Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_330
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: 91564
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3362 original size:25 final size:25
Alignment explanation
Indices: 3307--3379 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
3297 GACACACCAC
**
3307 AGCTCGTATGAGCTTACCGATTTGT
1 AGCTCGTACAAGCTTACCGATTTGT
*
3332 AGCTCGTGCAAGCTTACCGATTCTCG-
1 AGCTCGTACAAGCTTACCGATT-T-GT
**
3358 A-CTCGTATGAGCTTACCGATTT
1 AGCTCGTACAAGCTTACCGATTT
3380 ACAGTTTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 1 0.03
25 36 0.90
26 2 0.05
27 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.33
Consensus pattern (25 bp):
AGCTCGTACAAGCTTACCGATTTGT
Found at i:3413 original size:50 final size:49
Alignment explanation
Indices: 3307--3415 Score: 121
Period size: 50 Copynumber: 2.2 Consensus size: 49
3297 GACACACCAC
** *
3307 AGCTCGTATGAGCTTACCGATTTGTAGCTCGTGCAAGCTTACCGATTCT
1 AGCTCGTATGAGCTTACCGATTTACAGCTCGTGCAAGCATACCGATTCT
* * * *
3356 CGACTCGTATGAGCTTACCGATTTACAGTTTGTG-AGAGCATATCGATTCAT
1 AG-CTCGTATGAGCTTACCGATTTACAGCTCGTGCA-AGCATACCGATTC-T
3407 AGCTCGTAT
1 AGCTCGTAT
3416 AAGTGTACAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
49 2 0.04
50 45 0.92
51 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (49 bp):
AGCTCGTATGAGCTTACCGATTTACAGCTCGTGCAAGCATACCGATTCT
Found at i:6866 original size:111 final size:111
Alignment explanation
Indices: 6672--6894 Score: 437
Period size: 111 Copynumber: 2.0 Consensus size: 111
6662 CAAGCCAATA
6672 AATCAACTATTTTGAGCTGATTGGGTCAGCATGTTGGACGGTTTTGAGCAGCCCAATTGCTCGGT
1 AATCAACTATTTTGAGCTGATTGGGTCAGCATGTTGGACGGTTTTGAGCAGCCCAATTGCTCGGT
6737 TGGATCAGTCTCTCAGATTAGCATAACTGGGCCTCCTGTTCATAAT
66 TGGATCAGTCTCTCAGATTAGCATAACTGGGCCTCCTGTTCATAAT
*
6783 AATCAACTATTTTGAGCTGATTGGGTCAGCATGTTGGACGGTTTTGAGCAGCCCGATTGCTCGGT
1 AATCAACTATTTTGAGCTGATTGGGTCAGCATGTTGGACGGTTTTGAGCAGCCCAATTGCTCGGT
6848 TGGATCAGTCTCTCAGATTAGCATAACTGGGCCTCCTGTTCATAAT
66 TGGATCAGTCTCTCAGATTAGCATAACTGGGCCTCCTGTTCATAAT
6894 A
1 A
6895 TAATTAATAA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 111 1.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (111 bp):
AATCAACTATTTTGAGCTGATTGGGTCAGCATGTTGGACGGTTTTGAGCAGCCCAATTGCTCGGT
TGGATCAGTCTCTCAGATTAGCATAACTGGGCCTCCTGTTCATAAT
Found at i:6931 original size:111 final size:111
Alignment explanation
Indices: 6705--6924 Score: 275
Period size: 111 Copynumber: 2.0 Consensus size: 111
6695 GGTCAGCATG
6705 TTGGACGGTTTTGAGCAGCCCAATTGCTCGGTTGGATCAGTCTCTCAGATTAGCATAACTGGGCC
1 TTGGACGGTTTTGAGCAGCCCAATTGCTCGGTTGGATCAGTCTCTCAGATTAGCATAACTGGGCC
* *** * **** ** *
6770 TCCTGTTCATAATAATCAACTATTTTGAGCTGATTGGGTCAGCATG
66 TCCTGTTCATAATAATCAACTAATAACAGATGATTAACCCAAAATA
*
6816 TTGGACGGTTTTGAGCAGCCCGATTGCTCGGTTGGATCAGTCTCTCAGATTAGCATAACTGGGCC
1 TTGGACGGTTTTGAGCAGCCCAATTGCTCGGTTGGATCAGTCTCTCAGATTAGCATAACTGGGCC
* *
6881 TCCTGTTCATAAT-AT-AATTAATAACA-ATTATTTAACCCAAAATA
66 TCCTGTTCATAATAATCAACTAATAACAGATGA-TTAACCCAAAATA
6925 AATTGGATAA
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 2 0.02
109 12 0.13
110 2 0.02
111 77 0.83
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (111 bp):
TTGGACGGTTTTGAGCAGCCCAATTGCTCGGTTGGATCAGTCTCTCAGATTAGCATAACTGGGCC
TCCTGTTCATAATAATCAACTAATAACAGATGATTAACCCAAAATA
Found at i:15027 original size:33 final size:34
Alignment explanation
Indices: 14981--15047 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
14971 ACAATGCGTG
*
14981 CAGTAACAATCTGGGCCTGAGCCCTATTCAGTAA
1 CAGTAACAATCTGGGCCTGAGCCCTATACAGTAA
* *
15015 CAGT-ACAGTCTGGGCCTTAGCCCTATACAGTAA
