Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1370
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: 39074
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6332 original size:2 final size:2
Alignment explanation
Indices: 6325--6357 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6315 GATTGATGAT
6325 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6358 ATGCATCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8673 original size:2 final size:2
Alignment explanation
Indices: 8666--8702 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8656 AAGAGTGCAT
8666 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8703 CATCAATCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:14717 original size:2 final size:2
Alignment explanation
Indices: 14710--14734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14700 AATTAACAAA
14710 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 A
14735 ACTTAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25401 original size:173 final size:175
Alignment explanation
Indices: 25111--25455 Score: 425
Period size: 173 Copynumber: 2.0 Consensus size: 175
25101 TGGAAAATAA
* * * ** *
25111 CTAAAATGATATAAAAATGATGATGAAATGGCATAAAAGTTCCTAATCATGAAAAATTACTAAAA
1 CTAAAATGATATAAAAATGATGATGAAATGACATAAAAGTCCCCAATCACAAAAAATGACTAAAA
* * * * * * *
25176 TGGCTATAAAATGCATGAAATTGTATAAAAGTCTTTAATTTATGGAAAATGACTAAAACTG-TTC
66 TGGCAATAAAATGCATGAAATGGCATAAAAATCCTTAATCTATGAAAAATGACTAAAA-TGATTC
25240 AAAAAT-CACGAAATTACATAATAGTCCCTAATTCATGAAAAACAG
130 AAAAATACACGAAATTACATAATAGTCCCTAATTCATGAAAAACAG
25285 CTAAAATGATAT-AAAATG-TG-TGAAATGACATAAAAAGTCCCCAAGTCACAAAAAATGACTAA
1 CTAAAATGATATAAAAATGATGATGAAATGACAT-AAAAGTCCCCAA-TCACAAAAAATGACTAA
*
25347 AAT-GCAATTAAAATGTATGAAATGGCATAAAAATCCTTAAGTCT-TGAAAAATGACTAAAATGA
64 AATGGCAA-TAAAATGCATGAAATGGCATAAAAATCCTTAA-TCTATGAAAAATGACTAAAATGA
* * * * *
25410 TTCTAAAATACATGTAATTGCATAATTGTCCCTAATTCATGAAAAA
127 TTCAAAAATACACGAAATTACATAATAGTCCCTAATTCATGAAAAA
25456 TGACATAAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
171 10 0.07
172 17 0.12
173 73 0.50
174 46 0.32
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (175 bp):
CTAAAATGATATAAAAATGATGATGAAATGACATAAAAGTCCCCAATCACAAAAAATGACTAAAA
TGGCAATAAAATGCATGAAATGGCATAAAAATCCTTAATCTATGAAAAATGACTAAAATGATTCA
AAAATACACGAAATTACATAATAGTCCCTAATTCATGAAAAACAG
Found at i:25453 original size:58 final size:57
Alignment explanation
Indices: 25073--25465 Score: 246
Period size: 58 Copynumber: 6.8 Consensus size: 57
