Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014307.1 Kokia drynarioides strain JFW-HI SEQ_129343, 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: 14513
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:73 original size:28 final size:27
Alignment explanation
Indices: 27--80 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
17 TGTAAAAACA
* **
27 GTTATTATTATTATTAATATTAATTATG
1 GTTATTATTAATAACAATATT-ATTATG
55 GTTATTATTAATAACAATATTATTAT
1 GTTATTATTAATAACAATATTATTAT
81 TAAGTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (27 bp):
GTTATTATTAATAACAATATTATTATG
Found at i:819 original size:17 final size:17
Alignment explanation
Indices: 759--819 Score: 52
Period size: 17 Copynumber: 3.6 Consensus size: 17
749 ATTTTATTTC
759 AAAATAAATTTAAA-TT
1 AAAATAAATTTAAACTT
* ** *
775 CCAAATAAGCTTAAATTT
1 -AAAATAAATTTAAACTT
*
793 ACAATAAATTTAAACTT
1 AAAATAAATTTAAACTT
*
810 AAAATGAATT
1 AAAATAAATT
820 AAAAATTTAA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
17 31 0.94
18 2 0.06
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAATAAATTTAAACTT
Found at i:883 original size:16 final size:18
Alignment explanation
Indices: 852--884 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
842 GGTTTACTTT
852 CGATCTAAATATTGGGCC
1 CGATCTAAATATTGGGCC
870 CGATC-AAA-ATTGGGC
1 CGATCTAAATATTGGGC
885 TCCAACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (18 bp):
CGATCTAAATATTGGGCC
Found at i:1835 original size:102 final size:102
Alignment explanation
Indices: 1650--1846 Score: 261
Period size: 101 Copynumber: 1.9 Consensus size: 102
1640 AATTGTGTGC
** * * *
1650 GCCAATGCTTGGCCAACACCACCTTTTTGTTTAGATAAAAAAAAAATTGGTTTTGGTCATACATT
1 GCCAATGCTTGGCCAACACCACCTTTTTAATCAGATAAAAAAAAAATTGGTGTTGGCCATACATT
** **
1715 GGTCGACACCAGTATTTTTTATCAGATAAAAGTGTTG
66 GACCGACACCAACATTTTTTATCAGATAAAAGTGTTG
* * * *
1752 GCCAATGCTTGGTCAACATCACCTTTTTAATCAGAT-AAAAAAAATTTGGTGTTGGCCATGCATT
1 GCCAATGCTTGGCCAACACCACCTTTTTAATCAGATAAAAAAAAAATTGGTGTTGGCCATACATT
*
1816 GACCGACACTAACATTTTTTATCAGATAAAA
66 GACCGACACCAACATTTTTTATCAGATAAAA
1847 AAAAATTTGG
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
101 50 0.62
102 31 0.38
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (102 bp):
GCCAATGCTTGGCCAACACCACCTTTTTAATCAGATAAAAAAAAAATTGGTGTTGGCCATACATT
GACCGACACCAACATTTTTTATCAGATAAAAGTGTTG
Found at i:1890 original size:55 final size:56
Alignment explanation
Indices: 1775--1910 Score: 150
Period size: 56 Copynumber: 2.4 Consensus size: 56
1765 CAACATCACC
* *
1775 TTTTTAATCAGATAAAAAAAATTTGGTGTTGGCCATGCATTGACCGACACTAACAT
1 TTTTTAATCAGATAAAAAAAATTTGGTGTTGGCCATACATTGACCGACACCAACAT
** * *
1831 TTTTT-ATCAGATAAAAAAAAATTTGGTGTTGGCTTTACATT-AGTCGACACCAGCAT
1 TTTTTAATCAGAT-AAAAAAAATTTGGTGTTGGCCATACATTGA-CCGACACCAACAT
* ** *
1887 TTTTTTATTGGATAAAAAATATTT
