Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008988.1 Kokia drynarioides strain JFW-HI SEQ_123686, 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: 12691
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:2462 original size:129 final size:128
Alignment explanation
Indices: 2177--2472 Score: 343
Period size: 129 Copynumber: 2.3 Consensus size: 128
2167 CGCTATAGAA
* *
2177 CATGGT-TTTAGCGGCACTTTTTGCACAAACGCCTCTAAAAGCCATGATCTTTAGCGGCGCTTAT
1 CATGGTCTTTAGCAGCACTTTTTGCACAAACGCCTCTAAAAGCCATGATCTTTAGCGGCACTTAT
*
2241 CTCACAAACGTCGCTAAAGAACATGACCTTTAACGGCGCTTTCCCAAAAGCCCCGCTAAAGAC
66 CTCACAAACGTCGCTAAAGAACATGACCTTTAACGGCGCTTTCCCAAAAGCCCCACTAAAGAC
* * *
2304 CATGGTCTTTAGCGACGC-TTTTTTGCACAAACG-TTGCT-AAAGACCATGGTCTTTAGCGGCAC
1 CATGGTCTTTAGC-A-GCACTTTTTGCACAAACGCCT-CTAAAAG-CCATGATCTTTAGCGGCAC
** * * * * *
2366 TTATCTCACAAACG-CTGCTAAAGAACATGGTCTTTAGCGGTGATTTTCCCACAAA-CGCTACTA
62 TTATCTCACAAACGTC-GCTAAAGAACATGACCTTTAACGGCG-CTTTCCCA-AAAGCCCCACTA
2429 AAGAC
124 AAGAC
** *
2434 CATGGTCTTTAGCAGCACTTTTCCCACAAACGCCACTAA
1 CATGGTCTTTAGCAGCACTTTTTGCACAAACGCCTCTAA
2473 CATTAACAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
127 6 0.04
128 14 0.10
129 84 0.60
130 33 0.24
131 3 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (128 bp):
CATGGTCTTTAGCAGCACTTTTTGCACAAACGCCTCTAAAAGCCATGATCTTTAGCGGCACTTAT
CTCACAAACGTCGCTAAAGAACATGACCTTTAACGGCGCTTTCCCAAAAGCCCCACTAAAGAC
Found at i:2472 original size:43 final size:43
Alignment explanation
Indices: 2161--2472 Score: 274
Period size: 43 Copynumber: 7.3 Consensus size: 43
2151 TTATAAGGAA
* * **
2161 AAACGCCGCTATAGAACATGGT-TTTAGCGGCACTTTTTGCAC
1 AAACGCCGCTAAAGACCATGGTCTTTAGCGGCACTTTTCCCAC
* * * * *
2203 AAACGCCTCTAAA-AGCCATGATCTTTAGCGGCGCTTATCTCAC
1 AAACGCCGCTAAAGA-CCATGGTCTTTAGCGGCACTTTTCCCAC
* * ** * *
2246 AAACGTCGCTAAAGAACATGACCTTTAACGGCGC-TTTCCCA-
1 AAACGCCGCTAAAGACCATGGTCTTTAGCGGCACTTTTCCCAC
* * * **
2287 AAAGCCCCGCTAAAGACCATGGTCTTTAGCGACGCTTTTTTGCAC
1 AAA-CGCCGCTAAAGACCATGGTCTTTAGCGGCAC-TTTTCCCAC
** * *
2332 AAACGTTGCTAAAGACCATGGTCTTTAGCGGCACTTATCTCAC
1 AAACGCCGCTAAAGACCATGGTCTTTAGCGGCACTTTTCCCAC
* * *
2375 AAACGCTGCTAAAGAACATGGTCTTTAGCGGTGA-TTTTCCCAC
1 AAACGCCGCTAAAGACCATGGTCTTTAGCGG-CACTTTTCCCAC
** *
2418 AAACGCTACTAAAGACCATGGTCTTTAGCAGCACTTTTCCCAC
1 AAACGCCGCTAAAGACCATGGTCTTTAGCGGCACTTTTCCCAC
*
2461 AAACGCCACTAA
1 AAACGCCGCTAA
2473 CATTAACAAA
Statistics
Matches: 219, Mismatches: 42, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
41 4 0.02
42 46 0.21
43 133 0.61
44 33 0.15
45 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCATGGTCTTTAGCGGCACTTTTCCCAC
