Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010483.1 Kokia drynarioides strain JFW-HI SEQ_125386, 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: 65977
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:900 original size:24 final size:24
Alignment explanation
Indices: 864--944 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
854 TTAAACTCTG
864 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* * *
888 TTTGGGCTTGTAAGAGGTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* *
912 TCTGGGCTCGTAAGAGCTAATCAA
1 TCTGGGCTCGTAAGAGCTAACCAT
936 TCTGGGCTC
1 TCTGGGCTC
945 ATGTGGGCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Found at i:5510 original size:208 final size:209
Alignment explanation
Indices: 4834--5897 Score: 1325
Period size: 209 Copynumber: 5.1 Consensus size: 209
4824 TTTGGTCCTT
**
4834 TTCTCTGTATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCGTATTGAG-TTTCGCTTCATT
1 TTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTT-GCTTCATT
* * * *** *
4897 GATTTAGTCTATTTCTCTGTATCTCATCTGGAAGATGGTTGTTTCATT-ATTTTGATCCACTTCT
65 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGA-TTTGATCCACTTCT
* * * * * *
4961 CTGTATATCATCAGGAAGGCAGATTTGGTGCACTTCTCTATATCTCATCAGGAAGATGAACACTT
129 CTGTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTT
* *
5026 TATTGCTTTGACTCAC
194 TATTACTTTGACCCAC
* * *
5042 TTTTCTGTATCACATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
1 TTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
* * * * * * *
5107 ATTTGAGTCTACTTCTCTATATCTTATCAGAAAGATGATCGTTTCATTGATTTAATCCACTTTTC
66 ATTTG-GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTGATCCACTTCTC
* * * * * * * *
5172 TGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCTGTATCTCGTCAGAAAGATTATCGCTTT
130 TGTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTT
*
5237 ATTGCTTTGACCCAC
195 ATTACTTTGACCCAC
* ** * *
5252 TTCTATGTATCTCATCAAAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTACTTCATTG
1 TTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
* * * * *
5317 ATTTGGTTTACTTCTTTGTATCTCATCAGGAAGATAACCACTTCA-TGAATTTGATTCACTTCTC
66 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTG-ATTTGATCCACTTCTC
* * * ** * *
5381 TGTATCTCATTAAGAAGGTGGATTTGGTCTACTTCTCTGTATCTCATCAAAAAGATGATCGCTTT
130 TGTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTT
5446 ATTACTTT-ACCCAC
195 ATTACTTTGACCCAC
* * *
5460 TTTTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTTACTTCATTG
1 TTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
* *
5525 ATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGATTTGATTCACTTCTCT
66 ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTGATCCACTTCTCT
*
5590 GTATCTCATCAAGAAGGCAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
131 GTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
5655 TTACTTTGACCCAC
196 TTACTTTGACCCAC
* *
5669 TTCTCTGTATCTCATCA-GAAGGATAAGGGTTTGAAGTTTCACTCACATTGAG-TTTCGCTTTAT
1 TTCTCTGTATCTCATCAGGAA-GATAGGGGTTTGAAGTTTCACTCACATTGAGCTTT-GCTTCAT
* * * * * *
5732 TGATTTGGTCTACTTCTTTATTTCTCATCAGAAAGAAGACCGCTTCATTGATTTAATCCACTTCT
