Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3141
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: 46812
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Found at i:2168 original size:51 final size:51
Alignment explanation
Indices: 2106--2219 Score: 201
Period size: 51 Copynumber: 2.2 Consensus size: 51
2096 CTGATCACAT
2106 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
2157 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
2208 TTGTCGCTTGTC
1 TTATCACTTGTC
2220 GCTTGTCACT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:9965 original size:51 final size:51
Alignment explanation
Indices: 9894--10007 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
9884 CTGATCACAT
9894 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
9945 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCATTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
* *
9996 TTGTCGCTTGTC
1 TTATCACTTGTC
10008 GCTTGTCACT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:11107 original size:361 final size:361
Alignment explanation
Indices: 10443--11178 Score: 1337
Period size: 361 Copynumber: 2.0 Consensus size: 361
10433 AATGCCATAG
10443 TCACTAAATTATTTTTATCTTTAGCTAAAGAACTCCAAATTAGGATCCGCTAATTTTCCCTGAAA
1 TCACTAAATTATTTTTATCTTTAGCTAAAGAACTCCAAATTAGGATCCGCTAATTTTCCCTGAAA
* *
10508 CTACATTCATATTTCTTCTAATCATAAAATTTTTAGAATTTTTGGTTTATCTAATAAGTACAGTT
66 CTACATTCATATGTCCTCTAATCATAAAATTTTTAGAATTTTTGGTTTATCTAATAAGTACAGTT
*
10573 TATTCTTTAAAGTCACCCCTGTTCTACTGTCTGACAATTCCGACCCTTCTTCACTAAAAATTAAT
131 TATTCTTTAAAGTCACCCCTGTTCTACTGTCTGACAATTCCAACCCTTCTTCACTAAAAATTAAT
*
10638 TATCTCTTCGTACAGAATTCGGATAATGTCCATGTTTATTTCTATTGAAAATAGATTCATTAAGG
196 TATCTCTTCGTACAGAATTCGGATAATGTCCATGTTTATTTCTATTGAAAATAGACTCATTAAGG
10703 ATTTTAAAAATATAAATTTAAGCCCCTAATTATTTTTCTCCAATTTTTTTATGATTTTCAAAAGT
261 ATTTTAAAAATATAAATTTAAGCCCCTAATTATTTTTCTCCAATTTTTTTATGATTTTCAAAAGT
* *
10768 CAGAACAGGGGAACCCGAAATCATTCTGACATTGTC
326 CAGAACAGGGGAACCCAAAATCATTCTGACATTATC
*
10804 TCACTAAATTATTTTTATCTTTAGCTAAAGAGCTCCAAATTAGGATCCGCTAATTTTCCCTGAAA
1 TCACTAAATTATTTTTATCTTTAGCTAAAGAACTCCAAATTAGGATCCGCTAATTTTCCCTGAAA
* *
10869 CTAGATTCATATGTCCTCTTATCATAAAATTTTTAGAATTTTTGGTTTATCTAATAAGTACAGTT
66 CTACATTCATATGTCCTCTAATCATAAAATTTTTAGAATTTTTGGTTTATCTAATAAGTACAGTT
10934 TATTCTTTAAAGTCACCCCTGTTCTACTGTCTGACAATTCCAACCCTTCTTCACTAAAAATTAAT
131 TATTCTTTAAAGTCACCCCTGTTCTACTGTCTGACAATTCCAACCCTTCTTCACTAAAAATTAAT
* *
10999 TATCTCTTCGTACAGAATTCGGATGATGTCCATGTTTATTTCTATTGAAAATAGACTCATTAAGT
196 TATCTCTTCGTACAGAATTCGGATAATGTCCATGTTTATTTCTATTGAAAATAGACTCATTAAGG
11064 ATTTTAAAAATATAAATTTAAGCCCCTAATTATTTTTCTCCAATTTTTTTATGATTTTCAAAAGT
261 ATTTTAAAAATATAAATTTAAGCCCCTAATTATTTTTCTCCAATTTTTTTATGATTTTCAAAAGT
* *
11129 CAGAACAGGGGAACCCAAAATTATTCTGATATTATC
326 CAGAACAGGGGAACCCAAAATCATTCTGACATTATC
*
11165 TCACAAAATCTATT
1 TCACTAAAT-TATT
11179 ATATCTCATG
Statistics
Matches: 360, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
