Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1206
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: 146566
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:143367 original size:30 final size:30
Alignment explanation
Indices: 143331--143581 Score: 245
Period size: 30 Copynumber: 8.1 Consensus size: 30
143321 CAAATCTCTC
* *
143331 TTTTCTAAGTCCACGACTCAGTGGCATCTA
1 TTTTCAAAGTCCACGACTCAGTGGCATCTT
*
143361 TTTTCTAAGTCCACGACTCAGTGGCATCCTT
1 TTTTCAAAGTCCACGACTCAGTGGCAT-CTT
* * *
143392 TTCTTCCAAGTCCACGACTTAGTAGCATCTTTTT
1 TT-TTCAAAGTCCACGACTCAGTGGCATC---TT
* *
143426 TTCTTCAACGTCCACGACTCAGTGGCATCTC
1 TT-TTCAAAGTCCACGACTCAGTGGCATCTT
* * *
143457 TTCTCAAAGTCCACGATTTAGTGGCATCTT
1 TTTTCAAAGTCCACGACTCAGTGGCATCTT
*
143487 TTCTTCAAAGTCCACGACTCAATGGCAT-TT
1 TT-TTCAAAGTCCACGACTCAGTGGCATCTT
* *
143517 TTCTTCAAAGTTCACGACTCAGTGGCAATCTC
1 TT-TTCAAAGTCCACGACTCAGTGGC-ATCTT
* **
143549 TTCTCAAAGTCCATAACTTC-GTGGCATCTT
1 TTTTCAAAGTCCACGAC-TCAGTGGCATCTT
143579 TTT
1 TTT
143582 CCCTTTTAAA
Statistics
Matches: 185, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
30 84 0.45
31 47 0.25
32 27 0.15
34 27 0.15
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.35
Consensus pattern (30 bp):
TTTTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:143513 original size:61 final size:62
Alignment explanation
Indices: 143327--143561 Score: 264
Period size: 61 Copynumber: 3.8 Consensus size: 62
143317 TCTTCAAATC
* * *
143327 TCTCTT-TTCTAAGTCCACGACTCAGTGGCATCTATT-TTCTAAGTCCACGACTCAGTGGCA
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * * * *
143387 TCCTTTTCTTCCAAGTCCACGACTTAGTAGCATCTTTTTTTCTTCAACGTCCACGACTCAGTGGC
1 T-CTCTTCTTCAAAGTCCACGACTCAGTGGCATC---TTTTCTTCAAAGTCCACGACTCAGTGGC
143452 A
62 A
* * *
143453 TCTCTTC-TCAAAGTCCACGATTTAGTGGCATCTTTTCTTCAAAGTCCACGACTCAATGGCA
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
* * *
143514 T-TTTTCTTCAAAGTTCACGACTCAGTGGCAATCTCTTC-TCAAAGTCCA
1 TCTCTTCTTCAAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGTCCA
143562 TAACTTCGTG
Statistics
Matches: 149, Mismatches: 18, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
60 5 0.03
61 61 0.41
62 30 0.20
64 22 0.15
65 8 0.05
66 23 0.15
ACGTcount: A:0.23, C:0.29, G:0.14, T:0.34
Consensus pattern (62 bp):
TCTCTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA
Found at i:143714 original size:35 final size:35
Alignment explanation
Indices: 143648--143986 Score: 169
Period size: 33 Copynumber: 9.9 Consensus size: 35
143638 CTTTTTCTTT
* * *
143648 TTTTTTAAGTCCACAACTCCGTGGCACCTTTTT-C
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* *
143682 TTTTTAAAGCCCATAGCTCCGTTGCACTCTTTTTCC
1 TTTTTAAAGCCCATAACTCCGTGGCAC-CTTTTTCC
143718 TTTTTAAAGCCCATAACTCCGTGGCACCCTTGCACTCTTTTTTCC
1 TTTTTAAAGCCCATAACTCCGT-G-------GCAC-C-TTTTTCC
* * * *
143763 CTTTTAAAGCCCACAATTTCGTGGCA-C-----CC
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* * * **
143792 -TTTT-AAGTCCACAACTCCGTGACATATTTTTCC
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* * * *
143825 -TTTT-AAGTCCACAACTCTGTGGCACCTTGTTCC
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* *
143858 -TTTT-AAGTCCATAACTCCGTGGCATCTTTTTCC