64 TGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTGATCCACTTCT
* ** * * * * * *
5797 CTGTATCTAATCAAGAAGATGAATTTAGTCCACTTCTCTGTATCTCATTAGGGAGATGACCTCCT
129 CTGTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTT
*
5862 TATT-CTTCGACCCAC
194 TATTACTTTGACCCAC
5877 TTCTCTGTATCTCATCAGGAA
1 TTCTCTGTATCTCATCAGGAA
5898 TATGAGAGTT
Statistics
Matches: 751, Mismatches: 95, Indels: 19
0.87 0.11 0.02
Matches are distributed among these distances:
208 244 0.32
209 322 0.43
210 184 0.25
211 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (209 bp):
TTCTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTTGCTTCATTG
ATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTGATCCACTTCTCT
GTATCTCATCAAGAAGGCGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTA
TTACTTTGACCCAC
Found at i:5622 original size:37 final size:37
Alignment explanation
Indices: 5572--5642 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
5562 CCGCTTCATT
*
5572 GATTTGATTCACTTCTCTGTATCTCATCAAGAAGGCA
1 GATTTGATCCACTTCTCTGTATCTCATCAAGAAGGCA
* *
5609 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAG
1 GATTTGATCCACTTCTCTGTATCTCATCAAGAAG
5643 ATGACCACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (37 bp):
GATTTGATCCACTTCTCTGTATCTCATCAAGAAGGCA
Found at i:5632 original size:85 final size:84
Alignment explanation
Indices: 5524--5690 Score: 255
Period size: 85 Copynumber: 2.0 Consensus size: 84
5514 TTACTTCATT
* * * **
5524 GATTTGGTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGA-TTTGATTCACTTCT
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATT-ACTTTGACCCACTTCT
5588 CTGTATCTCATCAAGAAGGCA
65 CTGTATCTCATC-AGAAGGCA
*
5609 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTACTTTGACCCACTTCTC
1 GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTACTTTGACCCACTTCTC
5674 TGTATCTCATCAGAAGG
66 TGTATCTCATCAGAAGG
5691 ATAAGGGTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 7 0.09
85 68 0.91
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (84 bp):
GATTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTACTTTGACCCACTTCTC
TGTATCTCATCAGAAGGCA
Found at i:5701 original size:417 final size:414
Alignment explanation
Indices: 4834--5897 Score: 1337
Period size: 417 Copynumber: 2.5 Consensus size: 414
4824 TTTGGTCCTT
**
4834 TTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCGTATTGAGTTTCGCTTCATTGA
1 TTCTCTGTATCTCATCA-GAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATTGA
* * * * **** * * *
4899 TTTAGTCTATTTCTCTGTATCTCATCTGGAAGATGGTTGTTTCATTATTTTGATCCACTTCTCTG
65 TTTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGCTTCATGAATTTGATCCACTTCTCTG
* * ** *
4964 TATATCATCAGGAAGGCAGATTTGGTGCACTTCTCTATATCTCATCAGGAAGATGAACACTTTAT
130 TATCTCATCAAGAAGGTGGATTTGGT-CACTTCTCTGTATCTCATCAGGAAGATGAACACTTTAT
* * *
5029 TGCTTTGACTCACTTTTCTGTATCACATCAAGAAGATAGGGGTTTGAAGTTTCACTCACATTGAG
194 T-CTTT-ACCCACTTTTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAG
* * * *
5094 CTTTGCTTCATTGATTTGAGTCTACTTCTCTATATCTTATCAGAAAGATGATCGTTTCATTGATT
257 CTTTACTTCATTGATTTGAGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTGATT
* * * *
