Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold846
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: 33035
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:989 original size:20 final size:20
Alignment explanation
Indices: 964--1015 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
954 TTTACCCAGA
964 TGTATCGATACATTATTCAT
1 TGTATCGATACATTATTCAT
984 TGTATCGATACATTATTCAT
1 TGTATCGATACATTATTCAT
1004 TGTATCGATACA
1 TGTATCGATACA
1016 ATGTATCGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
TGTATCGATACATTATTCAT
Found at i:1022 original size:13 final size:13
Alignment explanation
Indices: 1004--1028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
994 CATTATTCAT
1004 TGTATCGATACAA
1 TGTATCGATACAA
1017 TGTATCGATACA
1 TGTATCGATACA
1029 TTCTGGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3548 original size:79 final size:78
Alignment explanation
Indices: 3350--3573 Score: 244
Period size: 78 Copynumber: 2.9 Consensus size: 78
3340 TTTTTCATCT
* * * * **
3350 CGGGGATACTCCAA-CCCGGTTTTATTTATAAAATATTGATTTCTCATAATCAGGGATACTCCAA
1 CGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCACAATTGGGGATACTCCAA
3414 CCCCGTTATTTGG
66 CCCCGTTATTTGG
* * * *
3427 CGGGGACACTCCAACCCCGGCCTTATTTCTAAAGCT-TCGATTTTTCACAATTGGGGATACTCCA
1 CGGGGATACTCCAACCCCGGCTTTATTTCTAAA-ATATTGATTTTTCACAATTGGGGATACTCCA
*
3491 ACCCCGTTATTT-T
65 ACCCCGTTATTTGG
** *
3504 CAAGGGGATACTTAAACCCCGGCTTTATTTCTAAAATATTGATTTTTTATC--TTGGGGATACT-
1 C--GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCA-CAATTGGGGATACTC
3566 CAACCCCG
63 CAACCCCG
3574 GTTTTATTTC
Statistics
Matches: 123, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
77 22 0.18
78 62 0.50
79 38 0.31
80 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCACAATTGGGGATACTCCAA
CCCCGTTATTTGG
Found at i:3610 original size:49 final size:49
Alignment explanation
Indices: 3507--3615 Score: 121
Period size: 49 Copynumber: 2.2 Consensus size: 49
3497 TTATTTTCAA
* * ** * * *
3507 GGGGATACTTAAACCCCGGCTTTATTTCTAAAATATTGATTTTTTATCTT
1 GGGGATAC-TCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATATC
*
3557 GGGGATACTCAACCCCGGTTTTATTTC-AAAACATCAATTTTTCATAATC
1 GGGGATACTCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCAT-ATC
3606 GGGGATACTC
1 GGGGATACTC
3616 CAATCCCGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
48 14 0.28
49 28 0.56
50 8 0.16
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (49 bp):
GGGGATACTCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATATC
Found at i:3639 original size:78 final size:78
Alignment explanation
Indices: 3557--3882 Score: 290
Period size: 79 Copynumber: 4.2 Consensus size: 78
3547 TTTTTATCTT
* *
3557 GGGGATACTCAACCCCGGTTTTATTTC-AAAACATCAATTTTTCATAATCGGGGATACTCCAATC
1 GGGGATACTCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAA-C
3621 CC-GTTATTTTCCGA
65 CCTGTTATTTT-CGA
* * * * * *
3635 GGGGATACTC--CTCCAGCTTTATTTCTAAAATATTAATTTCTCACAATTGGGGATACTCCAACC
1 GGGGATACTCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
* *
3698 CTGTTATTTTGGC
66 CTGTTATTTTCGA
* * * * * * *
3711 GAGGATACTCCAACCCCGGCCTTATTTCTAAAGCTTCGATTTTCCACAATCGGGGATACTCTAAC
1 GGGGATACT-CAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
3776 TCC-GTTATTTTCAA
65 -CCTGTTATTTTCGA
* * ** * * * *
3790 AGGGAAACTCAAACCCCGATTTTATTTC-AAAACA-CTGA-TTTTCTATAATCAGGGATGCTCCA
1 GGGGATACTC-AACCCCGGCTTTATTTCTAAAACATC-AATTTTTC-ACAATCGGGGATACTCCA
3852 ACCCTGTTATTTTCGA
63 ACCCTGTTATTTTCGA
3868 GGGGATACTCCAACC
1 GGGGATACT-CAACC
3883 TCGATTTTTA
Statistics
Matches: 195, Mismatches: 42, Indels: 22
0.75 0.16 0.08
Matches are distributed among these distances:
76 24 0.12
