Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2745
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: 48741
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:4907 original size:22 final size:22
Alignment explanation
Indices: 4873--4927 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
4863 TATTTTAAAA
* *
4873 AATATTAAAATATTTTTATAT-T
1 AATATTTAAATA-TATTATATGT
*
4895 AATATTTATATATATTATATGT
1 AATATTTAAATATATTATATGT
4917 AA-ATTTAAATA
1 AATATTTAAATA
4928 AAAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATATTTAAATATATTATATGT
Found at i:7440 original size:2 final size:2
Alignment explanation
Indices: 7433--7474 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
7423 GGGAGAAATA
7433 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7475 TAGCTTTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8213 original size:25 final size:24
Alignment explanation
Indices: 8153--8214 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
8143 ATAAAATATA
8153 AATT-AATTTAAAAATTATTATTT
1 AATTAAATTTAAAAATTATTATTT
*
8176 -ATTATAATATT-AAAATATATTTTTAT
1 AATTA-AAT-TTAAAAAT-TATTATT-T
8202 AATTAAATTTAAA
1 AATTAAATTTAAA
8215 TAAAAATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
22 3 0.10
24 8 0.26
25 10 0.32
26 6 0.19
27 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATTAAATTTAAAAATTATTATTT
Found at i:8215 original size:24 final size:26
Alignment explanation
Indices: 8153--8216 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 26
8143 ATAAAATATA
*
8153 AATT-AATTTAAAAATTATTATTTAT
1 AATTAAATTTAAATATTATTATTTAT
* *
8178 TA-TAATATTAAAATA-TATT-TTTAT
1 AATTAA-ATTTAAATATTATTATTTAT
8202 AATTAAATTTAAATA
1 AATTAAATTTAAATA
8217 AAAATATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
24 15 0.48
25 9 0.29
26 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTAAATTTAAATATTATTATTTAT
Found at i:8240 original size:25 final size:25
Alignment explanation
Indices: 8161--8242 Score: 62
Period size: 25 Copynumber: 3.1 Consensus size: 25
8151 TAAATTAATT
*
8161 TAAAAATTATTA-TTTATTA-TAATAT
1 TAAAAA-TATTATTTTATTATTAA-AA
*
8186 TAAAATATATT-TTTATAATTAAATTTAAA
1 TAAAA-ATATTATTT-T-ATT--ATTAAAA
8215 TAAAAATATTATTTTATTATTAAAA
1 TAAAAATATTATTTTATTATTAAAA
8240 TAA
1 TAA
8243 TAATTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
25 20 0.43
26 2 0.04
27 6 0.13
28 6 0.13
29 10 0.22
30 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAAAATATTATTTTATTATTAAAA
Found at i:15183 original size:30 final size:30
Alignment explanation
Indices: 15123--15211 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 30
15113 ATAAAAAATT
* *
15123 ATTAAAATTATTATCAATCTTAATTTTTTAATA
1 ATTAAAATTGTTA-AAAT-TTAA-TTTTTAATA
*
15156 ATTAAAATTGTTAAAATTTAATTTTTAATT
1 ATTAAAATTGTTAAAATTTAATTTTTAATA
*
15186 ATTAAAA--GTAAAAATTTAATATTTTA
1 ATTAAAATTGTTAAAATTTAAT-TTTTA
15212 TCAATTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
28 12 0.24
29 5 0.10
30 15 0.29
31 4 0.08
32 3 0.06
33 12 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTAAAATTGTTAAAATTTAATTTTTAATA
Found at i:17088 original size:15 final size:15
Alignment explanation
Indices: 17068--17097 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17058 CATATTGTAT