Found at i:2808 original size:24 final size:24
Alignment explanation
Indices: 2781--2853 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 24
2771 ATAACAAATG
2781 AGTACCATATGTGCATAAAGAAGA
1 AGTACCATATGTGCATAAAGAAGA
* *
2805 AGTACCATA-----A-CAA-ATG-
1 AGTACCATATGTGCATAAAGAAGA
2821 AGTACCATATGTGCATAAAGAAGA
1 AGTACCATATGTGCATAAAGAAGA
2845 AGTACCATA
1 AGTACCATA
2854 ACAAATGAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 16
0.65 0.07 0.28
Matches are distributed among these distances:
16 9 0.24
17 2 0.05
18 2 0.05
19 1 0.03
21 1 0.03
22 2 0.05
23 2 0.05
24 18 0.49
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.21
Consensus pattern (24 bp):
AGTACCATATGTGCATAAAGAAGA
Found at i:2808 original size:40 final size:40
Alignment explanation
Indices: 2758--2863 Score: 212
Period size: 40 Copynumber: 2.6 Consensus size: 40
2748 GTATTTTTCG
2758 AAGAAGAAGTACCATAACAAATGAGTACCATATGTGCATA
1 AAGAAGAAGTACCATAACAAATGAGTACCATATGTGCATA
2798 AAGAAGAAGTACCATAACAAATGAGTACCATATGTGCATA
1 AAGAAGAAGTACCATAACAAATGAGTACCATATGTGCATA
2838 AAGAAGAAGTACCATAACAAATGAGT
1 AAGAAGAAGTACCATAACAAATGAGT
2864 TCCAAATCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.19
Consensus pattern (40 bp):
AAGAAGAAGTACCATAACAAATGAGTACCATATGTGCATA
Found at i:6840 original size:28 final size:28
Alignment explanation
Indices: 6821--6930 Score: 105
Period size: 28 Copynumber: 3.8 Consensus size: 28
6811 TTGGATACCT
6821 GAGGGCAAAATGGTAATTTTGGACACTC
1 GAGGGCAAAATGGTAATTTTGGACACTC
* *
6849 GAGGGCAAAATGGTAATTTTGGAAAGGTTC
1 GAGGGCAAAATGGTAATTTTGGACA--CTC
* * * *
6879 AAGGTCAAAAATGG-AATTTTTAGACATTC
1 GAGGGC-AAAATGGTAA-TTTTGGACACTC
**
6908 GAGGATAAAATGGTAATTTTGGA
1 GAGGGCAAAATGGTAATTTTGGA
6931 AAGTTCGTGG
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
28 37 0.55
29 8 0.12
30 8 0.12
31 14 0.21
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.28
Consensus pattern (28 bp):
GAGGGCAAAATGGTAATTTTGGACACTC
Found at i:6911 original size:59 final size:57
Alignment explanation
Indices: 6837--7190 Score: 205
Period size: 58 Copynumber: 6.1 Consensus size: 57
6827 AAAATGGTAA
* * *
6837 TTTTGGACACTCGAGGGCAAAATGGTAATTTTGGAAAGGTTCAAGGTCAAAAATGGAAT
1 TTTTAGACA-TCGAGGGTAAAATGGTAATTTTGGAAA-GTTCAAGGTCAAAAATAGAAT
* ** **
6896 TTTTAGACATTCGAGGATAAAATGGTAATTTTGGAAAGTTCGTGGTTTAAAATAGAAT
1 TTTTAGACA-TCGAGGGTAAAATGGTAATTTTGGAAAGTTCAAGGTCAAAAATAGAAT
* * ** *
6954 TTTTAGACATCCAGGGGTAAAATAGTAATTTTGGAAAAATCAAAGTCAAAAATAGAA-
1 TTTTAGACATCGA-GGGTAAAATGGTAATTTTGGAAAGTTCAAGGTCAAAAATAGAAT
* * ** * ** * * *
7011 TTTTGGAAAGTTTAGGGGTAAAAAGGTAATTTATGGAAAAATCGAGGTTAAAAATAG-AC