1 CAGTAACAATCTGGGCCTGAGCCCTATACAGTAA
15048 TAGTGTGAGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (34 bp):
CAGTAACAATCTGGGCCTGAGCCCTATACAGTAA
Found at i:15221 original size:26 final size:26
Alignment explanation
Indices: 15192--15242 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
15182 CACCAATACC
* *
15192 GCAACAAAGCTACCAGTAATAGTAAT
1 GCAACAAAGCTACCAGAAACAGTAAT
*
15218 GCAACATAGCTACCAGAAACAGTAA
1 GCAACAAAGCTACCAGAAACAGTAA
15243 ATGTGGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.16
Consensus pattern (26 bp):
GCAACAAAGCTACCAGAAACAGTAAT
Found at i:15259 original size:27 final size:27
Alignment explanation
Indices: 15229--15316 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
15219 CAACATAGCT
* *
15229 ACCAGAAACAGTAAATGTGGCAAAGTC
1 ACCAGTAACAGTAAATGTGGCATAGTC
* * *
15256 ACCAGTATCAGTAATTGTGGCATAGCC
1 ACCAGTAACAGTAAATGTGGCATAGTC
* * * *
15283 ACTAGTAATAGTGAATGTGACATAGTC
1 ACCAGTAACAGTAAATGTGGCATAGTC
15310 ACCAGTA
1 ACCAGTA
15317 TAACTCACGA
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (27 bp):
ACCAGTAACAGTAAATGTGGCATAGTC
Found at i:16715 original size:27 final size:28
Alignment explanation
Indices: 16663--16731 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
16653 TTAAAATCAT
*
16663 CTTTTCCAAAA-CCAAATTTTAGGAAAAA
1 CTTTT-CAAAACCCAAATTTGAGGAAAAA
*
16691 CTTTTCAAAACCCTAATTTGA-GAAAAA
1 CTTTTCAAAACCCAAATTTGAGGAAAAA
*
16718 ATTTT-AGAAACCCA
1 CTTTTCA-AAACCCA
16732 TTCCACAGCC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.03
27 21 0.60
28 13 0.37
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (28 bp):
CTTTTCAAAACCCAAATTTGAGGAAAAA
Found at i:17387 original size:33 final size:34
Alignment explanation
Indices: 17344--17414 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
17334 ACAATGCGTG
* *
17344 CAGTAACAGTCTGGGCCTGAGCCTTATTCAGTAA
1 CAGTAACAGTCTGGGCCTGAGCCCTATACAGTAA
* *
17378 CAGT-ACAGTCTGGGCCTTATCCCTATACAGTAA
1 CAGTAACAGTCTGGGCCTGAGCCCTATACAGTAA
17411 CAGT
1 CAGT
17415 GTGGGCCTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (34 bp):
CAGTAACAGTCTGGGCCTGAGCCCTATACAGTAA
Found at i:17422 original size:28 final size:28
Alignment explanation
Indices: 17377--17442 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
17367 TTATTCAGTA
* * *
17377 ACAGT-ACAGTCTGGGCCTTATCCCTAT
1 ACAGTAACAGTCTGGGCCTAAGCCCAAT
*
17404 ACAGTAACAGTGTGGGCCTAAGCCCAAT
1 ACAGTAACAGTCTGGGCCTAAGCCCAAT
*
17432 ACAGTATCAGT
1 ACAGTAACAGT
17443 ATAGTGTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (28 bp):
ACAGTAACAGTCTGGGCCTAAGCCCAAT
Found at i:17663 original size:27 final size:26
Alignment explanation
Indices: 17599--17678 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
17589 CTGCCAGAAG
* *
17599 TAGTAAATGTGGCAAAGCCACCAGT-A
1 TAGT-AATGTGGCATATCCACCAGTAA
*
17625 TCAATAATTGTGGCATATCCACCAGTAA
1 T-AGTAA-TGTGGCATATCCACCAGTAA
*
17653 TAGTGAATGTGACATAGT-CACCAGTA
1 TAGT-AATGTGGCATA-TCCACCAGTA
17679 CAGCTCACGA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
26 3 0.07
27 36 0.82
28 5 0.11
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (26 bp):
TAGTAATGTGGCATATCCACCAGTAA
Found at i:20772 original size:46 final size:46
Alignment explanation
Indices: 20719--20811 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
20709 TTATTAAACT
* *
20719 CATGTTTATGTTGTTACAAATAAATTCACGGCAACTCGGTAATTTG
1 CATGTTTATGTTGTTACAAATAAATTCACGGAAACTCGATAATTTG
* *
20765 CATGTTTATGTTGTTACGAATAAATTCATGGAAACTCGATAATTTG
1 CATGTTTATGTTGTTACAAATAAATTCACGGAAACTCGATAATTTG
20811 C
1 C
20812 TAACTTATGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (46 bp):
