Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold627
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: 33720
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Found at i:266 original size:13 final size:13
Alignment explanation
Indices: 248--272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
238 ACATAAATGT
248 TGTATCGATACAA
1 TGTATCGATACAA
261 TGTATCGATACA
1 TGTATCGATACA
273 TATTTTTTGT
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:283 original size:32 final size:33
Alignment explanation
Indices: 228--293 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
218 TTCAACGATT
228 TGTATCGATTACATAAATGTTGTATCGATACAA
1 TGTATCGATTACATAAATGTTGTATCGATACAA
** *
261 TGTATCGA-TACATATTTTTTGTATCGATACAA
1 TGTATCGATTACATAAATGTTGTATCGATACAA
293 T
1 T
294 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATTACATAAATGTTGTATCGATACAA
Found at i:511 original size:52 final size:51
Alignment explanation
Indices: 365--539 Score: 293
Period size: 52 Copynumber: 3.5 Consensus size: 51
355 CACTGATCTT
*
365 TGTATCGATACATGCAGGCAATTTG-CC-GATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATAAAA
414 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATAAAA
**
465 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACACTATAAAA
517 TGTATCGATACATGCA-GCAATTT
1 TGTATCGATACATGCAGGCAATTT
540 TCATATTTCG
Statistics
Matches: 120, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
49 25 0.21
50 7 0.06
51 42 0.35
52 46 0.38
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:4635 original size:10 final size:10
Alignment explanation
Indices: 4620--4644 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4610 GCTAACTAAG
4620 TTTTGTTTGT
1 TTTTGTTTGT
4630 TTTTGTTTGT
1 TTTTGTTTGT
4640 TTTTG
1 TTTTG
4645 CTTGATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (10 bp):
TTTTGTTTGT
Found at i:14339 original size:1 final size:1
Alignment explanation
Indices: 14333--14442 Score: 85
Period size: 1 Copynumber: 110.0 Consensus size: 1
14323 GGCGTCCTCC
* ** ** ** **
14333 AAAAAAACAAAAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * *
14398 AAAAAAAAAACAAAAACAATAAAAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
14443 GGGGGTCCGG
Statistics
Matches: 85, Mismatches: 24, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 85 1.00
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:14375 original size:37 final size:37
Alignment explanation
Indices: 14333--14442 Score: 134
Period size: 36 Copynumber: 2.9 Consensus size: 37
14323 GGCGTCCTCC
14333 AAAAAAACAAAAAAAAAAAAAAAAAAACG-AAAAAAA
1 AAAAAAACAAAAAAAAAAAAAAAAAAACGAAAAAAAA
** * *
14369 TGAAAAACCAAAAAAAAAAAAAAAAAAGGAAAAAAAA
1 AAAAAAACAAAAAAAAAAAAAAAAAAACGAAAAAAAA
*
14406 AACAAAAACAATAAAAAAAACAAACAAAAAC-AAAAAA
1 AA-AAAAACAA-AAAAAAAA-AAAAAAAAACGAAAAAA
14443 GGGGGTCCGG
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
36 25 0.41
37 7 0.11
38 7 0.11
39 14 0.23
40 8 0.13
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (37 bp):
AAAAAAACAAAAAAAAAAAAAAAAAAACGAAAAAAAA
Found at i:14404 original size:48 final size:45
Alignment explanation
Indices: 14333--14444 Score: 131
Period size: 47 Copynumber: 2.4 Consensus size: 45
14323 GGCGTCCTCC
*
14333 AAAAAAACAAAAAAAAA--AAAAAAAAAACGAAAAA-AATGAAAAACCA
1 AAAAAAAAAAAAAAAAAGGAAAAAAAAAAC-AAAAACAAT-AAAAA--A
14379 AAAAAAAAAAAAAAAAAGGAAAAAAAAAACAAAAACAATAAAAAA
1 AAAAAAAAAAAAAAAAAGGAAAAAAAAAACAAAAACAATAAAAAA
*
14424 AACAAACAAAAACAAAAAAGG
1 AA-AAA-AAAAAAAAAAAAGG
14445 GGGTCCGGAT
Statistics
Matches: 59, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
45 3 0.05
46 19 0.32
47 23 0.39
48 14 0.24
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.02
Consensus pattern (45 bp):
AAAAAAAAAAAAAAAAAGGAAAAAAAAAACAAAAACAATAAAAAA
Found at i:15923 original size:30 final size:30
Alignment explanation
Indices: 15883--15963 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
15873 TCACCCTTCA
*
15883 AAAGTCCACAAGTCAGTGGCATTTTTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTCG
*
15913 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCATTTTTTTCG
15943 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
15964 ACCTTCAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 8 0.17
30 39 0.83
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTCG
Found at i:15985 original size:27 final size:27
Alignment explanation
Indices: 15943--16037 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 27
