Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1741
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: 42583
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:6935 original size:28 final size:29
Alignment explanation
Indices: 6895--6956 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
6885 ATATTTTTCA
*
6895 TTTTCTCTCACTTT-ATTTATATTTGAAAT
1 TTTTATCTCACTTTCATTTA-ATTTGAAAT
**
6924 TTTTATCT-ACTTTCATTTAATTTTTAAT
1 TTTTATCTCACTTTCATTTAATTTGAAAT
6952 TTTTA
1 TTTTA
6957 GAATTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATCTCACTTTCATTTAATTTGAAAT
Found at i:8675 original size:56 final size:56
Alignment explanation
Indices: 8627--8755 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 56
8617 AATCTATAAT
* *
8627 ATTATTAAATTTTAATAAAAAATTCAAATA-TTAAAAATTATTAAAAAATATATAAAA
1 ATTATAAAATTTT-AT-AAAAATTCAAAAATTTAAAAATTATTAAAAAATATATAAAA
* * *
8684 ATTGTAAAATTTTATAAAAATTTAAAAATTTAAAAA-TA-TATAGAAATATA-AAAA
1 ATTATAAAATTTTATAAAAATTCAAAAATTTAAAAATTATTA-AAAAATATATAAAA
8738 ATTATAAAATTTTATAAA
1 ATTATAAAATTTTATAAA
8756 GTCATAAGAA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
54 23 0.36
55 21 0.33
56 9 0.14
57 11 0.17
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (56 bp):
ATTATAAAATTTTATAAAAATTCAAAAATTTAAAAATTATTAAAAAATATATAAAA
Found at i:8702 original size:18 final size:18
Alignment explanation
Indices: 8681--8755 Score: 66
Period size: 18 Copynumber: 4.2 Consensus size: 18
8671 AAAATATATA
*
8681 AAAATTGTAAAATTTTAT
1 AAAATTATAAAATTTTAT
*
8699 AAAAATT-TAAAAATTTA-
1 -AAAATTATAAAATTTTAT
* *
8716 AAAATATATAGAAA-TATAA
1 AAAAT-TATA-AAATTTTAT
8735 AAAATTATAAAATTTTAT
1 AAAATTATAAAATTTTAT
8753 AAA
1 AAA
8756 GTCATAAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
16 5 0.11
17 4 0.09
18 24 0.51
19 14 0.30
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAATTATAAAATTTTAT
Found at i:8718 original size:7 final size:8
Alignment explanation
Indices: 8679--8749 Score: 52
Period size: 8 Copynumber: 8.1 Consensus size: 8
8669 AAAAAATATA
8679 TAAAAATT
1 TAAAAATT
*
8687 GTAAAATTTT
1 -TAAAA-ATT
8697 ATAAAAATT
1 -TAAAAATT
8706 TAAAAATT
1 TAAAAATT
8714 TAAAAATAT
1 TAAAAAT-T
* *
8723 ATAGAAATA
1 -TAAAAATT
*
8732 TAAAAAAT
1 TAAAAATT
8740 TATAAAATT
1 TA-AAAATT
8749 T
1 T
8750 TATAAAGTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
8 22 0.45
9 14 0.29
10 13 0.27
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (8 bp):
TAAAAATT
Found at i:8752 original size:10 final size:9
Alignment explanation
Indices: 8671--8755 Score: 59
Period size: 10 Copynumber: 9.3 Consensus size: 9
8661 AAATTATTAA
*
8671 AAAATATAT
1 AAAATTTAT
* *
8680 AAAAATTGT
1 AAAATTTAT
8689 AAAATTTTAT
1 AAAA-TTTAT
8699 AAAAATTTA-
1 -AAAATTTAT
8708 AAAATTTA-
1 AAAATTTAT
*
8716 AAAATATAT
1 AAAATTTAT
*
8725 AGAAATATA-
1 A-AAATTTAT
*
8734 AAAAATTAT
1 AAAATTTAT
8743 AAAATTTTAT
1 AAAA-TTTAT
8753 AAA
1 AAA
8756 GTCATAAGAA
