Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1288
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: 51228
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Found at i:6000 original size:40 final size:40
Alignment explanation
Indices: 5923--6348 Score: 721
Period size: 40 Copynumber: 10.7 Consensus size: 40
5913 GCAAACACCT
* * *
5923 TTGCCTTCGGGTCTTA-ACCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
5962 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
6002 TTGCCTTCGGGTCATAGCCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
6042 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
6082 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
6122 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
6162 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
6202 TTGCCTTCGGGTCTTAGCCCGGATATAT-AACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
6241 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
6281 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
6321 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
6349 TCCAATGCTC
Statistics
Matches: 364, Mismatches: 21, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
39 55 0.15
40 309 0.85
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:10801 original size:20 final size:20
Alignment explanation
Indices: 10776--10817 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10766 ACGTGTATGT
10776 AGTATGTCATACTCATAACC
1 AGTATGTCATACTCATAACC
10796 AGTATGTCATACTCATAACC
1 AGTATGTCATACTCATAACC
10816 AG
1 AG
10818 CCATATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.29
Consensus pattern (20 bp):
AGTATGTCATACTCATAACC
Found at i:14421 original size:22 final size:22
Alignment explanation
Indices: 14396--14466 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
14386 GTTCTAGGGT
14396 CACACGAGCATGTCCCTTGGAC
1 CACACGAGCATGTCCCTTGGAC
* * ** *
14418 CACACGGGCATGTTCCAAGG-T
1 CACACGAGCATGTCCCTTGGAC
*
14439 CACACGAGCGTGTCCCTTGGAC
1 CACACGAGCATGTCCCTTGGAC
14461 CACACG
1 CACACG
14467 GGTGTGTGAG
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
21 15 0.41
22 22 0.59
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (22 bp):
CACACGAGCATGTCCCTTGGAC
Found at i:18344 original size:27 final size:27
Alignment explanation
Indices: 18204--18332 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
18194 CCCCAGATTT
*
18204 TAAAATTACCGAAATACCCCTGGT-TTG
1 TAAAATTACCGAAATACCCCT-GTAGTG
** *
18231 TAAAATTACTAAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCTGTAGTG
*
18258 TAAAATTATCGAAATACCCCTGTAGTG
1 TAAAATTACCGAAATACCCCTGTAGTG
** * *
18285 TAAAATTATTGAAATACCCTTATAGTG
1 TAAAATTACCGAAATACCCCTGTAGTG
18312 TAAAATTACCGAAATACCCCT
1 TAAAATTACCGAAATACCCCT
18333 ATAGGGAAAA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
26 2 0.02
27 85 0.98
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCCTGTAGTG
Found at i:18344 original size:54 final size:54
Alignment explanation
Indices: 18204--18332 Score: 197
Period size: 54 Copynumber: 2.4 Consensus size: 54
18194 CCCCAGATTT
* *
18204 TAAAATTACCGAAATACCCCTGGT-TTGTAAAATTACTAAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCT-GTAGTGTAAAATTACTAAAATACCCTTATAGTG
* * *
18258 TAAAATTATCGAAATACCCCTGTAGTGTAAAATTATTGAAATACCCTTATAGTG
1 TAAAATTACCGAAATACCCCTGTAGTGTAAAATTACTAAAATACCCTTATAGTG
18312 TAAAATTACCGAAATACCCCT
1 TAAAATTACCGAAATACCCCT
18333 ATAGGGAAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 2 0.03
54 66 0.97
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCCTGTAGTGTAAAATTACTAAAATACCCTTATAGTG
Found at i:18359 original size:54 final size:54
Alignment explanation
Indices: 18204--18348 Score: 157
Period size: 54 Copynumber: 2.7 Consensus size: 54
18194 CCCCAGATTT
* ** * * * *
