Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold834
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: 65653
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:4150 original size:41 final size:41
Alignment explanation
Indices: 4027--4209 Score: 247
Period size: 41 Copynumber: 4.7 Consensus size: 41
4017 TCCTCGTTCA
* *
4027 AATGCCTTCGGGACATAGCCCGG-TTTTAGT-ACTC-CAC-
1 AATGCCTTCGGGACATAACCCGGATTTTAATAACTCGCACG
*
4064 AATGCCTTCGGGACATAACCCGGA--TTAACAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTTAATAACTCGCACG
* * *
4103 ACTGCCTTCGGGACTTAACCCGGATTTTAATAACTCGTACG
1 AATGCCTTCGGGACATAACCCGGATTTTAATAACTCGCACG
*
4144 AATGCCTTCGGGACTTAACCCGGA-TTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCGGATTTTAATAACTCGCACG
4184 AATGCCTTCGGGAC-TAACCCGGATTT
1 AATGCCTTCGGGACATAACCCGGATTT
4210 AGTATCTCGC
Statistics
Matches: 130, Mismatches: 9, Indels: 11
0.87 0.06 0.07
Matches are distributed among these distances:
36 3 0.02
37 26 0.20
38 3 0.02
39 31 0.24
40 31 0.24
41 36 0.28
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (41 bp):
AATGCCTTCGGGACATAACCCGGATTTTAATAACTCGCACG
Found at i:4185 original size:40 final size:40
Alignment explanation
Indices: 4027--4288 Score: 266
Period size: 39 Copynumber: 6.6 Consensus size: 40
4017 TCCTCGTTCA
* * * *
4027 AATGCCTTCGGGACATAGCCCGGTTTTAGT-ACTC-CAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
4064 AATGCCTTCGGGACATAACCCGGA-TTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
4103 ACTGCCTTCGGGACTTAACCCGGATTTTAATAACTCGTACG
1 AATGCCTTCGGGACTTAACCCGGA-TTTAATAACTCGCACG
4144 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
4184 AATGCCTTCGGGAC-TAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * * *
4223 AAGGCCTGTCGCGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCT-TCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
4265 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
4289 CAGCATTCAA
Statistics
Matches: 191, Mismatches: 25, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.02
37 26 0.14
38 3 0.02
39 50 0.26
40 43 0.23
41 42 0.22
42 19 0.10
43 5 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:4249 original size:81 final size:78
Alignment explanation
Indices: 4027--4223 Score: 265
Period size: 80 Copynumber: 2.5 Consensus size: 78
4017 TCCTCGTTCA
* * *
4027 AATGCCTTCGGGACATAGCCCGGTTTTAGTACTC-CACAATGCCTTCGGGACATAACCCGGA-TT
1 AATGCCTTCGGGACATAACCCGGATTTAGTACTCGCACAATGCCTTCGGGACTTAACCCGGATTT
4090 AACAACTCGCACG
66 AACAACTCGCACG
* * * *
4103 ACTGCCTTCGGGACTTAACCCGGATTTTAATAACTCGTACGAATGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACATAACCCGGA-TTTAGT-ACTCGCAC-AATGCCTTCGGGACTTAACCCGGA
*
4168 TTTAATAACTCGCACG
63 TTTAACAACTCGCACG
4184 AATGCCTTCGGGAC-TAACCCGGATTTAGTATCTCGCACAA
1 AATGCCTTCGGGACATAACCCGGATTTAGTA-CTCGCACAA
4224 AGGCCTGTCG
Statistics
Matches: 104, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
76 20 0.19
77 5 0.05
78 7 0.07
79 13 0.12
80 32 0.31
81 27 0.26
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (78 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTACTCGCACAATGCCTTCGGGACTTAACCCGGATTT
AACAACTCGCACG
Found at i:4272 original size:81 final size:81
Alignment explanation
Indices: 4030--4288 Score: 228
Period size: 81 Copynumber: 3.3 Consensus size: 81
4020 TCGTTCAAAT
* * * * * *
4030 GCCTTCGGGACATAGCCCGG-TTTTAGT-ACTC-CAC-AATGCCTTCGGGACATAACCCGGAT-T
1 GCCTTCGGGACTTAACCCGGATTTTAATAACTCGCACAAAGGCCTTCGCGACTTAACCCGGATAT
* * **
4090 AACAACTCGCACGACT
66 AATAACTAGCACGAAA
