Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014933.1 Kokia drynarioides strain JFW-HI SEQ_129976, 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: 464154
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 704 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:369680 original size:30 final size:30
Alignment explanation
Indices: 369584--369687 Score: 90
Period size: 30 Copynumber: 3.5 Consensus size: 30
369574 CCCCCGAATG
* * * *
369584 TCCAAAAATT-TCATTTTTGATCCCGGTTT
1 TCCAAAAATTACCATTTTTTATCCTGATTT
* * *
369613 TCCTAAAAATTACCA--TTTTACCCCTGAATG
1 TCC-AAAAATTACCATTTTTTA-TCCTGATTT
369643 TCCAAAAATT-CCATTTTTTATCCTGATTT
1 TCCAAAAATTACCATTTTTTATCCTGATTT
369672 TCCGAAAAATTACCAT
1 TCC-AAAAATTACCAT
369688 CTTACCCCCC
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 3 0.05
29 23 0.40
30 26 0.45
31 6 0.10
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTTTATCCTGATTT
Found at i:372720 original size:29 final size:30
Alignment explanation
Indices: 372677--372735 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
372667 GAATTGAATC
372677 AAATCAAAATTTCATATATAAAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
* * *
372707 AAATTAAAA-TTCATGTATACAATTGCACA
1 AAATCAAAATTTCATATATAAAATTGCACA
372736 TTAAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTGCACA
Found at i:372968 original size:22 final size:22
Alignment explanation
Indices: 372943--372989 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
372933 TACATAATTT
* *
372943 TTTTTAAATAAAATTAAAAATA
1 TTTTTAAACAAAATTAAAAAAA
**
372965 TTTTTTTACAAAATTAAAAAAA
1 TTTTTAAACAAAATTAAAAAAA
372987 TTT
1 TTT
372990 AAACGGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTTAAACAAAATTAAAAAAA
Found at i:382534 original size:55 final size:55
Alignment explanation
Indices: 382464--382600 Score: 130
Period size: 55 Copynumber: 2.5 Consensus size: 55
382454 ACTCATGTAC
* * ** * *
382464 AGCTCGAGTATAGCTTCTACATGCTTACGTCTTGGCTAGAGCATAATGCCTTTAT
1 AGCTCGGGTAGAGCTTCTACATGCTTACGTCTTGATTAGAGCGTAATGCCATTAT
* * * * * *
382519 AGCTCGAGTAGAGCTTCAACATGCTTACGTCTCGATTAGAGTGTAATGNCATTAC
1 AGCTCGGGTAGAGCTTCTACATGCTTACGTCTTGATTAGAGCGTAATGCCATTAT
* ** *
382574 AACTTAGGTAGAGCTTCAACATGCTTA
1 AGCTCGGGTAGAGCTTCTACATGCTTA
382601 TGCCTCAGTG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.31
Consensus pattern (55 bp):
AGCTCGGGTAGAGCTTCTACATGCTTACGTCTTGATTAGAGCGTAATGCCATTAT
Found at i:382695 original size:99 final size:99
Alignment explanation
Indices: 382510--382699 Score: 240
Period size: 99 Copynumber: 1.9 Consensus size: 99
382500 TAGAGCATAA
* * * * *
382510 TGCCTTTATAGCTCGAGTAGAGCTTCAACATGCTTACGTCTCGATTAGAGTGTAATGNCATTACA
1 TGCCATTATAGCTCGAGTAGAGCTTCAACATGCTTACATCTAGATTAGAGCGTAATGCCATTACA
382575 ACTTAGGTAGAGCTTCAACATGCTTATGCCTCAG
66 ACTTAGGTAGAGCTTCAACATGCTTATGCCTCAG
* * * * *
382609 TGCCATTATTGCTCGGGTATAGCTTCGACATGCTTACATCTTAG-TTAGAGCGTAATGCCATTAT
1 TGCCATTATAGCTCGAGTAGAGCTTCAACATGCTTACATC-TAGATTAGAGCGTAATGCCATTAC
* *
382673 AGC-TATGGTAGAGCTTCGACATGCTTA
65 AACTTA-GGTAGAGCTTCAACATGCTTA
382700 CGTCTTAGTT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
98 2 0.03
99 73 0.95
100 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (99 bp):
TGCCATTATAGCTCGAGTAGAGCTTCAACATGCTTACATCTAGATTAGAGCGTAATGCCATTACA
ACTTAGGTAGAGCTTCAACATGCTTATGCCTCAG
Found at i:382750 original size:154 final size:154
Alignment explanation
Indices: 382465--382754 Score: 386
Period size: 154 Copynumber: 1.9 Consensus size: 154
382455 CTCATGTACA
* * * *
382465 GCTCGAGTATAGCTTCTACATGCTTACGTCTTGGCTAGAGCATAATGCCTTTATAGCTCGAGTAG
1 GCTCGAGTATAGCTTCGACATGCTTACATCTTAGCTAGAGCATAATGCCATTATAGCTCGAGTAG
* * * *
382530 AGCTTCAACATGCTTACGTCTCGATTAGAGTGTAATGNCATTACAACTTAGGTAGAGCTTCAACA
66 AGCTTCAACATGCTTACGTCTAGATTAGAGCGTAATGCCATTACAACTCAGGTAGAGCTTCAACA
382595 TGCTTATGCCTCAGTGCCATTATT
131 TGCTTATGCCTCAGTGCCATTATT
* * * *
382619 GCTCGGGTATAGCTTCGACATGCTTACATCTTAGTTAGAGCGTAATGCCATTATAGCTATG-GTA
1 GCTCGAGTATAGCTTCGACATGCTTACATCTTAGCTAGAGCATAATGCCATTATAGCT-CGAGTA