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
8 20 0.33
9 16 0.26
10 21 0.34
11 4 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (9 bp):
AAAATTTAT
Found at i:8753 original size:28 final size:28
Alignment explanation
Indices: 8627--8793 Score: 123
Period size: 28 Copynumber: 5.9 Consensus size: 28
8617 AATCTATAAT
* * *
8627 ATTATTAAATTTTAATAAAAA-ATTCAAAT
1 ATTATAAAATTTT-ATAAAAATA-TAAAAA
8656 ATTA-AAAATTATTA-AAAAATATATAAAA
1 ATTATAAAATT-TTATAAAAATATA-AAAA
* *
8684 ATTGTAAAATTTTATAAAAAT-TTAAAA
1 ATTATAAAATTTTATAAAAATATAAAAA
* * *
8711 ATT-TAAAAATATATAGAAATATAAAAA
1 ATTATAAAATTTTATAAAAATATAAAAA
*
8738 ATTATAAAATTTTAT-AAAGTCATAAGAAA
1 ATTATAAAATTTTATAAAAAT-ATAA-AAA
*
8767 ATTATACAAATTGTA-AAGAAATATAAA
1 ATTATA-AAATTTTATAA-AAATATAAA
8794 TTTGGTAAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
26 14 0.13
27 24 0.22
28 30 0.27
29 28 0.25
30 12 0.11
31 3 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (28 bp):
ATTATAAAATTTTATAAAAATATAAAAA
Found at i:9101 original size:20 final size:20
Alignment explanation
Indices: 9074--9126 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
9064 TTAATAAGTT
9074 TTTA-AATTTTTAT-TAAAA
1 TTTATAATTTTTATCTAAAA
*
9092 TTTAATAATTTTTTTCTAAAA
1 TTT-ATAATTTTTATCTAAAA
*
9113 TTTATTATTTTTAT
1 TTTATAATTTTTAT
9127 GATTCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 3 0.10
19 1 0.03
20 17 0.59
21 8 0.28
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATAATTTTTATCTAAAA
Found at i:9328 original size:89 final size:87
Alignment explanation
Indices: 9158--9350 Score: 257
Period size: 89 Copynumber: 2.2 Consensus size: 87
9148 TAAGAGTAGG
*
9158 GGCTTAATTGCTTTTTTGAAAAAAATTTAAGGCCTTTTTATGCATTATGAAAGTTCAAGTACCCA
1 GGCTTAATTGCTTTTTTGAAAAAAAATTAAGGCCTTTTTATGCATTATGAAAGTTCAAGTACCCA
**
9223 AATTGAGTGGGGAAAAAATAGA
66 AATTGAGTGGAAAAAAAATAGA
**
9245 GGCTTAATTG-TTTCTTTGAAAAAAAAATTAAGGTTTTTTTTATGCATTATGAAAGTTCAAGTAC
1 GGCTTAATTGCTTT-TTTG-AAAAAAAATTAAGG-CCTTTTTATGCATTATGAAAGTTCAAGTAC
*
9309 CC-AATTGAGTGGAAAAAAAA-AGGGG
63 CCAAATTGAGTGGAAAAAAAATA--GA
*
9334 GGTTTAATTGCTTTTTT
1 GGCTTAATTGCTTTTTT
9351 TGAAGAAGTG
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
86 3 0.03
87 15 0.16
88 29 0.31
89 43 0.46
90 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.36
Consensus pattern (87 bp):
GGCTTAATTGCTTTTTTGAAAAAAAATTAAGGCCTTTTTATGCATTATGAAAGTTCAAGTACCCA
AATTGAGTGGAAAAAAAATAGA
Found at i:9373 original size:89 final size:87
Alignment explanation
Indices: 9192--9418 Score: 222
Period size: 89 Copynumber: 2.6 Consensus size: 87
9182 ATTTAAGGCC
* *
9192 TTTTTATGCATTATGAAAGTTCAAGTACCCAAATTGAGTGGGGAAAAAATAGAGGCTTAATTGTT
1 TTTTTATGCATTATGAAAGTTCAAGTACCC-AATTGAGT-GGAAAAAAAAAGAGGCTTAATTGTT
* * *
9257 TCTTTGAAAAAAAAATTAAGGTTT
64 TCTTTGAAAAAAAAATAAAGATAT
* *
9281 TTTTTATGCATTATGAAAGTTCAAGTACCCAATTGAGTGGAAAAAAAAAGGGGGGTTTAATTGCT
1 TTTTTATGCATTATGAAAGTTCAAGTACCCAATTGAGTGGAAAAAAAAA--GAGGCTTAATTG-T
* * ***