361 356 0.99
362 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (361 bp):
TCACTAAATTATTTTTATCTTTAGCTAAAGAACTCCAAATTAGGATCCGCTAATTTTCCCTGAAA
CTACATTCATATGTCCTCTAATCATAAAATTTTTAGAATTTTTGGTTTATCTAATAAGTACAGTT
TATTCTTTAAAGTCACCCCTGTTCTACTGTCTGACAATTCCAACCCTTCTTCACTAAAAATTAAT
TATCTCTTCGTACAGAATTCGGATAATGTCCATGTTTATTTCTATTGAAAATAGACTCATTAAGG
ATTTTAAAAATATAAATTTAAGCCCCTAATTATTTTTCTCCAATTTTTTTATGATTTTCAAAAGT
CAGAACAGGGGAACCCAAAATCATTCTGACATTATC
Found at i:13787 original size:89 final size:88
Alignment explanation
Indices: 13679--13970 Score: 248
Period size: 89 Copynumber: 3.3 Consensus size: 88
13669 TGGCTTCGAT
* * *
13679 CTGCTCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTTGAG
1 CTGCTCCAATGTAACTTCAGGGAGAA-AGATTTGTAGATTCGATCTACTCCGCTGGAACTTTAAG
13744 GAGATAAGAATTGGTAATTTCAAC
65 GAGATAAGAATTGGTAATTTCAAC
* * * * ** ** * *
13768 CTGCTCCACTGCAACTTCAGGGGGATAAGGTTTGT-GTATTTTATCCTACTCTACTGTAAC-TTC
1 CTGCTCCAATGTAACTTCAGGGAGA-AAGATTTGTAG-ATTCGAT-CTACTCCGCTGGAACTTTA
* *** * *
13831 AGAGAGATAAGGATT-GTGGCTTAAAT
63 AG-GAGATAAGAATTGGTAATTTCAAC
* * * * * * *
13857 CTGCTCCAATGTAATTTAAGGAAGAATATATTTGTAGTTTCGATCTACTCCGCTAGAACTTCAAG
1 CTGCTCCAATGTAACTTCAGGGAGAA-AGATTTGTAGATTCGATCTACTCCGCTGGAACTTTAAG
*
13922 GAGGTAAGAATTGGTAATTTCAAC
65 GAGATAAGAATTGGTAATTTCAAC
* *
13946 CTGCTCCACTGTAACTTCAGAGAGA
1 CTGCTCCAATGTAACTTCAGGGAGA
13971 TAAGGCTGGT
Statistics
Matches: 148, Mismatches: 47, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
88 23 0.16
89 100 0.68
90 25 0.17
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (88 bp):
CTGCTCCAATGTAACTTCAGGGAGAAAGATTTGTAGATTCGATCTACTCCGCTGGAACTTTAAGG
AGATAAGAATTGGTAATTTCAAC
Found at i:13861 original size:178 final size:178
Alignment explanation
Indices: 13590--14018 Score: 599
Period size: 178 Copynumber: 2.4 Consensus size: 178
13580 ATCTTTAACT
* * * * *
13590 TGCTCCAATGCAACTTCAGAGAGATAAGGTTTGTATATTTTTATCCTTCTCTGCTGCAACTTCAA
1 TGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTGTA-TTTTATCCTACTCTACTGCAACTTCAG
** * *
13655 AGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAGGGAGAAGAGATTTGTAGCTTC
65 AGAGATAAGGATTGTGGCTTAAATCTGCTCCAATGTAATTTAAGGAAGAAGAGATTTGTAGCTTC
* **
13720 GATCTACTCCGCTGGAACTTTGAGGAGATAAGAATTGGTAATTTCAACC
130 GATCTACTCCGCTAGAACTTCAAGGAGATAAGAATTGGTAATTTCAACC
* * *
13769 TGCTCCACTGCAACTTCAGGGGGATAAGGTTTGTGTATTTTATCCTACTCTACTGTAACTTCAGA
1 TGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTGTATTTTATCCTACTCTACTGCAACTTCAGA
* * *
13834 GAGATAAGGATTGTGGCTTAAATCTGCTCCAATGTAATTTAAGGAAGAATATATTTGTAGTTTCG
66 GAGATAAGGATTGTGGCTTAAATCTGCTCCAATGTAATTTAAGGAAGAAGAGATTTGTAGCTTCG
*
13899 ATCTACTCCGCTAGAACTTCAAGGAGGTAAGAATTGGTAATTTCAACC
131 ATCTACTCCGCTAGAACTTCAAGGAGATAAGAATTGGTAATTTCAACC
* * * ** ** *
13947 TGCTCCACTGTAACTTCAGAGAGATAAGGCTGGTGGCTTCAAT-CTACTCCACTGCAACTTCAGA
1 TGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTGTATTTTATCCTACTCTACTGCAACTTCAGA
