Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010806.1 Kokia drynarioides strain JFW-HI SEQ_125773, 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: 103385
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 124 characters in sequence are not A, C, G, or T
Found at i:116 original size:2 final size:2
Alignment explanation
Indices: 109--140 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
99 TCAAAAACGA
109 AT AT 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
141 CTCAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14848 original size:17 final size:18
Alignment explanation
Indices: 14816--14850 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
14806 AGGAAAAAGT
*
14816 AGTTACAAGAATATGAAA
1 AGTTACAAGAAGATGAAA
14834 AGTTA-AAGAAGATGAAA
1 AGTTACAAGAAGATGAAA
14851 GGTTGAACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.20
Consensus pattern (18 bp):
AGTTACAAGAAGATGAAA
Found at i:19519 original size:31 final size:31
Alignment explanation
Indices: 19451--19519 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
19441 ATTTGATACC
*
19451 TGAACTTGACACTTTTTCCTAATTTGGTACA
1 TGAACTTGACACTTTTTCCTAAGTTGGTACA
* ** *
19482 TAAACTTGACACTTTTTTTTAAGTTGGTACT
1 TGAACTTGACACTTTTTCCTAAGTTGGTACA
19513 TGAACTT
1 TGAACTT
19520 TTTGGGATCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (31 bp):
TGAACTTGACACTTTTTCCTAAGTTGGTACA
Found at i:19821 original size:58 final size:57
Alignment explanation
Indices: 19741--19885 Score: 168
Period size: 57 Copynumber: 2.5 Consensus size: 57
19731 AAATTGAATC
* * *
19741 TAAAAAAAA-TTAGGTACCAAATTAGGAAAAA-TGCCAAGTTCAGGTAACAAATTGGG
1 TAAAAAAAATTTAGGTACCAAATTA-AAAAAAGTACCAAGTTCAGGTAACAAATTGAG
* * *** *
19797 TCCAAAAAAATTTAGGTACCAAATTAAAAAAAGTATCAAGTTCAGGTTTTAACTTGAG
1 T-AAAAAAAATTTAGGTACCAAATTAAAAAAAGTACCAAGTTCAGGTAACAAATTGAG
*
19855 TAAAAAAAATTTAGATACCAAATTAAAAAAA
1 TAAAAAAAATTTAGGTACCAAATTAAAAAAA
19886 AAGGTCAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
56 1 0.01
57 40 0.53
58 34 0.45
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (57 bp):
TAAAAAAAATTTAGGTACCAAATTAAAAAAAGTACCAAGTTCAGGTAACAAATTGAG
Found at i:20975 original size:24 final size:24
Alignment explanation
Indices: 20947--20993 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
20937 ATCCAAACAA
20947 TAAATTTAAATTAATTTAAATTCT
1 TAAATTTAAATTAATTTAAATTCT
* *
20971 TAAATTTTAATTATTTTAAATTC
1 TAAATTTAAATTAATTTAAATTC
20994 CTAACAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATTTAAATTAATTTAAATTCT
Found at i:28044 original size:228 final size:228
Alignment explanation
Indices: 27697--28520 Score: 1055
Period size: 228 Copynumber: 3.6 Consensus size: 228