9346 TTTTTTG-AAGAAGTGTAAAGATAT
63 TTCTTTGAAAAAAAAATAAAGATAT
* * * * * * * *
9370 TTTTGATACATTTTAAAAGTTTAAGTGCTCAATTGAGTGTAAAAAAAAA
1 TTTTTATGCATTATGAAAGTTCAAGTACCCAATTGAGTGGAAAAAAAAA
9419 AGAAAAAAAA
Statistics
Matches: 115, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
87 9 0.08
88 8 0.07
89 91 0.79
90 7 0.06
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.35
Consensus pattern (87 bp):
TTTTTATGCATTATGAAAGTTCAAGTACCCAATTGAGTGGAAAAAAAAAGAGGCTTAATTGTTTC
TTTGAAAAAAAAATAAAGATAT
Found at i:14273 original size:28 final size:28
Alignment explanation
Indices: 14205--14273 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
14195 ATTATACTCA
* *
14205 TTTTCCCATGTTGGTACCTAAACTTATTT
1 TTTTCCCAAG-TGGTACATAAACTTATTT
* *
14234 TTGGTCACAAGTGGTACATAAAC-TACTTT
1 TT-TTCCCAAGTGGTACATAAACTTA-TTT
14263 TTTTCCCAAGT
1 TTTTCCCAAGT
14274 TACTACTGCC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
28 9 0.28
29 18 0.56
30 5 0.16
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (28 bp):
TTTTCCCAAGTGGTACATAAACTTATTT
Found at i:17179 original size:23 final size:25
Alignment explanation
Indices: 17142--17190 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
17132 TTTCTCAAAA
*
17142 TAATTTTTTCAAATTAAAAT-TTAT
1 TAATTATTTCAAATTAAAATGTTAT
*
17166 TAATTATTT-AAATTAAGATGTTAT
1 TAATTATTTCAAATTAAAATGTTAT
17190 T
1 T
17191 TTTTTATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (25 bp):
TAATTATTTCAAATTAAAATGTTAT
Found at i:18637 original size:28 final size:29
Alignment explanation
Indices: 18597--18658 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
18587 ATTTCCCTCA
*
18597 TTTTCTCTCACTTT-ATTTATATTTGAAAT
1 TTTTATCTCACTTTCATTTA-ATTTGAAAT
**
18626 TTTTATCT-ACTTTCATTTAATTTTTAAT
1 TTTTATCTCACTTTCATTTAATTTGAAAT
18654 TTTTA
1 TTTTA
18659 GAATTTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 17 0.59
29 12 0.41
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATCTCACTTTCATTTAATTTGAAAT
Found at i:21709 original size:54 final size:54
Alignment explanation
Indices: 21595--21710 Score: 223
Period size: 54 Copynumber: 2.1 Consensus size: 54
21585 TTGCTCAAAT
*
21595 TTCCAAAACATTGCGGAATTGTTCCACTCAAGTTATTGTGGGACAAATCAAGAA
1 TTCCAAGACATTGCGGAATTGTTCCACTCAAGTTATTGTGGGACAAATCAAGAA
21649 TTCCAAGACATTGCGGAATTGTTCCACTCAAGTTATTGTGGGACAAATCAAGAA
1 TTCCAAGACATTGCGGAATTGTTCCACTCAAGTTATTGTGGGACAAATCAAGAA
21703 TTCCAAGA
1 TTCCAAGA
21711 GAAGTGACAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (54 bp):
TTCCAAGACATTGCGGAATTGTTCCACTCAAGTTATTGTGGGACAAATCAAGAA
Found at i:22619 original size:72 final size:72
Alignment explanation
Indices: 22502--22650 Score: 253
Period size: 72 Copynumber: 2.1 Consensus size: 72
22492 GAATTGACGA
** *
22502 TGGAATTTGTCCACTCAATTGGTTCTGCGACAAGTCTAAAAGAGTGAGTTGCAAGTGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAAAGAGTGAGTTGCAAGAGGTTCCCCA
22567 ATGATCT
66 ATGATCT
*
22574 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAAAGAGTGAGTTGCAAGAGGTTCCCCA
