Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009763.1 Kokia drynarioides strain JFW-HI SEQ_124482, 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: 130903
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:4700 original size:25 final size:25
Alignment explanation
Indices: 4664--4717 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
4654 AAACACATTG
4664 TTTT-ATTAAAACTAAAACTCCCCA
1 TTTTGATTAAAACTAAAACTCCCCA
* *
4688 TTTTGATTAAAACTTAAACTTCCCA
1 TTTTGATTAAAACTAAAACTCCCCA
4713 TTTTG
1 TTTTG
4718 CTTATATCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (25 bp):
TTTTGATTAAAACTAAAACTCCCCA
Found at i:5681 original size:10 final size:10
Alignment explanation
Indices: 5666--5690 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5656 AGATTAGGTT
5666 GGTGGGGGGA
1 GGTGGGGGGA
5676 GGTGGGGGGA
1 GGTGGGGGGA
5686 GGTGG
1 GGTGG
5691 ATGCTGGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.80, T:0.12
Consensus pattern (10 bp):
GGTGGGGGGA
Found at i:9950 original size:27 final size:27
Alignment explanation
Indices: 9843--9996 Score: 120
Period size: 27 Copynumber: 5.7 Consensus size: 27
9833 AACGCCAAAA
*
9843 AAATGGAAGCCTTTGTGGCAATTTATG
1 AAATGGAAGCCTTTGTGGCAAATTATG
* ** *
9870 AAATGGAAGCATCAGT-G-ATAGTCTATG
1 AAATGGAAGCCTTTGTGGCA-AAT-TATG
* * * *
9897 AAATGGAAACCTTTATAGC-AGTCTATG
1 AAATGGAAGCCTTTGTGGCAAAT-TATG
9924 AAATGGAAGCCTTTGTGGCAAATTATG
1 AAATGGAAGCCTTTGTGGCAAATTATG
* *
9951 AAA-GGAATGCCTTCGTGGTAAATTATG
1 AAATGGAA-GCCTTTGTGGCAAATTATG
*
9978 AAA-GGAATGCCTTCGTGGC
1 AAATGGAA-GCCTTTGTGGC
9997 GCACTCTAAG
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
25 1 0.01
26 7 0.07
27 94 0.90
28 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (27 bp):
AAATGGAAGCCTTTGTGGCAAATTATG
Found at i:12219 original size:36 final size:36
Alignment explanation
Indices: 12177--12277 Score: 175
Period size: 36 Copynumber: 2.8 Consensus size: 36
12167 TAGTAACAAG
12177 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
*
12213 CATGACCTTTGAGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
* *
12249 CATGACCTTCGGGTCAATAGGGAGTAAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAAA
12278 CGAATATTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.35, C:0.17, G:0.27, T:0.22
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
Found at i:14338 original size:51 final size:51
Alignment explanation
Indices: 14254--14434 Score: 274
Period size: 51 Copynumber: 3.5 Consensus size: 51
14244 TAAACGAAAG
* * *
14254 GGTCCGATGACTAAGTGTCGTCGTGAGCAAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAT
* *
14305 GGTCCGATGATTAAGTGTCATCATGAGTGAATGAATCCTTTATGGATTAAT
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAT
*
14356 GGTTCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAAT
1 GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATT-AAT
* *
14408 -ATCCGATGACTAAGTGTCATCGTGAGT
1 GGTCCGATGACTAAGTGTCATCATGAGT
14435 TTATGGATTC
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 115 0.97
52 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTATGGATTAAT
Found at i:21498 original size:26 final size:26
Alignment explanation
Indices: 21408--21513 Score: 106
Period size: 26 Copynumber: 4.1 Consensus size: 26
21398 TTACTACTAA
*
21408 TGTCGTTGTATGAGCATGTCCAGAAT
1 TGTCGTTGTATGAACATGTCCAGAAT
* *
21434 TGTTGTTGTA-GAAACTTGTCCAGAAT
1 TGTCGTTGTATG-AACATGTCCAGAAT
* ** * *
21460 TATCACTGCATGAACATGTCCAGAGT
1 TGTCGTTGTATGAACATGTCCAGAAT
* *
21486 TGTCGTTGTATGAGCATGTCTAGAAT
1 TGTCGTTGTATGAACATGTCCAGAAT
21512 TG
1 TG
21514 AGCCCAGAAT
Statistics
Matches: 61, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
25 1 0.02
26 59 0.97
27 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (26 bp):
TGTCGTTGTATGAACATGTCCAGAAT
Found at i:25640 original size:36 final size:36
Alignment explanation
Indices: 25593--25693 Score: 175
Period size: 36 Copynumber: 2.8 Consensus size: 36
25583 TGGTAACATG
25593 CATGACCTTTGGGTCAACAGGGAGTAAAATAAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATAAGCAT
*
25629 CATGACCTTTGGGTCAACAGGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAATAAGCAT
* *
25665 CATGGCCTTTGGGTCAATAGGGAGTAAAA
1 CATGACCTTTGGGTCAACAGGGAGTAAAA
25694 CGAATAACGA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAATAAGCAT
Found at i:33690 original size:37 final size:37
Alignment explanation
Indices: 33640--33714 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
33630 AAATCCATCA
* *
33640 TCGTTTAAGAAGAAATAAAGAGTACAACGAAGCTTAC
1 TCGTTTAAGAAGAAATAAAGAGTACAACAAAACTTAC
*
33677 TCGTTTAAGAAGAATTAAAGAGTACAACAAAACTTAC
1 TCGTTTAAGAAGAAATAAAGAGTACAACAAAACTTAC
33714 T
1 T
33715 ATCTCTAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (37 bp):
TCGTTTAAGAAGAAATAAAGAGTACAACAAAACTTAC
Found at i:36165 original size:16 final size:16
Alignment explanation
Indices: 36144--36174 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36134 ATAATTTGAA
36144 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
36160 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
36175 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:37153 original size:38 final size:36
Alignment explanation
Indices: 37089--37159 Score: 97
Period size: 38 Copynumber: 1.9 Consensus size: 36
37079 ATTTATGCAA
**
37089 CGATAGTTTTGGCGTAATCTCGAGGTGCTCATGTGG
1 CGATAGTTTTGGCGTAATCTAAAGGTGCTCATGTGG
*
37125 CGATAGTTTTTGGGCGTAATCTAAAGGTGTTCATG
1 CGATAG-TTTT-GGCGTAATCTAAAGGTGCTCATG
37160 CGACGACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 6 0.20
37 4 0.13
38 20 0.67
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (36 bp):
CGATAGTTTTGGCGTAATCTAAAGGTGCTCATGTGG