27687 TGAGGTGGAA
* * * * * *
27697 AGCTCCGACACCATCGATAATGTCAAGGCCAAGATCCAAGATAAAGAAGG-AATCCCACCAGATC
1 AGCTCGGACACCATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATTCCC-CCAGACC
* * *
27761 AACAGAGGCTT-ATCTTTGCTGGTAAGCAGCTTGAAGATGGCCGCACTCTGGCTGACTACAACAT
65 AACAGAGG-TTGATCTTTGCTGGTAAGCAACTTGAAGATGGCAGCACTCTGGCAGACTACAACAT
*
27825 TCAAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTCGTGGTGGTATGCAAATTTTTGTGAAGA
129 CCAAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTCGTGGTGGTATGCAAATTTTTGTGAAGA
* * *
27890 CTCTTACCGGAAAAACCATTACTTTGGAGGTTGAG
194 CTCTTACAGGAAAAACCATCACTTTGGAAGTTGAG
* * * * * * *
27925 AGTTCAGATACCATTGACAATGTCAAGGCTAAGATCCAGGACAAGGAGGGTATTCCCCCAGACCA
1 AGCTCGGACACCATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATTCCCCCAGACCA
* * * *
27990 GCAGAGGTTGATCTTTGCTGGCAAGCAACTTGAAGATGGCCGCACTCTGGCTGACTACAACATCC
66 ACAGAGGTTGATCTTTGCTGGTAAGCAACTTGAAGATGGCAGCACTCTGGCAGACTACAACATCC
*
28055 AAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTCGTGGTGGTATGCAGATTTTTGTGAAGACT
131 AAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTCGTGGTGGTATGCAAATTTTTGTGAAGACT
* * *
28120 CTTACAGGGAAAACCATCACCTTAGAAGTTGAG
196 CTTACAGGAAAAACCATCACTTTGGAAGTTGAG
* * * *
28153 AGCTCGGACACCATTGATAATGTGAAGGCCAAAATCCAGGACAAGGAAGGTATCCCCCCAGACCA
1 AGCTCGGACACCATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATTCCCCCAGACCA
* * * * * * *
28218 ACAGAGGTTGAT-TTTCGCAGGTAAGCAGCTTGAGGATGGCAGGACACTTGCAGACTACAACATT
66 ACAGAGGTTGATCTTT-GCTGGTAAGCAACTTGAAGATGGCAGCACTCTGGCAGACTACAACATC
* * * * *
28282 CAAAAAGAGTCGACCCTCCATTTGGTGCTTCGTCTTCGTGGTGGGATGCAAATTTTTGTGAAGAC
130 CAAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTCGTGGTGGTATGCAAATTTTTGTGAAGAC
* * *
28347 AT-TGACAGGAAAGACCATCACTTTGGAAGTTGAA
195 -TCTTACAGGAAAAACCATCACTTTGGAAGTTGAG
* * *
28381 AGCTCGGACACCATTGATAATGTGAAGGCCAAGATCCAAGATAAGGAAGGAATTCCCCCAGACCA
1 AGCTCGGACACCATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATTCCCCCAGACCA
* * * * * *
28446 GCAGAGGTTGATTTTTGCGGGGAAGCAACTTGAAGATGGAAGGAC-CTTGGCAGACTACAACATC
66 ACAGAGGTTGATCTTTGCTGGTAAGCAACTTGAAGATGGCAGCACTC-TGGCAGACTACAACATC
*
28510 CAGAAGGAATC
130 CAAAAGGAATC
28521 GACTCTGCAC
Statistics
Matches: 519, Mismatches: 71, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
227 6 0.01
228 504 0.97
229 9 0.02
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (228 bp):
AGCTCGGACACCATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATTCCCCCAGACCA
ACAGAGGTTGATCTTTGCTGGTAAGCAACTTGAAGATGGCAGCACTCTGGCAGACTACAACATCC
AAAAGGAATCCACCCTCCACTTGGTGCTTCGTCTTCGTGGTGGTATGCAAATTTTTGTGAAGACT
CTTACAGGAAAAACCATCACTTTGGAAGTTGAG
