Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011254.1 Kokia drynarioides strain JFW-HI SEQ_126232, 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: 39310
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:2743 original size:11 final size:11
Alignment explanation
Indices: 2729--2753 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2719 AAATTAAATT
2729 TTTAAATATAA
1 TTTAAATATAA
2740 TTTAAATATAA
1 TTTAAATATAA
2751 TTT
1 TTT
2754 TAATTATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAATATAA
Found at i:2886 original size:18 final size:18
Alignment explanation
Indices: 2852--2889 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2842 TTTAAATTAA
*
2852 AAAATATCAATTTTTTTG
1 AAAATATCAATTATTTTG
2870 AAAAT-TCAATTAATTTTG
1 AAAATATCAATT-ATTTTG
2888 AA
1 AA
2890 TAAATCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
AAAATATCAATTATTTTG
Found at i:3070 original size:11 final size:11
Alignment explanation
Indices: 3054--3088 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3044 TGTCCTTTAA
3054 TTTTTTAATTT
1 TTTTTTAATTT
*
3065 TTTTTTAGTTT
1 TTTTTTAATTT
*
3076 TTATTTAATTT
1 TTTTTTAATTT
3087 TT
1 TT
3089 CATTTCTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTTTAATTT
Found at i:11239 original size:18 final size:19
Alignment explanation
Indices: 11216--11253 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
11206 TCCAATCCAC
*
11216 TCCTCCTCCA-AAAAACCA
1 TCCTCCACCATAAAAACCA
*
11234 TCCTCCACCATCAAAACCA
1 TCCTCCACCATAAAAACCA
11253 T
1 T
11254 TTCCTTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (19 bp):
TCCTCCACCATAAAAACCA
Found at i:11498 original size:18 final size:19
Alignment explanation
Indices: 11475--11512 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
11465 TCCAATCCAC
*
11475 TCCTCCTCCA-AAAAACCA
1 TCCTCCACCATAAAAACCA
*
11493 TCCTCCACCATCAAAACCA
1 TCCTCCACCATAAAAACCA
11512 T
1 T
11513 TTCCTTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.37, C:0.45, G:0.00, T:0.18
Consensus pattern (19 bp):
TCCTCCACCATAAAAACCA
Found at i:11519 original size:259 final size:259
Alignment explanation
Indices: 11060--11584 Score: 998
Period size: 259 Copynumber: 2.0 Consensus size: 259
11050 GAAAGGAGAA
* *
11060 AATAAAGAAGAAGAAAAACAAAAACTCTACTTAGTTAGAGTTTTATAAAATGTGGATGGTAGGAG
1 AATAAAGAAGAAGAAAAACAAAAAATCTACTCAGTTAGAGTTTTATAAAATGTGGATGGTAGGAG
11125 ATCCAACTATTGGATCATTTGGTGAGGACAATGAAAAATTTATTTACCTTGTGGATTATTCACGA
66 ATCCAACTATTGGATCATTTGGTGAGGACAATGAAAAATTTATTTACCTTGTGGATTATTCACGA
11190 AAGCCAGCATTAACAGTCCAATCCACTCCTCCTCCAAAAAACCATCCTCCACCATCAAAACCATT
131 AAGCCAGCATTAACAGTCCAATCCACTCCTCCTCCAAAAAACCATCCTCCACCATCAAAACCATT
*
11255 TCCTTTACAAAAATCACCAAAGTCTACTCTTCAAAAGACAAATCCTTTTCCTCAGCCCTGCTAT
196 TCCTTTACAAAAATCACCAAAGTCTACTCTTCAAAAGACAAATACTTTTCCTCAGCCCTGCTAT
*
11319 AATAAAGAAGAAGAAAAAGAAAAAATCTACTCAGTTAGAGTTTTATAAAATGTGGATGGTAGGAG
1 AATAAAGAAGAAGAAAAACAAAAAATCTACTCAGTTAGAGTTTTATAAAATGTGGATGGTAGGAG