17068 CATATTAACATAAAC
1 CATATTAACATAAAC
17083 CATATTAACATAAAC
1 CATATTAACATAAAC
17098 AGATCAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (15 bp):
CATATTAACATAAAC
Found at i:20957 original size:29 final size:27
Alignment explanation
Indices: 20899--20959 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 27
20889 AATTTATATA
***
20899 ATATAAATTATTAAAATTTTAAATTTT
1 ATATAAATTATTAAAATTTTAAAAAAT
20926 ATATAAATATAATTAAAATTTTAAAAAAT
1 ATATAAAT-T-ATTAAAATTTTAAAAAAT
20955 ATATA
1 ATATA
20960 TCAAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 8 0.28
28 1 0.03
29 20 0.69
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
ATATAAATTATTAAAATTTTAAAAAAT
Found at i:21499 original size:21 final size:20
Alignment explanation
Indices: 21448--21499 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
21438 GTTATAATTA
* *
21448 TTATTTTAT-AATTTTAATT
1 TTATTTTATAAAATTTAAAT
*
21467 TTTTTATTATAAACATTTAAAT
1 TTATT-TTATAAA-ATTTAAAT
21489 TTATTTTATAA
1 TTATTTTATAA
21500 TTAAATCATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.15
20 4 0.15
21 8 0.31
22 10 0.38
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTATAAAATTTAAAT
Found at i:29433 original size:15 final size:17
Alignment explanation
Indices: 29413--29454 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
29403 ATTATTTCAT
29413 AAATTTTATTT-A-TAA
1 AAATTTTATTTCATTAA
29428 AAATTTTAATTTCATTAA
1 AAATTTT-ATTTCATTAA
29446 AAATGTTTA
1 AAAT-TTTA
29455 AATAGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.30
16 4 0.17
17 1 0.04
18 8 0.35
19 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
AAATTTTATTTCATTAA
Found at i:31639 original size:14 final size:14
Alignment explanation
Indices: 31620--31650 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31610 CAAAATCATG
31620 ATATATATATATGT
1 ATATATATATATGT
*
31634 ATATATATGTATGT
1 ATATATATATATGT
31648 ATA
1 ATA
31651 CCATAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (14 bp):
ATATATATATATGT
Found at i:40875 original size:2 final size:2
Alignment explanation
Indices: 40870--40894 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40860 ACACACCCCA
40870 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
40895 GAGAGAGAGA
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:40899 original size:2 final size:2
Alignment explanation
Indices: 40894--40928 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
40884 ATATATATAT
*
40894 AG AG AG AG AG AG AG AT AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
40929 ACAGAAGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:43777 original size:2 final size:2
Alignment explanation
Indices: 43770--43809 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
43760 TTTTAATTAT
43770 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
43810 TAAAATTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44332 original size:16 final size:15
Alignment explanation
Indices: 44306--44335 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
44296 CATAATCTAA
44306 AAATAAAATATTTAT
1 AAATAAAATATTTAT
44321 AAATATAAATATTTA
1 AAATA-AAATATTTA
44336 AATTTTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATAAAATATTTAT
Found at i:44650 original size:3 final size:3
Alignment explanation
Indices: 44642--44668 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44632 TTGAATTAGT
44642 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
44669 TTATTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44920 original size:31 final size:29
Alignment explanation
Indices: 44849--44922 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 29
44839 ATTTATTTGT
*
44849 TTATATTTGTATTATTTTTTATTTAAAATA
1 TTATATTT-TATTATTTTTTATATAAAATA
*
44879 TTATATTTTTATATATTTTTTATATATTAATAA
1 TTATA-TTTTAT-TATTTTTTATATA-AAAT-A
44912 TT-TATTTTATT
1 TTATATTTTATT
44923 TAATATATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
30 9 0.24
31 21 0.55
32 5 0.13
33 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTATATTTTATTATTTTTTATATAAAATA
Found at i:45466 original size:494 final size:493
Alignment explanation
Indices: 44792--45695 Score: 1245
Period size: 488 Copynumber: 1.8 Consensus size: 493
44782 AGGAAAGGAG
** *
44792 AGAAAGGAGAAAAGAAGAAAAAGGAACAAAAGAAAGAAGAGAAAAAAATTTATTTGTTTATATTT
1 AGAAAGGAGAAAAGAAGAAAAAGGAACAAAAGAAAGAAGAGAAAAAAATTTAAGTGTTCATATTT
*
44857 GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTATATATTAATAATTTATTTTAT
66 GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTAT
* * * * *
44922 TTAATATATATTTTTATATGTACGTATATTTATATTATACGTATTTATTTTTATATTATATTTTT
131 TTAATATATATTTTTATATGTACATATATTCATATTATACGCATTTATTTTCAT-GT-TATTTTT
* *
44987 AAATATTTTTTATAAATATCGCGTTTATATTATTTTTTTATATTTAAAATAAAATAAATTTATAT
194 AAATATTTTTTATAAACATCGCG-TT-TA-T-GTTTTTTATATTTAAAATAAAATAAATTTATAT
* * * * * *
45052 AAATTTTTACATGTTAATTATTTATTTATCTATATTTTAACATATTCGTGTATACATACTATATT
255 AAATTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATT
* *
45117 TATATTATTTTTCATGTTATATTTTAATTTTTTATCTATATGTTAAATGTGTATTATATCTCAAT
320 TATATTATCTTTCATGTTATATTTTAATTTTTT-T-TATATGTTAAATGTATATTATATCTCAAT
45182 TCATGTTATATTTT-ATATAACTAATCACTATGATTCATATAAAATCAACTACACAAACTAATAT
383 TCATGTTATATTTTGA-ATAACTAATCACTATGATTCATATAAAATCAACTACACAAACTAATAT
45246 GGTGCTAACATGTGACTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
447 GGTGCTAACATGTGACTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
* *
45293 AGAAAGGAGAAGAA-AAGAAAGAGGAA-AGAAAG-AA-AA-AGAAAAAATTTTAAGTGTTCATA-
1 AGAAAGGAGAA-AAGAAGAAAAAGGAACA-AAAGAAAGAAGAGAAAAAAATTTAAGTGTTCATAT
*
45352 TT-TA-TGTTTTTTATTTAAAATATTATATTTTTATAT-TTTTTTACATATTAATAATTTATTTT
64 TTGTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTT
* * * * * **
45414 ATTTTATGTATA-TTTTATATGTACATGTATTCGTGTTATGTGCATATTATTTTCATGTTATTTT
129 ATTTAATATATATTTTTATATGTACATATATTCATATTATACGCAT-TTATTTTCATGTTATTTT
* * *
45478 TAAATATTTTTTATAAACATCGTGTTTATGTTTTTTATGTTTAAAATAAAATAAATTTTTATAAA
193 TAAATATTTTTTATAAACATCGCGTTTATGTTTTTTATATTTAAAATAAAATAAATTTATATAAA
* * * * *
45543 TTTTTACACGTTAATTATTCATATATCTATATTTTGACATATTCATGCATTCGTACCGTGTTTAT
258 TTTTTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATTTAT
* * * *
45608 ATTATCTTTCATGTTGTGTTTTAATTTTTTTTATATGTTAAATTTATATTATATCTCAATTTATG
323 ATTATCTTTCATGTTATATTTTAATTTTTTTTATATGTTAAATGTATATTATATCTCAATTCATG
*
45673 TTATATTTTGAATAGCTAATCAC
388 TTATATTTTGAATAACTAATCAC
45696 CGTGATTTAA
Statistics
