Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3616.1
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: 114881
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.32
Warning! 2281 characters in sequence are not A, C, G, or T
Found at i:224 original size:33 final size:32
Alignment explanation
Indices: 181--247 Score: 125
Period size: 33 Copynumber: 2.1 Consensus size: 32
171 TGACACCATA
181 AATTGGGTCACAATACGTAGTATAATGTAGGG
1 AATTGGGTCACAATACGTAGTATAATGTAGGG
213 ANATTGGGTCACAATACGTAGTATAATGTAGGG
1 A-ATTGGGTCACAATACGTAGTATAATGTAGGG
246 AA
1 AA
248 AAAATGTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.27
Consensus pattern (32 bp):
AATTGGGTCACAATACGTAGTATAATGTAGGG
Found at i:18006 original size:30 final size:30
Alignment explanation
Indices: 17971--18029 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
17961 CTTTGAGTAC
*
17971 TTATAAATAAATATTAA-TAAATTTATTTAA
1 TTATAAATAAA-AGTAATTAAATTTATTTAA
* *
18001 TTATAATTAAAAGTAATTAAATTTTTTTA
1 TTATAAATAAAAGTAATTAAATTTATTTA
18030 TTTCTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
TTATAAATAAAAGTAATTAAATTTATTTAA
Found at i:21763 original size:8 final size:9
Alignment explanation
Indices: 21742--21768 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21732 GTTTTTATTA
21742 AAAAAATTT
1 AAAAAATTT
21751 AAAAAATTT
1 AAAAAATTT
21760 AAAAAATTT
1 AAAAAATTT
21769 TTATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAAATTT
Found at i:29084 original size:18 final size:18
Alignment explanation
Indices: 29061--29119 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
29051 TTGTTTATTG
29061 TTATTCAATAACAATCAA
1 TTATTCAATAACAATCAA
* * *
29079 TTATTCAGTATCAAAC-A
1 TTATTCAATAACAATCAA
*
29096 --A-TCAATAAAAATCAA
1 TTATTCAATAACAATCAA
29111 TTATTCAAT
1 TTATTCAAT
29120 CTAGTAATAC
Statistics
Matches: 30, Mismatches: 7, Indels: 8
0.67 0.16 0.18
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
17 2 0.07
18 18 0.60
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (18 bp):
TTATTCAATAACAATCAA
Found at i:31660 original size:427 final size:427
Alignment explanation
Indices: 30842--32068 Score: 2229
Period size: 427 Copynumber: 2.9 Consensus size: 427
30832 CATATGACAT
* *
30842 ATCAGGTCGAATTTCAGTATCCACTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGA
1 ATCAGGTCGAATTTCAAT-TCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGA
* *
30907 GCATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACAATATGTA
65 GCATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCA
*
30972 ACTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAATGAGAACTTAGTTTTCCTTTTCG
130 ACTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCG
* *
31037 ACCGAATCTCATAATTTTCTTCCGAGGTGAAACTTTTAAAAATACCTTATCACCAACCGCGTACT
195 ACCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACT
31102 CAATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCT
260 CAATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCT
31167 CGAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAA
325 CGAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAA
31232 TTCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
390 TTCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
31270 ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
1 ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
31335 CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
66 CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
* * *
31400 TTGGTCCAACTCTATCAATAATCTCATATGGCCCAATAAAACGAGAATTTAGTTTTCCTTTTCGA
131 CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCGA
31465 CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
196 CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
31530 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
261 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
* *
31595 GAATCTTCTTAATAGTGTCTTCTATTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAAT
326 GAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAAT
*
31660 TCAGCTAACGGTAGATAACGTTCCCAACCGATTCAAG
391 TCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
*
31697 ATCAGGTCTAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
1 ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
* *
31762 CATAGAAACATGAAAAACATCATGAATTTTTTGCAATTCTGGAAGTAAAGCCAGACGATATGCAA
66 CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
*
31827 CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGGACTTAGTTTTCCTTTTCGA
131 CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCGA
* * *
31892 CCGAATCTCAGAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAATCGCATACTC
196 CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
* *
31957 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTACCTGTCAAAAGTTGCTTTCAATCTTTCTC
261 AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
* *
32022 GAATCTTCTTAACAGTATCTCCTGTTTCTTGAATTAATTCTGGCCCA
326 GAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCA
32069 ATCATTTTCT
Statistics
Matches: 770, Mismatches: 29, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
427 753 0.98
428 17 0.02
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (427 bp):
ATCAGGTCGAATTTCAATTCCTCTGTAGAAATAATAAGAAAAGGATCTGATCGATATCTTCTGAG
CATAGAAACATGAAAAACATCATGAATCTTTTGCAATTCTGGAAGCAAAGCCAGACGATATGCAA
CTGGTCCAACTCTCTCAATAATCTCATATGGCCCAATAAAACGAGAACTTAGTTTTCCTTTTCGA
CCGAATCTCATAATTTTCTTCCAAGGTGAAACTTTTAGAAATACCTTATCACCAACCGCGTACTC
AATGTCTCTACGTTTCAGATCTGCATATGACTTCTGCCTGTCAAAAGCTGCTTTCAATCTTTCTC
GAATCTTCTTAACAGTGTCTTCTGTTTCTTGAATTAATTCTGGCCCACTATTATTGCATACAAAT
TCAGCTAACGGTACATAACGTTCCCAACCGATTCAAG
Found at i:34929 original size:75 final size:75
Alignment explanation
Indices: 34806--34955 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 75
34796 TAACATAATA
34806 ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
1 ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
34871 CCATATTGTG
66 CCATATTGTG
* * * * *
34881 ATGTGATGATCTTGGATCTATTAAAGCATAAACGGGTTCTGAGTACAATAAAAATATACCCGTCA
1 ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
34946 CCATATTGTG
66 CCATATTGTG
34956 TACATCTCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (75 bp):
ATGTGACGATCCTAGATCTATTAAAGCATAAACGAGTTCTGAGTACAATAAAAATATACCAGTCA
CCATATTGTG
Found at i:36758 original size:47 final size:47
Alignment explanation
Indices: 36667--36758 Score: 114
Period size: 47 Copynumber: 2.0 Consensus size: 47
36657 CCAACACACC
* * * *
36667 AGTACGGCACTCAGTGCCTCATCGGCTTTATCGAAGTAAGTAGTAGT
1 AGTACGGCACTCAGTACCTCATCGGATTAACCGAAGTAAGTAGTAGT
* *
36714 AGTACGGTACTTAGTACCTCATCGGATTAAACCGAAGTAA-TAGTA
1 AGTACGGCACTCAGTACCTCATCGGATT-AACCGAAGTAAGTAGTA
36759 ACAGTATGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 29 0.76
48 9 0.24
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (47 bp):
AGTACGGCACTCAGTACCTCATCGGATTAACCGAAGTAAGTAGTAGT
Found at i:36803 original size:44 final size:44
Alignment explanation
Indices: 36755--36846 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
36745 CCGAAGTAAT
* *
36755 AGTAACAGTATGACACACA-AGGTGCCTCATCGACTCGAA-GTCGA
1 AGTAACAATACGACACACATA-GTGCCTCATCGACTC-AAGGTCGA
** *
36799 AGTAACAATACGACACTTATAGTGCTTCATCGACTCAAGGTCGA
