Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3483
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: 65574
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:9924 original size:27 final size:27
Alignment explanation
Indices: 9884--10042 Score: 185
Period size: 27 Copynumber: 5.9 Consensus size: 27
9874 CCGCACACTC
* *
9884 AGTCAACTCGCACACTTAGTGCTACGT
1 AGTCAAATCGCACACTTAGTGCTACAT
*
9911 AATCAAATCGCACACTTAGTGCTACAT
1 AGTCAAATCGCACACTTAGTGCTACAT
**
9938 AGTCAAACTCGCACACTTAGTGCCGCAT
1 AGTCAAA-TCGCACACTTAGTGCTACAT
* *
9966 GGTCAATTCGCACACTTAGTGC-ATCAT
1 AGTCAAATCGCACACTTAGTGCTA-CAT
* ** * *
9993 ATTCATTTCGCACACTTAGTGCAACAC
1 AGTCAAATCGCACACTTAGTGCTACAT
10020 AGTCAAATCGCACACTTAGTGCT
1 AGTCAAATCGCACACTTAGTGCT
10043 GTACAATTTA
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
27 88 0.79
28 24 0.21
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
AGTCAAATCGCACACTTAGTGCTACAT
Found at i:9977 original size:55 final size:55
Alignment explanation
Indices: 9884--10042 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 55
9874 CCGCACACTC
* * *
9884 AGTCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTA-CAT
1 AGTCAACTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTATCAT
** * *
9938 AGTCAAACTCGCACACTTAGTGCCGCATGGTCAATTCGCACACTTAGTGC-ATCAT
1 AGTC-AACTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTATCAT
* ** *
9993 ATTCATTTCGCACACTTAGTGCAACACAGTCAAATCGCACACTTAGTGCT
1 AGTCAACTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCT
10043 GTACAATTTA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
54 43 0.49
55 45 0.51
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (55 bp):
AGTCAACTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAGTGCTATCAT
Found at i:9980 original size:82 final size:81
Alignment explanation
Indices: 9885--10041 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
9875 CGCACACTCA
* * *
9885 GTCAACTCGCACACTTAGTGC-TACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCG
1 GTCAACTCGCACACTTAGTGCAT-CATAATCAAATCGCACACTTAGTGCAACACAGTCAAA-TCG
9949 CACACTTAGTGCCGCATG
64 CACACTTAGTGCCGCATG
* * **
9967 GTCAATTCGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACACAGTCAAATCGCA
1 GTCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACACAGTCAAATCGCA
10032 CACTTAGTGC
66 CACTTAGTGC
10042 TGTACAATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (81 bp):
GTCAACTCGCACACTTAGTGCATCATAATCAAATCGCACACTTAGTGCAACACAGTCAAATCGCA
CACTTAGTGCCGCATG
Found at i:12022 original size:23 final size:22
Alignment explanation
Indices: 11979--12022 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
11969 GAATGGAGAT
*
11979 TTATCACACTTTTACTGGCAGC
1 TTATCACACTTTTACTAGCAGC
*
12001 TTATCTACATTTTTACTAGCAG
1 TTATC-ACACTTTTACTAGCAG
12023 AATTTTTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (22 bp):
TTATCACACTTTTACTAGCAGC
Found at i:21364 original size:5 final size:5
Alignment explanation
Indices: 21354--21391 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
21344 AATTTGTGTG
*