* * * * *
4106 GCCTTCGGGACTTAACCCGGATTTTAATAACTCGTACGAATGCCTTCGGGACTTAACCCGGATTT
1 GCCTTCGGGACTTAACCCGGATTTTAATAACTCGCACAAAGGCCTTCGCGACTTAACCCGGATAT
* *
4171 AATAACTCGCACGAAT
66 AATAACTAGCACGAAA
* * *
4187 GCCTTCGGGAC-TAACCCGGA-TTTAGTATCTCGCACAAAGGCCTGTCGCGATCTTAATCCGGAT
1 GCCTTCGGGACTTAACCCGGATTTTAATAACTCGCACAAAGGCCT-TCGCGA-CTTAACCCGGAT
* *
4250 ATATTCACTTAGCAC-AAA
64 ATAATAAC-TAGCACGAAA
*
4268 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
4289 CAGCATTCAA
Statistics
Matches: 154, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
76 18 0.12
77 6 0.04
78 4 0.03
79 20 0.13
80 38 0.25
81 55 0.36
82 13 0.08
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (81 bp):
GCCTTCGGGACTTAACCCGGATTTTAATAACTCGCACAAAGGCCTTCGCGACTTAACCCGGATAT
AATAACTAGCACGAAA
Found at i:10866 original size:40 final size:40
Alignment explanation
Indices: 10768--11030 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
10758 TCCTCGTTCA
* * * * *
10768 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
10807 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
10847 ACTGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
10887 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
10927 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
10967 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
11007 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
11031 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 37 0.19
40 153 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:13118 original size:43 final size:43
Alignment explanation
Indices: 13038--13141 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 43
13028 ATGCCACTAT
* * * * *
13038 CCCAAACATGGTCTTACACGAAATCGATTAACGATGCCAATGC
1 CCCAGACATGGTCTTACACAAAATCCAATAACAATGCCAATGC
*
13081 CCCAGACATGGTCTTACACAAAATCTCAAT-ACAATGCCAATGT
1 CCCAGACATGGTCTTACACAAAATC-CAATAACAATGCCAATGC
* *
13124 CCCAGGCATGGTATTACA
1 CCCAGACATGGTCTTACA
13142 TGTAATCACA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
43 50 0.96
44 2 0.04
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (43 bp):
CCCAGACATGGTCTTACACAAAATCCAATAACAATGCCAATGC
Found at i:26344 original size:34 final size:34
Alignment explanation
Indices: 26306--26381 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
26296 GTGACAATCT
*
26306 AGTATCAGTGTGAGCCTTAGCCCATTACAATACC
1 AGTATCAGTGTGAGCCTTAGCCCATTACAATAAC
* *
26340 AGTATCAGTGTGGGCCTTAGCCCATTACAGTAAC
1 AGTATCAGTGTGAGCCTTAGCCCATTACAATAAC
26374 AGTATCAG
1 AGTATCAG
26382 AAATGCATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
AGTATCAGTGTGAGCCTTAGCCCATTACAATAAC
Found at i:29348 original size:22 final size:21
Alignment explanation
Indices: 29329--29379 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
29319 CCTCACACAT
29329 CCGTGTGGTCCAAGAGACACGC
1 CCGTGTGGTCCAAGAGACAC-C
* *
29351 CGGTGTGGTCCAAGGGACACGC
1 CCGTGTGGTCCAAGAGACAC-C
29373 CCGTGTG
1 CCGTGTG
29380 ACCCTAGGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.29, G:0.37, T:0.16
Consensus pattern (21 bp):
CCGTGTGGTCCAAGAGACACC
Found at i:32006 original size:44 final size:44
Alignment explanation
Indices: 31952--32035 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
31942 GTTAATTATG
*
31952 GCACTTAGTGTGCGAAACCAAGATAGCTTCGGATATATATATTT
1 GCACTAAGTGTGCGAAACCAAGATAGCTTCGGATATATATATTT
* *** *
31996 GCACTAAGTGTGCGAGATTGAGATAGCTTCGGCTATATAT
1 GCACTAAGTGTGCGAAACCAAGATAGCTTCGGATATATAT
32036 TTATATGCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (44 bp):