25063 CCTAATATGT
* * * * * *
25073 ATGAAATTGCAT-AAGGATTCCT-ATATCATGGAAAATAACTAAAATGATATAAAAATGATG
1 ATGAAATTGCATAAAAG-TCCCTAAT-TCATGAAAAATGACTAAAATGAT-TATAAA--ATC
* * * **
25133 ATGAAATGGCATAAAAGTTCCTAA-TCATGAAAAATTACTAAAATGGCTATAAAATGC
1 ATGAAATTGCATAAAAGTCCCTAATTCATGAAAAATGACTAAAATGATTATAAAAT-C
* ** * *
25190 ATGAAATTGTATAAAAGTCTTTAATTTATGGAAAATGACTAAAACTG-TTCA-AAAATC
1 ATGAAATTGCATAAAAGTCCCTAATTCATGAAAAATGACTAAAA-TGATT-ATAAAATC
* * * * *
25247 ACGAAATTACATAATAGTCCCTAATTCATGAAAAA-CAGCTAAAATGA-TATAAAATGT
1 ATGAAATTGCATAAAAGTCCCTAATTCATGAAAAATGA-CTAAAATGATTATAAAAT-C
* * * ** * *
25304 GTGAAA-TGACATAAAAAGTCCCCAAGTCACAAAAAATGACTAAAATGCAAT-TAAAATGT
1 ATGAAATTG-CAT-AAAAGTCCCTAATTCATGAAAAATGACTAAAATG-ATTATAAAAT-C
* * * * * *
25363 ATGAAATGGCATAAAAATCCTTAAGTCTTGAAAAATGACTAAAATGATTCTAAAATAC
1 ATGAAATTGCATAAAAGTCCCTAATTCATGAAAAATGACTAAAATGATTATAAAAT-C
* **
25421 ATGTAATTGCATAATTGTCCCTAATTCATGAAAAATGACATAAAA
1 ATGAAATTGCATAAAAGTCCCTAATTCATGAAAAATGAC-TAAAA
25466 ATGTATGAAA
Statistics
Matches: 260, Mismatches: 55, Indels: 37
0.74 0.16 0.11
Matches are distributed among these distances:
55 1 0.00
56 12 0.05
57 62 0.24
58 118 0.45
59 45 0.17
60 18 0.07
61 4 0.02
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (57 bp):
ATGAAATTGCATAAAAGTCCCTAATTCATGAAAAATGACTAAAATGATTATAAAATC
Found at i:28153 original size:354 final size:352
Alignment explanation
Indices: 27491--28552 Score: 1701
Period size: 354 Copynumber: 3.0 Consensus size: 352
27481 TTTACCTTTA
* * *
27491 ACCTTAGGAATGGTTTGATCCCAAAGCCCATTGTGAATATCACGCCAGAATCCAAGAGCACTCTA
1 ACCTTGGGAATGGTTTGATCCCAAAGCCCATTGTGAATATCATGCTAGAATCCAAGAGCACTCTA
*
27556 TCAAGGATTGTGTTGCATGAAAAACAAAGTTAAAAGCTTTATAAAAGTAGGAATACTAAAGTTTG
66 TCAAGGATTGTATTGCATGAAAAACAAAGTTAAAAGCTTTATAAAAGTAGGAATACTAAAGTTTG
* *
27621 AGGCAGAAAGTGGACCAAGTGACAAAGAGACCAATTACTTCTAAACCATTTAATCCATGCAAATT
131 AGGTAGAAAGTGGACCAAGTGACAAAGAGACCAATTACTTCTAAACCATTTAATCCAAGCAAATT
* * *
27686 AGGAAACAATTGAGATAAGATTCAAGCCAACCAAATTCCTATATCTTACATTAAACTACTACATT
196 AGGAAACAATTGAGATAAGAGTCAAGTCAACCAAATTCCTATATCTTACATT-AACTACTACCTT
* * * *
27751 GACTAATTTAAAATCACCCTCTAATCTCGTGCACATGGGGCCATTGAAACCTTCATGCCTAAGCT
260 GACTAATTCAAAATCACCTTCTAATC-CGTGCACATAGGGCCATTGAAACCTTCATACCTAAGCT
27816 AGTATAATGCTAATGAGAGTTGCGATTAT
324 AGTATAATGCTAATGAGAGTTGCGATTAT
*
27845 ACCTTGGGAATGGTTTGATCCCAAAGCCCATTGTGAATATCATGCTAGAATCCAAAAGCACTCTA
1 ACCTTGGGAATGGTTTGATCCCAAAGCCCATTGTGAATATCATGCTAGAATCCAAGAGCACTCTA
* * *
27910 TCAAGGATTGTATTGCATGTAAAACAAAGTTAAAAGCTTTATAAAAGTAGAAATACTAAGGTTTG