*
22639 GTGATCT
66 ATGATCT
22646 TGGAA
1 TGGAA
22651 CCGTTCCTGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (72 bp):
TGGAATTTGTCCACTCAATTGGTTCCCCGACAAGTCTAAAAGAGTGAGTTGCAAGAGGTTCCCCA
ATGATCT
Found at i:24304 original size:61 final size:61
Alignment explanation
Indices: 24211--24337 Score: 139
Period size: 61 Copynumber: 2.1 Consensus size: 61
24201 TATATTAAAA
* * * *
24211 TTTTTAGAATTAGAACTAAATTGCTAATTTTTGAAAATATTAAGGGTTAAATTTATTAATT
1 TTTTTAGAATTAGAACTAAAATGCTAAGTTTTGAAAACATTAAGGGCTAAATTTATTAATT
* * ** * * *
24272 TTTTTAGAATTTGAACTAAAATGAC-AGGTTTTGTTAACATTTAGGGCTAAATTTGTTGATT
1 TTTTTAGAATTAGAACTAAAATG-CTAAGTTTTGAAAACATTAAGGGCTAAATTTATTAATT
24333 TTTTT
1 TTTTT
24338 TATATCTAGG
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 53 0.98
62 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.47
Consensus pattern (61 bp):
TTTTTAGAATTAGAACTAAAATGCTAAGTTTTGAAAACATTAAGGGCTAAATTTATTAATT
Found at i:25648 original size:10 final size:10
Alignment explanation
Indices: 25645--25823 Score: 85
Period size: 10 Copynumber: 18.5 Consensus size: 10
25635 AAAAAATTGT
*
25645 AAAATTATTTA
1 AAAATTA-TAA
25656 AAAATTAATAA
1 AAAATT-ATAA
25667 AAAATTA-AA
1 AAAATTATAA
25676 AAAA-T-T-A
1 AAAATTATAA
*
25683 AAAATTATTA
1 AAAATTATAA
25693 AAAA-TATATA
1 AAAATTATA-A
*
25703 AAAATTGTAA
1 AAAATTATAA
**
25713 AATTTTATAA
1 AAAATTATAA
*
25723 AAAATTGTAA
1 AAAATTATAA
**
25733 AATTTTATAA
1 AAAATTATAA
25743 AAAAGTT-TAA
1 AAAA-TTATAA
*
25753 AAAATTTTAA
1 AAAATTATAA
*
25763 AATA-TAT-A
1 AAAATTATAA
*
25771 GAAA-TAT--
1 AAAATTATAA
* *
25778 AAAATTTTAT
1 AAAATTATAA
*
25788 AAAATCATAA
1 AAAATTATAA
*
25798 GAAAATTATAC
1 -AAAATTATAA
25809 AAAATGTA-AA
1 AAAAT-TATAA
25819 AAAAT
1 AAAAT
25824 AAATTTGTAA
Statistics
Matches: 128, Mismatches: 26, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
7 8 0.06
8 10 0.08
9 14 0.11
10 66 0.52
11 29 0.23
12 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (10 bp):
AAAATTATAA
Found at i:25648 original size:11 final size:12
Alignment explanation
Indices: 25624--25648 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25614 GCTCTTATAT
25624 AAAAATTGTAAA
1 AAAAATTGTAAA
25636 AAAAATTGTAAA
1 AAAAATTGTAAA
25648 A
1 A
25649 TTATTTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAAATTGTAAA
Found at i:25694 original size:27 final size:27
Alignment explanation
Indices: 25653--25728 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
25643 GTAAAATTAT
*
25653 TTAAAAATTAATAAAAAATTAAAAAAA
1 TTAAAAATTATTAAAAAATTAAAAAAA
*
25680 TTAAAAATTATT-AAAAATATATAAAAA
1 TTAAAAATTATTAAAAAAT-TAAAAAAA
* *
25707 TTGTAAAATTTTATAAAAAATT
1 TT-AAAAATTAT-TAAAAAATT
25729 GTAAAATTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 6 0.15
27 20 0.49
28 7 0.17
29 2 0.05
30 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (27 bp):
TTAAAAATTATTAAAAAATTAAAAAAA
Found at i:25753 original size:78 final size:77