Found at i:32281 original size:228 final size:228
Alignment explanation
Indices: 31884--33250 Score: 1055
Period size: 228 Copynumber: 6.0 Consensus size: 228
31874 GACACAACAG
* * * * * *
31884 ATGCAGATCTTTGTGAAAACTCTTACTGGTAAGACCATCACCCTCGAGGTAGAAAGCTCCGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACTGGAAAGACCATCACCCTTGAGGTGGAGAGCTCTGACAC
* * *
31949 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCCCCTGACCAACAGAGGCTT-
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATCCCACCTGACCAGCAGAGG-TTA
* * * *
32013 ATCTTCGCTGGGAAACAGCTTGAGGATGGCCGTACCCTTGCTGACTACAACATCCA-AAAGGAGT
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGCAGAACCCTTGCTGACTACAACATCCAGAAA-GAGT
* *
32077 CCACCCTCCACCTT-GTCCTTCGTCTCAGAGGTGGC
194 CTACCCTCCA-CTTGGTCCTTCGTCTCAGTGGTGGC
* * * * * *
32112 ATGCAGATCTTCGTGAAAACCCTTACTGGCAAGACAATCACCCTTGAGGTTGAAAGCTCCGACAC
1 ATGCAGATCTTTGTGAAAACCCTTACTGGAAAGACCATCACCCTTGAGGTGGAGAGCTCTGACAC
* * *
32177 AATTGATAATGTCAAGGCCAAGATCCAAGACAAAGAAGGTATCCCTCCTGACCAACAGAGGCTT-
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATCCCACCTGACCAGCAGAGG-TTA
* * * *
32241 ATCTTTGCTGGTAAACAACTGGAGGATGGCCGCACCCTTGCTGACTACAACATCCAGAAAGAGTC
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGCAGAACCCTTGCTGACTACAACATCCAGAAAGAGTC
* *
32306 TACCCTCCACCTT-GTCCTTCGTCTTAGGGGTGGC
195 TACCCTCCA-CTTGGTCCTTCGTCTCAGTGGTGGC
* * * * * * *
32340 ATGCAGATCTTTGTAAAAACACTCACTGGAAAAACCATCA-CTTTAGAGGTGGAGAGTTCTGATA
1 ATGCAGATCTTTGTGAAAACCCTTACTGGAAAGACCATCACCCTT-GAGGTGGAGAGCTCTGACA
* * * * * * * *
32404 CAATTGATAACGTTAAGGCCAAGATTCAGGACAAGGAGGGCATACCACCAGACCAGCAGAGGTTA
65 CAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATCCCACCTGACCAGCAGAGGTTA
* * * * * *
32469 ATTTTTGCTGGGAAACAGCTTGAAGATGGCAGAACCCTTGCAGACTATAACATTCA-AAAGGAGT
130 ATCTTTGCTGGGAAACAGCTGGAGGATGGCAGAACCCTTGCTGACTACAACATCCAGAAA-GAGT
* * * *
32533 CTACCCTCCATTTGGT-GTTGCGTCTCCGTGGTGGT
194 CTACCCTCCACTTGGTCCTT-CGTCTCAGTGGTGGC
* * * * * * * * * * * * *
32568 ATGCAAATTTTTGTGAAGACCCTCACAGGAAAGACTATTACCATGGAAGTTGAGAGTTCTGATAC
1 ATGCAGATCTTTGTGAAAACCCTTACTGGAAAGACCATCACCCTTGAGGTGGAGAGCTCTGACAC
* * * * * * * * * *
32633 GATTGACAATGTGAAAGCTAAGATCCAGGACAAGGAAGGTATTCCACCGGATCAGCAGAGGTTGA
66 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATCCCACCTGACCAGCAGAGGTTAA
* * * * * * * * * *
32698 TTTTTGCTGGCAAGCAGCTGGAGGATGGGAGGACCCTTGCTGATTATAATATTCAGAAAGAGTCA
131 TCTTTGCTGGGAAACAGCTGGAGGATGGCAGAACCCTTGCTGACTACAACATCCAGAAAGAGTCT
* * *
32763 ACCCTCCACTTGGTGCTTCGCCTGC-GTGGTGGA
196 ACCCTCCACTTGGTCCTTCGTCT-CAGTGGTGGC
* * * *
32796 ATGCAGATATTTGTGAAAA-CTTTGACTGGTAAA-ACCATTA-CGTTGGAGGTGGAGAGCTCTGA
