Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold877
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: 219531
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:191304 original size:29 final size:27
Alignment explanation
Indices: 191283--191336 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
191273 TAAATTTCAT
191283 ATTTAATTTTTAAAAATTTTAAAATATAA
1 ATTTAATTTTT-AAAATTTT-AAATATAA
* *
191312 ATTTTATTTTTAAAATTTTAGATAT
1 ATTTAATTTTTAAAATTTTAAATAT
191337 TGAATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 8 0.35
29 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTTAATTTTTAAAATTTTAAATATAA
Found at i:191461 original size:22 final size:22
Alignment explanation
Indices: 191409--191461 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
191399 TATAGTTTTC
*
191409 AAAATTGTTAAAAAATCATATAT
1 AAAATT-TTAAAAAATAATATAT
* *
191432 TAATTTTTAAAAATATAATA-AT
1 AAAATTTTAAAAA-ATAATATAT
191454 AAAATTTT
1 AAAATTTT
191462 CATATTTTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATTTTAAAAAATAATATAT
Found at i:191580 original size:27 final size:27
Alignment explanation
Indices: 191550--191601 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
191540 AAAATGTGGA
*
191550 ATTTAAATCATTTTTAAAATATTAAAT
1 ATTTAAATCATTTTTAAAAAATTAAAT
* *
191577 ATTTAAGTTATTTTTAAAAAATTAA
1 ATTTAAATCATTTTTAAAAAATTAA
191602 TATCTACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTTAAATCATTTTTAAAAAATTAAAT
Found at i:191822 original size:21 final size:22
Alignment explanation
Indices: 191796--191836 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
191786 TTATGATTTT
*
191796 AATTTATT-TAAATATTTATTA
1 AATTTATTCAAAATATTTATTA
191817 AATTTATTCAAAATATTTAT
1 AATTTATTCAAAATATTTAT
191837 CAAAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
AATTTATTCAAAATATTTATTA
Found at i:193839 original size:2 final size:2
Alignment explanation
Indices: 193832--193869 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
193822 ATTATCAATT
193832 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
193870 AAGATGTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:194489 original size:16 final size:16
Alignment explanation
Indices: 194463--194512 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
194453 AAATAACCCA
194463 AACTTGAAATGACTCG
1 AACTTGAAATGACTCG
194479 AACTTGAAATGA-TCCG
1 AACTTGAAATGACT-CG
*
194495 AA-TCCGAAATGACTCG
1 AACT-TGAAATGACTCG
194511 AA
1 AA
194513 TAATTAACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (16 bp):
AACTTGAAATGACTCG
Found at i:195347 original size:53 final size:53
Alignment explanation
Indices: 195247--195347 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 53
195237 TGAATCCGAT
* * *
195247 TTAACCCAAATGTTAAATCCAATTGAACCGAATCCAGAATGATCCGAAACTGA
1 TTAACCCAAATGTTAAACCCAATTGAACCGAATCCAGAATAACCCGAAACTGA
* *
195300 TTAACCCGAGTGTTAAACCCAATTG-ACTCGAATCC-GAAATAACCCGAA
1 TTAACCCAAATGTTAAACCCAATTGAAC-CGAATCCAG-AATAACCCGAA
195348 CCCAAAATGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
52 3 0.07
53 38 0.93
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.22
Consensus pattern (53 bp):
TTAACCCAAATGTTAAACCCAATTGAACCGAATCCAGAATAACCCGAAACTGA
Found at i:196008 original size:13 final size:14
Alignment explanation
Indices: 195990--196022 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
195980 AAAAAAATCA
195990 AATCAAATTAA-TT
1 AATCAAATTAATTT
196003 AATC-AATTAATTT
1 AATCAAATTAATTT
196016 AATCAAA
1 AATCAAA
196023 AATTAAAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 10 0.56
14 2 0.11