Found at i:40268 original size:15 final size:12
Alignment explanation
Indices: 40253--40282 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40243 AGAAAAAGAA
*
40253 GAAGAAGGAAAG
1 GAAGAAGGGAAG
40265 GAAGAAGGGAAG
1 GAAGAAGGGAAG
40277 GAAGAA
1 GAAGAA
40283 ACTAAACCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (12 bp):
GAAGAAGGGAAG
Found at i:45887 original size:16 final size:16
Alignment explanation
Indices: 45866--45896 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45856 TTGTGGATCC
45866 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
45882 CATTTTATCTTTATT
1 CATTTTACCTTTATT
45897 TTCACAATAT
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:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:64420 original size:20 final size:20
Alignment explanation
Indices: 64392--64436 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
64382 AGTCAACGGG
*
64392 TTCGAGTTGAGCC-GATTCGA
1 TTCGGGTTGAGCCAG-TTCGA
*
64412 TTCGGGTTGGGCCAGTTCGA
1 TTCGGGTTGAGCCAGTTCGA
64432 TTCGG
1 TTCGG
64437 TTTGGGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.13, C:0.20, G:0.36, T:0.31
Consensus pattern (20 bp):
TTCGGGTTGAGCCAGTTCGA
Found at i:67158 original size:19 final size:20
Alignment explanation
Indices: 67131--67168 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
67121 ACATGATTTC
*
67131 TTATTTTAT-ATGAGTTTTT
1 TTATGTTATCATGAGTTTTT
*
67150 TTATGTTATCTTGAGTTTT
1 TTATGTTATCATGAGTTTT
67169 GGAATGCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.18, C:0.03, G:0.13, T:0.66
Consensus pattern (20 bp):
TTATGTTATCATGAGTTTTT
Found at i:68820 original size:22 final size:21
Alignment explanation
Indices: 68776--68820 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
68766 CACCCACAAA
* *
68776 CCAATGGTCAAACTAAAGTAT
1 CCAATGGTCAAACAAAAGCAT
*
68797 CCAATTGTCAAATCAAAAGCAT
1 CCAATGGTCAAA-CAAAAGCAT
68819 CC
1 CC
68821 TTGAGAAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.22
Consensus pattern (21 bp):
CCAATGGTCAAACAAAAGCAT
Found at i:71454 original size:19 final size:19
Alignment explanation
Indices: 71426--71464 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
71416 TTACAAGCAG
71426 CATTGAGGAGATTCATCCT
1 CATTGAGGAGATTCATCCT
*
71445 CATTGTGGAGATTCATCCT
1 CATTGAGGAGATTCATCCT
71464 C
1 C
71465 TTGCCATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (19 bp):
CATTGAGGAGATTCATCCT
Found at i:72226 original size:10 final size:9
Alignment explanation
Indices: 72213--72237 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
72203 AACAAAATCG
72213 AAAAAAATA
1 AAAAAAATA
72222 AAAAAAATA
1 AAAAAAATA
72231 AAAAAAA
1 AAAAAAA
72238 CATTTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:73765 original size:30 final size:30
Alignment explanation
Indices: 73729--73785 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
