Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold278
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: 111759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:868 original size:48 final size:48
Alignment explanation
Indices: 754--976 Score: 211
Period size: 48 Copynumber: 4.4 Consensus size: 48
744 GGTAAGAGAT
*
754 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATC-ATGAGGG
1 CCCATGTAAGACCATGTCTGGGACATGGCA-TGGCA-CC--GAGA-CGA-GA-GG
*
808 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACGAGAGG
1 -CCCATGTAAGACCATGTCTGGGACATGGCAT-GGCACCGAGACGAGAGG
* *
858 -CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 CCCATGTAAGACCATGTCTGGGACATGGC-ATGGCACCGAGACGAGAGG
* * * **
906 TCCCCTATAAGACCATGTCT-GGACATGGCATGGCACC-ATCACGAGAACAT
1 -CCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGA-GACGAG-A-GG
956 CCCATGTAAGACCATGTCTGG
1 CCCATGTAAGACCATGTCTGG
977 ACAGGCTTTG
Statistics
Matches: 145, Mismatches: 14, Indels: 23
0.80 0.08 0.13
Matches are distributed among these distances:
47 1 0.01
48 54 0.37
49 28 0.19
50 19 0.13
51 3 0.02
52 4 0.03
54 3 0.02
55 33 0.23
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (48 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATGGCACCGAGACGAGAGG
Found at i:7961 original size:29 final size:30
Alignment explanation
Indices: 7902--7959 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
7892 TCCGAGCCTT
*
7902 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
7932 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
7960 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:8188 original size:13 final size:13
Alignment explanation
Indices: 8170--8201 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
8160 TTTCCAGCAA
8170 TTATGAATTTATT
1 TTATGAATTTATT
8183 TTATGAATTTATT
1 TTATGAATTTATT
*
8196 TGATGA
1 TTATGA
8202 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:8443 original size:50 final size:50
Alignment explanation
Indices: 8296--8543 Score: 302
Period size: 50 Copynumber: 4.8 Consensus size: 50
8286 ATTTGGGTAA
* *
8296 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--G
*
8352 AGAGGTCCC-TGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* *
8401 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
* * * *
8451 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-GACG
** *
8501 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
8544 TGTTATTATC
Statistics
Matches: 171, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
49 11 0.06
50 81 0.47
51 35 0.20
52 3 0.02
54 2 0.01
55 31 0.18
56 8 0.05
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACG
Found at i:8489 original size:105 final size:102
Alignment explanation
Indices: 8296--8544 Score: 353
Period size: 100 Copynumber: 2.4 Consensus size: 102
8286 ATTTGGGTAA
8296 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
8361 TGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 TATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
8401 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGT-CCCTA
8463 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
65 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
8501 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
8545 GTTATTATCA
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
99 10 0.08
100 43 0.33
101 37 0.28
104 2 0.02
105 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (102 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCTAT
AAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:13928 original size:112 final size:109
Alignment explanation
Indices: 13779--13991 Score: 295
Period size: 108 Copynumber: 1.9 Consensus size: 109
13769 TTGTCAATAT