1 TTTTTAATCAGATAAAAAAAATTT
1911 TTTGGTGTTG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
55 8 0.12
56 55 0.81
57 5 0.07
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (56 bp):
TTTTTAATCAGATAAAAAAAATTTGGTGTTGGCCATACATTGACCGACACCAACAT
Found at i:2045 original size:117 final size:117
Alignment explanation
Indices: 1897--2313 Score: 422
Period size: 117 Copynumber: 3.6 Consensus size: 117
1887 TTTTTTATTG
* *
1897 GATAAAAAATATTTTTT-GGTGTTGGCAAATGCTTGGCTAACACCACCTTTTTTATCTGAT-AAA
1 GATAAAAAATATTTTTTAGGTGTTGGCCAATGCTTGGCCAACACCACCTTTTTTATCTGATAAAA
* *
1960 AAATAAATTTTTTTTTTGTGTTAGCCATGCATTGACTGACACTATTTTTTTATCA
66 AAAT-AA--TTTTTTTTGTGTTGGCCATGCATTGACTGACACTATTTTTTAATCA
* * * * *
2015 AATAAAAAA-A-ATTTTAGGTGTTGGCCAATGCTTGGCCAACACTACCATTTTTATTTGATAAAA
1 GATAAAAAATATTTTTTAGGTGTTGGCCAATGCTTGGCCAACACCACCTTTTTTATCTGATAAAA
* * * *
2078 AAATAA-TTTTTTTGTGTTGGTCATACATT-AATCGACACTATTTTTTAATCT
66 AAATAATTTTTTTTGTGTTGGCCATGCATTGACT-GACACTATTTTTTAATCA
* * * * * *
2129 GATAAAAAATATTTTTTTA-GTGTTGACCAATGCTTGACCGACATCACTTTTTTTATATGATAAA
1 GATAAAAAATA-TTTTTTAGGTGTTGGCCAATGCTTGGCCAACACCACCTTTTTTATCTGATAAA
* * * * * * **
2193 AAAATAATTTTTTTGGTATCGGCCATGCATTGGCCGACACCACCTTTTAATCA
65 AAAATAATTTTTTTTGTGTTGGCCATGCATTGACTGACACTATTTTTTAATCA
* * *
2246 GAT-AAAAATAATTTTTTTGGTGTTGGTC-ATGCATTGGCCGACACCA-CTTATTTTATCTGATA
1 GATAAAAAAT-ATTTTTTAGGTGTTGGCCAATGC-TTGGCCAACACCACCTT-TTTTATCTGATA
2308 AAAAAA
63 AAAAAA
2314 AAAAATTTGT
Statistics
Matches: 245, Mismatches: 42, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
113 2 0.01
114 44 0.18
115 1 0.00
116 66 0.27
117 117 0.48
118 15 0.06
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (117 bp):
GATAAAAAATATTTTTTAGGTGTTGGCCAATGCTTGGCCAACACCACCTTTTTTATCTGATAAAA
AAATAATTTTTTTTGTGTTGGCCATGCATTGACTGACACTATTTTTTAATCA
Found at i:2132 original size:58 final size:59
Alignment explanation
Indices: 1800--2313 Score: 304
Period size: 57 Copynumber: 8.8 Consensus size: 59
1790 AAAAAATTTG
* * *
1800 GTGTTGGCCATGCATTGACCGACACTAACATTTTTTATCAGATAAAAAAA-AA----TTTG
1 GTGTTGGCCATGCATTGACCGACAC-CAC-TTTTTTATCTGATAAAAAAATAATTTTTTTA
** * * *
1856 GTGTTGGCTTTACATT-AGTCGACACCAGCATTTTTTTAT-TGGAT-AAAAAAT-A-TTTTTTG
1 GTGTTGGCCATGCATTGA-CCGACACCA-C--TTTTTTATCT-GATAAAAAAATAATTTTTTTA
* * ** *
1915 GTGTTGGCAAATGC-TTGGCTAACACCACCTTTTTTATCTGAT-AAAAAATAAATTTTTTTTTT
1 GTGTTGGC-CATGCATTGACCGACACCA-CTTTTTTATCTGATAAAAAAAT-AA--TTTTTTTA
* * * * **
1977 GTGTTAGCCATGCATTGACTGACACTATTTTTTTATCAAAT-AAAAAA-AA---TTTTA
1 GTGTTGGCCATGCATTGACCGACACCACTTTTTTATCTGATAAAAAAATAATTTTTTTA
* * * * *
2031 GGTGTTGGCCAATGC-TTGGCCAACACTACCATTTTTATTTGATAAAAAAATAATTTTTTT-
1 -GTGTTGGCC-ATGCATTGACCGACACCA-CTTTTTTATCTGATAAAAAAATAATTTTTTTA
* * * * *
2091 GTGTTGGTCATACATTAATCGACACTA-TTTTTTAATCTGAT-AAAAAAT-ATTTTTTTA
1 GTGTTGGCCATGCATTGACCGACACCACTTTTTT-ATCTGATAAAAAAATAATTTTTTTA