1 TTTTAGACA-TCGA-GGGTAAAATGGTAATTT-TGGAAAGTTCAAGGTCAAAAATAGAAT
* * * * * * *
7070 TTTTGGAAAGTTTGAGGGTAAAAAT-GTAATTTTTGGAAAATTCAGGGTTAAAAATGGAAT
1 TTTTAGACA--TCGAGGGT-AAAATGGTAA-TTTTGGAAAGTTCAAGGTCAAAAATAGAAT
* * ** * * **
7130 TTATAAAGTTCAAGGGTAAAAAT-GTAATTTTTGAAAAAATCAAGGTCAAAAA-AGGAAT
1 TTTTAGACATCGAGGGT-AAAATGGTAA-TTTTGGAAAGTTCAAGGTCAAAAATA-GAAT
7188 TTT
1 TTT
7191 GAAAAGTTTA
Statistics
Matches: 237, Mismatches: 49, Indels: 19
0.78 0.16 0.06
Matches are distributed among these distances:
57 10 0.04
58 121 0.51
59 91 0.38
60 15 0.06
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (57 bp):
TTTTAGACATCGAGGGTAAAATGGTAATTTTGGAAAGTTCAAGGTCAAAAATAGAAT
Found at i:6937 original size:29 final size:27
Alignment explanation
Indices: 6827--6990 Score: 89
Period size: 28 Copynumber: 5.7 Consensus size: 27
6817 ACCTGAGGGC
* * *
6827 AAAATGGTAATTTTGGACACTCGAGGGC
1 AAAATGGTAATTTTGGAAATTCGA-GGT
*
6855 AAAATGGTAATTTTGGAAAGGTTCAAGGT
1 AAAATGGTAATTTTGGAAA--TTCGAGGT
* *
6884 CAAAAATGG-AATTTTTAGACATTCGAGGAT
1 --AAAATGGTAA-TTTTGGAAATTCGAGG-T
*
6914 AAAATGGTAATTTTGGAAAGTTCGTGGTTT
1 AAAATGGTAATTTTGGAAA-TTCGAGG--T
* * * * *
6944 AAAATAG-AATTTTTAGACATCCAGGGGT
1 AAAATGGTAA-TTTTGGAAATTC-GAGGT
*
6972 AAAATAGTAATTTTGGAAA
1 AAAATGGTAATTTTGGAAA
6991 AATCAAAGTC
Statistics
Matches: 106, Mismatches: 18, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
28 47 0.44
29 22 0.21
30 23 0.22
31 14 0.13
ACGTcount: A:0.38, C:0.07, G:0.24, T:0.31
Consensus pattern (27 bp):
AAAATGGTAATTTTGGAAATTCGAGGT
Found at i:7028 original size:58 final size:59
Alignment explanation
Indices: 6966--7253 Score: 288
Period size: 59 Copynumber: 4.9 Consensus size: 59
6956 TTAGACATCC
*
6966 AGGGGT-AAAATAGTAA-TTTTGGAAAAATCAAAGTCAAAAATAGAATTTTGGAAAGTTT
1 AGGGGTAAAAAT-GTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTT
* * * * *
7024 AGGGGTAAAAAGGTAATTTATGGAAAAATCGAGGTTAAAAATAGACTTTTGGAAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTT
* * * * *
7083 -GAGGGTAAAAATGTAATTTTTGGAAAATTCAGGGTTAAAAATGGAATTTAT--AAAGTTC
1 AG-GGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTT-TGGAAAGTTT
* * *
7141 AAGGGTAAAAATGTAATTTTTGAAAAAATCAAGGTCAAAAA-AGGAATTTTGAAAAGTTT
1 AGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAATA-GAATTTTGGAAAGTTT
* * * * *
7200 AGGGGTTAAAATAT-ATTTTT-TAAAAAGTTCAAGGT-TAAAATGGAATTTTGGAAA
1 AGGGGTAAAAATGTAATTTTTGGAAAAA--TCAAGGTCAAAAATAGAATTTTGGAAA
7254 TTCGGGGACC
Statistics
Matches: 191, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
57 6 0.03
58 79 0.41
59 105 0.55
60 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (59 bp):
AGGGGTAAAAATGTAATTTTTGGAAAAATCAAGGTCAAAAATAGAATTTTGGAAAGTTT