13779 AATATAATAATAAAGAATAAAAGATATTTCCATCAATTCATATACATATCATATAATAATAAACT
1 AATATAATAATAAAGAATAAAAGATATTTCCATCAATTCATATACATAT--TAT-ATAATAAA-T
* *
13844 TTACATCCAATAAGTACTTCAATTATTTTATATAAAAAAACTCTAATG
62 TTACATACAATAAGCACTTCAATTATTTTATATAAAAAAACTCTAATG
* * *
13892 AATATAATAA-AAATAATAAAATATAATTT-CATCAATTCATATGCATATTATATAATAAATTTA
1 AATATAATAATAAAGAATAAAAGAT-ATTTCCATCAATTCATATACATATTATATAATAAATTTA
* * *
13955 CATACAATGAGCATTTTAATTATTTTATATAAAAAAA
65 CATACAATAAGCACTTCAATTATTTTATATAAAAAAA
13992 GCCTTATTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
108 36 0.40
109 8 0.09
110 3 0.03
112 30 0.33
113 14 0.15
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (109 bp):
AATATAATAATAAAGAATAAAAGATATTTCCATCAATTCATATACATATTATATAATAAATTTAC
ATACAATAAGCACTTCAATTATTTTATATAAAAAAACTCTAATG
Found at i:24773 original size:25 final size:26
Alignment explanation
Indices: 24745--24793 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
24735 TTTTCTTTCT
*
24745 TTATTATTTGTTTT-TAAAATTTTTA
1 TTATTATTTATTTTATAAAATTTTTA
*
24770 TTATTATTTATTTTATAATATTTT
1 TTATTATTTATTTTATAAAATTTT
24794 AAATGTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATTATTTATTTTATAAAATTTTTA
Found at i:27504 original size:19 final size:20
Alignment explanation
Indices: 27482--27530 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
27472 TTTAACTTTT
*
27482 TCTTT-ATGTTTTAAGTAAC
1 TCTTTCATGTTTTAAATAAC
* *
27501 TCTTTCATATTTTAAATAAT
1 TCTTTCATGTTTTAAATAAC
27521 TCTTTCATGT
1 TCTTTCATGT
27531 ATTACTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.55
Consensus pattern (20 bp):
TCTTTCATGTTTTAAATAAC
Found at i:34748 original size:22 final size:22
Alignment explanation
Indices: 34718--34760 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34708 AGATATAAAC
*
34718 TATTTTAAAT-TCTTTTATTATG
1 TATTGTAAATCTC-TTTATTATG
34740 TATTGTAAATCTCTTTATTAT
1 TATTGTAAATCTCTTTATTAT
34761 CATTTATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
TATTGTAAATCTCTTTATTATG
Found at i:39034 original size:13 final size:13
Alignment explanation
Indices: 39016--39046 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
39006 CCATATCCCT
39016 CTCAAAAAATTTC
1 CTCAAAAAATTTC
39029 CTC-AAAAATTTC
1 CTCAAAAAATTTC
39041 CTCAAA
1 CTCAAA
39047 TTTATCTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (13 bp):
CTCAAAAAATTTC
Found at i:39587 original size:5 final size:5
Alignment explanation
Indices: 39579--39605 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
39569 AAATTAAAAT
39579 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
39606 AAAATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:46146 original size:26 final size:28
Alignment explanation
Indices: 46098--46164 Score: 97
Period size: 26 Copynumber: 2.5 Consensus size: 28
46088 TTAAAGACAC
46098 TATTATAAATATAATAAATATTTTATTA
1 TATTATAAATATAATAAATATTTTATTA
*
46126 TATTATAAA-A-AGTAAATATTTTATTA
1 TATTATAAATATAATAAATATTTTATTA
46152 TA-T-TAAATATAAT
1 TATTATAAATATAAT
46165 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 4 0.11
25 2 0.06
26 19 0.54
27 1 0.03
28 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTATAAATATAATAAATATTTTATTA
Found at i:47714 original size:22 final size:23
Alignment explanation
Indices: 47687--47729 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
47677 TTATAATCAA
47687 ATATAAACACATAATT-TTATTT
1 ATATAAACACATAATTATTATTT
* *
47709 ATATAAATATATAATTATTAT
1 ATATAAACACATAATTATTAT
47730 ATTTTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATAAACACATAATTATTATTT
Found at i:49075 original size:26 final size:24
Alignment explanation
Indices: 49050--49098 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
49040 CACTTGCACC
49050 CCCCATTTT-TTTGACTTTTCAACA
1 CCCC-TTTTATTTGACTTTTCAACA
