Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3786
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: 68870
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:1253 original size:25 final size:26
Alignment explanation
Indices: 1223--1348 Score: 140
Period size: 25 Copynumber: 5.0 Consensus size: 26
1213 TGGATAAGTT
1223 GTAGAATTACCGAAATACCCCTGTA-
1 GTAGAATTACCGAAATACCCCTGTAG
*
1248 GTAGAATTACTGAAATA-CCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTA-G
**
1274 GTA-AATTATTGAAATA-CCCTGTAG
1 GTAGAATTACCGAAATACCCCTGTAG
*
1298 GTAGAATTACC--AATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTA-G
*
1323 GTAGAA-TACCAAAATACCCCTGTAG
1 GTAGAATTACCGAAATACCCCTGTAG
1348 G
1 G
1349 GTAGTACCGT
Statistics
Matches: 88, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
23 4 0.05
24 21 0.24
25 49 0.56
26 14 0.16
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (26 bp):
GTAGAATTACCGAAATACCCCTGTAG
Found at i:1344 original size:50 final size:51
Alignment explanation
Indices: 1223--1348 Score: 163
Period size: 50 Copynumber: 2.5 Consensus size: 51
1213 TGGATAAGTT
1223 GTAGAATTACCGAAATACCCCTGTA-GTAGAATTACTGAAATACCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGTAGAATTAC-GAAATACCCTGTAGG
** *
1274 GTA-AATTATTGAAATA-CCCTGTAGGTAGAATTAC-CAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGTAGAATTACGAAATACCC-TGTAGG
*
1323 GTAGAA-TACCAAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
1349 GTAGTACCGT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
48 7 0.11
49 23 0.35
50 32 0.49
51 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (51 bp):
GTAGAATTACCGAAATACCCCTGTAGGTAGAATTACGAAATACCCTGTAGG
Found at i:8698 original size:27 final size:27
Alignment explanation
Indices: 8664--8818 Score: 152
Period size: 27 Copynumber: 5.7 Consensus size: 27
8654 TGGATAAGTT
*
8664 GTAGAATTAGCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
*
8691 GTAGAATTACCAAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAAG
** * *
8718 GTAGAATTATTGACATACCCCTAT-AG
1 GTAGAATTACCGAAATACCCCTGTAAG
* * *
8744 GATAGAATTATCGAAATACCCTTGTATG
1 G-TAGAATTACCGAAATACCCCTGTAAG
* * *
8772 GTAGAAATACTGAAATACCCTTGT-AG
1 GTAGAATTACCGAAATACCCCTGTAAG
* *
8798 AGTGGAATTACCGAGATACCC
1 -GTAGAATTACCGAAATACCC
8819 TTGTGGGGTT
Statistics
Matches: 105, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
26 4 0.04
27 99 0.94
28 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAAG
Found at i:8817 original size:81 final size:81
Alignment explanation
Indices: 8665--8818 Score: 193
Period size: 81 Copynumber: 1.9 Consensus size: 81
8655 GGATAAGTTG
* **
8665 TAGAATTAGCGAAATACCCCTGTAAGGTAGAATTACCAAAATACCCCTGTAAGGTAGAATTATTG
1 TAGAATTAGCGAAATACCCCTGTAAGGTAGAAATACCAAAATACCCCTGTAAGGTAGAATTACCG
8730 ACATACCCCTATAGGA
66 ACATACCCCTATAGGA
* * * ** * *
8746 TAGAATTATCGAAATACCCTTGTATGGTAGAAATACTGAAATACCCTTGT-AGAGTGGAATTACC
1 TAGAATTAGCGAAATACCCCTGTAAGGTAGAAATACCAAAATACCCCTGTAAG-GTAGAATTACC
*
8810 GAGATACCC
65 GACATACCC
8819 TTGTGGGGTT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 2 0.03
81 59 0.97
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (81 bp):
TAGAATTAGCGAAATACCCCTGTAAGGTAGAAATACCAAAATACCCCTGTAAGGTAGAATTACCG
ACATACCCCTATAGGA
Found at i:8881 original size:27 final size:26
Alignment explanation
Indices: 8837--8890 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
8827 TTAAATTAAC
8837 ATTTTGCCCCTAGGGTGTTAAATGACT
1 ATTTTGCCCCTAGGGTG-TAAATGACT
* *
8864 ATTTTGCCCCTTGTGTGTAAATGACT
1 ATTTTGCCCCTAGGGTGTAAATGACT
8890 A
1 A
8891 ACTTGTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTTGCCCCTAGGGTGTAAATGACT
Found at i:14484 original size:47 final size:46
Alignment explanation
Indices: 14330--14542 Score: 162
Period size: 47 Copynumber: 4.5 Consensus size: 46
14320 TTTGTGCACT
* * * ** *