* * * * **
382683 GAGCTTCGACATGCTTACGTCTTAG-TTAGAGCGTAATGCCATTATAGCTCGGGTAGAGCTTTGA
65 GAGCTTCAACATGCTTACGTC-TAGATTAGAGCGTAATGCCATTACAACTCAGGTAGAGCTTCAA
382747 CATGCTTA
129 CATGCTTA
382755 CGTCTTCATT
Statistics
Matches: 116, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
154 113 0.97
155 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (154 bp):
GCTCGAGTATAGCTTCGACATGCTTACATCTTAGCTAGAGCATAATGCCATTATAGCTCGAGTAG
AGCTTCAACATGCTTACGTCTAGATTAGAGCGTAATGCCATTACAACTCAGGTAGAGCTTCAACA
TGCTTATGCCTCAGTGCCATTATT
Found at i:382831 original size:56 final size:55
Alignment explanation
Indices: 382609--382853 Score: 332
Period size: 55 Copynumber: 4.4 Consensus size: 55
382599 TATGCCTCAG
* * *
382609 TGCCATTATTGCTCGGGTATAGCTTCGACATGCTTACATCTTAGTTAGAGCGTAA
1 TGCCATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTTAGTTAGAGCGTAA
**
382664 TGCCATTATAGCTATGGTAGAGCTTCGACATGCTTACGTCTTAGTTAGAGCGTAA
1 TGCCATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTTAGTTAGAGCGTAA
*
382719 TGCCATTATAGCTCGGGTAGAGCTTTGACATGCTTACGTCTTCA-TTAGAGCGTAA
1 TGCCATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTT-AGTTAGAGCGTAA
* * * * *
382774 TGCTATTATAGCTCGGGTAGACCTTTGGACATGCTTACGTC-TCGATTAGAGCATAA
1 TGCCATTATAGCTCGGGTAGAGC-TTCGACATGCTTACGTCTTAG-TTAGAGCGTAA
* *
382830 TGCTATTATAGCTCGGGTACAGCT
1 TGCCATTATAGCTCGGGTAGAGCT
382854 CTAGCTTGCC
Statistics
Matches: 171, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
55 123 0.72
56 48 0.28
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (55 bp):
TGCCATTATAGCTCGGGTAGAGCTTCGACATGCTTACGTCTTAGTTAGAGCGTAA
Found at i:382878 original size:111 final size:111
Alignment explanation
Indices: 382609--382884 Score: 310
Period size: 111 Copynumber: 2.5 Consensus size: 111
382599 TATGCCTCAG
* * * * * *
382609 TGCCATTATTGCTCGGGTATAGCTTCGACATGCTTACATC-TTAGTTAGAGCGTAATGCCATTAT
1 TGCCATTATAGCTCGGGTACAGCTTAGACATGCCTACGTCGTCAGTTAGAGCGTAATGCCATTAT
* * * *
382673 AGCTATGGTAGAGCTTCGACATGCTTACGTCTTAGTTAGAGCGTAA
66 AGCTAGGGTAGACCTTCGACATGCTTACGTCTGAGTTAGAGCATAA
* * * * *
382719 TGCCATTATAGCTCGGGTAGAGCTTTGACATGCTTACGTCTTCA-TTAGAGCGTAATGCTATTAT
1 TGCCATTATAGCTCGGGTACAGCTTAGACATGCCTACGTCGTCAGTTAGAGCGTAATGCCATTAT
* *
382783 AGCTCGGGTAGACCTTTGGACATGCTTACGTCTCGA-TTAGAGCATAA
66 AGCTAGGGTAGACC-TTCGACATGCTTACGTCT-GAGTTAGAGCATAA
* * *
382830 TGCTATTATAGCTCGGGTACAGCTCTAG-CTTGCCTACGT-GTCAGTTAGAGTGTAA
1 TGCCATTATAGCTCGGGTACAGCT-TAGACATGCCTACGTCGTCAGTTAGAGCGTAA
382885 GGTTATTTCG
Statistics
Matches: 142, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
110 69 0.49
111 70 0.49
112 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (111 bp):
TGCCATTATAGCTCGGGTACAGCTTAGACATGCCTACGTCGTCAGTTAGAGCGTAATGCCATTAT
AGCTAGGGTAGACCTTCGACATGCTTACGTCTGAGTTAGAGCATAA
Found at i:385444 original size:30 final size:31
Alignment explanation
Indices: 385377--385459 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
385367 AATGTATGTG
* * *
385377 TATATATACAATATATATGCGTGAGTTCTGT
1 TATATATATAATATATATGCATGAGTTCTGA
*
385408 TATATATGTAATATATATGCATG-GTTCTTGA
1 TATATATATAATATATATGCATGAGTTC-TGA
385439 T-TATATATAATATATATGCAT
1 TATATATATAATATATATGCAT
385460 ATATGGGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 23 0.50
31 23 0.50
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (31 bp):
TATATATATAATATATATGCATGAGTTCTGA
Found at i:393563 original size:37 final size:36
Alignment explanation
Indices: 393513--393591 Score: 113
Period size: 37 Copynumber: 2.2 Consensus size: 36
393503 TTACTACTAA
* * *
393513 TGTCGTTGCATGAGCACTTCTAGATTGCGCCCGAAAT
1 TGTCGTTGCATGAGCACTTCCAG-TTGCACCCAAAAT
*
393550 TGTCGTTGCATGAGCACTTCCAGTTGCACCTAAAAT
1 TGTCGTTGCATGAGCACTTCCAGTTGCACCCAAAAT
393586 TGTCGT
1 TGTCGT
393592 CGCAGGTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
36 16 0.42
37 22 0.58
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (36 bp):
TGTCGTTGCATGAGCACTTCCAGTTGCACCCAAAAT
Found at i:395754 original size:17 final size:17
Alignment explanation
