Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 167 of 167
Found at i:55267281 original size:16 final size:17
Alignment explanation
Indices: 55267241--55267281 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
55267231 TTTATTTTTA
*
55267241 TATAAAATAATTTATTT
1 TATAAAATAATTCATTT
*
55267258 TATAAAATAATTCCTTT
1 TATAAAATAATTCATTT
55267275 T-TAAAAT
1 TATAAAAT
55267282 TTTGATGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (17 bp):
TATAAAATAATTCATTT
Found at i:55268803 original size:15 final size:15
Alignment explanation
Indices: 55268790--55268828 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 15
55268780 TTATTTTATT
55268790 TTTTGAATTTTTATAA
1 TTTT-AATTTTTATAA
55268806 TTTTAATTTTTTATATA
1 TTTTAA-TTTTTATA-A
55268823 TTTTAA
1 TTTTAA
55268829 ATTATCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.10
16 12 0.57
17 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTAATTTTTATAA
Found at i:55268816 original size:16 final size:17
Alignment explanation
Indices: 55268797--55268828 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55268787 ATTTTTTGAA
55268797 TTTTTATA-ATTTTAAT
1 TTTTTATATATTTTAAT
55268813 TTTTTATATATTTTAA
1 TTTTTATATATTTTAA
55268829 ATTATCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATATATTTTAAT
Found at i:55269950 original size:2 final size:2
Alignment explanation
Indices: 55269943--55269981 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55269933 TTGAAGACAA
55269943 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
55269982 AGGATGAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55272850 original size:22 final size:22
Alignment explanation
Indices: 55272825--55272868 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55272815 TTAATGATCT
55272825 TTACGTTTTTGGAGTCCCGATA
1 TTACGTTTTTGGAGTCCCGATA
55272847 TTACGTTTTTGGAGTCCCGATA
1 TTACGTTTTTGGAGTCCCGATA
55272869 ACTTGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (22 bp):
TTACGTTTTTGGAGTCCCGATA
Found at i:55275942 original size:47 final size:46
Alignment explanation
Indices: 55275884--55276061 Score: 191
Period size: 47 Copynumber: 3.8 Consensus size: 46
55275874 GCCACATTAT
55275884 GAGAGCCAGTGTAAGACCATGT-TGGGACATGGCATCGGCATTGAGA
1 GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TTGAGA
* * **
55275930 CGAGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCTGCTACAAGA
1 -GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCT-TGAGA
* * * * *
55275976 TGACAGTCAGTGTAAAACCATGTCTCGGACATGGCATCGACTTGAGA
1 -GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGA
* *
55276023 TATGAGCCAGTGTAAGACCATGTCTGGGATATGGCATCG
1 GA-GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
55276062 ACACCTTACC
Statistics
Matches: 106, Mismatches: 20, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
45 1 0.01
46 28 0.26
47 70 0.66
48 7 0.07
ACGTcount: A:0.29, C:0.19, G:0.30, T:0.22
Consensus pattern (46 bp):
GAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTTGAGA
Found at i:55275988 original size:46 final size:46
Alignment explanation
Indices: 55275840--55276060 Score: 154
Period size: 47 Copynumber: 4.7 Consensus size: 46
55275830 ATTTGTTTGT
* **
55275840 GAGCTAGTGTAAGA-CATGTC-GAGGACAT-GCACCAGCCACATTATGA
1 GAGC-AGTGTAAGACCATGTCTG-GGACATGGCATCAG-CACAAGATGA
* ** *
55275886 GAGCCAGTGTAAGACCATGT-TGGGACATGGCATCGGCATTGAGACGA
1 GAG-CAGTGTAAGACCATGTCTGGGACATGGCATCAGCA-CAAGATGA
*
55275933 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCTGCTACAAGATGA
1 GAGC-AGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACAAGATGA
* * * *
55275979 CAGTCAGTGTAAAACCATGTCTCGGACATGGCATC-G-ACTTGAGAT-A
1 GAG-CAGTGTAAGACCATGTCTGGGACATGGCATCAGCAC--AAGATGA
*
55276025 TGAGCCAGTGTAAGACCATGTCTGGGATATGGCATC
1 -GAG-CAGTGTAAGACCATGTCTGGGACATGGCATC
55276061 GACACCTTAC
Statistics
Matches: 141, Mismatches: 20, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
45 2 0.01
46 49 0.35
47 85 0.60
48 5 0.04
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (46 bp):
GAGCAGTGTAAGACCATGTCTGGGACATGGCATCAGCACAAGATGA
Found at i:55276021 original size:93 final size:93
Alignment explanation
Indices: 55275839--55276060 Score: 261
Period size: 93 Copynumber: 2.4 Consensus size: 93
55275829 CATTTGTTTG
* ** * *
55275839 TGAGCTAGTGTAAGACATGTC-GAGGACATGCACCAGCCACATTATGAGAGCCAGTGTAAGACCA
1 TGAGCTAGTGTAAGACATGTCTG-GGACATGCATCAGCCACAAGATGACAGCCAGTGTAAAACCA
* *
55275903 TGTTGGGACATGGCATCGGCATTGAGACGA
65 TGTTCGGACATGGCATCGACATTGAGA-GA
* * *
55275933 -GAGCTAGTGTAAGACATGTCTGGGACATGCATCTGCTACAAGATGACAGTCAGTGTAAAACCAT
1 TGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGACAGCCAGTGTAAAACCAT
*
55275997 GTCTCGGACATGGCATCGAC-TTGAGATA
66 GT-TCGGACATGGCATCGACATTGAGAGA
* *
55276025 TGAGCCAGTGTAAGACCATGTCTGGGATATGGCATC
1 TGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
55276061 GACACCTTAC
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
92 1 0.01
93 75 0.68
94 29 0.26
95 5 0.05
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (93 bp):
TGAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATGACAGCCAGTGTAAAACCAT
GTTCGGACATGGCATCGACATTGAGAGA
Found at i:55281903 original size:16 final size:16
Alignment explanation
Indices: 55281884--55281914 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55281874 CTTCTTCACT
55281884 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
55281900 TACTTACTTACTTAA
1 TACTCACTTACTTAA
55281915 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:55281920 original size:20 final size:20
Alignment explanation
Indices: 55281881--55281920 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55281871 AAACTTCTTC
* *
55281881 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
55281901 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
55281921 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:55282296 original size:55 final size:53
Alignment explanation
Indices: 55282106--55282360 Score: 245
Period size: 55 Copynumber: 4.8 Consensus size: 53
55282096 ACACGGGTAC
* * * * *
55282106 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA---T-CCTT-TTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAG-AA
* *
55282155 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAA
* * *
55282208 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AA
* * * * *
55282263 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGA-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAA
*
55282316 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA-CCTT
55282361 AAACCCTAAT
Statistics
Matches: 172, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
49 35 0.20
52 2 0.01
53 47 0.27
54 14 0.08
55 72 0.42
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAA
Found at i:55282297 original size:108 final size:110
Alignment explanation
Indices: 55282153--55282353 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
55282143 ATCCTTTTGA
* *
55282153 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
55282216 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
* * *
55282261 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
55282326 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