Matches: 357, Mismatches: 42, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
486 51 0.14
487 2 0.01
488 114 0.32
489 1 0.00
490 2 0.01
491 2 0.01
492 28 0.08
493 26 0.07
494 44 0.12
495 31 0.09
496 2 0.01
497 2 0.01
498 19 0.05
499 2 0.01
500 3 0.01
501 26 0.07
502 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (493 bp):
AGAAAGGAGAAAAGAAGAAAAAGGAACAAAAGAAAGAAGAGAAAAAAATTTAAGTGTTCATATTT
GTATTATTTTTTATTTAAAATATTATATTTTTATATATTTTTTACATATTAATAATTTATTTTAT
TTAATATATATTTTTATATGTACATATATTCATATTATACGCATTTATTTTCATGTTATTTTTAA
ATATTTTTTATAAACATCGCGTTTATGTTTTTTATATTTAAAATAAAATAAATTTATATAAATTT
TTACACGTTAATTATTCATATATCTATATTTTAACATATTCATGCATACATACCATATTTATATT
ATCTTTCATGTTATATTTTAATTTTTTTTATATGTTAAATGTATATTATATCTCAATTCATGTTA
TATTTTGAATAACTAATCACTATGATTCATATAAAATCAACTACACAAACTAATATGGTGCTAAC
ATGTGACTTTTTTTTTTTGGCAAGGCTGAAAAGAAAAT
Found at i:46433 original size:20 final size:17
Alignment explanation
Indices: 46402--46467 Score: 71
Period size: 17 Copynumber: 3.8 Consensus size: 17
46392 ATTTATTTGA
46402 ATAATT-TATTTATCAAATT
1 ATAATTATATTTA--AAA-T
46421 ATAATTATATTTAAAAT
1 ATAATTATATTTAAAAT
* *
46438 ATTATAATATTTAAAAT
1 ATAATTATATTTAAAAT
*
46455 ATTATTATATTTA
1 ATAATTATATTTA
46468 TATATATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
17 28 0.65
18 3 0.07
19 6 0.14
20 6 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATAATTATATTTAAAAT
Found at i:46449 original size:17 final size:17
Alignment explanation
Indices: 46427--46467 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
46417 AATTATAATT
46427 ATATTTAAAATATTATA
1 ATATTTAAAATATTATA
*
46444 ATATTTAAAATATTATT
1 ATATTTAAAATATTATA
46461 ATATTTA
1 ATATTTA
46468 TATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTTAAAATATTATA
Found at i:46500 original size:20 final size:20
Alignment explanation
Indices: 46452--46503 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
46442 TAATATTTAA
46452 AATATTATTATATTTATATAT
1 AATATTA-TATATTTATATAT
* *
46473 ATTTTTATATATTTATA-ATT
1 AATATTATATATTTATATA-T
46493 AATATTATATA
1 AATATTATATA
46504 AATTTTAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTATATATTTATATAT
Found at i:46511 original size:60 final size:58
Alignment explanation
Indices: 46424--46553 Score: 144
Period size: 60 Copynumber: 2.3 Consensus size: 58
46414 TCAAATTATA
* *
46424 ATTATA-TTTAA--AATATTATAATATTTAAAATATTATTATATT-TATATATATTTTT
1 ATTATATTTTAATTAATATTATAAAATTTAAAATATT-TAATATTATATATATATTTTT
* * *
46479 A-TATATTTATAATTAATATTATATAAATTTTAAAGTATTTAATATTATATTTTTATTTTT
1 ATTATATTT-TAATTAATATTATA-AAA-TTTAAAATATTTAATATTATATATATATTTTT
46539 ATTATATTTTAATTA
1 ATTATATTTTAATTA
46554 TTTTTTATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
54 4 0.06
55 3 0.05
56 3 0.05
58 9 0.15
59 8 0.13
60 28 0.45
61 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (58 bp):
ATTATATTTTAATTAATATTATAAAATTTAAAATATTTAATATTATATATATATTTTT
Found at i:46546 original size:11 final size:11
Alignment explanation
Indices: 46532--46565 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
46522 ATTATATTTT
46532 TATTTTTATTA
1 TATTTTTATTA
*
46543 TATTTTAATTA
1 TATTTTTATTA
46554 T-TTTTTATTA
1 TATTTTTATTA
46564 TA
1 TA