*
11384 ATCCAACTATTGGATCATTTGGTGAGGACAATGGAAAATTTATTTACCTTGTGGATTATTCACGA
66 ATCCAACTATTGGATCATTTGGTGAGGACAATGAAAAATTTATTTACCTTGTGGATTATTCACGA
11449 AAGCCAGCATTAACAGTCCAATCCACTCCTCCTCCAAAAAACCATCCTCCACCATCAAAACCATT
131 AAGCCAGCATTAACAGTCCAATCCACTCCTCCTCCAAAAAACCATCCTCCACCATCAAAACCATT
11514 TCCTTTACAAAAATCACCAAAGTCTACTCTTCAAAAGACAAATACTTTTCCTCAGCCCTGCTAT
196 TCCTTTACAAAAATCACCAAAGTCTACTCTTCAAAAGACAAATACTTTTCCTCAGCCCTGCTAT
11578 AA-AAAGA
1 AATAAAGA
11585 TCAGTAAATG
Statistics
Matches: 261, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
258 5 0.02
259 256 0.98
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.26
Consensus pattern (259 bp):
AATAAAGAAGAAGAAAAACAAAAAATCTACTCAGTTAGAGTTTTATAAAATGTGGATGGTAGGAG
ATCCAACTATTGGATCATTTGGTGAGGACAATGAAAAATTTATTTACCTTGTGGATTATTCACGA
AAGCCAGCATTAACAGTCCAATCCACTCCTCCTCCAAAAAACCATCCTCCACCATCAAAACCATT
TCCTTTACAAAAATCACCAAAGTCTACTCTTCAAAAGACAAATACTTTTCCTCAGCCCTGCTAT
Found at i:17177 original size:16 final size:18
Alignment explanation
Indices: 17151--17185 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17141 TCGTGAAATT
17151 TAATCATTTT-ATTAAAA
1 TAATCATTTTAATTAAAA
17168 TAAT-ATTTTAATTAAAA
1 TAATCATTTTAATTAAAA
17185 T
1 T
17186 TATTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATCATTTTAATTAAAA
Found at i:18907 original size:30 final size:30
Alignment explanation
Indices: 18673--19048 Score: 279
Period size: 30 Copynumber: 12.6 Consensus size: 30
18663 AAATTTGGAA
* *
18673 AAGTTTAGGGGTAAAAATGTAATTTT-GGG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
* * *
18702 AACATTTA-GGGTTAAAATGTGATTTT-GTA-
1 AA-GTTTAGGGGTCAAAATGTAATTTTAG-AG
* * *
18731 ATAGTTT-GGGGTCAAAATATTATTTT-GGG
1 A-AGTTTAGGGGTCAAAATGTAATTTTAGAG
** ** *
18760 AAGGTTTAAAGGTCAAAACATGATTTTAGAG
1 AA-GTTTAGGGGTCAAAATGTAATTTTAGAG
* * * * *
18791 AAG-TTCGAGGATCCAAATGTAATCTTGGA-
1 AAGTTTAG-GGGTCAAAATGTAATTTTAGAG
*
18820 AAGGTTTAGGGGGTTAAAATGTAATTTTAGAG
1 AA-GTTTA-GGGGTCAAAATGTAATTTTAGAG
* *
18852 AAGTTTTA-GGTTAAAACATG--ATTTTAGAG
1 AAG-TTTAGGGGTCAAA-ATGTAATTTTAGAG
18881 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
* * ** *
18911 AAGTTTAAGGGTTAAAATACAATTTTGGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
** *
18941 AAGTTTAAAGGTCAAAATGAAATTTTAGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
* * *
18971 AAGTTTAGAGGTTAAAATGTAACTTTAGAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
* * *
19001 AAGTTTAGGGATTAAAATGTAATTTTAAAG
1 AAGTTTAGGGGTCAAAATGTAATTTTAGAG
19031 AAGTTTAGGGGTCAAAAT
1 AAGTTTAGGGGTCAAAAT
19049 ATGATTTCTT
Statistics
Matches: 275, Mismatches: 54, Indels: 35
0.76 0.15 0.10
Matches are distributed among these distances:
28 8 0.03
29 66 0.24
30 168 0.61
31 26 0.09
32 7 0.03
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (30 bp):
AAGTTTAGGGGTCAAAATGTAATTTTAGAG
Found at i:21334 original size:32 final size:32
Alignment explanation
