Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3825
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: 144318
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:8367 original size:39 final size:39
Alignment explanation
Indices: 8322--8465 Score: 173
Period size: 39 Copynumber: 3.7 Consensus size: 39
8312 TACCAGCTCG
* * * * *
8322 AGCCTGCGGGA-CTTTAGCCCGGACATATTTCCAGCACGT
1 AGCCTGC-GGACCTTAAGTCCGGATATAATTCCAGCACAT
* *
8361 AGCCTGCAGACCTTAAGTCTGGATATAATTCCAGCACAT
1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
* *
8400 AGCCTGCTGACCCTAAGTCCGGATATAATTCCAGCACAT
1 AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
* *
8439 AGCCTGCGGACCCTAAGTCCGAATATA
1 AGCCTGCGGACCTTAAGTCCGGATATA
8466 CATCACTGAA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
38 2 0.02
39 90 0.98
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (39 bp):
AGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCACAT
Found at i:18508 original size:41 final size:39
Alignment explanation
Indices: 18429--18650 Score: 251
Period size: 38 Copynumber: 5.6 Consensus size: 39
18419 CGGGACTTTA
* * *
18429 AGCCCGAATATAATACCAGCACGAATG-CTTTGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
*
18467 AGCCTGGATATAACACCGAGCACGAAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACC-AGCACG-AATGCCTTCGGGGCTT
*
18508 AGCCCGGATAATAACACCAGCA--AATGCCTTCAGGGCTT
1 AGCCCGGAT-ATAACACCAGCACGAATGCCTTCGGGGCTT
*
18546 AAGCTCGGATATAACTATCC-G-ACGAATGCCTTCGGGAG-TT
1 -AGCCCGGATATAAC-A-CCAGCACGAATGCCTTCGGG-GCTT
*
18586 AG-CCGGATATAACACCAGCACGAATGCCTTCGGGAAACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGG--GCTT
18626 AGCCCGGATATAACACCAGCACGAA
1 AGCCCGGATATAACACCAGCACGAA
18651 GCCCCTTCGG
Statistics
Matches: 159, Mismatches: 10, Indels: 27
0.81 0.05 0.14
Matches are distributed among these distances:
36 2 0.01
37 2 0.01
38 60 0.38
39 19 0.12
40 23 0.14
41 45 0.28
42 8 0.05
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.19
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
Found at i:22844 original size:42 final size:39
Alignment explanation
Indices: 22780--22884 Score: 104
Period size: 39 Copynumber: 2.6 Consensus size: 39
22770 AGCGATTACC
* * * *
22780 AGTAACTCGTACAATTGCCTTCGGGACTTAAACTCGGATTTT
1 AGTAACTCGCACAAATGCCTTCGGG-CTT-AACCCGGA-ATT
*
22822 AGTAACTCGCAGCAAATG-CTTCGGGCTTACCCCGGAATT
1 AGTAACTCGCA-CAAATGCCTTCGGGCTTAACCCGGAATT
* *
22861 AGTATCTCGCACAAATGTCTTCGG
1 AGTAACTCGCACAAATGCCTTCGG
22885 ATTTAGTTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
38 6 0.11
39 18 0.33
40 6 0.11
41 3 0.05
42 17 0.31
43 5 0.09
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.29
Consensus pattern (39 bp):
AGTAACTCGCACAAATGCCTTCGGGCTTAACCCGGAATT
Found at i:43641 original size:28 final size:28
Alignment explanation
Indices: 43610--43728 Score: 91
Period size: 28 Copynumber: 4.2 Consensus size: 28
43600 GTGAACATGA
*
43610 ATATAATGTGATTTGGGCCGAATGGGCC
1 ATATAATGTGAATTGGGCCGAATGGGCC
** * *
43638 ATATAAAT-T-ATATTGATCCTAAAGGGCC
1 ATAT-AATGTGA-ATTGGGCCGAATGGGCC
*
43666 ATAGAATGTGAATTGGGCCTG-ATGGGCC
1 ATATAATGTGAATTGGGCC-GAATGGGCC
* * * *
43694 GTATGAACGTGAATTGGGTCGGATGGGCC
1 ATAT-AATGTGAATTGGGCCGAATGGGCC
43723 ATATAA
1 ATATAA
43729 ATGAGATTGG
Statistics
Matches: 69, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
27 4 0.06
28 38 0.55
29 27 0.39
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.28
Consensus pattern (28 bp):
ATATAATGTGAATTGGGCCGAATGGGCC
Found at i:51266 original size:14 final size:14
Alignment explanation