CATGTTTATGTTGTTACAAATAAATTCACGGAAACTCGATAATTTG
Found at i:23402 original size:79 final size:78
Alignment explanation
Indices: 23302--23524 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
23292 GCTCCTCGTT
* * *
23302 CAAATGCCTCCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
23367 ATTTAGTATCCCGCA
64 AATTAGTATCCCGCA
* *
23382 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAACTGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
*
23445 AATTAGTATCTCGCA
64 AATTAGTATCCCGCA
* * * * *
23460 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
23523 GA
63 GA
23525 CATCATCCAA
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
78 47 0.39
79 55 0.45
80 19 0.16
81 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTATCCCGCA
Found at i:23421 original size:39 final size:40
Alignment explanation
Indices: 23302--23524 Score: 248
Period size: 39 Copynumber: 5.7 Consensus size: 40
23292 GCTCCTCGTT
* * *
23302 CAAATGCCTCCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
23342 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCCCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
23382 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
23421 CAACTGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
23460 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
23501 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
23525 CATCATCCAA
Statistics
Matches: 163, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
38 2 0.01
39 88 0.54
40 62 0.38
41 11 0.07
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:31307 original size:79 final size:78
Alignment explanation
Indices: 31205--31427 Score: 274
Period size: 79 Copynumber: 2.8 Consensus size: 78
31195 GCTCCTCGTT
* *
31205 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
31270 ATTTAGTATCTCGCA
64 AATTAGTATCTCGCA
*
31285 CAAATGCCTTCGGGCTTAGCCCGGAATTAGT-ATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAAT-TCGCACAAATGCCTTCGGGACTTAGCCCGG
31348 AATTAGTATCTCGCA
64 AATTAGTATCTCGCA
* * * * *
31363 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGT-AATTCGCACAAATGCCTTCGGGACTTAGCCCG
31426 GA
63 GA
31428 CATCATCCAA
Statistics
Matches: 126, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
78 48 0.38
79 57 0.45
80 20 0.16
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAATTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTATCTCGCA
Found at i:31319 original size:39 final size:40
Alignment explanation
Indices: 31205--31427 Score: 275
Period size: 39 Copynumber: 5.7 Consensus size: 40
31195 GCTCCTCGTT
* *
31205 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* *
31245 CAAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
31285 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
31324 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
31363 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
31404 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31428 CATCATCCAA
Statistics
Matches: 168, Mismatches: 7, Indels: 17
0.88 0.04 0.09
Matches are distributed among these distances:
38 2 0.01
39 91 0.54
40 64 0.38
41 11 0.07
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:38935 original size:27 final size:27
Alignment explanation
Indices: 38904--39081 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38894 TAAATTGTAC
38904 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
38931 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
38957 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
