Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009805.1 Kokia drynarioides strain JFW-HI SEQ_124526, 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: 143196
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Warning! 172 characters in sequence are not A, C, G, or T
Found at i:12859 original size:2 final size:2
Alignment explanation
Indices: 12850--12883 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
12840 CAATATATTG
12850 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12884 TAATCTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13062 original size:16 final size:16
Alignment explanation
Indices: 13041--13074 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
13031 ATATTCAATG
13041 ATTTTA-TATATTTATA
1 ATTTTATTA-ATTTATA
13057 ATTTTATTAATTTATA
1 ATTTTATTAATTTATA
13073 AT
1 AT
13075 ATATTATGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTATTAATTTATA
Found at i:20843 original size:40 final size:40
Alignment explanation
Indices: 20798--20875 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
20788 AATTATGAAA
20798 TGTAACCATTGCATTAAAGAAGTTTCCATCCTTCTCTCAT
1 TGTAACCATTGCATTAAAGAAGTTTCCATCCTTCTCTCAT
20838 TGTAACCATTGCATTAAAGAAGTTTCCATCCTTCTCTC
1 TGTAACCATTGCATTAAAGAAGTTTCCATCCTTCTCTC
20876 GTTCATCCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.27, C:0.26, G:0.10, T:0.37
Consensus pattern (40 bp):
TGTAACCATTGCATTAAAGAAGTTTCCATCCTTCTCTCAT
Found at i:36311 original size:17 final size:17
Alignment explanation
Indices: 36289--36327 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
36279 AGGTGGAGAA
* *
36289 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
36306 CTTGTTTGTAGAGAATT
1 CTTGTTCGTAGAGAATT
36323 CTTGT
1 CTTGT
36328 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:36374 original size:41 final size:41
Alignment explanation
Indices: 36317--36412 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
36307 TTGTTTGTAG
* *
36317 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
36358 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
36399 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
36413 AATAAAATTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.36
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGAAGATTGTTAGAATTGGGTGACT
Found at i:41891 original size:2 final size:2
Alignment explanation
Indices: 41880--41912 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
41870 TCTTATTACA
41880 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41913 TCAAGTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:47183 original size:25 final size:26
Alignment explanation
Indices: 47149--47198 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
47139 CTTAAAATTA
* *
47149 AATTTTATTAATATTA-AATAAAAAT
1 AATTATATTAATATTAGAAAAAAAAT
47174 AATTATATTAATATTAGAAAAAAAA
1 AATTATATTAATATTAGAAAAAAAA
47199 AAACTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (26 bp):
AATTATATTAATATTAGAAAAAAAAT
Found at i:50448 original size:16 final size:15
Alignment explanation
Indices: 50396--50448 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
50386 TGTTTGTTTT
*
50396 AAATTTAATTAAAAA
1 AAATTTAATAAAAAA
*
50411 AATTTTAA-AAAATAA
1 AAATTTAATAAAA-AA
50426 AAA-TTAATAAAAAA
1 AAATTTAATAAAAAA
50440 ACAATTTAA
1 A-AATTTAA
50449 AAGTTAAGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 10 0.32
15 17 0.55
16 4 0.13
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATTTAATAAAAAA
Found at i:50825 original size:17 final size:18
Alignment explanation