77 46 0.24
78 54 0.28
79 69 0.35
80 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (78 bp):
GGGGATACTCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
CTGTTATTTTCGA
Found at i:3697 original size:127 final size:127
Alignment explanation
Indices: 3428--3698 Score: 327
Period size: 127 Copynumber: 2.1 Consensus size: 127
3418 GTTATTTGGC
* * * * *
3428 GGGGACACTCCAACCCCGGCCTTATTTCTAAAGCTTCGATTTTTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
* * * *
3493 CCCGTTATTTTCAAGGGGATACTTAAACCCCGGCTTTATTTCTAAAATATTGATTTTTTATCTT
66 CCCGTTATTTTCAAGGGGATACTT--ACCCCAGCTTTATTTCTAAAATATTAATTTCTCATCTT
** * *
3557 GGGGATACT-CAACCCCGGTTTTATTTC-AAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
3620 CCCGTTATTTTCCGAGGGGATAC-T-CCTCCAGCTTTATTTCTAAAATATTAATTTCTCA-CAAT
66 CCCGTTATTTT-CAAGGGGATACTTACC-CCAGCTTTATTTCTAAAATATTAATTTCTCATC--T
3682 T
127 T
3683 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
3699 TGTTATTTTG
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
124 3 0.02
125 27 0.22
126 11 0.09
127 48 0.39
128 26 0.21
129 8 0.07
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (127 bp):
GGGGATACTCCAACCCCGGCCTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCAAGGGGATACTTACCCCAGCTTTATTTCTAAAATATTAATTTCTCATCTT
Found at i:3706 original size:204 final size:205
Alignment explanation
Indices: 3339--3742 Score: 485
Period size: 204 Copynumber: 2.0 Consensus size: 205
3329 AAATTTCTAT
* * **
3339 ATTTTTCATCTCGGGGATACTCCAACCCGGTTTTATTTATAAAATATTGATTTCTCATAATCAGG
1 ATTTTTCATCTCGGGGATACTCCAACCCGGTTTTATTTACAAAACATCAATTTCTCATAATCAGG
* * * * *
3404 GATACTCCAACCCCGTTATTTGGCGGGGACACTCCAACCCCGGCCTTATTTCTAAAGCTTCGATT
66 GATACTCCAACCCCGTTATTTCGAGGGGACACTCC-ACCCCAGCCTTATTTCTAAAGATTCAATT
* * * *
3469 TTTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTTAAACCCCGGCTTTATTT
130 TCTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCAAACCCCGGCCTTATTT
3534 CTAAAATATTG
195 CTAAAATATTG
* * * *
3545 ATTTTTTATCTTGGGGATACT-CAACCCCGGTTTTATTT-CAAAACATCAATTTTTCATAATCGG
1 ATTTTTCATCTCGGGGATACTCCAA-CCCGGTTTTATTTACAAAACATCAATTTCTCATAATCAG
* * * * *
3608 GGATACTCCAATCCCGTTATTTTCCGAGGGGATACT-C-CTCCAGCTTTATTTCTAAA-ATATTA
65 GGATACTCCAACCCCGTTA-TTT-CGAGGGGACACTCCACCCCAGCCTTATTTCTAAAGAT-TCA
* *** *
3670 ATTTCTCACAATTGGGGATACTCCAACCCTGTTATTTTGGCGAGGATACTCCAACCCCGGCCTTA
127 ATTTCTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCAAACCCCGGCCTTA
3735 TTTCTAAA
192 TTTCTAAA
3743 GCTTCGATTT
Statistics
Matches: 167, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
203 1 0.01
204 81 0.49
205 40 0.24
206 36 0.22
207 9 0.05
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (205 bp):
ATTTTTCATCTCGGGGATACTCCAACCCGGTTTTATTTACAAAACATCAATTTCTCATAATCAGG
GATACTCCAACCCCGTTATTTCGAGGGGACACTCCACCCCAGCCTTATTTCTAAAGATTCAATTT
CTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGAGGATACTCAAACCCCGGCCTTATTTC
TAAAATATTG
Found at i:3888 original size:78 final size:77
Alignment explanation
Indices: 3557--3890 Score: 286
Period size: 78 Copynumber: 4.3 Consensus size: 77
3547 TTTTTATCTT
* * *
3557 GGGGATACT-CAACCCCGGTTTTATTTCAAAACATCAATTTT-TCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCGATTTTATTTCAAAACAT-GATTTTCTCACAATCGGGGATACTCCAA-
3620 CCCGTTATTTTCCGA
64 CCCGTTATTTT-CGA
* * * * * * *
3635 GGGGATACTCC--TCCAG-CTTTATTTCTAAAATATTAATTTCTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTC-AAAACATGATTTTCTCACAATCGGGGATACTCCAAC
* *
3697 CCTGTTATTTTGGC
65 CC-GTTATTTTCGA
* *** * * *
3711 GAGGATACTCCAACCCCGGCCTTATTTCTAAAGCTTCGATTTTC-CACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTC-AAAACAT-GATTTTCTCACAATCGGGGATACTCCAA
*
3775 CTCCGTTATTTTCAA