Indices: 395717--395775 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
395707 TAATTGCACC
* *
395717 TGCATTGTTATTGTCAC
1 TGCATTTTTATTGTCAT
*
395734 TGCATTTTTATTGTTAT
1 TGCATTTTTATTGTCAT
* **
395751 TGCATCTACATTGTCAT
1 TGCATTTTTATTGTCAT
395768 TGCATTTT
1 TGCATTTT
395776 CATATATATT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.53
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:395769 original size:23 final size:23
Alignment explanation
Indices: 395719--395769 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
395709 ATTGCACCTG
* *
395719 CATTGTTATTGTCACTGCATTTT
1 CATTGTTATTGTCACTACATTGT
*
395742 TATTGTTATTG-CATCTACATTGT
1 CATTGTTATTGTCA-CTACATTGT
395765 CATTG
1 CATTG
395770 CATTTTCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.51
Consensus pattern (23 bp):
CATTGTTATTGTCACTACATTGT
Found at i:396868 original size:37 final size:37
Alignment explanation
Indices: 396794--396868 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
396784 TTTGTACTAA
* **
396794 TGTCGCTGCATGAGCACTTCTAGATTACGCCCGAAAT
1 TGTCGCTGCATGAGCACTTCTAGATTACACCAAAAAT
*
396831 TGTCGCTGCATGAGCATTTCTAGATTACACCAAAAAT
1 TGTCGCTGCATGAGCACTTCTAGATTACACCAAAAAT
396868 T
1 T
396869 ATCCTCGCCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (37 bp):
TGTCGCTGCATGAGCACTTCTAGATTACACCAAAAAT
Found at i:396935 original size:38 final size:38
Alignment explanation
Indices: 396892--396979 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
396882 TGCACCAAAG
*
396892 ACTATCGCTGCATAATTATTCTTCAAAT-TACATCCA-GA
1 ACTATCGCTGCATAAGTATTCTTCAAATGTAC--CCAGGA
* * *
396930 ACTATCGCTACATAAGTATTTTTCAATTGTACCCAGGA
1 ACTATCGCTGCATAAGTATTCTTCAAATGTACCCAGGA
396968 A-TATCGCTGCAT
1 ACTATCGCTGCAT
396980 GAACATGTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 13 0.30
38 27 0.63
39 3 0.07
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (38 bp):
ACTATCGCTGCATAAGTATTCTTCAAATGTACCCAGGA
Found at i:397021 original size:26 final size:26
Alignment explanation
Indices: 396971--397022 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
396961 CCCAGGAATA
*
396971 TCGCTGCATGAACATGTACAGAATTG
1 TCGCTGCATGAACATGTACAAAATTG
* *
396997 TCGCTGCATGAACGTGTCCAAAATTG
1 TCGCTGCATGAACATGTACAAAATTG
397023 CACCAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (26 bp):
TCGCTGCATGAACATGTACAAAATTG
Found at i:397667 original size:16 final size:16
Alignment explanation
Indices: 397646--397676 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
397636 TTGTGGATCC
397646 CATTTTAACTTTATTA
1 CATTTTAACTTTATTA
*
397662 CATTTTATCTTTATT
1 CATTTTAACTTTATT
397677 TTCACATTAT
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:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTAACTTTATTA
Found at i:404745 original size:22 final size:23
Alignment explanation
Indices: 404720--404762 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
404710 ATCTTTTCCC
*
404720 ATTTCA-AAAAGCTTTGTAAACG
1 ATTTCATAAAAGCTTAGTAAACG
*
404742 ATTTCATAAAATCTTAGTAAA
1 ATTTCATAAAAGCTTAGTAAA
404763 TTAACTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (23 bp):
ATTTCATAAAAGCTTAGTAAACG
Found at i:404971 original size:30 final size:30
Alignment explanation
Indices: 404937--405012 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
404927 TTAAATTAGT
* * *
404937 AATGATAAAATTATATTTTTAC-CTCTTAAA
1 AATGATAAAAATATAATTTAACTCT-TTAAA
404967 AATGATAAAAATATAATTTAACTCTTTAAA
1 AATGATAAAAATATAATTTAACTCTTTAAA
* *
404997 AATTATAAAGATATAA
1 AATGATAAAAATATAA
405013 ACTATTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 38 0.95
31 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (30 bp):
AATGATAAAAATATAATTTAACTCTTTAAA
Found at i:421290 original size:3 final size:3
Alignment explanation
Indices: 421282--421377 Score: 87
Period size: 3 Copynumber: 33.7 Consensus size: 3
421272 TAGTAAAGTA
** * * *
421282 AAT AAT AAT AAT AAT AAT AAT AAT AAT ACG AA- AAC AAG AAT AA- AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