66 TCAAGGATTGTATTGCATGAAAAACAAAGTTAAAAGCTTTATAAAAGTAGGAATACTAAAGTTTG
* * *
27975 AGGTAGAAAGTGGACCAACTGACAAAGAGACCAATTACTTCTAAACCATTTAATCAAAGTAAATT
131 AGGTAGAAAGTGGACCAAGTGACAAAGAGACCAATTACTTCTAAACCATTTAATCCAAGCAAATT
* *
28040 AGGAAACAATTGAGATCAGAGTCAAGTTAACCAAATTCCTATATCTTACATTGAACTACTACCTT
196 AGGAAACAATTGAGATAAGAGTCAAGTCAACCAAATTCCTATATCTTACATT-AACTACTACCTT
* *
28105 GACTTATTCAAAATCACCTTCTAATCACGTGCACATAGGGCAATTGAAACCTTCATACCTAAGCT
260 GACTAATTCAAAATCACCTTCTAATC-CGTGCACATAGGGCCATTGAAACCTTCATACCTAAGCT
*
28170 AGTATAACGCTAATGAGAGTTGCGATTAT
324 AGTATAATGCTAATGAGAGTTGCGATTAT
* *
28199 ACCTTGGGAATGGTTTGATCCCAAAGCCCATTATGAATATCATGCTAGAATCTAAGAGCACTCTA
1 ACCTTGGGAATGGTTTGATCCCAAAGCCCATTGTGAATATCATGCTAGAATCCAAGAGCACTCTA
*
28264 TCAAGGATTGTATTGCATGAAAAACAAAGTTAAAAGCTTTATAAAAGTAGGAATACTAACGTTTG
66 TCAAGGATTGTATTGCATGAAAAACAAAGTTAAAAGCTTTATAAAAGTAGGAATACTAAAGTTTG
* *
28329 AGGTAGAAAGTGGACTAAGTGACAAAGAGACCAATTACTTATAAACCATTTAATCCAAGCAAATT
131 AGGTAGAAAGTGGACCAAGTGACAAAGAGACCAATTACTTCTAAACCATTTAATCCAAGCAAATT
*
28394 AGGAAACAATTAAGATAAGAGTCAAGTCAACCAAATTCCTATATCTTACATTAACTTACTACCTT
196 AGGAAACAATTGAGATAAGAGTCAAGTCAACCAAATTCCTATATCTTACATTAAC-TACTACCTT
** * * * ** * *
28459 GACTCGTTCAACATCGCCTTCTAATCCTATGCATTTAAGGCCATTGAAACCTTCATACTTAAGCT
260 GACTAATTCAAAATCACCTTCTAATCC-GTGCACATAGGGCCATTGAAACCTTCATACCTAAGCT
*
28524 AGTATAATGCTAATGAGAGTTACGATTAT
324 AGTATAATGCTAATGAGAGTTGCGATTAT
28553 CATTCTAGCA
Statistics
Matches: 653, Mismatches: 53, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
353 4 0.01
354 649 0.99
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (352 bp):
ACCTTGGGAATGGTTTGATCCCAAAGCCCATTGTGAATATCATGCTAGAATCCAAGAGCACTCTA
TCAAGGATTGTATTGCATGAAAAACAAAGTTAAAAGCTTTATAAAAGTAGGAATACTAAAGTTTG
AGGTAGAAAGTGGACCAAGTGACAAAGAGACCAATTACTTCTAAACCATTTAATCCAAGCAAATT
AGGAAACAATTGAGATAAGAGTCAAGTCAACCAAATTCCTATATCTTACATTAACTACTACCTTG
ACTAATTCAAAATCACCTTCTAATCCGTGCACATAGGGCCATTGAAACCTTCATACCTAAGCTAG
TATAATGCTAATGAGAGTTGCGATTAT
Found at i:29008 original size:20 final size:20
Alignment explanation
Indices: 28970--29008 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28960 AACAATGTTA
* *
28970 ATTCATTCATTCATCTATTT
1 ATTCATTCATGCATATATTT
28990 ATTCATTCATGCATATATT
1 ATTCATTCATGCATATATT
29009 CAACTCCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.18, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTCATTCATGCATATATTT
Found at i:30759 original size:15 final size:15
Alignment explanation
Indices: 30739--30861 Score: 53