14011 GAGATAAG
66 GAGATAAG
14019 ATTCGCCATA
Statistics
Matches: 220, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
177 27 0.12
178 160 0.73
179 33 0.15
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (178 bp):
TGCTCCACTGCAACTTCAGAGAGATAAGGTTTGTGTATTTTATCCTACTCTACTGCAACTTCAGA
GAGATAAGGATTGTGGCTTAAATCTGCTCCAATGTAATTTAAGGAAGAAGAGATTTGTAGCTTCG
ATCTACTCCGCTAGAACTTCAAGGAGATAAGAATTGGTAATTTCAACC
Found at i:13962 original size:45 final size:45
Alignment explanation
Indices: 13742--13964 Score: 118
Period size: 45 Copynumber: 5.0 Consensus size: 45
13732 TGGAACTTTG
* *
13742 AGGAGATAAGAATTGGTAATTTCAACCTGCTCCACTGCAACTTC-
1 AGGAGGTAAGAATTGGTAATTTCAACCTGCTCCACTGTAACTTCA
* ** * * * *
13786 AGGGGGATAAGGTTTGTGT-ATTTTATCCTACTCTACTGTAACTTC-
1 AGGAGG-TAAGAATTG-GTAATTTCAACCTGCTCCACTGTAACTTCA
* * *** * * * *
13831 AGAGAGATAAGGATT-GTGGCTTAAATCTGCTCCAATGTAA-TTTA
1 AG-GAGGTAAGAATTGGTAATTTCAACCTGCTCCACTGTAACTTCA
* * * * * * * *
13875 AGGAAG-AATATATTTGTAGTTTCGATCTACTCCGCTAG-AACTTCA
1 AGGAGGTAAGA-ATTGGTAATTTCAACCTGCTCCACT-GTAACTTCA
13920 AGGAGGTAAGAATTGGTAATTTCAACCTGCTCCACTGTAACTTCA
1 AGGAGGTAAGAATTGGTAATTTCAACCTGCTCCACTGTAACTTCA
13965 GAGAGATAAG
Statistics
Matches: 127, Mismatches: 41, Indels: 21
0.67 0.22 0.11
Matches are distributed among these distances:
42 2 0.02
43 9 0.07
44 37 0.29
45 72 0.57
46 7 0.06
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (45 bp):
AGGAGGTAAGAATTGGTAATTTCAACCTGCTCCACTGTAACTTCA
Found at i:14171 original size:143 final size:143
Alignment explanation
Indices: 13946--14310 Score: 527
Period size: 143 Copynumber: 2.6 Consensus size: 143
13936 TAATTTCAAC
* * * *
13946 CTGCTCCACTGTAACTTC-AGAGAGATAAGGCTGGTGGCTTCAATCTACTCCACTGCAACTTCAG
1 CTGCTCCACTCTAACTTCAAG-GAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTCAG
* * * *
14010 AGAGATAAGATTCGCCATAATTTTTAGCTTTAATCTGTTCCACTACAACTTTAGGGAAATAAGAT
65 GGAGATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCAACTACAACTTCAGGGAAATAAGAT
*
14075 TCGCTGTCTTTAGT
130 TCGCTGTCTTTAAT
* * *
14089 CTGCTCCGCTCTAACTTCAAGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTACAACTTTAGG
1 CTGCTCCACTCTAACTTCAAGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTCAGG
* *
14154 GAGGTAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCAACTGCAACTTCAGGGAAATAAGATT
66 GAGATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCAACTACAACTTCAGGGAAATAAGATT
14219 CGCTGTCTTTAAT
131 CGCTGTCTTTAAT
* * * *
14232 CTGCTCCACTGC-AACTTTAAAGAGATAAGACTTATGGCTTCAATCTGCTCCACTGCAACTTCAA
1 CTGCTCCACT-CTAACTTCAAGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTCAG
*
14296 GGAAATAAGATTCGC
65 GGAGATAAGATTCGC
14311 TGTCTTCAGT
Statistics
Matches: 197, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
143 194 0.98
144 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (143 bp):
CTGCTCCACTCTAACTTCAAGGAGATAAGACTTGTGGCTTCAATCTGCTCCACTGCAACTTCAGG
GAGATAAGATTCGCCATAATTTGTAGCTTTAATCTGTTCAACTACAACTTCAGGGAAATAAGATT
