Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2069
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: 37196
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Found at i:11058 original size:1 final size:1
Alignment explanation
Indices: 11052--11078 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
11042 TTTGCTTCCT
11052 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
11079 CTTTGGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12473 original size:86 final size:88
Alignment explanation
Indices: 12276--12541 Score: 314
Period size: 86 Copynumber: 3.1 Consensus size: 88
12266 GACAGATCAA
* * *
12276 TGAAGACAAAGGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAA-CCTTGCC
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAA-ACACAAAGCCTTGCC
** * * *
12340 TCTTTCGGTTG-TGATAGAGCTGGT
65 TCCATCGGTTGCAG-TGGAGCTAGT
* *
12364 TGAAGACAAAAGATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCAT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCT
*
12428 CCATCGATTGCAGTGGAGCTAGT
66 CCATCGGTTGCAGTGGAGCTAGT
*
12451 T-AA-A-AAAGTAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGC
1 TGAAGACAAA--AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGC
*
12512 CTCCATCGGTTGCATTGGAGC-AGAT
64 CTCCATCGGTTGCAGTGGAGCTAG-T
12537 TGAAG
1 TGAAG
12542 CCAGAGATCT
Statistics
Matches: 155, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
84 3 0.02
85 6 0.04
86 74 0.48
87 26 0.17
88 46 0.30
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.24
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAACACAAAGCCTTGCCT
CCATCGGTTGCAGTGGAGCTAGT
Found at i:12550 original size:86 final size:84
Alignment explanation
Indices: 12287--12586 Score: 291
Period size: 86 Copynumber: 3.5 Consensus size: 84
12277 GAAGACAAAG
* * * * **
12287 GATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAGACACAAACCTTGCCTCTTTCGGTTGT
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACA-AAGCCTTGCCTCCATCGGTTG-
* * * *
12352 GATAGAGCTGGTTGAAGACAAAA
64 CATGGAGC-AGTTGAAG-CAAGA
* * *
12375 GATCTTGCCTTCCTACATTAACAGCGAAGCAGATCGAAA-ACAAAGCCTTGCATCCATCGATTGC
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC-AAAGACAAAGCCTTGCCTCCATCGGTTGC
**
12439 AGTGGAGCTAGTT-AAAAAAGTA
65 A-TGGAGC-AGTTGAAGCAAG-A
12461 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
1 GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
*
12526 TTGGAGCAGATTGAAGCCAGA
66 -TGGAGCAG-TTGAAGCAAGA
** * * *
12547 GATCTTATCTCCCTGAGATT-ACAGCGGAGCAGATCAAAGA
1 GATCTTGCCTTCCTG-CATTAACAGCGAAGCAGATCAAAGA
12587 TAGTAATCCT
Statistics
Matches: 178, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
85 7 0.04
86 102 0.57
87 32 0.18
88 35 0.20
89 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (84 bp):
GATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCAAAGACAAAGCCTTGCCTCCATCGGTTGCA
TGGAGCAGTTGAAGCAAGA
Found at i:12681 original size:41 final size:41
Alignment explanation
Indices: 12633--12925 Score: 142
Period size: 46 Copynumber: 6.8 Consensus size: 41
12623 GATTAAAGGA
* * *
12633 TCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGAAGATCAAATCAGG
* * *
12674 TCTTATCTCCCTG-AGATTACAGTGGA-ACAGACCGAAGAATTGTAGA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGA-AGATC--A-AA-T-CAGG
* * * * **
12720 TCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGAAGATC-AA-ATCA-GG
* ** * *
12763 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGAAGA-TCAAAT-CAGG
* * * **
12806 ATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
1 -TCTTATCTCCCTGAAGTTACAGTGGAGAAGATCAAATCAGG
* * * * *
12848 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGAAGATC--A-AA-T-CAGG
* *
12894 TCTTATCCCCCTGAAGTTACAGTGGAGCAGAT
1 TCTTATCTCCCTGAAGTTACAGTGGAGAAGAT
12926 TGAAGCCAGA
Statistics
Matches: 191, Mismatches: 41, Indels: 35
0.72 0.15 0.13
Matches are distributed among these distances:
40 3 0.02
41 55 0.29
42 6 0.03
43 33 0.17
44 32 0.17
45 4 0.02
46 57 0.30
47 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGAAGATCAAATCAGG
Found at i:12752 original size:87 final size:87
Alignment explanation
Indices: 12624--13003 Score: 294
Period size: 87 Copynumber: 4.4 Consensus size: 87
12614 AATGGAGCGG
* *
12624 ATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAG
1 ATTAAA-GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCACATCAGGTCTTATCTCCCTGAG
*
12689 ATTACAGTGGAACAGACCGAAGA
65 ATTACAGTGGAGCAGACCGAAGA
** * * ** * ** *
12712 ATTGTAGATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGAT-ATAATCCTATCTCCCTG
1 ATTAAAGATCTTATCTCCCTGAAGTTACAGTAGAGCAGATC--ACATCA-GGTCTTATCTCCCTG
* **
12776 A-AGTTACAGTGGAGCGGA-TTAA-A
63 AGA-TTACAGTGGAGCAGACCGAAGA
* * * *
12799 A-TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTCTCTGAG
1 ATTAAA-GATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCACATCAGGTCTTATCTCCCTGAG
* *
12863 GTTACAGTGGAGTAGACCGAAGA
65 ATTACAGTGGAGCAGACCGAAGA
* * * * * *
12886 ATTACAGATCTTATCCCCCTGAAGTTACAGTGGAGCAGATTGA-AGCCAGAGATCTTATCTCCCC
1 ATTAAAGATCTTATCTCCCTGAAGTTACAGTAGAGCAGA-TCACA-TCAG-G-TCTTATCTCCCT
* * *
12950 GGGATTACAGCGGAGCAGATCGAAGA
62 GAGATTACAGTGGAGCAGACCGAAGA
* *
12976 CACT----ATCCTATCTCCCTGAAGTTACAGT
1 -ATTAAAGATCTTATCTCCCTGAAGTTACAGT
13004 GGAGTGGGTT
Statistics
Matches: 224, Mismatches: 53, Indels: 31
0.73 0.17 0.10
Matches are distributed among these distances:
85 27 0.12
86 5 0.02
87 114 0.51
88 15 0.07
89 30 0.13
90 31 0.14
91 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (87 bp):
ATTAAAGATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCACATCAGGTCTTATCTCCCTGAGA
TTACAGTGGAGCAGACCGAAGA
Found at i:12833 original size:174 final size:171
Alignment explanation
Indices: 12546--12930 Score: 542
Period size: 174 Copynumber: 2.2 Consensus size: 171
12536 TTGAAGCCAG
* * *
12546 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATT
12611 ACAAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
66 ACAAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
**
12676 TTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGT
131 TTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTAC
*
12717 AGATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATA-TAATCCTATCTCCCTGA-AGT
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGA-T
* * *
12780 TAC-AGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 TACAAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACAT
* * **
12844 CAGGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTAC
125 CAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTAC
* * * *
12891 AGATCTTATCCCCCTGAAGTTACAGTGGAGCAGATTGAAG
1 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAG
12931 CCAGAGATCT
Statistics
Matches: 190, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
169 11 0.06
170 21 0.11
171 40 0.21
174 118 0.62
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (171 bp):
AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATAGTAATCCTATCTCCCTGAGATT
ACAAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTC
TTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTAC
Found at i:12900 original size:46 final size:45
Alignment explanation
Indices: 12631--13007 Score: 221
Period size: 44 Copynumber: 8.6 Consensus size: 45
12621 CGGATTAAAG
* * * * *
12631 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATC--A-CAT-CA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATACA
* * **
12672 GGTCTTATCTCCCTG-AGATTACAGTGGAACAGACCGAAGAATTGTA
1 GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGACCGAAGAA-TACA
* * * * *
12718 GATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAG-ATATA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATACA
* * ** *
12762 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AATAAA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATACA
* * * * *
12804 GGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATC---GCAT-CA
1 -GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATACA
* * * *
