Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2529
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: 68136
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:298 original size:76 final size:76
Alignment explanation
Indices: 172--325 Score: 281
Period size: 76 Copynumber: 2.0 Consensus size: 76
162 CTATATGGCT
*
172 CATGCAAACGCTATCAAAGTAGAGACTAGGGCTTAGGACTGAATTTGAGAATTCAAGGCAGGTTT
1 CATGCAAACACTATCAAAGTAGAGACTAGGGCTTAGGACTGAATTTGAGAATTCAAGGCAGGTTT
237 TTAACCTAGGA
66 TTAACCTAGGA
* *
248 CATGCAAACACTATCAAAGTAGAGACTAGGGCTTAGGACTGAGTTTGAGAATTCAAGGCTGGTTT
1 CATGCAAACACTATCAAAGTAGAGACTAGGGCTTAGGACTGAATTTGAGAATTCAAGGCAGGTTT
313 TTAACCTAGGA
66 TTAACCTAGGA
324 CA
1 CA
326 GGCCTCTAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (76 bp):
CATGCAAACACTATCAAAGTAGAGACTAGGGCTTAGGACTGAATTTGAGAATTCAAGGCAGGTTT
TTAACCTAGGA
Found at i:1591 original size:2 final size:2
Alignment explanation
Indices: 1580--1630 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
1570 ATATATGTAC
* *
1580 AG AG AA AG AG AG AG AG AG AG AG AG -G CG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1621 AG AG AG AG AG
1 AG AG AG AG AG
1631 TGCCTTAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2614 original size:18 final size:17
Alignment explanation
Indices: 2605--2638 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2595 AATATTTATG
2605 AAATTAATAAATAATTAA
1 AAATTAAT-AATAATTAA
*
2623 AAATTAATAAAAATTA
1 AAATTAATAATAATTA
2639 TATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTAATAATAATTAA
Found at i:4232 original size:18 final size:19
Alignment explanation
Indices: 4209--4249 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
4199 TGGAAGAAAG
*
4209 TTTTTAGAGAATATA-ATT
1 TTTTTAAAGAATATATATT
*
4227 TTTTTAAAGAATTTATATT
1 TTTTTAAAGAATATATATT
4246 TTTT
1 TTTT
4250 ATTTATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTTAAAGAATATATATT
Found at i:6662 original size:125 final size:125
Alignment explanation
Indices: 6499--6800 Score: 315
Period size: 127 Copynumber: 2.4 Consensus size: 125
6489 TATTTTATTA
* * * * *
6499 ATTAGTTATTTTTATTTTCTATTTTTAAAATAATATATTTAAATGAATTAATTTGCATGTTAACT
1 ATTAATTATTTTTA-TTT-TA-TTTT-AAATAATATATTTAAAAGAATTAAATCGCATATTAACT
* * * *
6564 TGCTAG-TC-ATTTAAAATTTATACCTAA-AATT-ATGGAAAAAATTTAAAAAAAAAATTATATT
62 T-ATAGATCAATTTAAAATTCATACCTAACAATTGA-AGAAAAAAGTTAAAAAAAAAATT-TATT
6625 TT
124 TT
* * *
6627 ATTAATTATTTTTATTTTATTATTAAATTATATATTTAAAAGAGTTAAATCGTATATTAACTTAT
1 ATTAATTATTTTTATTTTATT-TTAAATAATATATTTAAAAGAATTAAATCGCATATTAACTTAT
* * * *
6692 AGATCAATTTAAAATTCATACTTAATCCATTGAAGAAAAAAGTTAAAATAATAATTTATTTT
65 AGATCAATTTAAAATTCATACCTAA-CAATTGAAGAAAAAAGTTAAAAAAAAAATTTATTTT
* * *
6754 ATTAATTATTTATATATTTGTTTTAAATAATATATTTAAAAAAATTA
1 ATTAATTATTTTTAT-TTTATTTTAAATAATATATTTAAAAGAATTA
6801 TTCACACGTT
Statistics
Matches: 146, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
124 3 0.02
125 36 0.25
126 21 0.14
127 45 0.31
128 40 0.27
129 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (125 bp):