5159 TAATCCACTTTTCTGTATCTCATCAGGAAGGCGAATTTGGTTCACTTCTCTGTATCTCGTCAGAA
322 TAATCCACTTCTCTGTATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGAA
* * * *
5224 AGATTATCGCTTTATTGCTTTGACCCAC
387 AGATGACCACTTTATTACTTTGACCCAC
* * *
5252 TTCTATGTATCTCATCAAAAAGATGGGGGTTTGAAGTTTCACTCACATTGAGCTTT-ACTTCATT
1 TTCTCTGTATCTCATC-AGAAGAT-GGGGTTTGAAGTTTCACTCACATTGAG-TTTCGCTTCATT
* * *
5316 GATTTGGTTTACTTCTTTGTATCTCATCAGGAAGATAACCACTTCATGAATTTGATTCACTTCTC
63 GATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGCTTCATGAATTTGATCCACTTCTC
* ** * *
5381 TGTATCTCATTAAGAAGGTGGATTTGGTCTACTTCTCTGTATCTCATCAAAAAGATGATCGCTTT
128 TGTATCTCATCAAGAAGGTGGATTTGGTC-ACTTCTCTGTATCTCATCAGGAAGATGAACACTTT
*
5446 ATTACTTTACCCACTTTTCTGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATTGA
192 ATT-CTTTACCCACTTTTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGA
* * *
5511 GCTTTACTTCATTGATTTG-GTCTACTTCTCTGTATCTCATTAGGAAGATGACCGCTTCATTGAT
256 GCTTTACTTCATTGATTTGAGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTGAT
* *
5575 TTGATTCACTTCTCTGTATCTCATCAAGAAGGC-AGATTTGGTCCACTTCTCTGTATCTCATCAG
321 TTAATCCACTTCTCTGTATCTCATCAAGAAGGCGA-ATTTGGTCCACTTCTCTGTATCTCATCAG
*
5639 GAAGATGACCACTTTATTACTTTGACCCAC
385 AAAGATGACCACTTTATTACTTTGACCCAC
* *
5669 TTCTCTGTATCTCATCAGAAGGATAAGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTTATTG
1 TTCTCTGTATCTCATCAGAA-GAT-GGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATTG
* * * *
5734 ATTTGGTCTACTTCTTTATTTCTCATCAGAAAGA-AGACCGCTTCATTG-ATTTAATCCACTTCT
64 ATTTGGTCTACTTCTTTGTATCTCATCAGGAAGATA-ACCGCTTCA-TGAATTTGATCCACTTCT
* * * * * * * * *
5797 CTGTATCTAATCAAGAAGATGAATTTAGTCCACTTCTCTGTATCTCATTAGGGAGATGACCTCCT
127 CTGTATCTCATCAAGAAGGTGGATTTGGT-CACTTCTCTGTATCTCATCAGGAAGATGAACACTT
* *
5862 TATTCTTCGACCCACTTCTCTGTATCTCATCAGGAA
191 TATTCTT-TACCCACTTTTCTGTATCTCATCAGGAA
5898 TATGAGAGTT
Statistics
Matches: 556, Mismatches: 79, Indels: 23
0.84 0.12 0.03
Matches are distributed among these distances:
416 11 0.02
417 303 0.54
418 95 0.17
419 144 0.26
420 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (414 bp):
TTCTCTGTATCTCATCAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGTTTCGCTTCATTGAT
TTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGCTTCATGAATTTGATCCACTTCTCTGT
ATCTCATCAAGAAGGTGGATTTGGTCACTTCTCTGTATCTCATCAGGAAGATGAACACTTTATTC
TTTACCCACTTTTCTGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACATTGAGCTTT
ACTTCATTGATTTGAGTCTACTTCTCTATATCTCATCAGAAAGATGACCGCTTCATTGATTTAAT
CCACTTCTCTGTATCTCATCAAGAAGGCGAATTTGGTCCACTTCTCTGTATCTCATCAGAAAGAT
GACCACTTTATTACTTTGACCCAC
Found at i:5996 original size:46 final size:45
Alignment explanation
Indices: 5910--5997 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
5900 TGAGAGTTTG
*
5910 ATCTGTCCCTCTTGACTAAAGGTAAAAGATCGGAATATGGCTTTA
1 ATCTGTCCCTCTTGACTAAAGGTAAAAGATCGGAAGATGGCTTTA
* *
5955 ATCTGTCCCTCTTGACTTAAAGGTAAAAGATTGGTAGATGGCT
1 ATCTGTCCCTCTTGAC-TAAAGGTAAAAGATCGGAAGATGGCT
5998 GCAATCTACC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 16 0.41
46 23 0.59
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (45 bp):
ATCTGTCCCTCTTGACTAAAGGTAAAAGATCGGAAGATGGCTTTA