1 AGTAACAATACGACACACATAGTGCCTCATCGACTCAAGGTCGA
36843 AGTA
1 AGTA
36847 TCCCTGAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 2 0.05
44 38 0.93
45 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (44 bp):
AGTAACAATACGACACACATAGTGCCTCATCGACTCAAGGTCGA
Found at i:37745 original size:3 final size:3
Alignment explanation
Indices: 37737--37761 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37727 TCGTTACTTT
37737 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
37762 AACATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:39294 original size:12 final size:12
Alignment explanation
Indices: 39277--39301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39267 CACAAGTTAG
39277 TGCATTTATGTA
1 TGCATTTATGTA
39289 TGCATTTATGTA
1 TGCATTTATGTA
39301 T
1 T
39302 ATAACTCATT
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:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TGCATTTATGTA
Found at i:40285 original size:17 final size:16
Alignment explanation
Indices: 40265--40303 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
40255 AAACCCAATT
40265 CAATATTATAATTCCAA
1 CAATATT-TAATTCCAA
*
40282 CAATAATTTATTTCCAA
1 CAAT-ATTTAATTCCAA
40299 CAATA
1 CAATA
40304 GAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.80
18 3 0.15
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
CAATATTTAATTCCAA
Found at i:49747 original size:33 final size:33
Alignment explanation
Indices: 49705--49770 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
49695 TGTAAAATTT
*
49705 TCCCTACATTTCCGCTACTCCCGAGGCTCAACG
1 TCCCTACATTTCCGCTACTCCCGAGGCACAACG
49738 TCCCTACATTTCCGCTACTCCCGAGGCACAACG
1 TCCCTACATTTCCGCTACTCCCGAGGCACAACG
49771 GTGAAGCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.42, G:0.15, T:0.23
Consensus pattern (33 bp):
TCCCTACATTTCCGCTACTCCCGAGGCACAACG
Found at i:71660 original size:15 final size:14
Alignment explanation
Indices: 71619--71667 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
71609 GAAATTTGTA
*
71619 TTTT-TTTTTCTTTT
1 TTTTCTTTTTC-TCT
71633 TTTTCTTTTTCTCT
1 TTTTCTTTTTCTCT
71647 TTTTCATTTTTCTCT
1 TTTTC-TTTTTCTCT
71662 GTTTTC
1 -TTTTC
71668 GGCTATAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.35
15 15 0.48
16 5 0.16
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTCTCT
Found at i:79581 original size:30 final size:30
Alignment explanation
Indices: 79547--79605 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
79537 GATTTTTTTA
** *
79547 GGTTTTATATATTATTATGATTATTATTAT
1 GGTTTTATATAAAATTATGATAATTATTAT
*
79577 GGTTTTATATAAAATTATTATAATTATTA
1 GGTTTTATATAAAATTATGATAATTATTA
79606 ATTAACATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (30 bp):
GGTTTTATATAAAATTATGATAATTATTAT
Found at i:79636 original size:21 final size:20
Alignment explanation
Indices: 79569--79637 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
79559 TATTATGATT
*
79569 ATTATTATGGTTTTATATAAA
1 ATTATTATGGTTTTATAT-TA
**
79590 ATTATTATAATTATTA-ATTA
1 ATTATTATGGTT-TTATATTA
*
79610 A-CATTATGGTTTTATATTA
1 ATTATTATGGTTTTATATTA
79629 GATTATTAT
1 -ATTATTAT
79638 TATTAGCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 11 0.30
20 3 0.08
21 17 0.46
22 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (20 bp):
ATTATTATGGTTTTATATTA
Found at i:80050 original size:12 final size:12
Alignment explanation
Indices: 80033--80063 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
80023 GAAGCAGGGG
80033 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
80045 AGAAAAAGGGAA
1 AGAAAAAGAGAA
80057 AGAAAAA
1 AGAAAAA
