Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3843.1
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: 98793
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 2887 characters in sequence are not A, C, G, or T
Found at i:338 original size:43 final size:43
Alignment explanation
Indices: 159--394 Score: 195
Period size: 43 Copynumber: 5.5 Consensus size: 43
149 AGAAAAACGT
* * * * * *
159 TGCTATAGAACATGACCTTTAGCGGTGTTTTTACTATAAATAC
1 TGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACAC
** * * * *
202 CACTATAGAACATGACTTTTAGCGGCGTTTTTCTCACTAACAC
1 TGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACAC
* * * * * **
245 TGCTACAAAACATGACCTTTAACGGC-ATTTTTCCACAAATGC
1 TGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACAC
* * *
287 TTCTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGC
1 TGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACAC
* * ** * *
330 TGCTATAGAACAAGACATTTAGCAACACTTTTCTCACAAACAC
1 TGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACAC
* *
373 CGTTATAGAACATGACCTTTAG
1 TGCTATAGAACATGACCTTTAG
395 TGTGCTCTCC
Statistics
Matches: 151, Mismatches: 41, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
42 31 0.21
43 120 0.79
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (43 bp):
TGCTATAGAACATGACCTTTAGCGGCGCTTTTCCCACAAACAC
Found at i:362 original size:85 final size:86
Alignment explanation
Indices: 204--369 Score: 199
Period size: 85 Copynumber: 1.9 Consensus size: 86
194 ATAAATACCA
* * * * * * * *
204 CTATAGAACATGACTTTTAGCGGCGTTTTTCTCACTAACACTGCTACAAAACATGACCTTTAACG
1 CTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACACTGCTACAAAACAAGACATTTAACA
* *
269 GCATTTTTC-CACAAATGCTT
66 ACACTTTTCTCACAAATGCTT
* * * *
289 CTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCTGCTATAGAACAAGACATTTAGCA
1 CTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACACTGCTACAAAACAAGACATTTAACA
354 ACACTTTTCTCACAAA
66 ACACTTTTCTCACAAA
370 CACCGTTATA
Statistics
Matches: 66, Mismatches: 14, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
85 60 0.91
86 6 0.09
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (86 bp):
CTATAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACACTGCTACAAAACAAGACATTTAACA
ACACTTTTCTCACAAATGCTT
Found at i:476 original size:42 final size:41
Alignment explanation
Indices: 428--522 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 41
418 ATAGAGTACG
*
428 ACCTTTAGCGACACTTTTTCCACAAACGCCTCTATAAAA-TAA
1 ACCTTTAGCGACACTTTTTCCA-AAA-ACCTCTATAAAATTAA
** *
470 ACCTTTAGCGACACTTTTTTTAAAAACCTTTATAAAATTAA
1 ACCTTTAGCGACACTTTTTCCAAAAACCTCTATAAAATTAA
*
511 ACCTTTAACGAC
1 ACCTTTAGCGAC
523 GCCTTCCTCA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
40 10 0.21
41 17 0.36
42 20 0.43
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (41 bp):
ACCTTTAGCGACACTTTTTCCAAAAACCTCTATAAAATTAA
Found at i:3644 original size:18 final size:18
Alignment explanation
Indices: 3621--3656 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3611 GCATTGTAAA
3621 ACAGATTCATGAATCGCT
1 ACAGATTCATGAATCGCT
3639 ACAGATTCATGAATCGCT
1 ACAGATTCATGAATCGCT
3657 TTCAGCAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
ACAGATTCATGAATCGCT
Found at i:4250 original size:35 final size:35
Alignment explanation
Indices: 4199--4268 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
4189 GACGAGCTTG
4199 CTGCTTGCGAGCTGCGCAACTGACTACCGATTGCA
1 CTGCTTGCGAGCTGCGCAACTGACTACCGATTGCA
* * *
4234 CTGCTTGCGAGTTGCGCCACTGACTACCTATTGCA
1 CTGCTTGCGAGCTGCGCAACTGACTACCGATTGCA
4269 AGGGCTGAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.26
Consensus pattern (35 bp):
CTGCTTGCGAGCTGCGCAACTGACTACCGATTGCA
Found at i:10601 original size:47 final size:47
Alignment explanation
Indices: 10503--10715 Score: 145