18204 TAAAATTACCGAAATACCCCTGGT-TTGTAAAATTACTAAAATACCCTTGTAGTG
1 TAAAATTACCGAAATACCCCT-ATAGGGAAAAATGACTGAAATACCCTTATAGTG
* * * * * *
18258 TAAAATTATCGAAATACCCCTGTAGTGTAAAATTATTGAAATACCCTTATAGTG
1 TAAAATTACCGAAATACCCCTATAGGGAAAAATGACTGAAATACCCTTATAGTG
18312 TAAAATTACCGAAATACCCCTATAGGGAAAAATGACT
1 TAAAATTACCGAAATACCCCTATAGGGAAAAATGACT
18349 ATTTTACCCT
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 2 0.03
54 77 0.97
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCCTATAGGGAAAAATGACTGAAATACCCTTATAGTG
Found at i:18793 original size:27 final size:28
Alignment explanation
Indices: 18763--18823 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
18753 ATGCCAATTG
*
18763 TATTTACTTG-TGGCTCTGTGTTGATCA
1 TATTTACTTGATGACTCTGTGTTGATCA
18790 TATTTA-TTGATGACTCTGTGTTGATCA
1 TATTTACTTGATGACTCTGTGTTGATCA
18817 TATTTAC
1 TATTTAC
18824 CCATGGCTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
26 3 0.10
27 28 0.90
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (28 bp):
TATTTACTTGATGACTCTGTGTTGATCA
Found at i:18836 original size:27 final size:27
Alignment explanation
Indices: 18773--18836 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
18763 TATTTACTTG
***
18773 TGGCTCTGTGTTGATCATATTTATTGA
1 TGGCTCTGTGTTGATCATATTTACCCA
*
18800 TGACTCTGTGTTGATCATATTTACCCA
1 TGGCTCTGTGTTGATCATATTTACCCA
*
18827 TGGCTGTGTG
1 TGGCTCTGTG
18837 CCGATTATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (27 bp):
TGGCTCTGTGTTGATCATATTTACCCA
Found at i:25835 original size:15 final size:15
Alignment explanation
Indices: 25815--25866 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
25805 AATACAAAAC
25815 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
25830 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
25849 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
25864 ATT
1 ATT
25867 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:25930 original size:16 final size:16
Alignment explanation
Indices: 25899--25935 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
25889 ATGTGAATAA
25899 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
25915 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
25931 TATTA
1 TATTA
25936 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:25987 original size:22 final size:22
Alignment explanation
Indices: 25947--26007 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
25937 AATAAAATTG
*
25947 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
25967 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
* * *
25989 TATTAATAATTTAT-TTTAT
1 AAATAATAAATTATATTTAT
26008 GACTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.26
21 7 0.20
22 19 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:26960 original size:21 final size:20
Alignment explanation
Indices: 26931--26989 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
26921 TAGAAGTCTG
*
26931 AGTTATATCGGTAGAAT-AC
1 AGTTGTATCGGTAGAATCAC
* *
26950 AGATTTGTATCGATAGAACTCCC
1 AG--TTGTATCGGTAGAA-TCAC
26973 AGTTGTATCGGTAGAAT
1 AGTTGTATCGGTAGAAT
26990 TTTGTAGCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 2 0.06
20 1 0.03
21 25 0.78
22 1 0.03
23 3 0.09
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (20 bp):
AGTTGTATCGGTAGAATCAC
Found at i:29078 original size:48 final size:46
Alignment explanation
Indices: 29026--29130 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 46
29016 CTTATTGATG
*
29026 CCAATGTCATATCCCAAATATGGTCTTACAAGGGATCACATATAGAC
1 CCAATGTCATATCCCAAATATGGTCTTACAAGGGATCACACATA-AC
* *
29073 TCCAAT-TCCATATCCCAGATATGGTCTTACATGGGATCACACATAAC
1 -CCAATGT-CATATCCCAAATATGGTCTTACAAGGGATCACACATAAC
29120 CCTAATGTCAT
1 CC-AATGTCAT
29131 GACATTTGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
46 2 0.04
47 9 0.18
48 40 0.78
