Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011873.1 Kokia drynarioides strain JFW-HI SEQ_126870, 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: 56819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:111 original size:10 final size:11
Alignment explanation
Indices: 83--111 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
73 TATATATATT
83 ATATTATTTAA
1 ATATTATTTAA
94 ATATTATTTAA
1 ATATTATTTAA
105 A-ATTATT
1 ATATTATT
112 ATTTCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.33
11 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTATTTAA
Found at i:129 original size:17 final size:17
Alignment explanation
Indices: 107--163 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
97 TTATTTAAAA
**
107 TTATTATTTCTATTTAG
1 TTATTATTGATATTTAG
124 TTATTATTGATATTTAG
1 TTATTATTGATATTTAG
*
141 TCTATT-TAGA-ATTTA-
1 T-TATTATTGATATTTAG
156 TTATTATT
1 TTATTATT
164 CAATTTAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 4 0.12
15 2 0.06
16 5 0.15
17 19 0.56
18 4 0.12
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (17 bp):
TTATTATTGATATTTAG
Found at i:187 original size:29 final size:28
Alignment explanation
Indices: 158--228 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
148 AGAATTTATT
158 ATTATTCAATTTAAGT-TAAATAGAAAATTA
1 ATTATT-AATTTAAGTAT-AAT-GAAAATTA
* * *
188 ATAATTTATTTAAGTATAATTAAAATTA
1 ATTATTAATTTAAGTATAATGAAAATTA
216 ATTATTAATTTAA
1 ATTATTAATTTAA
229 TAATTTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 18 0.51
29 11 0.31
30 6 0.17
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (28 bp):
ATTATTAATTTAAGTATAATGAAAATTA
Found at i:3962 original size:18 final size:18
Alignment explanation
Indices: 3935--3979 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
3925 CTTCTTTAGG
*
3935 ATCTTATTCAAGATCTTC
1 ATCTTCTTCAAGATCTTC
*
3953 ATCTTCTTCATGATCTTC
1 ATCTTCTTCAAGATCTTC
*
3971 TTCTTCTTC
1 ATCTTCTTC
3980 TTCTTCAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (18 bp):
ATCTTCTTCAAGATCTTC
Found at i:4358 original size:18 final size:18
Alignment explanation
Indices: 4331--4375 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
4321 CTTCTTTAGG
*
4331 ATCTTATTCAAGATCTTC
1 ATCTTCTTCAAGATCTTC
*
4349 ATCTTCTTCATGATCTTC
1 ATCTTCTTCAAGATCTTC
*
4367 TTCTTCTTC
1 ATCTTCTTC
4376 TTCTTCAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.04, T:0.51
Consensus pattern (18 bp):
ATCTTCTTCAAGATCTTC
Found at i:4382 original size:396 final size:386
Alignment explanation
Indices: 3650--4433 Score: 1478
Period size: 396 Copynumber: 2.0 Consensus size: 386