49074 CCCCTTTTAATTTGACTTTTCAACA
1 CCCCTTTT-ATTTGACTTTTCAACA
49099 TAATCCACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 15 0.65
ACGTcount: A:0.22, C:0.29, G:0.04, T:0.45
Consensus pattern (24 bp):
CCCCTTTTATTTGACTTTTCAACA
Found at i:50597 original size:3 final size:3
Alignment explanation
Indices: 50589--50638 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
50579 AATAAATAGG
* * *
50589 TAA TAA TAA TAA TAG TAG TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50637 TA
1 TA
50639 GGACTAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51438 original size:11 final size:11
Alignment explanation
Indices: 51412--51444 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
51402 AAACGATTGC
51412 AGAAAAAT-AA
1 AGAAAAATAAA
*
51422 ACAAAAATAAA
1 AGAAAAATAAA
51433 AGAAAAATAAA
1 AGAAAAATAAA
51444 A
1 A
51445 TGAATAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 7 0.35
11 13 0.65
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (11 bp):
AGAAAAATAAA
Found at i:52493 original size:87 final size:87
Alignment explanation
Indices: 52377--52538 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
52367 AAACTTGATG
* * * * * *
52377 CGATCTACTCTGCTGTGACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
52441 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * * *
52464 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
52529 CAGGGAGATA
66 CAGGGAGATA
52539 AGATCTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
87 62 0.98
88 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:52524 original size:44 final size:43
Alignment explanation
Indices: 52389--52757 Score: 236
Period size: 44 Copynumber: 8.6 Consensus size: 43
52379 ATCTACTCTG
* * * ** * *
52389 CTGTGACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGAT-CTCTGCTTCAATCTGCTCCA
* * ** * *
52433 CTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCTG-CTTCAATCTGCTCCA
*
52476 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCT-GCTTCAATCTGCTCCA
* * * ** *
52520 CTGTAACCTCAGGGAGATAAGATCTGAAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCT---CTGCTTCAATCTGCTCCA
* * * * *
52566 CTGTAACCTCAGGGAAATAAGA-C-CTGATGT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCTCTGCT-TCAATCTGCTCCA
* * *
52607 CTGTAACTTCAGAGAGATAAGATC-CT--TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGCTTCAATCTGCTCCA
* * * * * ** *
52646 TTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGC-CCG
1 CTGTAACCTCAGGGAGATAAGATCT-CT-GCTTCAATCTGCTCCA
* *
52689 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCT-GCTTCAATCTGCTCCA
52733 CTGTAACCTCAGGGAGATAAGATCT
1 CTGTAACCTCAGGGAGATAAGATCT
52758 GAAATTCTTT
Statistics
Matches: 251, Mismatches: 58, Indels: 32
0.74 0.17 0.09
Matches are distributed among these distances:
39 25 0.10
40 3 0.01
41 29 0.12
42 4 0.02
43 65 0.26
44 90 0.36
45 2 0.01
46 32 0.13
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCTCTGCTTCAATCTGCTCCA
Found at i:52707 original size:213 final size:214
Alignment explanation
Indices: 52338--52804 Score: 661
Period size: 213 Copynumber: 2.2 Consensus size: 214
52328 GTTGTTTTCA
* * * * * * *
52338 GTCTATTCCACTGCATCTTCAGGGAAATAAAACTTGATGCGATCTACTCTGCTGTGACCTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* * *
52403 AGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGAT
66 AGATAAGATCC----TTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGAT
52468 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGG
127 CTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGG
52533 GAGATAAGATCTGAAATTCTCCG
192 GAGATAAGATCTGAAATTCTCCG
* * * *
52556 GTCTACTCCACTGTAACCTCAGGGAAATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
* *
52621 AGATAAGATCC-TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTTTGATCT
66 AGATAAGATCCTTTTAATCCGCTCCACTGTAACT-TCAAGGAGATAGGA-TACTATCTTCGATCT
*
52684 GC-CCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCGCTGTAACCTCAGGGA
129 GCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
**
52748 GATAAGATCTGAAATTCTTTG
194 GATAAGATCTGAAATTCTCCG
* * *
52769 GTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG
1 GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTG
52805 TATAATAAAC
Statistics
Matches: 224, Mismatches: 23, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
212 1 0.00
213 144 0.64
214 14 0.06
218 65 0.29
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (214 bp):
GTCTATTCCACTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAG
AGATAAGATCCTTTTAATCCGCTCCACTGTAACTTCAAGGAGATAGGATACTATCTTCGATCTGC
TCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
TAAGATCTGAAATTCTCCG
Found at i:63975 original size:24 final size:25
Alignment explanation
Indices: 63928--63977 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
63918 GGATTTATGC
63928 TTGAAAAGTCAAATTAAAAAGGGGTG
1 TTGAAAAGTCAAA-TAAAAAGGGGTG
*
63954 TTGAAAAGTCAAA-AAAATGGGGTG
1 TTGAAAAGTCAAATAAAAAGGGGTG
63978 CAAGTGGGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.43
26 13 0.57
ACGTcount: A:0.46, C:0.04, G:0.28, T:0.22
Consensus pattern (25 bp):
TTGAAAAGTCAAATAAAAAGGGGTG
Found at i:66888 original size:19 final size:20
Alignment explanation
Indices: 66841--66893 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
66831 CAAAATATAA
66841 AATTTTA-AAAATTATATTT
1 AATTTTATAAAATTATATTT
* *
66860 AATATAATAAAATTAT-TTT
1 AATTTTATAAAATTATATTT
* *
66879 ACTTTTATAATATTA
1 AATTTTATAAAATTA
66894 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTTTATAAAATTATATTT
Found at i:68993 original size:13 final size:13
Alignment explanation
Indices: 68971--69004 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
68961 TGGATTTTTA
*
68971 ATTATTTATATAT
1 ATTATATATATAT
68984 ATTATATATATAT
1 ATTATATATATAT
68997 ATT-TATAT
1 ATTATATAT
69005 TTGAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:74011 original size:13 final size:13
Alignment explanation
Indices: 73993--74024 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
73983 ATTTAATAAA
*
73993 TTTGAGGACAATT
1 TTTGAGGAAAATT
74006 TTTGAGGAAAATT
1 TTTGAGGAAAATT
74019 TTTGAG
1 TTTGAG
74025 AGGGAATGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.41
Consensus pattern (13 bp):
TTTGAGGAAAATT
Found at i:75814 original size:9 final size:9
Alignment explanation
Indices: 75800--75824 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
75790 TTAAATTAAA
75800 ATTTATTTT
1 ATTTATTTT
75809 ATTTATTTT
1 ATTTATTTT
75818 ATTTATT
1 ATTTATT
75825 AAAATCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
ATTTATTTT
Found at i:82540 original size:24 final size:23
Alignment explanation
Indices: 82513--82560 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
82503 TTAGATATTA
82513 TTATAAATATAA-ATATATATAATT
1 TTATAAAT-TAACATATAT-TAATT
*
82537 TTATTAATTAACATATATTAATT
1 TTATAAATTAACATATATTAATT
82560 T
1 T
82561 ATTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TTATAAATTAACATATATTAATT
Found at i:83790 original size:28 final size:30
Alignment explanation
Indices: 83733--83791 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
83723 ATAATTTTTA
* *
83733 ATTTCTTTTATAATTTATTTTAAATTAAAT
1 ATTTCTTTTATAATGTATTTTAAATAAAAT
83763 ATTT-TTTTATAA-GTATTTATAAA-AAAAT
1 ATTTCTTTTATAATGTATTT-TAAATAAAAT
83791 A
1 A
83792 AGACTACGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 10 0.38
29 12 0.46
30 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTTCTTTTATAATGTATTTTAAATAAAAT
Found at i:86985 original size:3 final size:3