421328 AA- AAT AAT AATT AA- AAT AAT AAT AAT CAT -AT AAT AA- AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
421370 AAT AAT AA
1 AAT AAT AA
421378 GAAAATAAAG
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
2 12 0.15
3 65 0.81
4 3 0.04
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:421778 original size:27 final size:27
Alignment explanation
Indices: 421706--421771 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
421696 GCGAATTGAG
421706 AAGAGGAGGCAGACGGTGGAGATCTAA
1 AAGAGGAGGCAGACGGTGGAGATCTAA
*
421733 AAGAGGAGGGC-GACGGTGGAGATCTGA
1 AAGAGGA-GGCAGACGGTGGAGATCTAA
*
421760 AAGAGGTGGCAG
1 AAGAGGAGGCAG
421772 TCAGTGGCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 29 0.83
28 3 0.09
ACGTcount: A:0.33, C:0.11, G:0.45, T:0.11
Consensus pattern (27 bp):
AAGAGGAGGCAGACGGTGGAGATCTAA
Found at i:423169 original size:3 final size:3
Alignment explanation
Indices: 423155--423246 Score: 104
Period size: 3 Copynumber: 32.0 Consensus size: 3
423145 ATTTTCTCAA
*
423155 TAT TAT TTT TAT TA- TAT TAT TAT TAT TAT TATT TAT T-T TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
* * *
423198 TAT T-T TAT TCT TGT T-T TCT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
423244 TAT
1 TAT
423247 ATTTACTTTA
Statistics
Matches: 78, Mismatches: 5, Indels: 12
0.82 0.05 0.13
Matches are distributed among these distances:
2 10 0.13
3 65 0.83
4 3 0.04
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:423188 original size:48 final size:51
Alignment explanation
Indices: 423135--423251 Score: 127
Period size: 51 Copynumber: 2.3 Consensus size: 51
423125 AATTTTTCTT
*
423135 TTATTTA-TTTATTTTCTCAATATT-AT-TTTTATTA-TATTATTATTATTA
1 TTATTTATTTTATTTTAT-AATATTCATGTTTTATTATTATTATTATTATTA
** * *
423183 TTATTTATTTTATTTTATTTTATTCTTGTTTTCTTATTATTATTATTATTA
1 TTATTTATTTTATTTTATAATATTCATGTTTTATTATTATTATTATTATTA
423234 TTA-TTATTATTATATTTA
1 TTATTTATT-TTAT-TTTA
423252 CTTTACTGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
48 11 0.19
49 10 0.17
50 12 0.21
51 21 0.36
52 4 0.07
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (51 bp):
TTATTTATTTTATTTTATAATATTCATGTTTTATTATTATTATTATTATTA
Found at i:429114 original size:17 final size:16
Alignment explanation
Indices: 429092--429132 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
429082 TCTTCATTTG
429092 ATTTTATTTCAATTTTT
1 ATTTTATTT-AATTTTT
*
429109 ATTTTATTTACTTTTT
1 ATTTTATTTAATTTTT
429125 -TTTTATTT
1 ATTTTATTT
429133 TTTATATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.35
16 6 0.26
17 9 0.39
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTATTTAATTTTT
Found at i:431319 original size:22 final size:22
Alignment explanation
Indices: 431274--431319 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
431264 ACAAAATAAC
* *
431274 AAAGACATAAATCAACCAATAA
1 AAAGACATAAAGCAACCAACAA
* *
431296 AAAGACATAAAGCAGCCAGCAA
1 AAAGACATAAAGCAACCAACAA
431318 AA
1 AA
431320 TATCCCAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.20, G:0.11, T:0.09
Consensus pattern (22 bp):
AAAGACATAAAGCAACCAACAA
Found at i:431525 original size:3 final size:3
Alignment explanation
Indices: 431517--431603 Score: 58
Period size: 3 Copynumber: 28.7 Consensus size: 3
431507 ACTCTGAATG
*
431517 AAT AAT AAT AAT AAT AAT AAT AA- AAC AGAT CAA- AA- AAT AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT AAT A-AT
* *
431562 ATAT AA- AAA AAGT AA- AAA AAT AAAT AAT AAT AAT AAT AAT AA
1 A-AT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
431604 CAAAAGTAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
2 10 0.14
3 47 0.66
4 13 0.18
5 1 0.01
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:431556 original size:29 final size:27
Alignment explanation
Indices: 431523--431597 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 27
431513 AATGAATAAT
*
431523 AATAATAATAATAATAAAACAGATCAAAA
1 AATAATAATAATAATAAAA-AG-TAAAAA
431552 AATAATAGATATATAA-AAAAAGTAAAAA
1 AATAATA-ATA-ATAATAAAAAGTAAAAA
431580 AATAAATAATAATAATAA
1 AAT-AATAATAATAATAA