1 ATGCAGATCTTTGTGAAAACCCTT-ACTGG-AAAGACCATCACCCTT-GAGGTGGAGAGCTCTGA
* * * *
32858 CACGATTGATAATGTTAAGGCCAAGATCCAAGATAAGGAGGGTATCCCACCTGACCAGCAGAGGT
63 CACAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATCCCACCTGACCAGCAGAGGT
* * * * * * * * * * *
32923 TGATTTTTGC-CGGAAAGCAGCTCGAGGACGGGAGGACTCTTGCAGACTATAACATTCA-AAAGG
128 TAATCTTTGCTGGGAAA-CAGCTGGAGGATGGCAGAACCCTTGCTGACTACAACATCCAGAAA-G
* * * * * * * * *
32986 AGTCAACCCTGCATTTGGT-TTTGCGCCTTAGAGGAGGG
191 AGTCTACCCTCCACTTGGTCCTT-CGTCTCAGTGGTGGC
* * * * * * *
33024 ATGCAGATATTTGTCAAGA-CCTTGACTGGGAAA-ACCATCACCCTGGAGGTTGAGAGCTCGGAT
1 ATGCAGATCTTTGTGAAAACCCTT-ACT-GGAAAGACCATCACCCTTGAGGTGGAGAGCTCTGAC
* * * * ** * * * * * * *
33087 ACGATCGACAATGTAAAATCGAAGATTCAGGACAAGGAGGGAATTCCC-CCGGATCAGCAGAGGT
64 ACAATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTA-TCCCACCTGACCAGCAGAGGT
* * * * * * * *
33151 TGATCTTTGCTGGGAAGCAGTTGGAGGACGGTC-GAACTCTAGCTGACTACAATATCCAGAAGGA
128 TAATCTTTGCTGGGAAACAGCTGGAGGATGG-CAGAACCCTTGCTGACTACAACATCCAGAAAGA
* * * *
33215 GTCTACTCTGCATCTT-GTCCTTCGCCTCCGTGGTGG
192 GTCTACCCTCCA-CTTGGTCCTTCGTCTCAGTGGTGG
33251 TTTCTGATTT
Statistics
Matches: 936, Mismatches: 178, Indels: 50
0.80 0.15 0.04
Matches are distributed among these distances:
227 24 0.03
228 880 0.94
229 32 0.03
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (228 bp):
ATGCAGATCTTTGTGAAAACCCTTACTGGAAAGACCATCACCCTTGAGGTGGAGAGCTCTGACAC
AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGTATCCCACCTGACCAGCAGAGGTTAA
TCTTTGCTGGGAAACAGCTGGAGGATGGCAGAACCCTTGCTGACTACAACATCCAGAAAGAGTCT
ACCCTCCACTTGGTCCTTCGTCTCAGTGGTGGC
Found at i:33249 original size:456 final size:451
Alignment explanation
Indices: 31884--33250 Score: 1405
Period size: 456 Copynumber: 3.0 Consensus size: 451
31874 GACACAACAG
* * * * * *
31884 ATGCAGATCTTTGTGAAAACTCTTACTGGTAAGACCATCACCCTCGAGGTAGAAAGCTCCGACAC
1 ATGCAGATCTTTGTGAAAACT-TTACTGGTAAAACCATCACCTTAGAGGTGGAGAGCTCTGACAC
* * *
31949 AATTGATAATGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCCCCTGACCAACAGAGGCTTA
65 AATTGATAATGTTAAGGCCAAGATCCAAGACAAGG-AGGGATCCCACCTGACCAGCAGAGG-TTA
* * * * * * * *
32014 TCTTCGCTGGGAAACAGCTTGAGGATGGCCGTACCCTTGCTGACTACAACATCCAAAAGGAGTCC
128 TTTTTGCTGGGAAACAGCTTGAGGATGGCAGAACCCTTGCAGACTATAACATTCAAAAGGAGTCA
* * * * *
32079 ACCCTCCACCTT-GTCCTT-CGTCTCAGAGGTGGCATGCAGATCTTCGTGAAAACCCTTACTGGC
193 ACCCTCCA-TTTGGT-CTTGCGTCTCAGAGGTGGCATGCAGATATTTGTGAAGA-CCTTACTGGG
* * * * * * * * *
32142 AAGACAATCACCCTTGAGGTTGAAAGCTCCGACACAATTGATAATGTCAAGGCCAAGATCCAAGA
255 AAAACAATCACCCTGGAGGTTGAGAGCTCCGATACGATTGACAATGTAAAAGCCAAGATCCAGGA
* * * * * * *
32207 CAAAGAAGGTA-TCCCTCCTGACCAACAGAGGCTT-ATCTTTGCTGGTAAACAACTGGAGGATGG