3640 ATGGTTCAAA
3650 TATGTAATTTGAAAATTCAAGCACAAAAATATATGGTTCACGAAATACTTTTTCAAGTGCATATG
1 TATGTAATTTGAAAATTCAAGCACAAAAATATATGGTTCACGAAATACTTTTTCAAGTGCATATG
3715 TAAAAGCGTCATCTCGTATTTTCATGTATCTCCAATAAGATTGTTGCTACCATTGCATATGTTGC
66 TAAAAGCGTCATCTCGTATTTTCATGTATCTCCAATAAGATTGTTGCTACCATTGCATATGTTGC
3780 ACGCAATCTATCATCTTTGACAGCTGATCTCAAAGTTCTAAGTGAGGTGACTGAGGTCTAGGTAT
131 ACGCAATCTATCATCTTTGACAGCTGATCTCAAAGTTCTAAGTGAGGTGACTGAGGTCTAGGTAT
3845 GGATATGTCAGGTTCGAACATTCATTAAGTAGACTCTACCTCATCAGGAATTCCTATTGGCTCTG
196 GGATATGTCAGGTTCGAACATTCATTAAGTAGACTCTACCTCATCAGGAATTCCTATTGGCTCTG
3910 TTTCTGAAAGATCTTCTTCTTTAGGATCTTATTCAAGATCTTCATCTTCTTCATGATCTTCTTCT
261 TTTCTGAAAGATCTTCTTCTTTAGGATCTTATTCAAGATCTTCATCTTCTTCATGATCTTCTTCT
3975 TCTTCTTCTTCAGCTTGCTGTTGAAGAATGAAATTTCCTGCTACTCGAATGAGGTCTAAAT
326 TCTTCTTCTTCAGCTTGCTGTTGAAGAATGAAATTTCCTGCTACTCGAATGAGGTCTAAAT
4036 NNNNNNNNNNTATGTAATTTGAAAATTCAAGCACAAAAATATATGGTTCACGAAATACTTTTTCA
1 ----------TATGTAATTTGAAAATTCAAGCACAAAAATATATGGTTCACGAAATACTTTTTCA
4101 AGTGCATATGTAAAAGCGTCATCTCGTATTTTCATGTATCTCCAATAAGATTGTTGCTACCATTG
56 AGTGCATATGTAAAAGCGTCATCTCGTATTTTCATGTATCTCCAATAAGATTGTTGCTACCATTG
4166 CATATGTTGCACGCAATCTATCATCTTTGACAGCTGATCTCAAAGTTCTAAGTGAGGTGACTGAG
121 CATATGTTGCACGCAATCTATCATCTTTGACAGCTGATCTCAAAGTTCTAAGTGAGGTGACTGAG
4231 GTCTAGGTATGGATATGTCAGGTTCGAACATTCATTAAGTAGACTCTACCTCATCAGGAATTCCT
186 GTCTAGGTATGGATATGTCAGGTTCGAACATTCATTAAGTAGACTCTACCTCATCAGGAATTCCT
4296 ATTGGCTCTGTTTCTGAAAGATCTTCTTCTTTAGGATCTTATTCAAGATCTTCATCTTCTTCATG
251 ATTGGCTCTGTTTCTGAAAGATCTTCTTCTTTAGGATCTTATTCAAGATCTTCATCTTCTTCATG
4361 ATCTTCTTCTTCTTCTTCTTCAGCTTGCTGTTGAAGAATGAAATTTCCTGCTACTCGAATGAGGT
316 ATCTTCTTCTTCTTCTTCTTCAGCTTGCTGTTGAAGAATGAAATTTCCTGCTACTCGAATGAGGT
4426 CTAAAT
381 CTAAAT
4432 TA
1 TA
4434 ATTATCGCAC
Statistics
Matches: 388, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
386 2 0.01
396 386 0.99
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (386 bp):
TATGTAATTTGAAAATTCAAGCACAAAAATATATGGTTCACGAAATACTTTTTCAAGTGCATATG
TAAAAGCGTCATCTCGTATTTTCATGTATCTCCAATAAGATTGTTGCTACCATTGCATATGTTGC
ACGCAATCTATCATCTTTGACAGCTGATCTCAAAGTTCTAAGTGAGGTGACTGAGGTCTAGGTAT
GGATATGTCAGGTTCGAACATTCATTAAGTAGACTCTACCTCATCAGGAATTCCTATTGGCTCTG
TTTCTGAAAGATCTTCTTCTTTAGGATCTTATTCAAGATCTTCATCTTCTTCATGATCTTCTTCT
TCTTCTTCTTCAGCTTGCTGTTGAAGAATGAAATTTCCTGCTACTCGAATGAGGTCTAAAT
Found at i:5117 original size:26 final size:24
Alignment explanation
Indices: 5088--5147 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 24
5078 TTAATTAGTC
5088 TAAAATATTAATAATTTAAAATAAAT
1 TAAAA-ATTAATAATTT-AAATAAAT
*