73719 TAGGTCCCTG
*
73729 AATTTTTTAAAAATAATATTTTGACCCGTA
1 AATTTTTTAAAAATAATATTTTAACCCGTA
* *
73759 AATTTTTTAGAAATTATATTTTAACCC
1 AATTTTTTAAAAATAATATTTTAACCC
73786 CCAAACTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.46
Consensus pattern (30 bp):
AATTTTTTAAAAATAATATTTTAACCCGTA
Found at i:73808 original size:30 final size:30
Alignment explanation
Indices: 73769--73910 Score: 155
Period size: 30 Copynumber: 4.8 Consensus size: 30
73759 AATTTTTTAG
*
73769 AAATTATATTTTAACCCCCAAACTTCTCCA
1 AAATTATATTTTAACCCCCAAACTTTTCCA
* * *
73799 AAATCATATTTTAA-CACTAAACTTTTCCA
1 AAATTATATTTTAACCCCCAAACTTTTCCA
* * *
73828 AAATTACATTTTAACCCCTAAACTTTCCCA
1 AAATTATATTTTAACCCCCAAACTTTTCCA
* **
73858 AAATTACATTGTT-ACCTTCAAACTTTTCCA
1 AAATTATATT-TTAACCCCCAAACTTTTCCA
*
73888 AAATTATATTTTGA-CCCCAAACT
1 AAATTATATTTTAACCCCCAAACT
73911 CTCTGAAACT
Statistics
Matches: 94, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
29 33 0.35
30 59 0.63
31 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.36
Consensus pattern (30 bp):
AAATTATATTTTAACCCCCAAACTTTTCCA
Found at i:73840 original size:59 final size:60
Alignment explanation
Indices: 73769--73910 Score: 177
Period size: 59 Copynumber: 2.4 Consensus size: 60
73759 AATTTTTTAG
*
73769 AAATTATATTTTAACCCCCAAAC-TTCTCCAAAATCATATT-TTAACAC-T-AAACTTTTCCA
1 AAATTATATTTTAACCCCCAAACTTTC-CCAAAATCACATTGTT-AC-CTTCAAACTTTTCCA
* * *
73828 AAATTACATTTTAACCCCTAAACTTTCCCAAAATTACATTGTTACCTTCAAACTTTTCCA
1 AAATTATATTTTAACCCCCAAACTTTCCCAAAATCACATTGTTACCTTCAAACTTTTCCA
*
73888 AAATTATATTTTGA-CCCCAAACT
1 AAATTATATTTTAACCCCCAAACT
73911 CTCTGAAACT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
58 1 0.01
59 43 0.60
60 28 0.39
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.36
Consensus pattern (60 bp):
AAATTATATTTTAACCCCCAAACTTTCCCAAAATCACATTGTTACCTTCAAACTTTTCCA
Found at i:86772 original size:15 final size:15
Alignment explanation
Indices: 86752--86780 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
86742 CTAGCTGAAG
86752 GAAAAGGAAGAAGAA
1 GAAAAGGAAGAAGAA
86767 GAAAAGGAAGAAGA
1 GAAAAGGAAGAAGA
86781 GAATAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
GAAAAGGAAGAAGAA
Found at i:88413 original size:26 final size:26
Alignment explanation
Indices: 88384--88436 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
88374 TTGAATGAGT
88384 AAACTCAAGCTGAATTTACATATGGA
1 AAACTCAAGCTGAATTTACATATGGA
88410 AAACTCAAGCTGAATTTACATATGGA
1 AAACTCAAGCTGAATTTACATATGGA
88436 A
1 A
88437 GCACCAACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.26
Consensus pattern (26 bp):
AAACTCAAGCTGAATTTACATATGGA
Found at i:93244 original size:203 final size:206
Alignment explanation
Indices: 92890--93331 Score: 629
Period size: 203 Copynumber: 2.1 Consensus size: 206
92880 ATTCCCGATA