320 CAAGGAAGGTATTCCC-CCGGATCAGCAGAGG-TTGATCTTTGCTGGCAAGCAGCTGGAGGATGG
* * * ** *
32270 CCGCACCCTTGCTGACTACAACATCCAGAAAGAGTCTACCCTCCACCTTGTCCTTCGTCTTAGGG
383 CCGAACCCTTGCTGACTACAATATCCAGAAAGAGTCTACCCTCCA-CTTGTCCTTCGCCTCCGTG
*
32335 GTGGC
447 GTGGA
* * * * * * *
32340 ATGCAGATCTTTGTAAAAACACTCACTGGAAAAACCATCACTTTAGAGGTGGAGAGTTCTGATAC
1 ATGCAGATCTTTGTGAAAAC-TTTACTGGTAAAACCATCACCTTAGAGGTGGAGAGCTCTGACAC
* * * * *
32405 AATTGATAACGTTAAGGCCAAGATTCAGGACAAGGAGGGCATACCACCAGACCAGCAGAGGTTAA
65 AATTGATAATGTTAAGGCCAAGATCCAAGACAAGGAGGG-ATCCCACCTGACCAGCAGAGGTT-A
* *
32470 TTTTTGCTGGGAAACAGCTTGAAGATGGCAGAACCCTTGCAGACTATAACATTCAAAAGGAGTCT
128 TTTTTGCTGGGAAACAGCTTGAGGATGGCAGAACCCTTGCAGACTATAACATTCAAAAGGAGTCA
* * * * * * * *
32535 ACCCTCCATTTGGTGTTGCGTCTCCGTGGTGGTATGCAAATTTTTGTGAAGACCCTCAC-AGGAA
193 ACCCTCCATTTGGTCTTGCGTCTCAGAGGTGGCATGCAGATATTTGTGAAGA-CCTTACTGGGAA
* * * * * * * *
32599 AGACTATTACCATGGAAGTTGAGAGTTCTGATACGATTGACAATGTGAAAGCTAAGATCCAGGAC
257 A-ACAATCACCCTGGAGGTTGAGAGCTCCGATACGATTGACAATGTAAAAGCCAAGATCCAGGAC
* * **
32664 AAGGAAGGTATTCCACCGGATCAGCAGAGGTTGATTTTTGCTGGCAAGCAGCTGGAGGATGGGAG
321 AAGGAAGGTATTCCCCCGGATCAGCAGAGGTTGATCTTTGCTGGCAAGCAGCTGGAGGATGGCCG
* * * * * * *
32729 GACCCTTGCTGATTATAATATTCAGAAAGAGTCAACCCTCCACTTGGTGCTTCGCCTGCGTGGTG
386 AACCCTTGCTGACTACAATATCCAGAAAGAGTCTACCCTCCACTT-GTCCTTCGCCTCCGTGGTG
32794 GA
450 GA
* * * *
32796 ATGCAGATATTTGTGAAAACTTTGACTGGTAAAACCATTACGTTGGAGGTGGAGAGCTCTGACAC
1 ATGCAGATCTTTGTGAAAACTTT-ACTGGTAAAACCATCACCTTAGAGGTGGAGAGCTCTGACAC
* *
32861 GATTGATAATGTTAAGGCCAAGATCCAAGATAAGGAGGGTATCCCACCTGACCAGCAGAGGTTGA
65 AATTGATAATGTTAAGGCCAAGATCCAAGACAAGGAGGG-ATCCCACCTGACCAGCAGAGGTT-A
* * * * * *
32926 TTTTTGC-CGGAAAGCAGCTCGAGGACGGGAGGACTCTTGCAGACTATAACATTCAAAAGGAGTC
128 TTTTTGCTGGGAAA-CAGCTTGAGGATGGCAGAACCCTTGCAGACTATAACATTCAAAAGGAGTC
* * * * * * *
32990 AACCCTGCATTTGGTTTTGCGCCTTAGAGGAGGGATGCAGATATTTGTCAAGACCTTGACTGGGA
192 AACCCTCCATTTGGTCTTGCGTCTCAGAGGTGGCATGCAGATATTTGTGAAGACCTT-ACTGGGA
* * * * * *
33055 AAACCATCACCCTGGAGGTTGAGAGCTCGGATACGATCGACAATGTAAAATCGAAGATTCAGGAC
256 AAACAATCACCCTGGAGGTTGAGAGCTCCGATACGATTGACAATGTAAAAGCCAAGATCCAGGAC
* * * * * *
33120 AAGGAGGGAATTCCCCCGGATCAGCAGAGGTTGATCTTTGCTGGGAAGCAGTTGGAGGACGGTCG
321 AAGGAAGGTATTCCCCCGGATCAGCAGAGGTTGATCTTTGCTGGCAAGCAGCTGGAGGATGGCCG
* * * * *
33185 AACTCTAGCTGACTACAATATCCAGAAGGAGTCTACTCTGCATCTTGTCCTTCGCCTCCGTGGTG
386 AACCCTTGCTGACTACAATATCCAGAAAGAGTCTACCCTCCA-CTTGTCCTTCGCCTCCGTGGTG
33250 G
450 G
33251 TTTCTGATTT
Statistics
Matches: 744, Mismatches: 153, Indels: 28
0.80 0.17 0.03
Matches are distributed among these distances:
455 27 0.04
456 706 0.95
457 11 0.01