80064 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:82634 original size:33 final size:32
Alignment explanation
Indices: 82560--82677 Score: 94
Period size: 33 Copynumber: 3.6 Consensus size: 32
82550 ATGAACTTGA
* ** * **
82560 GCCGAGAGGAGTAGAATATGGAGGTGAATATAG
1 GCCG-GAGGAGTAGAGTACAGAGGTGGATACGG
* *
82593 GCCGGGAGGAGTAGAGTACGGCGGTGGATAC-G
1 GCC-GGAGGAGTAGAGTACAGAGGTGGATACGG
* *
82625 GCTCTGGAGGAGTTGAGTACATAGGTGGATACGG
1 GC-C-GGAGGAGTAGAGTACAGAGGTGGATACGG
82659 GCCGGAAGGAGTAGAGTAC
1 GCCGG-AGGAGTAGAGTAC
82678 TGAGATAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
32 5 0.07
33 61 0.87
34 4 0.06
ACGTcount: A:0.28, C:0.12, G:0.43, T:0.17
Consensus pattern (32 bp):
GCCGGAGGAGTAGAGTACAGAGGTGGATACGG
Found at i:87298 original size:22 final size:22
Alignment explanation
Indices: 87264--87327 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
87254 TCAACATTTT
*
87264 AATAAATCA-ATAAAAATTATCA
1 AATAAAT-ATATAAAAATTATAA
*
87286 AATAAATATATAATAA-TATAA
1 AATAAATATATAAAAATTATAA
*
87307 AATTACATTATATAAAAATTA
1 AA-TA-AATATATAAAAATTA
87328 CATTAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 15 0.44
23 10 0.29
24 2 0.06
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATATATAAAAATTATAA
Found at i:87321 original size:15 final size:16
Alignment explanation
Indices: 87301--87332 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
87291 ATATATAATA
87301 ATAT-AAAATTACATT
1 ATATAAAAATTACATT
87316 ATATAAAAATTACATT
1 ATATAAAAATTACATT
87332 A
1 A
87333 AAAAATCACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAAATTACATT
Found at i:87566 original size:115 final size:113
Alignment explanation
Indices: 87390--87833 Score: 653
Period size: 115 Copynumber: 3.9 Consensus size: 113
87380 ATACTAACAC
* * * ** *
87390 AAAATAACTATAAAATTATTTTTTT-GAATGCATTACTAAAAAAAAATCACAATACATTAATACA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT--AAAAAAATCACAATACACTAAT--A
87454 CACTAAACCACTAAACACTAACAA-TATATAACCTAATCTTAAATTACTAAT
62 CACTAAACCACTAAACACTAACAATTATATAACCTAATCTTAAATTACTAAT
*
87505 AAAATAGCTATAAAAATATTTTTTTTAAATATATTACTAAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT-AAAAAAATCACAATACACTAATACAC
87570 TAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
65 TAAACCACTAAACACTAACAA-TTATATAACCTAATCTTAAATTACTAAT
* * * *
87620 AAAATATCTATAAAAATATTTTTTAAAAATATATTACTAAAAAAATTACAATACGCTAAT--ACT
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACT
87683 AAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 AAACCACTAAACACTAACAA-TTATATAACCTAATCTTAAATTACTAAT
*
87732 AAAATAGCTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAAATATTTTTTT-AAAATATATTACTAAAAAAATCACAATACACTAATACAC
* *
87797 TAAACTACTAAACACTAACAATTTATATAACCAAATC
65 TAAACCACTAAACACTAACAA-TTATATAACCTAATC
87834 AACTATAAAA
Statistics
Matches: 305, Mismatches: 18, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
112 74 0.24
113 58 0.19
114 20 0.07
115 144 0.47
116 9 0.03
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (113 bp):
AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATACACT
AAACCACTAAACACTAACAATTATATAACCTAATCTTAAATTACTAAT
Found at i:89027 original size:131 final size:129
Alignment explanation
Indices: 88759--89013 Score: 357
Period size: 131 Copynumber: 2.0 Consensus size: 129
88749 CAATTATTCA
* * * * *
88759 TTTAAAAATTCTTTAAAACGAAGGCAATACTTGATGTTTGGCAATTCGGAATCGTGCCCTATCGT
1 TTTAAAAACTCTTCAAAACAAAGGCAATACTCGATGTTTAGCAATTCGGAATCGTGCCCTATCGT
* *
88824 GCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCAAATATTCCTTTGAAATTTTACTCATGTC
66 GCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCAAATATCCCTTTGAAATTTCACTCATGTC