GCACTAAGTGTGCGAAACCAAGATAGCTTCGGATATATATATTT
Found at i:32071 original size:45 final size:46
Alignment explanation
Indices: 31972--32082 Score: 138
Period size: 45 Copynumber: 2.5 Consensus size: 46
31962 TGCGAAACCA
* * *
31972 AGATAGCTTCGG--ATATATATATTTGCACTAAGTGTGCGAGATTG
1 AGATAGCTTCGGCTATATATTTATATGCACTAAGTATGCGAGATTG
* *
32016 AGATAGCTTCGGCTATATATTTATATGCTCTTAGTATG-GAGATTG
1 AGATAGCTTCGGCTATATATTTATATGCACTAAGTATGCGAGATTG
* *
32061 ATATAGCTTCGGCTATTTATTT
1 AGATAGCTTCGGCTATATATTT
32083 GGCACTAAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
44 12 0.21
45 27 0.47
46 19 0.33
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.40
Consensus pattern (46 bp):
AGATAGCTTCGGCTATATATTTATATGCACTAAGTATGCGAGATTG
Found at i:33050 original size:51 final size:52
Alignment explanation
Indices: 32969--33148 Score: 281
Period size: 51 Copynumber: 3.4 Consensus size: 52
32959 GATGATGAAA
*
32969 AAAGGAAAAGAAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
1 AAAGAAAAAG-AAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
33022 AAAGAAAAAGAAG-AAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
1 AAAGAAAAAGAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
33073 AAAGAAAAAGAAGAAAAAAAAAGAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
1 AAAGAAAAAGAAG----AAAAA-AAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
*
33130 AAAGAAAAAGAAGGAAAAA
1 AAAGAAAAAGAAGAAAAAA
33149 GAGCTTTGAG
Statistics
Matches: 119, Mismatches: 2, Indels: 13
0.89 0.01 0.10
Matches are distributed among these distances:
51 51 0.43
52 4 0.03
53 13 0.11
56 4 0.03
57 47 0.39
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.17
Consensus pattern (52 bp):
AAAGAAAAAGAAGAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAG
Found at i:33086 original size:13 final size:13
Alignment explanation
Indices: 33068--33097 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33058 TTGGCCGAAT
*
33068 AGAAGAAAGAAAA
1 AGAAGAAAAAAAA
33081 AGAAGAAAAAAAA
1 AGAAGAAAAAAAA
33094 AGAA
1 AGAA
33098 AAGCTCTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAA
Found at i:33106 original size:57 final size:56
Alignment explanation
Indices: 33017--33148 Score: 212
Period size: 57 Copynumber: 2.3 Consensus size: 56
33007 TTGGCCGAAT
33017 AGAAGAAAGAA-AAAGAAGAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAA
1 AGAA-AAAGAAGAAA-AA-AAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAA
33075 AGAAAAAGAAGAAAAAAAAAGAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAA
1 AGAAAAAGAAGAAAAAAAAA-AAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAA
*
33132 AGAAAAAGAAGGAAAAA
1 AGAAAAAGAAGAAAAAA
33149 GAGCTTTGAG
Statistics
Matches: 71, Mismatches: 1, Indels: 5
0.92 0.01 0.06
Matches are distributed among these distances:
56 4 0.06
57 60 0.85
58 7 0.10
ACGTcount: A:0.54, C:0.09, G:0.22, T:0.15
Consensus pattern (56 bp):
AGAAAAAGAAGAAAAAAAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAAGAA
Found at i:34447 original size:40 final size:40
Alignment explanation
Indices: 34391--34612 Score: 286
Period size: 40 Copynumber: 5.5 Consensus size: 40
34381 TGGATGATAA
* *
34391 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTA-TAT
* * * *
34431 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTACAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
* *
34471 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
* *
34511 CCGGGCTAAGTCCCGAAGGCATTGGTG-TGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGTTACTATAT
* * *
34551 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
*
34591 CCGGGCTATGTCCCGAAGGCAT
1 CCGGGCTAAGTCCCGAAGGCAT
34613 AGAGCGAGTA
Statistics
Matches: 162, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATAT
Found at i:34604 original size:120 final size:120
Alignment explanation
Indices: 34391--34612 Score: 340
Period size: 120 Copynumber: 1.9 Consensus size: 120
34381 TGGATGATAA
* * *
34391 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGTTTCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTGGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
34456 TGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATAT
66 TGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATAT
* * *
34511 CCGGGCTAAGTCCCGAAGGCATTGGTG-TGAGTTATTA-TATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTGGCGCT-AGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATT
* *
34574 GGTGCGAGTTATTATATCCGGGCTATGTCCCGAAGGCAT
64 GGTGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCAT
34613 AGAGCGAGTA
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
119 2 0.02
120 90 0.98
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.27
Consensus pattern (120 bp):
CCGGGCTAAGTCCCGAAGGCATTGGCGCTAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
TGCGAGTTATTACATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGCTACTATAT
Found at i:37092 original size:25 final size:25
Alignment explanation
Indices: 37029--37096 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
37019 AATAAACACA
*
37029 AGAT-TCTCTGGAAAGCCTTTGTGG
1 AGATCTCTCTGGAAAGCCTTTGTAG
* * *
37053 TGATCTATCTTGAAAGCCTTTGTAG
1 AGATCTCTCTGGAAAGCCTTTGTAG
37078 AGAATC-CTCTGGAAAGCCT
1 AG-ATCTCTCTGGAAAGCCT
37097 ATGTGGCTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
24 3 0.09
25 29 0.83
26 3 0.09
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (25 bp):
AGATCTCTCTGGAAAGCCTTTGTAG
Found at i:41298 original size:49 final size:47
Alignment explanation
Indices: 41238--41739 Score: 806
Period size: 47 Copynumber: 10.6 Consensus size: 47
41228 GATAATTGTG
* *
41238 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41285 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41332 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41379 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41426 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41473 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41522 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41571 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41620 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * * *
41667 ATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41714 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
41740 TCCCGAAGGG
Statistics
Matches: 433, Mismatches: 20, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 288 0.67
49 145 0.33
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41373 original size:38 final size:39
Alignment explanation
Indices: 41331--41648 Score: 114
Period size: 49 Copynumber: 6.8 Consensus size: 39
41321 CGATGTGATG
41331 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGA
1 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC------A
41376 TGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGA
1 --AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC------A
*
41423 TGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 --AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCC------A