Alignment explanation
Indices: 25619--25778 Score: 173
Period size: 78 Copynumber: 2.1 Consensus size: 77
25609 CCCCTGCTCT
* *
25619 TATATAAAAATTGTAAAAAAAATTGTAAAATTATTTAAAAATTAATAAAAAATTAAAAAAATTAA
1 TATATAAAAATTGT-AAAAAAATTATAAAATAATTTAAAAATTAATAAAAAATTAAAAAAATTAA
25684 AAAT-TATTAAAAA
65 AAATATA-TAAAAA
** * * *
25697 TATATAAAAATTGT-AAAATTTTATAAAA-AATTGTAAAATTTTATAAAAAAGTTTAAAAAATTT
1 TATATAAAAATTGTAAAAAAATTATAAAATAATT-TAAAAATTAATAAAAAA--TTAAAAAAATT
* *
25760 TAAAATATATAGAAA
63 AAAAATATATAAAAA
25775 TATA
1 TATA
25779 AAATTTTATA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
75 3 0.04
76 26 0.38
78 38 0.55
79 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (77 bp):
TATATAAAAATTGTAAAAAAATTATAAAATAATTTAAAAATTAATAAAAAATTAAAAAAATTAAA
AATATATAAAAA
Found at i:26054 original size:19 final size:19
Alignment explanation
Indices: 26032--26082 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
26022 TTTTGATGGA
*
26032 TTTTATATATTTTTATGAT
1 TTTTATATATTTTTATAAT
* *
26051 TTTTATAAAATTTTATAAT
1 TTTTATATATTTTTATAAT
*
26070 TTTT-TTTATTTTT
1 TTTTATATATTTTT
26083 TGACGATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTATATATTTTTATAAT
Found at i:26312 original size:87 final size:88
Alignment explanation
Indices: 26204--26364 Score: 272
Period size: 89 Copynumber: 1.8 Consensus size: 88
26194 TAAGAGCAGG
*
26204 GGCTTAATTGCTTTTTTG-AAAAAAATTTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
1 GGCTTAATTGCTTTTTTGAAAAAAAAATTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
26268 CAATTGAGTGGGAAAAAACTAAA
66 CAATTGAGTGGGAAAAAACTAAA
*
26291 GGCTTAATTG-TTTCTTTGAAAAAAAAAATTAAGGTCTTTTTGATGCATTATGAAAGTTCAAGTA
1 GGCTTAATTGCTTT-TTTG-AAAAAAAAATTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTA
26355 CCCAATTGAG
64 CCCAATTGAG
26365 CAGAAAAAGT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
86 3 0.04
87 14 0.20
89 52 0.75
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (88 bp):
GGCTTAATTGCTTTTTTGAAAAAAAAATTAAGGCCTTTTTGATGCATTATGAAAGTTCAAGTACC
CAATTGAGTGGGAAAAAACTAAA
Found at i:28747 original size:18 final size:20
Alignment explanation
Indices: 28726--28762 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28716 TATTTTGTTT
28726 TATTT-ATTTCTA-AACCCA
1 TATTTCATTTCTACAACCCA
*
28744 TATTTCTTTTCTACAACCC
1 TATTTCATTTCTACAACCC
28763 CAATTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 6 0.38
20 5 0.31
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTTCATTTCTACAACCCA
Found at i:35022 original size:28 final size:29
Alignment explanation
Indices: 34960--35022 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 29
34950 ATTTCCCTCA
*
34960 TTTTCTCTCACTTTATTTATATTTGAAAT
1 TTTTATCTCACTTTATTTATATTTGAAAT
* **
34989 TCTTATCT-ACTTTCATTTA-ATTTTTAAT
1 TTTTATCTCACTTT-ATTTATATTTGAAAT
35017 TTTTAT
1 TTTTAT
35023 AATTTTGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.24, C:0.13, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATCTCACTTTATTTATATTTGAAAT