Found at i:6004 original size:46 final size:43
Alignment explanation
Indices: 5910--6047 Score: 136
Period size: 46 Copynumber: 3.1 Consensus size: 43
5900 TGAGAGTTTG
* *
5910 ATCTGTCCCTCTTGAC-TAAAGGTAAAAGATCGGAATATGGCTTTA
1 ATCTGTCCCTCTTGACTTAAAGGTAAAAGATTGG-A-ATGGC-TCA
5955 ATCTGTCCCTCTTGACTTAAAGGTAAAAGATTGGTAGATGGCTGCA
1 ATCTGTCCCTCTTGACTTAAAGGTAAAAGATTGG-A-ATGGCT-CA
** * ** *
6001 ATCTACCCCTCTTTA-TTAGGGGTAAAATATTGGAATGGCTCA
1 ATCTGTCCCTCTTGACTTAAAGGTAAAAGATTGGAATGGCTCA
6043 ATCTG
1 ATCTG
6048 CCCCCTGATC
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
42 6 0.08
43 6 0.08
44 1 0.01
45 32 0.40
46 35 0.44
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (43 bp):
ATCTGTCCCTCTTGACTTAAAGGTAAAAGATTGGAATGGCTCA
Found at i:6297 original size:96 final size:96
Alignment explanation
Indices: 6087--6330 Score: 253
Period size: 96 Copynumber: 2.5 Consensus size: 96
6077 TCTTCAATCT
* * * *
6087 TTCTAAAGGTA-CCGGTTTGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTTATGGTACCAAT
1 TTCT-AAGGTATCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTT-ATATCTCTATGGTACCAAT
*
6151 TCACTGTCATCCCTTAATCCTTCCCATCACATC
64 TCACTGTCATCCCTCAATCCTTCCCATCACATC
* * * *
6184 TTTTAAGTTATCGGGTTCGTCATTGCGGCCTCAACCTTTCCCTT-TTTC-CTATGGTACCAAATT
1 TTCTAAGGTATCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTATATCTCTATGGTACC-AATT
* ** * *
6247 CATTGTTGTAGCCTCGATCCTTCCCATCACATC
65 CACTGTCAT-CCCTCAATCCTTCCCATCACATC
* * *
6280 TTCTAAGGTA-CTTGGTTCGCCTTTACGGCCTCAACCTTTCCCTTCATATCT
1 TTCTAAGGTATC-GGGTTCGCCATTGCGGCCTCAACCTTTCCCTT-ATATCT
6331 TAATGTTTCC
Statistics
Matches: 119, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
94 9 0.08
95 14 0.12
96 61 0.51
97 32 0.27
98 3 0.03
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (96 bp):
TTCTAAGGTATCGGGTTCGCCATTGCGGCCTCAACCTTTCCCTTATATCTCTATGGTACCAATTC
ACTGTCATCCCTCAATCCTTCCCATCACATC
Found at i:7241 original size:22 final size:21
Alignment explanation
Indices: 7213--7268 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 21
7203 TCTTTTTCCC
7213 TTTTTTTCTTTTT-TTCACTTTT
1 TTTTTTTCTTTTTCTT--CTTTT
7235 TTATTTTTCTTTTTCTTC-TTT
1 TT-TTTTTCTTTTTCTTCTTTT
*
7256 TTTCTTTCTTTTT
1 TTTTTTTCTTTTT
7269 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 10 0.32
21 5 0.16
22 3 0.10
23 11 0.35
24 2 0.06
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTTCTTTTTCTTCTTTT
Found at i:11254 original size:73 final size:73
Alignment explanation
Indices: 11135--11278 Score: 279
Period size: 73 Copynumber: 2.0 Consensus size: 73
11125 CGAGTTTAAA
*
11135 TTAATAACTTTTCTTGTATGATGATACAAATGCAAGCAAAAGGGATAAAATAAAATAAGTTAGCA
1 TTAATAACTTTTCTTGTATGATGATACAAATGCAAGCAAAAGGGATAAAATAAAACAAGTTAGCA
11200 AAAACAAG
66 AAAACAAG
11208 TTAATAACTTTTCTTGTATGATGATACAAATGCAAGCAAAAGGGATAAAATAAAACAAGTTAGCA
1 TTAATAACTTTTCTTGTATGATGATACAAATGCAAGCAAAAGGGATAAAATAAAACAAGTTAGCA
11273 AAAACA
66 AAAACA
11279 TCAGTATCAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.49, C:0.10, G:0.15, T:0.26
Consensus pattern (73 bp):
TTAATAACTTTTCTTGTATGATGATACAAATGCAAGCAAAAGGGATAAAATAAAACAAGTTAGCA
AAAACAAG
Found at i:12695 original size:29 final size:29