Indices: 21293--21354 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
21283 TGGTGAAAGA
21293 GATTGGATAGTTGCAATCTGCCCCTACGCAGG
1 GATTGGATAGTTGCAATCTGCCCCTACGCAGG
*
21325 GATTGGATAGTTGCAATTTGCCCCTACGCA
1 GATTGGATAGTTGCAATCTGCCCCTACGCA
21355 AGGTAAGAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (32 bp):
GATTGGATAGTTGCAATCTGCCCCTACGCAGG
Found at i:21486 original size:77 final size:74
Alignment explanation
Indices: 21329--21517 Score: 200
Period size: 77 Copynumber: 2.5 Consensus size: 74
21319 CGCAGGGATT
* ** * * *
21329 GGATAGTTGCAATTTGCCCCTACGCAAGGTAAGAGATTGGCTGACGATCCGCTTCATGATCGGGG
1 GGATGGTTGCAATTTGCCCCTACGCGGGGTAAAAGATTGGCTGACGATCCGCTCCAGGATCGGGG
21394 TAAAAGATC
66 TAAAAGATC
* * * *
21403 GAATGGTTGCAATCTGCCCCTATCGCGGGGTAAAAGATTGGCTGACGGTGATTCGC-CCAGGCTC
1 GGATGGTTGCAATTTGCCCCTA-CGCGGGGTAAAAGATTGGCTGAC---GATCCGCTCCAGGATC
21467 GGGGTAAAAGATC
62 GGGGTAAAAGATC
* * * *
21480 GGATGGTTGTAATTTGCCCCAAGCTCGGGATAAAAGAT
1 GGATGGTTGCAATTTGCCCCTA-CGCGGGGTAAAAGAT
21518 CGGATGACTG
Statistics
Matches: 94, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
74 19 0.20
75 20 0.21
77 49 0.52
78 6 0.06
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (74 bp):
GGATGGTTGCAATTTGCCCCTACGCGGGGTAAAAGATTGGCTGACGATCCGCTCCAGGATCGGGG
TAAAAGATC
Found at i:21515 original size:39 final size:39
Alignment explanation
Indices: 21388--22185 Score: 322
Period size: 39 Copynumber: 20.5 Consensus size: 39
21378 CGCTTCATGA
* * * * *
21388 TCGGGGTAAAAGATCGAATGGTTGCAATCTGCCCCTATC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * ** * *
21427 GCGGGGTAAAAGATTGGCTGACGGTGAT-T-CGCCCAGGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGC-CCCAAGC
* *
21465 TCGGGGTAAAAGATCGGATGGTTGTAATTTGCCCCAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * *
21504 TCGGGATAAAAGATCGGATGACTGTAATCTACCCCAGGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * * * ** * **
21543 TTGAGGTAAGAGATTGGCTGACGGTGATCTATCCCAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * *
21582 TAGGGGTAAAAGATCGGATGACTGCAATTTGCCCC-AGTC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAG-C
** * * * * *
21621 TAAGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* ** *
21660 TCGGGGTAAAAGATCGGAT-AGCTACAATCTGCCCTAAGC
1 TCGGGGTAAAAGATCGGATGA-TTGTAATCTGCCCCAAGC
* * * * * * * *
21699 TAGGGGTAAGAGATTGGCTAATAGTGAT-TGCCTCAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
** * * * *
21737 TTAGGGTAAAAGATCGGAT-AGCTGCAATTTGCCCCAGGC
1 TCGGGGTAAAAGATCGGATGA-TTGTAATCTGCCCCAAGC
* * * * * * * *
21776 TAGAGGTAAGAGATCGGTTGATGGTGATTTGCCCTAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* ** * * *
21815 TTGGGGTAAAAGATCAAATGGTTGTTATCTGCCCCAAAC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * ** * * * * ***
21854 TCGGGGTAAGAGCTTAGCTGATGGTAATTTACCCTGGGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * *
21893 TCAGGATAAAAGATCGGATGACTGCAATCTGCCCC-AGCC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAG-C
* * * * * * * *
21932 TCGGGGTAAGAA-ATTGGTTGATGGTGATTTGCCCTAGGT
1 TCGGGGTAA-AAGATCGGATGATTGTAATCTGCCCCAAGC
* * * ** * *
21971 TCAGGATAAAAGATCGGAT-AGCTACAATCTG-CCCAGGT
1 TCGGGGTAAAAGATCGGATGA-TTGTAATCTGCCCCAAGC
** * * * * *
22009 TAAGGGTAAGAGATTGGATGATGGTGATTTGCCCCAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * * * * *
22048 TCGGAGTAAAAGATTGGCTAATGGTAATCCGCCTCAAGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
** * * *
22087 TCGGGGTAAAAGATCGGATGGCTGCAATCTGTCCCAGGC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
* * * * *
22126 TCGGGGTAAAAGATTGGCTGATAGTGATTTGCCCC-AGTC
1 TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAG-C
22165 TCGGGGTAAAAGATCGGATGA
1 TCGGGGTAAAAGATCGGATGA
22186 CTATGATCCG
Statistics
Matches: 533, Mismatches: 208, Indels: 36
0.69 0.27 0.05
Matches are distributed among these distances:
37 2 0.00
38 84 0.16
39 439 0.82
40 8 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (39 bp):
TCGGGGTAAAAGATCGGATGATTGTAATCTGCCCCAAGC
Found at i:21581 original size:78 final size:77
Alignment explanation
Indices: 21491--22061 Score: 433
Period size: 78 Copynumber: 7.3 Consensus size: 77
21481 GATGGTTGTA
* * *
21491 ATTTGCCCCAAGCTCGGGATAAAAGATCGGATGACTGTAATCTACCCCAGGCTTGAGGTAAGAGA
1 ATTT-CCCTAAGCTCGGGATAAAAGATCGGATGACTGCAATCTGCCCCAGGCTTGAGGTAAGAGA
*
21556 TTGGCTGACGGTG
65 TTGGCTGATGGTG
* * * * *
21569 ATCTATCCC-AAGCTAGGGGTAAAAGATCGGATGACTGCAATTTGCCCCAGTC-TAAGGGTAAGA
1 AT-T-TCCCTAAGCTCGGGATAAAAGATCGGATGACTGCAATCTGCCCCAGGCTTGA-GGTAAGA
*
21632 GATTGGCTGATGGTA
63 GATTGGCTGATGGTG
* * * * * * *
21647 ATCTGCCCTAAGCTCGGGGTAAAAGATCGGAT-AGCTACAATCTGCCCTAAGCTAGGGGTAAGAG
1 AT-TTCCCTAAGCTCGGGATAAAAGATCGGATGA-CTGCAATCTGCCCCAGGCTTGAGGTAAGAG
* *
21711 ATTGGCTAATAGTG
64 ATTGGCTGATGGTG
* * * *
21725 A-TTGCCTCAAGCTTAGGG-TAAAAGATCGGAT-AGCTGCAATTTGCCCCAGGCTAGAGGTAAGA
1 ATTTCCCT-AAGC-TCGGGATAAAAGATCGGATGA-CTGCAATCTGCCCCAGGCTTGAGGTAAGA
* *
21787 GATCGGTTGATGGTG
63 GATTGGCTGATGGTG
* * ** ** ** ** * * *
21802 ATTTGCCCTAAGCTTGGGGTAAAAGATCAAATGGTTGTTATCTGCCCCAAACTCGGGGTAAGAGC
1 ATTT-CCCTAAGCTCGGGATAAAAGATCGGATGACTGCAATCTGCCCCAGGCTTGAGGTAAGAGA
* *
21867 TTAGCTGATGGTA
65 TTGGCTGATGGTG
** * * * * *
21880 ATTTACCCTGGGCTCAGGATAAAAGATCGGATGACTGCAATCTGCCCCAGCCTCGGGGTAAGAAA
1 ATTT-CCCTAAGCTCGGGATAAAAGATCGGATGACTGCAATCTGCCCCAGGCTTGAGGTAAGAGA
*
21945 TTGGTTGATGGTG
65 TTGGCTGATGGTG
* * * * *
21958 ATTTGCCCTAGGTTCAGGATAAAAGATCGGAT-AGCTACAATCTG-CCCAGG-TTAAGGGTAAGA
1 ATTT-CCCTAAGCTCGGGATAAAAGATCGGATGA-CTGCAATCTGCCCCAGGCTTGA-GGTAAGA
*
22020 GATTGGATGATGGTG
63 GATTGGCTGATGGTG
*
22035 ATTTGCCCCAAGCTC-GGAGTAAAAGAT
1 ATTT-CCCTAAGCTCGGGA-TAAAAGAT
22062 TGGCTAATGG
Statistics
Matches: 394, Mismatches: 84, Indels: 31
0.77 0.17 0.06
Matches are distributed among these distances:
76 8 0.02
77 111 0.28
78 267 0.68
79 7 0.02
80 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (77 bp):