*
41470 TGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGA
1 --AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCC------A
*
41519 TGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGA
1 --AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCC------A
*
41568 TGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGA
1 --AATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCC------A
41617 TGAATGTGAAAGTGTATATATGTGATAAGGCC
1 --AATGTGAAAGTGTATATATGTGATAAGGCC
41649 TAATAGCCGA
Statistics
Matches: 267, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
47 122 0.46
49 145 0.54
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (39 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
Found at i:41376 original size:22 final size:22
Alignment explanation
Indices: 41348--41423 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
41338 AAGTGTATAT
41348 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* * ***
41370 ATGTGATGAATG-TGAAAGTGTATA
1 ATGTGAT-AAGGCCG-AA-TGGCCA
41394 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
41417 ATGTGAT
1 ATGTGAT
41424 GAATGTGAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 15 0.38
23 8 0.21
24 8 0.21
25 8 0.21
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:44689 original size:164 final size:164
Alignment explanation
Indices: 44494--44821 Score: 484
Period size: 164 Copynumber: 2.0 Consensus size: 164
44484 TTTTTGAATA
*
44494 TTTTCCCCTATTTACTTTCCGCTCAAAATTTTATTCCCCCAACCCTCAAAACTTTTTATTTCCCC
1 TTTTCCCCTATTTACTTTCCGCTCAAAATTTTATTCCCCCAACCCTCAAAACTTATTATTTCCCC
* *
44559 CCTAAACTTTTACTTTTCACTATTTACCCCAAATAAAAAATCATCAAAAAAAAATCCCTAAACAT
66 CCTAAACTTTTACTTTTCACCATTTACCCCAAATAAAAAACCATC-AAAAAAAATCCCTAAACAT
*
44624 AAACT-GTAATAAATTTATTTATATCTACTATTTAT
130 AAA-TAGTAATAAATTTATTTAGATCTACTATTTAT
* * *
44659 TTTTCCCC-ATTTACTTTCTC-C-CAAAAATTTTATTCTCCCAACCTTCAAAACTTATTATTTTC
1 TTTTCCCCTATTTACTTTC-CGCTC-AAAATTTTATTCCCCCAACCCTCAAAACTTATTATTTCC
* * * *
44721 CCCCTAAACTTTTACTTTTCACCCTTTACCCCAAATAAAAAGCCATCTAAAAAAATCCCTAAATA
64 CCCCTAAACTTTTACTTTTCACCATTTACCCCAAATAAAAAACCATCAAAAAAAATCCCTAAACA
*
44786 TAAATAGTAATAATTTTATTTAGATCTACTATTTAT
129 TAAATAGTAATAAATTTATTTAGATCTACTATTTAT
44822 ATTATTAAAT
Statistics
Matches: 148, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
162 1 0.01
163 49 0.33
164 89 0.60
165 9 0.06
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (164 bp):
TTTTCCCCTATTTACTTTCCGCTCAAAATTTTATTCCCCCAACCCTCAAAACTTATTATTTCCCC
CCTAAACTTTTACTTTTCACCATTTACCCCAAATAAAAAACCATCAAAAAAAATCCCTAAACATA
AATAGTAATAAATTTATTTAGATCTACTATTTAT
Found at i:44731 original size:20 final size:20
Alignment explanation
Indices: 44706--44745 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
44696 CCAACCTTCA
*
44706 AAACTTATTA-TTTTCCCCCT
1 AAACTT-TTACTTTTCACCCT
44726 AAACTTTTACTTTTCACCCT
1 AAACTTTTACTTTTCACCCT
44746 TTACCCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (20 bp):
AAACTTTTACTTTTCACCCT
Found at i:45174 original size:19 final size:19
Alignment explanation
Indices: 45150--45187 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
45140 AAGTTAATAA
*
45150 CAAATTTGATTACGGTGGG
1 CAAATTTAATTACGGTGGG
45169 CAAATTTAATTACGGTGGG
1 CAAATTTAATTACGGTGGG
45188 TGACATTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (19 bp):
CAAATTTAATTACGGTGGG
Found at i:50602 original size:40 final size:40
Alignment explanation
Indices: 50555--50777 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
50545 CTACTCGCTC
* * *