ATTAATTATTTTTATTTTATTTTAAATAATATATTTAAAAGAATTAAATCGCATATTAACTTATA
GATCAATTTAAAATTCATACCTAACAATTGAAGAAAAAAGTTAAAAAAAAAATTTATTTT
Found at i:7103 original size:16 final size:17
Alignment explanation
Indices: 7057--7111 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
7047 ATATTTATAA
*
7057 TTTATTAA--AATTTAA
1 TTTATTAATTAATTTAT
*
7072 TTTA-AAATTAATTTAT
1 TTTATTAATTAATTTAT
7088 TTTATTAATTAA-TTAT
1 TTTATTAATTAATTTAT
*
7104 TTTTTTAA
1 TTTATTAA
7112 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.64
17 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTAATTAATTTAT
Found at i:19557 original size:13 final size:13
Alignment explanation
Indices: 19539--19564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19529 AGGATGATGG
19539 CTATAAGAGACTA
1 CTATAAGAGACTA
19552 CTATAAGAGACTA
1 CTATAAGAGACTA
19565 TGTTATTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CTATAAGAGACTA
Found at i:21297 original size:28 final size:30
Alignment explanation
Indices: 21265--21361 Score: 73
Period size: 28 Copynumber: 3.4 Consensus size: 30
21255 TAATTCTTAC
*
21265 TATATAATAAATTTTATTAT-GTAAT-AAA
1 TATATAATAAATTTTATTATAATAATCAAA
* * * *
21293 TATATATTTACTTTTA-TATAATAATCTAA
1 TATATAATAAATTTTATTATAATAATCAAA
* *
21322 TAAATATATAAATTTTATTATTATAA--AAA
1 TATATA-ATAAATTTTATTATAATAATCAAA
21351 T-TAT-ATAAATT
1 TATATAATAAATT
21362 AATTAAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
26 7 0.13
27 3 0.06
28 19 0.36
29 10 0.19
30 7 0.13
31 7 0.13
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (30 bp):
TATATAATAAATTTTATTATAATAATCAAA
Found at i:21373 original size:26 final size:28
Alignment explanation
Indices: 21344--21411 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
21334 TTTTATTATT
*
21344 ATAAAAATTATATAAAT-TAATTAA-AA
1 ATAAAAATTATATAAATATAATAAATAA
* *
21370 ATAAATAGTTACATAAATAATAATAAATAA
1 ATAAA-AATTATATAAAT-ATAATAAATAA
21400 ATACAAAATTAT
1 ATA-AAAATTAT
21412 TAATTGATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
26 5 0.16
27 10 0.31
29 6 0.19
30 9 0.28
31 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (28 bp):
ATAAAAATTATATAAATATAATAAATAA
Found at i:22673 original size:5 final size:5
Alignment explanation
Indices: 22662--22700 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
22652 AGTAGTCATG
* *
22662 AAAAGC AAAGC AAAAC AAAGC AAAAC AAAAC AAAAC AAA
1 AAAA-C AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAA
22701 TGTAACATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 26 0.90
6 3 0.10
ACGTcount: A:0.74, C:0.18, G:0.08, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:22682 original size:10 final size:10
Alignment explanation
Indices: 22662--22700 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
22652 AGTAGTCATG
22662 AAAAGCAAAGC
1 AAAA-CAAAGC
22673 AAAACAAAGC
1 AAAACAAAGC
*
22683 AAAACAAAAC
1 AAAACAAAGC
22693 AAAACAAA
1 AAAACAAA
22701 TGTAACATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.74, C:0.18, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAACAAAGC
Found at i:22683 original size:15 final size:15
Alignment explanation
Indices: 22663--22700 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
22653 GTAGTCATGA
*
22663 AAAGCAAAGCAAAAC
1 AAAGCAAAACAAAAC
22678 AAAGCAAAACAAAAC
1 AAAGCAAAACAAAAC
*
22693 AAAACAAA
1 AAAGCAAA
22701 TGTAACATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.74, C:0.18, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAGCAAAACAAAAC
Found at i:25999 original size:6 final size:7
Alignment explanation
Indices: 25973--26008 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
25963 ATTTGTGTTT
25973 TATAAAA
1 TATAAAA
25980 TATAAAA
1 TATAAAA
25987 TATAAAA
1 TATAAAA
25994 -ATAAAA
1 TATAAAA
26000 -ATAAAA
1 TATAAAA
26006 TAT
1 TAT
26009 GTGTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TATAAAA
Found at i:27109 original size:91 final size:92
Alignment explanation
Indices: 26947--27125 Score: 342
Period size: 92 Copynumber: 2.0 Consensus size: 92
26937 TTTTTAAGCA
26947 AAAAAAAAAAGGCGGTTTATGATTCATGGAGGATGCAACCAAACTTTTTTTTGAAAATTTTCAAG
1 AAAAAAAAAAGGCGGTTTATGATTCATGGAGGATGCAACCAAACTTTTTTTTGAAAATTTTCAAG
27012 TAATTATATTAGATTTGATAATTTGTG
66 TAATTATATTAGATTTGATAATTTGTG
*
27039 AAAAAAAAAAGGCGGTTTATGATTCATGGAGGATGCAACCAAACTTTTTTTT-CAAATTTTCAAG
1 AAAAAAAAAAGGCGGTTTATGATTCATGGAGGATGCAACCAAACTTTTTTTTGAAAATTTTCAAG
27103 TAATTATATTAGATTTGATAATT
66 TAATTATATTAGATTTGATAATT
27126 CATGTCTTTA
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 34 0.40
92 52 0.60
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (92 bp):
AAAAAAAAAAGGCGGTTTATGATTCATGGAGGATGCAACCAAACTTTTTTTTGAAAATTTTCAAG
TAATTATATTAGATTTGATAATTTGTG
Found at i:27369 original size:18 final size:17
Alignment explanation
Indices: 27348--27381 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
27338 GTATTAAATC
27348 TTAAATATTATATTTTAA
1 TTAAATATT-TATTTTAA
27366 TTAAATATTTATTTTA
1 TTAAATATTTATTTTA
27382 TAATTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAATATTTATTTTAA
Found at i:27377 original size:19 final size:18
Alignment explanation
Indices: 27348--27386 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
27338 GTATTAAATC
27348 TTAAATATTATATTT-TAA
1 TTAAATATTAT-TTTATAA
27366 TTAAATATTTATTTTATAA
1 TTAAATA-TTATTTTATAA
27385 TT
1 TT
27387 TGTTAGACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAAATATTATTTTATAA
Found at i:45994 original size:33 final size:33
Alignment explanation
Indices: 45936--45998 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
45926 TCATCCTTTT
***
45936 AAGCCCACATAAATTGGTGGCATCCTTTCTCAA
1 AAGCCCACATAAATTGGTCAAATCCTTTCTCAA
*
45969 AAGCCCACATAAGTTGGTCAAATCCTTTCT
1 AAGCCCACATAAATTGGTCAAATCCTTTCT
45999 TTCAAAGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (33 bp):
AAGCCCACATAAATTGGTCAAATCCTTTCTCAA
Found at i:46033 original size:130 final size:130
Alignment explanation
Indices: 45796--46256 Score: 545
Period size: 130 Copynumber: 3.5 Consensus size: 130
45786 TAGACGTTCA
* * * * ** * *
45796 TCATCCTTCTAAGCCTAAACAAGTTGGTGGCATTTTTTCTCAGAAGCCCACACAAGTTGGTGGCA
