Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold991
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: 40522
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:232 original size:15 final size:17
Alignment explanation
Indices: 214--247 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
204 TTTAAAAATA
214 AAATATAT-C-TATATT
1 AAATATATACATATATT
229 AAATATATACATATATT
1 AAATATATACATATATT
246 AA
1 AA
248 TACTTGCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATATACATATATT
Found at i:1191 original size:25 final size:25
Alignment explanation
Indices: 1149--1201 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1139 GTTGCTTGTA
*
1149 TTATTTATTTTAATTTTTAGATTTT
1 TTATTTATTTTAATTTTTAGAATTT
* *
1174 TTATTT-TTTTATTTTTTTATAATTT
1 TTATTTATTTTA-ATTTTTAGAATTT
1199 TTA
1 TTA
1202 AAAATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (25 bp):
TTATTTATTTTAATTTTTAGAATTT
Found at i:1785 original size:16 final size:16
Alignment explanation
Indices: 1766--1796 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1756 CGGGTTCGAA
1766 TTATTTCGAGTTCGGG
1 TTATTTCGAGTTCGGG
*
1782 TTATTTTGAGTTCGG
1 TTATTTCGAGTTCGG
1797 ACAATTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.29, T:0.48
Consensus pattern (16 bp):
TTATTTCGAGTTCGGG
Found at i:2545 original size:19 final size:17
Alignment explanation
Indices: 2521--2559 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
2511 ATAAAATAAA
*
2521 TTATTAATTTATATTATTT
1 TTATTAACTTA-ATT-TTT
2540 TTATTAACTTAATTTTT
1 TTATTAACTTAATTTTT
2557 TTA
1 TTA
2560 AATAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTAACTTAATTTTT
Found at i:5156 original size:13 final size:13
Alignment explanation
Indices: 5134--5165 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5124 GCAGCCATGT
*
5134 TCCAAAAATTTTG
1 TCCAAGAATTTTG
5147 TCCAAGAATTTTG
1 TCCAAGAATTTTG
5160 TCCAAG
1 TCCAAG
5166 TAGAACCGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (13 bp):
TCCAAGAATTTTG
Found at i:9681 original size:2 final size:2
Alignment explanation
Indices: 9636--9663 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9626 GTCTCCATTT
9636 TA TA TA 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
9664 AAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9816 original size:19 final size:20
Alignment explanation
Indices: 9791--9835 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
9781 GTAATAGTAC
*
9791 TTTTTTTAAGAGA-ATGATAA
1 TTTTTTTAAGA-ATATGAAAA
9811 TTTTTTTAA-AATATGAAAA
1 TTTTTTTAAGAATATGAAAA
9830 TTTTTT
1 TTTTTT
9836 AAGTGGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 13 0.57
20 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTTTTTAAGAATATGAAAA
Found at i:9973 original size:64 final size:64
Alignment explanation
Indices: 9905--10036 Score: 167
Period size: 64 Copynumber: 2.1 Consensus size: 64
9895 TAAATTTTTT
* * * * * *
9905 TAAAATATATTACAT-AAAATAATTGAAAGATATAAATATTTTTATAATATTATTATTTAATTTA
1 TAAAAGATATTACATAAAAAT-ATTAAAAAATACAAATATTCTTATAATATTATTACTTAATTTA
* * *
9969 TAAAAGATATTATATAAAAATATTAAAAAATACAAATATTCTTATAATATTGTTGCTTAATTTA
1 TAAAAGATATTACATAAAAATATTAAAAAATACAAATATTCTTATAATATTATTACTTAATTTA
10033 TAAA
1 TAAA
10037 GAATTTGATT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 53 0.91
65 5 0.09
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (64 bp):
TAAAAGATATTACATAAAAATATTAAAAAATACAAATATTCTTATAATATTATTACTTAATTTA
Found at i:10551 original size:19 final size:19
Alignment explanation
Indices: 10527--10565 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
10517 ATACTATTGG
10527 TATATAAGAGATATGCTTA
1 TATATAAGAGATATGCTTA
*
10546 TATATAAGAGATATGTTTA
1 TATATAAGAGATATGCTTA
10565 T
1 T
10566 GGGTCGGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (19 bp):
TATATAAGAGATATGCTTA
Found at i:11350 original size:13 final size:13
Alignment explanation