64 C-CCGTTATTTTCGA
* * * * * *
3790 AGGGAAACTCAAACCCCGATTTTATTTCAAAACACTGATTTTCT-ATAATCAGGGATGCTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCAAAACA-TGATTTTCTCACAATCGGGGATACTCCAAC
3854 CCTGTTATTTTCGA
65 CC-GTTATTTTCGA
*
3868 GGGGATACTCCAACCTCGATTTT
1 GGGGATACTCCAACCCCGATTTT
3891 TAATTCCAGA
Statistics
Matches: 202, Mismatches: 42, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
76 26 0.13
77 38 0.19
78 68 0.34
79 63 0.31
80 7 0.03
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGATTTTATTTCAAAACATGATTTTCTCACAATCGGGGATACTCCAACC
CGTTATTTTCGA
Found at i:17540 original size:61 final size:61
Alignment explanation
Indices: 17420--17608 Score: 263
Period size: 61 Copynumber: 3.1 Consensus size: 61
17410 GAGCAGGATG
* *
17420 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGATGCCTTCT
* * * * * *
17482 CCTTTTAAAGCACACACAAGTTAGTGACACCTTCCAGTCCTCAAAGAGTAGGATGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTCT
* *
17543 CCTCTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATG-CTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCT-TCT
17604 CCTTT
1 CCTTT
17609 CACCCTTTAG
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
60 2 0.02
61 80 0.73
62 27 0.25
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGATGCCTTCT
Found at i:17688 original size:55 final size:55
Alignment explanation
Indices: 17617--17928 Score: 216
Period size: 55 Copynumber: 5.3 Consensus size: 55
17607 TTCACCCTTT
* * * *
17617 AGTCCTCAAAGTGCAGGACGCCTTTCAAAGCCCACCCTAA-TTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACAC-AAGTTGGTGGCACTTTCC
* *
17672 AGTCCTTAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* * *
17727 AGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-C
1 AGTCCTCAAAGAGCAGGACACC-TTT-C----AAAGCCCACACAAGTTGGTGGCACTTTCC
* * * * * * *
17787 AGTCCTTAAAGAGTAAGATGCCTTTTCCTTTTAAAACCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAG-CAG--GAC---ACCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * ** *
17849 AGTCCTCAAAAAGCAGGATACCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTT-T
1 AGTCCTCAAAGAGCAGGACA-C-----C-TTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCC
17911 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
17929 TGCCTTTTCT
Statistics
Matches: 203, Mismatches: 31, Indels: 39
0.74 0.11 0.14
Matches are distributed among these distances:
54 2 0.01
55 66 0.33
56 3 0.01
57 1 0.00
59 1 0.00
60 35 0.17
61 31 0.15
62 30 0.15
63 28 0.14
64 1 0.00
65 3 0.01
66 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:17763 original size:210 final size:212
Alignment explanation
Indices: 17300--17799 Score: 616
Period size: 210 Copynumber: 2.4 Consensus size: 212
17290 TTTCATTTTT
* * * * ** *
17300 CAGTCCTAAAAGAGCAGGACGCTTTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAA
1 CAGTCCTCAAAGAGTAGGACGC-CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAG
* * * *
17365 TCCTCAAAGAGCAGGACGCTCTCCTTTCAACCTTTATTCCTGAAAGAGCAGGATGCCTTTTAAAG
65 TCCTCAAAGAGCAGGACGCTCTCCTTTCAACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAG
* * *
17430 CCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTTCCTTTTAAAGCAC
130 CCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGA-GAC--TACCTTTTAAAGCAC
17495 ACACAAGTTAGTGACACCTTC
192 ACACAAGTTAGTGACACCTTC
* * * *
17516 CAGTCCTCAAAGAGTAGGATGCCTTCTCCTCTTAAAGCCCACACAAGTTGGTGGCACTTTTTAGT
1 CAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGT
* * *
17581 CCTCAAAGAGCAGGATGCTCTCTCCTTTCACCCTTTAGTCCTCAAAGTGCAGGACGCCTTTCAAA
66 CCTCAAAGAGCAGGA--CGCTCTCCTTTCAACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAA
* * *