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* * *
143891 -TTTT-AAGTCCACAACTCCGTGGCACCTTATTCC
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* *
143924 -TTTT-AAGTCCACAACTCCGTGGCACC-TTTT-C
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
* * ** *
143955 TTTTT-GAGTCCACGACTCCGTGGCACCCTTTT
1 TTTTTAAAGCCCATAACTCCGTGGCACCTTTTT
143987 AAGCCCACAA
Statistics
Matches: 255, Mismatches: 31, Indels: 39
0.78 0.10 0.12
Matches are distributed among these distances:
27 16 0.06
28 4 0.02
29 2 0.01
31 1 0.00
32 27 0.11
33 119 0.47
34 22 0.09
35 7 0.03
36 22 0.09
37 3 0.01
44 7 0.03
45 25 0.10
ACGTcount: A:0.19, C:0.31, G:0.13, T:0.37
Consensus pattern (35 bp):
TTTTTAAAGCCCATAACTCCGTGGCACCTTTTTCC
Found at i:143753 original size:44 final size:45
Alignment explanation
Indices: 143703--143793 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
143693 CATAGCTCCG
* *
143703 TTGCACTC-TTTTTCCTTTTTAAAGCCCATAACTCCGTGGCACCC
1 TTGCACTCTTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCC
* *
143747 TTGCACTCTTTTTTCCCTTTTAAAGCCCACAATTTCGTGGCACCC
1 TTGCACTCTTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCC
143792 TT
1 TT
143794 TTAAGTCCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 8 0.19
45 34 0.81
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (45 bp):
TTGCACTCTTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCC
Found at i:143827 original size:33 final size:33
Alignment explanation
Indices: 143790--144048 Score: 298
Period size: 33 Copynumber: 8.0 Consensus size: 33
143780 TTCGTGGCAC
* **
143790 CCTTTTAAGTCCACAACTCCGTGACATATTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
143823 CCTTTTAAGTCCACAACTCTGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* *
143856 CCTTTTAAGTCCATAACTCCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
*
143889 CCTTTTAAGTCCACAACTCCGTGGCACCTTATT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
143922 CCTTTTAAGTCCACAACTCCGTGGCACC-TTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
143954 CTTTTTGAGTCCACGACTCCGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
143981 CCTTTTAAGCCCACAACTCTGTGGCACTTTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTT
* * * *
144015 CCTTTTAAGCCCACAAGTCAGTGGCACCCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
144048 C
1 C
144049 AAAAGCCCAC
Statistics
Matches: 193, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
27 21 0.11
31 1 0.01
32 26 0.13
33 120 0.62
34 25 0.13
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:143901 original size:99 final size:92
Alignment explanation
Indices: 143757--144048 Score: 323
Period size: 99 Copynumber: 3.1 Consensus size: 92
143747 TTGCACTCTT
* * * *
143757 TTTTCCCTTTTAAAGCCCACAATTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGACATATTTT
1 TTTT-CCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATATTTT
*
143822 TCCTTTTAAGTCCACAACTCTGTGGCACC
64 TCCTTTTAAGTCCACAACTCAGTGGCACC
* *
143851 TTGTTCCTTTTAAGTCCATAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
1 TT-TTCCTTTTAAGTCCACAACTCCGTGGCA-C-----CCTTTTAAGTCCACAACTCCGTGGCAT
* * *
143916 CTTATTCCTTTTAAGTCCACAACTCCGTGGCACC