Indices: 50775--50832 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
50765 TTTTTGAAAA
* *
50775 TTTTTGAAAATTGTTTAAT
1 TTTTTAAAAATT-TATAAT
*
50794 ATTTTAAAAATTTATAAT
1 TTTTTAAAAATTTATAAT
* *
50812 TTTTTTAAAA-TTATTAT
1 TTTTTAAAAATTTATAAT
50829 TTTT
1 TTTT
50833 ATAATTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 10 0.30
18 13 0.39
19 10 0.30
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTTAAAAATTTATAAT
Found at i:57775 original size:15 final size:17
Alignment explanation
Indices: 57745--57776 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
57735 TTCAAGGAGA
57745 GAATCTAATCATTTTTT
1 GAATCTAATCATTTTTT
57762 GAAT-TAAT-ATTTTTT
1 GAATCTAATCATTTTTT
57777 CTCGAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
GAATCTAATCATTTTTT
Found at i:61758 original size:38 final size:38
Alignment explanation
Indices: 61716--61792 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
61706 GTTTAAACCC
** *
61716 AATCTACTTTTACACAAAGGAGCAGCTGCAACCCTAAT
1 AATCTACCCTTACACAAAGGAGCAACTGCAACCCTAAT
* *
61754 AATCTACCCTTACACAAAGGGGTAACTGCAACCCTAAT
1 AATCTACCCTTACACAAAGGAGCAACTGCAACCCTAAT
61792 A
1 A
61793 CCTACTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (38 bp):
AATCTACCCTTACACAAAGGAGCAACTGCAACCCTAAT
Found at i:62525 original size:46 final size:46
Alignment explanation
Indices: 62474--62566 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
62464 TGAACATTTT
* * * *
62474 CAAATTACATATATTACATCATAAAAGTATAGATACCAAATTTATG
1 CAAATTACATATACTACATAATAAAAGTAGAGATACCAAATGTATG
62520 CAAATTACATATACTACATAATAAAAGTAGAGATACCAAATGTATG
1 CAAATTACATATACTACATAATAAAAGTAGAGATACCAAATGTATG
62566 C
1 C
62567 GACAAAGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (46 bp):
CAAATTACATATACTACATAATAAAAGTAGAGATACCAAATGTATG
Found at i:68660 original size:3 final size:3
Alignment explanation
Indices: 68652--68677 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
68642 TATTTTACCC
68652 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
68678 TAAACTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:80607 original size:21 final size:21
Alignment explanation
Indices: 80583--80636 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
80573 AGAGTTTTTA
*
80583 GTATCGGTAGAAGTATGACTT
1 GTATCGGTAGAAGTATCACTT
* *
80604 GTATCGGTAGATGTCTCACTT
1 GTATCGGTAGAAGTATCACTT
*
80625 GTATCGATAGAA
1 GTATCGGTAGAA
80637 CTGTCATAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACTT
Found at i:86700 original size:29 final size:29
Alignment explanation
Indices: 86658--86731 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
86648 CTCTCTGTCT
86658 AATTTTATGTCAAAGGCTCATTCAAAAAA
1 AATTTTATGTCAAAGGCTCATTCAAAAAA
86687 AATTTTATGTCAAAGGCTCATTCAAAAAA
1 AATTTTATGTCAAAGGCTCATTCAAAAAA
86716 AATTTTATGTCAAAGG
1 AATTTTATGTCAAAGG
86732 TAAAATAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (29 bp):
AATTTTATGTCAAAGGCTCATTCAAAAAA
Found at i:89678 original size:24 final size:26
Alignment explanation
Indices: 89642--89689 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
89632 AGAGAAATGT
89642 AAATGTGATATATGA-A-ATTATGAG
1 AAATGTGATATATGAGAGATTATGAG
89666 AAATGATGA-ATATGAGAGATTATG
1 AAATG-TGATATATGAGAGATTATG
89690 CCCATGTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGTGATATATGAGAGATTATGAG
Found at i:89782 original size:23 final size:22
Alignment explanation
Indices: 89763--89895 Score: 133
Period size: 23 Copynumber: 5.9 Consensus size: 22
89753 TTACTGTTCA
* *
89763 GCACTGTGTGTGCTTACTGTTT
1 GCACTGTGTGTGCCTACTGATT
* *
89785 CGCACT-TCGTGTTCCTATTGATTT