Found at i:7033 original size:29 final size:29
Alignment explanation
Indices: 7001--7165 Score: 108
Period size: 30 Copynumber: 5.7 Consensus size: 29
6991 AATCAAAGTC
7001 AAAAATAG-AATTTTGGAAAGTTTAGGGGT
1 AAAAAT-GTAATTTTGGAAAGTTTAGGGGT
* ** * *
7030 AAAAAGGTAATTTATGGAAA-AATCGAGGTT
1 AAAAATGTAATTT-TGGAAAGTTTAG-GGGT
*
7060 AAAAATAG-ACTTTTGGAAAGTTT-GAGGGT
1 AAAAAT-GTAATTTTGGAAAGTTTAG-GGGT
* * *
7089 AAAAATGTAATTTTTGGAAAATTCAGGGTT
1 AAAAATGTAA-TTTTGGAAAGTTTAGGGGT
* * *
7119 AAAAATGGAATTTAT--AAAGTTCAAGGGT
1 AAAAATGTAATTT-TGGAAAGTTTAGGGGT
*
7147 AAAAATGTAATTTTTGAAA
1 AAAAATGTAATTTTGGAAA
7166 AAATCAAGGT
Statistics
Matches: 106, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
27 1 0.01
28 24 0.23
29 36 0.34
30 43 0.41
31 2 0.02
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (29 bp):
AAAAATGTAATTTTGGAAAGTTTAGGGGT
Found at i:7063 original size:30 final size:30
Alignment explanation
Indices: 6978--7189 Score: 93
Period size: 30 Copynumber: 7.2 Consensus size: 30
6968 GGGTAAAATA
* * * *
6978 GTAATTT-TGGAAAAATCAAAGTCAAAAATA
1 GTAATTTATGGAAAATTCAAGGTTAAAAA-G
* * * *
7008 G-AATTT-TGGAAAGTTTAGGGGTAAAAAG
1 GTAATTTATGGAAAATTCAAGGTTAAAAAG
* *
7036 GTAATTTATGGAAAAATCGAGGTTAAAAA-
1 GTAATTTATGGAAAATTCAAGGTTAAAAAG
* ** * *
7065 -TAGACTTT-TGGAAAGTTTGAGGGTAAAAAT
1 GTA-A-TTTATGGAAAATTCAAGGTTAAAAAG
* *
7095 GTAATTTTTGGAAAATTCAGGGTTAAAAATG
1 GTAATTTATGGAAAATTCAAGGTTAAAAA-G
* * *
7126 G-AATTTAT--AAAGTTCAAGGGTAAAAAT
1 GTAATTTATGGAAAATTCAAGGTTAAAAAG
* * * *
7153 GTAATTTTTGAAAAAATCAAGGTCAAAAAAG
1 GTAATTTATGGAAAATTCAAGGT-TAAAAAG
7184 G-AATTT
1 GTAATTT
7190 TGAAAAGTTT
Statistics
Matches: 135, Mismatches: 35, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
27 1 0.01
28 24 0.18
29 45 0.33
30 56 0.41
31 9 0.07
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (30 bp):
GTAATTTATGGAAAATTCAAGGTTAAAAAG
Found at i:7150 original size:28 final size:28
Alignment explanation
Indices: 7026--7166 Score: 99
Period size: 29 Copynumber: 4.9 Consensus size: 28
7016 GAAAGTTTAG
* *
7026 GGGTAAAAAGGTAATTTATGGAAAAATCGA
1 GGGTAAAAATGTAATTTAT-GAAAATTC-A
* * * *
7056 GGTTAAAAATAG-ACTTT-TGGAAAGTTTGA
1 GGGTAAAAAT-GTAATTTAT-GAAA-ATTCA
*
7085 GGGTAAAAATGTAATTTTTGGAAAATTCA
1 GGGTAAAAATGTAATTTAT-GAAAATTCA
* *
7114 GGGTTAAAAATGGAATTTAT-AAAGTTCAA
1 GGG-TAAAAATGTAATTTATGAAAATTC-A
*
7143 GGGTAAAAATGTAATTTTTGAAAA
1 GGGTAAAAATGTAATTTATGAAAA
7167 AATCAAGGTC
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
28 21 0.24
29 33 0.38
30 33 0.38
31 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (28 bp):
GGGTAAAAATGTAATTTATGAAAATTCA