59 ATTTTTCCTTTTAAGTCCACAACTCAGTGGCACC
* * * * * *
143950 TTTTCTTTTTGAGTCCACGACTCCGTGGCACCCTTTTAAGCCCACAACTCTGTGGCACTTTTTTT
1 TTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-TATTTTT
* *
144015 CCTTTTAAGCCCACAAGTCAGTGGCACCC
65 CCTTTTAAGTCCACAACTCAGTGGCA-CC
144044 TTTTC
1 TTTTC
144049 AAAAGCCCAC
Statistics
Matches: 168, Mismatches: 21, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
92 24 0.14
93 43 0.26
94 16 0.10
95 2 0.01
97 1 0.01
98 24 0.14
99 58 0.35
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (92 bp):
TTTTCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATATTTTTC
CTTTTAAGTCCACAACTCAGTGGCACC
Found at i:144013 original size:27 final size:27
Alignment explanation
Indices: 143891--144013 Score: 75
Period size: 27 Copynumber: 4.1 Consensus size: 27
143881 ATCTTTTTCC
*
143891 TTTTAAGTCCACAACTCCGTGGCACCTTATT
1 TTTTAAGCCCACAACTCCGTGGCACC----T
*
143922 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTCT
1 --TTTTAAGCCCACAACTCCGTGGCA-C----CT
* * * *
143956 TTTTGAGTCCACGACTCCGTGGCACCC
1 TTTTAAGCCCACAACTCCGTGGCACCT
* *
143983 TTTTAAGCCCACAACTCTGTGGCACTT
1 TTTTAAGCCCACAACTCCGTGGCACCT
144010 TTTT
1 TTTT
144014 TCCTTTTAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
27 26 0.34
31 1 0.01
32 22 0.29
33 24 0.32
34 2 0.03
38 1 0.01
ACGTcount: A:0.19, C:0.32, G:0.15, T:0.35
Consensus pattern (27 bp):
TTTTAAGCCCACAACTCCGTGGCACCT
Found at i:144086 original size:28 final size:28
Alignment explanation
Indices: 144021--144113 Score: 141
Period size: 28 Copynumber: 3.2 Consensus size: 28
144011 TTTTCCTTTT
*
144021 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC--TTCAA
*
144051 AAGCCCACAAGTTAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
*
144079 AAGCCCACAAGTCAGTGGCAACTTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTCAA
144107 AAGCCCA
1 AAGCCCA
144114 AACAAGTTGG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
28 38 0.64
30 21 0.36
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTCAA
Found at i:144305 original size:49 final size:49
Alignment explanation
Indices: 144154--145208 Score: 397
Period size: 49 Copynumber: 21.4 Consensus size: 49
144144 ACTATCACTA
* * * *
144154 GCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAA-ATCCAATGTCGTTG
1 GCCTTGAATCAGCACATTGGCACC-TT-T-ATCTTTAAGA-CCAATATCGCTG
* * * * * * * *
144206 GCCATAAATCAGCACATTGTCATTCTTCGCACCTTCAAGCCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCA-CCTT--TATCTTTAAGACCAATATCGCTG
* * * * *
144258 CCCTTGAATCAGCATATTGGTACCTTTGTCTTTAAGACCAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
*
144307 GCCTTGAATCAGCACA-TGG--GC---A----TAAG-CTCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGAC-CAATATCGCTG
* * * * * *
144346 GCCTTGAATCAGTATATTGGCACCTTCATCTTTAAGACCCATGTCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* * * * * *
144395 GCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTA
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* ** **
144444 TCCTTGAATCAGCACATCAGCACCTCAACCATCTTTAAG-CCTAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACCT---TTATCTTTAAGACC-AATATCGCTG
* * * *