431598 TAATAACAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
27 4 0.10
28 13 0.32
29 13 0.32
30 7 0.17
31 4 0.10
ACGTcount: A:0.71, C:0.03, G:0.04, T:0.23
Consensus pattern (27 bp):
AATAATAATAATAATAAAAAGTAAAAA
Found at i:431596 original size:38 final size:37
Alignment explanation
Indices: 431550--431631 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
431540 AACAGATCAA
431550 AAAATAATAGATATATAAAAAAAGTAAA-AAAAT-AAAT
1 AAAATAATA-ATA-ATAAAAAAAGTAAAGAAAATAAAAT
*
431587 AATAATAATAATAATAACAAAAGTAAAGAAAATAAAAT
1 AA-AATAATAATAATAAAAAAAGTAAAGAAAATAAAAT
431625 AAAATAA
1 AAAATAA
431632 AAACTAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
36 13 0.32
37 15 0.37
38 13 0.32
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (37 bp):
AAAATAATAATAATAAAAAAAGTAAAGAAAATAAAAT
Found at i:431608 original size:29 final size:27
Alignment explanation
Indices: 431523--431643 Score: 75
Period size: 31 Copynumber: 4.2 Consensus size: 27
431513 AATGAATAAT
*
431523 AATAATAATAATAATAAAACAGATCAAAA
1 AATAATAATAATAATAAAACA-A-AAAAA
* *
431552 AATAATAGATATATAAAAAAAGTAAAAAAATA
1 AATAATA-ATA-ATAATAAAA--CAAAAAA-A
**
431584 AATAATAATAATAATAATAACAAAAGTA
1 AATAATAATAATAATAA-AACAAAAAAA
* *
431612 AAGAA-AATAA-AATAAAATAAAAACTAA
1 AATAATAATAATAATAAAACAAAAA--AA
431639 AATAA
1 AATAA
431644 AATCAAAGGA
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
25 6 0.08
26 5 0.07
27 10 0.14
28 5 0.07
29 11 0.15
30 9 0.12
31 16 0.22
32 9 0.12
33 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (27 bp):
AATAATAATAATAATAAAACAAAAAAA
Found at i:431622 original size:9 final size:8
Alignment explanation
Indices: 431564--431634 Score: 52
Period size: 9 Copynumber: 7.9 Consensus size: 8
431554 TAATAGATAT
431564 ATAAAAAA
1 ATAAAAAA
431572 AGTAAAAAA
1 A-TAAAAAA
431581 ATAAATAATA
1 ATAAA-AA-A
*
431591 ATAATAATA
1 ATAA-AAAA
431600 ATAACAAAA
1 ATAA-AAAA
*
431609 GTAAAGAAA
1 ATAAA-AAA
431618 ATAAAATAAA
1 AT-AAA-AAA
431628 ATAAAAA
1 ATAAAAA
431635 CTAAAATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
8 8 0.16
9 28 0.55
10 14 0.27
11 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (8 bp):
ATAAAAAA
Found at i:431623 original size:5 final size:5
Alignment explanation
Indices: 431578--431646 Score: 52
Period size: 5 Copynumber: 13.0 Consensus size: 5
431568 AAAAAGTAAA
* *
431578 AAAAT -AAAT AATAAT AATAAT AATAAC AAAAGT -AAAG AAAAT AAAAT
1 AAAAT AAAAT AA-AAT AA-AAT AA-AAT AAAA-T AAAAT AAAAT AAAAT
431625 AAAAT AAAAACT AAAAT AAAAT
1 AAAAT -AAAA-T AAAAT AAAAT
431647 CAAAGGAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.07
5 25 0.46
6 24 0.44
7 1 0.02
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:431641 original size:12 final size:11
Alignment explanation
Indices: 431578--431645 Score: 50
Period size: 12 Copynumber: 5.8 Consensus size: 11
431568 AAAAAGTAAA
431578 AAAATAAATAAT
1 AAAATAAA-AAT
*
431590 AATAATAATAAT
1 AA-AATAAAAAT
*
431602 AACAA-AAGTAAAG
1 AA-AATAA--AAAT
431615 AAAAT-AAAAT
1 AAAATAAAAAT
431625 AAAATAAAAACT
1 AAAATAAAAA-T
431637 AAAATAAAA
1 AAAATAAAA
431646 TCAAAGGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
10 8 0.18
11 6 0.13
12 22 0.49
13 9 0.20
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:431641 original size:17 final size:16
Alignment explanation
Indices: 431615--431646 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
431605 AAAAGTAAAG
431615 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
431631 AAAACTAAAATAAAAT
1 AAAA-TAAAATAAAAT
431647 CAAAGGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:431646 original size:64 final size:64
Alignment explanation
Indices: 431520--431640 Score: 153
Period size: 64 Copynumber: 1.9 Consensus size: 64
431510 CTGAATGAAT
* * *
431520 AATAATAATAATAATAATAAAACAGATCAAAAAATAATAGATATATAAAAAAAGTAAAAAAATA
1 AATAATAATAATAATAATAAAAAAGATAAAAAAATAATAGATATATAAAAAAACTAAAAAAATA
431584 AATAATAATAATAATAATAACAAAAG-TAAAGAAAATAA-A-ATA-A-AATAAAAACTAAAA
1 AATAATAATAATAATAATAA-AAAAGATAAA-AAAATAATAGATATATAA-AAAAACTAAAA