* * * *
2148 GTGTTGACCAATGC-TTGACCGACATCACTTTTTTTATATGATAAAAAAATAATTTTTTTG
1 GTGTTGGCC-ATGCATTGACCGACACCAC-TTTTTTATCTGATAAAAAAATAATTTTTTTA
* * * * * * *
2208 GTATCGGCCATGCATTGGCCGACACCACCTTTTAATCAGAT--AAAAATAATTTTTTTG
1 GTGTTGGCCATGCATTGACCGACACCACTTTTTTATCTGATAAAAAAATAATTTTTTTA
* *
2265 GTGTTGGTCATGCATTGGCCGACACCACTTATTTTATCTGATAAAAAAA
1 GTGTTGGCCATGCATTGACCGACACCACTT-TTTTATCTGATAAAAAAA
2314 AAAAATTTGT
Statistics
Matches: 355, Mismatches: 66, Indels: 70
0.72 0.13 0.14
Matches are distributed among these distances:
54 4 0.01
55 20 0.06
56 48 0.14
57 105 0.30
58 30 0.08
59 67 0.19
60 33 0.09
61 25 0.07
62 23 0.06
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (59 bp):
GTGTTGGCCATGCATTGACCGACACCACTTTTTTATCTGATAAAAAAATAATTTTTTTA
Found at i:2335 original size:57 final size:56
Alignment explanation
Indices: 1746--2353 Score: 269
Period size: 57 Copynumber: 10.6 Consensus size: 56
1736 TCAGATAAAA
* * * * * *
1746 GTGTTGGCCAATGC-TTGGTCAACATCACCTTTTTAATCAGAT--AAAAAAAA-TTTG
1 GTGTTGG-CAATGCATTGGCCGACACCA-CTTTTTTATCTGATAAAAAAAAAATTTTT
* * * * *
1800 GTGTTGGCCATGCATTGACCGACACTAACATTTTTTATCAGAT-AAAAAAAAA-TTTG
1 GTGTTGGCAATGCATTGGCCGACAC-CAC-TTTTTTATCTGATAAAAAAAAAATTTTT
** * * * * *
1856 GTGTTGGCTTTACATTAGTCGACACCAGCATTTTTTTAT-TGGAT-AAAAAATATTTTTT
1 GTGTTGGCAATGCATTGGCCGACACCA-C--TTTTTTATCT-GATAAAAAAAAAATTTTT
** *
1914 GGTGTTGGCAAATGC-TTGGCTAACACCACCTTTTTTATCTGATAAAAAATAAATTTTTTTTTT
1 -GTGTTGGC-AATGCATTGGCCGACACCA-CTTTTTTATCTGATAAAAAA-AAA----ATTTTT
* * * * * * *
1977 GTGTTAGCCATGCATTGACTGACACTATTTTTTTATC--A-AATAAAAAAAATTTTAG
1 GTGTTGGCAATGCATTGGCCGACACCACTTTTTTATCTGATAA-AAAAAAAATTTT-T
* * * * *
2032 GTGTTGGCCAATGC-TTGGCCAACACTACCATTTTTATTTGATAAAAAAATAATTTTTTT
1 GTGTTGG-CAATGCATTGGCCGACACCA-CTTTTTTATCTGATAAAAAAA-AA-ATTTTT
* *** * * **
2091 GTGTTGGTC-ATACATTAATCGACACTA-TTTTTTAATCTGATAAAAAATATTTTTTT
1 GTGTTGG-CAATGCATTGGCCGACACCACTTTTTT-ATCTGATAAAAAAAAAATTTTT
* * * * *
2147 AGTGTTGACCAATGC-TTGACCGACATCACTTTTTTTATATGATAAAAAAATAATTTTT
1 -GTGTTG-GCAATGCATTGGCCGACACCAC-TTTTTTATCTGATAAAAAAAAAATTTTT
* * * * * * **
2205 TTGGTATCGGCCATGCATTGGCCGACACCACCTTTTAATCAGATAAAAATAATTTTTTT
1 GT-GT-T-GGCAATGCATTGGCCGACACCACTTTTTTATCTGATAAAAAAAAAATTTTT
**
2264 GGTGTTGGTC-ATGCATTGGCCGACACCACTTATTTTATCTGATAAAAAAAAAAAATTT
1 -GTGTTGG-CAATGCATTGGCCGACACCACTT-TTTTATCTGATAAAAAAAAAATTTTT
* *
2322 GTGTTGGCAATGCATTAGCTGACACCAACTTT
1 GTGTTGGCAATGCATTGGCCGACACC-ACTTT
2354 CCCTCCTTGC
Statistics
Matches: 420, Mismatches: 91, Indels: 83
0.71 0.15 0.14
Matches are distributed among these distances:
53 5 0.01
54 19 0.05
55 30 0.07
56 51 0.12
57 97 0.23
58 82 0.20
59 80 0.19
60 20 0.05
61 13 0.03
62 17 0.04
63 6 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (56 bp):
GTGTTGGCAATGCATTGGCCGACACCACTTTTTTATCTGATAAAAAAAAAATTTTT