1 -GCACTGT-GTGTGCCTACTGA-TT
* * *
89809 GCGCTATGTGCGCCTACTGATT
1 GCACTGTGTGTGCCTACTGATT
*
89831 GCACTGTGTGTGCCTGCTGGATT
1 GCACTGTGTGTGCCTACT-GATT
89854 GCACTGTGTGTGCCTACTGGATT
1 GCACTGTGTGTGCCTACT-GATT
*
89877 GCACTGTGTGTGCTTACTG
1 GCACTGTGTGTGCCTACTG
89896 TTTCTCAACA
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
22 18 0.20
23 71 0.77
24 3 0.03
ACGTcount: A:0.11, C:0.23, G:0.28, T:0.38
Consensus pattern (22 bp):
GCACTGTGTGTGCCTACTGATT
Found at i:95279 original size:23 final size:23
Alignment explanation
Indices: 95244--95300 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
95234 TTTATTCATG
* *
95244 CATTGATAGATCCAGCTTCTACA
1 CATTCATACATCCAGCTTCTACA
* *
95267 CATTCATACATCCGGGTTCTACA
1 CATTCATACATCCAGCTTCTACA
95290 CATTCATACAT
1 CATTCATACAT
95301 GAGAACTAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.32
Consensus pattern (23 bp):
CATTCATACATCCAGCTTCTACA
Found at i:100017 original size:51 final size:51
Alignment explanation
Indices: 99962--100066 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
99952 AAGCTTATTG
99962 TTAATTAATTACTTTTATTAACTAATCTATATTTAATACTTATGTAATGAT
1 TTAATTAATTACTTTTATTAACTAATCTATATTTAATACTTATGTAATGAT
100013 TTAATTAATTACTTTTATTAACTAATCTATATTTAATACTTATGTAATGAT
1 TTAATTAATTACTTTTATTAACTAATCTATATTTAATACTTATGTAATGAT
100064 TTA
1 TTA
100067 TATGATATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (51 bp):
TTAATTAATTACTTTTATTAACTAATCTATATTTAATACTTATGTAATGAT
Found at i:102592 original size:23 final size:23
Alignment explanation
Indices: 102566--102610 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
102556 TAAACTATTG
102566 AAATACATTT-AATATTATAAATT
1 AAATACATTTAAATATT-TAAATT
*
102589 AAATATATTTAAATATTTAAAT
1 AAATACATTTAAATATTTAAAT
102611 ATTATTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
AAATACATTTAAATATTTAAATT
Found at i:103818 original size:3 final size:3
Alignment explanation
Indices: 103810--103836 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
103800 CTTTTCCCTG
103810 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
103837 GAATTTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:106418 original size:15 final size:15
Alignment explanation
Indices: 106400--106450 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
106390 AAAAATATAT
106400 AAAATATAAATTTTA
1 AAAATATAAATTTTA
* *
106415 AAAATAT-AATCAATCA
1 AAAATATAAAT--TTTA
*
106431 AAGATATAAATTTTA
1 AAAATATAAATTTTA
106446 AAAAT
1 AAAAT
106451 CTAATCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 3 0.11
15 13 0.48
16 8 0.30
17 3 0.11
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAATATAAATTTTA
Found at i:106441 original size:31 final size:31
Alignment explanation
Indices: 106403--106465 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
106393 AATATATAAA
106403 ATATAAATTTTAAAAATATAATCAATCAAAG
1 ATATAAATTTTAAAAATATAATCAATCAAAG
* *
106434 ATATAAATTTTAAAAATCTAATCAATTAAAG
1 ATATAAATTTTAAAAATATAATCAATCAAAG
106465 A
1 A
106466 GACTATAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.33
Consensus pattern (31 bp):
ATATAAATTTTAAAAATATAATCAATCAAAG
Found at i:115195 original size:39 final size:39
Alignment explanation
Indices: 115141--115215 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
115131 GGGCAACAAA
*
115141 GAGCACACAAAGTGCTACA-CAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTA-ATCAGAGAGCACACAAAGTACT
115180 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGT
115216 GCTAATCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTACT
Found at i:115206 original size:23 final size:23