431641 TAAAATCAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 2 0.04
62 11 0.22
63 3 0.06
64 24 0.47
65 11 0.22
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (64 bp):
AATAATAATAATAATAATAAAAAAGATAAAAAAATAATAGATATATAAAAAAACTAAAAAAATA
Found at i:432348 original size:75 final size:73
Alignment explanation
Indices: 432187--432356 Score: 191
Period size: 75 Copynumber: 2.3 Consensus size: 73
432177 AACAAACATC
* * * *
432187 TCACACAGTCTGGCAAATGCCCGTGTGTCTAGGCCGTGCCATTTCGAATTAATAACAAATTATTG
1 TCACACAGTCTGGCACATGCCCGTGTGTCCAGGCCGTGCAATTTCGAATTAATAACAAATTATTA
*
432252 CCCAATGG
66 CCCAATAG
* *
432260 TTACACAGTCTGGCACACGCCCGTGTGTCCAGGCCGTGTGCAATTTCGAATTAAAATAA-AAA-T
1 TCACACAGTCTGGCACATGCCCGTGTGTCCAGGCC--GTGCAATTTCGAATT--AATAACAAATT
*
432323 ATTACCCAGTAG
62 ATTACCCAATAG
* **
432335 TCATATGGTCTGGCACATGCCC
1 TCACACAGTCTGGCACATGCCC
432357 ATTTGTCTAG
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
73 31 0.39
75 41 0.51
76 3 0.04
77 5 0.06
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (73 bp):
TCACACAGTCTGGCACATGCCCGTGTGTCCAGGCCGTGCAATTTCGAATTAATAACAAATTATTA
CCCAATAG
Found at i:432703 original size:118 final size:117
Alignment explanation
Indices: 432481--432721 Score: 394
Period size: 118 Copynumber: 2.1 Consensus size: 117
432471 CCTTGTGCTA
* * * *
432481 TTTTAATAATAAAACATACAAAATAAGTATAAAATATTAAAAATAAAAATAAATTAAATTTAAAC
1 TTTTGATAATAAAACATACAAAATAAGTATAAAATAATAAAAATAAAAATAAAATAAATTAAAAC
*
432546 ATTCGGATTGCCTCCCGATAAGCGCTTGTTTAAAATCTAAGCTCGACTTCCC
66 ACTCGGATTGCCTCCCGATAAGCGCTTGTTTAAAATCTAAGCTCGACTTCCC
432598 TTTTGATAATAAAACATA-AAAATTAAGTATAAAATAATAAAAATAAAAATGAAAATAAATTAAA
1 TTTTGATAATAAAACATACAAAA-TAAGTATAAAATAATAAAAATAAAAAT-AAAATAAATTAAA
* *
432662 ACACTCGGATTGCCTCTCGATAAGCGCTTGTTTAAAGTCTAAGCTCGACTTCCC
64 ACACTCGGATTGCCTCCCGATAAGCGCTTGTTTAAAATCTAAGCTCGACTTCCC
432716 TTTTGA
1 TTTTGA
432722 AACTCACAAT
Statistics
Matches: 115, Mismatches: 7, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
116 4 0.03
117 43 0.37
118 68 0.59
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.31
Consensus pattern (117 bp):
TTTTGATAATAAAACATACAAAATAAGTATAAAATAATAAAAATAAAAATAAAATAAATTAAAAC
ACTCGGATTGCCTCCCGATAAGCGCTTGTTTAAAATCTAAGCTCGACTTCCC
Found at i:436222 original size:108 final size:106
Alignment explanation
Indices: 436026--436225 Score: 251
Period size: 106 Copynumber: 1.9 Consensus size: 106
436016 ATTATTTTCT
* * * *
436026 TTTAGGGAATTCAAGAAATTATGCCCTAACGTATTAGGTATGATTTTTTTTAACCTAAATAATCA
1 TTTAGGGAACTCAAGAAATTATGCCCAAACGTATGAGGTATCATTTTTTTTAACCTAAATAATCA
** *
436091 AGTATCCAATTTAAAATCAATAAATGTTCGATTTTCTTTTA
66 AACACCCAATTTAAAATCAATAAATGTTCGATTTTCTTTTA
*
436132 TTTAGGGAACTCGAAG-AATTGTGCCCAAACGTACTGA-GTATCATTTTTCTTTAAACCTAAATA
1 TTTAGGGAACTC-AAGAAATTATGCCCAAACGTA-TGAGGTATCATTTTT-TTT-AACCTAAATA
* * *
436195 ATTAAACACCCTATTTAAAATCGATAAATGT
62 ATCAAACACCCAATTTAAAATCAATAAATGT
436226 CCTTTGTTTT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
106 36 0.46
107 8 0.10
108 35 0.44
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (106 bp):
TTTAGGGAACTCAAGAAATTATGCCCAAACGTATGAGGTATCATTTTTTTTAACCTAAATAATCA
AACACCCAATTTAAAATCAATAAATGTTCGATTTTCTTTTA
Found at i:446443 original size:39 final size:39
Alignment explanation
Indices: 446403--446528 Score: 103
Period size: 39 Copynumber: 3.2 Consensus size: 39
446393 CATGGGACAG
*
446403 ATTGAAATCATCCAATCTTTTACTCTAACCAAAGGTCAG
1 ATTGAAATCATCCAATCTTTTACTCTAACCAAAGGTCAA
* * * * * **
446442 ATTAAAGACACCATCCAATCTCTTACTCCACCCACGGGTCAA
1 ATT---GAAATCATCCAATCTTTTACTCTAACCAAAGGTCAA
* *
446484 ATTG-AATCCATCCAATCTTTTA-TACTAACCAGAGGGCAA
1 ATTGAAAT-CATCCAATCTTTTACT-CTAACCAAAGGTCAA
446523 ATTGAA
1 ATTGAA
446529 TACACTATCA
Statistics
Matches: 65, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
38 2 0.03
39 31 0.48
40 1 0.02
42 31 0.48
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (39 bp):
ATTGAAATCATCCAATCTTTTACTCTAACCAAAGGTCAA
Found at i:446505 original size:81 final size:80
Alignment explanation
Indices: 446370--447032 Score: 411