17646 GCCCACCCTAA-TTGGTGGCA-TTTTCCAGTCCTTAAAGAGC-AG-GAC-ACCTTTTAAAGCCCA
129 GCCCACAC-AAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGAGACTACCTTTTAAAGCACA
* * *
17706 CACAAGTTGGTGGCACTTTC
193 CACAAGTTAGTGACACCTTC
* * *
17726 CAGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCAC-CTTCAGT
1 CAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGT
*
17790 CCTTAAAGAG
66 CCTCAAAGAG
17800 TAAGATGCCT
Statistics
Matches: 246, Mismatches: 35, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
209 14 0.06
210 82 0.33
213 2 0.01
215 52 0.21
216 37 0.15
217 57 0.23
218 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (212 bp):
CAGTCCTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGT
CCTCAAAGAGCAGGACGCTCTCCTTTCAACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
CCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAAGAGACTACCTTTTAAAGCACACAC
AAGTTAGTGACACCTTC
Found at i:17958 original size:61 final size:61
Alignment explanation
Indices: 17692--17983 Score: 338
Period size: 61 Copynumber: 4.8 Consensus size: 61
17682 GAGCAGGACA
* * *
17692 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGTAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGATACCTTTT
* * * * * *
17753 CCTTTTAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTTAAAGAGTAAGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATACCTTTT
* * *
17813 CCTTTTAAAACCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGATACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGATACCTTTT
* ** *
17875 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATACCTTTT
* ** * *
17937 -CTTTTCAAAGTCCACATGAGTTAGTGGCACTTTTTAGTCCTCAAAGA
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA
17984 ATAGGACACC
Statistics
Matches: 203, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
60 51 0.25
61 76 0.37
62 52 0.26
63 24 0.12
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATACCTTTT
Found at i:18070 original size:42 final size:42
Alignment explanation
Indices: 18023--18349 Score: 222
Period size: 41 Copynumber: 7.7 Consensus size: 42
18013 CAGGACGCCT
* * *
18023 TTTCCTTTTTTCCTTTGTCCTCAAAAAGTAGGACACATTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* *
18065 TTTCCTTCTTTTCCCTTTTGTCCTCGAAGAGCAGGATTC-CCTTT--
1 TTTCCTT-TTTT-CC-TTTGTCCTCAAAGAGCAGGA--CGCATTTCA
* * * *
18109 TTT-CTTTTTTCCTTTATCCTCAAGGAGTAGGACGCACTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* *
18150 TTTCCTTCTTTTCCCTTCTAGTTCTCAAAGAGTAGGACGCACTTT-A
1 TTTCCTT-TTTT-CCTT-T-GTCCTCAAAGAGCAGGACGCA-TTTCA
* * * *
18196 TTCTCC-TTTTTCCTTTATCCTCAAAAAGCAGGACACATTTAA
1 TT-TCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* ** * * *
18238 TTTCCTATTTT-CTTTGTTTTCAAAGGGCAGGATGCATTTTA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* * * * *
18279 TTTCTTTTTTTCCTTAGTCCCCAAAGAACAGGACCCATTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
** *
18321 -TT-CTCTTTTTCCTTAATCCTCGAAGAGCA
1 TTTCCT-TTTTTCCTTTGTCCTCAAAGAGCA
18350 AGATGCTCCC
Statistics
Matches: 222, Mismatches: 44, Indels: 39
0.73 0.14 0.13
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
40 17 0.08
41 64 0.29
42 58 0.26
43 12 0.05
44 13 0.06
45 22 0.10
46 26 0.12
47 6 0.03
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
Found at i:18229 original size:88 final size:85
Alignment explanation
Indices: 18010--18243 Score: 276
Period size: 85 Copynumber: 2.7 Consensus size: 85
18000 TTGCCCTCTT
*
18010 GAGCAGGACGC-C--TTTTCCTTTTTTCCTTTGTCCTCAAAAAGTAGGACACATTTCATTTCCTT
1 GAGCAGGACGCACTTTTTTCC-TTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCTT
* *
18072 CTTTTCCCTTTTGTCCTCGAA
65 CTTTTCCCTTTAGTCCTCAAA