Found at i:3223 original size:30 final size:30
Alignment explanation
Indices: 3182--3304 Score: 192
Period size: 30 Copynumber: 4.1 Consensus size: 30
3172 AAAAAATAAT
*
3182 AATTAGAAATTAAATTTAAAGTATAAACAA
1 AATTAGAAATTAAATTTAAAATATAAACAA
*
3212 AATTAGTAATTAAATTTAAAATATAAACAA
1 AATTAGAAATTAAATTTAAAATATAAACAA
3242 AATTAGAAATTAAATTTAAAATATAAACAA
1 AATTAGAAATTAAATTTAAAATATAAACAA
* * *
3272 AATTACAAATTAAATCTAAAAAATAAACGAA
1 AATTAGAAATTAAATTTAAAATATAAAC-AA
3303 AA
1 AA
3305 AAATCAAAAT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
30 82 0.95
31 4 0.05
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACAA
Found at i:4333 original size:56 final size:55
Alignment explanation
Indices: 4179--4347 Score: 157
Period size: 56 Copynumber: 3.0 Consensus size: 55
4169 ACCAAAAAAA
* * * * * *
4179 TTATTTGATTAAAAAGGTGGTGTCGACTAAACATTAGCCAGCACCAAAA-ATTTTT
1 TTATTTGA-AAAAAAGTTGGTGTCGACCAAGCATTAGCCAACACCAAAATTTTTTT
* * * *
4234 TTATCTGATAAAAAA-TACTGGTATCGACCAATGCA-TGGGCAACACCAAAATTTTTTT
1 TTATTTGA-AAAAAAGT--TGGTGTCGACCAA-GCATTAGCCAACACCAAAATTTTTTT
*
4291 TTATTTGAACAAAAAGTTGGTGTCGGCCAAGCATTAGCCAACACC-AAATTTTTTT
1 TTATTTGAA-AAAAAGTTGGTGTCGACCAAGCATTAGCCAACACCAAAATTTTTTT
4346 TT
1 TT
4348 GAAAATCTCG
Statistics
Matches: 92, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
55 28 0.30
56 44 0.48
57 19 0.21
58 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (55 bp):
TTATTTGAAAAAAAGTTGGTGTCGACCAAGCATTAGCCAACACCAAAATTTTTTT
Found at i:5539 original size:90 final size:89
Alignment explanation
Indices: 5438--5806 Score: 465
Period size: 88 Copynumber: 4.2 Consensus size: 89
5428 ATGGCTCATC
* * * * * *
5438 TGTAAATCAATTTTAATATGTATTATTTGTTGGTCGAATTTTATATTTTTATATATCAGTTTTAT
1 TGTAAATCAATTTTAGTCTATATTATTTGTTGGTCGAATTTTATATTTTCATATATCAATTTTCT
*
5503 AAAATGTTCATATTATTTTTGGATT
66 AAAATGTTCATATT-TTTTTGTATT
* * **
5528 TGTAAATCAATTTTAGTCTGTATTATTTGTTCGTCGAATTTTATATTTTTGTATATCAATTTTCT
1 TGTAAATCAATTTTAGTCTATATTATTTGTTGGTCGAATTTTATATTTTCATATATCAATTTTCT
* * *
5593 AGAATGTT-TTATTTTTTTTGTATA
66 AAAATGTTCATA-TTTTTTTGTATT
* * * * *
5617 TATAAATCAA-TTTAGTCTATATTATTTATTGGTAGAATTTTATATTGTCATATATCAATTTTTT
1 TGTAAATCAATTTTAGTCTATATTATTTGTTGGTCGAATTTTATATTTTCATATATCAATTTTCT
5681 AAAATGTTCAT-TTTTTTTGTATT
66 AAAATGTTCATATTTTTTTGTATT
* *
5704 TGTAAATCATTTTTAGTCTATATTATTTGTTGGTCAAATTTTATATTTTCATATATCAATTTTCT
1 TGTAAATCAATTTTAGTCTATATTATTTGTTGGTCGAATTTTATATTTTCATATATCAATTTTCT
* * *
5769 AAAATGTTCGTATTTTCTTGTATC
66 AAAATGTTCATATTTTTTTGTATT
* *
5793 TATAAATTAATTTT
1 TGTAAATCAATTTT
5807 GTTGGGTTTT
Statistics
Matches: 240, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
87 19 0.08
88 112 0.47
89 41 0.17
90 68 0.28
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (89 bp):
TGTAAATCAATTTTAGTCTATATTATTTGTTGGTCGAATTTTATATTTTCATATATCAATTTTCT
AAAATGTTCATATTTTTTTGTATT