5114 TAAAAAGTTAATAATTTAAATAAGT
1 TAAAAA-TTAATAATTTAAATAAAT
5139 TAAAAATTA
1 TAAAAATTA
5148 GAAAATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 3 0.09
25 14 0.44
26 15 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
TAAAAATTAATAATTTAAATAAAT
Found at i:5126 original size:16 final size:16
Alignment explanation
Indices: 5107--5152 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
5097 AATAATTTAA
5107 AATAAATTAAAAAGTT
1 AATAAATTAAAAAGTT
*
5123 AATAATTTAAATAAGTT
1 AATAAATTAAA-AAGTT
5140 AA-AAATTAGAAAA
1 AATAAATTA-AAAA
5153 TAATTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (16 bp):
AATAAATTAAAAAGTT
Found at i:5136 original size:35 final size:35
Alignment explanation
Indices: 5063--5144 Score: 87
Period size: 35 Copynumber: 2.3 Consensus size: 35
5053 TGGAAACAAG
**
5063 TAATTTAAAAAAAAATTAATTAGTCTAAAATATTAA
1 TAATTT-AAAAAAAATTAAAAAGTCTAAAATATTAA
*
5099 TAATTTAAAATAAATTAAAAAGT-TAATAAT-TTAAA
1 TAATTTAAAAAAAATTAAAAAGTCTAA-AATATT-AA
*
5134 TAAGTTAAAAA
1 TAATTTAAAAA
5145 TTAGAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 5 0.13
35 28 0.72
36 6 0.15
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.35
Consensus pattern (35 bp):
TAATTTAAAAAAAATTAAAAAGTCTAAAATATTAA
Found at i:5140 original size:17 final size:16
Alignment explanation
Indices: 5107--5146 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5097 AATAATTTAA
*
5107 AATAAATTAAAAAGTT
1 AATAATTTAAAAAGTT
5123 AATAATTTAAATAAGTT
1 AATAATTTAAA-AAGTT
*
5140 AAAAATT
1 AATAATT
5147 AGAAAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (16 bp):
AATAATTTAAAAAGTT
Found at i:5141 original size:25 final size:26
Alignment explanation
Indices: 5095--5144 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
5085 GTCTAAAATA
5095 TTAATAATTTAAAATAAATTAAAAAG
1 TTAATAATTTAAAATAAATTAAAAAG
*
5121 TTAATAATTT-AAATAAGTTAAAAA
1 TTAATAATTTAAAATAAATTAAAAA
5145 TTAGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
TTAATAATTTAAAATAAATTAAAAAG
Found at i:5620 original size:120 final size:121
Alignment explanation
Indices: 5479--5719 Score: 450
Period size: 120 Copynumber: 2.0 Consensus size: 121
5469 CACAAGGCAG
5479 CTACCATTCGCGAGCTGAAGCTGGAGCAAGGAGTGGCATGCATAACACAGGTGCAAGACTTAGTA
1 CTACCATTCGCGAGCTGAAGCTGGAGCAAGGAGTGGCATGCATAACACAGGTGCAAGACTTAGTA
*
5544 GCACGC-A-AAGGGAAACAACATGCCTGAGGTGTGCGATAGTGTGCGAGGGCGACT
66 GCACACAACAAGGGAAACAACATGCCTGAGGTGTGCGATAGTGTGCGAGGGCGACT
5598 NCTACCATTCGCGAGCTGAAGCTGGAGCAAGGAGTGGCATGCATAACACAGGTGCAAGACTTAGT
1 -CTACCATTCGCGAGCTGAAGCTGGAGCAAGGAGTGGCATGCATAACACAGGTGCAAGACTTAGT
5663 AGCACACAACAAGGGAAACAACATGCCTGAGGTGTGCGATAGTGTGCGAGGGCGACT