Indices: 11321--11362 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
11311 TGAATAGATA
*
11321 AAAAAAATA-TGT
1 AAAAAAATATTTT
*
11333 AAAAAATATTTTTT
1 AAAAAA-ATATTTT
11347 AAAAAAATATTTT
1 AAAAAAATATTTT
11360 AAA
1 AAA
11363 TTTGCGTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.24
13 11 0.44
14 8 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
AAAAAAATATTTT
Found at i:11434 original size:17 final size:17
Alignment explanation
Indices: 11414--11446 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11404 AAAATGGATA
11414 ATTTTTTAAAATTAAAT
1 ATTTTTTAAAATTAAAT
*
11431 ATTTTTTAAATTTAAA
1 ATTTTTTAAAATTAAA
11447 AATACATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTAAAATTAAAT
Found at i:13464 original size:29 final size:28
Alignment explanation
Indices: 13419--13480 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
13409 TTTTTACTAA
*
13419 AAATATTATCATTTTTATATTTATTTTT
1 AAATATTATCATTTTTATATTTATATTT
* * *
13447 AAATATTGTTATTATTTATTTTTATATTT
1 AAATATTATCATT-TTTATATTTATATTT
*
13476 CAATA
1 AAATA
13481 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 11 0.39
29 17 0.61
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (28 bp):
AAATATTATCATTTTTATATTTATATTT
Found at i:13715 original size:16 final size:16
Alignment explanation
Indices: 13689--13731 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
13679 CAATTGATCT
* * *
13689 GAACTCGAAATGACTT
1 GAACTCAAAATAACTC
*
13705 GAACTTAAAATAACTC
1 GAACTCAAAATAACTC
13721 GAACTCAAAAT
1 GAACTCAAAAT
13732 CACCCAAAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.23
Consensus pattern (16 bp):
GAACTCAAAATAACTC
Found at i:14335 original size:29 final size:29
Alignment explanation
Indices: 14294--14353 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
14284 TTATTATAAA
14294 TATTATTAGGCTATTAGAAAGGATCCACT
1 TATTATTAGGCTATTAGAAAGGATCCACT
*
14323 TATTATTAGGCTATTAGAAGGGATCCACT
1 TATTATTAGGCTATTAGAAAGGATCCACT
14352 TA
1 TA
14354 GACGTATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (29 bp):
TATTATTAGGCTATTAGAAAGGATCCACT
Found at i:15260 original size:22 final size:22
Alignment explanation
Indices: 15226--15277 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
15216 AATAAGTCAT
* * *
15226 TAATTCATGAATTGTATTATAA
1 TAATTTATAAATTATATTATAA
* *
15248 TGATTTATAAATTATGTTATAA
1 TAATTTATAAATTATATTATAA
15270 TAATTTAT
1 TAATTTAT
15278 TTATAATAAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (22 bp):
TAATTTATAAATTATATTATAA
Found at i:15281 original size:14 final size:15
Alignment explanation
Indices: 15254--15286 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
15244 ATAATGATTT
15254 ATAAATTATGTTATA
1 ATAAATTATGTTATA
*
15269 ATAATTTAT-TTATA
1 ATAAATTATGTTATA
15283 ATAA
1 ATAA
15287 GTAGGTGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATAAATTATGTTATA
Found at i:17079 original size:16 final size:16
Alignment explanation
Indices: 17042--17088 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
17032 TTTCTTTAAT
17042 AATTAATTATAT-T-A
1 AATTAATTATATATAA
17056 AA-TAATTATATATAA
1 AATTAATTATATATAA
17071 AATTAATTATATATAA
1 AATTAATTATATATAA
17087 AA
1 AA
17089 ATAAATAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.30
14 3 0.10
15 3 0.10
16 15 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTAATTATATATAA
Found at i:17101 original size:29 final size:28
Alignment explanation
Indices: 17042--17120 Score: 74
Period size: 29 Copynumber: 2.8 Consensus size: 28
17032 TTTCTTTAAT
* *
17042 AATTAATTATAT-TAAATAATTATATATAA
1 AATTAATTATATATAAA-AA-TAAATAAAA
17071 AATTAATTATATATAAAAATAAATAGAAA
1 AATTAATTATATATAAAAATAAATA-AAA
* *
17100 AAAT-ATGA-ATATAAAAATAAA
1 AATTAATTATATATAAAAATAAA
17121 ATGTATAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
27 13 0.30
28 8 0.18
29 19 0.43
30 4 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AATTAATTATATATAAAAATAAATAAAA