* * *
92890 TTCCCGATGAGATACAGAAAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATT
1 TTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATT
* ** * *
92955 AAATCAATGAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAAATCAATGAAGCAAAG
66 AAATCAATGAAACGGTCATCTTCCAAATGAGATACAAAGAAGTAAACCAAATCAATAAAGCAAAG
*
93020 CTCAATGTAAGGGAAACTTCAAACCCC-ACCTTCC-T-GATACAGAGAAATGGGTCAAAGCAATA
131 CTCAATGCAAGGGAAACTTCAAACCCCTACCTTCCATAGATACAGAGAAATGGGTCAAAGCAATA
93082 AAGAGGTAATC
196 AAGAGGTAATC
* *
93093 TTCCTGATGAGATACAGAGAAGTAAACCAAATCCGTCTTCCTGATGAGATATAGAGAAGTGGATT
1 TTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATT
* *
93158 AAATCAATGAAACGGTCATCTTCCAAATGAGATACAAAGAAGTAGACCAAATTAATAAAGCAAAG
66 AAATCAATGAAACGGTCATCTTCCAAATGAGATACAAAGAAGTAAACCAAATCAATAAAGCAAAG
* * * * * * *
93223 TTCAATGCGAGTGAAACTTCAAACCCCTATCTTCCTGATGAGATACAGAGAAGTGGGTCGAAGTA
131 CTCAATGCAAGGGAAACTTCAAACCCCTACCTTCC--AT-AGATACAGAGAAATGGGTCAAAGCA
* *
93288 ATAAAGCGGTCATC
193 ATAAAGAGGTAATC
*
93302 TTCCTGATAAGATACAGAGAAGTAGACCAA
1 TTCCTGATGAGATACAGAGAAGTAGACCAA
93332 GAAATGAAGC
Statistics
Matches: 209, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
203 141 0.67
204 6 0.03
207 1 0.00
209 61 0.29
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (206 bp):
TTCCTGATGAGATACAGAGAAGTAGACCAAATCCGTCTTCCTGATGAGATACAGAGAAGTGGATT
AAATCAATGAAACGGTCATCTTCCAAATGAGATACAAAGAAGTAAACCAAATCAATAAAGCAAAG
CTCAATGCAAGGGAAACTTCAAACCCCTACCTTCCATAGATACAGAGAAATGGGTCAAAGCAATA
AAGAGGTAATC
Found at i:94566 original size:12 final size:12
Alignment explanation
Indices: 94549--94573 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94539 TTAGGATTTG
94549 TAAAATCTAGTT
1 TAAAATCTAGTT
94561 TAAAATCTAGTT
1 TAAAATCTAGTT
94573 T
1 T
94574 TACTTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TAAAATCTAGTT
Found at i:95316 original size:30 final size:29
Alignment explanation
Indices: 95292--95720 Score: 327
Period size: 30 Copynumber: 14.5 Consensus size: 29
95282 CAAAAATAAT
* *
95292 ATTTTGACCCATAAACTTTCC-AAAAACTAG
1 ATTTTGACCC-TAAACTTTCCTAAAATC-AC
* * *
95322 AATTTGATCCCCAAACTTTTCC-AAAACCAC
1 ATTTTGA-CCCTAAAC-TTTCCTAAAATCAC
*
95352 ATTTTGA-CCTAAACTTTTCC-AAAATAAC
1 ATTTTGACCCTAAAC-TTTCCTAAAATCAC
* ***
95380 ATTTTGACCCAAAACTTATCC-AAAATTTT
1 ATTTTGACCCTAAACTT-TCCTAAAATCAC
* * *
95409 AGTTTGATCCTTAAACTTTCCCAAAATCAC
1 ATTTTGA-CCCTAAACTTTCCTAAAATCAC
* * *
95439 ATTTTAAACCCTAAACTTTCTTAAAATTAC
1 ATTTT-GACCCTAAACTTTCCTAAAATCAC
* *
95469 ATTTTAACCCTTAAACTTTTCC-AAAATTAC
1 ATTTTGACCC-TAAAC-TTTCCTAAAATCAC
* * *
95499 ATTTTGATCCTCAATTTTCCTAAAATCAC
1 ATTTTGACCCTAAACTTTCCTAAAATCAC
* *
95528 ATTTTAACACTTAAACTTTCCTAAAATCAC
1 ATTTTGAC-CCTAAACTTTCCTAAAATCAC
*
95558 ATTTTAACCCTTAAACTTTCCTAAAATCAC
1 ATTTTGACCC-TAAACTTTCCTAAAATCAC
*
95588 ATTTTGACCCCTAAA-TTTCTCTAAAATCAA