1 TCATCCTTTTAAGCCCACACAAATTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTTGGTGACA
* *
45861 TCCTTTCTTTCAAAGCCCATAACTCCT-TGGCACCTTCTTTTCACAGTCCATGACTCCATGGCAT
66 TCCTTTCTTTCAAAGCCCATAACT-CTGTGGCACCTTCCTTTCAAAGTCCATGACTCCATGGCAT
45925 C
130 C
* * * *
45926 TCATCCTTTTAAGCCCACATAAATTGGTGGCATCCTTTCTCAAAAGCCCACATAAGTTGGTCAAA
1 TCATCCTTTTAAGCCCACACAAATTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTTGGTGACA
* ** * *
45991 TCCTTTCTTTCAAAGCCCATAACTCTGTGGCACCTTCCTTTCAAAGCCCATGACTTTATAGCACC
66 TCCTTTCTTTCAAAGCCCATAACTCTGTGGCACCTTCCTTTCAAAGTCCATGACTCCATGGCATC
* * * *
46056 TTATCCTTTTAAGCCCACACAAGTTGGTGGCATCCTTTCTCAAAAGCCCACACAAATCGGTGACA
1 TCATCCTTTTAAGCCCACACAAATTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTTGGTGACA
* * * * * **
46121 -CCTTTTTCTTTTAAAGTCCATAA-TTTCGTGGCACATTCCTTTGAAAGTCCACAACTCCATGGC
66 TCC--TTTCTTTCAAAGCCCATAACTCT-GTGGCACCTTCCTTTCAAAGTCCATGACTCCATGGC
*
46184 ATT
128 ATC
* *
46187 TCATCCTTTTAAGCCCACA-AAAGTTGGTGGCATTCTTTCTCAAAAGCCCACACAAGTTGGTGGC
1 TCATCCTTTTAAGCCCACACAAA-TTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTTGGTGAC
46251 A-CCTTT
65 ATCCTTT
46257 GCGAAGTCCA
Statistics
Matches: 280, Mismatches: 46, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
129 7 0.03
130 169 0.60
131 104 0.37
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (130 bp):
TCATCCTTTTAAGCCCACACAAATTGGTGGCATCCTTTCTCAAAAGCCCACACAAGTTGGTGACA
TCCTTTCTTTCAAAGCCCATAACTCTGTGGCACCTTCCTTTCAAAGTCCATGACTCCATGGCATC
Found at i:46055 original size:31 final size:31
Alignment explanation
Indices: 45992--46057 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
45982 TTGGTCAAAT
* * *
45992 CCTTTCTTTCAAAGCCCATAACTCTGTGGCA
1 CCTTCCTTTCAAAGCCCATAACTCTATAGCA
* *
46023 CCTTCCTTTCAAAGCCCATGACTTTATAGCA
1 CCTTCCTTTCAAAGCCCATAACTCTATAGCA
46054 CCTT
1 CCTT
46058 ATCCTTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.33
Consensus pattern (31 bp):
CCTTCCTTTCAAAGCCCATAACTCTATAGCA
Found at i:46435 original size:32 final size:32
Alignment explanation
Indices: 46379--46443 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
46369 CATAAGCCAA
* * *
46379 TGGCAACCTTCCTCAAAGCTCACACAAGTTGG
1 TGGCAACCTTCCTCAAAACCCACACAAATTGG
46411 TGGCAACCTT-CTCAAAAACCCACACAAATTGG
1 TGGCAACCTTCCTC-AAAACCCACACAAATTGG
46443 T
1 T
46444 AGCATCCCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 3 0.10
32 26 0.90
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (32 bp):
TGGCAACCTTCCTCAAAACCCACACAAATTGG
Found at i:46638 original size:50 final size:52
Alignment explanation
Indices: 46584--46699 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 52
46574 GATGTTGCTA
* *
46584 GCCTTGAATCAGCACATT-G-TCCTTCACCATCTCTAAGTCCAATATCGTTG
1 GCCTTGAATCAGCACATTGGCACCTTCACCATCTCTAAGTCCAATATCGCTG
* * * *** *
46634 GCCTTAAATCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTG
1 GCCTTGAATCAGCACATTGGCACCTTCACCATCTCTAAGTCCAATATCGCTG
46686 GCCTTGAATCAGCA
1 GCCTTGAATCAGCA
46700 TATTAGTATC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 15 0.28