Alignment explanation
Indices: 86977--87031 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
86967 ATAAATTATG
* * *
86977 TAA TAA TAA TAAA TAGT TAG TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
87024 TAA TAA TA
1 TAA TAA TA
87032 GACTGAATTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
3 42 0.89
4 5 0.11
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:87492 original size:10 final size:9
Alignment explanation
Indices: 87479--87503 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
87469 ATGAAAAGAG
87479 AAAAAAAAT
1 AAAAAAAAT
87488 AAAAAAAAT
1 AAAAAAAAT
87497 AAAAAAA
1 AAAAAAA
87504 GAAACAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:88933 original size:44 final size:43
Alignment explanation
Indices: 88840--89159 Score: 181
Period size: 44 Copynumber: 7.7 Consensus size: 43
88830 TTTAATCCGC
* * **
88840 CCACTGTAACTTCA-GGAGATAGGAT-AGTGTCTTCGATCTGCT
1 CCACTGTAACCTCAGGGAGATAAGATCTCTG-CTTCGATCTGCT
* * *
88882 CCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCT
1 CCACTGTAACCTCAGGGAGATAAGATCTCT-GCTTCGATCTGCT
* * * *
88926 CCACTGTAACCTCAGGGAGATAAGATCTGAAATTC-TCGGTCTACT
1 CCACTGTAACCTCAGGGAGATAAGATCT---CTGCTTCGATCTGCT
* * * *
88971 CCACTGTAACCTCAGGGAAATAAGACCTATG--T-GATCTTCT
1 CCACTGTAACCTCAGGGAGATAAGATCTCTGCTTCGATCTGCT
* * * * *
89011 CTTACTGTAACTTCAGAGAGATAAGATC-CT--TT-AATCCGCT
1 C-CACTGTAACCTCAGGGAGATAAGATCTCTGCTTCGATCTGCT
* * * * * *
89051 CCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGC-
1 CCACTGTAACCTCAGGGAGATAAGATCT-CT-GCTTCGATCTGCT
* *
89094 CC-C-GTGAATCTCA-GGAGATAAGATCTCTGCTTCAATC-GCT
1 CCACTGT-AACCTCAGGGAGATAAGATCTCTGCTTCGATCTGCT
89134 -C-CTGTAACCTCAGGGAGATAAGATCT
1 CCACTGTAACCTCAGGGAGATAAGATCT
89160 GAAATTTTTG
Statistics
Matches: 216, Mismatches: 43, Indels: 40
0.72 0.14 0.13
Matches are distributed among these distances:
39 28 0.13
40 38 0.18
41 36 0.17
42 21 0.10
43 14 0.06
44 43 0.20
45 34 0.16
46 1 0.00
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (43 bp):
CCACTGTAACCTCAGGGAGATAAGATCTCTGCTTCGATCTGCT
Found at i:89182 original size:206 final size:210
Alignment explanation
Indices: 88830--89204 Score: 559
Period size: 206 Copynumber: 1.8 Consensus size: 210
88820 GATCCTTTAT
* * *
88830 TTTAATCCGCCCACTGTAACTTCAGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTC
1 TTTAATCCGCCCACTGTAACTTCAGGAGATAGGATACTATCTTCGATCTGCCCCGCTGTAATCTC
88895 AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
66 AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
88960 CTCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTATGTGATCTTCTCTTACTGTAACTTC
131 CTCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTATGTGATCTTCTCTTACTGTAACTTC
89025 AGAGAGATAAGATCC
196 AGAGAGATAAGATCC
* *
89040 TTTAATCCGCTCCATTGTAA-TCTCAAGGAGATAGGATTACTATCTTTGATCTGCCCCG-TG-AA
1 TTTAATCCGC-CCACTGTAACT-TC-AGGAGATAGGA-TACTATCTTCGATCTGCCCCGCTGTAA
89102 TCTCA-GGAGATAAGATCTCT-GCTTCAATC-GCT-C-CTGTAACCTCAGGGAGATAAGATCTGA
62 TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGA
* * ** * *
89162 AATTTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCT
127 AATTCTCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCT
89205 GTATAATAAA
Statistics
Matches: 150, Mismatches: 11, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
206 64 0.43
207 1 0.01
208 3 0.02
209 9 0.06
210 26 0.17
211 17 0.11
212 13 0.09
213 17 0.11
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (210 bp):
TTTAATCCGCCCACTGTAACTTCAGGAGATAGGATACTATCTTCGATCTGCCCCGCTGTAATCTC
AGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
CTCGGTCTACTCCACTGTAACCTCAGGGAAATAAGACCTATGTGATCTTCTCTTACTGTAACTTC
AGAGAGATAAGATCC
Found at i:107885 original size:1 final size:1
Alignment explanation