65 AGCACACAACAAGGGAAACAACATGCCTGAGGTGTGCGATAGTGTGCGAGGGCGACT
5720 GACGATCGCT
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
120 70 0.59
121 1 0.01
122 47 0.40
ACGTcount: A:0.30, C:0.21, G:0.32, T:0.17
Consensus pattern (121 bp):
CTACCATTCGCGAGCTGAAGCTGGAGCAAGGAGTGGCATGCATAACACAGGTGCAAGACTTAGTA
GCACACAACAAGGGAAACAACATGCCTGAGGTGTGCGATAGTGTGCGAGGGCGACT
Found at i:6450 original size:51 final size:51
Alignment explanation
Indices: 6374--6477 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
6364 CTTAAGTTCC
6374 AAACTCCTAGACAGAATTCATTTCAACATACTAATCAAGAAAACATACCCT
1 AAACTCCTAGACAGAATTCATTTCAACATACTAATCAAGAAAACATACCCT
6425 AAACTCCTAGACAGAATTCATTTCAACATACTAATCAAGAAAACATACCCT
1 AAACTCCTAGACAGAATTCATTTCAACATACTAATCAAGAAAACATACCCT
6476 AA
1 AA
6478 GTTCTTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (51 bp):
AAACTCCTAGACAGAATTCATTTCAACATACTAATCAAGAAAACATACCCT
Found at i:12272 original size:31 final size:31
Alignment explanation
Indices: 12237--12314 Score: 147
Period size: 31 Copynumber: 2.5 Consensus size: 31
12227 GTATCAATCT
12237 AAACTAAAATTAATTTGAGTTAAAAAAAATA
1 AAACTAAAATTAATTTGAGTTAAAAAAAATA
12268 AAACTAAAATTAATTTGAGTTAAAAAAAATA
1 AAACTAAAATTAATTTGAGTTAAAAAAAATA
*
12299 AAAATAAAATTAATTT
1 AAACTAAAATTAATTT
12315 CAATGCACGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (31 bp):
AAACTAAAATTAATTTGAGTTAAAAAAAATA
Found at i:17630 original size:40 final size:40
Alignment explanation
Indices: 17586--17675 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
17576 GGACCTATTC
* *
17586 TGACTTGTTTGAAAATAATTTTGA--TGTGTTAAAATGATTT
1 TGACTTGATTG-AAATAATTTTGACTTGT-TTAAAATCATTT
*
17626 TGACTTGATTGAAATTATTTTGACTTGTTTAAAATCATTT
1 TGACTTGATTGAAATAATTTTGACTTGTTTAAAATCATTT
**
17666 AAACTTGATT
1 TGACTTGATT
17676 TTAAAATTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
39 11 0.26
40 29 0.67
41 3 0.07
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (40 bp):
TGACTTGATTGAAATAATTTTGACTTGTTTAAAATCATTT
Found at i:17645 original size:20 final size:20
Alignment explanation
Indices: 17581--17675 Score: 77
Period size: 20 Copynumber: 4.8 Consensus size: 20
17571 GGCCTGGACC
* *
17581 TATTCTGACTTGTTTGAAAAT
1 TATTTTGACTTGATT-AAAAT
*
17602 AATTTTGA-TGTG-TTAAAAT
1 TATTTTGACT-TGATTAAAAT
* *
17621 GATTTTGACTTGATTGAAAT
1 TATTTTGACTTGATTAAAAT
*
17641 TATTTTGACTTGTTTAAAAT
1 TATTTTGACTTGATTAAAAT
* **
17661 CATTTAAACTTGATT
1 TATTTTGACTTGATT
17676 TTAAAATTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 14 0.23
20 38 0.63
21 8 0.13
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (20 bp):
