Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 25 of 25
Found at i:3969459 original size:1 final size:1
Alignment explanation
Indices: 3969453--3969478 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
3969443 TCTAAAAGAG
3969453 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
3969479 CAACTATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3973410 original size:2 final size:2
Alignment explanation
Indices: 3973403--3973449 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
3973393 AACTCTTGAA
3973403 AT AT AT 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
3973445 AT AT A
1 AT AT A
3973450 ACATGATGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3974096 original size:14 final size:15
Alignment explanation
Indices: 3974072--3974101 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3974062 AGGAAGTTTG
3974072 ATTGATTTAAAATTT
1 ATTGATTTAAAATTT
3974087 ATTG-TTTAAAATTT
1 ATTGATTTAAAATTT
3974101 A
1 A
3974102 ATTTAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTGATTTAAAATTT
Found at i:3974119 original size:10 final size:11
Alignment explanation
Indices: 3974095--3974127 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3974085 TTATTGTTTA
3974095 AAATTTAATTT
1 AAATTTAATTT
3974106 AAATTTAA-TT
1 AAATTTAATTT
*
3974116 AAATTTTATTT
1 AAATTTAATTT
3974127 A
1 A
3974128 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:3974120 original size:16 final size:16
Alignment explanation
Indices: 3974096--3974279 Score: 57
Period size: 16 Copynumber: 11.8 Consensus size: 16
3974086 TATTGTTTAA
*
3974096 AATTTAATTTAAATTT
1 AATTAAATTTAAATTT
*
3974112 AATTAAATTT-TATTT
1 AATTAAATTTAAATTT
* **
3974127 -ATAAAATAAAAATTT
1 AATTAAATTTAAATTT
* *
3974142 ATTTTGAAAAATTAAA-TT
1 A-ATT--AAATTTAAATTT
*
3974160 ATTTAAATTT--ATTT
1 AATTAAATTTAAATTT
* * *
3974174 GATTAGATATAAATTT
1 AATTAAATTTAAATTT
* * *
3974190 AATAAAAATTAAATTA
1 AATTAAATTTAAATTT
* *
3974206 AATTTATTTTAAATTT
1 AATTAAATTTAAATTT
*
3974222 AATT--ATTTATA-TT
1 AATTAAATTTAAATTT
*
3974235 ATTTTAAATTTAAA-TT
1 A-ATTAAATTTAAATTT
*
3974251 -ATT-AATTATTAATATT
1 AATTAAATT-TAAAT-TT
*
3974267 AATTAAAATTAAA
1 AATTAAATTTAAA
3974280 ATAATAAATA
Statistics
Matches: 117, Mismatches: 35, Indels: 31
0.64 0.19 0.17
Matches are distributed among these distances:
13 8 0.07
14 26 0.22
15 13 0.11
16 48 0.41
17 10 0.09
18 6 0.05
19 6 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
AATTAAATTTAAATTT
Found at i:3974188 original size:48 final size:45
Alignment explanation
Indices: 3974104--3974206 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 45
3974094 AAAATTTAAT
*
3974104 TTAAATTTAATTAAATTTTATTTATAAAATAAAAATTTATTTTGAAAAA
1 TTAAA-TTAATTAAATTTTATTTATAAAATAAAAATTTA--AT-AAAAA
* * * *
3974153 TTAAATTATTTAAA-TTTATTTGATTAGATATAAATTTAATAAAAA
1 TTAAATTAATTAAATTTTATTT-ATAAAATAAAAATTTAATAAAAA
3974198 TTAAATTAA
1 TTAAATTAA
3974207 ATTTATTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
45 13 0.28
46 1 0.02
47 7 0.15
48 21 0.45
49 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (45 bp):
TTAAATTAATTAAATTTTATTTATAAAATAAAAATTTAATAAAAA
Found at i:3974241 original size:24 final size:23
Alignment explanation
Indices: 3974209--3974260 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
3974199 TAAATTAAAT
3974209 TTATTTTAAATTT-AATTATTTATA
1 TTATTTTAAATTTAAATTA-TTA-A
3974233 TTATTTTAAATTTAAATTATTAA
1 TTATTTTAAATTTAAATTATTAA
3974256 TTATT
1 TTATT
3974261 AATATTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 6 0.22
24 16 0.59
25 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTTAAATTTAAATTATTAA
Found at i:3974266 original size:32 final size:31
Alignment explanation
Indices: 3974213--3974281 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 31
3974203 TTAAATTTAT
* * *
3974213 TTTAAA-TTTAATTATTTATATTATTTTAAA
1 TTTAAATTTTAATTATTAATATTAATTAAAA
3974243 TTTAAATTATTAATTATTAATATTAATTAAAA
1 TTTAAATT-TTAATTATTAATATTAATTAAAA
*
3974275 TTAAAAT
1 TTTAAAT
3974282 AATAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
31 1 0.03
32 26 0.79