** * * ** * *
18093 GAGCAGGATTCCCTTTTTTCTTTTTTCCTTTATCCTCAAGGAGTAGGACGCACTTCATTTCCTTC
1 GAGCAGGACGCACTTTTTTCCTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCTTC
*
18158 TTTTCCCTTCTAGTTCTCAAA
66 TTTTCCCTT-TAGTCCTCAAA
* * *
18179 GAGTAGGACGCACTTTATTCTCCTTTTTCCTTTATCCTCAAAAAGCAGGACACATTTAATTTCCT
1 GAGCAGGACGCACTTT-TT-TCCTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCT
18244 ATTTTCTTTG
Statistics
Matches: 123, Mismatches: 22, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
83 9 0.07
84 1 0.01
85 48 0.39
86 25 0.20
87 2 0.02
88 38 0.31
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (85 bp):
GAGCAGGACGCACTTTTTTCCTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCTTC
TTTTCCCTTTAGTCCTCAAA
Found at i:19016 original size:20 final size:20
Alignment explanation
Indices: 18991--19049 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
18981 TACCCAAATG
18991 TATCGATACATTGTTCATTA
1 TATCGATACATTGTTCATTA
19011 TATCGATACATTGTTCATTA
1 TATCGATACATTGTTCATTA
*
19031 TATCGATACATTATTCATT
1 TATCGATACATTGTTCATT
19050 GTATTGTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (20 bp):
TATCGATACATTGTTCATTA
Found at i:23485 original size:27 final size:27
Alignment explanation
Indices: 23448--23505 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
23438 CCATATTTTT
* *
23448 CTACTCAACCTCTATACCCGTCATATC
1 CTACTCAACCTCCATACCCATCATATC
* *
23475 CTACTTAACCTCCATACCCATTATATC
1 CTACTCAACCTCCATACCCATCATATC
23502 CTAC
1 CTAC
23506 CACGACCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.40, G:0.02, T:0.31
Consensus pattern (27 bp):
CTACTCAACCTCCATACCCATCATATC
Found at i:24311 original size:13 final size:13
Alignment explanation
Indices: 24293--24318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24283 TACACAAAGT
24293 ATGTATCGATACA
1 ATGTATCGATACA
24306 ATGTATCGATACA
1 ATGTATCGATACA
24319 CAAAAAAATT
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):
ATGTATCGATACA
Found at i:24337 original size:34 final size:32
Alignment explanation
Indices: 24275--24339 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
24265 TAGCCAAACT
**
24275 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
24307 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
24340 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:26571 original size:21 final size:21
Alignment explanation
Indices: 26538--26587 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
26528 TTGCAAGTTG
*
26538 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
26560 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
26581 AAATAAA
1 AAATAAA
26588 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:28400 original size:15 final size:15
Alignment explanation
Indices: 28380--28410 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28370 TAAAAATGTC
*
28380 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
28395 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
28410 C
1 C
28411 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:30765 original size:13 final size:13
Alignment explanation
Indices: 30747--30772 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30737 TACAGCAAGT
30747 ATGTATCGATACA
1 ATGTATCGATACA
30760 ATGTATCGATACA
1 ATGTATCGATACA
30773 CAAAAAATTG
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):
ATGTATCGATACA
Found at i:31293 original size:34 final size:35
Alignment explanation
Indices: 31230--31296 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
31220 CTAAGTGATT
31230 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
31266 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
31297 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Done.