12846 GGTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTACA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAA-TACA
* ** ** *
12892 GATCTTATCCCCCTGAAGTTACAGTGGAGCAGATTGAAG-CCAGA
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATACA
* * * * *
12936 GATCTTATCTCCCCG-GGATTACAGCGGAGCAGATCGAAG-ACAC-
1 GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGACCGAAGAATACA
* *
12979 TATCCTATCTCCCTGAAGTTACAGTGGAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAG
13008 TGGGTTAAAA
Statistics
Matches: 259, Mismatches: 58, Indels: 36
0.73 0.16 0.10
Matches are distributed among these distances:
40 2 0.01
41 57 0.22
42 7 0.03
43 53 0.20
44 70 0.27
45 3 0.01
46 66 0.25
47 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (45 bp):
GATCTTATCTCCCTGAAGTTACAGTGGAGCAGACCGAAGAATACA
Found at i:12970 original size:131 final size:128
Alignment explanation
Indices: 12720--12971 Score: 274
Period size: 131 Copynumber: 1.9 Consensus size: 128
12710 GAATTGTAGA
* * * *
12720 TCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATACAATCCTATCCCCCTGAAGTTACAG
* * * * * *
12785 TGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 TGGAGCAGATTAAAACAAAGGATCTTATCTCCCGGAAGTTACAGCAGAGCAGATCGCATCAGG
* * * *
12848 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTACAGATCTTATCCCCCTGAAGTTA
1 TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAG-A-TACA-ATCCTATCCCCCTGAAGTTA
* * * * *
12913 CAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCCGGGA-TTACAGCGGAGCAGATCG
63 CAGTGGAGCAGATTAAAACAAAG-GATCTTATCT-CCCGGAAGTTACAGCAGAGCAGATCG
12972 AAGACACTAT
Statistics
Matches: 100, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
128 32 0.32
129 1 0.01
130 5 0.05
131 58 0.58
132 4 0.04
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (128 bp):
TCTTATCTCCCTGAGGTTACAGCGGAGCAGACCGAAGATACAATCCTATCCCCCTGAAGTTACAG
TGGAGCAGATTAAAACAAAGGATCTTATCTCCCGGAAGTTACAGCAGAGCAGATCGCATCAGG
Found at i:12997 original size:174 final size:174
Alignment explanation
Indices: 12546--13008 Score: 458
Period size: 174 Copynumber: 2.7 Consensus size: 174
12536 TTGAAGCCAG
* * * **
12546 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTG-AGA
1 AGATCTTATCCCCCTGAAG-TTACAGCGGAGCAGATCGAAGACAG-AATCCTATCTCCCGGAAG-
** * * *
12609 TTACAAATGGAGCGGATT-AAAG----GATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACA
63 TTAC-AGCGGAGCAGATTAAAAGAAACGATCCTATCTCTCTGAAGTTACAGTAGAGTAGATCACA
**
12669 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTGT
127 TCAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTAC
* * * * * *
12717 AGATCTTGTCTCCCTGAGGTTACAGCGGAGCAGATCGAAGATATAATCCTATCTCCCTGAAGTTA
1 AGATCTTATCCCCCTGAAGTTACAGCGGAGCAGATCGAAGACAGAATCCTATCTCCCGGAAGTTA
* * * * * *
12782 CAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
66 CAGCGGAGCAGATTAAAAGAAACGATCCTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAG
* * **
12847 GTCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTAC
131 GTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTAC
* * * * *
12891 AGATCTTATCCCCCTGAAGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCCGGGA-T
1 AGATCTTATCCCCCTGAAGTTACAGCGGAGCAGATCGAAGACAGA-ATCCTATCT-CCCGGAAGT
** * * * *
12955 TACAGCGGAGCAGA-TCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGT
64 TACAGCGGAGCAGATTAAAAGAAACGATCCTATCTCTCTGAAGTTACAGTAGAGT
13009 GGGTTAAAAT
Statistics
Matches: 246, Mismatches: 37, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
169 12 0.05
170 21 0.09
171 40 0.16
172 1 0.00
174 146 0.59
175 21 0.09
176 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (174 bp):
AGATCTTATCCCCCTGAAGTTACAGCGGAGCAGATCGAAGACAGAATCCTATCTCCCGGAAGTTA
CAGCGGAGCAGATTAAAAGAAACGATCCTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAG
GTCTTATCTCCCTGAGATTACAGTGGAACAGACCGAAGAATTAC
Found at i:13045 original size:87 final size:90
Alignment explanation
Indices: 12848--13047 Score: 203
Period size: 87 Copynumber: 2.3 Consensus size: 90
12838 TCGCATCAGG
* * * *
12848 TCTTATCTCTCTGAGGTTACAGTGGAGTAGACCGAAGAATTACAGATCTTATCCCCCTGAAGTTA