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTAAATTTTAATTATTAATATTAATTAAAA
Found at i:3974302 original size:20 final size:19
Alignment explanation
Indices: 3974267--3974317 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
3974257 TATTAATATT
*
3974267 AATTAAAATT-AAAATAATA
1 AATT-AAATTAAAAATAAAA
*
3974286 AATATATATTAAAAATAAAA
1 AAT-TAAATTAAAAATAAAA
3974306 AATTAAATTAAA
1 AATTAAATTAAA
3974318 TTTATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAATTAAAAATAAAA
Found at i:3974340 original size:22 final size:21
Alignment explanation
Indices: 3974301--3974356 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
3974291 ATATTAAAAA
* *
3974301 TAAAAAATT-AAATTAAAT-T
1 TAAAATATTCAAATCAAATAT
3974320 TATAAATTATTCAAATCAAATAT
1 TA-AAA-TATTCAAATCAAATAT
*
3974343 TAAAATATTTAAAT
1 TAAAATATTCAAAT
3974357 TTAAATTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.07
20 3 0.10
21 11 0.37
22 11 0.37
23 3 0.10
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAATATTCAAATCAAATAT
Found at i:3974362 original size:22 final size:22
Alignment explanation
Indices: 3974308--3974363 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
3974298 AAATAAAAAA
3974308 TTAAATTAAATTTATAAATTAT
1 TTAAATTAAATTTATAAATTAT
* *
3974330 TCAAATCAAATATTA-AAA-TAT
1 TTAAATTAAAT-TTATAAATTAT
3974351 TTAAATTTAAATT
1 TTAAA-TTAAATT
3974364 ACACTTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 8 0.29
22 17 0.61
23 3 0.11
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAATTAAATTTATAAATTAT
Found at i:3977198 original size:2 final size:2
Alignment explanation
Indices: 3977159--3977190 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3977149 TATAATAGTA
3977159 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
3977191 GAATATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3977299 original size:14 final size:14
Alignment explanation
Indices: 3977280--3977306 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3977270 TGATATATAA
3977280 AAATATAAAAATAC
1 AAATATAAAAATAC
3977294 AAATATAAAAATA
1 AAATATAAAAATA
3977307 GTTAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
AAATATAAAAATAC
Found at i:3977652 original size:13 final size:15
Alignment explanation
Indices: 3977622--3977653 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
3977612 TTTAATTTTA
3977622 AATTTATTAAATAAT
1 AATTTATTAAATAAT
3977637 AATTT-TTAAA-AAT
1 AATTTATTAAATAAT
3977650 AATT
1 AATT
3977654 ATATAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTATTAAATAAT
Found at i:3978737 original size:19 final size:15
Alignment explanation
Indices: 3978696--3978727 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3978686 TGGTCAACAA
3978696 AAATTTTTATTTATT
1 AAATTTTTATTTATT
3978711 AAATTTTTATTTATT
1 AAATTTTTATTTATT
3978726 AA
1 AA
3978728 GAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATTTTTATTTATT
Found at i:3978759 original size:17 final size:18
Alignment explanation
Indices: 3978737--3978771 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3978727 AGAATATTTT
3978737 TTAAATAAACT-TAATTA
1 TTAAATAAACTATAATTA
*
3978754 TTAAATAATCTATAATTA
1 TTAAATAAACTATAATTA
3978772 ACAAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATAAACTATAATTA
Found at i:3979172 original size:8 final size:8
Alignment explanation
Indices: 3979159--3979191 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3979149 AATTTTTTTT
3979159 AATAAAAA
1 AATAAAAA
3979167 AAT-AAAA
1 AATAAAAA
*
3979174 AATAAATA
1 AATAAAAA
3979182 AATAAAAA
1 AATAAAAA
3979190 AA
1 AA
3979192 CGAATGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:3979177 original size:15 final size:15
Alignment explanation
Indices: 3979159--3979190 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3979149 AATTTTTTTT
3979159 AATAAAAAAATAAAA
1 AATAAAAAAATAAAA
*
3979174 AATAAATAAATAAAA
1 AATAAAAAAATAAAA
3979189 AA
1 AA
3979191 ACGAATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AATAAAAAAATAAAA
Found at i:3979264 original size:153 final size:159
Alignment explanation
Indices: 3979091--3979402 Score: 377
Period size: 160 Copynumber: 2.0 Consensus size: 159