21354 TTATT TTATT TTTTCT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TTATT TT
21392 TTTCACACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:21944 original size:3 final size:3
Alignment explanation
Indices: 21936--21964 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
21926 ACTTTATAGT
21936 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
21965 AATAAACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:22495 original size:44 final size:43
Alignment explanation
Indices: 22405--22495 Score: 166
Period size: 42 Copynumber: 2.1 Consensus size: 43
22395 TAAAGTACAT
22405 TCTCTATTGCTTTCATATTTTCTTTGTTCTTTATTCTTTCCATC
1 TCTCTATTGC-TTCATATTTTCTTTGTTCTTTATTCTTTCCATC
22449 TCTCTATTGC-TCATATTTTCTTTGTTCTTTATTCTTTCCATC
1 TCTCTATTGCTTCATATTTTCTTTGTTCTTTATTCTTTCCATC
22491 TCTCT
1 TCTCT
22496 TTATTTTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 37 0.79
44 10 0.21
ACGTcount: A:0.11, C:0.24, G:0.04, T:0.60
Consensus pattern (43 bp):
TCTCTATTGCTTCATATTTTCTTTGTTCTTTATTCTTTCCATC
Found at i:28946 original size:20 final size:20
Alignment explanation
Indices: 28912--28952 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
28902 ATCTCTCTTT
28912 ATTTTATAACAA-TTTGATA
1 ATTTTATAACAATTTTGATA
*
28931 ATTTTAATAACTATTTTGATA
1 ATTTT-ATAACAATTTTGATA
28952 A
1 A
28953 GGTCTTAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
ATTTTATAACAATTTTGATA
Found at i:29893 original size:5 final size:5
Alignment explanation
Indices: 29883--29916 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
29873 ATCTGTGTTT
29883 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
29917 TCACAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:35090 original size:40 final size:41
Alignment explanation
Indices: 35034--35149 Score: 150
Period size: 40 Copynumber: 2.9 Consensus size: 41
35024 AGCTTTAGTG
*
35034 GCATTAGTGGCACTTTT-TAAAAAATGTCGCTATAGACCGA
1 GCATTAGCGGCACTTTTCTAAAAAATGTCGCTATAGACCGA
* * *
35074 GCATTAGCGGCTCTTTTCT-AAAAATGCCGCTATAGATCGA
1 GCATTAGCGGCACTTTTCTAAAAAATGTCGCTATAGACCGA
*
35114 GCATTAGCGGCGCTTTTCTAAAAACA--TCGCTATAGA
1 GCATTAGCGGCACTTTTCTAAAAA-ATGTCGCTATAGA
35150 TCAGGCATTG
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
40 61 0.91
41 5 0.07
42 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
GCATTAGCGGCACTTTTCTAAAAAATGTCGCTATAGACCGA
Found at i:35262 original size:194 final size:194
Alignment explanation
Indices: 34899--35392 Score: 497
Period size: 194 Copynumber: 2.5 Consensus size: 194
34889 CGTTTGGATA
*
34899 AAAAATGCCACTATAGATCGAGCATTAGCGGTACTTTTTGAAAAACTCCGCTATAGATCGAGCAT
1 AAAAATGCCACTATAGATCGAGCATTAGCGGCACTTTTTGAAAAACTCCGCTATAGATCGAGCAT
* ** * * * * *
34964 TAGCGGCGTTTTTCAAGAAGGCCGTAAAAAAATTAAGCATAACGTCGTCGTTTTATGTTGAGCTT
66 TAGCGGCGTTTTTCAAAAACACCGCAAAAAAATTAACCACAACGCCGTCGTTTTATGTTGACCTT
* * * *
35029 TAGTGGCATTAGTGGCACTTTTTAAAAAATGTCGCTATAGACCGAGCATTAGCGGCTCTTTTCT
131 TAGCGGCATTAGTAGCACTTTTTAAAAAATCTCGCTATAGACCGAGCATTAACGGCTCTTTTCT
* *
35093 AAAAATGCCGCTATAGATCGAGCATTAGCGGCGCTTTTCT-AAAAACAT-CGCTATAGATC-AGG