ATTTCCCTAAGCTCGGGATAAAAGATCGGATGACTGCAATCTGCCCCAGGCTTGAGGTAAGAGAT
TGGCTGATGGTG
Found at i:21823 original size:233 final size:232
Alignment explanation
Indices: 21491--22061 Score: 591
Period size: 233 Copynumber: 2.4 Consensus size: 232
21481 GATGGTTGTA
* * * *
21491 ATTTGCCCCAAGC-TCGGGATAAAAGATCGGAT-GACTGTAATCTACCCCAGGCTTGAGGTAAGA
1 ATTTG-CCCAAGCTTAGGG-TAAAAGATCGGATAG-CTGCAATCTGCCCCAGGCTAGAGGTAAGA
* * ** *
21554 GATTGGCTGACGGTGATCTAT-CCCAAGCTAGGGGTAAAAGATCGGATGACTGCAATTTGCCCCA
63 GATTGGATGATGGTGAT-T-TGCCCAAGCTAGGGGTAAAAGATCAAATGACTGCAATCTGCCCCA
** * * * *
21618 GTCTAAGGGTAAGAGATTGGCTGATGGTAATCTGCCCTAAGCTCGGGGTAAAAGATCGGAT-AGC
126 AACTAAGGGTAAGAGATTAGCTGATGGTAATCTACCCTAAGCTCAGGATAAAAGATCGGATGA-C
*
21682 TACAATCTGCCCTAAG-CTAGGGGTAAGAGATTGGCTAATAGTG
190 TACAATCTGCCC-AAGCCTAGGGGTAAGAAATTGGCTAATAGTG
*
21725 A-TTGCCTCAAGCTTAGGGTAAAAGATCGGATAGCTGCAATTTGCCCCAGGCTAGAGGTAAGAGA
1 ATTTGCC-CAAGCTTAGGGTAAAAGATCGGATAGCTGCAATCTGCCCCAGGCTAGAGGTAAGAGA
* * * ** **
21789 TCGGTTGATGGTGATTTGCCCTAAGCTTGGGGTAAAAGATCAAATGGTTGTTATCTGCCCCAAAC
65 TTGGATGATGGTGATTTGCCC-AAGCTAGGGGTAAAAGATCAAATGACTGCAATCTGCCCCAAAC
** * * ** *
21854 TCGGGGTAAGAGCTTAGCTGATGGTAATTTACCCTGGGCTCAGGATAAAAGATCGGATGACTGCA
129 TAAGGGTAAGAGATTAGCTGATGGTAATCTACCCTAAGCTCAGGATAAAAGATCGGATGACTACA
* * * * *
21919 ATCTGCCCCAGCCTCGGGGTAAGAAATTGGTTGATGGTG
194 ATCTGCCCAAGCCTAGGGGTAAGAAATTGGCTAATAGTG
* * * * *
21958 ATTTGCCCTAGGTTCAGGATAAAAGATCGGATAGCTACAATCTG-CCCAGGTTA-AGGGTAAGAG
1 ATTTGCCCAAGCTT-AGGGTAAAAGATCGGATAGCTGCAATCTGCCCCAGGCTAGA-GGTAAGAG
* *
22021 ATTGGATGATGGTGATTTGCCCCAAGCTCGGAGTAAAAGAT
64 ATTGGATGATGGTGATTTG-CCCAAGCTAGGGGTAAAAGAT
22062 TGGCTAATGG
Statistics
Matches: 281, Mismatches: 45, Indels: 23
0.81 0.13 0.07
Matches are distributed among these distances:
231 1 0.00
232 9 0.03
233 230 0.82
234 41 0.15
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (232 bp):
ATTTGCCCAAGCTTAGGGTAAAAGATCGGATAGCTGCAATCTGCCCCAGGCTAGAGGTAAGAGAT
TGGATGATGGTGATTTGCCCAAGCTAGGGGTAAAAGATCAAATGACTGCAATCTGCCCCAAACTA
AGGGTAAGAGATTAGCTGATGGTAATCTACCCTAAGCTCAGGATAAAAGATCGGATGACTACAAT
CTGCCCAAGCCTAGGGGTAAGAAATTGGCTAATAGTG
Found at i:22042 original size:38 final size:39
Alignment explanation
Indices: 21935--22042 Score: 96
Period size: 38 Copynumber: 2.8 Consensus size: 39
21925 CCCAGCCTCG
* * *
21935 GGGTAAGAAATTGGTTGATGGTGATTTGCCCTAGGTTCA
1 GGGTAAGAGATTGGATGATGGTGATTTGCCCTAGGTTAA
* * * * * *
21974 GGATAAAAGATCGGAT-A-GCTACAATCTGCCC-AGGTTAA
1 GGGTAAGAGATTGGATGATGGT--GATTTGCCCTAGGTTAA
22012 GGGTAAGAGATTGGATGATGGTGATTTGCCC
1 GGGTAAGAGATTGGATGATGGTGATTTGCCC
22043 CAAGCTCGGA
Statistics
Matches: 50, Mismatches: 15, Indels: 9
0.68 0.20 0.12
Matches are distributed among these distances:
37 2 0.04
38 27 0.54
39 19 0.38
40 2 0.04
ACGTcount: A:0.28, C:0.13, G:0.31, T:0.28
Consensus pattern (39 bp):
GGGTAAGAGATTGGATGATGGTGATTTGCCCTAGGTTAA
Found at i:22138 original size:233 final size:230