55282354 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 28 0.33
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGT
Found at i:55284877 original size:27 final size:27
Alignment explanation
Indices: 55284847--55285024 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
55284837 ATATTGAGTC
* * * *
55284847 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
55284874 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
55284901 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
55284929 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
55284956 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
55284983 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
55285010 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
55285025 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:55284986 original size:82 final size:81
Alignment explanation
Indices: 55284868--55285023 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
55284858 TGCTATATAA
* *
55284868 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
55284933 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
55284950 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
55285014 CACTTAGTGC
65 CACTTAGTGC
55285024 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:55287112 original size:20 final size:20
Alignment explanation
Indices: 55287087--55287135 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
55287077 CATGAAAAAT
*
55287087 TTTGTGAGCTAATTTTAATG
1 TTTGTGAGCTAATTTTAACG
55287107 TTTGTGAGCTAATTTTAACG
1 TTTGTGAGCTAATTTTAACG
55287127 TTTGTGAGC
1 TTTGTGAGC
55287136 CCAATAGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTGTGAGCTAATTTTAACG
Found at i:55288275 original size:47 final size:47
Alignment explanation
Indices: 55288202--55288330 Score: 181
Period size: 47 Copynumber: 2.7 Consensus size: 47
55288192 ATTTGTTTGT
* *
55288202 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCACGA-GATGA
*
55288248 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTACGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCACGAGATGA
* *
55288295 CAGTCAGTGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCG
55288331 ACACCTTACC
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
46 13 0.17
47 55 0.73
48 7 0.09
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCACGAGATGA
Found at i:55296792 original size:24 final size:24
Alignment explanation
Indices: 55296760--55296900 Score: 185
Period size: 24 Copynumber: 5.9 Consensus size: 24
55296750 TCGGTCAAGG
*
55296760 AAATTCGCACACATAGTGCCATGC
1 AAATCCGCACACATAGTGCCATGC
* * *
55296784 TAACCCGCACACATAGTGCCTTGC
1 AAATCCGCACACATAGTGCCATGC
* * * *
55296808 TAATCCACACACGTAGTGCCATTC
1 AAATCCGCACACATAGTGCCATGC
*
55296832 AAATCCGCACACATAGTGCCATTC
1 AAATCCGCACACATAGTGCCATGC
55296856 AAATCCGCACACATAGTGCCATTG-
1 AAATCCGCACACATAGTGCCA-TGC
55296880 AAATCCGCACACATAGTGCCA
1 AAATCCGCACACATAGTGCCA
55296901 ATGTCATTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 102 0.99
25 1 0.01
ACGTcount: A:0.32, C:0.33, G:0.15, T:0.21
Consensus pattern (24 bp):
AAATCCGCACACATAGTGCCATGC
Found at i:55298252 original size:17 final size:17
Alignment explanation
Indices: 55298230--55298265 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
55298220 CTTCACTTAA
*
55298230 TATTTTATAACTTATTT
1 TATTTTATAACATATTT
55298247 TATTTTATAACATATTT
1 TATTTTATAACATATTT
55298264 TA
1 TA
55298266 AATATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
TATTTTATAACATATTT
Found at i:55313835 original size:24 final size:24