Period size: 15 Copynumber: 8.4 Consensus size: 15
30729 TCATATAATT
*
30739 AATTTA-TTATCTTTC
1 AATTTACTT-TCTTAC
30754 AATTTACTTTCTTAC
1 AATTTACTTTCTTAC
* *
30769 AATTTAAC---CAATGC
1 AATTT-ACTTTC-TTAC
*
30783 AATTTACTTTCTTGC
1 AATTTACTTTCTTAC
* *
30798 AATTTA-ATT-TAAGC
1 AATTTACTTTCTTA-C
* * *
30812 AATTTATTTTTTTGC
1 AATTTACTTTCTTAC
* *
30827 AATTTAATTT-ATAC
1 AATTTACTTTCTTAC
*
30841 AATTTACTTTCTTGC
1 AATTTACTTTCTTAC
30856 AATTTA
1 AATTTA
30862 ATTTAAGCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
13 4 0.05
14 27 0.33
15 45 0.55
16 6 0.07
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (15 bp):
AATTTACTTTCTTAC
Found at i:30787 original size:29 final size:29
Alignment explanation
Indices: 30753--30891 Score: 153
Period size: 29 Copynumber: 4.9 Consensus size: 29
30743 TATTATCTTT
* **
30753 CAATTTACTTTCTTACAATTTAACCAATG
1 CAATTTACTTTCTTGCAATTTAATTAATG
30782 CAATTTACTTTCTTGCAATTTAATTTAA-G
1 CAATTTACTTTCTTGCAATTTAA-TTAATG
* * * *
30811 CAATTTATTTTTTTGCAATTTAATTTATA
1 CAATTTACTTTCTTGCAATTTAATTAATG
30840 CAATTTACTTTCTTGCAATTTAATTTAA-G
1 CAATTTACTTTCTTGCAATTTAA-TTAATG
30869 CAATTT--TTT-TTAGCAATTTAATT
1 CAATTTACTTTCTT-GCAATTTAATT
30892 TTTTGCAGTT
Statistics
Matches: 95, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
26 4 0.04
27 12 0.13
28 3 0.03
29 71 0.75
30 5 0.05
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (29 bp):
CAATTTACTTTCTTGCAATTTAATTAATG
Found at i:30830 original size:58 final size:58
Alignment explanation
Indices: 30753--30889 Score: 188
Period size: 58 Copynumber: 2.4 Consensus size: 58
30743 TATTATCTTT
* * * *
30753 CAATTTACTTTCTTACAATTTAACCAATGCAATTTACTTTCTTGCAATTTAATTTAAG
1 CAATTTATTTTTTTGCAATTTAACCAATACAATTTACTTTCTTGCAATTTAATTTAAG
***
30811 CAATTTATTTTTTTGCAATTTAATTTATACAATTTACTTTCTTGCAATTTAATTTAAG
1 CAATTTATTTTTTTGCAATTTAACCAATACAATTTACTTTCTTGCAATTTAATTTAAG
*
30869 CAA-TT-TTTTTTAGCAATTTAA
1 CAATTTATTTTTTTGCAATTTAA
30890 TTTTTTGCAG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
56 15 0.21
57 2 0.03
58 54 0.76
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (58 bp):
CAATTTATTTTTTTGCAATTTAACCAATACAATTTACTTTCTTGCAATTTAATTTAAG
Found at i:30898 original size:42 final size:43
Alignment explanation
Indices: 30739--30936 Score: 154
Period size: 44 Copynumber: 4.6 Consensus size: 43
30729 TCATATAATT
* * * **
30739 AATTTATTATCTTTCAATTTACTTTCTTACAATTTAA-CCAATGC
1 AATTTATT-TCTTGCAATTTAATTTCTTGCAATTTAATTTAA-GC
** * **
30783 AATTTACTTTCTTGCAATTTAATTT-AAGCAATTTATTTTTTTGC
1 AATTTA-TTTCTTGCAATTTAATTTCTTGCAATTTA-ATTTAAGC