15933 ATTTTTTTCG
*
15943 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
15970 AAAGCCCACAAATCAGTGGC-ACCATTTTCC
1 AAAGCCCACAAATCAGTGGCAACC---TT-C
*
16000 AAAGCCCACACAAGTCGGTGGCAACCCTTC
1 AAAGCCCACA-AA-TCAGTGGCAA-CCTTC
*
16030 TAAGCCCA
1 AAAGCCCA
16038 ATATAGCTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
26 3 0.05
27 19 0.33
29 2 0.04
30 19 0.33
31 4 0.07
32 7 0.12
33 1 0.02
34 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.17, T:0.16
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:15989 original size:57 final size:60
Alignment explanation
Indices: 15910--16037 Score: 163
Period size: 57 Copynumber: 2.2 Consensus size: 60
15900 GGCATTTTTT
* * *** *
15910 TTCAAAGCCCACAAGTCGGTGGCATTTTTTTCGAAAG-CC-CACAAGTCAGTGGCAA-CC
1 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
15967 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
16027 TTCTAAGCCCA
1 TTCAAAGCCCA
16038 ATATAGCTGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 31 0.52
58 2 0.03
59 15 0.25
60 12 0.20
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (60 bp):
TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
Found at i:16005 original size:30 final size:30
Alignment explanation
Indices: 15883--16009 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
15873 TCACCCTTCA
* ** *
15883 AAAGTCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
* ** *
15913 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
15943 AAAGCCCACAAGTCAGTGGCAACC---TT-C
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTCC
* *
15970 AAAGCCCACAAATCAGTGGCACCATTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
16000 AAAGCCCACA
1 AAAGCCCACA
16010 CAAGTCGGTG
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
26 3 0.04
27 19 0.23
28 2 0.02
29 2 0.02
30 56 0.67
31 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTTCC
Found at i:16035 original size:30 final size:30
Alignment explanation
Indices: 15949--16037 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
15939 TTCGAAAGCC
15949 CACAAGTCAGTGGCAA-CCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
*
15978 CA-AA-TCAGTGGC-ACCATTTTCCAAAGCCCA
1 CACAAGTCAGTGGCAACC--CTT-CAAAGCCCA
* *
16008 CACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
16038 ATATAGCTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 1 0.02
27 9 0.18
28 2 0.04
29 4 0.08
30 19 0.39
31 4 0.08
32 7 0.14
33 3 0.06
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (30 bp):
CACAAGTCAGTGGCAACCCTTCAAAGCCCA
Found at i:16092 original size:49 final size:49
Alignment explanation
Indices: 16030--16281 Score: 281
Period size: 49 Copynumber: 5.0 Consensus size: 49
16020 GCAACCCTTC
* *
16030 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
16079 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
16128 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * * *
16180 TAAGTTCAATGTAGCTGGCCTTAAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * *
16235 TAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCAACTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
16282 ACTTCTCTCA
Statistics
Matches: 174, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
49 89 0.51
50 3 0.02
51 2 0.01
52 38 0.22
53 2 0.01
54 2 0.01
55 37 0.21
56 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:16260 original size:107 final size:99
Alignment explanation
Indices: 16025--16278 Score: 296
Period size: 107 Copynumber: 2.5 Consensus size: 99
16015 CGGTGGCAAC
*
16025 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACC-TTTATCTTTAAGTCCAAT
1 CCTT-TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAAT
* * *
16089 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
65 ATAGCTGGCCTTAAATCAGCACATTGACACCTTCA
* *
16124 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT--ATCTTTAAGTCCAA
*
16189 TGTAGCTGGCCTTAAATCAGCACATTGACATCCTTTTTCTCA
64 TATAGCTGGCCTTAAATCAGCACATTGACA-CC----T-TCA
* * * * *
16231 TCTTTAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCAACTTT
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTT
16279 ATCACTTCTC
Statistics
Matches: 132, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
98 39 0.30
99 7 0.05
101 39 0.30
102 2 0.02
106 2 0.02
107 43 0.33
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (99 bp):
CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAATA
TAGCTGGCCTTAAATCAGCACATTGACACCTTCA