Alignment explanation
Indices: 55313806--55313915 Score: 114
Period size: 24 Copynumber: 4.6 Consensus size: 24
55313796 AGGAAATTCA
*
55313806 CACACATAGTGCCATGCTAACCCG
1 CACACATAGTGCCATGCAAACCCG
* * * *
55313830 CACACATAGTGCCTTGCTAATCCA
1 CACACATAGTGCCATGCAAACCCG
* *
55313854 CACACGTAGTGCCATTCAAATCCC-
1 CACACATAGTGCCATGCAAA-CCCG
* * *
55313878 TACACATAGTGCCATTCAAATCCG
1 CACACATAGTGCCATGCAAACCCG
55313902 CACACATAGTGCCA
1 CACACATAGTGCCA
55313916 ATGTCATTTC
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
23 2 0.03
24 68 0.94
25 2 0.03
ACGTcount: A:0.31, C:0.35, G:0.14, T:0.21
Consensus pattern (24 bp):
CACACATAGTGCCATGCAAACCCG
Found at i:55313866 original size:48 final size:48
Alignment explanation
Indices: 55313799--55313915 Score: 139
Period size: 48 Copynumber: 2.4 Consensus size: 48
55313789 TCGGTCAAGG
* *
55313799 AAATTCACACACATAGTGCCATGCTAA-CCCGCACACATAGTGCC-TTGC
1 AAATCCACACACATAGTGCCATGCAAATCCC-CACACATAGTGCCATT-C
* * * *
55313847 TAATCCACACACGTAGTGCCATTCAAATCCCTACACATAGTGCCATTC
1 AAATCCACACACATAGTGCCATGCAAATCCCCACACATAGTGCCATTC
*
55313895 AAATCCGCACACATAGTGCCA
1 AAATCCACACACATAGTGCCA
55313916 ATGTCATTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
48 53 0.91
49 5 0.09
ACGTcount: A:0.32, C:0.33, G:0.13, T:0.21
Consensus pattern (48 bp):
AAATCCACACACATAGTGCCATGCAAATCCCCACACATAGTGCCATTC
Found at i:55315256 original size:17 final size:17
Alignment explanation
Indices: 55315234--55315267 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55315224 CCCCACTTAA
*
55315234 TATATTATAACTTATTT
1 TATATTATAACATATTT
55315251 TATATTATAACATATTT
1 TATATTATAACATATTT
55315268 CAAATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATTATAACATATTT
Found at i:55318401 original size:18 final size:18
Alignment explanation
Indices: 55318378--55318414 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55318368 CTATTTTTCG
55318378 AGCCTTTGGTCACCCTCT
1 AGCCTTTGGTCACCCTCT
55318396 AGCCTTTGGTCACCCTCT
1 AGCCTTTGGTCACCCTCT
55318414 A
1 A
55318415 TCATCCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.14, C:0.38, G:0.16, T:0.32
Consensus pattern (18 bp):
AGCCTTTGGTCACCCTCT
Found at i:55323098 original size:18 final size:18
Alignment explanation
Indices: 55323075--55323111 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55323065 CTATTTTTCG
55323075 AGCCTTTGGTCACCCTCT
1 AGCCTTTGGTCACCCTCT
55323093 AGCCTTTGGTCACCCTCT
1 AGCCTTTGGTCACCCTCT
55323111 A
1 A
55323112 TCATCCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.14, C:0.38, G:0.16, T:0.32
Consensus pattern (18 bp):
AGCCTTTGGTCACCCTCT
Found at i:55347040 original size:22 final size:21
Alignment explanation
Indices: 55347000--55347040 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
55346990 CACTTGACAT
*
55347000 AGGGGCACACGCCCATGTGGG
1 AGGGGCACACACCCATGTGGG
*
55347021 AGGGGCAACACACCCCTGTG
1 AGGGGC-ACACACCCATGTG
55347041 AGCATTCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.22, C:0.32, G:0.37, T:0.10
Consensus pattern (21 bp):
AGGGGCACACACCCATGTGGG
Found at i:55347693 original size:35 final size:35
Alignment explanation
Indices: 55347647--55347725 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
55347637 TTTATAAATT
*
55347647 CAAAGTGAATGTTAGCCATCACTAAAGGCTTAATA
1 CAAAGTGAATGTTAGCCATCACTAAAGACTTAATA
*
55347682 CAAAGTGAATGTTAGCCATCATTAAAGACTTAATA
1 CAAAGTGAATGTTAGCCATCACTAAAGACTTAATA
*
55347717 CAAATTGAA
1 CAAAGTGAA
55347726 GGGTTTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (35 bp):
CAAAGTGAATGTTAGCCATCACTAAAGACTTAATA