Alignment explanation
Indices: 21640--22139 Score: 498
Period size: 233 Copynumber: 2.1 Consensus size: 230
21630 GAGATTGGCT
* * *
21640 GATGGTAATCTGCCCTAAGCTCGGGGTAAAAGATCGGATAGCTACAATCTGCCCTAAGCTAGGGG
1 GATGGTAATTTACCCTAGGCTCGGGGTAAAAGATCGGATAGCTACAATCTGCCCTAAGCTAGGGG
* * * *
21705 TAAGAGATTGGCTAATAGTGATTGCCTCAAGCTTAGGGTAAAAGATCGGATAGCTGCAATTTGCC
66 TAAGAAATTGGCTAATAGTGATTGCCTCAAGCTTAGGATAAAAGATCGGATAGCTACAATCTGCC
* * * *
21770 CCAGGCTAGAGGTAAGAGATCGGTTGATGGTGATTTGCCCTAAGCTTGGGGTAAAAGATCAAATG
131 CCAGGCTAGAGGTAAGAGATCGGATGATGGTGATTTGCCCCAAGCTCGGAGTAAAAGATCAAATG
* * * *
21835 GTTGTTATCTGCCCCAAACTCGGGGTAAGAGCTTAGCT
196 G-TGTAATCCGCCCCAAACTCGGGGTAAAAG--TAGCG
* * * * * *
21873 GATGGTAATTTACCCTGGGCTCAGGATAAAAGATCGGAT-GACTGCAATCTGCCC-CAGCCTCGG
1 GATGGTAATTTACCCTAGGCTCGGGGTAAAAGATCGGATAG-CTACAATCTGCCCTAAG-CTAGG
* * * * *
21936 GGTAAGAAATTGGTTGATGGTGATTTGCC-CTAGGTTCAGGATAAAAGATCGGATAGCTACAATC
64 GGTAAGAAATTGGCTAATAGTGA-TTGCCTCAAGCTT-AGGATAAAAGATCGGATAGCTACAATC
* *
22000 TG-CCCAGGTTA-AGGGTAAGAGATTGGATGATGGTGATTTGCCCCAAGCTCGGAGTAAAAGATT
127 TGCCCCAGGCTAGA-GGTAAGAGATCGGATGATGGTGATTTGCCCCAAGCTCGGAGTAAAAGA-T
* * * *
22063 GGCTAAT-G-GTAATCCGCCTCAAGCTCGGGGTAAAAG-ATCG
190 --CAAATGGTGTAATCCGCCCCAAACTCGGGGTAAAAGTAGCG
22103 GATGGCTGCAATCTGT-CCC-AGGCTCGGGGTAAAAGAT
1 GATGG-T--AAT-T-TACCCTAGGCTCGGGGTAAAAGAT
22140 TGGCTGATAG
Statistics
Matches: 219, Mismatches: 35, Indels: 26
0.78 0.12 0.09
Matches are distributed among these distances:
230 7 0.03
231 1 0.00
232 4 0.02
233 165 0.75
234 36 0.16
235 2 0.01
236 4 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (230 bp):
GATGGTAATTTACCCTAGGCTCGGGGTAAAAGATCGGATAGCTACAATCTGCCCTAAGCTAGGGG
TAAGAAATTGGCTAATAGTGATTGCCTCAAGCTTAGGATAAAAGATCGGATAGCTACAATCTGCC
CCAGGCTAGAGGTAAGAGATCGGATGATGGTGATTTGCCCCAAGCTCGGAGTAAAAGATCAAATG
GTGTAATCCGCCCCAAACTCGGGGTAAAAGTAGCG
Found at i:22195 original size:117 final size:116
Alignment explanation
Indices: 21977--22219 Score: 292
Period size: 117 Copynumber: 2.1 Consensus size: 116
21967 AGGTTCAGGA
* * *
21977 TAAAAGATCGGATAGCTACAATCTGCCCAGGTTAAGGGTAAGAGATTGGATGATGGTGATTTGCC
1 TAAAAGATCGGATAGCTACAATCTGCCCAGGCTAAGGGTAAAAGATTGGATGATAGTGATTTGCC
* * * *
22042 CCAAGCTCGGAGTAAAAGATTGGCTAATGGTAATCCGCCTCAAGCTCGGGG
66 CCAAGCTCGGAGTAAAAGATCGGATAATGATAATCCGCCTCAAGATCGGGG
* * ** *
22093 TAAAAGATCGGATGGCTGCAATCTGTCCCAGGCTCGGGGTAAAAGATTGGCTGATAGTGATTTGC
1 TAAAAGATCGGATAGCTACAATCTG-CCCAGGCTAAGGGTAAAAGATTGGATGATAGTGATTTGC
* * * *
22158 CCC-AGTCTCGGGGTAAAAGATCGGATGACT-ATGATCCGCCTCATGATCGGGG
65 CCCAAG-CTCGGAGTAAAAGATCGGAT-AATGATAATCCGCCTCAAGATCGGGG
*
22210 TAAGAGATCG
1 TAAAAGATCG
22220 AAATCTTCAA
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
116 25 0.23
117 80 0.75
118 2 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (116 bp):
TAAAAGATCGGATAGCTACAATCTGCCCAGGCTAAGGGTAAAAGATTGGATGATAGTGATTTGCC
CCAAGCTCGGAGTAAAAGATCGGATAATGATAATCCGCCTCAAGATCGGGG