51 1 0.02
52 37 0.70
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.32
Consensus pattern (52 bp):
GCCTTGAATCAGCACATTGGCACCTTCACCATCTCTAAGTCCAATATCGCTG
Found at i:46910 original size:61 final size:62
Alignment explanation
Indices: 46816--46938 Score: 185
Period size: 61 Copynumber: 2.0 Consensus size: 62
46806 TTGGAATTCT
* *
46816 TCATATTTTAACCCCAATATCGCTAGCCTTGAATCAACATATTGGCACCTTTATCATTCTTC
1 TCATATTTTAAACCCAATATCGCTAGCCGTGAATCAACATATTGGCACCTTTATCATTCTTC
* * * *
46878 TCATA-TTTAAACCCAATATCGTTGGCCGTGAATTAGCATATTGGCACCTTTATCATTCTTC
1 TCATATTTTAAACCCAATATCGCTAGCCGTGAATCAACATATTGGCACCTTTATCATTCTTC
46939 GCATCCTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
61 50 0.91
62 5 0.09
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (62 bp):
TCATATTTTAAACCCAATATCGCTAGCCGTGAATCAACATATTGGCACCTTTATCATTCTTC
Found at i:50279 original size:98 final size:96
Alignment explanation
Indices: 50143--50402 Score: 308
Period size: 98 Copynumber: 2.7 Consensus size: 96
50133 GAATACTCTA
* * * * *
50143 TTTTTCGAGGGGATATTCTAACTCCGTTTTTAAAAATTATCAAGATTTAAATCTTAATTTTGCTT
1 TTTTTTGAGGGGATACTCCAACCCCATTTTT-AAAATTATCAAGATTTAAATCTTAATTTTGCTT
** *
50208 AAATTATCATCATTGGGGATACTCTAACCCTAT
65 AAATTATCATCATTAAGGATACTC-AACCCCAT
* *
50241 TTTTTTGAGGGGATACTCCAACCCCATTTTTACAAATTATCAAGATTTAAACCTTAATTTTGCCT
1 TTTTTTGAGGGGATACTCCAACCCCATTTTTA-AAATTATCAAGATTTAAATCTTAATTTTGCTT
*
50306 AAATTATCGTCATTAAGGATACTCAACCCCAT
65 AAATTATCATCATTAAGGATACTCAACCCCAT
* * * * * * * *
50338 TATTCTAAGGGGATACTCCAACCCCATTTTTAAACTCATTAAGA--TAATTCTTATTTTTGCTTA
1 TTTTTTGAGGGGATACTCCAACCCCATTTTTAAAATTATCAAGATTTAAATCTTAATTTTGCTTA
50401 AA
66 AA
50403 ATGTCATCGT
Statistics
Matches: 140, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
94 17 0.12
96 9 0.06
97 37 0.26
98 77 0.55
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (96 bp):
TTTTTTGAGGGGATACTCCAACCCCATTTTTAAAATTATCAAGATTTAAATCTTAATTTTGCTTA
AATTATCATCATTAAGGATACTCAACCCCAT
Found at i:55386 original size:51 final size:51
Alignment explanation
Indices: 55327--55462 Score: 191
Period size: 51 Copynumber: 2.7 Consensus size: 51
55317 TTTTAACTAG
* *
55327 ATGTATCGATACATTGAAAAATATATCGATATATCTGGGCAAAAGGATAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGCAAAAAGATAGA
* * *
55378 ATGTATCGATACATTGAAGAATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGCAAAAAGATAGA
* * * *
55429 ATGTATCGATACATTCATACATGTATCGATACAT
1 ATGTATCGATACATTGAAAAATATATCGATACAT
55463 TGAAAAATGT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTGGGCAAAAAGATAGA
Found at i:55454 original size:20 final size:20
Alignment explanation
Indices: 55428--55482 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
55418 AAAAAGATAG
*
55428 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
55448 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
55468 AATGTATCGATACAT
1 AATGTATCGATACAT
55483 CTGGGTACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:59487 original size:78 final size:78