1 ATTTTGA-CCCTAAACTTTC-CTAAAATCAC
* * *
95618 ATTTTAACCCTAAACATTCCTAAAATCAT
1 ATTTTGACCCTAAACTTTCCTAAAATCAC
* * * *
95647 ATTTTAACCCCTAACCTTTCCTAAAATTAAA
1 ATTTTGA-CCCTAAACTTTCCTAAAA-TCAC
*
95678 ATTTT-ACCCCTAAACTTTTCC-AAAATTAC
1 ATTTTGA-CCCTAAAC-TTTCCTAAAATCAC
*
95707 ATTTTTACCCTAAA
1 ATTTTGACCCTAAA
95721 TTCTCTAAAA
Statistics
Matches: 332, Mismatches: 48, Indels: 39
0.79 0.11 0.09
Matches are distributed among these distances:
28 32 0.10
29 86 0.26
30 181 0.55
31 33 0.10
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (29 bp):
ATTTTGACCCTAAACTTTCCTAAAATCAC
Found at i:95518 original size:89 final size:89
Alignment explanation
Indices: 95292--95720 Score: 387
Period size: 89 Copynumber: 4.8 Consensus size: 89
95282 CAAAAATAAT
* * * * * * *
95292 ATTTTGACCCATAAACTTTCCAAAAACTAGAATTTGATCCCCAAACTTTT-CCAAAACCACATTT
1 ATTTTAACCCTTAAACTTTCCTAAAATTACATTTTGATCCCCAAA-TTTTCCCAAAATCACATTT
* *
95356 TGA-CCTAAACTTTTCC-AAAATAAC
65 TAACCCTAAAC-TTTCCTAAAATCAC
* * ** * ** *
95380 ATTTTGACCC-AAAACTTATCC-AAAATTTTAGTTTGATCCTTAAACTTTCCCAAAATCACATTT
1 ATTTTAACCCTTAAACTT-TCCTAAAATTACATTTTGATCCCCAAATTTTCCCAAAATCACATTT
* *
95443 TAAACCCTAAACTTTCTTAAAATTAC
65 T-AACCCTAAACTTTCCTAAAATCAC
* *
95469 ATTTTAACCCTTAAACTTTTCC-AAAATTACATTTTGATCCTC-AATTTTCCTAAAATCACATTT
1 ATTTTAACCCTTAAAC-TTTCCTAAAATTACATTTTGATCCCCAAATTTTCCCAAAATCACATTT
*
95532 TAACACTTAAACTTTCCTAAAATCAC
65 TAAC-CCTAAACTTTCCTAAAATCAC
* * *
95558 ATTTTAACCCTTAAACTTTCCTAAAATCACATTTTGA-CCCCTAAA-TTTCTCTAAAATCAAATT
1 ATTTTAACCCTTAAACTTTCCTAAAATTACATTTTGATCCCC-AAATTTTC-CCAAAATCACATT
* *
95621 TTAACCCTAAACATTCCTAAAATCAT
64 TTAACCCTAAACTTTCCTAAAATCAC
* * * *
95647 ATTTTAACCCCTAACCTTTCCTAAAATTAAAATTTT-A-CCCCTAAACTTTT-CCAAAATTACAT
1 ATTTTAACCCTTAAACTTTCCTAAAATT-ACATTTTGATCCCC-AAA-TTTTCCCAAAATCACAT
*
95709 TTTTACCCTAAA
63 TTTAACCCTAAA
95721 TTCTCTAAAA
Statistics
Matches: 289, Mismatches: 37, Indels: 29
0.81 0.10 0.08
Matches are distributed among these distances:
86 3 0.01
87 37 0.13
88 29 0.10
89 167 0.58
90 48 0.17
91 5 0.02
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.36
Consensus pattern (89 bp):
ATTTTAACCCTTAAACTTTCCTAAAATTACATTTTGATCCCCAAATTTTCCCAAAATCACATTTT
AACCCTAAACTTTCCTAAAATCAC
Found at i:95524 original size:119 final size:119
Alignment explanation
Indices: 95334--95720 Score: 321
Period size: 119 Copynumber: 3.3 Consensus size: 119
95324 TTTGATCCCC
* *
95334 AAACTTTTCC-AAAACCACATTTTGA--CCTAAACTTTTCCAAAATAACATTTTGACCCAAAACT
1 AAAC-TTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATAACATTTTGACCCAAAACT
*** *
95396 TATCCAAAATTTTAGTTTGATC-CTTAAACTTTCCCAAAATCACATTTTAAACCC-T
65 TATCCAAAATCACA-TTTGAACACTTAAACTTTCCCAAAATCACATTTT-AACCCTT
* * * * * **
95451 AAACTTTCTTAAAATTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTGATCCTCAA-TT