Found at i:17156 original size:15 final size:14
Alignment explanation
Indices: 17129--17159 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
17119 AAATGTATAA
17129 TAATATAAATAAAT
1 TAATATAAATAAAT
17143 TAATATACAATAAAT
1 TAATATA-AATAAAT
17158 TA
1 TA
17160 TCATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATATAAATAAAT
Found at i:17169 original size:15 final size:16
Alignment explanation
Indices: 17131--17176 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
17121 ATGTATAATA
17131 ATATAAATAAATTA--
1 ATATAAATAAATTATC
17145 ATATACAATAAATTATC
1 ATATA-AATAAATTATC
17162 AT-TAAAT-AATTATC
1 ATATAAATAAATTATC
17176 A
1 A
17177 ATTTTAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 13 0.45
15 12 0.41
16 2 0.07
17 2 0.07
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAAATAAATTATC
Found at i:17302 original size:2 final size:2
Alignment explanation
Indices: 17295--17319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17285 ATTTGTATGC
17295 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
17320 CACATCTAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24693 original size:41 final size:40
Alignment explanation
Indices: 24614--24699 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 40
24604 ACCGTCATCC
*
24614 TTTTATTAAAAATTTTAAAATAAATAAAATTAAGTTTTACT
1 TTTTATTAAAAATTTTAAAATAAATAAAAATAAGTTTTA-T
*
24655 TTTTATTAAAATTTTTTAAAATAAATAAAAATAA-TTTTAT
1 TTTTATTAAAA-ATTTTAAAATAAATAAAAATAAGTTTTAT
24695 TTTTA
1 TTTTA
24700 ATGAATAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
40 6 0.14
41 16 0.38
42 20 0.48
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (40 bp):
TTTTATTAAAAATTTTAAAATAAATAAAAATAAGTTTTAT
Found at i:24789 original size:15 final size:15
Alignment explanation
Indices: 24734--24800 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 15
24724 AATTTTATAG
*
24734 TTTAATTTAAAATAA
1 TTTAATTTAAATTAA
*
24749 TTATAATTCAAA-TAA
1 TT-TAATTTAAATTAA
24764 TTTTTTAAATTTAAATTAA
1 ---TTT-AATTTAAATTAA
24783 TTTAATTTAATATTAA
1 TTTAATTTAA-ATTAA
24799 TT
1 TT
24801 ATTATTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
15 12 0.28
16 18 0.42
17 1 0.02
18 9 0.21
19 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAATTTAAATTAA
Found at i:24827 original size:18 final size:18
Alignment explanation
Indices: 24775--24831 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 18
24765 TTTTTAAATT
24775 TAAA-TTAATTTAATTTAA
1 TAAATTTAATTT-ATTTAA
*
24793 TATTAATTATTATTTATTTAA
1 TA--AATT-TAATTTATTTAA
24814 TAAATTTAATTTATTTAA
1 TAAATTTAATTTATTTAA
24832 ATTTAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 13 0.39
19 4 0.12
20 2 0.06
21 9 0.27
22 5 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAAATTTAATTTATTTAA
Found at i:24832 original size:15 final size:15
Alignment explanation
Indices: 24761--24839 Score: 67
Period size: 15 Copynumber: 5.3 Consensus size: 15
24751 ATAATTCAAA
24761 TAATTT-TTTAAATT
1 TAATTTATTTAAATT
*
24775 TAAATTAATTT-AATT
1 T-AATTTATTTAAATT
* *
24790 TAATATTAATTATTATT
1 TAAT-TTATTTA-AATT
*
24807 T-ATTTA-ATAAATT
1 TAATTTATTTAAATT
24820 TAATTTATTTAAATT
1 TAATTTATTTAAATT
24835 TAATT
1 TAATT
24840 ATAAAAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
13 4 0.08
14 11 0.22
15 27 0.53
16 5 0.10
17 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TAATTTATTTAAATT
Found at i:24864 original size:22 final size:22
Alignment explanation
Indices: 24829--24870 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
24819 TTAATTTATT
24829 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
24851 TAAATATTAA-TATAAAAATA
1 TAAAT-TTAATTATAAAAATA
24871 ATTTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:25052 original size:14 final size:13
Alignment explanation
Indices: 25035--25141 Score: 51
Period size: 16 Copynumber: 7.6 Consensus size: 13