Alignment explanation
Indices: 59224--59720 Score: 428
Period size: 78 Copynumber: 6.4 Consensus size: 78
59214 ATGAAAATAC
* * * **
59224 GAGATGATCAAAATATGGACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAG-AAACGTCTCG
1 GAGATGATCAAAGTCTAGACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGCAATTGTCTCG
*
59288 AGCCT-AAAAGAC
66 AGCCTAAAAAGAT
* * * * * * *
59300 AAGATGATCAAAGTTTAGACTTTTAGGAACGTCAAAGTCTTTAGGAAGGCATAGCAATTGTATCG
1 GAGATGATCAAAGTCTAGACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGCAATTGTCTCG
* *
59365 AGCTTGAAAATG-T
66 AGCCT-AAAAAGAT
* * * * * * * * *
59378 GAGATAATTAAGGTTTGGACCCTT-GAAAAGGTCAATGCCTTTAGGAAGGCATAACAATTGTTTC
1 GAGATGATCAAAGTCTAGACCTTTAG-GAAGGTCAATGCCTTTAGGAAGGCATAGCAATTGTCTC
* *
59442 AAGCCTAAAAAAAT
65 GAGCCTAAAAAGAT
* * * * * * * *
59456 GATATGGTCAAAGTCTAGACCTTTGGGAAGGTCCATGCTTTTAGGAAGGCATAGTAATTATCTTG
1 GAGATGATCAAAGTCTAGACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGCAATTGTCTCG
* *
59521 AGCCTAAAATGAC
66 AGCCTAAAAAGAT
* * * * * * * ** * *
59534 AAGATGATGAAAGTCTAGACCTTTGGGAAGTTTAGTGCCTATAAAAAGGCGTAGCAATTGTCTCA
1 GAGATGATCAAAGTCTAGACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGCAATTGTCTCG
* *
59599 AGCCTGAAAAGGT
66 AGCCTAAAAAGAT
* * *
59612 GAGATGATCAAGGTCTAGACCTTTAGGAAAG-CTAATGCCTTTGGGAAGGCATAGCAATTGTCTC
1 GAGATGATCAAAGTCTAGACCTTTAGGAAGGTC-AATGCCTTTAGGAAGGCATAGCAATTGTCTC
*
59676 GAGCCTAAAAGGAT
65 GAGCCTAAAAAGAT
* *
59690 GAGATGATCAAAGTTTGGACCTTTTAGGAAG
1 GAGATGATCAAAGTCTAGACC-TTTAGGAAG
59721 ACATAGCAAC
Statistics
Matches: 320, Mismatches: 93, Indels: 13
0.75 0.22 0.03
Matches are distributed among these distances:
76 46 0.14
77 16 0.05
78 245 0.77
79 13 0.04
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (78 bp):
GAGATGATCAAAGTCTAGACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGCAATTGTCTCG
AGCCTAAAAAGAT
Found at i:59661 original size:234 final size:232
Alignment explanation
Indices: 59177--59720 Score: 556
Period size: 234 Copynumber: 2.3 Consensus size: 232
59167 GCTAAGTAGG
** * ** * * * * * *
59177 TCAATGCCTTTAGGAAGGTGTAACAAATG-CTTCAAGTATGAAAATACGAGATGATCAAAATATG
1 TCAATGCCTTTAGGAAGGCATAACAATTGTC-TCAAGCCTAAAAAAATGAGATGATCAAAGTCTA
*
59241 GACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGAAACGTCTCGAGCCTAAAAGACAAGATG
65 GACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGAAACATCTCGAGCCTAAAAGACAAGATG
* * * ** * *
59306 ATCAAAGTTTAGACTTTTAGGAACGTCAAAGTCTTTAGGAAGGCATAGCAATTGTATCGAGCTTG
130 ATCAAAGTCTAGACCTTTAGGAACGTCAAAGTCTATAAAAAGGCATAGCAATTGTATCAAGCCTG
* * * * *
59371 AAAATGTGAGATAATTAAGGTTTGGACCCTTGAAAAGG
195 AAAAGGTGAGATAATCAAGGTCTAGACCCTTGAAAAGC
* * *
59409 TCAATGCCTTTAGGAAGGCATAACAATTGTTTCAAGCCTAAAAAAATGATATGGTCAAAGTCTAG
1 TCAATGCCTTTAGGAAGGCATAACAATTGTCTCAAGCCTAAAAAAATGAGATGATCAAAGTCTAG
* * * ** *
59474 ACCTTTGGGAAGGTCCATGCTTTTAGGAAGGCATAGTAATTATCTTGAGCCTAAAATGACAAGAT
66 ACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAG-AAACATCTCGAGCCTAAAA-GACAAGAT
* * ** * *
59539 GATGAAAGTCTAGACCTTTGGGAA-GT-TTAGTGCCTATAAAAAGGCGTAGCAATTGTCTCAAGC