Alignment explanation
Indices: 12654--12889 Score: 141
Period size: 29 Copynumber: 8.2 Consensus size: 29
12644 ATAAGGTCGA
12654 AAAATG-AAGTTTTTGAGAA-TTTCAAGGTT
1 AAAATGTAA-TTTTTGAGAAGTTT-AAGGTT
* * * *
12683 AAAATGTGA-TTTTGGGAAGTTTAGGGTC
1 AAAATGTAATTTTTGAGAAGTTTAAGGTT
** *
12711 AAAATGTAATTTTAAAGAAGTTTAGGGGTT
1 AAAATGTAATTTTTGAGAAGTTTA-AGGTT
* *
12741 AAAATGTAAATTTAG-GAAAGTTTAAGGTT
1 AAAATGTAATTTTTGAG-AAGTTTAAGGTT
* *
12770 AAAATGTAATTTTTGA-AGAGTTGAGGGGTT
1 AAAATGTAATTTTTGAGA-AGTTTA-AGGTT
* * *
12800 AAAATGTAA-TTTTG-GAAGAGTTAGGGGTC
1 AAAATGTAATTTTTGAGAAG-TTTA-AGGTT
*
12829 AAAATGTAA-TTTTGAAAAGTTTAAGG-T
1 AAAATGTAATTTTTGAGAAGTTTAAGGTT
* * * * *
12856 -CAATATAATTTTGGAAAAGTTCAAGGGTT
1 AAAATGTAATTTTTGAGAAGTTTAA-GGTT
12885 AAAAT
1 AAAAT
12890 CAAATTTCTA
Statistics
Matches: 164, Mismatches: 28, Indels: 29
0.74 0.13 0.13
Matches are distributed among these distances:
26 6 0.04
27 13 0.08
28 27 0.16
29 74 0.45
30 44 0.27
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTTAAGGTT
Found at i:12747 original size:30 final size:30
Alignment explanation
Indices: 12679--12851 Score: 182
Period size: 29 Copynumber: 5.9 Consensus size: 30
12669 AGAATTTCAA
* *
12679 GGTTAAAATGTGATTTTG-GGAAGTTTA-G
1 GGTTAAAATGTAATTTTGAAGAAGTTTAGG
* *
12707 GGTCAAAATGTAATTTTAAAGAAGTTTAGG
1 GGTTAAAATGTAATTTTGAAGAAGTTTAGG
* * *
12737 GGTTAAAATGTAAATTT-AGGAAAGTTTA-A
1 GGTTAAAATGTAATTTTGAAG-AAGTTTAGG
*
12766 GGTTAAAATGTAATTTTTGAAG-AGTTGAGG
1 GGTTAAAATGTAA-TTTTGAAGAAGTTTAGG
12796 GGTTAAAATGTAATTTTGGAAG-AG-TTAGG
1 GGTTAAAATGTAATTTT-GAAGAAGTTTAGG
*
12825 GGTCAAAATGTAATTTTGAA-AAGTTTA
1 GGTTAAAATGTAATTTTGAAGAAGTTTA
12852 AGGTCAATAT
Statistics
Matches: 122, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
28 20 0.16
29 55 0.45
30 45 0.37
31 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.26, T:0.36
Consensus pattern (30 bp):
GGTTAAAATGTAATTTTGAAGAAGTTTAGG
Found at i:12774 original size:59 final size:58
Alignment explanation
Indices: 12679--12941 Score: 234
Period size: 59 Copynumber: 4.5 Consensus size: 58
12669 AGAATTTCAA
* * *
12679 GGTTAAAATGTGATTTTGGGAAGTTTAGGGTCAAAATGTAATTTTAAAGAAGTTTAGG
1 GGTTAAAATGTAATTTTGGAAAGTTTAGGGTCAAAATGTAATTTTGAAGAAGTTTAGG
* * * *
12737 GGTTAAAATGTAAATTTAGGAAAGTTTAAGGTTAAAATGTAATTTTTGAAG-AGTTGAGG
1 GGTTAAAATGT-AATTTTGGAAAGTTTAGGGTCAAAATGTAA-TTTTGAAGAAGTTTAGG
*
12796 GGTTAAAATGTAATTTTGGAAGAG-TTAGGGGTCAAAATGTAATTTTGAA-AAGTTTA-A
1 GGTTAAAATGTAATTTTGGAA-AGTTTA-GGGTCAAAATGTAATTTTGAAGAAGTTTAGG
* * * * ** * *
12853 GG-T-CAATATAATTTTGGAAAAGTTCAAGGGTTAAAATCAAATTTCT-AAAAAATTTAGG
1 GGTTAAAATGTAATTTTGG-AAAGTT-TAGGGTCAAAATGTAATTT-TGAAGAAGTTTAGG
* **
12911 GGTTAATATCAAATTTTTGGAAAGTTTAGGG
1 GGTTAAAATGTAA-TTTTGGAAAGTTTAGGG
12942 ACCTCTTGAG
Statistics
Matches: 166, Mismatches: 25, Indels: 27
0.76 0.11 0.12
Matches are distributed among these distances:
55 14 0.08
56 20 0.12
57 10 0.06
58 37 0.22
59 62 0.37
60 17 0.10
61 6 0.04
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (58 bp):
GGTTAAAATGTAATTTTGGAAAGTTTAGGGTCAAAATGTAATTTTGAAGAAGTTTAGG
Found at i:12939 original size:30 final size:29
Alignment explanation