Period size: 81 Copynumber: 8.2 Consensus size: 80
446360 AGGCAAAGCT
* * * *
446370 ACCATCCAATCTCTTA-TCGTGACCATGGGACAGATTGAAATCATCCAATCTTTTACTCTAACCA
1 ACCATCCAATCTCTTACTCCT-ACCATGGGTCAAATTG-AATCATCCAATCTTTTACCCTAACCA
* *
446434 AAGGTCAGATTAAAGAC
64 AAGGACAAATTAAAGAC
* **
446451 ACCATCCAATCTCTTACTCC-ACCCACGGGTCAAATTGAATCCATCCAATCTTTTATACTAACCA
1 ACCATCCAATCTCTTACTCCTA-CCATGGGTCAAATTGAAT-CATCCAATCTTTTACCCTAACCA
* * * *
446515 GAGGGCAAATTGAATAC
64 AAGGACAAATTAAAGAC
* * * ** * * * **
446532 ACTATCAAATCTCTTACCCCGCCCAT-GGTACAGATTGAAGCTATCCAATTTTTTACCCTAATTA
1 ACCATCCAATCTCTTACTCCTACCATGGGT-CAAATTGAATC-ATCCAATCTTTTACCCTAACCA
* * * *
446596 GAGGACATATTAAGGGC
64 AAGGACAAATTAAAGAC
* * * * * * *
446613 ATCATCCAACCTCTAAC-CCTGACCATAGGGT-AAATTAAAGTCATTCAACCTTTTACCCTAATC
1 ACCATCCAATCTCTTACTCCT-ACCAT-GGGTCAAATTGAA-TCATCCAATCTTTTACCCTAACC
*
446676 AGTAA--ATAAATTAAAGAC
63 A--AAGGACAAATTAAAGAC
* * * * * * *
446694 ACTATCTAATCTCTTAC-CCTGCCCATTGAGT-AGATTGAAGCCATCTAATCTTTTACCCTAACC
1 ACCATCCAATCTCTTACTCCT-ACCA-TGGGTCAAATTGAA-TCATCCAATCTTTTACCCTAACC
* *
446757 AGA-GAGCAAATTAAAAAC
63 AAAGGA-CAAATTAAAGAC
* * * * *
446775 ACCATCCAATCTCTTAC-CTCGATCATGAGG-CAGATTGAAGTCATCCAATCTTTTATCCTAAAC
1 ACCATCCAATCTCTTACTC-CTACCATG-GGTCAAATTGAA-TCATCCAATCTTTTACCCTAACC
*
446838 AAAAGACAAATTAAAGAC
63 AAAGGACAAATTAAAGAC
* * * * * * *
446856 ACCATCCAATCTCTTACCCCTACCATAGGACAAATTAAAGTCACCCAATATTTTACCTTAACCAA
1 ACCATCCAATCTCTTACTCCTACCATGGGTCAAATTGAA-TCATCCAATCTTTTACCCTAACC-A
* * *
446921 AAGG-TAGATTGAAGAC
64 AAGGACAAATTAAAGAC
* * * * *
446937 ACCATCCAATCTCTT--TCCTTAACAATGGGGCAAATTGAACTCATCCAATTTTTTACCTTAACT
1 ACCATCCAATCTCTTACTCC-T-ACCATGGGTCAAATTGAA-TCATCCAATCTTTTACCCTAACC
* *
447000 AGAGGACAAATTGAAGAC
63 AAAGGACAAATTAAAGAC
447018 ACCATCCAATCTCTT
1 ACCATCCAATCTCTT
447033 CAATCTACCC
Statistics
Matches: 454, Mismatches: 103, Indels: 50
0.75 0.17 0.08
Matches are distributed among these distances:
79 3 0.01
80 20 0.04
81 415 0.91
82 12 0.03
83 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.27
Consensus pattern (80 bp):
ACCATCCAATCTCTTACTCCTACCATGGGTCAAATTGAATCATCCAATCTTTTACCCTAACCAAA
GGACAAATTAAAGAC
Found at i:446974 original size:42 final size:43
Alignment explanation
Indices: 446734--447032 Score: 156
Period size: 42 Copynumber: 7.3 Consensus size: 43
446724 TAGATTGAAG
* * * * *
446734 CCATCTAATCT-TTTACCCTAACCAGA-GAGCAAATTAAAAACA
1 CCATCCAATCTCTTTACCTTAACAAGAGGA-CAAATTGAAGACA
* * * *
446776 CCATCCAATCTC-TTACCTCGATCATGAGG-CAGATTGAAG---
1 CCATCCAATCTCTTTACCT-TAACAAGAGGACAAATTGAAGACA
* * * *
446815 TCATCCAATCT-TTTATCCTAAACAA-AAGACAAATTAAAGACA
1 CCATCCAATCTCTTTA-CCTTAACAAGAGGACAAATTGAAGACA
* * * * *
446857 CCATCCAATCTC-TTACCCCT-ACCATAGGACAAATTAAAGTCA
1 CCATCCAATCTCTTTA-CCTTAACAAGAGGACAAATTGAAGACA
* * * *
446899 -C--CCAATAT-TTTACCTTAACCAAAAGG-TAGATTGAAGACA
1 CCATCCAATCTCTTTACCTTAA-CAAGAGGACAAATTGAAGACA
*
446938 CCATCCAATCTCTTT-CCTTAACAATG-GGGCAAATTG-A-AC-
1 CCATCCAATCTCTTTACCTTAACAA-GAGGACAAATTGAAGACA
* * *
446977 TCATCCAAT-TTTTTACCTTAACTAGAGGACAAATTGAAGACA
1 CCATCCAATCTCTTTACCTTAACAAGAGGACAAATTGAAGACA
447019 CCATCCAATCTCTT
1 CCATCCAATCTCTT
447033 CAATCTACCC
Statistics
Matches: 190, Mismatches: 41, Indels: 51
0.67 0.15 0.18
Matches are distributed among these distances:
38 10 0.05
39 68 0.36
40 12 0.06
41 12 0.06
42 77 0.41
43 10 0.05
44 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.10, T:0.27
Consensus pattern (43 bp):
CCATCCAATCTCTTTACCTTAACAAGAGGACAAATTGAAGACA
Found at i:446993 original size:243 final size:241
Alignment explanation
Indices: 446370--447032 Score: 619
Period size: 243 Copynumber: 2.7 Consensus size: 241
446360 AGGCAAAGCT
* * * *
446370 ACCATCCAATCTCTTATCGTGACCATGGGACAGATTGAAA-TCATCCAATCTTTTA-CTCTAACC
1 ACCATCCAATCTCTTACCCTGACCATAGGACAAATT-AAAGTCATCCAATCTTTTACCT-TAACC
* *
446433 -AAAGGTCAGATTAAAGACACCATCCAATCTCTTACTCC-ACCCACGGGTCAAATTGAA-TCCAT
64 AAAAGGT-AGATTAAAGACACCATCCAATCTCTT--TCCTACCCATGGGGCAAATTGAACT-CAT
** * * * *
446495 CCAATCTTTTATACTAACCAGAGGGCAAATTGAATACACTATCAAATCTCTTACCCCGCCCATGG