Indices: 51246--51283 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
51236 TTTAATATCA
*
51246 TTTAAAAACC-AGT
1 TTTAAAAACCAAGG
51259 TCTTAAAAACCAAGG
1 T-TTAAAAACCAAGG
51274 TTTAAAAACC
1 TTTAAAAACC
51284 CAAAATTCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.26
Consensus pattern (14 bp):
TTTAAAAACCAAGG
Found at i:62002 original size:12 final size:12
Alignment explanation
Indices: 61985--62012 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
61975 TTATGAGCCT
61985 ACCACATGGGTG
1 ACCACATGGGTG
61997 ACCACATGGGTG
1 ACCACATGGGTG
62009 ACCA
1 ACCA
62013 TACGCTAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (12 bp):
ACCACATGGGTG
Found at i:62566 original size:5 final size:5
Alignment explanation
Indices: 62552--62582 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
62542 AAGGAGACAG
62552 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
62583 TGATAACTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:65807 original size:13 final size:13
Alignment explanation
Indices: 65789--65813 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65779 ACAAATGATA
65789 AAATTTTCACACG
1 AAATTTTCACACG
65802 AAATTTTCACAC
1 AAATTTTCACAC
65814 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:76931 original size:38 final size:38
Alignment explanation
Indices: 76797--77017 Score: 198
Period size: 39 Copynumber: 5.7 Consensus size: 38
76787 TTGAATGCTG
* * *
76797 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGT-ATTAAA
*
76837 TCCGGACTAAGATCCGAAGGCATTTGTGCGAG-A-TACAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTATTA-AA
* * *
76875 GTTCCGGGTTAAGCCCGAAGGCCTTTGTGCGAGTATTAAA
1 --TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTATTAAA
* *
76915 TCCGGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAG-TATTAAA
* * *
76954 TCCGGGTTAAGTCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAG-TATTAAA
* *
76992 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
77018 AACGAGGAGC
Statistics
Matches: 155, Mismatches: 16, Indels: 20
0.81 0.08 0.10
Matches are distributed among these distances:
37 2 0.01
38 53 0.34
39 55 0.35
40 35 0.23
41 10 0.06
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (38 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTATTAAA
Found at i:76943 original size:77 final size:76
Alignment explanation
Indices: 76797--77015 Score: 215
Period size: 77 Copynumber: 2.8 Consensus size: 76
76787 TTGAATGCTG
* * * * *
76797 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAG-CCCGAAGGCTTTGTGC-GAGT-AATAAATCCGGGCTAAG-TCCGAAGGCATTC
*
76862 GTGCGAGATA-CAAGT
62 GTGCGAGATATCAA-A
* *
76877 TCCGGGTTAAGCCCGAAGGCCTTTGTGCGAGTATTAAATCCGGGTTAAGTCCGAAGGCATTCGTG
1 TCCGGGTTAAGCCCGAAGG-CTTTGTGCGAGTAATAAATCCGGGCTAAGTCCGAAGGCATTCGTG
* *
76942 CGAGTTATTAAA
65 CGAGATATCAAA
* * * * * *
76954 TCCGGGTTAAGTCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGCCCGAAGGCTTTGTGCGAG-TAATAAATCCGGGCTAAGT-CCGAAGGCATT
77016 TGAACGAGGA
Statistics
Matches: 118, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
76 9 0.08
77 54 0.46
78 26 0.22
79 11 0.09
80 18 0.15
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (76 bp):
TCCGGGTTAAGCCCGAAGGCTTTGTGCGAGTAATAAATCCGGGCTAAGTCCGAAGGCATTCGTGC
GAGATATCAAA
Found at i:77715 original size:1 final size:1
Alignment explanation
Indices: 77709--77802 Score: 98
Period size: 1 Copynumber: 94.0 Consensus size: 1
77699 GGCTTTTCAG
* * * * **
77709 TTTTTTTTTTTTTGTTTTTTTTTTTTTATTTTTTTTTGTTTTGTTTTTTTTTTTTTTTCGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
77774 TTTTTGTTTTTTGTTTCTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
77803 GATGCTTCGA
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.01, C:0.02, G:0.07, T:0.89
Consensus pattern (1 bp):
T
Found at i:77744 original size:29 final size:28
Alignment explanation
Indices: 77709--77802 Score: 125
Period size: 28 Copynumber: 3.3 Consensus size: 28
77699 GGCTTTTCAG
77709 TTTTTTTTTTTTTGTTTTTTTTTTTTTAT
1 TTTTTTTTTTTTTGTTTTTTTTTTTTT-T
*
77738 TTTTTTTTGTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTGTTTTTTTTTTTTTT
** * *
77766 TCGTTTTTTTTTTGTTTTTTGTTTCTTT
1 TTTTTTTTTTTTTGTTTTTTTTTTTTTT
*
77794 TTTTGTTTT
1 TTTTTTTTT
77803 GATGCTTCGA
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
28 30 0.54
29 26 0.46
ACGTcount: A:0.01, C:0.02, G:0.07, T:0.89
Consensus pattern (28 bp):
TTTTTTTTTTTTTGTTTTTTTTTTTTTT
Found at i:77773 original size:40 final size:37
Alignment explanation
Indices: 77708--77802 Score: 120
Period size: 39 Copynumber: 2.5 Consensus size: 37
77698 CGGCTTTTCA
77708 GTTTTTTTTTTTTTGTTTTTTTTTTTTTATTT-TTTTTT
1 GTTTTTTTTTTTTT-TTTTTTTTTTTTT-TTTGTTTTTT
77746 GTTTTGTTTTTTTTTTTTTTTCGTTTTTTTTTTGTTTTTT
1 GTTTT-TTTTTTTTTTTTTTT--TTTTTTTTTTGTTTTTT
* *
77786 GTTTCTTTTTTTGTTTT
1 GTTTTTTTTTTTTTTTT
77803 GATGCTTCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
38 11 0.22
39 23 0.45
40 17 0.33
ACGTcount: A:0.01, C:0.02, G:0.08, T:0.88
Consensus pattern (37 bp):
GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTT
Found at i:82724 original size:40 final size:40
Alignment explanation
Indices: 82600--82824 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
82590 TTGAATGCTG
* * * *
82600 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
* * * *
82640 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATA-CAAGT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAA-A
* * *
82680 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
82720 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
82760 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
82799 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
82825 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 34 0.22
40 112 0.72
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:82842 original size:79 final size:80
Alignment explanation
Indices: 82680--82857 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
82670 AGATACAAGT
* * * * *
82680 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
82745 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * *
82760 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
82824 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
82839 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
82858 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:92255 original size:27 final size:28
Alignment explanation
Indices: 92225--92287 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
92215 GGGCATAATT
92225 GTCATTTTACCATACAGG-GGTATTACG
1 GTCATTTTACCATACAGGAGGTATTACG
* *
92252 GTCATTTTACCCTATAGGAGGTATTACG
1 GTCATTTTACCATACAGGAGGTATTACG
92280 GTCATTTT
1 GTCATTTT
92288 GCCTATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (28 bp):
GTCATTTTACCATACAGGAGGTATTACG
Found at i:94306 original size:14 final size:14
Alignment explanation
Indices: 94287--94321 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
94277 CACCCTTAAA
*
94287 GAAATTTTAGCCTC
1 GAAATTTCAGCCTC
94301 GAAATTTCAGCCTC
1 GAAATTTCAGCCTC
94315 GAAATTT
1 GAAATTT
94322 ACCTAATCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (14 bp):