ACGTcount: A:0.33, C:0.26, G:0.13, T:0.28
Consensus pattern (46 bp):
CCAATGTCATATCCCAAATATGGTCTTACAAGGGATCACACATAAC
Found at i:35646 original size:48 final size:48
Alignment explanation
Indices: 35468--35791 Score: 296
Period size: 48 Copynumber: 7.0 Consensus size: 48
35458 CACATAGTAA
** * *
35468 GATGCCAATGTAATATCCCAGATATGGTCTTACATGGGATCACAGATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * * *
35516 GAAGCC---G--ATAGCCCAG-CTATGGTCTTACATGATG-TCTCATATC
1 GATGCCAATGCCATATCCCAGAC-ATGGTCTTACATG-GGATCACATATC
* * * ** *
35559 GATGCC-ATGCC-T-T---AAACATGGTGTTAGATGAAATAACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * * *
35601 AATGCCAATGCCATATCCCAGATATGATCTTACATGTGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * *
35649 GATGCCAATGTCATATCCCAGATATGGTCTTACGTGGGATCACATATC
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
* * ** *
35697 GATGCCAATGCCATGTCCCAGACAAGGTCTTATGTGGGATCACATATT
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
*
35745 GATGCCAACGCCATATCCCAGACATGGTCTTACATGGGATCACATAT
1 GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATAT
35792 AACCCTAATA
Statistics
Matches: 222, Mismatches: 40, Indels: 28
0.77 0.14 0.10
Matches are distributed among these distances:
42 24 0.11
43 39 0.18
44 2 0.01
45 3 0.01
46 1 0.00
48 153 0.69
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.27
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAGACATGGTCTTACATGGGATCACATATC
Found at i:36065 original size:10 final size:9
Alignment explanation
Indices: 36038--36086 Score: 62
Period size: 9 Copynumber: 5.1 Consensus size: 9
36028 TACATATATT
*
36038 AAAACATAA
1 AAAAAATAA
36047 AAGAAAATACA
1 AA-AAAATA-A
36058 AAAAAATAA
1 AAAAAATAA
36067 AAAAAATAA
1 AAAAAATAA
36076 AAAAATATAA
1 AAAAA-ATAA
36086 A
1 A
36087 TTTTTACCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 17 0.47
10 16 0.44
11 3 0.08
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:36072 original size:19 final size:19
Alignment explanation
Indices: 36038--36086 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
36028 TACATATATT
*
36038 AAAACATAAAAGAAAATACA
1 AAAAAATAAAAGAAAATA-A
36058 AAAAAATAAAA-AAAATAA
1 AAAAAATAAAAGAAAATAA
36076 AAAAATATAAA
1 AAAAA-ATAAA
36087 TTTTTACCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.22
19 11 0.41
20 10 0.37
ACGTcount: A:0.82, C:0.04, G:0.02, T:0.12
Consensus pattern (19 bp):
AAAAAATAAAAGAAAATAA
Found at i:36200 original size:11 final size:11
Alignment explanation
Indices: 36184--36223 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
36174 CCCTTCCCCC
36184 CTCCCTTCTCT
1 CTCCCTTCTCT
36195 CTCCCTTCTCT
1 CTCCCTTCTCT
36206 CTTCCC-TCTCT
1 C-TCCCTTCTCT
*
36217 CTTCCTT
1 CTCCCTT
36224 TTTTCTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 19 0.73
12 4 0.15
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
CTCCCTTCTCT
Found at i:36218 original size:22 final size:23
Alignment explanation
Indices: 36185--36238 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
36175 CCTTCCCCCC
36185 TCCCTTCTCTCTCCCTTCTCTC-T
1 TCCC-TCTCTCTCCCTTCTCTCTT
* * *
36208 TCCCTCTCTCTTCCTTTTTTCTT
1 TCCCTCTCTCTCCCTTCTCTCTT
36231 TCCCTCTC
1 TCCCTCTC
36239 CCCAAATGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (23 bp):
TCCCTCTCTCTCCCTTCTCTCTT
Found at i:36704 original size:3 final size:3
Alignment explanation
Indices: 36696--36732 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
36686 TGTATTTCAA
36696 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
36733 GTACATTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:36888 original size:127 final size:129
Alignment explanation
Indices: 36705--36942 Score: 315
Period size: 127 Copynumber: 1.9 Consensus size: 129
36695 ATATTATTAT
* * * * *
36705 TATTATTATTATTATTATTATTATTATTGTACATTAGTGTATATCTTCATGTATGTATATATATA