38985 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39013 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39040 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39067 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39082 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39018 original size:82 final size:81
Alignment explanation
Indices: 38905--39060 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38895 AAATTGTACA
* *
38905 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
38969 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
38986 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39051 TGCGAGTTGA
65 TGCGAATTGA
39061 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39072 original size:82 final size:81
Alignment explanation
Indices: 38901--39081 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
38891 GATTAAATTG
* *
38901 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
38966 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
38982 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39046 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39064 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
39082 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41838 original size:24 final size:24
Alignment explanation
Indices: 41806--41905 Score: 139
Period size: 24 Copynumber: 4.0 Consensus size: 24
41796 TGACATTGTG
41806 CTAAGTGAAATAA-TACCATGGCAT
1 CTAAGTGAAATAAGT-CCATGGCAT
41830 CTAAGTGAAATAAGTCCATGGCAATGT
1 CTAAGTGAAATAAGTCCATGGC-A--T
41857 GCTAAGTGAAATAAGTCCATGGCAT
1 -CTAAGTGAAATAAGTCCATGGCAT
*
41882 CTAAGTGAAATAAGCCCATGGCAT
1 CTAAGTGAAATAAGTCCATGGCAT
41906 TGTGTTAAGT
Statistics
Matches: 70, Mismatches: 1, Indels: 10
0.86 0.01 0.12
Matches are distributed among these distances:
24 43 0.61
25 3 0.04
27 2 0.03
28 22 0.31
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (24 bp):
CTAAGTGAAATAAGTCCATGGCAT
Found at i:41865 original size:52 final size:52
Alignment explanation
Indices: 41802--41917 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
41792 GATATGACAT
*
41802 TGTGCTAAGTGAAATAA-TACCATGGCATCTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAAGT-CCATGGCATCTAAGTGAAATAAGCCCATGGCAA
*
41854 TGTGCTAAGTGAAATAAGTCCATGGCATCTAAGTGAAATAAGCCCATGGCAT
1 TGTGCTAAGTGAAATAAGTCCATGGCATCTAAGTGAAATAAGCCCATGGCAA
*
41906 TGTGTTAAGTGA
1 TGTGCTAAGTGA
41918 GAAATTTCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 59 0.98
53 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (52 bp):
TGTGCTAAGTGAAATAAGTCCATGGCATCTAAGTGAAATAAGCCCATGGCAA
Found at i:41870 original size:28 final size:27
Alignment explanation
Indices: 41802--41917 Score: 138
Period size: 24 Copynumber: 4.4 Consensus size: 27
41792 GATATGACAT
41802 TGTGCTAAGTGAAATAA-TACCATGGCA
1 TGTGCTAAGTGAAATAAGT-CCATGGCA
41829 --T-CTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAAGTCCATGGC-A
41854 TGTGCTAAGTGAAATAAGTCCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGCA
*
41881 --T-CTAAGTGAAATAAGCCCATGGCA
1 TGTGCTAAGTGAAATAAGTCCATGGCA
*
41905 TTGTGTTAAGTGA
1 -TGTGCTAAGTGA
41918 GAAATTTCCC
Statistics
Matches: 78, Mismatches: 2, Indels: 17
0.80 0.02 0.18
Matches are distributed among these distances:
24 42 0.54
25 4 0.05
27 3 0.04
28 29 0.37
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (27 bp):
TGTGCTAAGTGAAATAAGTCCATGGCA
Found at i:41983 original size:30 final size:30
Alignment explanation
Indices: 41947--42006 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
41937 TTAGGAATAA
41947 AATAGCTTTGAACACAAGTATGGTACTATG
1 AATAGCTTTGAACACAAGTATGGTACTATG
*
41977 AATAGCTTTGAACATAAGTATGGTACTATG
1 AATAGCTTTGAACACAAGTATGGTACTATG