TATTTTGACTTGATTAAAAT
Found at i:18896 original size:21 final size:22
Alignment explanation
Indices: 18848--18895 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 22
18838 AAATAATTTC
18848 AATCATGCAAATTAAACAATTAAAA
1 AATCATGCAAATTAAAC-A--AAAA
18873 AATCATGCAAATTAAACAAAAA
1 AATCATGCAAATTAAACAAAAA
18895 A
1 A
18896 TAAAAAAGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.22
24 1 0.04
25 17 0.74
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.21
Consensus pattern (22 bp):
AATCATGCAAATTAAACAAAAA
Found at i:20000 original size:222 final size:222
Alignment explanation
Indices: 19677--20121 Score: 854
Period size: 222 Copynumber: 2.0 Consensus size: 222
19667 AATAGAATAT
19677 AAATATATATGTAATAGTATACATTGAGGAAAAAAATGTTGATTCTCTTTGTATTTCGAAATGAA
1 AAATATATATGTAATAGTATACATTGAGGAAAAAAATGTTGATTCTCTTTGTATTTCGAAATGAA
*
19742 TTTGTAGGTTTTTGATTGCCGAAAATCTCAAATGCTATTTTCTCCTCTCTATTTTTCAAGTATTT
66 TTTGTAGGTTTTTGATTGCCGAAAATCTCAAATGCTATTTTCTCCTCTCCATTTTTCAAGTATTT
19807 TTTCAGTACTTTACATTTATTTTTTTTGTGTATTTATAACACTATTTTACAATCTTTTCTCGGAT
131 TTTCAGTACTTTACATTTATTTTTTTTGTGTATTTATAACACTATTTTACAATCTTTTCTCGGAT
*
19872 TTTTCGGTTCGAGATTGGGTTACGTGC
196 TTTTCGATTCGAGATTGGGTTACGTGC
19899 AAATATATATGTAATAGTATACATTGAGGAAAAAAATGTTGATTCTCTTTGTATTTCGAAATGAA
1 AAATATATATGTAATAGTATACATTGAGGAAAAAAATGTTGATTCTCTTTGTATTTCGAAATGAA
* *
19964 TTTGTAGGTTTTTGATTGCCGAAAATTTCGAATGCTATTTTCTCCTCTCCATTTTTCAAGTATTT
66 TTTGTAGGTTTTTGATTGCCGAAAATCTCAAATGCTATTTTCTCCTCTCCATTTTTCAAGTATTT
20029 TTTCAGTACTTTACATTTATTTTTTTTGTGTATTTATAACACTATTTTACAATCTTTTCTCGGAT
131 TTTCAGTACTTTACATTTATTTTTTTTGTGTATTTATAACACTATTTTACAATCTTTTCTCGGAT
20094 TTTTCGATTCGAGATTGGGTTACGTGC
196 TTTTCGATTCGAGATTGGGTTACGTGC
20121 A
1 A
20122 GATTGTGGAG
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
222 219 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (222 bp):
AAATATATATGTAATAGTATACATTGAGGAAAAAAATGTTGATTCTCTTTGTATTTCGAAATGAA
TTTGTAGGTTTTTGATTGCCGAAAATCTCAAATGCTATTTTCTCCTCTCCATTTTTCAAGTATTT
TTTCAGTACTTTACATTTATTTTTTTTGTGTATTTATAACACTATTTTACAATCTTTTCTCGGAT
TTTTCGATTCGAGATTGGGTTACGTGC
Found at i:20971 original size:101 final size:101
Alignment explanation
Indices: 20790--21032 Score: 258
Period size: 101 Copynumber: 2.4 Consensus size: 101
20780 TAATGTAGCC
* * *
20790 TCAATCCAATCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTAGATTTATCTTGCTTCACT
1 TCAATCCAACCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTAGATCTATCTTACTTCACT
* * * ** *
20855 GCAGCTTTAGGGAGATAAAGATTTGCTTTCATGA-CT
66 GCAACTTCAGAGAGATAAAGATTCACCTTCAT-ATCT