50555 AATGCCTTCGGGACATAGCCCGAATATAATAACTAGCACC
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACA
*
50595 AATGCCTTCGGGACTTAGCCCGGATATAATAACTCA-CACC
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACT-AGCACA
* *
50635 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACA
* *
50675 AATGCCTTCGGGACTTATCCCGGATGTAATAACTCA-CACA
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACT-AGCACA
* * **
50715 AATGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGTGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAATAACTAGCACA
50755 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
50778 TTATCATCTG
Statistics
Matches: 163, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.01
40 159 0.98
41 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACA
Found at i:50654 original size:80 final size:80
Alignment explanation
Indices: 50554--50777 Score: 324
Period size: 80 Copynumber: 2.8 Consensus size: 80
50544 GCTACTCGCT
* * *
50554 CAATGCCTTCGGGACATAGCCCGAATATAATAACTAGCACCAATGCCTTCGGGACTTAGCCCGGA
1 CAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGA
50619 TATAATAACTCACAC
66 TATAATAACTCACAC
* * *
50634 CAATGCCTTCGGGACTTAGCCCGGATATAGTAGCTAGCACAAATGCCTTCGGGACTTATCCCGGA
1 CAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGA
*
50699 TGTAATAACTCACAC
66 TATAATAACTCACAC
* * * **
50714 AAATGCCTTCGGGACTTAGCCCGGAA-CTAGTCACTAGTGCAAATGCCTTCGGGACTTAGCCCGG
1 CAATGCCTTCGGGACTTAGCCC-GAATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
50778 TTATCATCTG
Statistics
Matches: 128, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
80 126 0.98
81 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (80 bp):
CAATGCCTTCGGGACTTAGCCCGAATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGA
TATAATAACTCACAC
Found at i:52091 original size:13 final size:13
Alignment explanation
Indices: 52073--52102 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52063 ATGAGAGCTT
*
52073 TTCTTTTTTTTTC
1 TTCTTTTTCTTTC
52086 TTCTTTTTCTTTC
1 TTCTTTTTCTTTC
52099 TTCT
1 TTCT
52103 ATTCGGCCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTCTTTC
Found at i:52105 original size:57 final size:56
Alignment explanation
Indices: 52022--52143 Score: 217
Period size: 57 Copynumber: 2.2 Consensus size: 56
52012 CTCAAAGCTC
*
52022 TTTTTCCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTCTTT
1 TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTT-TTT
52079 TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTTTT
1 TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTTTT
*
52135 TTCTTTCTT
1 TTTTTTCTT
52144 TTCCTTTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 11 0.17
57 52 0.83
ACGTcount: A:0.16, C:0.21, G:0.10, T:0.52
Consensus pattern (56 bp):
TTTTTTCTTCTTTTTCTTTCTTCTATTCGGCCAAGAACAACATGAGAGCTTTTTTT
Found at i:61276 original size:53 final size:53
Alignment explanation
Indices: 61168--61292 Score: 168
Period size: 53 Copynumber: 2.4 Consensus size: 53
61158 TGTGATGAAA
*
61168 AAAGGAAAAGAA-AGAAAAAAAAAAGTCTCATGTTGTTTCTTGGCAATAGAGAG
1 AAAGAAAAAGAAGA-AAAAAAAAAAGTCTCATGTTGTTTCTTGGCAATAGAGAG
61221 AAAGAAAAAGAAGAAAAAAAAGAAAGCTCTCATGTTG-TTCTT-GCGAATAGA-AG
1 AAAGAAAAAGAAGAAAAAAAA-AAAG-TCTCATGTTGTTTCTTGGC-AATAGAGAG
*
61274 AAAGAAAAAGAAGGAAAAA
1 AAAGAAAAAGAAGAAAAAA
61293 GAGCTTTGAG
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
53 40 0.61
54 16 0.24
55 10 0.15
ACGTcount: A:0.54, C:0.07, G:0.22, T:0.17
Consensus pattern (53 bp):
AAAGAAAAAGAAGAAAAAAAAAAAGTCTCATGTTGTTTCTTGGCAATAGAGAG
Done.