Found at i:17095 original size:33 final size:33
Alignment explanation
Indices: 17058--17124 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
17048 TTCAACGATT
17058 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
17091 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
17124 T
1 T
17125 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:17096 original size:13 final size:13
Alignment explanation
Indices: 17078--17102 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17068 CATAAAATGT
17078 TGTATCGATACAA
1 TGTATCGATACAA
17091 TGTATCGATACA
1 TGTATCGATACA
17103 TATTTTTTTG
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:17183 original size:13 final size:13
Alignment explanation
Indices: 17165--17189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17155 ATTACTCAAA
17165 TGTATCGATACAT
1 TGTATCGATACAT
17178 TGTATCGATACA
1 TGTATCGATACA
17190 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17353 original size:52 final size:51
Alignment explanation
Indices: 17198--17372 Score: 314
Period size: 51 Copynumber: 3.4 Consensus size: 51
17188 CACTGATCTT
17198 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
17249 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
* *
17300 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
*
17352 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
17373 CTTTTCATAT
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 72 0.60
52 48 0.40
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:21523 original size:10 final size:10
Alignment explanation
Indices: 21508--21534 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21498 TGCTAACTAA
21508 GTTTTTGTTT
1 GTTTTTGTTT
21518 GTTTTTGTTT
1 GTTTTTGTTT
21528 GTTTTTG
1 GTTTTTG
21535 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:31229 original size:1 final size:1
Alignment explanation
Indices: 31223--31336 Score: 93
Period size: 1 Copynumber: 114.0 Consensus size: 1
31213 GGCGTCCTCC
* ** ** **
31223 AAAAAAACAAAAAAAAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACCAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * * *
31288 AAAGGAAAAAAAAAACAAAAACAATAAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31337 GGGGGGTCCG
Statistics
Matches: 89, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 89 1.00
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:31269 original size:40 final size:37
Alignment explanation
Indices: 31225--31336 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 37
31215 CGTCCTCCAA
*
31225 AAAAACAAAAAAAAAAAAAAAAAAAAAAACGAAAAAAATG
1 AAAAACAAAAAAAAAAAAAAAAAAAAAAA--AAAAAAA-C
*
31265 AAAAACCAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAC
1 AAAAA-CAAAAAAAAAAAAAAAAAAA-AAAAAAAAAAAC
* * * *
31304 AAAAACAATAAAAAAAACAAACAAAAACAAAAA
1 AAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAA
31337 GGGGGGTCCG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
37 6 0.10
38 17 0.27
39 5 0.08
40 12 0.19
41 20 0.32
42 3 0.05
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (37 bp):
AAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAC
Found at i:31276 original size:49 final size:49
Alignment explanation
Indices: 31221--31336 Score: 152
Period size: 49 Copynumber: 2.4 Consensus size: 49
31211 ACGGCGTCCT
31221 CCAAAAAAACAAAAAAAAAAAA-AAAAAAAAAAACGAAAAA-AATGAAAAA
1 CCAAAAAAACAAAAAAAAAAAAGAAAAAAAAAAAC-AAAAACAAT-AAAAA
*
31270 CCAAAAAAA-AAAAAAAAAAAAGGAAAAAAAAAACAAAAACAATAAAAA
1 CCAAAAAAACAAAAAAAAAAAAGAAAAAAAAAAACAAAAACAATAAAAA
* *
31318 --AAACAAACAAAAACAAAAA
1 CCAAAAAAACAAAAAAAAAAA
31337 GGGGGGTCCG
Statistics
Matches: 61, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
46 6 0.10
47 10 0.16
48 22 0.36
49 23 0.38
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.02
Consensus pattern (49 bp):
CCAAAAAAACAAAAAAAAAAAAGAAAAAAAAAAACAAAAACAATAAAAA
Found at i:31285 original size:38 final size:39
Alignment explanation
Indices: 31223--31336 Score: 123
Period size: 37 Copynumber: 3.1 Consensus size: 39
31213 GGCGTCCTCC
31223 AAAAAAAC--AAA-AAAAAAAAAAAAAAAAAAAACG--A
1 AAAAAAACAAAAACAAAAAAAAAAAAAAAAAAAACGAAA
** * *
31257 AAAAAATGAAAAACCAAAAAAAAAAAAAAAAAAAGGAAA
1 AAAAAAACAAAAACAAAAAAAAAAAAAAAAAAAACGAAA
* *
31296 AAAAAAACAAAAACAATAAAAAAAACAAACAAAAAC-AAA
1 AAAAAAACAAAAACAA-AAAAAAAAAAAAAAAAAACGAAA
31335 AA
1 AA
31337 GGGGGGTCCG
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
34 6 0.09
36 3 0.05