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (14 bp):
AATCAAATTAATTT
Found at i:196423 original size:18 final size:18
Alignment explanation
Indices: 196402--196443 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
196392 TCATTACTTA
*
196402 TTTAATATTAAAAATATT
1 TTTAATAATAAAAATATT
* *
196420 TTTAATAATATAAATTTT
1 TTTAATAATAAAAATATT
196438 TTTAAT
1 TTTAAT
196444 TAAATTAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTAATAATAAAAATATT
Found at i:196651 original size:14 final size:16
Alignment explanation
Indices: 196616--196653 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
196606 AGGTAAACTG
*
196616 TATTAAAAATAATGAC
1 TATTAAAAATAATCAC
196632 TATTAAAAAT-ATCA-
1 TATTAAAAATAATCAC
196646 TATTAAAA
1 TATTAAAA
196654 GATGTTGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 3 0.14
16 10 0.48
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (16 bp):
TATTAAAAATAATCAC
Found at i:196787 original size:49 final size:48
Alignment explanation
Indices: 196731--196825 Score: 172
Period size: 49 Copynumber: 2.0 Consensus size: 48
196721 TATTTGTATA
*
196731 AAAATTAAAAATAAATTCCTAAAAATTATATTTGTATTAAATAATAATT
1 AAAATTAAAAATAAATTCCTAAAAATTATAGTTGTATTAAA-AATAATT
196780 AAAATTAAAAATAAATTCCTAAAAATTATAGTTGTATTAAAAATAA
1 AAAATTAAAAATAAATTCCTAAAAATTATAGTTGTATTAAAAATAA
196826 AATTAATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 5 0.11
49 40 0.89
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (48 bp):
AAAATTAAAAATAAATTCCTAAAAATTATAGTTGTATTAAAAATAATT
Found at i:196847 original size:44 final size:47
Alignment explanation
Indices: 196732--196851 Score: 151
Period size: 49 Copynumber: 2.6 Consensus size: 47
196722 ATTTGTATAA
*
196732 AAATTAAAAATAAATTCCTAAAAATTATATTTGTATTAAATAATAATT
1 AAATTAAAAATAAATT-CTAAAAATTATAGTTGTATTAAATAATAATT
196780 AAAATTAAAAATAAATTCCTAAAAATTATAGTTGTATTAAA-AATAAAATT
1 -AAATTAAAAATAAATT-CTAAAAATTATAGTTGTATTAAATAAT--AATT
196830 -AA-TAAAAAT-AATT-TAAAAATTA
1 AAATTAAAAATAAATTCTAAAAATTA
196852 AAAAATGGAA
Statistics
Matches: 68, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
44 9 0.13
46 4 0.06
47 7 0.10
48 5 0.07
49 39 0.57
50 4 0.06
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (47 bp):
AAATTAAAAATAAATTCTAAAAATTATAGTTGTATTAAATAATAATT
Found at i:200182 original size:17 final size:17
Alignment explanation
Indices: 200160--200195 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
200150 TGGAAAAACG
200160 TGTTCATACCAGACATT
1 TGTTCATACCAGACATT
200177 TGTTCATACCAGACATT
1 TGTTCATACCAGACATT
200194 TG
1 TG
200196 GTCTTATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (17 bp):
TGTTCATACCAGACATT
Found at i:200271 original size:20 final size:20
Alignment explanation
Indices: 200246--200370 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
200236 TTTTAACTAG
200246 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
200266 ATGTATCGATACATCTGGGTAACACGACAAA
1 ATGTATCGATACAT-T--G----A--A-A-A
*
200297 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
200317 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
* *
200337 ATGTATCGATATATTAAAAA
1 ATGTATCGATACATTGAAAA
*
200357 ATATATCGATACAT
1 ATGTATCGATACAT
200371 CTGGGTAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 59 0.71
21 1 0.01
22 1 0.01
23 1 0.01
24 1 0.01
27 1 0.01
28 1 0.01
29 1 0.01
30 2 0.02
31 15 0.18
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:200418 original size:90 final size:91
Alignment explanation
Indices: 200246--200420 Score: 262
Period size: 91 Copynumber: 1.9 Consensus size: 91
200236 TTTTAACTAG
* * *