Found at i:7220 original size:117 final size:116
Alignment explanation
Indices: 6966--7249 Score: 299
Period size: 117 Copynumber: 2.4 Consensus size: 116
6956 TTAGACATCC
* * * * * * *
6966 AGGGG-TAAAATAGTAATTTTGGAAAAATCAAAGTCAAAAATAGAATTTTGGAAAGTTTAGGGGT
1 AGGGGTTAAAATA-TATTTTTGGAAAATTCAAGGTTAAAAATGGAATTTT-GAAAGTTCAAGGGT
* * * * *
7030 AAAAAGGTAATTTATGGAAAAATCGAGGTTAAAAATAGACTTTTGGAAAGTTT
64 AAAAAGGTAATTTATGAAAAAATCAAGGTCAAAAATAGAATTTTGAAAAGTTT
* * *
7083 -GAGGGTAAAAATGTAATTTTTGGAAAATTCAGGGTTAAAAATGGAATTTAT-AAAGTTCAAGGG
1 AG-GGGTTAAAATAT-ATTTTTGGAAAATTCAAGGTTAAAAATGGAATTT-TGAAAGTTCAAGGG
* *
7146 TAAAAATGTAATTTTTGAAAAAATCAAGGTCAAAAA-AGGAATTTTGAAAAGTTT
63 TAAAAAGGTAATTTATGAAAAAATCAAGGTCAAAAATA-GAATTTTGAAAAGTTT
**
7200 AGGGGTTAAAATATATTTTTTAAAAAGTTCAAGGTT-AAAATGGAATTTTG
1 AGGGGTTAAAATATATTTTTGGAAAA-TTCAAGGTTAAAAATGGAATTTTG
7250 GAAATTCGGG
Statistics
Matches: 137, Mismatches: 22, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
115 1 0.01
116 24 0.18
117 77 0.56
118 34 0.25
119 1 0.01
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.31
Consensus pattern (116 bp):
AGGGGTTAAAATATATTTTTGGAAAATTCAAGGTTAAAAATGGAATTTTGAAAGTTCAAGGGTAA
AAAGGTAATTTATGAAAAAATCAAGGTCAAAAATAGAATTTTGAAAAGTTT
Found at i:7248 original size:30 final size:30
Alignment explanation
Indices: 7090--7248 Score: 84
Period size: 30 Copynumber: 5.4 Consensus size: 30
7080 TTTGAGGGTA
* ** *
7090 AAAATGTAATTTTTGGAAAA-TTCAGGGTT
1 AAAATGGAATTTTTTAAAAAGTTCAAGGTT
* *
7119 AAAAATGGAA---TTTATAAAGTTCAAGGGTA
1 -AAAATGGAATTTTTTAAAAAGTTCAA-GGTT
* * * *
7148 AAAATGTAATTTTTGAAAAA-ATCAAGGTCA
1 AAAATGGAATTTTTTAAAAAGTTCAAGGT-T
* * * *
7178 AAAAAGGAA--TTTTGAAAAGTTTAGGGGTT
1 AAAATGGAATTTTTTAAAAAGTTCA-AGGTT
7207 AAAAT--ATATTTTTTAAAAAGTTCAAGGTT
1 AAAATGGA-ATTTTTTAAAAAGTTCAAGGTT
7236 AAAATGGAATTTT
1 AAAATGGAATTTT
7249 GGAAATTCGG
Statistics
Matches: 94, Mismatches: 22, Indels: 26
0.66 0.15 0.18
Matches are distributed among these distances:
27 6 0.06
28 20 0.21
29 21 0.22
30 40 0.43
31 7 0.07
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTTAAAAAGTTCAAGGTT
Found at i:8282 original size:3 final size:3
Alignment explanation
Indices: 8270--8318 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
8260 TTTCAAATTC
* * * *
8270 TAT T-T TAT TAT TAT TAA TAT TAA AAT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8317 TA
1 TA
8319 ATGCTATTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:9011 original size:17 final size:17
Alignment explanation
Indices: 8953--9032 Score: 79
Period size: 17 Copynumber: 4.6 Consensus size: 17
8943 TAAATAAATT
* *
8953 TAAACTTAATATTTATAA
1 TAAATTTAA-ATTTAAAA