25025 TAAATTTTTA
25035 ATATTAAATATATT
1 ATATTAAATATA-T
25049 ATATTAAA-ATA-
1 ATATTAAATATAT
*
25060 ATA-TAAATA-AA
1 ATATTAAATATAT
25071 ATAATTAAAATATAAT
1 AT-ATT-AAATAT-AT
25087 ATAATATAAATATAT
1 AT-AT-TAAATATAT
*
25102 ATTTTAAAATTTATAT
1 ATATT-AAA--TATAT
*
25118 AATATTAATTATTAAT
1 -ATATTAAATA-T-AT
25134 ATATTAAA
1 ATATTAAA
25142 ATTTATAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 27
0.70 0.05 0.25
Matches are distributed among these distances:
10 5 0.07
11 6 0.08
12 1 0.01
13 5 0.07
14 19 0.26
15 12 0.16
16 21 0.28
17 5 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATATAT
Found at i:25117 original size:18 final size:18
Alignment explanation
Indices: 25096--25148 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
25086 TATAATATAA
*
25096 ATATATATTTTAAAATTT
1 ATATATATATTAAAATTT
25114 ATATA-ATATT--AA-TT
1 ATATATATATTAAAATTT
25128 AT-TAATATATTAAAATTT
1 ATAT-ATATATTAAAATTT
25146 ATA
1 ATA
25149 AAAATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 11
0.70 0.03 0.28
Matches are distributed among these distances:
13 1 0.04
14 5 0.18
15 7 0.25
17 6 0.21
18 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATATATATTAAAATTT
Found at i:25146 original size:32 final size:30
Alignment explanation
Indices: 25057--25148 Score: 107
Period size: 30 Copynumber: 3.0 Consensus size: 30
25047 TTATATTAAA
* *
25057 ATAATATAAATAAAATA-ATTAAAATATAAT
1 ATAATATAAATATAATATATTAAAAT-TTAT
*
25087 ATAATATAAATAT-ATATTTTAAAATTTAT
1 ATAATATAAATATAATATATTAAAATTTAT
*
25116 ATAATATTAATTATTAATATATTAAAATTTAT
1 ATAATA-TAAATA-TAATATATTAAAATTTAT
25148 A
1 A
25149 AAAATTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
29 12 0.23
30 24 0.45
31 1 0.02
32 16 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (30 bp):
ATAATATAAATATAATATATTAAAATTTAT
Found at i:25857 original size:22 final size:23
Alignment explanation
Indices: 25830--25892 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 23
25820 TTGGTAGTTC
25830 TTTTTAAGTAAAAAAATA-TGCT
1 TTTTTAAGTAAAAAAATAGTGCT
* *
25852 TTTTTATGTAAAAGGTAAATAGTTCT
1 TTTTTAAGTAAAA---AAATAGTGCT
*
25878 TTTTGAAGTAAAAAA
1 TTTTTAAGTAAAAAA
25893 TGTGGGTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 12 0.36
23 2 0.06
25 5 0.15
26 14 0.42
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (23 bp):
TTTTTAAGTAAAAAAATAGTGCT
Found at i:25888 original size:26 final size:22
Alignment explanation
Indices: 25824--25892 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
25814 AAAATGTTGG
25824 TAGTTCTTTTTAAGTAAAAAAA
1 TAGTTCTTTTTAAGTAAAAAAA
* *
25846 TA-TGCTTTTTTATGTAAAAGGTAAA
1 TAGTTC-TTTTTAAGTAAAA---AAA
25871 TAGTTCTTTTTGAAGTAAAAAA
1 TAGTTCTTTTT-AAGTAAAAAA
25893 TGTGGGTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
21 2 0.05
22 14 0.38
23 2 0.05
25 10 0.27
26 9 0.24
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (22 bp):
TAGTTCTTTTTAAGTAAAAAAA
Found at i:26161 original size:2 final size:2
Alignment explanation
Indices: 26150--26196 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
26140 AAATTAAAAA
*
26150 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26192 AT AT A
1 AT AT A
26197 GTTGCATGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28803 original size:2 final size:2
Alignment explanation
Indices: 28796--28825 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28786 CAATGCAATG
28796 TA TA TA TA 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
28826 ATACCTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31912 original size:13 final size:14
Alignment explanation
Indices: 31884--31913 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
31874 CCTAGAGGAC
31884 AAAAAGAAAGACAAA
1 AAAAAGAAAGA-AAA
31899 AAAAAGAAAGAAAA
1 AAAAAGAAAGAAAA
31913 A
1 A
31914 TAAGAAAGCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Done.