Alignment explanation
Indices: 115180--115274 Score: 129
Period size: 23 Copynumber: 4.1 Consensus size: 23
115170 ACAAAGTACT
115180 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
115203 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* * *
115226 GAGCACGA-GACGTGCTAAACAGA
1 GAGCAC-ACAAAGTGCTAATCAGA
* *
115249 GAGCACACACAGTGCTAATCAAA
1 GAGCACACAAAGTGCTAATCAGA
115272 GAG
1 GAG
115275 AGCGCTAGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.02
23 60 0.97
24 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:118778 original size:24 final size:24
Alignment explanation
Indices: 118748--118796 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
118738 TGAGAAATAA
* *
118748 TATTTCAGTTAAACTCTATTTATT
1 TATTTCAATTAAACTCCATTTATT
*
118772 TATTTCAATTGAACTCCATTTATT
1 TATTTCAATTAAACTCCATTTATT
118796 T
1 T
118797 GTTTGAGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (24 bp):
TATTTCAATTAAACTCCATTTATT
Found at i:120213 original size:27 final size:27
Alignment explanation
Indices: 120169--120222 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
120159 AGATGTCAGG
* *
120169 TATGTACTTGATTCACGAAAGAATATC
1 TATGTACCTAATTCACGAAAGAATATC
*
120196 TATGTACCTAATTTACGAAAGAATATC
1 TATGTACCTAATTCACGAAAGAATATC
120223 GTCTCTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (27 bp):
TATGTACCTAATTCACGAAAGAATATC
Found at i:120812 original size:24 final size:24
Alignment explanation
Indices: 120738--120812 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
120728 AGAAATAATC
*
120738 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
* *
120762 TTACAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
*
120786 TTTCAATTAAACTCCATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
120810 TTT
1 TTT
120813 GAGTCGAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:122027 original size:89 final size:89
Alignment explanation
Indices: 121875--122050 Score: 262
Period size: 89 Copynumber: 2.0 Consensus size: 89
121865 TCTAGTCCAA
* * * * *
121875 GAGTAGAGAGGAAGAAGAAAATCCAAATCGGGTCTCTTTCAGTACTGTCCCTTTCCCCGCGGTAT
1 GAGTAGAGAGGAAGAAGAAAATCCAAACCGAGTCTCTTTCAATACCGTCCCTTTCCCCACGGTAT
*
121940 CAACGGTAGTGAAGAAAGAGGGAC
66 CAACGGTAATGAAGAAAGAGGGAC
* * * *
121964 GAGTAGAGAGGAAGAAGACAATCTAAACCGAGTCTCTTTCAATTCCGTCCCTTTCTCCACGGTAT
1 GAGTAGAGAGGAAGAAGAAAATCCAAACCGAGTCTCTTTCAATACCGTCCCTTTCCCCACGGTAT
122029 CAACGGTAATGAAGAAAGAGGG
66 CAACGGTAATGAAGAAAGAGGG
122051 GACAAGTCTT
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 77 1.00
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (89 bp):
GAGTAGAGAGGAAGAAGAAAATCCAAACCGAGTCTCTTTCAATACCGTCCCTTTCCCCACGGTAT
CAACGGTAATGAAGAAAGAGGGAC
Found at i:124314 original size:91 final size:92
Alignment explanation
Indices: 124153--124327 Score: 280
Period size: 91 Copynumber: 1.9 Consensus size: 92
124143 ATTGAGTTTC
* * ** * *
124153 ATATTATAATGGCTTCTTGCTTTCTTCCCCCATGTTTATTTTCTTCTTATTTATACTGATTTTTA
1 ATATGATAATGGCCTCTTGCTTTCTTCCCCCATCATTATTTGCTTCTTATCTATACTGATTTTTA
124218 ATAGTTAATATTTTTGTAGGTATTTTG
66 ATAGTTAATATTTTTGTAGGTATTTTG
*
124245 ATATGATAATGGCCTCTTGCTTTC-TCCCCCCTCATTATTTGCTTCTTATCTATACTGATTTTTA
1 ATATGATAATGGCCTCTTGCTTTCTTCCCCCATCATTATTTGCTTCTTATCTATACTGATTTTTA
124309 ATAGTTAATATTTTTGTAG
66 ATAGTTAATATTTTTGTAG
124328 ATGTTTTCAC
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
91 54 0.71
92 22 0.29
ACGTcount: A:0.21, C:0.16, G:0.11, T:0.52
Consensus pattern (92 bp):
ATATGATAATGGCCTCTTGCTTTCTTCCCCCATCATTATTTGCTTCTTATCTATACTGATTTTTA
ATAGTTAATATTTTTGTAGGTATTTTG
Done.