200246 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAACACGACAAAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAACAAGACAAAATGTATCGATACAT
200311 TGAAGAATGTATCGATACATTCATAC
66 TGAAGAATGTATCGATACATTCATAC
* *
200337 ATGTATCGATATATTAAAAAATATATCGATACATCTGGGTAA-AAGACAGAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAACAAGACAAAATGTATCGATACAT
****
200401 TTTTTAATGTATCGATACAT
66 TGAAGAATGTATCGATACAT
200421 CTAGGTAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 36 0.48
91 39 0.52
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (91 bp):
ATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAACAAGACAAAATGTATCGATACAT
TGAAGAATGTATCGATACATTCATAC
Found at i:200790 original size:14 final size:14
Alignment explanation
Indices: 200773--200800 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
200763 GATAAAGTGT
200773 TTGAAAAAAAAAAA
1 TTGAAAAAAAAAAA
200787 TTGAAAAAAAAAAA
1 TTGAAAAAAAAAAA
200801 ATTCCAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (14 bp):
TTGAAAAAAAAAAA
Found at i:200833 original size:21 final size:21
Alignment explanation
Indices: 200807--200863 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
200797 AAAAATTCCA
200807 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
200828 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
200849 AATGTATCGATACAT
1 AATGTATCGATACAT
200864 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:200943 original size:19 final size:19
Alignment explanation
Indices: 200919--200986 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
200909 AATTCAACAA
200919 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
200938 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
200953 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
200970 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
200987 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:200958 original size:13 final size:13
Alignment explanation
Indices: 200940--200964 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
200930 ACATAAGTTT
200940 TGTATCGATACAA
1 TGTATCGATACAA
200953 TGTATCGATACA
1 TGTATCGATACA
200965 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:200962 original size:32 final size:32
Alignment explanation
Indices: 200921--200983 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
200911 TTCAACAATT
*
200921 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
200953 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
200984 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:201044 original size:13 final size:13
Alignment explanation
Indices: 201026--201051 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
201016 CATTTTTCTG
201026 TGTATCGATACAT
1 TGTATCGATACAT
201039 TGTATCGATACAT
1 TGTATCGATACAT
201052 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:201048 original size:33 final size:33
Alignment explanation
Indices: 201006--201072 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
200996 GCCAAGGAAA
***
201006 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
201039 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
201072 T
1 T
201073 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:203726 original size:52 final size:51
Alignment explanation
Indices: 203402--203736 Score: 189
Period size: 52 Copynumber: 6.4 Consensus size: 51
203392 ATCAATTCTC
* * * *
203402 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAA-TTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
* *
203452 CTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAACACCAATTT-TT
* * * * ** * *
203508 CACAATCGGGGATGCTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACACCAA-----TT-TTT
* * * ** * *
203566 C-CGA--GGGTATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
* * * *
203614 CCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTC
1 -CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTTT
** *
203666 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTTT
* *
203719 CACAATCGAGGATGCTCC
1 CACAATCGGGGATACTCC
203737 GACCTCGTTA
Statistics
Matches: 212, Mismatches: 48, Indels: 48
0.69 0.16 0.16
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 3 0.01
51 34 0.16
52 72 0.34
53 27 0.13
54 17 0.08
55 37 0.17
56 4 0.02
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
Found at i:203784 original size:212 final size:212
Alignment explanation
Indices: 203400--203806 Score: 595
Period size: 212 Copynumber: 1.9 Consensus size: 212
203390 TTATCAATTC
* *
203400 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
203465 TACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGATGCTCCAACC
66 TACTCCAACTCCGATTTTATTTCC-AAAAAACACCAATTTCTTCACAATCGAGGATGCTCCAACC
* * * *
203530 CCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGTATACTCCAACTCCGGTTTTAT
130 CCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTAT
203595 CGCTAAAACACTAATTTT
195 CGCTAAAACACTAATTTT
* * * *
203613 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
203677 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATGCTCCGAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATGCTCCAAC
* * * *
203740 CTCGTTATTGCATTGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCCCGGCTTT
129 CCCGTTAAT-CATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
203805 AT
193 AT
203807 TCCCAAAATA
Statistics
Matches: 173, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
211 28 0.16
212 67 0.39
213 43 0.25
214 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATGCTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:216314 original size:20 final size:19
Alignment explanation
Indices: 216289--216341 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
216279 ACTTCTCTTC
216289 AAAAAAAAAAAAAGAGCAAA
1 AAAAAAAAAAAAAGA-CAAA
*
216309 AAAAAAACAAAAA-ACAAA
1 AAAAAAAAAAAAAGACAAA
* *
216327 AAAACAAAACAAAGA
1 AAAAAAAAAAAAAGA
216342 AAAGAGAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.50
19 2 0.07
20 12 0.43
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAGACAAA
Found at i:216327 original size:15 final size:14
Alignment explanation
Indices: 216288--216363 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
216278 CACTTCTCTT
216288 CAAAAAAAAAAAAA
1 CAAAAAAAAAAAAA
* **
216302 GAGCAAAAAAAAAA
1 CAAAAAAAAAAAAA
216316 CAAAAAACAAAAAAA
1 CAAAAAA-AAAAAAA
216331 CAAAACAAAGAAAAGAGA
1 CAAAA-AAA-AAAA-A-A
* *
216349 GAAAAGAAAAAAAA
1 CAAAAAAAAAAAAA
216363 C
1 C
216364 TACGTAAGCT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
14 16 0.33
15 14 0.29
16 10 0.21
17 3 0.06
18 5 0.10
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAA
Found at i:216344 original size:17 final size:16
Alignment explanation
Indices: 216288--216344 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
216278 CACTTCTCTT
216288 CAAAAAAAAAA-AAAGA
1 CAAAAAAAAAACAAA-A
216304 GCAAAAAAAAAACAAAA
1 -CAAAAAAAAAACAAAA
*
216321 -AACAAAAAAACAAAA
1 CAAAAAAAAAACAAAA
*
216336 CAAAGAAAA
1 CAAAAAAAA
216345 GAGAGAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 14 0.40
16 6 0.17
17 12 0.34
18 3 0.09
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (16 bp):
CAAAAAAAAAACAAAA