Period size: 47 Copynumber: 4.6 Consensus size: 47
10493 GTGCCAATGT
* **
10503 CATGTCCCAGACATGGTCTTACACTGGCTCATATCTAAAGTTGATGC
1 CATGTCCCAGACATGGTCTTACACTGACTCATATCTAAAGCCGATGC
* *
10550 CATGTCCCAGACATGGTCTTACACTGACT-ATCATTTCATAGCCGATG-
1 CATGTCCCAGACATGGTCTTACACTGACTCAT-ATCT-AAAGCCGATGC
* * *** * *
10597 CATGTCCCAAACAT-GTCTTACACT-AGCTTACGCCTCGAGGCCGATG-
1 CATGTCCCAGACATGGTCTTACACTGA-CTCATATCT-AAAGCCGATGC
* * * *
10643 CATGTCCCA-AGCAT-GTCTTACACTAGCCCTCGTCTC-AATGCCGATGC
1 CATGTCCCAGA-CATGGTCTTACACT-G-ACTCATATCTAAAGCCGATGC
* *
10690 CATGTTCCAGACATGATCTTACACTG
1 CATGTCCCAGACATGGTCTTACACTG
10716 GCTCTCATAA
Statistics
Matches: 132, Mismatches: 23, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
45 2 0.02
46 53 0.40
47 57 0.43
48 20 0.15
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACTGACTCATATCTAAAGCCGATGC
Found at i:10640 original size:46 final size:46
Alignment explanation
Indices: 10590--10714 Score: 153
Period size: 46 Copynumber: 2.7 Consensus size: 46
10580 TCATTTCATA
* *
10590 GCCGATGCATGTCCCAAACATGTCTTACACTAG-CTTACGCCTCGAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCCCT-CGCCTCAAG
* * *
10636 GCCGATGCATGTCCCAAGCATGTCTTACACTAGCCCTCGTCTCAAT
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCCCTCGCCTCAAG
* *
10682 GCCGATGCCATGTTCCAGACATGATCTTACACT
1 GCCGATG-CATGTCCCAAACATG-TCTTACACT
10715 GGCTCTCATA
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
46 45 0.66
47 14 0.21
48 9 0.13
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (46 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCCCTCGCCTCAAG
Found at i:25612 original size:20 final size:19
Alignment explanation
Indices: 25589--25647 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 19
25579 TTAAATTCTA
25589 AAAGATAAATACAAATAAAT
1 AAAGATAAATA-AAATAAAT
*
25609 AAAGATAATTAAAGATAAAT
1 AAAGATAAATAAA-ATAAAT
*
25629 AAGGATAAATAAAAATAAA
1 AAAGATAAAT-AAAATAAA
25648 AGCTAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.85
21 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.20
Consensus pattern (19 bp):
AAAGATAAATAAAATAAAT
Found at i:25623 original size:30 final size:30
Alignment explanation
Indices: 25589--25646 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
25579 TTAAATTCTA
*
25589 AAAGATAAATACA-AATAAATAAAGATAATT
1 AAAGATAAATA-AGAATAAATAAAAATAATT
*
25619 AAAGATAAATAAGGATAAATAAAAATAA
1 AAAGATAAATAAGAATAAATAAAAATAA
25647 AAGCTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.69, C:0.02, G:0.09, T:0.21
Consensus pattern (30 bp):
AAAGATAAATAAGAATAAATAAAAATAATT
Found at i:26144 original size:33 final size:32
Alignment explanation
Indices: 26003--26365 Score: 120
Period size: 33 Copynumber: 10.8 Consensus size: 32
25993 ACATTCGTAG
* *
26003 TGCCATAACCCAGTTATGGTCTTATCGTCAGAA
1 TGCCATAACCCAGTTATGGTCTTA-CATTAGAA
* * * * *
26036 TGTCATAGCCTAGCTATGGTCTTACATATAAACA
1 TGCCATAACCCAGTTATGGTCTTACAT-TAGA-A
*** *** * * *
26070 CTGCCATGGTCCAACCATGGTCTTACGTTTATAG
1 -TGCCATAACCCAGTTATGGTCTTAC-ATTAGAA
*
26104 TGTCATAACCCAGTTATGGTCTTATCATTAGAA
1 TGCCATAACCCAGTTATGGTCTTA-CATTAGAA
* * *
26137 TGCCATAACCCAACTT-TGGTCTTACATAAAAACA
1 TGCCATAACCC-AGTTATGGTCTTACAT-TAGA-A
*** * *** * * *
26171 TTGCCATGGTCTAACCATGGTCTTACGTTCATAG
1 -TGCCATAACCCAGTTATGGTCTTACATT-AGAA
*
26205 TGTCATAACCCAGTTATGGTCTTATCATTAGAA
1 TGCCATAACCCAGTTATGGTCTTA-CATTAGAA
* * *
26238 TGCCATAACCCAACTT-TGGTCTTACATAAAAACA
1 TGCCATAACCC-AGTTATGGTCTTACAT-TAGA-A
*** * *** * * *
26272 TTGCCATGGTCTAACCATGGTCTTACGTTCATAG
1 -TGCCATAACCCAGTTATGGTCTTACATT-AGAA
*
26306 TGTCATAACCCAGTTATGGTCTTATCATTAGAA
1 TGCCATAACCCAGTTATGGTCTTA-CATTAGAA
*
26339 TGCCATAACCCAACTT-TGGTCTTACAT
1 TGCCATAACCC-AGTTATGGTCTTACAT
26366 AAAAACATTG
Statistics
Matches: 230, Mismatches: 80, Indels: 41