3979081 AAAATTTTAA
* ***
3979091 TTTAATAGTAATTAAAGATAATTTTAAAATTAATTAAATTCTCACTATTTTGTAATT-AAATTTT
1 TTTAATAGTAATTAAAGATAATTTTAAAATTAATTAAATTCTCACTATTTTATAATTAAAAAAAT
* *
3979155 TTTTAAT-AA-AAAAAT-AAAAAATAA-ATAAATAAAAAAACGAATGATTAATAATGAATAAA-A
66 TTTTAATAAAGAAAAATAAAAAAAAAACATAAATAAAAAAACCAATGATTAATAATGAATAAAGA
*
3979215 GATATATTTGTATCCTCTTTTAAAATTATC
131 -ATATATTCGTATCCTCTTTTAAAATTATC
* * * * * *
3979245 TTTAATTG-AATTAAAGATAATTTTAAAATTACTTATATTTTTATTATTTTATAATTAAAAAAAT
1 TTTAATAGTAATTAAAGATAATTTTAAAATTAATTAAATTCTCACTATTTTATAATTAAAAAAAT
* * * *
3979309 TTTTAATAAAAGAAAAATGAAAAAAAAAACATAAATAGAGAAACCAGTGATTAATACTGAATAAA
66 TTTTAAT-AAAGAAAAAT-AAAAAAAAAACATAAATAAAAAAACCAATGATTAATAATGAATAAA
* *
3979374 GAATTTATTCGTATCTTCTTTTAAAATTA
129 GAATATATTCGTATCCTCTTTTAAAATTA
3979403 ACATAGTCAA
Statistics
Matches: 131, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
153 42 0.32
154 18 0.14
156 2 0.02
157 6 0.05
159 8 0.06
160 54 0.41
161 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (159 bp):
TTTAATAGTAATTAAAGATAATTTTAAAATTAATTAAATTCTCACTATTTTATAATTAAAAAAAT
TTTTAATAAAGAAAAATAAAAAAAAAACATAAATAAAAAAACCAATGATTAATAATGAATAAAGA
ATATATTCGTATCCTCTTTTAAAATTATC
Found at i:3981279 original size:139 final size:139
Alignment explanation
Indices: 3981020--3981306 Score: 369
Period size: 139 Copynumber: 2.1 Consensus size: 139
3981010 GTATTTTCTC
* * * * *
3981020 TAAA-CTTTAAGATCATTTTTATTGCATACTTGGCTATCTTATTGCCTTGCCTCCTTGCTCTACA
1 TAAATCTTTAAAATCAATTTTATTGCATACTTGACTATCTTATTACCTTGCCTCCTTACTCTACA
* ** * * ** * *
3981084 AAGCTCTTATTAATTTAGGTATTGAAATGTTTTAAAGTTTCAATTTTGATGCATTTTTAACTTTT
66 AAGCTCTTACTAATTTAAATATTGAAATGTTTTAAAATTTCAACTTCCATACATTTTTAACTCTT
*
3981149 TTTATCTTA
131 TTCATCTTA
* * * * *
3981158 TAGATCTTTAAAATCAATTTTATTGCATACTTGATTATCTTATTACCTTGCCTCCTTATTTTATA
1 TAAATCTTTAAAATCAATTTTATTGCATACTTGACTATCTTATTACCTTGCCTCCTTACTCTACA
* *
3981223 AAGCTCTTACTAATTTAAATATTGAAGTGTTTTAAAATTTCAACTTCCATATATTTTTAACTCTT
66 AAGCTCTTACTAATTTAAATATTGAAATGTTTTAAAATTTCAACTTCCATACATTTTTAACTCTT
3981288 TTCATCTTA
131 TTCATCTTA
3981297 TAAATCTTTA
1 TAAATCTTTA
3981307 TGCTGCATAG
Statistics
Matches: 125, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
138 3 0.02
139 122 0.98
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (139 bp):
TAAATCTTTAAAATCAATTTTATTGCATACTTGACTATCTTATTACCTTGCCTCCTTACTCTACA
AAGCTCTTACTAATTTAAATATTGAAATGTTTTAAAATTTCAACTTCCATACATTTTTAACTCTT
TTCATCTTA
Found at i:3982406 original size:20 final size:20
Alignment explanation
Indices: 3982381--3982422 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3982371 TGCTAACATA
* *
3982381 TCTCTCCAGTTTCCTTGATC
1 TCTCTCAAGTTTCCTTAATC
3982401 TCTCTCAAGTTTCCTTAATC
1 TCTCTCAAGTTTCCTTAATC
3982421 TC
1 TC
3982423 ATTGCGATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.33, G:0.07, T:0.45
Consensus pattern (20 bp):
TCTCTCAAGTTTCCTTAATC
Found at i:3983049 original size:15 final size:15
Alignment explanation
Indices: 3983025--3983102 Score: 54
Period size: 15 Copynumber: 5.3 Consensus size: 15
3983015 CAATATTAAT
*
3983025 TATATAATATATTTA
1 TATATTATATATTTA
3983040 TATATTATATATTTA
1 TATATTATATATTTA
* ** *
3983055 CATAAAATA-ACTTA
1 TATATTATATATTTA
* *
3983069 TGTATTGATATATATA
1 TATATT-ATATATTTA
*
3983085 TATA-T-TGTATTTA
1 TATATTATATATTTA
3983098 TATAT
1 TATAT
3983103 GATAAATTAA
Statistics
Matches: 46, Mismatches: 14, Indels: 7
0.69 0.21 0.10
Matches are distributed among these distances:
13 10 0.22
14 6 0.13
15 24 0.52
16 6 0.13
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (15 bp):
TATATTATATATTTA
Found at i:3984289 original size:33 final size:31
Alignment explanation
Indices: 3984238--3984299 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 31
3984228 TTATTTATAA
3984238 AATTTTTAAATTACATTATCCATATATAAAAT
1 AATTTTTAAATTACATTATCCAT-TATAAAAT
3984270 AATTATTTAAAATTA-ATTATCCATTATAAA
1 AATT-TTT-AAATTACATTATCCATTATAAA
3984300 TTAGCAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 10 0.36
33 12 0.43
34 6 0.21
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (31 bp):