Found at i:217502 original size:55 final size:54
Alignment explanation
Indices: 217430--218486 Score: 984
Period size: 53 Copynumber: 19.4 Consensus size: 54
217420 CTTAAACTTC
*
217430 AAGCCCACAC-AGTTGGTGGC-TTTTCAAGTCCTCAAA-AGGACA-GACACCTTTAA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA-G-CAGGACACCTTT-A
*
217483 AAGCCCAC-CTAAGTGTGGTGGCAATTTTCCAGT-CTCAAAGAGCAGGACAACTCCTTA
1 AAGCCCACAC-AAGT-TGGTGGC-ATTTTCCAGTCCTCAAAGAGCAGGAC-AC-CTTTA
*
217540 AAG-CCACACAAGTTGGTGGCCTTTTCCAGTCCTCAAAGAGCAGGAC-CCTTT-
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTA
** *
217591 CCGCCCAC-CGAGTTGGTGGCATTTTCCAGT-CTCAAAGAGCAGGAACACCTCTTA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGG-ACACCT-TTA
*
217645 AAGCCCACAACAAGTT-GTGGCATTTTCCAGTCCTC-AAGAGCAGGACACCTTCCA
1 AAGCCCAC-ACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTT-TA
217699 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTT-A
* *
217754 AAGCCCACAC-AGTTTGGGGGTTATTTTTCCAGTCCTCAAAGAGCAGGACACCTCTTA
1 AAGCCCACACAAG-TTGGTGG-CA-TTTTCCAGTCCTCAAAGAGCAGGACACCT-TTA
*
217811 AAG-CCACACAAGTTGGT-GCATTTTCCAGTCCTCAAAGAAGCAGGACACCGTTCA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAG-AGCAGGACACC-TTTA
*
217865 AAGCCC-CACAAG-T-GTGGCTATTTTCCAGTCCTCAAAGA-CAATGACACCTCTTA
1 AAGCCCACACAAGTTGGTGGC-ATTTTCCAGTCCTCAAAGAGC-AGGACACCT-TTA
* *
217918 AAG-CC-CAC-AGTTGGTGGCACCTTT-CAGTCCCTCAAAGAGCAGGACCCCTTTCCA
1 AAGCCCACACAAGTTGGTGGCA-TTTTCCAGT-CCTCAAAGAGCAGGACACCTTT--A
*
217972 AA-CCCACACAAGTGGGTGGGCGGCATTTTTCCAGTCCTCAAA-AGCAGGGACACCTCTTA
1 AAGCCCACACAAGT---T-GGTGGCA-TTTTCCAGTCCTCAAAGAGCA-GGACACCT-TTA
*
218031 AAGCCCACACAA-TTGGTGGCATTTT-CAGTCCTCAAAGA-CAGGACACCTTCA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTA
* *
218082 AAGCCCACACAAATTGGTGGCATGTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAATTA
1 AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACA-C-C-T---TTA
* * *
218142 AAGCCCACACAAGTTTGGTGGCACATTT-CAGTCCCCAAAG-GC-GGACACCTTTC
1 AAGCCCACACAAG-TTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTA
* * *
218195 AAGCCCACCCAAGTTGGTGGAAGTTTTCTAG-CCTCAAAGAGCAGGACACCTCTTA
1 AAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCT-TTA
* *
218250 AAGACC-CAC-AGTTGGTGGGCACCTTT-CAGTCC-CAAAGAGCA-GACACCATCTT-
1 AAGCCCACACAAGTTGGT-GGCA-TTTTCCAGTCCTCAAAGAGCAGGACACC-T-TTA
* *
218302 AAG-CCACACAAGTTGGTGGCAATTTTCTAGTCCTC-AAGAAACAGGACACCTTTCA
1 AAGCCCACACAAGTTGGTGGC-ATTTTCCAGTCCTCAAAG-AGCAGGACACCTTT-A
218357 AAG-CCACACAAGTTGGT-GCATTTGTCCAGTCCTCAAAGAGCAAGGACAACCTTTA
1 AAGCCCACACAAGTTGGTGGCATTT-TCCAGTCCTCAAAGAGC-AGGAC-ACCTTTA
* * * * *
218412 AAGCCCACACAAGTTGGTGGAACCTGTT-CA-TTC-CAAAGAGCAGGTCACTTTTCA
1 AAGCCCACACAAGTTGGTGG--CATTTTCCAGTCCTCAAAGAGCAGGACACCTTT-A
*
218466 AA-CCCACACAAGTGGGTGGCA
1 AAGCCCACACAAGTTGGTGGCA
218487 CCTGTCAAGT
Statistics
Matches: 853, Mismatches: 61, Indels: 182
0.78 0.06 0.17
Matches are distributed among these distances:
50 13 0.02
51 42 0.05
52 84 0.10
53 185 0.22
54 156 0.18
55 152 0.18
56 65 0.08
57 56 0.07
58 7 0.01
59 17 0.02
60 48 0.06
61 26 0.03
62 2 0.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (54 bp):
AAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTA
Found at i:218025 original size:220 final size:217
Alignment explanation
Indices: 217426--218433 Score: 972
Period size: 220 Copynumber: 4.6 Consensus size: 217
217416 ACCTCTTAAA
* *
217426 CTTC-AAGCCCACAC-AGTTGGTGGC-TTTTCAAGTCCTCAAAAGGACA-GACACCTTTAAAAGC
1 CTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAGA-G-CAGGACACCTTT-AAAGC
*
217487 CCAC-CTAAGTGTGGTGGCAATTTTCCAGT-CTCAAAGAGCAGGACAACTCCTT-AAAG-CCACA