CGCTGTCTTTAAT
Found at i:14335 original size:89 final size:89
Alignment explanation
Indices: 14179--14400 Score: 268
Period size: 89 Copynumber: 2.5 Consensus size: 89
14169 ATAATTTGTA
* * * * *
14179 GCTTTAATCTGTTCAACTGCAACTTCAGGGAAATAAGATTCGCTGTCTTTAATCTGCTCCACTGC
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTGTCTTCAATCTGCTCCACTGC
*
14244 AACTTTAAAGAGATAAGACTTA-TG
66 AACTTCAAAGAGATAAGAC-TAGTG
* * *
14268 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTGTCTTCAGTCTGTTCCGCTGC
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTGTCTTCAATCTGCTCCACTGC
** * *
14333 AACTTCAGGGAGATATGGCTAGTG
66 AACTTCAAAGAGATAAGACTAGTG
** *
14357 GCTTCAATCTGCTCCTTTGCAACTTC-AGAAAGATAAGATTCGCT
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAA-ATAAGATTCGCT
14401 ATGATGACTT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
88 6 0.05
89 109 0.95
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTGTCTTCAATCTGCTCCACTGC
AACTTCAAAGAGATAAGACTAGTG
Found at i:14380 original size:44 final size:45
Alignment explanation
Indices: 14179--14384 Score: 175
Period size: 45 Copynumber: 4.6 Consensus size: 45
14169 ATAATTTGTA
* * * * *
14179 GCTTTAATCTGTTCAACTGCAACTTCAGGGAAATAAGATTCGCTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGACTAGCTG
* * * ** *
14224 TCTTTAATCTGCTCCACTGCAACTTTAAAGAGATAAGACTTA--TG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGAC-TAGCTG
* * *
14268 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGACTAGCTG
* * * * * * *
14313 TCTTCAGTCTGTTCCGCTGCAACTTCAGGGAGATATGGCTAG-TG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGACTAGCTG
**
14357 GCTTCAATCTGCTCCTTTGCAACTTCAG
1 GCTTCAATCTGCTCCACTGCAACTTCAG
14385 AAAGATAAGA
Statistics
Matches: 127, Mismatches: 31, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
43 1 0.01
44 60 0.47
45 65 0.51
46 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (45 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGACTAGCTG
Found at i:14815 original size:46 final size:46
Alignment explanation
Indices: 14785--14930 Score: 204
Period size: 46 Copynumber: 3.2 Consensus size: 46
14775 AAATTTGTGG
* *
14785 TTTCTTCCATCCATCCTACTACAACTCAGGGGTATAGGATTTGTAC
1 TTTCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGTAC
** * *
14831 CATCTTCAATCCATCCCACTACAGCTCAGGGGTATAGGATTTGTAT
1 TTTCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGTAC
* *
14877 TTTCTTCAATCCATCCCACTGCAACTCAGGGGTACAGGATTTGTA-
1 TTTCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGTAC
14922 TCTTCTTCA
1 T-TTCTTCA
14931 TTGATCTGAG
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 1 0.01
46 87 0.99
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.34
Consensus pattern (46 bp):
TTTCTTCAATCCATCCCACTACAACTCAGGGGTATAGGATTTGTAC
Found at i:15393 original size:25 final size:25
Alignment explanation
Indices: 15365--15414 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
15355 CAAATATAAT