42007 TGAAGGCCAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (30 bp):
AATAGCTTTGAACACAAGTATGGTACTATG
Found at i:42036 original size:51 final size:51
Alignment explanation
Indices: 41977--42168 Score: 323
Period size: 51 Copynumber: 3.8 Consensus size: 51
41967 TGGTACTATG
* * * *
41977 AATAGCTTTGAACATAAGTATGGTACTATGTGAAGGCCACTTTGTGAATAT
1 AATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAA
42028 AATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAA
1 AATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAA
42079 AATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAA
1 AATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAA
*
42130 AATAGCTTTGG-CTACAAGGGTGGTACTATGTGAAGGCCA
1 AATAGCTTTGGAC-ACAAGTGTGGTACTATGTGAAGGCCA
42169 TTGTGTATCT
Statistics
Matches: 135, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
50 1 0.01
51 134 0.99
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (51 bp):
AATAGCTTTGGACACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAATAA
Found at i:44163 original size:5 final size:5
Alignment explanation
Indices: 44155--44182 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
44145 TAAAAAAATA
44155 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
44183 GTTTGGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:49203 original size:33 final size:33
Alignment explanation
Indices: 49166--49232 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
49156 GCTACGAGTT
49166 AAAGATTCAGATGTCTC-AAAGACAGCTTTCAGA
1 AAAGATTCAGATGTC-CGAAAGACAGCTTTCAGA
* *
49199 AAAGATTCAGATGTCCGGAAGACAGGTTTCAGA
1 AAAGATTCAGATGTCCGAAAGACAGCTTTCAGA
49232 A
1 A
49233 CCAAATATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (33 bp):
AAAGATTCAGATGTCCGAAAGACAGCTTTCAGA
Found at i:54208 original size:44 final size:44
Alignment explanation
Indices: 54156--54241 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
54146 TATGTAATCT
* *
54156 GAACTCATTGAGTTATGGTCTGAGTTCATGTTATATGTGACATC
1 GAACTCATTGAGTTATGGTCTGAGTTCATGATACATGTGACATC
* *
54200 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATACATGTGACA
1 GAACTCATTGAGTTATGGTCTGAGTTCATGATACATGTGACA
54242 CATGTTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (44 bp):
GAACTCATTGAGTTATGGTCTGAGTTCATGATACATGTGACATC
Found at i:57463 original size:46 final size:44
Alignment explanation
Indices: 57367--57586 Score: 185
Period size: 46 Copynumber: 4.8 Consensus size: 44
57357 CTATCAGTGT
* * * *
57367 CGATGCCATGTCCCAGACATGGCCTTACACTGACACAACTCTT-A-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTC--GTCTTAAGGC
*
57413 CGATGCAAGTCCCAGACATGTCTTACACTGGCTTACGTCTTAAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGC-T-CGTCTTAAGGC
* * * *
57459 CGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGT
1 CGATGCATGTCCCAGACATGTCTTACACT-G-GCTCGTCTTAAGGC
* * *
57505 CAATGCCATGTCCCAAACATGGTCTTACACTGGCTC-TCATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCGTCTTAA---GGC
*
57553 CGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTC
57587 ACATAAGTGA
Statistics
Matches: 143, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 15 0.10
45 18 0.13
46 65 0.45
47 29 0.20
48 16 0.11
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.26
Consensus pattern (44 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCGTCTTAAGGC
Found at i:66927 original size:40 final size:40
Alignment explanation
Indices: 66719--66921 Score: 318
Period size: 40 Copynumber: 5.1 Consensus size: 40
66709 CGGGCTTTAA
** *
66719 CCGGATATAGCCACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