125 CCAATCTTTTACCCTAACCAGA-GGCAAATTGAAAACACCATCCAATCTCTTACCCCGACCATGG
* ** * * * * *
446560 TACAGATTGAAGCTATCCAATTTTTTACCCTAATTAGAGGACATATTAAGGGC
189 TACAGATTGAAGCTATCCAATCTTTTACCCTAAACAAAAGACAAATTAAAGAC
* * * ** * * * *
446613 ATCATCCAACCTCTAACCCTGACCATAGGGTAAATTAAAGTCATTCAACCTTTTACCCTAATCAG
1 ACCATCCAATCTCTTACCCTGACCATAGGACAAATTAAAGTCATCCAATCTTTTACCTTAACCA-
* * * * * * * * * *
446678 TAAA--TAAATTAAAGACACTATCTAATCTCTTACCCTGCCCATTGAGTAGATTGAAGC-CATCT
65 -AAAGGTAGATTAAAGACACCATCCAATCTCTT-TCCTACCCATGGGGCAAATTGAA-CTCATCC
* * *
446740 AATCTTTTACCCTAACCAGAGAGCAAATTAAAAACACCATCCAATCTCTTACCTCGATCATGAG-
127 AATCTTTTACCCTAACCAGAG-GCAAATTGAAAACACCATCCAATCTCTTACCCCGACCATG-GT
* *
446804 GCAGATTGAAG-TCATCCAATCTTTTATCCTAAACAAAAGACAAATTAAAGAC
190 ACAGATTGAAGCT-ATCCAATCTTTTACCCTAAACAAAAGACAAATTAAAGAC
* *
446856 ACCATCCAATCTCTTACCCCT-ACCATAGGACAAATTAAAGTCACCCAATATTTTACCTTAACCA
1 ACCATCCAATCTCTTA-CCCTGACCATAGGACAAATTAAAGTCATCCAATCTTTTACCTTAACCA
* * *
446920 AAAGGTAGATTGAAGACACCATCCAATCTCTTTCCTTAACAATGGGGCAAATTGAACTCATCCAA
65 AAAGGTAGATTAAAGACACCATCCAATCTCTTTCC-TACCCATGGGGCAAATTGAACTCATCCAA
* * * *
446985 TTTTTTACCTTAACTAGAGGACAAATTGAAGACACCATCCAATCTCTT
129 TCTTTTACCCTAACCAGAGG-CAAATTGAAAACACCATCCAATCTCTT
447033 CAATCTACCC
Statistics
Matches: 329, Mismatches: 74, Indels: 34
0.75 0.17 0.08
Matches are distributed among these distances:
241 3 0.01
242 11 0.03
243 305 0.93
244 7 0.02
246 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.27
Consensus pattern (241 bp):
ACCATCCAATCTCTTACCCTGACCATAGGACAAATTAAAGTCATCCAATCTTTTACCTTAACCAA
AAGGTAGATTAAAGACACCATCCAATCTCTTTCCTACCCATGGGGCAAATTGAACTCATCCAATC
TTTTACCCTAACCAGAGGCAAATTGAAAACACCATCCAATCTCTTACCCCGACCATGGTACAGAT
TGAAGCTATCCAATCTTTTACCCTAAACAAAAGACAAATTAAAGAC
Found at i:448494 original size:26 final size:26
Alignment explanation
Indices: 448440--448507 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
448430 ATTCTGGATG
* *
448440 CAATTTTGGACGTGCTCATGCAACAA
1 CAATTTTGGACATGTTCATGCAACAA
*
448466 CAATTTTGGACATGTTCATGTAA-AGA
1 CAATTTTGGACATGTTCATGCAACA-A
* *
448492 CAATTCTGAACATGTT
1 CAATTTTGGACATGTT
448508 AATACAACGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (26 bp):
CAATTTTGGACATGTTCATGCAACAA
Found at i:456567 original size:108 final size:109
Alignment explanation
Indices: 456365--456579 Score: 267
Period size: 108 Copynumber: 2.0 Consensus size: 109
456355 AAAAACAAAA
** *
456365 AACATTTATCGATTTTAAATAAGGTGTTCAATTATTTAAATTTAAAGAAAAATCATACCTAGCAC
1 AACATTTATCGATTTTAAATAAGGTACTCAATTATTTAAATTTAAAGAAAAATCATACCTAACAC
* * * **
456430 GTTTGGACACAATTCTTCAAGTTTTCT-AAATAAAAGAACATCG
66 ATTAGGACACAATTCTTCAAATTACCTAAAATAAAAGAACATCG
* * *
456473 AACATTTATTGATTTTAAAT-AGGATACTCGATTATTTAAATTTAAAGAAAAATCATA-CTCAAT
1 AACATTTATCGATTTTAAATAAGG-TACTCAATTATTTAAATTTAAAGAAAAATCATACCT-AAC
*
456536 ACATTAGGACACAATT-TCTCAAATTACCTAAAATAAAATAACAT
64 ACATTAGGACACAATTCT-TCAAATTACCTAAAATAAAAGAACAT
456580 TGTCTCTTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
107 6 0.07
108 72 0.79
109 13 0.14
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (109 bp):
AACATTTATCGATTTTAAATAAGGTACTCAATTATTTAAATTTAAAGAAAAATCATACCTAACAC
ATTAGGACACAATTCTTCAAATTACCTAAAATAAAAGAACATCG
Found at i:460036 original size:70 final size:69
Alignment explanation
Indices: 459894--460027 Score: 182
Period size: 70 Copynumber: 2.0 Consensus size: 69
459884 ATCCGAATAA
* * * *
459894 TAAAAGGTAAAATTACGTCGTTTTGATAAATGTTTACACTTTCAAAAGTTAAAAGTTAAAACCAT
1 TAAAAGATAAAATTACGTCATTTTGATAAATGTTTACACATT-AAAAGTTAAAAGGTAAAACCAT
459959 TAAGT
65 TAAGT
* * *
459964 TAAAAGATAAAATTATGTCATTTTGATAAATGTTTACCCATT-AAA-TTAAAAGGTAAAATCATT
1 TAAAAGATAAAATTACGTCATTTTGATAAATGTTTACACATTAAAAGTTAAAAGGTAAAACCATT
460027 A
66 A
460028 TATTGTTAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
67 17 0.30
68 3 0.05
70 37 0.65
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (69 bp):
TAAAAGATAAAATTACGTCATTTTGATAAATGTTTACACATTAAAAGTTAAAAGGTAAAACCATT
AAGT
Done.