**
8971 TAAATTTAAATTCCAAA
1 TAAATTTAAATTTAAAA
** *
8988 TGGATTTAAATTTAATA
1 TAAATTTAAATTTAAAA
*
9005 TATATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
9022 TAAATTTAAAT
1 TAAATTTAAAT
9033 CTGTTGGGCC
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
17 41 0.84
18 8 0.16
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:9621 original size:49 final size:49
Alignment explanation
Indices: 9544--10220 Score: 470
Period size: 49 Copynumber: 13.8 Consensus size: 49
9534 GGATTTGCCT
* * * * *
9544 TTGCGGCTTAAATCTTTCCCATT-TTGTCTTGGTGGTACTAGATTCGCCG
1 TTGCGACTTAAATCTTTCCC-TTCATGTCTTTGAGGTACTAGATTCACCG
* **
9593 TTGC-AGCTTAAATCTTTCCCTTCATGTC-TTCATGGTACTAGATTCATAG
1 TTGCGA-CTTAAATCTTTCCCTTCATGTCTTTGA-GGTACTAGATTCACCG
* * * * * *
9642 TTG-AAGCTTAAATCTTTTTCACTTTATG-CTTCTGAGGTACTAGGTTCGCCA
1 TTGCGA-CTTAAATC--TTTCCCTTCATGTCTT-TGAGGTACTAGATTCACCG
* ** * *
9693 TTGCGACTTAAACCTTTCCCTTTGTGTCTTGGCGGTACTAGATTCACCG
1 TTGCGACTTAAATCTTTCCCTTCATGTCTTTGAGGTACTAGATTCACCG
* * *
9742 TTAC-AGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACTAGATTCACCG
1 TTGCGA-CTTAAATCTTTCCCTTCATGTCTTTGAGGTACTAGATTCACCG
* * *
9791 TTACGACTTAAATCTTTCCCTTTATG-CTTTTGAGGTA-TAAGGTTCACCG
1 TTGCGACTTAAATCTTTCCCTTCATGTC-TTTGAGGTACT-AGATTCACCG
* * ** *
9840 TTACGACTTAAACCTTTCTCC-TCATGTCTTTCCGGTACTGGATTCACCG
1 TTGCGACTTAAATCTTTC-CCTTCATGTCTTTGAGGTACTAGATTCACCG
* * * *
9889 TTGC-AGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCA
1 TTGCGA-CTTAAATCTTTCCCTTCATGTCTTTGAGGTACTAGATTCACCG
* * * *
9938 TTGCGACTTAAACCTTTCCCTTTATG-CTTCTGAGGTA-TAAGGTTCACTG
1 TTGCGACTTAAATCTTTCCCTTCATGTCTT-TGAGGTACT-AGATTCACCG
* * * * * **
9987 TTGCGACTTAAACCTTTCTGC-TCGTGTCTTTGTGGTACTGGATTCGTCG
1 TTGCGACTTAAATCTTTC-CCTTCATGTCTTTGAGGTACTAGATTCACCG
* * * ** *
10036 TTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTTGCCA
1 TTGCGACTTAAATCTTTCCCTTCATGTCTTTGAGGTACTAGATTCACCG
* * * * *
10085 TTGTGACTTAAACCTTTCCCTTTATG-CTTCTGAGGTAC-ACGGTTTACCG
1 TTGCGACTTAAATCTTTCCCTTCATGTCTT-TGAGGTACTA-GATTCACCG
* * * * * * *
10134 TTGCGACTTAAACCTTTCCCTCCATATC-TTCATGGTAATGGATTCGCCG
1 TTGCGACTTAAATCTTTCCCTTCATGTCTTTGA-GGTACTAGATTCACCG
* * * *
10183 TTGCGGCTTAGATCTTTCCCTTCAT-TCTTCGAAGTACT
1 TTGCGACTTAAATCTTTCCCTTCATGTCTTTGAGGTACT
10221 GAAACCTATA
Statistics
Matches: 495, Mismatches: 101, Indels: 65
0.75 0.15 0.10
Matches are distributed among these distances:
48 24 0.05
49 420 0.85
50 16 0.03
51 32 0.06
52 3 0.01
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (49 bp):
TTGCGACTTAAATCTTTCCCTTCATGTCTTTGAGGTACTAGATTCACCG
Found at i:9886 original size:147 final size:146
Alignment explanation