Found at i:39945 original size:72 final size:72
Alignment explanation
Indices: 39842--40082 Score: 401
Period size: 72 Copynumber: 3.3 Consensus size: 72
39832 GAATTGACAA
* *
39842 TGGAATTTGTCCACTCAATTGGTTCATCGGCAAGTGTAAATGAGTGAGATGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
39907 ATGATCT
66 ATGATCT
* *
39914 TGGAATTTTTCCACTCAATTGGTTCACCGGCAACTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
39979 ATGATCT
66 ATGATCT
* *** *
39986 TGGAATTTGTCCGCTCAATTGGTTCACCAATAAGTCTAAATGAGTGAGTTGCAAGAGGTTCCCCA
1 TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
40051 ATGATCT
66 ATGATCT
40058 TGGAATTTGTCCACTCAATTGGTTC
1 TGGAATTTGTCCACTCAATTGGTTC
40083 CCCAATGATC
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 157 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (72 bp):
TGGAATTTGTCCACTCAATTGGTTCACCGGCAAGTGTAAATGAGTGAGTTGCAAGAGGTTCCCCA
ATGATCT
Found at i:40082 original size:36 final size:36
Alignment explanation
Indices: 39970--40190 Score: 161
Period size: 36 Copynumber: 6.1 Consensus size: 36
39960 AGTTGCAAGA
*
39970 GGTTCCCCAATGATCTTGGAATTTGTCCGCTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
* * * ** * * **
40006 GGTTCACCAATAAGTC-T-AAATGAGT-GAGTTGCAAGA
1 GGTTCCCCAATGA-TCTTGGAATTTGTCCA-CT-CAATT
40042 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
40078 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
* ** * * **
40114 GGTTCACCGACAA-G-TC-T-AAATGAGT-GAGTTGCAAGA
1 GGTTC-CC--CAATGATCTTGGAATTTGTCCA-CT-CAATT
40150 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
40186 GGTTC
1 GGTTC
40191 ACCGACAAGT
Statistics
Matches: 136, Mismatches: 33, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
33 3 0.02
34 2 0.01
35 18 0.13
36 89 0.65
37 18 0.13
38 3 0.02
39 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (36 bp):
GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
Found at i:40105 original size:108 final size:108
Alignment explanation
Indices: 39970--40190 Score: 415
Period size: 108 Copynumber: 2.0 Consensus size: 108
39960 AGTTGCAAGA
* *
39970 GGTTCCCCAATGATCTTGGAATTTGTCCGCTCAATTGGTTCACCAATAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCAACAAGTCTAAATGAGTGAGT
40035 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
66 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
*
40078 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCAACAAGTCTAAATGAGTGAGT
40143 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
66 TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
40186 GGTTC
1 GGTTC
40191 ACCGACAAGT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (108 bp):
GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCAACAAGTCTAAATGAGTGAGT
TGCAAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATT
Found at i:40195 original size:72 final size:72
Alignment explanation
Indices: 40078--40465 Score: 577