1 AAAAATGCCACTATAGATCGAGCATTAGCGGCACTTTT-TGAAAAAC-TCCGCTATAGATCGA-G
* * * * *
35155 CATT-GTGGTGTTTTTTTGAAAAACACCGCAAAAACATTAACCACAATGCCGTCGTTTTATGTTG
63 CATTAGCGGCG--TTTTTCAAAAACACCGCAAAAAAATTAACCACAACGCCGTCGTTTTATGTTG
* *
35219 ACCTTTAGCGGCA-TAGTAGC-CTTTATTGAAAAACA-CT-GCTATAGATCGAGCATTAACGGCG
126 ACCTTTAGCGGCATTAGTAGCACTTT-TT-AAAAA-ATCTCGCTATAGACCGAGCATTAACGGCT
*
35280 GTTTT-T
188 CTTTTCT
** * * * * * * * *
35286 GAAAAACACCACTATAGGTCGACCGTTAGCGACGCTTTTTG-AAAACGCCGCTATAGGTC-AACT
1 -AAAAATGCCACTATAGATCGAGCATTAGCGGCACTTTTTGAAAAACTCCGCTATAGATCGAGC-
* *
35349 GTTAGCGGCGCTTTTTCAAAAACACCGCAAAAAAATTAAGCACA
64 ATTAGCGGCG-TTTTTCAAAAACACCGCAAAAAAATTAACCACA
35393 GTCCCATAAT
Statistics
Matches: 247, Mismatches: 40, Indels: 27
0.79 0.13 0.09
Matches are distributed among these distances:
192 1 0.00
193 59 0.24
194 125 0.51
195 61 0.25
196 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (194 bp):
AAAAATGCCACTATAGATCGAGCATTAGCGGCACTTTTTGAAAAACTCCGCTATAGATCGAGCAT
TAGCGGCGTTTTTCAAAAACACCGCAAAAAAATTAACCACAACGCCGTCGTTTTATGTTGACCTT
TAGCGGCATTAGTAGCACTTTTTAAAAAATCTCGCTATAGACCGAGCATTAACGGCTCTTTTCT
Found at i:35301 original size:40 final size:40
Alignment explanation
Indices: 35239--35374 Score: 103
Period size: 40 Copynumber: 3.4 Consensus size: 40
35229 GCATAGTAGC
** * *
35239 CTTTATTGAAAAACACTGCTATAGATCGAGCATTAACGGCG
1 CTTT-TTGAAAAACACCACTATAGATCGACCATTAACGACG
* * * *
35280 GTTTTTGAAAAACACCACTATAGGTCGACCGTTAGCGACG
1 CTTTTTGAAAAACACCACTATAGATCGACCATTAACGACG
* * * * ** * *
35320 CTTTTTG-AAAACGCCGCTATAGGTCAACTGTTAGCGGCG
1 CTTTTTGAAAAACACCACTATAGATCGACCATTAACGACG
*
35359 CTTTTTCAAAAACACC
1 CTTTTTGAAAAACACC
35375 GCAAAAAAAT
Statistics
Matches: 78, Mismatches: 16, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
39 33 0.42
40 42 0.54
41 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (40 bp):
CTTTTTGAAAAACACCACTATAGATCGACCATTAACGACG
Found at i:35342 original size:39 final size:39
Alignment explanation
Indices: 35281--35374 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 39
35271 TTAACGGCGG
*
35281 TTTTTGAAAAACACCACTATAGGTCGACCGTTAGCGACGC
1 TTTTTG-AAAACACCACTATAGGTCAACCGTTAGCGACGC
* * * *
35321 TTTTTGAAAACGCCGCTATAGGTCAACTGTTAGCGGCGC
1 TTTTTGAAAACACCACTATAGGTCAACCGTTAGCGACGC
*
35360 TTTTTCAAAAACACC
1 TTTTT-GAAAACACC
35375 GCAAAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
39 33 0.72
40 13 0.28
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (39 bp):
TTTTTGAAAACACCACTATAGGTCAACCGTTAGCGACGC
Found at i:36235 original size:14 final size:14
Alignment explanation
Indices: 36212--36292 Score: 58
Period size: 14 Copynumber: 5.8 Consensus size: 14
36202 GTTTCAGCAC
36212 CTAAACCCTAAACT
1 CTAAACCCTAAACT
* *
36226 CTAAAGCCTAATC-
1 CTAAACCCTAAACT
*
36239 CTTAAACCGTAACAC-
1 C-TAAACCCTAA-ACT
*
36254 CTAAACCCTAAAAT
1 CTAAACCCTAAACT
* *
36268 CTAAAGCCTAACCT
1 CTAAACCCTAAACT
* *
36282 TTAAATCCTAA
1 CTAAACCCTAA
36293 CCCATGAACT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
13 2 0.04
14 48 0.92
15 2 0.04