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.23
Consensus pattern (451 bp):
ATGCAGATCTTTGTGAAAACTTTACTGGTAAAACCATCACCTTAGAGGTGGAGAGCTCTGACACA
ATTGATAATGTTAAGGCCAAGATCCAAGACAAGGAGGGATCCCACCTGACCAGCAGAGGTTATTT
TTGCTGGGAAACAGCTTGAGGATGGCAGAACCCTTGCAGACTATAACATTCAAAAGGAGTCAACC
CTCCATTTGGTCTTGCGTCTCAGAGGTGGCATGCAGATATTTGTGAAGACCTTACTGGGAAAACA
ATCACCCTGGAGGTTGAGAGCTCCGATACGATTGACAATGTAAAAGCCAAGATCCAGGACAAGGA
AGGTATTCCCCCGGATCAGCAGAGGTTGATCTTTGCTGGCAAGCAGCTGGAGGATGGCCGAACCC
TTGCTGACTACAATATCCAGAAAGAGTCTACCCTCCACTTGTCCTTCGCCTCCGTGGTGGA
Found at i:52726 original size:23 final size:24
Alignment explanation
Indices: 52675--52726 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
52665 TAATAAGATG
** *
52675 AATTAAAAATAAATTTTTGGTGAA
1 AATTAAAAATAAAAATTTGGTAAA
*
52699 TATTAAAAATAAAAATTT-GTAAA
1 AATTAAAAATAAAAATTTGGTAAA
52722 AATTA
1 AATTA
52727 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (24 bp):
AATTAAAAATAAAAATTTGGTAAA
Found at i:60311 original size:29 final size:31
Alignment explanation
Indices: 60279--60338 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
60269 GATTTAATGA
* *
60279 GTAATTATATACATG-AACTTTAATT-TGGT
1 GTAATTATACACATGAAACTCTAATTGTGGT
60308 GTAATTATACACATGAAACTCTAATTGTGGT
1 GTAATTATACACATGAAACTCTAATTGTGGT
60339 TCAAATGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (31 bp):
GTAATTATACACATGAAACTCTAATTGTGGT
Found at i:69290 original size:3 final size:3
Alignment explanation
Indices: 69282--69356 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
69272 GCCATCTTAC
69282 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
69330 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
69357 AGGTTTTTTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:69607 original size:137 final size:138
Alignment explanation
Indices: 69360--69628 Score: 477
Period size: 137 Copynumber: 2.0 Consensus size: 138
69350 AGAAGAAAGG
* * *
69360 TTTTTTTTTCTTAGTTTAATTTACGTAACAATTTATGTTAAATTCTTTTTTCCTTGAATCAATAT
1 TTTTTTTTTCTTAGTTTAATATACGTAAAAATTTATGTTAAATTCTTTTTTCCTTGAACCAATAT
* *
69425 CAATCAAAATGATAGAAAAATATTTATAAAATATAAAATAAAAAAGTTGAGAAACAGATAAAATC
66 CAATCAAAATGATAGAAAAATATTTAAAAAATATAAAATAAAAAAGTTGAAAAACAGATAAAATC
69490 ATAATGAA
131 ATAATGAA
69498 TTTTTTTTT-TTAGTTTAATATACGTAAAAATTTATGTTAAATTCTTTTTTCCTTGAACCAATAT
1 TTTTTTTTTCTTAGTTTAATATACGTAAAAATTTATGTTAAATTCTTTTTTCCTTGAACCAATAT
*
69562 CAATCAAAATGATAGAAAAATCTTTAAAAAATATAAAATAAAAAAGTTGAAAAACAGATAAAATC
66 CAATCAAAATGATAGAAAAATATTTAAAAAATATAAAATAAAAAAGTTGAAAAACAGATAAAATC
69627 AT
131 AT
69629 CTATAATTAA
Statistics
Matches: 125, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
137 116 0.93
138 9 0.07