1 TCTTATCTCTCTGAGGTTACAGCGGAGCAGACCGAAGAATCACAGATCCTATCCCCCTGAAGTTA
* **
12913 CAGTGGAGCAGATTGAAGCCAGAGA
66 CAGTGGAGCAGATTAAAGAAAGAGA
* * * * *
12938 TCTTATCTCCCCG-GGATTACAGCGGAGCAGATCGAAG-A-CAC-TATCCTATCTCCCTGAAGTT
1 TCTTATCTCTCTGAGG-TTACAGCGGAGCAGACCGAAGAATCACAGATCCTATCCCCCTGAAGTT
** * *
12999 ACAGTGGAGTGGGTTAAAATAAAG-GA
65 ACAGTGGAGCAGATT-AAAGAAAGAGA
13025 TCTTATCTCTCTGAGGTTACAGC
1 TCTTATCTCTCTGAGGTTACAGC
13048 AGAGTAGGTC
Statistics
Matches: 89, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
87 49 0.55
88 8 0.09
89 3 0.03
90 29 0.33
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (90 bp):
TCTTATCTCTCTGAGGTTACAGCGGAGCAGACCGAAGAATCACAGATCCTATCCCCCTGAAGTTA
CAGTGGAGCAGATTAAAGAAAGAGA
Found at i:14512 original size:3 final size:3
Alignment explanation
Indices: 14504--14542 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
14494 AATCTAGTCC
* *
14504 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14543 CCTTTTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:19434 original size:24 final size:24
Alignment explanation
Indices: 19402--19451 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
19392 GAATTGGCAA
19402 GTAAGTTCTTTTATTTGTTTTATT
1 GTAAGTTCTTTTATTTGTTTTATT
19426 GTAAGTTCTTTTATTTGTTTTATT
1 GTAAGTTCTTTTATTTGTTTTATT
19450 GT
1 GT
19452 GCATAGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.16, C:0.04, G:0.14, T:0.66
Consensus pattern (24 bp):
GTAAGTTCTTTTATTTGTTTTATT
Found at i:28193 original size:10 final size:11
Alignment explanation
Indices: 28177--28206 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
28167 TTTTCCTAAT
28177 ATGTGAATTGA
1 ATGTGAATTGA
28188 AT-TGAATTGA
1 ATGTGAATTGA
28198 ATGTGAATT
1 ATGTGAATT
28207 TTATTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (11 bp):
ATGTGAATTGA
Found at i:28216 original size:21 final size:21
Alignment explanation
Indices: 28177--28218 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28167 TTTTCCTAAT
*
28177 ATGTGAATTGAATTGAATTGA
1 ATGTGAATTGAATTAAATTGA
**
28198 ATGTGAATTTTATTAAATTGA
1 ATGTGAATTGAATTAAATTGA
28219 GTTAAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
ATGTGAATTGAATTAAATTGA
Found at i:31430 original size:52 final size:51
Alignment explanation
Indices: 31359--31665 Score: 409
Period size: 52 Copynumber: 6.1 Consensus size: 51
31349 ATCAAGTGAT
* *
31359 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
31411 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTG---A-T-
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
31457 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
31503 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
*
31555 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* *
31606 AAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC-AAGTG
31659 ATAAGTG
1 A-AAGTG
31666 GCTACACTTA
Statistics
Matches: 232, Mismatches: 12, Indels: 21
0.88 0.05 0.08
Matches are distributed among these distances:
46 87 0.38
48 1 0.00
49 1 0.00
51 1 0.00
52 132 0.57
53 10 0.04
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:31465 original size:98 final size:97
Alignment explanation
Indices: 31345--31665 Score: 445
Period size: 98 Copynumber: 3.3 Consensus size: 97
31335 TTTGAGTACT
* **
31345 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-
* * *
31410 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
31443 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
31503 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
66 AAAGTGATAAGTGATAGCTTCAGCTACACTTA
31535 TCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 TCTGATCAAGTG---A-T--AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
31600 CAAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTA
60 CAAGTG-AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
31639 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGTGATAAAGTGATAAGTG
31666 GCTACACTTA
Statistics
Matches: 200, Mismatches: 11, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