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:36292 original size:21 final size:20
Alignment explanation
Indices: 36226--36292 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 20
36216 ACCCTAAACT
36226 CTAAAGCCTAATCCTTAAA-C
1 CTAAAGCCTAA-CCTTAAATC
*
36246 CGTAACA-CCTAAACCCTAAAAT-
1 C-TAA-AGCCT-AA-CCTTAAATC
36268 CTAAAGCCTAACCTTTAAATC
1 CTAAAGCCTAACC-TTAAATC
36289 CTAA
1 CTAA
36293 CCCATGAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 13
0.70 0.06 0.25
Matches are distributed among these distances:
19 2 0.05
20 9 0.24
21 16 0.43
22 10 0.27
ACGTcount: A:0.42, C:0.30, G:0.04, T:0.24
Consensus pattern (20 bp):
CTAAAGCCTAACCTTAAATC
Found at i:37018 original size:149 final size:149
Alignment explanation
Indices: 36813--37095 Score: 335
Period size: 150 Copynumber: 1.9 Consensus size: 149
36803 GCCAAAAACA
* * * * *
36813 CCGCAAACATGTGTTAAGTGTTAGTAAAACAGTGTCGTTTTATGCTTTATTTTTTAGTGG-AGCT
1 CCGCAAAAATGTGTTAAGTGTTAGCAAAACAGCGCCGTTTTATGCTTTATTATTTAGTGGCA-CT
* * ** *
36877 T-TGTTAAAATGCCATAAATATGTATTAGGAGTTCC-CAAAATGGCACCG-TTTAGCCTTGTTAT
65 TGTG-TAAAACGCCACAAATATGTATTACAAG-TCCAC-AAATGACACCGTTTTAGCCTTGTTAT
36939 TAGTGGCGTTTCACCAAAAAATG
127 TAGTGGCGTTTCACCAAAAAATG
* *
36962 CCGCAAAAAATGTTTTAAGTGTTAGCAAAACGGCGCCGTTTTAT-CATTT-TTATTTAGTGGCAC
1 CCGC-AAAAATGTGTTAAGTGTTAGCAAAACAGCGCCGTTTTATGC-TTTATTATTTAGTGGCAC
* *
37025 TTGTGTAAAACGCCACAAATGTGTATTACAAGTCCATCAAATGACACCGTTTTATCCTTGTTATT
64 TTGTGTAAAACGCCACAAATATGTATTACAAGTCCA-CAAATGACACCGTTTTAGCCTTGTTATT
37090 AGTGGC
128 AGTGGC
37096 ATTTTGTCCA
Statistics
Matches: 113, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
148 3 0.03
149 50 0.44
150 60 0.53
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (149 bp):
CCGCAAAAATGTGTTAAGTGTTAGCAAAACAGCGCCGTTTTATGCTTTATTATTTAGTGGCACTT
GTGTAAAACGCCACAAATATGTATTACAAGTCCACAAATGACACCGTTTTAGCCTTGTTATTAGT
GGCGTTTCACCAAAAAATG
Found at i:37116 original size:149 final size:149
Alignment explanation
Indices: 36794--37095 Score: 330
Period size: 149 Copynumber: 2.0 Consensus size: 149
36784 ATGCATTACC
* * * * * *
36794 GGCGTTTGAGCCAAAAACACCGC-AAACATGTGTTAAGTGTTAGTAAAACAGTGTCGTTTTATGC
1 GGCGTTTCA-CCAAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACAGCGCCGTTTTATGC
* * * ** *
36858 TTTATTTTTTAGTGGAGCTTTGTTAAAATGCCATAAATATGTATTAGGAGTTCCCAAAATGGCAC
65 TTTATTATTTAGTGGAGCTTTGTTAAAACGCCACAAATATGTATTACAAGTTCCCAAAATGACAC
36923 CGTTTAGCCTTGTTATTAGT
130 CGTTTAGCCTTGTTATTAGT
* * *
36943 GGCGTTTCACCAAAAAATGCCGCAAAAAATGTTTTAAGTGTTAGCAAAACGGCGCCGTTTTAT-C
1 GGCGTTTCACC-AAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACAGCGCCGTTTTATGC
*
37007 ATTT-TTATTTAGTGGCA-C-TTGTGTAAAACGCCACAAATGTGTATTACAAG-T-CCATCAAAT
65 -TTTATTATTTAGTGG-AGCTTTGT-TAAAACGCCACAAATATGTATTACAAGTTCCCA--AAAT
*
37067 GACACCGTTTTATCCTTGTTATTAGT
125 GACACCG-TTTAGCCTTGTTATTAGT
37093 GGC
1 GGC
37096 ATTTTGTCCA
Statistics
Matches: 128, Mismatches: 17, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
147 3 0.02
148 7 0.05
149 61 0.48
150 57 0.45
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (149 bp):
GGCGTTTCACCAAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACAGCGCCGTTTTATGCT
TTATTATTTAGTGGAGCTTTGTTAAAACGCCACAAATATGTATTACAAGTTCCCAAAATGACACC
GTTTAGCCTTGTTATTAGT
Found at i:37209 original size:189 final size:189
Alignment explanation
Indices: 36955--37301 Score: 440
Period size: 189 Copynumber: 1.8 Consensus size: 189
36945 CGTTTCACCA
* *
36955 AAAAATGCCGCAAAAAATGTTTTAAGTGTTAGCAAAACGGCGCCGTTTTATCATTTTTATTTAGT
1 AAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACGGCGCCGTTTTATCATTTTTATTTAGT
* *
37020 GGCAC-TTGTGT-AAAACGCCACAAATGTGTATTACAAG-TCCATC-AAATGACACCGTTTTATC
66 GGCACTTTGT-TAAAAACGCCACAAATATGTATTACAAGTTCC--CGAAATGACACCG-TTTAGC
*
37081 CTTGTTATTAGTGGCATTTTGTCC-AAAACGCCGCAATAGGCTATGCATTATCTGTATTTTGGCC
127 CTTGTTATTAGTAGCA-TTT-TCCAAAAACGCCGCAATAGGCTATGCATTATCTGTATTTTGGCC
* * * **
37145 AAAAACGCCGC-AAATATGTGTTAGGTGTTAGTAAAACGGCGTTGTTTTATGC-TTTATT-TTTA
1 AAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACGGCGCCGTTTTAT-CATTT-TTATTTA
* ** *
37207 GTGGCACTTTGTTAAAAACGCTACAAATATGTATTAGGAGTTCCCGAAATGACACCGTTTAGCTT
64 GTGGCACTTTGTTAAAAACGCCACAAATATGTATTACAAGTTCCCGAAATGACACCGTTTAGCCT
37272 TGTTATTAGTAGCATTTTCCAAAAACGCCG
129 TGTTATTAGTAGCATTTTCCAAAAACGCCG
37302 TAAATATGTG
Statistics
Matches: 136, Mismatches: 14, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
187 3 0.02
188 12 0.09
189 68 0.50
190 50 0.37
191 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (189 bp):
AAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACGGCGCCGTTTTATCATTTTTATTTAGT
GGCACTTTGTTAAAAACGCCACAAATATGTATTACAAGTTCCCGAAATGACACCGTTTAGCCTTG
TTATTAGTAGCATTTTCCAAAAACGCCGCAATAGGCTATGCATTATCTGTATTTTGGCC
Found at i:37545 original size:336 final size:337
Alignment explanation
Indices: 36749--37569 Score: 1058
Period size: 336 Copynumber: 2.4 Consensus size: 337
36739 AGTTTAACAA
* * * * *
36749 TAGTGGTGTTTTTGTCCAAAAAGCCGCAATAGGCTATGCATTACCGGCGTTTGAGCCAAAAACAC
1 TAGTGGCG-TTTTGTCCAAAACGCCGCAATAGGCTATGCATTACC-GTGTTTTAGCCAAAAACGC
* * *
36814 CGCAAACATGTGTTAAGTGTTAGTAAAACAGTGTCGTTTTATGCTTTATTTTTTAGTGG-AGCTT
64 CGCAAATATGTGTTAGGTGTTAGTAAAACGGTGTCGTTTTATGCTTTA-TTTTTAGTGGCA-CTT
* * *
36878 TGTTAAAATGCCATAAATATGTATTAGGAGTTCCCAAAATGGCACCGTTTAGCCTTGTTATTAGT
127 TGTTAAAACGCCACAAATATGTATTAGGAGTTCCCAAAATGACACCGTTTAGCCTTGTTATTAGT
* * * * *
36943 GGCGTTTCACCAAAAAATGCCGCAAAAAATGTTTTAAGTGTTAGCAAAACGGCGCCGTTTTATCA
192 AGCATTTCACCAAAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACGGCGCCATTTTATCA
* * * * *
37008 TTTTTATTTAGTGGCACTTGTGTAAAACGCCACAAATGTGTATTACAAGTCCATCAAATGACACC
257 TTTGTATTTAGTGGCACTTCTATAAAACGCCACAAATGTGTATTACAAGTCCATAAAACGACACC
37073 GTTTTATCCTTGTTAT
322 GTTTTATCCTTGTTAT
* * * *
37089 TAGTGGCATTTTGTCCAAAACGCCGCAATAGGCTATGCATTATCTGTATTTTGGCCAAAAACGCC
1 TAGTGGCGTTTTGTCCAAAACGCCGCAATAGGCTATGCATTA-CCGTGTTTTAGCCAAAAACGCC
* *
37154 GCAAATATGTGTTAGGTGTTAGTAAAACGGCGTTGTTTTATGCTTTATTTTTAGTGGCACTTTGT
65 GCAAATATGTGTTAGGTGTTAGTAAAACGGTGTCGTTTTATGCTTTATTTTTAGTGGCACTTTGT
* * *
37219 TAAAAACGCTACAAATATGTATTAGGAGTTCCCGAAATGACACCGTTTAGCTTTGTTATTAGTAG