Found at i:8022 original size:49 final size:50
Alignment explanation
Indices: 7965--8064 Score: 175
Period size: 49 Copynumber: 2.0 Consensus size: 50
7955 ATAAATATCG
*
7965 AATAATTGGTCATGAAGTATATAAAAAATAAGGG-TTTTTTTATCTAAGT
1 AATAATTGGTCACGAAGTATATAAAAAATAAGGGTTTTTTTTATCTAAGT
8014 AATAATTGGTCACGAAGTATATAAAAAATAAGGGTTTTTTTTTATCTAAGT
1 AATAATTGGTCACGAAGTATATAAAAAATAAGGG-TTTTTTTTATCTAAGT
8065 GACCCAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 33 0.69
51 15 0.31
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (50 bp):
AATAATTGGTCACGAAGTATATAAAAAATAAGGGTTTTTTTTATCTAAGT
Found at i:8443 original size:54 final size:55
Alignment explanation
Indices: 8362--8638 Score: 201
Period size: 54 Copynumber: 5.0 Consensus size: 55
8352 GAAAACAAAA
* * * *
8362 TTGGTGTTGGCCAATGCGTGATC-GACACCACCTTTTTGATCAGATAAAAAAATT
1 TTGGTATTGGCCAATGCTTGGTCAGACACCACCTTTTTAATCAGATAAAAAAATT
* * * *
8416 TTGGTATTGG-CTATGCATTGG-CAGACACCAGCATTTTTTATCGGATAAAAAAA-T
1 TTGGTATTGGCCAATGC-TTGGTCAGACACCA-CCTTTTTAATCAGATAAAAAAATT
* *
8470 TTGGTGTTGGCCAATGCTTGGTCA-ACACCATCTTTTTAATCAGATAAAAAATATTTTTT
1 TTGGTATTGGCCAATGCTTGGTCAGACACCACCTTTTTAATCAGATAAAAAA-A----TT
* * * * * *
8529 TTGGTGTTGGCCAATGCCTAG-CCGACACTACCTTTTTTATCAGATAAAAAAAATATT
1 TTGGTATTGGCCAATGCTTGGTCAGACACCACCTTTTTAATCAGAT--AAAAAA-ATT
* * * * * * *
8586 TTGATGTTGGCTAACGCTTGGCCA-ACACCA-CTTTTTTATCAGACAAAAAAATT
1 TTGGTATTGGCCAATGCTTGGTCAGACACCACCTTTTTAATCAGATAAAAAAATT
8639 ATTTTTTTGG
Statistics
Matches: 181, Mismatches: 27, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
53 26 0.14
54 45 0.25
55 26 0.14
56 13 0.07
57 23 0.13
58 2 0.01
59 38 0.21
61 8 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (55 bp):
TTGGTATTGGCCAATGCTTGGTCAGACACCACCTTTTTAATCAGATAAAAAAATT
Found at i:8538 original size:59 final size:58
Alignment explanation
Indices: 8362--8823 Score: 389
Period size: 59 Copynumber: 8.0 Consensus size: 58
8352 GAAAACAAAA
* * *
8362 TTGGTGTTGGCCAATGCGTGATCGACACCACCTTTTTGATCAGATAAAAAAA----TT
1 TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAAATTTTTT
* * * *
8416 TTGGTATTGG-CTATGCATTGG-CAGACACCAGCATTTTTTATCGGATAAAAAAA-----T
1 TTGGTGTTGGCCAATGC-TTGGTC-GACACCA-CCTTTTTTATCAGATAAAAAAATTTTTT
* * *
8470 TTGGTGTTGGCCAATGCTTGGTCAACACCATCTTTTTAATCAGATAAAAAATATTTTTT
1 TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAA-ATTTTTT
* * * * * *
8529 TTGGTGTTGGCCAATGCCTAGCCGACACTACCTTTTTTATCAGATAAAAAAA-ATATT
1 TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAAATTTTTT
* * * * * *
8586 TTGATGTTGGCTAACGCTTGGCCAACACCA-CTTTTTTATCAGACAAAAAAATTATTTTT
1 TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAAA-T-TTTTT
* * *
8645 TTGGTGTTAGCCAATGCTTGGTTGACACCACCTTTTTTATGTA-ATAAAAAAATATTTTT
1 TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTAT-CAGATAAAAAAAT-TTTTT