Found at i:55348322 original size:47 final size:46
Alignment explanation
Indices: 55348271--55348482 Score: 173
Period size: 46 Copynumber: 4.5 Consensus size: 46
55348261 TGATGCCACA
* *
55348271 TCCCAGACATGGTCTTACACT-GACTATCATCTCGTAGCCGATGCATG
1 TCCCAGACAT-GTCTTACACTAG-CTCTCATCTCGTAGCCAATGCATG
* * *
55348318 TCCCAAACATTTCTTACACTAGCT-TACGTCTCG-AGCCAATTGCATG
1 TCCCAGACATGTCTTACACTAGCTCT-CATCTCGTAGCCAA-TGCATG
* * * *
55348364 TCCTAGACATGTCTTACACTAGCCCTCGTCTC-AATGCCAATGCCATG
1 TCCCAGACATGTCTTACACTAGCTCTCATCTCGTA-GCCAATG-CATG
* * * * **
55348411 TCCCAGACATGGCCTTACACTGGCTCTCATAAT-GTGGCTGATGCATG
1 TCCCAGACAT-GTCTTACACTAGCTCTCAT-CTCGTAGCCAATGCATG
*
55348458 TCCCAGACATGTCTTACATTAGCTC
1 TCCCAGACATGTCTTACACTAGCTC
55348483 ACACACGAAT
Statistics
Matches: 134, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
45 6 0.04
46 64 0.48
47 43 0.32
48 20 0.15
49 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.29
Consensus pattern (46 bp):
TCCCAGACATGTCTTACACTAGCTCTCATCTCGTAGCCAATGCATG
Found at i:55350549 original size:14 final size:14
Alignment explanation
Indices: 55350530--55350566 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
55350520 GTAATCGTCG
55350530 TACGTCATTAGATT
1 TACGTCATTAGATT
55350544 TACGTCATTAGATT
1 TACGTCATTAGATT
*
55350558 TACATCATT
1 TACGTCATT
55350567 TCATAACACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (14 bp):
TACGTCATTAGATT
Found at i:55350738 original size:16 final size:17
Alignment explanation
Indices: 55350717--55350748 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
55350707 ATTTAGGGGC
55350717 ATTTTGTT-AATTTTCT
1 ATTTTGTTAAATTTTCT
55350733 ATTTTGTTAAATTTTC
1 ATTTTGTTAAATTTTC
55350749 ACCCGATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (17 bp):
ATTTTGTTAAATTTTCT
Found at i:55355260 original size:46 final size:47
Alignment explanation
Indices: 55355195--55355407 Score: 174
Period size: 46 Copynumber: 4.6 Consensus size: 47
55355185 TGAGAGCCAA
* * *
55355195 TGTAAGATCATGTCTGGGACATGGTATCGGCATTGAGAGA-GAACTAG
1 TGTAAGACCATGTCTAGGACATGGCATCGGC-TTGAGAGATGAACTAG
* * * * *
55355242 TGTAAGA-CATGTCTGGGACAT-GTATGGGCCTCG-G-GACGTAAGCTAG
1 TGTAAGACCATGTCTAGGACATGGCATCGG-CTTGAGAGATG-AA-CTAG
*
55355288 TGTAAGA-CATGTCTAGGACAT-GCATCGGC-T-ACGAGATGACAGTCAG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCTTGA-GAGATGA-ACT-AG
* * * *
55355334 TGTAAGACCATGTCTAGGACATGACATCGACTTGAGATATGAGCTAG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCTTGAGAGATGAACTAG
*
55355381 TGTAAGACCATGTTTAGGACATGGCAT
1 TGTAAGACCATGTCTAGGACATGGCAT
55355408 TGACACGTTA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
43 2 0.01
44 2 0.01
45 14 0.10
46 57 0.41
47 48 0.35
48 7 0.05
49 7 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (47 bp):
TGTAAGACCATGTCTAGGACATGGCATCGGCTTGAGAGATGAACTAG
Found at i:55362698 original size:20 final size:21
Alignment explanation
Indices: 55362660--55362698 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55362650 TCGAGTTGGT
55362660 CACAAGGGCGTGTTGCCCTTC
1 CACAAGGGCGTGTTGCCCTTC
*
55362681 CACACGGGCGTG-TGCCCT
1 CACAAGGGCGTGTTGCCCT
55362699 GTCTTAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.13, C:0.36, G:0.31, T:0.21
Consensus pattern (21 bp):
CACAAGGGCGTGTTGCCCTTC
Found at i:55364658 original size:32 final size:32
Alignment explanation
Indices: 55364617--55364682 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
55364607 ACCCCTAAAA
*
55364617 AAAATTTCGGCCCCAAAATTTTACCTGATCAG
1 AAAATTTCGGCCCCAAAATTGTACCTGATCAG
*
55364649 AAAATTTCGGCCCCAAAATTGTACCTGATTAG
1 AAAATTTCGGCCCCAAAATTGTACCTGATCAG