63 CCACAC-AAGT-TGGTGGC-ATTTTCCAGTCCTCAAAGAGCAGGAC-AC-CTTTCAAAGCCCACA
* ** ** *
217548 CAAGT-TGGTGG-CCTTTTCCAGTCCTCAAAGAGCAGGAC-CCT-TT-CCG-CCCACCGAGTTGG
123 CAAGTGTGGGGGAATTTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGACCCA-CAAGTTGG
217607 TGGCATTTTCCAGT-CTCAAAGAGCAGGAACAC
187 TGGCATTTT-CAGTCCTCAAAGAGCAGG-ACAC
* *
217639 CTCTTAAAGCCCACAACAAGTT-GTGGCATTTTCCAGTCCTCAAGAGCAGGACACCTTCCAAAGC
1 CT-TCAAAGCCCAC-ACAAGTTGGTGGCATTTTCCAGTCCTCAAGAGCAGGACACCTT-TAAAGC
217703 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACAC-AGT
63 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGT
* *
217767 TTGGGGGTTATTTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAG-CCACACAAGTTGGT-GC
128 GTGGGGG-AATTTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGACC-CACAAGTTGGTGGC
217830 ATTTTCCAGTCCTCAAAGAAGCAGGACAC
191 ATTTT-CAGTCCTCAAAG-AGCAGGACAC
*
217859 CGTTCAAAGCCC-CACAAG-T-GTGGCTATTTTCCAGTCCTCAA-AGACAATGACACCTCTTAAA
1 C-TTCAAAGCCCACACAAGTTGGTGGC-ATTTTCCAGTCCTCAAGAG-C-AGGACACCT-TTAAA
* *
217920 G-CC-CAC-AGTTGGTGGCACCTTT-CAGTCCCTCAAAGAGCAGGACCCCTTTCCAAA-CCCACA
61 GCCCACACAAGTTGGTGGCA-TTTTCCAGT-CCTCAAAGAGCAGGACACCTTT-CAAAGCCCACA
* *
217980 CAAGTGGGTGGGCGGCATTTTTCCAGTCCTCAAA-AGCAGGGACACCTCTTAAAG-CCCACACAA
123 CAAGT--GTGGG-GGAATTTTTCCAGTCCTCAAAGAGCA-GGACACCTCTTAAAGACCCACA-AG
218043 TTGGTGGCATTTTCAGTCCTCAAAGA-CAGGACAC
183 TTGGTGGCATTTTCAGTCCTCAAAGAGCAGGACAC
* *
218077 CTTCAAAGCCCACACAAATTGGTGGCATGTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAATTA
1 CTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC-AAGAGCAGGACA-C-C-T---TTA
* *
218142 AAGCCCACACAAGTTTGGTGGCACATTT-CAGTCCCCAAAG-GC-GGACACCTTTC-AAGCCCAC
59 AAGCCCACACAAG-TTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCAC
* * * *
218203 CCAAGT-TGGTGGAAGTTTTCTAG-CCTCAAAGAGCAGGACACCTCTTAAAGACCCAC-AGTTGG
122 ACAAGTGTGGGGGAATTTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGACCCACAAGTTGG
*
218265 TGGGCACCTTTCAGTCC-CAAAGAGCA-GACAC
187 T-GGCA-TTTTCAGTCCTCAAAGAGCAGGACAC
* * * *
218296 CATCTTAAG-CCACACAAGTTGGTGGCAATTTTCTAGTCCTCAAGAAACAGGACACCTTTCAAAG
1 CTTC-AAAGCCCACACAAGTTGGTGGC-ATTTTCCAGTCCTCAAG-AGCAGGACACCTTT-AAAG
218360 -CCACACAAGTTGGT-GCATTTGTCCAGTCCTCAAAGAGCAAGGACAACCTTT-AAAGCCCACAC
62 CCCACACAAGTTGGTGGCATTT-TCCAGTCCTCAAAGAGC-AGGAC-ACCTTTCAAAGCCCACAC
*
218422 AAGT-TGGTGGAA
124 AAGTGTGGGGGAA
218434 CCTGTTCATT
Statistics
Matches: 687, Mismatches: 42, Indels: 128
0.80 0.05 0.15
Matches are distributed among these distances:
211 2 0.00
212 4 0.01
213 21 0.03
214 33 0.05
215 47 0.07
216 48 0.07
217 125 0.18
218 55 0.08
219 115 0.17
220 151 0.22
221 24 0.03
222 1 0.00
223 2 0.00
224 17 0.02
225 11 0.02
226 5 0.01
227 9 0.01
228 17 0.02
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (217 bp):
CTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAGAGCAGGACACCTTTAAAGCCCA
CACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTGTG
GGGGAATTTTTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGACCCACAAGTTGGTGGCATTTT
CAGTCCTCAAAGAGCAGGACAC
Found at i:219213 original size:29 final size:30
Alignment explanation
Indices: 219166--219225 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 30
219156 CATAAGTTTT
219166 TGTATCGATACATAATATTGTATC-ATACA
1 TGTATCGATACATAATATTGTATCGATACA
219195 TGTATC-ATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAA-TATTGTATCGATACA
219225 T
1 T
219226 AATTACTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 8 0.28
29 15 0.52
30 6 0.21
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (30 bp):
TGTATCGATACATAATATTGTATCGATACA
Done.