Indices: 12679--12941 Score: 178
Period size: 30 Copynumber: 9.0 Consensus size: 29
12669 AGAATTTCAA
** *
12679 GGTTAAAATGTGATTTTGGGAAGTTTA-G
1 GGTTAAAATGAAATTTTGGAAAGTTTAGG
* * **
12707 GGTCAAAATGTAATTTTAAAGAAGTTTAGG
1 GGTTAAAATGAAATTTTGGA-AAGTTTAGG
* *
12737 GGTTAAAATGTAAATTTAGGAAAGTTTA-A
1 GGTTAAAATG-AAATTTTGGAAAGTTTAGG
* * *
12766 GGTTAAAATGTAATTTTTGAAGAGTTGAGG
1 GGTTAAAATGAAATTTTGGAA-AGTTTAGG
*
12796 GGTTAAAATGTAATTTTGGAAGAG-TTAGG
1 GGTTAAAATGAAATTTTGGAA-AGTTTAGG
* * * *
12825 GGTCAAAATGTAATTTTGAAAAGTTTA-A
1 GGTTAAAATGAAATTTTGGAAAGTTTAGG
* * * *
12853 GGTCAATAT--AATTTTGGAAAAGTTCAAG
1 GGTTAAAATGAAATTTTGG-AAAGTTTAGG
* ** *
12881 GGTTAAAATCAAATTTCTAAAAAATTTAGG
1 GGTTAAAATGAAATTT-TGGAAAGTTTAGG
* *
12911 GGTTAATATCAAATTTTTGGAAAGTTTAGG
1 GGTTAAAATGAAA-TTTTGGAAAGTTTAGG
12941 G
1 G
12942 ACCTCTTGAG
Statistics
Matches: 187, Mismatches: 36, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
26 7 0.04
27 7 0.04
28 40 0.21
29 48 0.26
30 75 0.40
31 10 0.05
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (29 bp):
GGTTAAAATGAAATTTTGGAAAGTTTAGG
Found at i:15422 original size:23 final size:23
Alignment explanation
Indices: 15396--15442 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
15386 CGAAAATAGA
15396 GGTTTCGAGACCACAACTTCGAT
1 GGTTTCGAGACCACAACTTCGAT
*
15419 GGTTTCGAGACCATAACTTCGAT
1 GGTTTCGAGACCACAACTTCGAT
15442 G
1 G
15443 ATTCGGGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (23 bp):
GGTTTCGAGACCACAACTTCGAT
Found at i:25634 original size:2 final size:2
Alignment explanation
Indices: 25629--25659 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
25619 ATATATATAT
*
25629 AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
25660 AAATTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29044 original size:19 final size:18
Alignment explanation
Indices: 28996--29046 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
28986 GTTTCCGAAA
*
28996 AATAATTTCTGGAAAATG
1 AATATTTTCTGGAAAATG
*
29014 AATTACTTTTCTGGAAAAGTT
1 AA-TA-TTTTCTGGAAAA-TG
29035 AATATTTTCTGG
1 AATATTTTCTGG
29047 TGTTTGGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 13 0.46
21 3 0.11
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (18 bp):
AATATTTTCTGGAAAATG
Found at i:32397 original size:40 final size:40
Alignment explanation
Indices: 32341--32543 Score: 226
Period size: 40 Copynumber: 5.1 Consensus size: 40
32331 GTTATGTTTC
** *
32341 AATAAATTCAAGCTTCGGCTTAGCATTCTACGAGCCGGTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGGTG
* * * * * * * *
32381 GATAAATTCAAACTTCGACTTAGAAAGCTACGAGTCGGTT
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGGTG
* * *
32421 AATAAATTCAAGCTTCGGCTTAGTAGGCTAAGAGTCGCTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGGTG
*
32461 AATAAATTCAAGCTTTGGCTTAGCAGGCTAAGAGCCGGTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGGTG
* * * * *
32501 AATAAATTGAAGCTTCGGCTTAGTAGTCTATGAGCCAGTG
1 AATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGGTG
32541 AAT
1 AAT
32544 GGATTAGTAA
Statistics
Matches: 137, Mismatches: 26, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.28