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGTATGTATATATACA
* * *
36770 TGTAGTAATGTTTTT-ATTACTTTATTTTAATAT-TTTTTATTATAATAGCTTTTGTATTTCAA
66 TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
*
36832 TATTATTATTATTTTTATTATTATCATT-AACATTACTATATATTCTT-AT-TAGATGTATATAT
1 TATTATTATTATTATTATTATTATCATTGAACATTACTATATA-TCTTCATGT--ATGTATATAT
* *
36894 ACATATATTACTGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
63 ACATATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATA
36943 TTTACTTTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
125 1 0.01
126 13 0.14
127 54 0.57
128 17 0.18
129 10 0.11
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (129 bp):
TATTATTATTATTATTATTATTATCATTGAACATTACTATATATCTTCATGTATGTATATATACA
TATAGTAATGTTTTTAATGACTTTATTTTAATATCATTTTATTATAATAGCTTTTGTATTTCAA
Found at i:49478 original size:68 final size:69
Alignment explanation
Indices: 49305--49478 Score: 215
Period size: 70 Copynumber: 2.5 Consensus size: 69
49295 CTTTCCAAGG
* ** * * *
49305 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTTTTTTATTTTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTTTTTTAGTTTATG
49370 TTTT
66 TTTT
* ** *
49374 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTTTTTTAGTTTAT
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTTTTTTAGTTTAT
49439 GTTTT
65 GTTTT
** *
49444 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
49479 TTTAATTTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
68 31 0.34
70 59 0.66
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (69 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCCGAGGTTTTTTAGTTTATG
TTTT
Found at i:49603 original size:70 final size:69
Alignment explanation
Indices: 49482--49742 Score: 352
Period size: 70 Copynumber: 3.7 Consensus size: 69
49472 TAAGCCTTTT
*
49482 AATTTTTGTTTTTC-AAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAAATCAACTCATATTGC--GAGGTGAGTTGAGCCTCAGGACACGCTGAG
49546 GTAATTTC
63 GT-ATTTC
* * * *
49554 AATTTCT-TTTTCAAAATTCAACT-ATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAG--GTGAGTTGAGCCTCAGGACACGCTGAGG
49617 TATTTC
64 TATTTC
*
49623 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGGTGAGTTGAGCCTC-GGACATGCTGAGGTA
1 AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
49687 TTTC
66 TTTC
*
49691 AATTTCTGTTTTAAAAAAAATCAACTCATATTGCGAGGTGAGTTGAG-CTCAG
1 AATTTCTGTTTT--CAAAAATCAACTCATATTGCGAGGTGAGTTGAGCCTCAG
49743 ATTACACACT
Statistics
Matches: 170, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
68 31 0.18
69 28 0.16
70 86 0.51
71 19 0.11
72 6 0.04
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (69 bp):
AATTTCTGTTTTCAAAAATCAACTCATATTGCGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
TTTC
Found at i:50266 original size:70 final size:69
Alignment explanation
Indices: 50132--50324 Score: 286
Period size: 70 Copynumber: 2.8 Consensus size: 69
50122 GAAGAATCAA
*
50132 TCAA-TTCTGTTTTTCAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAAGACACGTTGAGG
1 TCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGATGAGTTGAGCCTC-AGACACGCTGAGG
50196 T-ATT
65 TAATT
50200 TCAATTTCTGCTTTTTCAAAATTCAACTCATATTGCGAGATGAGTTGAGCCTCAGACACGCTGAG
1 TCAATTTCTG-TTTTTCAAAA-TCAACTCATATTGCGAGATGAGTTGAGCCTCAGACACGCTGAG
50265 GTAATT
64 GTAATT
*
50271 TCAATTTCTG-TTGTCAAAAAATCAACTCATATTGCGA-AGTGAGTTGAGCCTCAG
1 TCAATTTCTGTTTTTC--AAAATCAACTCATATTGCGAGA-TGAGTTGAGCCTCAG
50325 TTCACATGTT
Statistics
Matches: 116, Mismatches: 2, Indels: 12
0.89 0.02 0.09
Matches are distributed among these distances:
68 4 0.03
69 10 0.09
70 54 0.47
71 48 0.41
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (69 bp):
TCAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGATGAGTTGAGCCTCAGACACGCTGAGGT
AATT
Done.