AATTTTTAAATTACATTATCCATTATAAAAT
Found at i:3984887 original size:2 final size:2
Alignment explanation
Indices: 3984880--3984904 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3984870 CTAAAATGGG
3984880 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
3984905 GTCACGGAGG
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:3986102 original size:2 final size:2
Alignment explanation
Indices: 3986095--3986130 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3986085 TTAAGTATTT
*
3986095 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3986131 AAAGAACTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3988475 original size:19 final size:18
Alignment explanation
Indices: 3988450--3988517 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3988440 AATTCAACGA
3988450 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3988468 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
3988484 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3988500 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
3988518 TTAGCTACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:3988488 original size:32 final size:32
Alignment explanation
Indices: 3988452--3988514 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3988442 TTCAACGATT
*
3988452 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3988484 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3988515 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3988489 original size:13 final size:13
Alignment explanation
Indices: 3988471--3988495 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3988461 ACATAAGTGT
3988471 TGTATCGATACAA
1 TGTATCGATACAA
3988484 TGTATCGATACA
1 TGTATCGATACA
3988496 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3993474 original size:28 final size:28
Alignment explanation
Indices: 3993431--3993485 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
3993421 TTATGGCACC
3993431 AAGTATGCCTTATATCACAATAACATAA
1 AAGTATGCCTTATATCACAATAACATAA
*
3993459 AAGTATGCCTTTTATCACAATAACATA
1 AAGTATGCCTTATATCACAATAACATA
3993486 CAACTCATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.18, G:0.07, T:0.31
Consensus pattern (28 bp):
AAGTATGCCTTATATCACAATAACATAA
Found at i:3994188 original size:27 final size:27
Alignment explanation
Indices: 3994154--3994231 Score: 72
Period size: 27 Copynumber: 2.9 Consensus size: 27
3994144 AAACTTTTTT
3994154 TAACTTATCTTAGTTTACAATTTGATG
1 TAACTTATCTTAGTTTACAATTTGATG
** *
3994181 TAACTTA--TTA-TTTACAAACTTTTTTTT
1 TAACTTATCTTAGTTTAC-AA--TTTGATG
*
3994208 TAACTTATCTTAGTTTAAAATTTG
1 TAACTTATCTTAGTTTACAATTTG
3994232 TTGTGACTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
24 5 0.12
25 5 0.12
27 21 0.52
29 5 0.12
30 4 0.10
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (27 bp):
TAACTTATCTTAGTTTACAATTTGATG
Found at i:3994836 original size:3 final size:3
Alignment explanation
Indices: 3994822--3994859 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
3994812 CCTTTTCTAA
*
3994822 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3994860 CTCTCGATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:3997698 original size:3 final size:3
Alignment explanation
Indices: 3997690--3997729 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
3997680 AAATCGAGAG
*
3997690 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3997730 TTAGAAAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3998394 original size:27 final size:27
Alignment explanation
Indices: 3998319--3998401 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
3998309 AAATAGTCAC
*
3998319 AACAAATTTTAAACTAAGATAAGTTAAA
1 AACAAATTGTAAACTAAGATAAGTT-AA
* *
3998347 AAAAAAGTTTGTAAA-T-A-ATAAGTTAC
1 AACAAA--TTGTAAACTAAGATAAGTTAA
*
3998373 ATCAAATTGTAAACTAAGATAAGTTAA
1 AACAAATTGTAAACTAAGATAAGTTAA
3998400 AA
1 AA
3998402 AAAGTTTGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
24 7 0.16
25 1 0.02
26 6 0.14
27 16 0.37
28 6 0.14
29 1 0.02
30 6 0.14
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (27 bp):
AACAAATTGTAAACTAAGATAAGTTAA
Done.