* * * * * *
20891 TTAATCCGACCCACTGTAACTTCAGGGGTATAGGATTTGGTTTTGTAGCTCCT-TCTTAC-TCTA
1 TCAATCCAACCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTAGAT-CTATCTTACTTC-A
* * *
20954 CTGTAACTTCAGAGAGATAATGATTCACCTTCGTATCT
64 CTGCAACTTCAGAGAGATAAAGATTCACCTTCATATCT
* *
20992 TCAATCCAATCCACTGTAACTTTAGGGATATAGGATTTGAT
1 TCAATCCAACCCACTGTAACTTCAGGGATATAGGATTTGAT
21033 TTCGTAACTT
Statistics
Matches: 115, Mismatches: 24, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
100 3 0.03
101 111 0.97
102 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (101 bp):
TCAATCCAACCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTAGATCTATCTTACTTCACT
GCAACTTCAGAGAGATAAAGATTCACCTTCATATCT
Found at i:21044 original size:50 final size:50
Alignment explanation
Indices: 20759--21066 Score: 130
Period size: 50 Copynumber: 6.1 Consensus size: 50
20749 TCCATTATAT
* * *
20759 CTTTAGGGATATAGGACTTG-TTAAT-GTAGCCTCAATCCAATCCACTGTAA
1 CTTTAGGGATATAGGATTTGATT--TCGTAACTTCAATCCAATCCACTGTAA
* * *** * * *
20809 CTTCAGGGATATAGGATTTGATGTT-GTAGA-TT-TATCTTGCTTCACTGCAG
1 CTTTAGGGATATAGGATTTGAT-TTCGTA-ACTTCAATC-CAATCCACTGTAA
* * * * * * * *
20859 CTTTAGGGAGATAAAGATTTGCTTTCATGACTTTAATCCGACCCACTGTAA
1 CTTTAGGGATAT-AGGATTTGATTTCGTAACTTCAATCCAATCCACTGTAA
* * * * * ** * * *
20910 CTTCAGGGGTATAGGATTTGGTTTTGTAGC-TCCTTCTTACTCTACTGTAA
1 CTTTAGGGATATAGGATTTGATTTCGTAACTTCAATC-CAATCCACTGTAA
* * * * *
20960 CTTCAGAGAGATA-ATGA-TTCACCTTCGTATCTTCAATCCAATCCACTGTAA
1 CTTTAG-G-GATATAGGATTTGA-TTTCGTAACTTCAATCCAATCCACTGTAA
* *
21011 CTTTAGGGATATAGGATTTGATTTCGTAACTTCAATCCATTCTACT-TCAA
1 CTTTAGGGATATAGGATTTGATTTCGTAACTTCAATCCAATCCACTGT-AA
21061 CTTTAG
1 CTTTAG
21067 TGGAGATCGA
Statistics
Matches: 182, Mismatches: 60, Indels: 32
0.66 0.22 0.12
Matches are distributed among these distances:
49 11 0.06
50 104 0.57
51 56 0.31
52 11 0.06
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (50 bp):
CTTTAGGGATATAGGATTTGATTTCGTAACTTCAATCCAATCCACTGTAA
Found at i:21055 original size:101 final size:100
Alignment explanation
Indices: 20790--21063 Score: 227
Period size: 101 Copynumber: 2.7 Consensus size: 100
20780 TAATGTAGCC
*
20790 TCAATCCAATCCACTGTAACTTCAGGGATATAGGATTTGATGTTGTAGA-TT-TAT-C-TTGCTT
1 TCAATCCAATCCACTGTAACTTCAGGGATATAGGATTTGAT-TTGTA-ACTTCAATCCATT-C-T
* * * ** *
20851 CACTGCAGCTTTAGGGAGATAAAGATTTGCTTTCATGACT
62 -ACTGCAACTTCAGAGAGATAAAGATTCACCTTCATGACT
* * * * * * ** * *
20891 TTAATCCGACCCACTGTAACTTCAGGGGTATAGGATTTGGTTTTGTAGC-TCCTTCTTACTCTAC
1 TCAATCCAATCCACTGTAACTTCAGGGATATAGGATTT-GATTTGTAACTTCAATC-CATTCTAC
* * *
20955 TGTAACTTCAGAGAGATAATGATTCACCTTCGT-ATCT