14330 AGTGTAAGACATGCCTTGGACATACTTTGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCC
* * * * * * *
14376 AGTGTAAGACCATGTTTGGGACATGGCATC-GGCATCCA-GACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCTTCAGCCAT--ATTATGAGAGCC
*
14424 AGTATAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCC
* * * * *
14470 AGTGTAAGACCATGTCTGGGACATGGTGTTAGCACAGAGT-TGAGTGCC
1 AGTGTAAGA-CATGTCTGGGACATGCT-TCAGC-CATATTATGAGAGCC
*
14518 AGAGTAAGACATGTCTGGGACATGC
1 AGTGTAAGACATGTCTGGGACATGC
14543 ATCGGCCTCG
Statistics
Matches: 130, Mismatches: 28, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
45 1 0.01
46 27 0.21
47 62 0.48
48 35 0.27
49 5 0.04
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTATGAGAGCC
Found at i:14490 original size:94 final size:91
Alignment explanation
Indices: 14359--14690 Score: 289
Period size: 94 Copynumber: 3.5 Consensus size: 91
14349 ACATACTTTG
* *
14359 GCCACATTATGAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCCAGACGAGGGCT
1 GCCACA-TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-CAGA-GAGTGCT
*
14424 AGTATAAGACATGTCTGGGACATGCTTCA
63 AGTATAAGACATGTCTGGGACATGCATCA
* ** **
14453 GCCATATTATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGTGTTAGCA-CAGAGTTGAGTGC
1 GCCACA-TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAGA---GAGTGC
* *
14517 CAG-AGTAAGACATGTCTGGGACATGCATCG
62 TAGTA-TAAGACATGTCTGGGACATGCATCA
* * * * * * * *
14547 GCCTCGACAGA-GACAGCCAGTGTAA-AACGTGCCTGGGACA-CGCATCGGC-TAAGAGTTGTGC
1 G-C-C-ACATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAGAG-AGTGC
*
14608 TAGTGTAAGACATGTCTGGGACATGCATCA
62 TAGTATAAGACATGTCTGGGACATGCATCA
* * *
14638 GCACGCACATATGAGAGTCAGTATAAAACCATGTCTGGGACATGGCATCGGCA
1 G--C-CACATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
14691 ATATATCCCA
Statistics
Matches: 187, Mismatches: 37, Indels: 27
0.75 0.15 0.11
Matches are distributed among these distances:
90 1 0.01
91 35 0.19
92 17 0.09
93 20 0.11
94 96 0.51
95 14 0.07
96 2 0.01
97 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.21
Consensus pattern (91 bp):
GCCACATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATCAGAGAGTGCTAGT
ATAAGACATGTCTGGGACATGCATCA
Found at i:14628 original size:44 final size:46
Alignment explanation
Indices: 14372--14689 Score: 141
Period size: 47 Copynumber: 6.8 Consensus size: 46
14362 ACATTATGAG
* * *
14372 AGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATC-CAGACGAG
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCACAGA-GAC
* * * * * *
14420 GGCTAGTATAAGACATGTCTGGGACATGCTTCAGCCAT-ATTATGAG--
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-TCA-CA-GAGAC
* **** *
14466 AGCCAGTGTAAGACCATGTCTGGGACATG-GT-GTTAGCACAGAGTTGAG
1 AGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCACAGA---GAC
* *
14514 TGCCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGAC
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTC-ACAGAGAC
* * * * **
14561 AGCCAGTGTAAAACGTGCCTGGGACACGCATCGG-CT-A-AGAGTTG
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCACAGAG-AC
* * * * * *
14605 TGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCACATATGAG
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGC-CTCACAGA-GAC
* * *
14653 AGTCAGTATAAAACCATGTCTGGGACATGGCATCGGC
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
14690 AATATATCCC
Statistics
Matches: 198, Mismatches: 50, Indels: 42
0.68 0.17 0.14
Matches are distributed among these distances:
43 6 0.03
44 29 0.15
45 1 0.01
46 21 0.11
47 75 0.38
48 35 0.18
49 19 0.10
50 12 0.06
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (46 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCACAGAGAC
Found at i:22308 original size:31 final size:31
Alignment explanation
Indices: 22273--22336 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
22263 TGATTTAATG