55364681 AA
1 AA
55364683 CAAATAGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (32 bp):
AAAATTTCGGCCCCAAAATTGTACCTGATCAG
Found at i:55379865 original size:30 final size:31
Alignment explanation
Indices: 55379830--55379889 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
55379820 ACGAAGTCAC
* *
55379830 CAGATACAGATA-GTGGCTAGGCCACCAGAA
1 CAGATACAGATATGTGGCGAAGCCACCAGAA
* *
55379860 CAGATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATATGTGGCGAAGCCACCAGA
55379890 TTGCAGCGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.17
Consensus pattern (31 bp):
CAGATACAGATATGTGGCGAAGCCACCAGAA
Found at i:55379953 original size:27 final size:26
Alignment explanation
Indices: 55379905--55379956 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
55379895 GCGAGGCTGC
*
55379905 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
55379931 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
55379957 TTGCAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:55380472 original size:10 final size:10
Alignment explanation
Indices: 55380443--55380473 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
55380433 ACACACCTGG
*
55380443 TTGATGACGG
1 TTGATGACGA
55380453 TTGATGACGA
1 TTGATGACGA
55380463 TTGATGACGA
1 TTGATGACGA
55380473 T
1 T
55380474 ATTTCCCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.32
Consensus pattern (10 bp):
TTGATGACGA
Found at i:55382467 original size:28 final size:28
Alignment explanation
Indices: 55382427--55382481 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
55382417 GTGAAGTCGT
55382427 ACTATTTCCGCCACATACAGTTTCGCTC
1 ACTATTTCCGCCACATACAGTTTCGCTC
*
55382455 ACTATTTCCGCCATATACAGTTTCGCT
1 ACTATTTCCGCCACATACAGTTTCGCT
55382482 AACTTCTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.35
Consensus pattern (28 bp):
ACTATTTCCGCCACATACAGTTTCGCTC
Found at i:55391876 original size:22 final size:21
Alignment explanation
Indices: 55391830--55391878 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
55391820 ATTCTTCTTC
*
55391830 ATTTTTCTCTCAACTCCACAC
1 ATTTTTCTCTCAACTCCACAA
*
55391851 ATTTTTCTCTCCAATTCC-CATA
1 ATTTTTCTCT-CAACTCCACA-A
55391873 ATTTTT
1 ATTTTT
55391879 TTAGCCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTTTCTCTCAACTCCACAA
Found at i:55397579 original size:69 final size:70
Alignment explanation
Indices: 55397447--55397579 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
55397437 TAGTTTATTA
* * * * *
55397447 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
55397512 CTTAG
66 CTTAG
55397517 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
55397580 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:55415461 original size:19 final size:19
Alignment explanation
Indices: 55415437--55415474 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
55415427 TATAGTACCC
55415437 AGCTAAAC-CTAGAAAACTT
1 AGCTAAACTC-AGAAAACTT
55415456 AGCTAAACTCAGAAAACTT
1 AGCTAAACTCAGAAAACTT
55415475 CGAATTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (19 bp):
AGCTAAACTCAGAAAACTT
Found at i:55421438 original size:20 final size:19
Alignment explanation
Indices: 55421415--55421461 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
55421405 GTTCCAATCT
55421415 TTTATTTA-TT-GTT-CTA
1 TTTATTTATTTAGTTACTA
*
55421431 TTTATTTATCTTAGTTATTA
1 TTTATTTAT-TTAGTTACTA
55421451 TTTATTTATTT
1 TTTATTTATTT
55421462 TATTTGTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.31
18 2 0.08
19 5 0.19
20 11 0.42
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTATTTATTTAGTTACTA
Done.