Found at i:26766 original size:39 final size:40
Alignment explanation
Indices: 26712--26792 Score: 155
Period size: 39 Copynumber: 2.0 Consensus size: 40
26702 AAAGGAGGTC
26712 TAAAGAACAAAATAAATTTACGAAAGAATGA-TTATATGG
1 TAAAGAACAAAATAAATTTACGAAAGAATGATTTATATGG
26751 TAAAGAACAAAATAAATTTACGAAAGAATGATTTATATGG
1 TAAAGAACAAAATAAATTTACGAAAGAATGATTTATATGG
26791 TA
1 TA
26793 TGAGTATGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 31 0.76
40 10 0.24
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (40 bp):
TAAAGAACAAAATAAATTTACGAAAGAATGATTTATATGG
Found at i:34285 original size:30 final size:30
Alignment explanation
Indices: 34241--34640 Score: 332
Period size: 30 Copynumber: 13.4 Consensus size: 30
34231 ATACGGAATC
* *
34241 AAAATGTAAATTTGGAAAAGTTTAGGGGTA
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
34271 AAAATATAATTTTGGGAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * *
34301 AAAATGTGATTTTGTAGAAGTTTA-GGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* * * * *
34330 AAAATATGATTTTTG-AAAGATTTAAGGGTC
1 AAAATGTAATTTTGGAAAAG-TTTAGGGGTT
** * * *
34360 AAAACATAATTTTAGAGAAGTTT-GAGGATT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGGTT
* *
34390 TAAATGTAATTTTGGAAAGGTTTAGCGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGGTT
*
34421 AAAATGTAATTTTGGAGAAGTTTA-GGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
** * *
34450 AAAATGTGGTTTT-AAAGAAGTTTA-AGGTT
1 AAAATGTAATTTTGGAA-AAGTTTAGGGGTT
* * * * *
34479 AAAATATAATTTTAGAGAAGTTTAAGGGTG
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
34509 AAAATGTAATTTTAGAAAAGTTTAGGGGTC
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
34539 AAAATGTAAGTTTGGAGAAGTTT-GAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAG-GGGTT
* *
34569 AAAATGTAATTTTGGAGAAGTTTAAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGGTT
* *
34599 AAAATGTTATTTT--AAAGATGTTTAGGGGTC
1 AAAATGTAATTTTGGAAA-A-GTTTAGGGGTT
*
34629 AAAATATAATTT
1 AAAATGTAATTT
34641 CTTGAAAGGT
Statistics
Matches: 298, Mismatches: 60, Indels: 24
0.78 0.16 0.06
Matches are distributed among these distances:
28 6 0.02
29 67 0.22
30 196 0.66
31 29 0.10
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGGTT
Found at i:34413 original size:119 final size:118
Alignment explanation
Indices: 34271--34602 Score: 420
Period size: 119 Copynumber: 2.8 Consensus size: 118
34261 TTTAGGGGTA
* * * *
34271 AAAATATAATTTTGGGAAAGTTTAGGGGTTAAAATGTGATTTTGTAGAAGTTTAGGGTTAAAATA
1 AAAATGTAATTTT-GGAAAGTTTAGGGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAAAATG
* * *
34336 TGATTTTTGAAAGATTTAAGGGTCAAAACATAATTTTAGAGAAGTTTGAGGATT
65 TGATTTTTGAAAGATTTAAGGGTTAAAACATAATTTTAGAGAAGTTTAAGGATG
*
34390 TAAATGTAATTTTGGAAAGGTTTAGCGGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAAAAT
1 AAAATGTAATTTTGGAAA-GTTTAG-GGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAAAAT
* * *