144496 GCCTTGAATCAGCATATGGGCA-CATTGTCTTTAAGACCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* * * **
144544 GCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCATTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* * * * * * * * *
144593 GCCTTGCATTAGTATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTTATC-TT--TAAGACCAATATCGCTG
** * * *
144645 GCCTTGTCTCAGCACATTGGCA--TTCT-TCTTCAAGTCCAATGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCTT-TATCTTTAAGACCAATATCGCTG
* *
144692 GCCTTGAATCAGCACATTGG---C---A----TAAGCCCAATATCGCTT
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* * * *
144731 ACCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAACATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
** * ** ** *
144779 GCCTTGAATCAGCACATTGGCATAAGCCCAATATCGTTCATATTGGCACCTTTATCTTTAA
1 GCCTTGAATCAGCACATTGGC---A--CCTTTATC-TT--TA--AG-ACCAATATCGCT-G
* * * * ** * * *
144840 G--ATCAATGTCACTGGC-C-TTGAATCAGCACATTGGC-ATAAGCCCAATATCGTTG
1 GCCTTGAA--TCA---GCACATTG--GCA-C-CTTTATCTTTAAGACCAATATCGCTG
** * * * * *
144893 GCCTTGAATCAATATATTGGCAACTTCATCTTTAAGACCAATGTCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* *** *
144942 GCCTTGAATCAGCACATCGGCACGTCAACCATATTTAAG-CCTAATATCGCTG
1 GCCTTGAATCAGCACATTGGCAC--C-TTTATCTTTAAGACC-AATATCGCTG
* * **
144994 GCCTTGAATCAGCATATTGGCA--TATTGTCTTTAAGACCAACGTCGCTG
1 GCCTTGAATCAGCACATTGGCACCT-TTATCTTTAAGACCAATATCGCTG
* *
145042 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
* * * * * * *
145091 GCCTTGCATCAGCATATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTA
1 GCCTTGAATCAGCACATTGGCACCTTTATC-TT--TAAGACCAATATCGCTG
** * * * * *
145143 GCCTTGTCTCAGCACATTGGCA--TTCT-TCTTCAAGTCTAATGTCGTTG
1 GCCTTGAATCAGCACATTGGCACCTT-TATCTTTAAGACCAATATCGCTG
*
145190 GCCATGAATCAGCACATTG
1 GCCTTGAATCAGCACATTG
145209 TTATTCTTCA
Statistics
Matches: 750, Mismatches: 179, Indels: 153
0.69 0.17 0.14
Matches are distributed among these distances:
38 1 0.00
39 59 0.08
40 3 0.00
42 2 0.00
45 1 0.00
46 1 0.00
47 60 0.08
48 112 0.15
49 240 0.32
50 14 0.02
51 12 0.02
52 188 0.25
53 8 0.01
54 11 0.01
55 6 0.01
57 4 0.01
59 4 0.01
60 8 0.01
61 9 0.01
62 3 0.00
63 1 0.00
64 3 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
GCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGACCAATATCGCTG
Found at i:144397 original size:88 final size:88
Alignment explanation
Indices: 144242--144814 Score: 267
Period size: 88 Copynumber: 6.1 Consensus size: 88
144232 TCGCACCTTC
* **
144242 AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGTACCTTTGTCTTTAAGACCAATGTCGCTG
1 AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTG
144307 GCCTTGAATCAGCACATGGGCAT
66 GCCTTGAATCAGCACATGGGCAT
* * * * *
144330 AAGCTCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTCATCTTTAAGACCCATGTCGTTG
1 AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTG
* *
144395 GCCTTGAATCAGCATATTGGCACCTTCATCTTT
66 GCCTTGAATCAGCACA-TGG-----GCA----T
* * * * ** * ** * *
144428 AAGACCGATGTCGTTATCCTTGAATCAGCACATCAGCACCTCAACCATCTTTAAG-CCTAATATC
1 AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGCACCT---TCATCTTTAAGACC-AATGTC
*
144492 GCTGGCCTTGAATCAGCATATGGGCACATTGTCTTT