129 GATCAAAGTCTAGACCTTTAGGAACGTCAAAGT--CTATAAAAAGGCATAGCAATTGTATCAAGC
* * *
59602 CTGAAAAGGTGAGATGATCAAGGTCTAGACCTTTAGGAAAGC
192 CTGAAAAGGTGAGATAATCAAGGTCTAGACCCTT-GAAAAGC
* * * ** * *
59644 T-AATGCCTTTGGGAAGGCATAGCAATTGTCTCGAGCCTAAAAGGATGAGATGATCAAAGTTTGG
1 TCAATGCCTTTAGGAAGGCATAACAATTGTCTCAAGCCTAAAAAAATGAGATGATCAAAGTCTAG
59708 ACCTTTTAGGAAG
66 ACC-TTTAGGAAG
59721 ACATAGCAAC
Statistics
Matches: 252, Mismatches: 53, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
232 86 0.34
233 17 0.07
234 135 0.54
235 14 0.06
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (232 bp):
TCAATGCCTTTAGGAAGGCATAACAATTGTCTCAAGCCTAAAAAAATGAGATGATCAAAGTCTAG
ACCTTTAGGAAGGTCAATGCCTTTAGGAAGGCATAGAAACATCTCGAGCCTAAAAGACAAGATGA
TCAAAGTCTAGACCTTTAGGAACGTCAAAGTCTATAAAAAGGCATAGCAATTGTATCAAGCCTGA
AAAGGTGAGATAATCAAGGTCTAGACCCTTGAAAAGC
Found at i:59758 original size:139 final size:139
Alignment explanation
Indices: 59585--59842 Score: 349
Period size: 139 Copynumber: 1.9 Consensus size: 139
59575 TAAAAAGGCG
* * * * * * *
59585 TAGCAATTGTCTCAAGCCTGAAAAGGTGAGATGATCAAGGTCTAGACCTTTAGGAAAGCT-AATG
1 TAGCAACTGTCTCAAGCCTGAAAAAGTGAGATGATCAAAGTCTAAACC-TTAGCAAAGATCAATA
* * * *
59649 CCTTTGGGAAGGCATAGCAATTGTCTCGAGCCT-AAAAGGATGAGATGATCAAAGTTTGGACCTT
65 CATTTGGGAAGACATAACAATTGTCTCAAGCCTGAAAA-GATGAGATGATCAAAGTTTGGACCTT
59713 TTAGGAAGACA
129 TTAGGAAGACA
*
59724 TAGCAACTGTCTCAAGCCTGAAAAAGTGAGATGATCAAAGTTTAAACCTTAGCAAAGATCAATAC
1 TAGCAACTGTCTCAAGCCTGAAAAAGTGAGATGATCAAAGTCTAAACCTTAGCAAAGATCAATAC
* * *
59789 ATTTGGGAAGACTTAACAATTGTTTCAAGCCTGAAAATATGAGATGATCAAAGT
66 ATTTGGGAAGACATAACAATTGTCTCAAGCCTGAAAAGATGAGATGATCAAAGT
59843 CTAAACCTTT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
138 9 0.09
139 89 0.87
140 4 0.04
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (139 bp):
TAGCAACTGTCTCAAGCCTGAAAAAGTGAGATGATCAAAGTCTAAACCTTAGCAAAGATCAATAC
ATTTGGGAAGACATAACAATTGTCTCAAGCCTGAAAAGATGAGATGATCAAAGTTTGGACCTTTT
AGGAAGACA
Found at i:59773 original size:61 final size:61
Alignment explanation
Indices: 59655--59773 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
59645 AATGCCTTTG
* * * * **
59655 GGAAGGCATAGCAATTGTCTCGAGCCTAAAAGGATGAGATGATCAAAGTTTGGACCTTTTA
1 GGAAGACATAGCAACTGTCTCAAGCCTAAAAAGATGAGATGATCAAAGTTTAAACCTTTTA
59716 GGAAGACATAGCAACTGTCTCAAGCCTGAAAAAG-TGAGATGATCAAAGTTTAAACCTT
1 GGAAGACATAGCAACTGTCTCAAGCCT-AAAAAGATGAGATGATCAAAGTTTAAACCTT
59774 AGCAAAGATC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
61 46 0.90
62 5 0.10
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (61 bp):
GGAAGACATAGCAACTGTCTCAAGCCTAAAAAGATGAGATGATCAAAGTTTAAACCTTTTA
Found at i:62516 original size:20 final size:21
Alignment explanation
Indices: 62491--62530 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
62481 ATGATATTTG
*
62491 TATATACAGCT-AGGTTTTTA
1 TATATACAACTAAGGTTTTTA
*
62511 TATATATAACTAAGGTTTTT
1 TATATACAACTAAGGTTTTT
62531 GCATATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (21 bp):
TATATACAACTAAGGTTTTTA
Done.