34455 GTG-GTTTT-AAAGAAGTTTAA-GGTTAAAATATAATTTTAGAGAAGTTTAAGGGTG
64 GTGATTTTTGAAAG-A-TTTAAGGGTTAAAACATAATTTTAGAGAAGTTTAAGGATG
* * *
34509 AAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAAGTTTGGAGAAGTTTGAGGGTTAAAAT
1 AAAATGTAATTTT-GGAAAGTTTAGGGGTTAAAATGTAATTTTGGAGAAGTTT-AGGGTTAAAAT
* *
34574 GTAATTTTGGAGAAG-TTTAAGGGTTAAAA
64 GTGATTTTTGA-AAGATTTAAGGGTTAAAA
34603 TGTTATTTTA
Statistics
Matches: 185, Mismatches: 18, Indels: 19
0.83 0.08 0.09
Matches are distributed among these distances:
118 35 0.19
119 87 0.47
120 59 0.32
121 1 0.01
122 3 0.02
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (118 bp):
AAAATGTAATTTTGGAAAGTTTAGGGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAAAATGT
GATTTTTGAAAGATTTAAGGGTTAAAACATAATTTTAGAGAAGTTTAAGGATG
Found at i:34449 original size:149 final size:146
Alignment explanation
Indices: 34238--34648 Score: 504
Period size: 149 Copynumber: 2.7 Consensus size: 146
34228 AGGATACGGA
* *
34238 ATCAAAATGTAAATTTGGAAAAGTTTAGGGGTAAAAATATAATTTTGG-GAAAGTTTAGGGGTTA
1 ATCAAAATGTAAATTTGG-AAAGTTTAGGGGTTAAAATGTAATTTTGGAG-AAGTTTA-GGGTTA
** *
34302 AAATGTGATTTTGTAGAAGTTTAGGGTTAAAATATGATTTTTGAAAGATTTAAGGGTCAAAACAT
63 AAATGTGATTTTAAAGAAGTTTAGGGTTAAAATATAATTTTTGAAAG-TTTAAGGGTCAAAACAT
*
34367 AATTTTAGAGAAGTTT-GAGG
127 AATTTTAGAAAAGTTTAG-GG
** *
34387 ATTTAAATGTAATTTTGGAAAGGTTTAGCGGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAA
1 ATCAAAATGTAAATTTGGAAA-GTTTAG-GGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAA
* * * * **
34452 AATGTGGTTTTAAAGAAGTTTAAGGTTAAAATATAATTTTAGAGAAGTTTAAGGGTGAAAATGTA
64 AATGTGATTTTAAAGAAGTTTAGGGTTAAAATATAATTTTTGA-AAGTTTAAGGGTCAAAACATA
34517 ATTTTAGAAAAGTTTAGGG
128 ATTTTAGAAAAGTTTAGGG
* *
34536 GTCAAAATGTAAGTTTGGAGAAGTTT-GAGGGTTAAAATGTAATTTTGGAGAAGTTTAAGGGTTA
1 ATCAAAATGTAAATTTGGA-AAGTTTAG-GGGTTAAAATGTAATTTTGGAGAAGTTT-AGGGTTA
* * *
34600 AAATGTTATTTTAAAGATGTTTAGGGGTCAAAATATAATTTCTTGAAAG
63 AAATGTGATTTTAAAGAAGTTTA-GGGTTAAAATATAATTT-TTGAAAG
34649 GTAAGGGACC
Statistics
Matches: 227, Mismatches: 26, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
148 32 0.14
149 142 0.63
150 49 0.22
151 4 0.02
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (146 bp):
ATCAAAATGTAAATTTGGAAAGTTTAGGGGTTAAAATGTAATTTTGGAGAAGTTTAGGGTTAAAA
TGTGATTTTAAAGAAGTTTAGGGTTAAAATATAATTTTTGAAAGTTTAAGGGTCAAAACATAATT
TTAGAAAAGTTTAGGG
Found at i:35677 original size:11 final size:11
Alignment explanation
Indices: 35641--35700 Score: 56
Period size: 11 Copynumber: 5.6 Consensus size: 11
35631 AAATGGCAGT
35641 TAATAAATATA
1 TAATAAATATA
35652 T--T-AATATA
1 TAATAAATATA
35660 TAATAAATA-A
1 TAATAAATATA
35670 TAAGTAAATATA
1 TAA-TAAATATA
*
35682 TTAACAAATATA
1 -TAATAAATATA
*
35694 TATTAAA
1 TAATAAA
35701 AAAACTTTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
8 7 0.17
9 1 0.03
10 5 0.12
11 16 0.40
12 8 0.20
13 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (11 bp):
TAATAAATATA
Done.