62 GCTGGCCTTGAATCAGCACATGGG--CA-------T
* * * * * * **
144528 AAGACCAATATCGCTGGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCATTG
1 AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTG
* * * * *
144593 GCCTTGCATTAGTATATTGGCAT
66 GCCTTGAATCAGCACATGGGCAT
** * * ** ** * * * *
144616 ---CTTTAACATTC-CTAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGGCATTCTTCTTCA
1 AAGC-CCAATA-TCGCT--GCCC-TTG-AATCAG-CATAT-T-GGCACCTT--CA-TC-T-TT-A
* *
144677 AGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAT
51 AGACCAATGTCGCTGGCCTTGAATCAGCACATGGGCAT
** * **
144715 AAGCCCAATATCGCTTACCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAACATCGCTG
1 AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTG
*
144779 GCCTTGAATCAGCACATTGGCAT
66 GCCTTGAATCAGCACATGGGCAT
144802 AAGCCCAATATCG
1 AAGCCCAATATCG
144815 TTCATATTGG
Statistics
Matches: 364, Mismatches: 82, Indels: 79
0.69 0.16 0.15
Matches are distributed among these distances:
86 5 0.01
87 51 0.14
88 78 0.21
89 6 0.02
90 4 0.01
91 1 0.00
92 1 0.00
93 6 0.02
94 8 0.02
95 5 0.01
96 5 0.01
97 39 0.11
98 37 0.10
99 34 0.09
100 45 0.12
101 38 0.10
102 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (88 bp):
AAGCCCAATATCGCTGCCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCAATGTCGCTG
GCCTTGAATCAGCACATGGGCAT
Found at i:144632 original size:149 final size:150
Alignment explanation
Indices: 144329--144713 Score: 411
Period size: 149 Copynumber: 2.6 Consensus size: 150
144319 CACATGGGCA
* * * * *
144329 TAAGCTCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTCATCTTTAAGACCCATGTCGTT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGCT
* * * * *
144394 GGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTATCCTTGAATCAGCAC
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCATTAGCCTTGAATCAGCAC
*
144459 ATCAGCACCTCAACCATCTT
131 ATCAGCACCTCAACCATCTC
* * * *
144479 TAAGCCTAATATCGCTGGCCTTGAATCAGCATATGGGCACATT-GTCTTTAAGACCAATATCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGCT
* * * * * * *
144543 GGCCTTGAATCAGTACATTGGCACCTTCATCTTTAAGTCCAATATCATTGGCCTTGCATTAGTAT
66 GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCATTAGCCTTGAATCAGCAC
** * *
144608 ATTGGCATCTTTAA-CAT-TCC
131 ATCAGCA-CCTCAACCATCT-C
* * ** * * * *
144628 TAAGCCCAATGTCGTTGGCCTTGTCTCAGCACATTGG--CATTCTTCTTCAAGTCCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGCT
144691 GGCCTTGAATCAGCACATTGGCA
66 GGCCTTGAATCAGCACATTGGCA
144714 TAAGCCCAAT
Statistics
Matches: 194, Mismatches: 38, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
147 4 0.02
148 40 0.21
149 108 0.56
150 42 0.22
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (150 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTCATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGACCAATATCATTAGCCTTGAATCAGCAC
ATCAGCACCTCAACCATCTC
Found at i:144711 original size:99 final size:97
Alignment explanation
Indices: 144473--144801 Score: 245
Period size: 99 Copynumber: 3.5 Consensus size: 97
144463 GCACCTCAAC
* * **
144473 CATCTTTAAG-CCTAATATCGCTGGCCTTGAATCAGCATATGGGCA-CATTGTCTTTAAGACCAA
1 CATCTTCAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCATCATTAACTTTAAGACCAA
*
144536 TATCGCTGGCCTTGAATCAGTACATTGGCACCTT
65 TATCGCTGGCCTTGAATCAGCACATTGGCA-CTT
* ** * * * * *
144570 CATCTTTAAGTCCAATATCATTGGCCTTGCATTAGTATATTGGCATCTTTAACATTCCTAAGCCC
1 CATCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATTAAC-TT--TAAGACC
* * **
144635 AATGTCGTTGGCCTTGTCTCAGCACATTGGCA-TT
63 AATATCGCTGGCCTTGAATCAGCACATTGGCACTT
* * * *
144669 CTTCTTCAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG---C----A---TAAGCCCAAT
1 CATCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATTAACTTTAAGACCAAT
** *
144724 ATCGCTTACCTTGAATCAGCATATTGGCACCTT
66 ATCGCTGGCCTTGAATCAGCACATTGGCA-CTT
* * * * *
144757 -GTCTTTAAGACCAACATCGCTGGCCTTGAATCAGCACATTGGCAT
1 CATCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT
144802 AAGCCCAATA
Statistics
Matches: 186, Mismatches: 36, Indels: 27
0.75 0.14 0.11
Matches are distributed among these distances:
86 32 0.17
87 37 0.20
88 2 0.01
92 1 0.01
96 1 0.01
97 36 0.19
98 6 0.03
99 38 0.20
101 33 0.18
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (97 bp):
CATCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCATTAACTTTAAGACCAAT
ATCGCTGGCCTTGAATCAGCACATTGGCACTT
Found at i:144736 original size:39 final size:39
Alignment explanation
Indices: 144680--144814 Score: 126
Period size: 39 Copynumber: 3.2 Consensus size: 39
144670 TTCTTCAAGT
* *
144680 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGACCTTGAATCAGCACATTGGCATAAGC
* * *
144719 CCAATATCGCTTACCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGACCTTGAATCAGCACATTGGCA---------TAAGC
* *
144767 CCAACATCGCTGGCCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGACCTTGAATCAGCACATTGGCATAAGC
144806 CCAATATCG
1 CCAATATCG
144815 TTCATATTGG
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
39 42 0.55
48 34 0.45
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (39 bp):
CCAATATCGCTGACCTTGAATCAGCACATTGGCATAAGC
Found at i:144865 original size:75 final size:74
Alignment explanation
Indices: 144743--144891 Score: 244
Period size: 75 Copynumber: 2.0 Consensus size: 74
144733 CTTGAATCAG
* *
144743 CATATTGGCACCTTGTCTTTAAGACCAACATCGCTGGCCTTGAATCAGCACATTGGCATAAGCCC
1 CATATTGGCACCTTATCTTTAAGACCAACATCACTGGCCTTGAATCAGCACATTGGCATAAGCCC
144808 AATATCGTT
66 AATATCGTT
* **
144817 CATATTGGCACCTTTATCTTTAAGATCAATGTCACTGGCCTTGAATCAGCACATTGGCATAAGCC
1 CATATTGGCACC-TTATCTTTAAGACCAACATCACTGGCCTTGAATCAGCACATTGGCATAAGCC
144882 CAATATCGTT
65 CAATATCGTT
144892 GGCCTTGAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 12 0.17
75 57 0.83
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (74 bp):
CATATTGGCACCTTATCTTTAAGACCAACATCACTGGCCTTGAATCAGCACATTGGCATAAGCCC
AATATCGTT
Found at i:145162 original size:52 final size:48
Alignment explanation
Indices: 144908--145165 Score: 164
Period size: 52 Copynumber: 5.2 Consensus size: 48
144898 GAATCAATAT
* * * * *
144908 ATTGGCAACTTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCAC
1 ATTGGCATCTTTAACTTTAAGACCAATGTCGCTGGCCTTG-CTCAGCAC
* * * * * *
144957 ATCGGCA-CGTCAACCATATTTAAG-CCTAATATCGCTGGCCTTGAATCAGCAT
1 ATTGGCATCTTTAA-C---TTTAAGACC-AATGTCGCTGGCCTTG-CTCAGCAC
* * *