37 20 0.31
39 19 0.30
40 16 0.25
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (39 bp):
AAAAAAACAAAAACAAAAAAAAAAAAAAAAAAAACGAAA
Found at i:31287 original size:39 final size:37
Alignment explanation
Indices: 31233--31336 Score: 120
Period size: 39 Copynumber: 2.7 Consensus size: 37
31223 AAAAAAACAA
**
31233 AAAAAAAAAAAAAAAAAAAAACGAAAAAAATGAAAAACC
1 AAAAAAAAAAAAAAAAAAAAAC-AAAAAAAACAAAAA-C
31272 AAAAAAAAAAAAAAAAAAAGGAA-AAAAAAAACAAAAAC
1 AAAAAAAAAAAAAAAAAAA--AACAAAAAAAACAAAAAC
* * *
31310 AATAAAAAAAACAAACAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAACAAAAA
31337 GGGGGGTCCG
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
36 2 0.04
37 5 0.09
38 17 0.30
39 31 0.54
41 2 0.04
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (37 bp):
AAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAAAC
Found at i:32847 original size:29 final size:30
Alignment explanation
Indices: 32780--32859 Score: 119
Period size: 29 Copynumber: 2.7 Consensus size: 30
32770 TCACCCTTCA
*
32780 AAAGTCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
*
32810 AAAGCCCACAAGTCGGTGGCA-TTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
32839 GAAAG-CCACAAGTCAGTGGCA
1 -AAAGCCCACAAGTCAGTGGCA
32860 ACCTTCAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 23 0.50
30 23 0.50
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTTC
Found at i:32885 original size:56 final size:59
Alignment explanation
Indices: 32807--32933 Score: 152
Period size: 56 Copynumber: 2.2 Consensus size: 59
32797 GGCATTTTTT
* * *** *
32807 TTCAAAGCCCACAAGTCGGTGGCATTTTTTTCGAAAG-C-CACAAGTCAGTGGCAA-CC
1 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCACACAAGTCAGTGGCAACCC
*
32863 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAG-CCACACAAGTCAGTGGCAACCC
*
32923 TTCTAAGCCCA
1 TTCAAAGCCCA
32934 ATATAGCTGG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 31 0.53
58 1 0.02
59 15 0.25
60 12 0.20
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.20
Consensus pattern (59 bp):
TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCACACAAGTCAGTGGCAACCC
Found at i:32901 original size:30 final size:30
Alignment explanation
Indices: 32780--32905 Score: 118
Period size: 30 Copynumber: 4.3 Consensus size: 30
32770 TCACCCTTCA
* ** *
32780 AAAGTCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
* ** *
32810 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
32840 AAAG-CCACAAGTCAGTGGCAACC---TT-C
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTCC
* *
32866 AAAGCCCACAAATCAGTGGCACCATTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
32896 AAAGCCCACA
1 AAAGCCCACA
32906 CAAGTCGGTG
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
26 7 0.09
27 16 0.20
29 16 0.20
30 42 0.52
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTTCC
Found at i:32931 original size:30 final size:30
Alignment explanation
Indices: 32845--32933 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
32835 TTTCGAAAGC
32845 CACAAGTCAGTGGCAA-CCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
*
32874 CA-AA-TCAGTGGC-ACCATTTTCCAAAGCCCA
1 CACAAGTCAGTGGCAACC--CTT-CAAAGCCCA
* *
32904 CACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
32934 ATATAGCTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 1 0.02
27 9 0.18
28 2 0.04
29 4 0.08
30 19 0.39
31 4 0.08
32 7 0.14
33 3 0.06
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (30 bp):
CACAAGTCAGTGGCAACCCTTCAAAGCCCA
Found at i:32988 original size:49 final size:49
Alignment explanation
Indices: 32926--33176 Score: 272
Period size: 49 Copynumber: 5.0 Consensus size: 49
32916 GCAACCCTTC
*
32926 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* * *
32975 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
33024 TAAG-CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
** * * * *
33075 TAAGTTCAATGTAGCTGGCCTTAAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * *
33130 TAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCAACTTTATC
1 TAAGCCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
33177 ACTTCTCTCA
Statistics
Matches: 172, Mismatches: 21, Indels: 18
0.82 0.10 0.09
Matches are distributed among these distances:
48 36 0.21
49 54 0.31
50 1 0.01
51 10 0.06
52 29 0.17
53 2 0.01
54 2 0.01
55 37 0.22
56 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (49 bp):
TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Done.