46566 ATGATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:46554 original size:20 final size:20
Alignment explanation
Indices: 46456--46565 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 20
46446 ATTTAAAATA
46456 TTATTATA-TTTATATATATTT
1 TTATTATATTTTA-AT-TATTT
* *
46477 TTA-TATATTTATAATTAATA
1 TTATTATATTT-TAATTATTT
* *
46497 TTATATAAATTTTAAAGTATTT
1 TTAT-TATATTTT-AATTATTT
*
46519 AATATTATA-TTT--TTATTT
1 -TTATTATATTTTAATTATTT
46537 TTATTATATTTTAATTATTTT
1 TTATTATATTTTAATTA-TTT
46558 TTATTATA
1 TTATTATA
46566 ATGATAATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
17 7 0.10
18 8 0.12
20 13 0.19
21 22 0.32
22 16 0.23
23 3 0.04
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATTATATTTTAATTATTT
Found at i:46687 original size:19 final size:19
Alignment explanation
Indices: 46663--46700 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
46653 TATGTAGTGG
46663 GAAAGAAAGAAGAAAAAAA
1 GAAAGAAAGAAGAAAAAAA
46682 GAAAGAAAGAAGAAAAAAA
1 GAAAGAAAGAAGAAAAAAA
46701 AATTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAGAAAGAAGAAAAAAA
Found at i:46760 original size:23 final size:23
Alignment explanation
Indices: 46730--46807 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 23
46720 TGTTTGTATT
46730 TTATATTTTTTTATTTTTAAATA
1 TTATATTTTTTTATTTTTAAATA
*
46753 TTATATTTTTGTATATTTTTGACATA
1 TTATATTTTT-T-TATTTTT-AAATA
*
46779 TTAATAATTTATTTTATTTTATATATA
1 TT-AT-ATTT-TTTTATTTT-TAAATA
46806 TT
1 TT
46808 TTTATGTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
23 10 0.22
24 1 0.02
25 7 0.15
26 6 0.13
27 14 0.30
28 6 0.13
29 2 0.04
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (23 bp):
TTATATTTTTTTATTTTTAAATA
Found at i:46908 original size:17 final size:17
Alignment explanation
Indices: 46873--46910 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
46863 TATTATTTAA
46873 AATATTATAAATTTATGT
1 AATATTATAAA-TTATGT
46891 AATATTTATAAA-TATGT
1 AATA-TTATAAATTATGT
46908 AAT
1 AAT
46911 TATATTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
AATATTATAAATTATGT
Found at i:48260 original size:54 final size:54
Alignment explanation
Indices: 48196--48305 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
48186 CCACAAACTT
48196 AAATAAAAATAATATGATTTATAAAAAATATACGAAATTAAATTAAAATACCCG
1 AAATAAAAATAATATGATTTATAAAAAATATACGAAATTAAATTAAAATACCCG
48250 AAATAAAAATAATATGATTTATAAAAAATATACGAAATTAAATTAAAATACCCG
1 AAATAAAAATAATATGATTTATAAAAAATATACGAAATTAAATTAAAATACCCG
48304 AA
1 AA
48306 GCGAAGCGTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.27
Consensus pattern (54 bp):
AAATAAAAATAATATGATTTATAAAAAATATACGAAATTAAATTAAAATACCCG
Found at i:48299 original size:20 final size:18
Alignment explanation
Indices: 48218--48291 Score: 57
Period size: 20 Copynumber: 4.1 Consensus size: 18
48208 TATGATTTAT
48218 AAAAAATATACGAAATTA
1 AAAAAATATACGAAATTA
**
48236 AATTAAAATACCCGAAA-TA
1 AA--AAAATATACGAAATTA
*
48255 AAAATAATAT--G-ATTTA
1 AAAA-AATATACGAAATTA
48271 TAAAAAATATACGAAATTA
1 -AAAAAATATACGAAATTA
48290 AA
1 AA
48292 TTAAAATACC
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
15 1 0.02
16 8 0.19
17 6 0.14
18 9 0.21
19 8 0.19
20 11 0.26
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAAATATACGAAATTA
Done.