*
15365 AATAAGGAAATTAACTCAAAATGAA
1 AATAAAGAAATTAACTCAAAATGAA
15390 AATAAAGAAATTAACTCAAAATGAA
1 AATAAAGAAATTAACTCAAAATGAA
15415 TAAGTTAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.62, C:0.08, G:0.10, T:0.20
Consensus pattern (25 bp):
AATAAAGAAATTAACTCAAAATGAA
Found at i:15797 original size:18 final size:19
Alignment explanation
Indices: 15776--15814 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
15766 TTTGTCTAGC
15776 TTCTCAT-TTTTTTTTCTT
1 TTCTCATCTTTTTTTTCTT
* *
15794 TTCTCTTCTTTTTTTTGTT
1 TTCTCATCTTTTTTTTCTT
15813 TT
1 TT
15815 TTGTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (19 bp):
TTCTCATCTTTTTTTTCTT
Found at i:15805 original size:19 final size:20
Alignment explanation
Indices: 15783--15828 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
15773 AGCTTCTCAT
15783 TTTTTTTTCTTTTCT-CTTC
1 TTTTTTTTCTTTTCTGCTTC
* * *
15802 TTTTTTTTGTTTTTTGTTTC
1 TTTTTTTTCTTTTCTGCTTC
15822 TTTTTTT
1 TTTTTTT
15829 GGAAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (20 bp):
TTTTTTTTCTTTTCTGCTTC
Found at i:15805 original size:20 final size:20
Alignment explanation
Indices: 15782--15828 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
15772 TAGCTTCTCA
15782 TTTTTTTT-TCTTTTCTCTTC
1 TTTTTTTTGTCTTTTCT-TTC
* *
15802 TTTTTTTTGTTTTTTGTTTC
1 TTTTTTTTGTCTTTTCTTTC
15822 TTTTTTT
1 TTTTTTT
15829 GGAAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.85
Consensus pattern (20 bp):
TTTTTTTTGTCTTTTCTTTC
Found at i:16358 original size:10 final size:10
Alignment explanation
Indices: 16331--16361 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
16321 CCCTACAATC
16331 TTTTTTTTGT
1 TTTTTTTTGT
*
16341 TTTGTTTTGT
1 TTTTTTTTGT
16351 TTTTTTTTGT
1 TTTTTTTTGT
16361 T
1 T
16362 GTCTCTCATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (10 bp):
TTTTTTTTGT
Found at i:19209 original size:83 final size:83
Alignment explanation
Indices: 19070--19237 Score: 300
Period size: 83 Copynumber: 2.0 Consensus size: 83
19060 GTTCATCATG
* *
19070 TTTCTTTGTGATTCCAGCATTTGGTCTCTCATATCTTGTTGGATTTTAGCCAATTGCTCTTGCAT
1 TTTCTTTGTGATTCCAGCATTTGATCCCTCATATCTTGTTGGATTTTAGCCAATTGCTCTTGCAT
* *
19135 TTGTGTTTGCATCTGTTC
66 TTGTGATTGCATCTATTC
19153 TTTCTTTGTGATTCCAGCATTTGATCCCTCATATCTTGTTGGATTTTAGCCAATTGCTCTTGCAT
1 TTTCTTTGTGATTCCAGCATTTGATCCCTCATATCTTGTTGGATTTTAGCCAATTGCTCTTGCAT
19218 TTGTGATTGCATCTATTC
66 TTGTGATTGCATCTATTC
19236 TT
1 TT
19238 GCATCTCCTT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.49
Consensus pattern (83 bp):
TTTCTTTGTGATTCCAGCATTTGATCCCTCATATCTTGTTGGATTTTAGCCAATTGCTCTTGCAT
TTGTGATTGCATCTATTC
Found at i:19419 original size:19 final size:20
Alignment explanation
Indices: 19395--19433 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
19385 TTGTGACATT
*
19395 CAATGCATATG-ATGAAATG
1 CAATGCAGATGCATGAAATG
19414 CAATGCAGATGCATGAAATG
1 CAATGCAGATGCATGAAATG
19434 AATTCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (20 bp):