Indices: 107879--107907 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
107869 TTTGCTTCCT
107879 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
107908 CTTTGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:109173 original size:46 final size:46
Alignment explanation
Indices: 109106--109313 Score: 175
Period size: 46 Copynumber: 4.7 Consensus size: 46
109096 CTATAAAAGG
109106 TCTTAT-TCCCCTGAGATTACAGTGGAACAGACTAAAGAATTTCAGA
1 TCTTATCT-CCCTGAGATTACAGTGGAACAGACTAAAGAATTTCAGA
* * * * * *
109152 TCTTATCTCCCTGA-AGTTACAGTAGAGCAGA-T--CGCA--CCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGACTAAAGAATTTCAGA
* *
109193 TCTTATTTCCCTGAGATTACAGTGAAACAGACTAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACTAAAGAATTTCAGA
* * * * * *
109239 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA---GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACTAAAG-AATTTCAGA
* *
109283 TCTTATCTCCCTGAGATTACAGCGGAGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGA
109314 TCGAAGACAC
Statistics
Matches: 129, Mismatches: 24, Indels: 20
0.75 0.14 0.12
Matches are distributed among these distances:
41 28 0.22
42 2 0.02
43 2 0.02
44 34 0.26
45 2 0.02
46 59 0.46
47 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGACTAAAGAATTTCAGA
Found at i:109249 original size:87 final size:88
Alignment explanation
Indices: 109103--109304 Score: 316
Period size: 87 Copynumber: 2.3 Consensus size: 88
109093 TCACTATAAA
* *
109103 AGGTCTTATTCCCCTGAGATTACAGTGGAACAGACTAAAGAATTTCAGATCTTATCTCCCTGAAG
1 AGGTCTTATTTCCCTGAGATTACAGTGAAACAGACTAAAGAATTTCAGATCTTATCTCCCTGAAG
*
109168 TTACAGTAGAGCAGATCGCA-CC
66 TTACAGTAGAGCAGATCGAAGCC
*
109190 AGGTCTTATTTCCCTGAGATTACAGTGAAACAGACTAAAGAATTTCAGATCTTATCTCCCTGAGG
1 AGGTCTTATTTCCCTGAGATTACAGTGAAACAGACTAAAGAATTTCAGATCTTATCTCCCTGAAG
* *
109255 TTACAGTGGAGCAGATTGAAGCC
66 TTACAGTAGAGCAGATCGAAGCC
*
109278 AGAGATCTTATCTCCCTGAGATTACAG
1 AG-G-TCTTATTTCCCTGAGATTACAG
109305 CGGAGCAGAT
Statistics
Matches: 105, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
87 79 0.75
88 4 0.04
89 1 0.01
90 21 0.20
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (88 bp):
AGGTCTTATTTCCCTGAGATTACAGTGAAACAGACTAAAGAATTTCAGATCTTATCTCCCTGAAG
TTACAGTAGAGCAGATCGAAGCC
Found at i:109295 original size:44 final size:44
Alignment explanation
Indices: 109149--109391 Score: 183
Period size: 44 Copynumber: 5.6 Consensus size: 44
109139 AAAGAATTTC
* * * * *
109149 AGATCTTATCTCCCTGAAGTTACAGTAGAGCAGATCGCA-CCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAG
* * * * * * *
109192 -G-TCTTATTTCCCTGAGATTACAGTGAAACAGACTAAAGA-ATTTC
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACA---G
*
109236 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAG
* * *
109280 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAG
** * * * * * *
109323 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATT-AAAATAA
1 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAG
*
109366 AGGATCTTATCTCTCTGAGGTTACAG
1 A-GATCTTATCTCCCTGAGGTTACAG
109392 CAGAGTAGAT
Statistics
Matches: 152, Mismatches: 39, Indels: 17
0.73 0.19 0.08
Matches are distributed among these distances:
41 27 0.18
42 5 0.03
43 28 0.18
44 59 0.39
45 1 0.01
46 31 0.20
47 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGACAG
Found at i:109333 original size:87 final size:87
Alignment explanation
Indices: 109242--109403 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
109232 TTTCAGATCT
* * * *
109242 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
109306 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
109329 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
109394 GAGTAGATCG
66 GAGCAGATCG
109404 CATCAGGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Done.