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (138 bp):
TTTTTTTTTCTTAGTTTAATATACGTAAAAATTTATGTTAAATTCTTTTTTCCTTGAACCAATAT
CAATCAAAATGATAGAAAAATATTTAAAAAATATAAAATAAAAAAGTTGAAAAACAGATAAAATC
ATAATGAA
Found at i:79807 original size:34 final size:31
Alignment explanation
Indices: 79739--79805 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
79729 ATATTAAATA
* *
79739 ATCATTATTTTATTATATCCTAATCATTGTC
1 ATCATTATTTGATTATATCCTAATCATTATC
*
79770 ATCATTATTTGATTATATCCTAATCATCATC
1 ATCATTATTTGATTATATCCTAATCATTATC
79801 ATCAT
1 ATCAT
79806 CAATGCCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.48
Consensus pattern (31 bp):
ATCATTATTTGATTATATCCTAATCATTATC
Found at i:83498 original size:32 final size:32
Alignment explanation
Indices: 83417--83517 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 32
83407 TTCTAAATAG
* *
83417 TAATTAATATCTT-AAATCTATGTTTATATTAAA
1 TAATAAATAT-TTAAAAT-TATATTTATATTAAA
*
83450 -AATAAATATTTTAAATTATATTTTATATTAAA
1 TAATAAATATTTAAAATTATA-TTTATATTAAA
* * * *
83482 TGATATATA-TTAAAATTTTATTTATTTTAAA
1 TAATAAATATTTAAAATTATATTTATATTAAA
83513 TAATA
1 TAATA
83518 CTTTCATCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
31 19 0.33
32 32 0.56
33 6 0.11
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (32 bp):
TAATAAATATTTAAAATTATATTTATATTAAA
Found at i:83506 original size:31 final size:33
Alignment explanation
Indices: 83439--83517 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 33
83429 TAAATCTATG
*
83439 TTTATATTAAA-AATAAATATTTTAAATTATAT
1 TTTATATTAAATAATAAATATTTAAAATTATAT
* * *
83471 TTTATATTAAATGATATATA-TTAAAATTTTA-
1 TTTATATTAAATAATAAATATTTAAAATTATAT
*
83502 TTTATTTTAAATAATA
1 TTTATATTAAATAATA
83518 CTTTCATCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 14 0.35
32 20 0.50
33 6 0.15
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (33 bp):
TTTATATTAAATAATAAATATTTAAAATTATAT
Found at i:95063 original size:23 final size:21
Alignment explanation
Indices: 95014--95063 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
95004 ATTTATAGAT
95014 GATTTTATCTGTTTTTTCAAA
1 GATTTTATCTGTTTTTTCAAA
** *
95035 TTTTTTATTTTGTATTTTTCAAA
1 GATTTTA-TCTGT-TTTTTCAAA
95058 GATTTT
1 GATTTT
95064 TCAATCATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 5 0.23
22 4 0.18
23 13 0.59
ACGTcount: A:0.22, C:0.06, G:0.08, T:0.64
Consensus pattern (21 bp):
GATTTTATCTGTTTTTTCAAA
Found at i:95526 original size:37 final size:37
Alignment explanation
Indices: 95484--95554 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
95474 TGAAAATCAT
* *
95484 AAAAATTGAGTCTCCTTTATGCAAGTGAACGTAACTA
1 AAAAATCGAGTCTCCGTTATGCAAGTGAACGTAACTA
*
95521 AAAAATCGAGTTTCCGTTATGCAAGTGAACGTAA