** * * * *
8704 TTTCTGTTGGTC-ATACATTGGTCGACACTACCTTTTTTATCAGATAAAAAATAATTTTT
1 TTGGTGTTGGCCAATGC-TTGGTCGACACCACCTTTTTTATCAGATAAAAAA-ATTTTTT
* * * *
8763 TTGGTGTTGACCAATGCTTGATCGACACAATCTTTTTTATCTA-ATAAAAAATATTTTTT
1 TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTATC-AGATAAAAAA-ATTTTTT
8822 TT
1 TT
8824 TGTATTAGTC
Statistics
Matches: 327, Mismatches: 60, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
53 23 0.07
54 39 0.12
55 25 0.08
56 20 0.06
57 26 0.08
58 5 0.02
59 166 0.51
60 22 0.07
61 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (58 bp):
TTGGTGTTGGCCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAAATTTTTT
Found at i:8841 original size:118 final size:114
Alignment explanation
Indices: 8474--8826 Score: 370
Period size: 116 Copynumber: 3.0 Consensus size: 114
8464 AAAAATTTGG
* * * *
8474 TGTTGGCCAATGCTTGGTCAACACCATCTTTTTAATCAGATAAAAAATATTTTTTTTGGTGTTGG
1 TGTTGGTC-ATGCTTGGTCAACACCA-CTTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGA
* * * * * **
8539 CCAATGCCT-AGCCGACACTACCTTTTTTATC-AGATAAAAAAAATATTTTGA
64 CCAATGCTTGA-TCGACACAACCTTTTTTATCTA-ATAAAAAATATTTTTTTT
* * * * *
8590 TGTTGGCTAACGCTTGGCCAACACCACTTTTTTATCAGACAAAAAAATTATTTTTTTGGTGTT-A
1 TGTTGG-TCATGCTTGGTCAACACCACTTTTTTATCAGA-TAAAAAATAATTTTTTTGGTGTTGA
* * * *
8654 GCCAATGCTTGGTTGACACCACCTTTTTTATGTAATAAAAAAATATTTTTTTT
64 -CCAATGCTTGATCGACACAACCTTTTTTATCTAAT-AAAAAATATTTTTTTT
* * *
8707 CTGTTGGTCATACATTGGTCGACACTACCTTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTG
1 -TGTTGGTCATGC-TTGGTCAACACCA-CTTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTG
*
8772 ACCAATGCTTGATCGACACAATCTTTTTTATCTAATAAAAAATATTTTTTTT
63 ACCAATGCTTGATCGACACAACCTTTTTTATCTAATAAAAAATATTTTTTTT
8824 TGT
1 TGT
8827 ATTAGTCATG
Statistics
Matches: 195, Mismatches: 32, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
115 12 0.06
116 70 0.36
117 32 0.16
118 67 0.34
119 14 0.07
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (114 bp):
TGTTGGTCATGCTTGGTCAACACCACTTTTTTATCAGATAAAAAATAATTTTTTTGGTGTTGACC
AATGCTTGATCGACACAACCTTTTTTATCTAATAAAAAATATTTTTTTT
Found at i:8848 original size:59 final size:57
Alignment explanation
Indices: 8668--8849 Score: 179
Period size: 59 Copynumber: 3.1 Consensus size: 57
8658 ATGCTTGGTT
* * * * *
8668 GACACCACCTTTTTTATGTAATAAAAAAATATTTTTTTTCTGTTGGTCATACATTGGTC
1 GACACAACCTTTTTTATCTAAT-AAAAAATATTTTTTTT-TGTTTGTCATGCATTGATC
* * * *
8727 GACACTACCTTTTTTATC-AGATAAAAAATAATTTTTTTGGTGTTGACCAATGC-TTGATC
1 GACACAACCTTTTTTATCTA-ATAAAAAATATTTTTTTTTGT-TTG-TC-ATGCATTGATC
* *
8786 GACACAATCTTTTTTATCTAATAAAAAATATTTTTTTTTGTATTAGTCATGCATTGACC
1 GACACAACCTTTTTTATCTAATAAAAAATATTTTTTTTTGT-TT-GTCATGCATTGATC
8845 GACAC
1 GACAC
8850 GAACTTTCCT
Statistics
Matches: 101, Mismatches: 15, Indels: 14
0.78 0.12 0.11
Matches are distributed among these distances:
57 2 0.02
58 22 0.22
59 72 0.71
60 5 0.05
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (57 bp):
GACACAACCTTTTTTATCTAATAAAAAATATTTTTTTTTGTTTGTCATGCATTGATC
Found at i:8976 original size:31 final size:31
Alignment explanation
Indices: 8927--8985 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
8917 CAATCGAATT
* *
8927 TCGGGGTTGAACTCTATACTGTCATGTATTG
1 TCGGAGTTGAACTATATACTGTCATGTATTG
*
8958 TCGGAGTTGAATTATATACTGTCATGTA
1 TCGGAGTTGAACTATATACTGTCATGTA
8986 AAGTTGGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.39
Consensus pattern (31 bp):
TCGGAGTTGAACTATATACTGTCATGTATTG
Found at i:10113 original size:4 final size:4
Alignment explanation
Indices: 10104--10169 Score: 62
Period size: 4 Copynumber: 16.2 Consensus size: 4
10094 AAATAAACGG
* * *
10104 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* *
10154 G-AA GAAG GAAA TAAA G
1 GAAA GAAA GAAA GAAA G
10170 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:10129 original size:21 final size:21
Alignment explanation
Indices: 10105--10156 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
10095 AATAAACGGG
10105 AAAGAAAGAAAGAAA-AGAAAG
1 AAAGAAAGAAAGAAAGAG-AAG
* * *
10126 AAAGAAAGGAAGAAGGAGAGG
1 AAAGAAAGAAAGAAAGAGAAG
10147 AAAGAAAGAA
1 AAAGAAAGAA
10157 GAAGGAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAGAAAGAGAAG
Found at i:10138 original size:25 final size:25
Alignment explanation
Indices: 10104--10164 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
10094 AAATAAACGG
10104 GAAAGAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
* * * *
10129 GAAAGGAAGAAGGAGAGGAAAGAAA
1 GAAAGAAAGAAAGAAAAGAAAGAAA
*
10154 G-AAGAAGGAAA
1 GAAAGAAAGAAA
10165 TAAAGGTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 7 0.24
25 22 0.76
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (25 bp):
GAAAGAAAGAAAGAAAAGAAAGAAA
Found at i:10157 original size:17 final size:15
Alignment explanation
Indices: 10108--10169 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 15
10098 AAACGGGAAA
10108 GAAAGAAAGAA-AA-
1 GAAAGAAAGAAGAAG
10121 GAAAGAAAG-A-AAG
1 GAAAGAAAGAAGAAG
*
10134 G-AAG-AAGGAG-AG
1 GAAAGAAAGAAGAAG
10146 GAAAGAAAGAAGAAG
1 GAAAGAAAGAAGAAG
*
10161 GAAATAAAG
1 GAAAGAAAG
10170 GTAATGTGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
11 3 0.07
12 10 0.24
13 13 0.32
14 5 0.12
15 10 0.24
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (15 bp):
GAAAGAAAGAAGAAG
Found at i:13012 original size:21 final size:21
Alignment explanation
Indices: 12988--13028 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12978 TAGGGTCTAT
*
12988 TTGCCCCGGAGGAGTAGAGTC
1 TTGCCCCGGAGGAATAGAGTC
*
13009 TTGCCCGGGAGGAATAGAGT
1 TTGCCCCGGAGGAATAGAGT
13029 ATCGCGATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.20
Consensus pattern (21 bp):
TTGCCCCGGAGGAATAGAGTC
Done.