130 T-AAAACGCCACAAATATGTATTAGGAGTTCCCAAAATGACACCGTTTAGCCTTGTTATTAGTAG
* * * * *
37284 CATTT-TCC-AAAAACGCCG-TAAATATGTGTTAAGTGTTAGCAAAATGGTGCCATTTTATTC-T
194 CATTTCACCAAAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACGGCGCCATTTTA-TCAT
* * * **
37345 TTGTATTTAGTGGCGCTTCTATAAAACGCCGCAAATGTGTATTACGAGTCCATAAAACGTTACCG
258 TTGTATTTAGTGGCACTTCTATAAAACGCCACAAATGTGTATTACAAGTCCATAAAACGACACCG
37410 TTTTATCCTTGTTAT
323 TTTTATCCTTGTTAT
* * * *
37425 TAGTGGCGTTTTGTCCAAAACGCCGCAATAGGCTATTCATTACCGATGTTTTAGCTAAAAATGCT
1 TAGTGGCGTTTTGTCCAAAACGCCGCAATAGGCTATGCATTACCG-TGTTTTAGCCAAAAACGCC
* ** * * * *
37490 GTAAATATGTGTTAGGTGTTAGTAAAACGGTGTCGTTTTATGAATTGTATTTAGTGGCGCTTTAT
65 GCAAATATGTGTTAGGTGTTAGTAAAACGGTGTCGTTTTATGCTTTATTTTTAGTGGCACTTTGT
*
37555 TAGAAATGCCACAAA
130 TA-AAACGCCACAAA
37570 CGGAATTCAG
Statistics
Matches: 416, Mismatches: 59, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
335 3 0.01
336 225 0.54
337 11 0.03
338 19 0.05
339 151 0.36
340 7 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (337 bp):
TAGTGGCGTTTTGTCCAAAACGCCGCAATAGGCTATGCATTACCGTGTTTTAGCCAAAAACGCCG
CAAATATGTGTTAGGTGTTAGTAAAACGGTGTCGTTTTATGCTTTATTTTTAGTGGCACTTTGTT
AAAACGCCACAAATATGTATTAGGAGTTCCCAAAATGACACCGTTTAGCCTTGTTATTAGTAGCA
TTTCACCAAAAAACGCCGCAAAAAATGTGTTAAGTGTTAGCAAAACGGCGCCATTTTATCATTTG
TATTTAGTGGCACTTCTATAAAACGCCACAAATGTGTATTACAAGTCCATAAAACGACACCGTTT
TATCCTTGTTAT
Found at i:39756 original size:9 final size:9
Alignment explanation
Indices: 39744--39857 Score: 76
Period size: 9 Copynumber: 13.0 Consensus size: 9
39734 ATATCATATA
39744 ATAACTTAC
1 ATAACTTAC
*
39753 ATAAATTAC
1 ATAACTTAC
*
39762 AAAACTTAC
1 ATAACTTAC
39771 ATAA--TAC
1 ATAACTTAC
* *
39778 ATAA-ATAT
1 ATAACTTAC
* *
39786 ATATCATATC
1 ATAACTTA-C
39796 ATAACTTAC
1 ATAACTTAC
*
39805 AGAACTTAC
1 ATAACTTAC
*
39814 AAAACTTAC
1 ATAACTTAC
*
39823 TTAACTTAC
1 ATAACTTAC
39832 ATAA--TAC
1 ATAACTTAC
*
39839 ATAAATATAC
1 ATAACT-TAC
*
39849 ACAACTTAC
1 ATAACTTAC
39858 CTGAATTAGT
Statistics
Matches: 83, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
7 14 0.17
8 5 0.06
9 51 0.61
10 13 0.16
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.31
Consensus pattern (9 bp):
ATAACTTAC
Found at i:41579 original size:13 final size:13
Alignment explanation
Indices: 41561--41588 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
41551 ACATATTATA
41561 AATATTTTGTGTT
1 AATATTTTGTGTT
41574 AATATTTTGTGTT
1 AATATTTTGTGTT
41587 AA
1 AA
41589 AAATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (13 bp):
AATATTTTGTGTT
Found at i:43086 original size:40 final size:40
Alignment explanation
Indices: 43005--43208 Score: 333
Period size: 40 Copynumber: 5.2 Consensus size: 40
42995 GGACTAAGAT
43005 CGAAGGCATTTGTGCTAGTGACTATA-CCGGGCTAAGTCC
1 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
*
43044 CGAAGGCATTTGTGCTAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
43084 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
* *
43124 CGAAGGCATTTGTGCTAGTGATTATATCTGGGCTAAGTCC