* * *
30827 AATTTAATTT-ATACAATTTACTTTCTTGCAATTTAATTTAAGC
1 AATTT-ATTTCTTGCAATTTAATTTCTTGCAATTTAATTTAAGC
* * *
30870 AATTT-TTT-TTAGCAATTTAATTTTTTGCAGTTTAATTTATGC
1 AATTTATTTCTT-GCAATTTAATTTCTTGCAATTTAATTTAAGC
30912 AATTTAATTTCTTGCAATTTAATTT
1 AATTT-ATTTCTTGCAATTTAATTT
30937 AAGCAATTTA
Statistics
Matches: 121, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
41 4 0.03
42 31 0.26
43 28 0.23
44 53 0.44
45 5 0.04
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.53
Consensus pattern (43 bp):
AATTTATTTCTTGCAATTTAATTTCTTGCAATTTAATTTAAGC
Found at i:30898 original size:100 final size:101
Alignment explanation
Indices: 30781--30975 Score: 295
Period size: 100 Copynumber: 1.9 Consensus size: 101
30771 TTTAACCAAT
* * *
30781 GCAATTTACTTTCTTGCAATTTAATTTAAGCAATTTATTTTTTTGCAATTTAATTTATA-CAATT
1 GCAATTTAATTTCTTGCAATTTAATTTAAGCAATTTAATTTCTTGCAATTTAATTTA-AGCAATT
30845 TACTTTCTTGCAA-TTTAATTTAAGCAATTTTTTTTA
65 TACTTTCTTGCAATTTTAATTTAAGCAATTTTTTTTA
* * *
30881 GCAATTTAATTTTTTGCAGTTTAATTTATGCAATTTAATTTCTTGCAATTTAATTTAAGCAATTT
1 GCAATTTAATTTCTTGCAATTTAATTTAAGCAATTTAATTTCTTGCAATTTAATTTAAGCAATTT
* *
30946 ATTTTCTTGCAATTTTAATTTATGCAATTT
66 ACTTTCTTGCAATTTTAATTTAAGCAATTT
30976 ATTTCCTTAT
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
99 1 0.01
100 68 0.80
101 16 0.19
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (101 bp):
GCAATTTAATTTCTTGCAATTTAATTTAAGCAATTTAATTTCTTGCAATTTAATTTAAGCAATTT
ACTTTCTTGCAATTTTAATTTAAGCAATTTTTTTTA
Found at i:30903 original size:15 final size:15
Alignment explanation
Indices: 30780--30976 Score: 151
Period size: 15 Copynumber: 13.6 Consensus size: 15
30770 ATTTAACCAA
* *
30780 TGCAATTTACTTTCT
1 TGCAATTTAATTTTT
*
30795 TGCAATTTAA-TTTA
1 TGCAATTTAATTTTT
* *
30809 AGCAATTTATTTTTT
1 TGCAATTTAATTTTT
*
30824 TGCAATTTAA-TTTA
1 TGCAATTTAATTTTT
* * *
30838 TACAATTTACTTTCT
1 TGCAATTTAATTTTT
*
30853 TGCAATTTAA-TTTA
1 TGCAATTTAATTTTT
*
30867 AGCAATTT--TTTTT
1 TGCAATTTAATTTTT
*
30880 AGCAATTTAATTTTT
1 TGCAATTTAATTTTT
* *
30895 TGCAGTTTAA-TTTA
1 TGCAATTTAATTTTT
*
30909 TGCAATTTAATTTCT
1 TGCAATTTAATTTTT
*
30924 TGCAATTTAA-TTTA
1 TGCAATTTAATTTTT
*
30938 AGCAATTT-ATTTTCT
1 TGCAATTTAATTTT-T
*
30953 TGCAATTTTAA-TTTA
1 TGCAA-TTTAATTTTT
30968 TGCAATTTA
1 TGCAATTTA
30977 TTTCCTTATA
Statistics
Matches: 141, Mismatches: 31, Indels: 21
0.73 0.16 0.11
Matches are distributed among these distances:
13 12 0.09
14 58 0.41
15 64 0.45
16 6 0.04
17 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (15 bp):
TGCAATTTAATTTTT