GAAATTTCAGCCTC
Found at i:100282 original size:27 final size:28
Alignment explanation
Indices: 100242--100317 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
100232 CGGAGCACAA
* *
100242 GGGTATAATCGTCATTTTACCATATA-G
1 GGGTATTATGGTCATTTTACCATATAGG
*
100269 GGGTATTATGGTCATTTTACCCTATAGG
1 GGGTATTATGGTCATTTTACCATATAGG
*
100297 GGGTATTACGGTCATTTTACC
1 GGGTATTATGGTCATTTTACC
100318 TATTTTGGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 23 0.52
28 21 0.48
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (28 bp):
GGGTATTATGGTCATTTTACCATATAGG
Found at i:100309 original size:28 final size:27
Alignment explanation
Indices: 100252--100317 Score: 105
Period size: 28 Copynumber: 2.4 Consensus size: 27
100242 GGGTATAATC
*
100252 GTCATTTTACCATATAGGGGTATTATG
1 GTCATTTTACCATATAGGGGTATTACG
*
100279 GTCATTTTACCCTATAGGGGGTATTACG
1 GTCATTTTACCATATA-GGGGTATTACG
100307 GTCATTTTACC
1 GTCATTTTACC
100318 TATTTTGGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (27 bp):
GTCATTTTACCATATAGGGGTATTACG
Found at i:100327 original size:28 final size:28
Alignment explanation
Indices: 100252--100328 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
100242 GGGTATAATC
* *
100252 GTCATTTTACC-ATATAGGGGTATTATG
1 GTCATTTTACCTATTTAGGGGTATTACG
100279 GTCATTTTACCCTA--TAGGGGGTATTACG
1 GTCATTTTA-CCTATTTA-GGGGTATTACG
*
100307 GTCATTTTACCTATTTTGGGGT
1 GTCATTTTACCTATTTAGGGGT
100329 TTCAACTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
27 15 0.35
28 26 0.60
29 2 0.05
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (28 bp):
GTCATTTTACCTATTTAGGGGTATTACG
Found at i:104049 original size:42 final size:42
Alignment explanation
Indices: 104003--104116 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 42
103993 TGAGATCACG
* * **
104003 TGTAAGACCAAATTTGGGATATAGCATTGACATGAGACTT-CA
1 TGTAAGACCATATTTGGGATATGGCATTGACACAAGA-TTACA
* * *
104045 TGTAAGACCATAGTTGGGCTATTGGCATTGATACAAGATTACA
1 TGTAAGACCATATTTGGGATA-TGGCATTGACACAAGATTACA
* *
104088 TGTAAGACCATATCTAGGATATGGCATTG
1 TGTAAGACCATATTTGGGATATGGCATTG
104117 GTACAATACT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 28 0.47
43 31 0.53
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (42 bp):
TGTAAGACCATATTTGGGATATGGCATTGACACAAGATTACA
Found at i:107800 original size:7 final size:7
Alignment explanation
Indices: 107784--107814 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
107774 TAATAATGTT
*
107784 ATATATA
1 ATATAAA
107791 ATATAAA
1 ATATAAA
107798 ATATAAA
1 ATATAAA
107805 ATATAAA
1 ATATAAA
107812 ATA
1 ATA
107815 AATTAAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATATAAA
Found at i:109264 original size:23 final size:23
Alignment explanation
Indices: 109195--109264 Score: 60
Period size: 23 Copynumber: 3.1 Consensus size: 23
109185 TAATAGATAC
109195 ATGTATATTCGACCAAGGTAAAA
1 ATGTATATTCGACCAAGGTAAAA
*
109218 AT-TATATAT-G--GAA-GTATATTAA
1 ATGTATAT-TCGACCAAGGTA-A--AA
109240 ATGTATATTCGACCAAGGTAAAA
1 ATGTATATTCGACCAAGGTAAAA
109263 AT
1 AT
109265 TATGAGCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 18
0.64 0.04 0.32
Matches are distributed among these distances:
19 3 0.08
20 3 0.08
22 11 0.31
23 13 0.36
25 3 0.08
26 3 0.08
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (23 bp):
ATGTATATTCGACCAAGGTAAAA
Found at i:114949 original size:43 final size:43
Alignment explanation
Indices: 114901--115043 Score: 134
Period size: 43 Copynumber: 3.4 Consensus size: 43
114891 AGTGTTCTCA
*
114901 TGTAAGACCATGTCTGAGACATTGACATCGATATGCGATTACG