1 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
* *
43164 CGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATCC
1 CGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTCC
43203 CGAAGG
1 CGAAGG
43209 TACTTGGGTT
Statistics
Matches: 155, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
39 40 0.26
40 113 0.73
41 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (40 bp):
CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
Found at i:56794 original size:79 final size:81
Alignment explanation
Indices: 56670--56853 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
56660 GCTACTCGTT
* *
56670 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTC-GGATCTTAACCCG
* *
56733 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
56749 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCAC-AATGCCTTCGGATCTTAACCCG
* *
56812 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
56829 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
56854 CATCATTCAA
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 48 0.53
80 19 0.21
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:56853 original size:40 final size:40
Alignment explanation
Indices: 56651--56853 Score: 229
Period size: 39 Copynumber: 5.1 Consensus size: 40
56641 CGGAATTTAA
** *
56651 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56691 CCGGTTATAGTAACTCGCAC-AATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
56730 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
56769 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
56809 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
56849 CCGGA
1 CCGGA
56854 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.01
39 68 0.49
40 57 0.41
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:64671 original size:78 final size:81
Alignment explanation
Indices: 64550--64731 Score: 230
Period size: 78 Copynumber: 2.3 Consensus size: 81
64540 TACTCGTTCA
* *
64550 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
64613 ATTTAGTAAC-TCGCAC
65 ATATAGTAACTTAGCAC
* **
64629 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
64692 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
64708 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
64732 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.03
78 46 0.52
79 29 0.33
80 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:64731 original size:40 final size:40
Alignment explanation
Indices: 64529--64731 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
64519 CGGAATTTAA
** *
64529 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
64569 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
64609 CCGGATTTAGTAACTCGCAC-AATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
64647 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
64687 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
64727 CCGGA
1 CCGGA
64732 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
38 24 0.17
39 22 0.16
40 81 0.58
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.