Found at i:30904 original size:71 final size:73
Alignment explanation
Indices: 30796--30976 Score: 253
Period size: 71 Copynumber: 2.5 Consensus size: 73
30786 TTACTTTCTT
* * * *
30796 GCAATTTAATTT-AAGCAATTTATTTTTTTGCAATTTAATTTATACAATTTACTTTCTTGCAATT
1 GCAATTTATTTTCTAGCAATTTAATTTTTTGCAATTTAATTTATACAATTTAATTTCTTGCAATT
30860 TAATTTAA
66 TAATTTAA
* *
30868 GCAATTT-TTTT-TAGCAATTTAATTTTTTGCAGTTTAATTTATGCAATTTAATTTCTTGCAATT
1 GCAATTTATTTTCTAGCAATTTAATTTTTTGCAATTTAATTTATACAATTTAATTTCTTGCAATT
30931 TAATTTAA
66 TAATTTAA
* *
30939 GCAATTTATTTTCTTGCAATTTTAA-TTTATGCAATTTA
1 GCAATTTATTTTCTAGCAA-TTTAATTTTTTGCAATTTA
30977 TTTCCTTATA
Statistics
Matches: 97, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
71 65 0.67
72 11 0.11
73 16 0.16
74 5 0.05
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (73 bp):
GCAATTTATTTTCTAGCAATTTAATTTTTTGCAATTTAATTTATACAATTTAATTTCTTGCAATT
TAATTTAA
Found at i:30919 original size:29 final size:29
Alignment explanation
Indices: 30780--30976 Score: 161
Period size: 29 Copynumber: 6.8 Consensus size: 29
30770 ATTTAACCAA
* * *
30780 TGCAATTTACTTTCTTGCAATTTAA-TTTA
1 TGCAATTTAATTT-ATGCAATTTAATTTTT
* * * *
30809 AGCAATTTATTTTTTTGCAATTTAA-TTTA
1 TGCAATTTA-ATTTATGCAATTTAATTTTT
* * * *
30838 TACAATTTACTTTCTTGCAATTTAA-TTTA
1 TGCAATTTAATTT-ATGCAATTTAATTTTT
* **
30867 AGCAATTTTTTTTA-GCAATTTAATTTTT
1 TGCAATTTAATTTATGCAATTTAATTTTT
* *
30895 TGCAGTTTAATTTATGCAATTTAATTTCT
1 TGCAATTTAATTTATGCAATTTAATTTTT
*
30924 TGCAATTTAATTTAAGCAATTT-ATTTTCT
1 TGCAATTTAATTTATGCAATTTAATTTT-T
30953 TGCAATTTTAATTTATGCAATTTA
1 TGCAA-TTTAATTTATGCAATTTA
30977 TTTCCTTATA
Statistics
Matches: 141, Mismatches: 20, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
27 9 0.06
28 20 0.14
29 93 0.66
30 19 0.13
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (29 bp):
TGCAATTTAATTTATGCAATTTAATTTTT
Found at i:35989 original size:51 final size:51
Alignment explanation
Indices: 35921--36043 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 51
35911 ATCAATATAT
* * * * * *
35921 TGAAGAATGTATAGATACATTTAGGTCAAAACCTAGAATGCATCTATGCAA
1 TGAAAAATGTATCGATACATTTAGGTAAAAACCCAGAATGCATCGATACAA
* *
35972 TGAAAAATGTATCGATACAATTAGGTAAAAACCCAGAATGTATCGATACAA
1 TGAAAAATGTATCGATACATTTAGGTAAAAACCCAGAATGCATCGATACAA
* *
36023 T-AGAAATATATCGATACATTT
1 TGAAAAATGTATCGATACATTT
36044 CCTTCAAGAA
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 17 0.28
51 44 0.72
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (51 bp):
TGAAAAATGTATCGATACATTTAGGTAAAAACCCAGAATGCATCGATACAA
Done.