1 AAACTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATAACATTTTGACCCAAAACTT
* * *
95515 TTCCTAAAATCACATTTTAACACTTAAACTTTCCTAAAATCACATTTTAACCCTT
66 ATCC-AAAATCACATTTGAACACTTAAACTTTCCCAAAATCACATTTTAACCCTT
* * * *
95570 AAACTTTCCTAAAATCACATTTTGACCCCTAAA-TTTCTCTAAAATCAA-ATTTTAACCCTAAAC
1 AAACTTTCCTAAAATCACATTTTAACCCCTAAACTTT-TCCAAAAT-AACATTTTGACCCAAAAC
* * * * * * * * * *
95633 AT-TCCTAAAATCATATTTTAACCCCTAACCTTTCCTAAAATTAAAATTTT-ACCCCT
64 TTATCC-AAAATCACATTTGAACACTTAAACTTTCCCAAAA-TCACATTTTAACCCTT
* *
95689 AAACTTTTCC-AAAATTACATTTTTA-CCCTAAA
1 AAAC-TTTCCTAAAATCACATTTTAACCCCTAAA
95721 TTCTCTAAAA
Statistics
Matches: 224, Mismatches: 35, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
116 4 0.02
117 16 0.07
118 25 0.11
119 165 0.74
120 14 0.06
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (119 bp):
AAACTTTCCTAAAATCACATTTTAACCCCTAAACTTTTCCAAAATAACATTTTGACCCAAAACTT
ATCCAAAATCACATTTGAACACTTAAACTTTCCCAAAATCACATTTTAACCCTT
Found at i:102495 original size:22 final size:22
Alignment explanation
Indices: 102470--102511 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
102460 ATTATGTATT
*
102470 TAGTATAAGTTTTTTTTTTAAA
1 TAGTATAAGTTTATTTTTTAAA
*
102492 TAGTATAGGTTTATTTTTTA
1 TAGTATAAGTTTATTTTTTA
102512 TTGTGTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.60
Consensus pattern (22 bp):
TAGTATAAGTTTATTTTTTAAA
Found at i:106998 original size:229 final size:228
Alignment explanation
Indices: 106669--107128 Score: 893
Period size: 229 Copynumber: 2.0 Consensus size: 228
106659 TTTTTGCTTT
*
106669 AAAGTAGGTTTTAAAAATTTATCACCAACTTATATGTTTTCATTTTTTTTTTTCAGATGTTTTCT
1 AAAGTAGGTTTTAAAAATTTATCACAAACTTATATGTTTTCATTTTTTTTTTTCAGATGTTTTCT
106734 TATATTTTTTAAAAACAATGTAAGTTTGAACATTATAAATTCAAGTAGTGTGATTGTCTAAAAGA
66 TATATTTTTTAAAAACAATGTAAGTTTGAACATTATAAATTCAAGTAGTGTGATTGTCTAAAAGA
106799 AATACACTATTTATAACAATTGTTTAAAAAAAATTATGACCTTTGATTGCCTCCGGACGTATCAA
131 AATACACTATTTATAACAATTGTTTAAAAAAAATTATGACCTTTGATTGCCTCCGGACGTATCAA
106864 CGTCCAGAATAAGAATACTGCACAAAAGATATG
196 CGTCCAGAATAAGAATACTGCACAAAAGATATG
106897 AAAGTAGGTTTTAAAAATTTATCACAAACTTATATGTTTTCATTTTTTTTTTTTCAGATGTTTTC
1 AAAGTAGGTTTTAAAAATTTATCACAAACTTATATGTTTTCA-TTTTTTTTTTTCAGATGTTTTC
*
106962 TTATATTTTTTAAAAACAATGTAAGTTTGAACATTATAAATTCAGGTAGTGTGATTGTCTAAAAG
65 TTATATTTTTTAAAAACAATGTAAGTTTGAACATTATAAATTCAAGTAGTGTGATTGTCTAAAAG
107027 AAATACACTATTTATAACAATTGTTTAAAAAAAATTATGACCTTTGATTGCCTCCGGACGTATCA
130 AAATACACTATTTATAACAATTGTTTAAAAAAAATTATGACCTTTGATTGCCTCCGGACGTATCA
107092 ACGTCCAGAATAAGAATACTGCACAAAAGATATG
195 ACGTCCAGAATAAGAATACTGCACAAAAGATATG
107126 AAA
1 AAA
107129 TAAAATGGTG
Statistics
Matches: 229, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
228 41 0.18
229 188 0.82
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (228 bp):
AAAGTAGGTTTTAAAAATTTATCACAAACTTATATGTTTTCATTTTTTTTTTTCAGATGTTTTCT