92 41 0.20
95 1 0.00
96 1 0.00
98 114 0.57
101 1 0.00
104 42 0.21
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (97 bp):
TCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:31673 original size:37 final size:37
Alignment explanation
Indices: 31629--31737 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
31619 GATAGCTTTA
31629 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
31666 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
31703 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
31738 ATCATACGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:33053 original size:49 final size:49
Alignment explanation
Indices: 32992--33135 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
32982 ATGTGAACAT
*
32992 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
33042 GTGATATGTGATTTCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * *
33091 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
33136 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 84 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Found at i:36356 original size:50 final size:48
Alignment explanation
Indices: 36289--36548 Score: 308
Period size: 50 Copynumber: 5.4 Consensus size: 48
36279 GGTAGCTTTA
36289 GCTACACTTATCTGATCAAGTGACAAGTGGAAAGTGGATAAGATACTTCG
1 GCTACACTTATCTGATCAAGTGACAAGT-GAAAGT-GATAAGATACTTCG
* * *
36339 GCTATACTTATCTGATCAAGTGAAAAGTGATAAGTGAT-AG---CTTCA
1 GCTACACTTATCTGATCAAGTGACAAGTGA-AAGTGATAAGATACTTCG
36384 GCTACACTTATCTGATCAAGTGACAAGT-ATAAGTGAT-AG---CTTCG
1 GCTACACTTATCTGATCAAGTGACAAGTGA-AAGTGATAAGATACTTCG
36428 GCTACACTTATCTGATCAAGTGACAAGT-AAAGTGATAAGTGATAGCTTCG
1 GCTACACTTATCTGATCAAGTGACAAGTGAAAGTGATAA--GATA-CTTCG
*
36478 GCTACACTTATCTGATCAAGTGACAAAGTGAAAGTGATAAGTGATAGCTT-A
1 GCTACACTTATCTGATCAAGTGAC-AAGTGAAAGTGATAA--GATA-CTTCG
36529 GCTACACTTATCTGATCAAG
1 GCTACACTTATCTGATCAAG
36549 AAACAAAGTG
Statistics
Matches: 193, Mismatches: 7, Indels: 19
0.88 0.03 0.09
Matches are distributed among these distances:
43 7 0.04
44 45 0.23
45 30 0.16
46 1 0.01
48 2 0.01
49 5 0.03
50 59 0.31
51 24 0.12
52 20 0.10
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (48 bp):
GCTACACTTATCTGATCAAGTGACAAGTGAAAGTGATAAGATACTTCG
Found at i:36406 original size:38 final size:38
Alignment explanation
Indices: 36363--36455 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 38
36353 ATCAAGTGAA
36363 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
1 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
*
36401 AAGTGACAAGTATAAGTGATAGCTTCGGCTACACTTATCTGATC
1 AAGT-----G-ATAAGTGATAGCTTCAGCTACACTTATCTGATC
*
36445 AAGTGACAAGT
1 AAGTGATAAGT
36456 AAAGTGATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
38 9 0.19
39 1 0.02
43 1 0.02
44 36 0.77
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (38 bp):
AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC
Found at i:36432 original size:44 final size:45
Alignment explanation
Indices: 36330--36639 Score: 284
Period size: 37 Copynumber: 7.1 Consensus size: 45
36320 AAGTGGATAA
* *
36330 GATA-CTTCGGCTATACTTATCTGATCAAGTGAAAAGTGATAAGT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGATAAGT
*
36374 GATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-ATAAGT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGATAAGT
36418 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTAAAGTGATAAGT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGAC-----AAGTGATAAGT
36468 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGAAAGTGATAAGT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGAC-------AAGTGATAAGT
* *
36520 GATAGCTT-AGCTACACTTATCTGATCAA--GA-AA--CA-AAGT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGATAAGT
*
36558 GATAAG--T-GGCTACACTTATCTGATCAA--GA-AA--CA-AAGT
1 GAT-AGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGATAAGT
* *
36595 GATAG-GT-GGCTACACTTATCTGATC-AGGGACAAGTGATAAGT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGATAAGT
36637 GAT
