAATTGGG-CCAAGCCCATTTGGGCCCCTT
* ***
29590 TTTTTTCTCTCTCTCTTTTCCCGTTGGGCCAAGCCCATTTGGGCC
1 TTTTTTCTCTCTCCCTTTTCAAATTGGGCCAAGCCCATTTGGGCC
29635 AAAGACCTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 5 0.13
49 33 0.87
ACGTcount: A:0.09, C:0.32, G:0.17, T:0.43
Consensus pattern (49 bp):
TTTTTTCTCTCTCCCTTTTCAAATTGGGCCAAGCCCATTTGGGCCCCTT
Done.