* *
88888 TTTAAAAACTCTTCAAAACAAAGGTAATACTCGATGTTTAGCAATTAGGAGAATCGTGCCCTATC
1 TTTAAAAACTCTTCAAAACAAAGGCAATACTCGATGTTTAGCAATT-CG-GAATCGTGCCCTATC
* * * ** *
88953 GTGCTGGGTTGCGATTTCCTGTTTGTTCAAAATAATTGAATATCCCTTTGGAATTTCACTC
64 GTGCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCAAATATCCCTTTGAAATTTCACTC
89014 GTGTTTCCTA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
129 40 0.37
130 1 0.01
131 68 0.62
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (129 bp):
TTTAAAAACTCTTCAAAACAAAGGCAATACTCGATGTTTAGCAATTCGGAATCGTGCCCTATCGT
GCTGGGTTGCAATTTCCCGTTTGTTCAAAACAATCAAATATCCCTTTGAAATTTCACTCATGTC
Found at i:92754 original size:25 final size:25
Alignment explanation
Indices: 92720--92769 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
92710 ATACCCAATG
92720 AAGTCAACTGAAAAACTGTTGTTTT
1 AAGTCAACTGAAAAACTGTTGTTTT
*
92745 AAGTCAACTGAAAACCTGTTGTTTT
1 AAGTCAACTGAAAAACTGTTGTTTT
92770 CTTAAGAGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (25 bp):
AAGTCAACTGAAAAACTGTTGTTTT
Found at i:96064 original size:3 final size:3
Alignment explanation
Indices: 96058--96884 Score: 1654
Period size: 3 Copynumber: 275.7 Consensus size: 3
96048 ATAATAATAA
96058 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96106 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96154 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96202 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96250 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96298 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96346 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96394 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96442 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96490 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96538 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96586 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96634 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96682 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96730 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96778 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96826 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
96874 TAG TAG TAG TA
1 TAG TAG TAG TA
96885 ACAACAGTGG
Statistics
Matches: 824, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 824 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:100459 original size:25 final size:26
Alignment explanation
Indices: 100431--100486 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
100421 CATTTAGGTC
**
100431 AATTTAAC-CCTAGGGGTATTTCAGT
1 AATTTAACACCTAGGGGTATAACAGT
**
100456 AATTTTGCACCTAGGGGTATAACAGT
1 AATTTAACACCTAGGGGTATAACAGT
100482 AATTT
1 AATTT
100487 TCCATGCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (26 bp):
AATTTAACACCTAGGGGTATAACAGT
Found at i:100468 original size:26 final size:27
Alignment explanation
Indices: 100439--100514 Score: 84
Period size: 26 Copynumber: 2.8 Consensus size: 27
100429 TCAATTTAAC
*
100439 CCTAGGGGTATTTCAGTAATTTTGCA-
1 CCTAGGGGTATTTCAGTAATTTTCCAG
**
100465 CCTAGGGGTATAACAGTAATTTTCCATG
1 CCTAGGGGTATTTCAGTAATTTTCCA-G
*
100493 CATAGGGGTATTAT-AGTAATTT
1 CCTAGGGGTATT-TCAGTAATTT
100515 AGCTGTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 23 0.56
28 18 0.44
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (27 bp):
CCTAGGGGTATTTCAGTAATTTTCCAG
Found at i:101993 original size:26 final size:26
Alignment explanation
Indices: 101957--102012 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