Consensus pattern (40 bp):
AATAAATTCAAGCTTCGGCTTAGCAGGCTAAGAGCCGGTG
Found at i:54084 original size:15 final size:15
Alignment explanation
Indices: 54061--54090 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54051 CCCTATGATA
*
54061 ACAATATGCAAACCC
1 ACAACATGCAAACCC
54076 ACAACATGCAAACCC
1 ACAACATGCAAACCC
54091 CAAACTTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.37, G:0.07, T:0.10
Consensus pattern (15 bp):
ACAACATGCAAACCC
Found at i:57912 original size:20 final size:21
Alignment explanation
Indices: 57856--57931 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
57846 AACAGTGTAG
57856 ACTTCTATCGATACAAGTGAT
1 ACTTCTATCGATACAAGTGAT
* *
57877 AGTTCTATCGGTACAAGT-ACT
1 ACTTCTATCGATACAAGTGA-T
* *
57898 -CTTCTATCGAAACAAGTCAT
1 ACTTCTATCGATACAAGTGAT
* *
57918 GCTTCTACCGATAC
1 ACTTCTATCGATAC
57932 TAAAAACTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (21 bp):
ACTTCTATCGATACAAGTGAT
Found at i:61727 original size:45 final size:45
Alignment explanation
Indices: 61663--61749 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
61653 ATTTTGTGTG
*
61663 TTAGCTTAATGGTCATGAAGTTCATTGCTACAGGTGTGATCTAGA
1 TTAGCTTAATGGTCATGAAGTTCATTGCTACAGGTATGATCTAGA
* * *
61708 TTAGCTTAATGGTTATGAAGTTCATTGTTACATGTATGATCT
1 TTAGCTTAATGGTCATGAAGTTCATTGCTACAGGTATGATCT
61750 GAGTTTAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.40
Consensus pattern (45 bp):
TTAGCTTAATGGTCATGAAGTTCATTGCTACAGGTATGATCTAGA
Found at i:65333 original size:27 final size:26
Alignment explanation
Indices: 65294--65369 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 26
65284 CGGCTAGGTT
65294 AGGAAAAAGAAAAAGTAGAAAAGAAAA
1 AGGAAAAA-AAAAAGTAGAAAAGAAAA
65321 AGGAAGAAAAAAAAG-AGGAAAAATGAAAA
1 AGGAA-AAAAAAAAGTA-G-AAAA-GAAAA
*
65350 A-GAAAAGAAAAAGTA-AAAAG
1 AGGAAAAAAAAAAGTAGAAAAG
65370 CTGCAAATAG
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
24 1 0.02
25 4 0.09
26 1 0.02
27 20 0.47
28 11 0.26
29 6 0.14
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (26 bp):
AGGAAAAAAAAAAGTAGAAAAGAAAA
Found at i:65350 original size:7 final size:6
Alignment explanation
Indices: 65296--65369 Score: 60
Period size: 7 Copynumber: 11.2 Consensus size: 6
65286 GCTAGGTTAG
*
65296 GAAAAA GAAAAA GTAGAAAA GAAAAA GGAAGAAA AAAAAGA GGAAAAA
1 GAAAAA GAAAAA G-A-AAAA GAAAAA -GAA-AAA GAAAA-A -GAAAAA
65344 TGAAAAA G-AAAA GAAAAA GTAAAAA G
1 -GAAAAA GAAAAA GAAAAA G-AAAAA G
65370 CTGCAAATAG
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
5 5 0.09
6 19 0.33
7 21 0.37
8 12 0.21
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:65361 original size:19 final size:20
Alignment explanation
Indices: 65296--65362 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
65286 GCTAGGTTAG
*
65296 GAAAAAGAA-AAAGTAGAAAA
1 GAAAAAGAAGAAA-AAGAAAA
65316 GAAAAAGGAAGAAAAA-AAAGA
1 GAAAAA-GAAGAAAAAGAAA-A
* *
65337 GGAAAA-ATGAAAAAGAAAA
1 GAAAAAGAAGAAAAAGAAAA
65356 GAAAAAG
1 GAAAAAG
65363 TAAAAAGCTG
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
19 13 0.34
20 12 0.32
21 10 0.26
22 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.03
Consensus pattern (20 bp):
GAAAAAGAAGAAAAAGAAAA
Done.