64 TGCAACTTCAGAGAGATAAAGATTCACCTTCATGA-CT
*
20992 TCAATCCAATCCACTGTAACTTTAGGGATATAGGATTTGATTTCGTAACTTCAATCCATTCTACT
1 TCAATCCAATCCACTGTAACTTCAGGGATATAGGATTTGATTT-GTAACTTCAATCCATTCTACT
*
21057 TCAACTT
65 GCAACTT
21064 TAGTGGAGAT
Statistics
Matches: 132, Mismatches: 32, Indels: 18
0.73 0.18 0.10
Matches are distributed among these distances:
100 6 0.05
101 117 0.89
102 7 0.05
103 1 0.01
104 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (100 bp):
TCAATCCAATCCACTGTAACTTCAGGGATATAGGATTTGATTTGTAACTTCAATCCATTCTACTG
CAACTTCAGAGAGATAAAGATTCACCTTCATGACT
Found at i:21197 original size:50 final size:50
Alignment explanation
Indices: 21143--21332 Score: 170
Period size: 50 Copynumber: 3.8 Consensus size: 50
21133 GCTTCTGTAG
* *
21143 CTTCAATATG-TCCCTCTACAGCTTTAGGAGTATAAGATTTGCCCTTGCAT
1 CTTCAATATGCT-CCTCTACAGATTTAGGAGTATAAGATTCGCCCTTGCAT
* * *
21193 CTTCAATCTGCTCCTCTACAGATTTAGGAGTATAAGATTCGCCCTTACAA
1 CTTCAATATGCTCCTCTACAGATTTAGGAGTATAAGATTCGCCCTTGCAT
* * * * * * * **
21243 CTTAAATCTACTACTCTACA-ACTTTAGGTA-TATGAGATTCGCCATTACGG
1 CTTCAATATGCTCCTCTACAGA-TTTAGG-AGTATAAGATTCGCCCTTGCAT
* * * *
21293 CTTCAATCTACTCCTCTACAGTTTTAGGTGTATAAGATTC
1 CTTCAATATGCTCCTCTACAGATTTAGGAGTATAAGATTC
21333 ATTGTTTTGT
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
49 1 0.01
50 115 0.97
51 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (50 bp):
CTTCAATATGCTCCTCTACAGATTTAGGAGTATAAGATTCGCCCTTGCAT
Found at i:29447 original size:51 final size:51
Alignment explanation
Indices: 29371--29473 Score: 163
Period size: 51 Copynumber: 2.0 Consensus size: 51
29361 TTTCAATACA
* *
29371 TGAAATGCGATTCAAAACTTTATGAATGTATGAATGCATATGCAAGAAAGG
1 TGAAATGCGATTCAAAACTCTATGAATGTATGAATGCATAAGCAAGAAAGG
*
29422 TGAAATGCG-TTGCAAAACTCTATGAATGTATGTATGCATAAGCAAGAAAGG
1 TGAAATGCGATT-CAAAACTCTATGAATGTATGAATGCATAAGCAAGAAAGG
29473 T
1 T
29474 ATTGACTGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
50 2 0.04
51 46 0.96
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (51 bp):
TGAAATGCGATTCAAAACTCTATGAATGTATGAATGCATAAGCAAGAAAGG
Found at i:42574 original size:18 final size:18
Alignment explanation
Indices: 42551--42597 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
42541 TTTGAAACAA
42551 AATAAGAGTTAAAACGAT
1 AATAAGAGTTAAAACGAT
42569 AATAAGAGTTAAAACGAT
1 AATAAGAGTTAAAACGAT
* *
42587 GATAAAAGTTA
1 AATAAGAGTTA
42598 GAAGATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (18 bp):
AATAAGAGTTAAAACGAT
Found at i:47976 original size:20 final size:20
Alignment explanation
Indices: 47921--47999 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 20