CAATGCAGATGCATGAAATG
Found at i:26309 original size:31 final size:31
Alignment explanation
Indices: 26271--26336 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
26261 TTAGGAGTAT
*
26271 AAAATTCACAATTAGCATCGAATAATCATCC
1 AAAATTCACAATTAACATCGAATAATCATCC
* *
26302 AAAATTCACAATTAACATTGAATAATCATTC
1 AAAATTCACAATTAACATCGAATAATCATCC
26333 AAAA
1 AAAA
26337 GTACGTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (31 bp):
AAAATTCACAATTAACATCGAATAATCATCC
Found at i:36759 original size:124 final size:124
Alignment explanation
Indices: 36539--36787 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
36529 TTGAAGGAGC
36539 AAGATTGACAACATCTTTTAAACAAACCCAACTATAAAAAATTATGATTATAATTACAAAGAAGT
1 AAGATTGACAACATCTTTTAAACAAACCCAACTATAAAAAATTATGATTATAATTACAAAGAAGT
36604 CATGAATTGGACTATCAAATCATTTGTTAAACCATTATTTTCATTGTCTCCACCATGAA
66 CATGAATTGGACTATCAAATCATTTGTTAAACCATTATTTTCATTGTCTCCACCATGAA
36663 AAGATTGACAACATCTTTTAAACAAACCCAACTATAAAAAATTATGATTATAATTACAAAGAAGT
1 AAGATTGACAACATCTTTTAAACAAACCCAACTATAAAAAATTATGATTATAATTACAAAGAAGT
36728 CATGAATTGGACTATCAAATCATTTGTTAAACCATTATTTTCATTGTCTCCACCATGAA
66 CATGAATTGGACTATCAAATCATTTGTTAAACCATTATTTTCATTGTCTCCACCATGAA
36787 A
1 A
36788 GCAATGTAAC
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (124 bp):
AAGATTGACAACATCTTTTAAACAAACCCAACTATAAAAAATTATGATTATAATTACAAAGAAGT
CATGAATTGGACTATCAAATCATTTGTTAAACCATTATTTTCATTGTCTCCACCATGAA
Found at i:37120 original size:110 final size:111
Alignment explanation
Indices: 36833--37164 Score: 657
Period size: 110 Copynumber: 3.0 Consensus size: 111
36823 CCTCTGCCAG
36833 CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
1 CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
36898 AAATCATCCTTACTGTGCTACCCAAATTGGGATCAATTAAATACTA
66 AAATCATCCTTACTGTGCTACCCAAATTGGGATCAATTAAATACTA
36944 CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
1 CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
37009 AAATCATCCTTACTGTGCTACCCAAATT-GGATCAATTAAATACTA
66 AAATCATCCTTACTGTGCTACCCAAATTGGGATCAATTAAATACTA
37054 CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
1 CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
37119 AAATCATCCTTACTGTGCTACCCAAATTGGGATCAATTAAATACTA
66 AAATCATCCTTACTGTGCTACCCAAATTGGGATCAATTAAATACTA
37165 TGGAAAACAA
Statistics
Matches: 220, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
110 110 0.50
111 110 0.50
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (111 bp):
CCTATTGGTAACATGCAATTCTTTCATCCATCATCTTCAGGTTGCCAATAATTCATCAAAAATCA
AAATCATCCTTACTGTGCTACCCAAATTGGGATCAATTAAATACTA
Found at i:43350 original size:21 final size:21
Alignment explanation
Indices: 43324--43364 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
43314 ATCTGCTCAA
* *
43324 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
43345 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
43365 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Done.