Period size: 72 Copynumber: 5.3 Consensus size: 72
40068 CCACTCAATT
40078 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
40143 TGCAAGA
66 TGCAAGA
40150 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAG--TAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
40213 TGCAAGA
66 TGCAAGA
* * *
40220 TGTTCCCCAATGATCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAATCTAA
1 -G---------GTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAA
40285 ATGAGTGAGTTGCAAGA
56 ATGAGTGAGTTGCAAGA
40302 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTC-CACGACAAGTCTAAATGAGTGAG
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCAC-CGACAAGTCTAAATGAGTGAG
*
40366 TTGAAAGA
65 TTGCAAGA
* **
40374 GGTTCCCCAATAATCTTGGAATTTGTCCACTCAATTGGTTCTGCGACAAGTCTAAATGAGTGAGT
1 GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
40439 TGCAAGA
66 TGCAAGA
*
40446 GGTT-CCCAGTGATCTTGGAA
1 GGTTCCCCAATGATCTTGGAA
40466 CCGGTCCTGA
Statistics
Matches: 290, Mismatches: 12, Indels: 29
0.88 0.04 0.09
Matches are distributed among these distances:
70 20 0.07
71 15 0.05
72 188 0.65
80 46 0.16
81 1 0.00
82 20 0.07
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (72 bp):
GGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGT
TGCAAGA
Found at i:40326 original size:152 final size:150
Alignment explanation
Indices: 40081--40465 Score: 594
Period size: 152 Copynumber: 2.6 Consensus size: 150
40071 CTCAATTGGT
*
40081 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCACCGACAAGTCTAAATGAGTGAGTTGC
1 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAGTCTAAATGAGTGAGTTGC
40146 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTT-CACCGACAAG-TAAATGAGT
66 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCA-CGACAAGCTAAATGAGT
* *
40209 GAGTTGCAAGATGTTCCCCAATGA
130 GAGTTGAAAGAGGTTCCCC-A--A
*
40233 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAATCTAAATGAGTGAGTTGC
1 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAGTCTAAATGAGTGAGTTGC
40298 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCACGACAAGTCTAAATGAGT
66 AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCACGACAAG-CTAAATGAGT
40363 GAGTTGAAAGAGGTTCCCCAA
130 GAGTTGAAAGAGGTTCCCCAA
40384 T-----A--ATCTTGGAATTTGTCCACTCAATTGGTTC-TGCGACAAGTCTAAATGAGTGAGTTG
1 TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCAT-CGACAAGTCTAAATGAGTGAGTTG
*
40441 CAAGAGGTT-CCCAGTGATCTTGGAA
65 CAAGAGGTTCCCCAATGATCTTGGAA
40466 CCGGTCCTGA
Statistics
Matches: 223, Mismatches: 6, Indels: 17
0.91 0.02 0.07
Matches are distributed among these distances:
143 16 0.07
144 61 0.27
146 1 0.00
151 2 0.01
152 114 0.51
153 3 0.01
154 26 0.12
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.30
Consensus pattern (150 bp):
TCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCATCGACAAGTCTAAATGAGTGAGTTGC
AAGAGGTTCCCCAATGATCTTGGAATTTGTCCACTCAATTGGTTCCACGACAAGCTAAATGAGTG
AGTTGAAAGAGGTTCCCCAA
Done.