1 GAT
36640 CATACGTAAG
Statistics
Matches: 238, Mismatches: 11, Indels: 36
0.84 0.04 0.13
Matches are distributed among these distances:
36 3 0.01
37 52 0.22
38 9 0.04
39 5 0.02
41 3 0.01
42 7 0.03
44 43 0.18
45 30 0.13
49 6 0.03
50 40 0.17
51 19 0.08
52 21 0.09
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (45 bp):
GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGATAAGT
Found at i:36477 original size:139 final size:137
Alignment explanation
Indices: 36254--36585 Score: 398
Period size: 139 Copynumber: 2.4 Consensus size: 137
36244 TTTGAGTACT
* *
36254 TCTGATCAAGTGATAAAGTGATAA-TGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTG--AAAGT-ATAAGTGATAGC-TTGGCTACACTTATCTGATCAAGTGACAAGT-
*
36318 GAAAGTGGATAAGATACTTCGGCTATACTTATCTGATCAAGTG-A-AAAGTGATAAGTGATAGCT
61 GAAAGTGGATAAGATACTTCGGCTACACTTATCTGATCAAGTGAAGAAAGTGATAAGTGATAGCT
36381 TCAGCTACACTTA
126 T-AGCTACACTTA
36394 TCTGATCAAGTGACAAGTATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT-AA
1 TCTGATCAAGTGA-AAGTATAAGTGATAGCTT-GGCTACACTTATCTGATCAAGTGACAAGTGAA
36458 AGT-GATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAAGTGAAAGTGATAAGTGA
64 AGTGGATAA--GATA-CTTCGGCTACACTTATCTGATCAAGTG---AA--GAAAGTGATAAGTGA
36522 TAGCTTAGCTACACTTA
121 TAGCTTAGCTACACTTA
*
36539 TCTGATCAA--GAAA-CA-AAGTGATAAG--TGGCTACACTTATCTGATCAAG
1 TCTGATCAAGTGAAAGTATAAGTGAT-AGCTTGGCTACACTTATCTGATCAAG
36586 AAACAAAGTG
Statistics
Matches: 174, Mismatches: 4, Indels: 30
0.84 0.02 0.14
Matches are distributed among these distances:
136 5 0.03
137 5 0.03
138 32 0.18
139 65 0.37
140 19 0.11
141 3 0.02
142 2 0.01
143 3 0.02
145 20 0.11
146 20 0.11
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (137 bp):
TCTGATCAAGTGAAAGTATAAGTGATAGCTTGGCTACACTTATCTGATCAAGTGACAAGTGAAAG
TGGATAAGATACTTCGGCTACACTTATCTGATCAAGTGAAGAAAGTGATAAGTGATAGCTTAGCT
ACACTTA
Found at i:36482 original size:94 final size:91
Alignment explanation
Indices: 36330--36565 Score: 291
Period size: 94 Copynumber: 2.5 Consensus size: 91
36320 AAGTGGATAA
*
36330 GATA-CTTCGGCTATACTTATCTGATCAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTT
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTT
36393 ATCTGATCAAGTGACAAGT-ATAAGT
66 ATCTGATCAAGTGACAAGTGATAAGT
*
36418 GATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTAAAGTGATAAGTGATAGCTTCGGCTAC
1 GATAGCTTCGGCTACACTTATCTGATCAAGTG---A-TAAAGTGATAAGTGATAGCTTCAGCTAC
36483 ACTTATCTGATCAAGTGACAAAGTGAAAGTGATAAGT
62 ACTTATCTGATCAAGTGAC-------AAGTGATAAGT
* ** *
36520 GATAGCTT-AGCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GATAGCTTCGGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
36566 GCTACACTTA
Statistics
Matches: 128, Mismatches: 6, Indels: 19
0.84 0.04 0.12
Matches are distributed among these distances:
88 4 0.03
89 26 0.20
92 1 0.01
94 45 0.35
97 13 0.10
98 1 0.01
101 24 0.19
102 14 0.11
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (91 bp):
GATAGCTTCGGCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGATAGCTTCAGCTACACTT
ATCTGATCAAGTGACAAGTGATAAGT
Found at i:36555 original size:51 final size:53
Alignment explanation
Indices: 36401--36565 Score: 252
Period size: 50 Copynumber: 3.2 Consensus size: 53
36391 TTATCTGATC
36401 AAGTGACAAGT-ATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-
1 AAGTGACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACA
36452 AAGT-A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACA
1 AAGTGACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACA
* **
36503 AAGTGA-AAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAAACA
1 AAGTGACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACA
*
36554 AAGTGATAAGTG
1 AAGTGACAAGTG
36566 GCTACACTTA
Statistics
Matches: 107, Mismatches: 3, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
49 4 0.04
50 41 0.38
51 37 0.35
52 25 0.23
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.27
Consensus pattern (53 bp):
AAGTGACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACA
Done.