22273 TAAACATTATTAGTTTACACTTTCCAAAATA
1 TAAACATTATTAGTTTACACTTTCCAAAATA
22304 TAAACATTATTAGTTTACACTTTCCAAAATA
1 TAAACATTATTAGTTTACACTTTCCAAAATA
22335 TA
1 TA
22337 TAGTTTGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (31 bp):
TAAACATTATTAGTTTACACTTTCCAAAATA
Found at i:23812 original size:40 final size:40
Alignment explanation
Indices: 23763--23842 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
23753 TCATAAAAGA
* * *
23763 AACCGTTACTTACACGAAATGGAATAG-AAAACAAATCAAT
1 AACCATTACTTACACAAAATGGAATAGCAAAA-AAAACAAT
*
23803 AACCATTACTTACACAAAATGGAGTAGCAAAAAAAACAAT
1 AACCATTACTTACACAAAATGGAATAGCAAAAAAAACAAT
23843 CATCAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.89
41 4 0.11
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (40 bp):
AACCATTACTTACACAAAATGGAATAGCAAAAAAAACAAT
Found at i:25165 original size:19 final size:19
Alignment explanation
Indices: 25141--25180 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
25131 ATACCTCACT
25141 ATAGCTATTATTGAAATAA
1 ATAGCTATTATTGAAATAA
25160 ATAGCTATTATTGAAATAA
1 ATAGCTATTATTGAAATAA
25179 AT
1 AT
25181 TCATGTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.38
Consensus pattern (19 bp):
ATAGCTATTATTGAAATAA
Found at i:34176 original size:40 final size:40
Alignment explanation
Indices: 34139--34284 Score: 152
Period size: 40 Copynumber: 3.7 Consensus size: 40
34129 TGAGGAATTG
*
34139 TATCCGAGCTTAAAGACCCACAGGCTATATACTGGAATGT
1 TATCCGGGCTTAAAGACCCACAGGCTATATACTGGAATGT
* * * *
34179 TATCTGGGCTTAAAGACTCGCAGGCTATATGCTGGAATGT
1 TATCCGGGCTTAAAGACCCACAGGCTATATACTGGAATGT
** * * * *
34219 TATCCGGGCTTAAAGACCTGCAGGCT-TCGTGCTAGAATGC
1 TATCCGGGCTTAAAGACCCACAGGCTAT-ATACTGGAATGT
* *
34259 TATCCGGGC-TAGAGACCCGCAGGCTA
1 TATCCGGGCTTAAAGACCCACAGGCTA
34285 CGAGCTGGTA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 15 0.16
40 76 0.84
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCACAGGCTATATACTGGAATGT
Found at i:37226 original size:26 final size:26
Alignment explanation
Indices: 37190--37239 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
37180 CAATGGCTAG
37190 TTTGAACAACTGATTCTATTAACTAA
1 TTTGAACAACTGATTCTATTAACTAA
* *
37216 TTTGACCAACTGATTTTATTAACT
1 TTTGAACAACTGATTCTATTAACT
37240 GTTTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (26 bp):
TTTGAACAACTGATTCTATTAACTAA
Found at i:44162 original size:42 final size:42
Alignment explanation
Indices: 44103--44266 Score: 233
Period size: 42 Copynumber: 3.9 Consensus size: 42
44093 TTAGGGTTAC
*
44103 TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCTATA
1 TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCGATA
*
44145 TGAGATT-TCGTGTAAGACCATATTTGGGATATGGCATCGATA
1 TGAGATTAT-GTGTAAGACCATATCTGGGATATGGCATCGATA
* *
44187 TGAGACTT-TGTGTAAGACCATAACTGGGCTATTGGCATCGATA
1 TGAGA-TTATGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* *
44230 CGAGATTATATGTAAGACCATATCTGGGATATGGCAT
1 TGAGATTATGTGTAAGACCATATCTGGGATATGGCAT
44267 TGGTACGGTA
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.64
43 38 0.35
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (42 bp):
TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:44250 original size:85 final size:84
Alignment explanation
Indices: 44103--44266 Score: 233
Period size: 85 Copynumber: 1.9 Consensus size: 84
44093 TTAGGGTTAC
* * * *
44103 TGAGATTATGTGTAAGACCATATCTGGGATATGGCATCTATATGAGATTTCGTGTAAGACCATAT
1 TGAGATTATGTGTAAGACCATAACTGGGATATGGCATCGATACGAGATTTCATGTAAGACCATAT
*
44168 TTGGGATATGGCATCGATA
66 CTGGGATATGGCATCGATA
*
44187 TGAGACTT-TGTGTAAGACCATAACTGGGCTATTGGCATCGATACGAGATTAT-ATGTAAGACCA
1 TGAGA-TTATGTGTAAGACCATAACTGGGATA-TGGCATCGATACGAGATT-TCATGTAAGACCA
44250 TATCTGGGATATGGCAT
63 TATCTGGGATATGGCAT
44267 TGGTACGGTA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
84 26 0.37
85 44 0.62
86 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.32