101947 TGAAATTCCA
*
101957 ATCATGGAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
101983 ATCATGAAACATTTACCTAACCCATT
1 ATCATGAAACATTTACCTAACCCATT
102009 ATCA
1 ATCA
102013 ATTTGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (26 bp):
ATCATGAAACATTTACCTAACCCATT
Found at i:107168 original size:131 final size:130
Alignment explanation
Indices: 107000--107259 Score: 430
Period size: 131 Copynumber: 2.0 Consensus size: 130
106990 AATTTAGAGA
* *
107000 ACATGAGTGAAATTCTAAACGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCTAGCAC
1 ACATGAGTGAAATTCCAAACGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGCAC
* *
107065 GATAGGGCACGATTGCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTGAAGAGTCTTTAAA
66 GATAGGGCACGATT-CCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTAAAGAATCTTTAAA
107130 G
130 G
* * *
107131 ACATGAGTGAAATTCCAAAGGAATATTCGATTGTTTTGAACAAACGGGAAATCGCAACCCAGCAC
1 ACATGAGTGAAATTCCAAACGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGCAC
* *
107196 GATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTGCCTTCGTTTTAAAGAATTTTTAAA
66 GATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTAAAGAATCTTTAAA
107260 TGAATAATTA
Statistics
Matches: 120, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 46 0.38
131 74 0.62
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (130 bp):
ACATGAGTGAAATTCCAAACGAATATTCGATTATTTTGAACAAACAGGAAATCGCAACCCAGCAC
GATAGGGCACGATTCCCGAATTGCCAAACATCGAGTATTACCTTCGTTTTAAAGAATCTTTAAAG
Found at i:107771 original size:16 final size:15
Alignment explanation
Indices: 107750--107795 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
107740 CTAGAGATAT
107750 ATACATAATTATTAAA
1 ATACAT-ATTATTAAA
*
107766 ATACATGTTA-TAAA
1 ATACATATTATTAAA
*
107780 ATAAATATT-TTAAA
1 ATACATATTATTAAA
107794 AT
1 AT
107796 CGAATAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 17 0.65
15 3 0.12
16 6 0.23
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (15 bp):
ATACATATTATTAAA
Found at i:112881 original size:22 final size:23
Alignment explanation
Indices: 112852--112985 Score: 116
Period size: 22 Copynumber: 5.7 Consensus size: 23
112842 CACTAATGAA
112852 CAGAGAGCACTGAAGTGCTATAT
1 CAGAGAGCACTGAAGTGCTATAT
*
112875 -AGAGAGCAC-AAATGTGCTA-AT
1 CAGAGAGCACTGAA-GTGCTATAT
*
112896 CAGAGAGCACTGATGTGCTAAATAT
1 CAGAGAGCACTGAAGTGCT--ATAT
*
112921 CAGAGAGCAC-AAATGTGCTA-AT
1 CAGAGAGCACTGAA-GTGCTATAT
* *
112943 CAAAGAGCACTGACGTGCTAATATT
1 CAGAGAGCACTGAAGTGCT-ATA-T
112968 CAGAGAGCATGCTGAAGT
1 CAGAGAGCA--CTGAAGT
112986 CCCTTAACAT
Statistics
Matches: 88, Mismatches: 10, Indels: 22
0.73 0.08 0.18
Matches are distributed among these distances:
21 4 0.05
22 45 0.51
23 4 0.05
24 3 0.03
25 26 0.30
27 6 0.07
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (23 bp):
CAGAGAGCACTGAAGTGCTATAT
Found at i:112929 original size:47 final size:46
Alignment explanation
Indices: 112852--112976 Score: 191
Period size: 47 Copynumber: 2.7 Consensus size: 46
112842 CACTAATGAA
112852 CAGAGAGCACTGAAGTGCT-ATAT-AGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGAAGTGCTAATATCAGAGAGCACAAATGTGCTAAT
*
112896 CAGAGAGCACTGATGTGCTAAATATCAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACTGAAGTGCT-AATATCAGAGAGCACAAATGTGCTAAT
* *
112943 CAAAGAGCACTGACGTGCTAATATTCAGAGAGCA
1 CAGAGAGCACTGAAGTGCTAATA-TCAGAGAGCA
112977 TGCTGAAGTC
Statistics
Matches: 74, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
44 18 0.24
46 8 0.11
47 48 0.65
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (46 bp):
CAGAGAGCACTGAAGTGCTAATATCAGAGAGCACAAATGTGCTAAT
Done.