** *
66759 CCGGATATAGTAGTTCGCACAAATGTCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
66799 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
66839 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
66879 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
66919 CCG
1 CCG
66922 AAATTATCAT
Statistics
Matches: 151, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 1 0.01
40 150 0.99
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:74178 original size:46 final size:45
Alignment explanation
Indices: 73997--74174 Score: 146
Period size: 46 Copynumber: 3.8 Consensus size: 45
73987 ACAACTCTTA
* ** *
73997 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACTTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACTAAT-GTG
* * * * *
74043 GCTGATGCATGTCCTAGATATTTCTTACACTAGCACTCGTCTCAA--T-
1 GCCGATGCATGTCCCAGACATGTCTTACACTAG--CTC-ACT-AATGTG
* * *
74089 GCCGATGCCATGTCCCAGATATGATCTTACACTGGCTCTCATAATGTG
1 GCCGATG-CATGTCCCAGACATG-TCTTACACTAGCTCAC-TAATGTG
*
74137 GCCAATGCATGTCCCAGACATGTCTTACACTAGCTCAC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCAC
74175 ATAAGTGACC
Statistics
Matches: 105, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
45 4 0.04
46 53 0.50
47 28 0.27
48 18 0.17
49 2 0.02
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (45 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTCACTAATGTG
Found at i:81216 original size:40 final size:40
Alignment explanation
Indices: 81023--81248 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
81013 TTGAATGATG
* * * *
81023 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAGGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA-GTTACTAAA
* *
81063 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
81103 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
81143 TCTGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
81183 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
81224 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
81249 AATGAGTAGC
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.01
40 158 0.93
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:89141 original size:37 final size:39
Alignment explanation
Indices: 89085--89228 Score: 204
Period size: 40 Copynumber: 3.7 Consensus size: 39
89075 AGATGTCATT
*
89085 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA
89124 ATCCGGG-TAAG-CCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-A
*
89162 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* *
89201 TAACCGGGCTATGTCCCGAAGGCATTTG
1 -ATCCGGGCTAAGTCCCGAAGGCATTTG
89229 AACGAGTAGC
Statistics
Matches: 96, Mismatches: 4, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
37 24 0.25
38 12 0.12
39 11 0.11
40 49 0.51
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
Found at i:89247 original size:80 final size:76
Alignment explanation
Indices: 89099--89261 Score: 211
Period size: 77 Copynumber: 2.1 Consensus size: 76
89089 GGACTAAGAT
* **
89099 CCGAAGGCATTTGTGCGAGTTACTAATCCGGGTAAGCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGAAGGCATTTGTGCGAGTTACTAAACCGGGTAAGCCCGAAGGCATTTGAACGAGTTACTAAAT
*
89164 CCGGGTTAAGTC
66 CC-GGTTAAATC
*
89176 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGTTACTA-AACCGGG-TAAG-CCCGAAGGCATTTGAACGAGTTA-CT
* *
89240 ATATCCGGTTAAATT
62 AAATCCGGTTAAATC
89255 CCGAAGG
1 CCGAAGG
89262 TACGTGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
77 25 0.33
78 6 0.08
79 19 0.25
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (76 bp):
CCGAAGGCATTTGTGCGAGTTACTAAACCGGGTAAGCCCGAAGGCATTTGAACGAGTTACTAAAT
CCGGTTAAATC
Done.