Consensus pattern (84 bp):
TGAGATTATGTGTAAGACCATAACTGGGATATGGCATCGATACGAGATTTCATGTAAGACCATAT
CTGGGATATGGCATCGATA
Found at i:44766 original size:15 final size:15
Alignment explanation
Indices: 44746--44779 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
44736 AATAGAAAGT
44746 TACATGGGTTAGGGA
1 TACATGGGTTAGGGA
44761 TACATGGGTTAGGGA
1 TACATGGGTTAGGGA
44776 TACA
1 TACA
44780 GGCGTGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.09, G:0.35, T:0.26
Consensus pattern (15 bp):
TACATGGGTTAGGGA
Found at i:48650 original size:12 final size:13
Alignment explanation
Indices: 48628--48656 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
48618 TTATTAAATG
48628 AATTAAAAAGCCA
1 AATTAAAAAGCCA
48641 AATT-AAAAGCCA
1 AATTAAAAAGCCA
48653 AATT
1 AATT
48657 CTGTACATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTAAAAAGCCA
Found at i:52803 original size:42 final size:42
Alignment explanation
Indices: 52740--52845 Score: 149
Period size: 42 Copynumber: 2.5 Consensus size: 42
52730 TTAAGGTTAC
* * ** *
52740 TGAGATTACGTGTAAGGCCATATCTGGGATATGGCATCTATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGAAATCGATA
*
52782 TGAGATTTCGTGTAAGACCATATTTGGGATATGAAATCGATA
1 TGAGATTTCGTGTAAGACCATATCTGGGATATGAAATCGATA
*
52824 TGAGACTTCGTGTAAGACCATA
1 TGAGATTTCGTGTAAGACCATA
52846 GCTGAGCTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (42 bp):
TGAGATTTCGTGTAAGACCATATCTGGGATATGAAATCGATA
Found at i:62012 original size:45 final size:45
Alignment explanation
Indices: 61951--62124 Score: 285
Period size: 45 Copynumber: 3.9 Consensus size: 45
61941 TGATCTCATT
*
61951 TCACCAGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATC
1 TCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* * *
61996 TCACCGGCATTATAGCCTGCTCGGCTTAAAGGCCCGAATAGTATC
1 TCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
* *
62041 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAGTATC
1 TCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
*
62086 TCACCAGCATCATAGCCTGCTAGGCTCAAAGGCCCGAAT
1 TCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAAT
62125 TGTAACACTC
Statistics
Matches: 119, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 119 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (45 bp):
TCACCAGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAGTATC
Found at i:63953 original size:39 final size:39
Alignment explanation
Indices: 63737--63931 Score: 268
Period size: 39 Copynumber: 5.0 Consensus size: 39
63727 AGAAAGCATG
* * *
63737 CGGGACTTTAAGCCCGGACATAATACCAGCATAAA-GCCTG
1 CGGGAC-TT-AGCCCAGATATAATACCAGCATAAATGCCTT
63777 CGGGACTTTAGCCCAGATATAATACCAGCATAAATGCCTT
1 CGGGAC-TTAGCCCAGATATAATACCAGCATAAATGCCTT
* * *
63817 CGAGACTTAGCCCAGATATAACACCAGCACAAATGCCTT
1 CGGGACTTAGCCCAGATATAATACCAGCATAAATGCCTT
*
63856 CGGGACTTAGCCCAGATATAATACCAGCACAAATGCCTT
1 CGGGACTTAGCCCAGATATAATACCAGCATAAATGCCTT
* *
63895 CAGGACTTAGCCCGGATATAATACCAGCATAAA-GCCT
1 CGGGACTTAGCCCAGATATAATACCAGCATAAATGCCT
63932 GCGGACCTCA
Statistics
Matches: 143, Mismatches: 11, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
38 4 0.03
39 121 0.85
40 18 0.13
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (39 bp):
CGGGACTTAGCCCAGATATAATACCAGCATAAATGCCTT
Found at i:68787 original size:38 final size:39
Alignment explanation
Indices: 68741--68829 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 39
68731 TCCTCGTTCA
* * *
68741 AATGCCTTCGGGACATAGCCCGGTTTTAGTAAC-CACAC
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACAC
* *
68779 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACATAACCCGGATTTAATAACTCACAC
* *
68818 AAAGGCTTCGGG
1 AATGCCTTCGGG
68830 GGCGGGGGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 29 0.67
39 14 0.33
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACATAACCCGGATTTAATAACTCACAC
Done.