1 AAAAATCGAGTCTCCGTTATGCAAGTGAACGTAA
95555 GTGTTTTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (37 bp):
AAAAATCGAGTCTCCGTTATGCAAGTGAACGTAACTA
Found at i:101856 original size:259 final size:259
Alignment explanation
Indices: 101148--101930 Score: 1334
Period size: 259 Copynumber: 3.0 Consensus size: 259
101138 GAAAATAGTA
* *
101148 TGCAAGGGGACGGTAAGTGGCATGGCCTCTCACCAGGAATGTAAAATGGAATATGTGCAATCATT
1 TGCAAAGGGAGGGTAAGTGGCATGGCCTCTCACCAGGAATGTAAAATGGAATATGTGCAATCATT
* **
101213 TTTGTGCCTCCATCAATTCAGTTGATGGTGCCTGGTTTGTGTGGGTGCCCATGTGAAGGCCGAAA
66 TTTGTGCCTCCATCATTTCAGTTGATGGTGCCTAATTTGTGTGGGTGCCCATGTGAAGGCCGAAA
* * * * * * *
101278 AGACCTCAAGACAGACAAACAAAAAGTGGGGTCATACATTAATCCCAAATAATCACGAGCTTATC
131 AGATCTCAAGACAGACAAACAGAAAGCGGGGTCATCCATTAATCTCAAATAATCATGAGCTTGTC
* *
101343 TTCAAACCCTTAAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
196 TCCAAACCCTTGAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
* * *
101407 TGCAAGGGGAGAGTAAGTGGCATGGCCTCTCACCTGGAATGTAAAATGGAATATGTGCAATCA-T
1 TGCAAAGGGAGGGTAAGTGGCATGGCCTCTCACCAGGAATGTAAAATGGAATATGTGCAATCATT
* *
101471 TTTCTGCCTCCATCATTTCAGTTGATGGTGCCTAATTTGTGTGGGTGCCCATGTGAAGGCCGGAA
66 TTTGTGCCTCCATCATTTCAGTTGATGGTGCCTAATTTGTGTGGGTGCCCATGTGAAGGCCGAAA
101536 AGATCTCAAGACAGACAAACAGAAAGCGGGGTCATCCATTAATCTCAAATAATCATGAGCTTGTC
131 AGATCTCAAGACAGACAAACAGAAAGCGGGGTCATCCATTAATCTCAAATAATCATGAGCTTGTC
101601 TCCAAACCCTTGAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
196 TCCAAACCCTTGAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
*
101665 TGCAAAGGGAGGGTAAGTGGCATGACCTCTCACCAGGAATGTAAAATGGAATATGTGCAATCATT
1 TGCAAAGGGAGGGTAAGTGGCATGGCCTCTCACCAGGAATGTAAAATGGAATATGTGCAATCATT
* *
101730 TTTGTGCCTCCATCATTTCAGTTGATGGTGCCTAATTTGTGTGGGTACCCATGTGAAGGCCGTAA
66 TTTGTGCCTCCATCATTTCAGTTGATGGTGCCTAATTTGTGTGGGTGCCCATGTGAAGGCCGAAA
* *
101795 AGATCTCAAGACAGACAAATAGAAAGCAGGGTCATCCATTAATCTCAAATAATCATGAGCTTGTC
131 AGATCTCAAGACAGACAAACAGAAAGCGGGGTCATCCATTAATCTCAAATAATCATGAGCTTGTC
101860 TCCAAACCCTTGAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
196 TCCAAACCCTTGAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
*
101924 TGAAAAG
1 TGCAAAG
101931 CAACATTAGT
Statistics
Matches: 496, Mismatches: 27, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
258 240 0.48
259 256 0.52
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (259 bp):
TGCAAAGGGAGGGTAAGTGGCATGGCCTCTCACCAGGAATGTAAAATGGAATATGTGCAATCATT
TTTGTGCCTCCATCATTTCAGTTGATGGTGCCTAATTTGTGTGGGTGCCCATGTGAAGGCCGAAA
AGATCTCAAGACAGACAAACAGAAAGCGGGGTCATCCATTAATCTCAAATAATCATGAGCTTGTC
TCCAAACCCTTGAATCCGATATTTGAGATCGAGCAACTTGAATATGAGAACAAAGAATTCTTAG
Done.