1 TGTAAGACCATGTCTGAGACATTGACATCGATATGTGATTACG
* ** *
114944 TGTAAGACTATGTCTG-GCACATCAACATCG-TATTTGATT-CG
1 TGTAAGACCATGTCTGAG-ACATTGACATCGATATGTGATTACG
* * * *
114985 TGTAAGACCCTGTCT-AGGACAGTGGCATCGATATGTGA-TAGCA
1 TGTAAGACCATGTCTGA-GACATTGACATCGATATGTGATTA-CG
*
115028 TGTAAGACCACGTCTG
1 TGTAAGACCATGTCTG
115044 GGACGTTGGC
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
41 24 0.31
42 15 0.19
43 39 0.50
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATGTCTGAGACATTGACATCGATATGTGATTACG
Found at i:121526 original size:14 final size:13
Alignment explanation
Indices: 121504--121556 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
121494 GAATTATTAT
*
121504 TTAATTAATTATAA
1 TTAAATAATTA-AA
121518 TTAAATAATTAAA
1 TTAAATAATTAAA
* *
121531 TTTAAAAAATGAAA
1 -TTAAATAATTAAA
121545 TTAAATTAATTA
1 TTAAA-TAATTA
121557 GTCATTATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 7 0.22
14 25 0.78
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:125712 original size:27 final size:27
Alignment explanation
Indices: 125681--125858 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
125671 TAAATTGTAC
125681 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
125708 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
125734 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
125762 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
125790 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
125817 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
125844 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
125859 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:125795 original size:82 final size:81
Alignment explanation
Indices: 125682--125837 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
125672 AAATTGTACA
* *
125682 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
125746 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
125763 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
125828 TGCGAGTTGA
65 TGCGAATTGA
125838 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:125849 original size:82 final size:81
Alignment explanation
Indices: 125678--125858 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
125668 GATTAAATTG
* *
125678 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
125743 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
125759 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
125823 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
125841 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
125859 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:133662 original size:27 final size:27
Alignment explanation
Indices: 133631--133800 Score: 153
Period size: 27 Copynumber: 6.6 Consensus size: 27
133621 TAAATTGTAC
*
133631 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
133658 TGCACTAAGTGTGCGA--TGAATATG-
1 AGCACTAAGTGTGCGAGTTGACTATGT
* *
133682 ATGCACTAA-TG-GCGAATTGAC-CTG-
1 A-GCACTAAGTGTGCGAGTTGACTATGT
133706 -GCACTAAGCTGTGCGAGTTGACTATGT
1 AGCACTAAG-TGTGCGAGTTGACTATGT
* * *
133733 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
133760 AGCAC-AAGTGTGCGAGTTGATTAT-T
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
133785 AAGCACTGAGTGTGCG
1 -AGCACTAAGTGTGCG
133801 GACTCAATAT
Statistics
Matches: 119, Mismatches: 13, Indels: 22
0.77 0.08 0.14
Matches are distributed among these distances:
22 7 0.06
23 4 0.03
24 6 0.05
25 27 0.23
26 24 0.20
27 43 0.36
28 8 0.07
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Done.