Indices: 9577--10220 Score: 719
Period size: 147 Copynumber: 4.4 Consensus size: 146
9567 TTGTCTTGGT
* *
9577 GGTACTAGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTC-ATGGTACTAGATTCA-T
1 GGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTCGA-GGTACTAGATTCACC
* * * * *
9640 AGTTGAAG-CTTAAATCTTTTTCACTTTATGCTTCTGAGGTACT-AGGTTCGCCATTGCGACTTA
65 A-TT-ACGACTTAAA-C-CTTTCCCTTTATGCTTCTGAGGTA-TAAGGTTCACCGTTGCGACTTA
** **
9703 AACCTTTCCCTTTGTGTCTTGGC
125 AACCTTTCCC-TCATGTCTTTCC
* * * * *
9726 GGTACTAGATTCACCGTTACAGCTTAAATCTTTCCCTTCATGTCTTCGTGGTACTAGATTCACCG
1 GGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTCGAGGTACTAGATTCACCA
* * *
9791 TTACGACTTAAATCTTTCCCTTTATGCTTTTGAGGTATAAGGTTCACCGTTACGACTTAAACCTT
66 TTACGACTTAAACCTTTCCCTTTATGCTTCTGAGGTATAAGGTTCACCGTTGCGACTTAAACCTT
9856 TCTCCTCATGTCTTTCC
131 TC-CCTCATGTCTTTCC
* * *
9873 GGTACTGGATTCACCGTTGCAGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGGTTCGCC
1 GGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTC-GAGGTACTAGATTCACC
* *
9937 ATTGCGACTTAAACCTTTCCCTTTATGCTTCTGAGGTATAAGGTTCACTGTTGCGACTTAAACCT
65 ATTACGACTTAAACCTTTCCCTTTATGCTTCTGAGGTATAAGGTTCACCGTTGCGACTTAAACCT
* * **
10002 TTCTGCTCGTGTCTTTGT
130 TTC-CCTCATGTCTTTCC
* * * **
10020 GGTACTGGATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGGTTTGCC
1 GGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTC-GAGGTACTAGATTCACC
** * * *
10084 ATTGTGACTTAAACCTTTCCCTTTATGCTTCTGAGGTACACGGTTTACCGTTGCGACTTAAACCT
65 ATTACGACTTAAACCTTTCCCTTTATGCTTCTGAGGTATAAGGTTCACCGTTGCGACTTAAACCT
* *
10149 TTCCCTCCATATC-TTCAT
130 TTCCCT-CATGTCTTTC-C
* * * *
10167 GGTAATGGATTCGCCGTTGCGGCTTAGATCTTTCCCTTCAT-TCTTCGAAGTACT
1 GGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTCGAGGTACT
10221 GAAACCTATA
Statistics
Matches: 437, Mismatches: 49, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
146 16 0.04
147 351 0.80
148 4 0.01
149 66 0.15
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.39
Consensus pattern (146 bp):
GGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTCTTCGAGGTACTAGATTCACCA
TTACGACTTAAACCTTTCCCTTTATGCTTCTGAGGTATAAGGTTCACCGTTGCGACTTAAACCTT
TCCCTCATGTCTTTCC
Found at i:10607 original size:29 final size:29
Alignment explanation
Indices: 10575--10630 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
10565 TGGGCAGTGT
*
10575 GGGAAAGAATGAAATTGTATTTGAGTCAA
1 GGGAAAGAATGAAATTGTATTAGAGTCAA
*
10604 GGGAAAGAATGAGATTGTATTAGAGTC
1 GGGAAAGAATGAAATTGTATTAGAGTC
10631 CAAGCTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.30, T:0.27
Consensus pattern (29 bp):
GGGAAAGAATGAAATTGTATTAGAGTCAA
Done.