TATATTTTTTAAAAACAATGTAAGTTTGAACATTATAAATTCAAGTAGTGTGATTGTCTAAAAGA
AATACACTATTTATAACAATTGTTTAAAAAAAATTATGACCTTTGATTGCCTCCGGACGTATCAA
CGTCCAGAATAAGAATACTGCACAAAAGATATG
Found at i:108494 original size:314 final size:314
Alignment explanation
Indices: 107917--108540 Score: 899
Period size: 314 Copynumber: 2.0 Consensus size: 314
107907 AACTAAAAAG
*
107917 AAATCTAAAACCTAAGTAAAGGGAAAAACTAAAAACTAAAACGTACAAAGAAAACAAAATTTTCA
1 AAATCCAAAACCTAAGTAAAGGGAAAAACTAAAAACTAAAACGTACAAAGAAAACAAAATTTTCA
* *
107982 AAAACTATCCTTTAACAAGTGTGTAGTAGCCTATTTAAAGAATTAGGGTTGTCATCATCCTCAAC
66 AAAACTATCATTTAACAAGTGTGTAGGAGCCTATTTAAAGAATTAGGGTTGTCATCATCCTCAAC
** * *
108047 CCTAGGTTAGCTGACGCCCTCATGTATAATGGTTATTGTGCGGTCCAAAATTTCCTCTGCTCGTA
131 CCTAGGTTAGCTGACGCCCTCATGTATAACAGTTATTGTGCAGACCAAAATTTCCTCTGCTCGTA
* * *
108112 AGTATCTCCCATACAGGGCCAATGTCACAACACCCTAGTGCTTGTGTAACAACATCGATGACAGT
196 AGTATCTCCCATACAAGGCCAATGTCACAACACCCTAGTGCTTGTATAACAACATCGAGGACAGT
* *
108177 ATGTGTAGTTCAAGGATGGCTTCATGGGTGTG-CTGCGACATCCTATGGCTGTGT
261 ATGTATAGTTCAAGGATGGCTTCATAGGTGTGTC-GCGACATCCTATGGCTGTGT
* * * *
108231 AAATCCAAAACCTAAGTAAAGGGAAAAACTTAAAATTAAAACGTACAAAGAAACCAGAATTTTCA
1 AAATCCAAAACCTAAGTAAAGGGAAAAACTAAAAACTAAAACGTACAAAGAAAACAAAATTTTCA
** * *
108296 AAAGTTGTCATTTAACAAGTGTGTAGGAGCCTATTTAAAGAATTAGGGTTGTCGTCATCCTCAAC
66 AAAACTATCATTTAACAAGTGTGTAGGAGCCTATTTAAAGAATTAGGGTTGTCATCATCCTCAAC
* * * * * *
108361 CCTAGGTTAGTTGATGCCCTCGTGTTTAACATTTATTGTGCAGACCAAAATTTCCTTTGCTCGTA
131 CCTAGGTTAGCTGACGCCCTCATGTATAACAGTTATTGTGCAGACCAAAATTTCCTCTGCTCGTA
** * * * ** * **
108426 AGTATCTCCTGTACAAGGCCAATGTCGCGACACCTTAGTGCTTGTATCGCGACATCGAGGGTAGT
196 AGTATCTCCCATACAAGGCCAATGTCACAACACCCTAGTGCTTGTATAACAACATCGAGGACAGT
*
108491 ATGTATAGTTCAGGGATGGCTTCATAGGTGTGTCGCGACATCCTATGGCT
261 ATGTATAGTTCAAGGATGGCTTCATAGGTGTGTCGCGACATCCTATGGCT
108541 ATGCCGTGAC
Statistics
Matches: 272, Mismatches: 37, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
314 271 1.00
315 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (314 bp):
AAATCCAAAACCTAAGTAAAGGGAAAAACTAAAAACTAAAACGTACAAAGAAAACAAAATTTTCA
AAAACTATCATTTAACAAGTGTGTAGGAGCCTATTTAAAGAATTAGGGTTGTCATCATCCTCAAC
CCTAGGTTAGCTGACGCCCTCATGTATAACAGTTATTGTGCAGACCAAAATTTCCTCTGCTCGTA
AGTATCTCCCATACAAGGCCAATGTCACAACACCCTAGTGCTTGTATAACAACATCGAGGACAGT
ATGTATAGTTCAAGGATGGCTTCATAGGTGTGTCGCGACATCCTATGGCTGTGT
Found at i:115550 original size:29 final size:29
Alignment explanation
Indices: 115508--115566 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
115498 TTTATTTTAA
115508 AGCATTCAAACGAATTGCAAGTCATACAT
1 AGCATTCAAACGAATTGCAAGTCATACAT
*
115537 AGCATTCAAACGAATTGCAAGTTATACAT
1 AGCATTCAAACGAATTGCAAGTCATACAT
115566 A
1 A
115567 CTCTAAGGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (29 bp):
AGCATTCAAACGAATTGCAAGTCATACAT
Done.