47911 GACTTGTTTG
* *
47921 AAAATCATTTTGACGTG-TT
1 AAAATCATTTTAACTTGATT
* * *
47940 AACATGATTTTGACTTGATT
1 AAAATCATTTTAACTTGATT
* * *
47960 GAAATCATTTTACCTTGTTT
1 AAAATCATTTTAACTTGATT
47980 AAAATCATTTTAACTTGATT
1 AAAATCATTTTAACTTGATT
48000 TTAAAATTGT
Statistics
Matches: 47, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
19 14 0.30
20 33 0.70
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (20 bp):
AAAATCATTTTAACTTGATT
Found at i:47990 original size:40 final size:40
Alignment explanation
Indices: 47910--47999 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 40
47900 AGAGCTATTC
* * *
47910 TGACTTGTTTGAAAATCATTTTGACGTGTTAACATGATTT
1 TGACTTGATTGAAAATCATTTTGACGTGTTAAAATCATTT
*
47950 TGACTTGATTG-AAATCATTTT-ACCTTGTTTAAAATCATTT
1 TGACTTGATTGAAAATCATTTTGA-CGTG-TTAAAATCATTT
*
47990 TAACTTGATT
1 TGACTTGATT
48000 TTAAAATTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
38 1 0.02
39 13 0.30
40 29 0.67
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (40 bp):
TGACTTGATTGAAAATCATTTTGACGTGTTAAAATCATTT
Found at i:48497 original size:36 final size:37
Alignment explanation
Indices: 48457--48544 Score: 88
Period size: 41 Copynumber: 2.3 Consensus size: 37
48447 TGATGACTGT
48457 TGTGAAAGTGAATATGGGGGTATGTTATTCATGCCATG
1 TGTGAAAGTGAATATGGGGGTATGTTATTCATGCCA-G
* * * *
48495 TGATAGTAAAGTAAATATGTGGGTGTGTTTTTCATGCCA-
1 TG-T-G-AAAGTGAATATGGGGGTATGTTATTCATGCCAG
*
48534 TGTGACAGTGA
1 TGTGAAAGTGA
48545 TTATATTGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
36 5 0.12
37 1 0.02
38 3 0.07
39 3 0.07
40 1 0.02
41 28 0.68
ACGTcount: A:0.27, C:0.08, G:0.30, T:0.35
Consensus pattern (37 bp):
TGTGAAAGTGAATATGGGGGTATGTTATTCATGCCAG
Found at i:48506 original size:41 final size:41
Alignment explanation
Indices: 48461--48538 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
48451 GACTGTTGTG
*
48461 AAAGTGAATATGGGGGTATGTTATTCATGCCATGTGATAGT
1 AAAGTAAATATGGGGGTATGTTATTCATGCCATGTGATAGT
* * *
48502 AAAGTAAATATGTGGGTGTGTTTTTCATGCCATGTGA
1 AAAGTAAATATGGGGGTATGTTATTCATGCCATGTGA
48539 CAGTGATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (41 bp):
AAAGTAAATATGGGGGTATGTTATTCATGCCATGTGATAGT
Found at i:55374 original size:17 final size:17
Alignment explanation
Indices: 55345--55378 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55335 AGGGGAAATC
55345 GAAAAGGGAATGGAAGG
1 GAAAAGGGAATGGAAGG
55362 GAAAATGGG-ATGGAAGG
1 GAAAA-GGGAATGGAAGG
55379 CTAGAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.44, C:0.00, G:0.47, T:0.09
Consensus pattern (17 bp):
GAAAAGGGAATGGAAGG
Done.