145009 ATTGGCATATTGT--CTTTAAGACCAACGTCGCTGGCCTTGAATCAGCAC
1 ATTGGCATCTT-TAACTTTAAGACCAATGTCGCTGGCCTTG-CTCAGCAC
* * * * * *
145057 ATTGGCACCTTTATCTTTAAGTCCAATATCGTTGGCCTTGCATCAGCAT
1 ATTGGCATCTTTAACTTTAAGACCAATGTCGCTGGCCTTGC-TCAGCAC
* *
145106 ATTGGCATCTTTAACATTCCTAAGCCCAATGTCGCTAGCCTTGTCTCAGCAC
1 ATTGGCATCTTTAAC-TT--TAAGACCAATGTCGCTGGCCTTG-CTCAGCAC
145158 ATTGGCAT
1 ATTGGCAT
145166 TCTTCTTCAA
Statistics
Matches: 166, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
47 1 0.01
48 41 0.25
49 50 0.30
50 2 0.01
51 3 0.02
52 67 0.40
53 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (48 bp):
ATTGGCATCTTTAACTTTAAGACCAATGTCGCTGGCCTTGCTCAGCAC
Found at i:145162 original size:149 final size:148
Alignment explanation
Indices: 144891--145208 Score: 354
Period size: 149 Copynumber: 2.1 Consensus size: 148
144881 CCAATATCGT
** * *
144891 TGGCCTTGAATCAATATATTGGCAACTTCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCA
1 TGGCCTTGAATCAGCACATTGGCAACTTCATCTTTAAGACCAATATCGTTGGCCTTGAATCAGCA
* * * *
144956 CATCGGCACGTCAACCATATTTAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCATAT-T
66 CATCGGCACGTCAACCATATCTAAGCCCAATATCGCTAGCCTTGAATCAGCACATTGGCAT-TCT
*
145020 GTCTTTAAGACCAACGTCGC
130 -TCTTCAAGACCAACGTCGC
* * * *
145040 TGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAGTCCAATATCGTTGGCCTTGCATCAGCA
1 TGGCCTTGAATCAGCACATTGGCAACTTCATCTTTAAGACCAATATCGTTGGCCTTGAATCAGCA
* * * * * **
145105 TATTGGCATCTTTAA-CAT-TCCTAAGCCCAATGTCGCTAGCCTTGTCTCAGCACATTGGCATTC
66 CATCGGCA-CGTCAACCATAT-CTAAGCCCAATATCGCTAGCCTTGAATCAGCACATTGGCATTC
* * * *
145168 TTCTTCAAGTCTAATGTCGT
129 TTCTTCAAGACCAACGTCGC
*
145188 TGGCCATGAATCAGCACATTG
1 TGGCCTTGAATCAGCACATTG
145209 TTATTCTTCA
Statistics
Matches: 141, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
148 36 0.26
149 101 0.72
150 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (148 bp):
TGGCCTTGAATCAGCACATTGGCAACTTCATCTTTAAGACCAATATCGTTGGCCTTGAATCAGCA
CATCGGCACGTCAACCATATCTAAGCCCAATATCGCTAGCCTTGAATCAGCACATTGGCATTCTT
CTTCAAGACCAACGTCGC
Found at i:145981 original size:19 final size:21
Alignment explanation
Indices: 145934--145988 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
145924 AATTTTAACA
145934 TTTGTATCGATACAAACAGTG
1 TTTGTATCGATACAAACAGTG
** *
145955 AATGTATCGATACATA-AGT-
1 TTTGTATCGATACAAACAGTG
145974 TTTGTATCGATACAA
1 TTTGTATCGATACAA
145989 TGTATCGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (21 bp):
TTTGTATCGATACAAACAGTG
Found at i:145994 original size:13 final size:13
Alignment explanation
Indices: 145976--146001 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
145966 ACATAAGTTT
145976 TGTATCGATACAA
1 TGTATCGATACAA
145989 TGTATCGATACAA
1 TGTATCGATACAA
146002 AAGCTATCCT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:146039 original size:20 final size:20
Alignment explanation
Indices: 146014--146060 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
146004 GCTATCCTGC
*
146014 ATACATTACTCAATGTATTG
1 ATACATTACTCAATGTATAG
146034 ATACATTACTCAATGTATAG
1 ATACATTACTCAATGTATAG
146054 ATACATT
1 ATACATT
146061 GTATCGATAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (20 bp):
ATACATTACTCAATGTATAG
Done.