0.66 0.23 0.12
Matches are distributed among these distances:
32 11 0.05
33 137 0.60
34 21 0.09
35 60 0.26
36 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (32 bp):
TGCCATAACCCAGTTATGGTCTTACATTAGAA
Found at i:26176 original size:101 final size:101
Alignment explanation
Indices: 25991--26432 Score: 758
Period size: 101 Copynumber: 4.4 Consensus size: 101
25981 AATTCATCCT
* * * * * * * * * *
25991 TTACATTCGTAGTGCCATAACCCAGTTATGGTCTTATCGTCAGAATGTCATAGCCTAGCTATGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
* * *
26056 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
*
26092 TTACGTTTATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
26157 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
66 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
26193 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
26258 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
66 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
26294 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
26359 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
66 CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
26395 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATC
26433 CGTCAATTCA
Statistics
Matches: 326, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 326 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (101 bp):
TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATTAGAATGCCATAACCCAACTTTGGT
CTTACATAAAAACATTGCCATGGTCTAACCATGGTC
Found at i:28390 original size:19 final size:19
Alignment explanation
Indices: 28366--28408 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
28356 TTTCTTTCCT
28366 TATATA-CTAAATAAAATAA
1 TATATATCT-AATAAAATAA
*
28385 TATATATCTAATTAAATAA
1 TATATATCTAATAAAATAA
28404 T-TATA
1 TATATA
28409 AAATATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 16 0.73
20 2 0.09
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATATCTAATAAAATAA
Found at i:36579 original size:30 final size:29
Alignment explanation
Indices: 36545--36633 Score: 112
Period size: 26 Copynumber: 3.1 Consensus size: 29
36535 ATAAATTTGG
36545 ATAATTTTTTAATTATTTAAATAATGAAAA
1 ATAATTTTTT-ATTATTTAAATAATGAAAA
*
36575 ATAATGTTATTTATTATTTAAATTAT-AAAA
1 ATAAT-TT-TTTATTATTTAAATAATGAAAA
*
36605 AT-A-TATTTATTATTTAAATAATGAAAA
1 ATAATTTTTTATTATTTAAATAATGAAAA
36632 AT
1 AT
36634 TTTAGAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
26 16 0.30
27 7 0.13
29 1 0.02
30 11 0.21
31 15 0.28
32 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
ATAATTTTTTATTATTTAAATAATGAAAA
Found at i:36667 original size:8 final size:8
Alignment explanation
Indices: 36654--36701 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
36644 AAATACATTG
36654 TTTTTAAT
1 TTTTTAAT
36662 TTTTTAATT
1 TTTTTAA-T
36671 TTTTTAAT
1 TTTTTAAT
**
36679 TTTAAAAT
1 TTTTTAAT
*
36687 ATTTTAAT
1 TTTTTAAT
36695 TTTTTAA
1 TTTTTAA
36702 ATGATGAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
8 25 0.76
9 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTTTAAT
Found at i:36676 original size:17 final size:17
Alignment explanation
Indices: 36654--36703 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
36644 AAATACATTG
*
36654 TTTTTAATTTTTTAATT
1 TTTTTAATTTTTTAAAT
*
36671 TTTTTAA-TTTTAAAAT
1 TTTTTAATTTTTTAAAT
*
36687 ATTTTAATTTTTTAAAT
1 TTTTTAATTTTTTAAAT
36704 GATGAGATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTAATTTTTTAAAT
Found at i:48539 original size:122 final size:120
Alignment explanation
Indices: 48324--48547 Score: 344
Period size: 122 Copynumber: 1.9 Consensus size: 120
48314 CCAAAATAAC
* * *
48324 CATGAGAATGAGAATAGTAATGTAATGGGTATGAGGTTTTCCTAATCTCTATTTAACACGGAACG
1 CATGAGAATGAAAATAGTAATGTAATGGGTATGAGGTTTTCCTAATCTCAATTTAACACGAAACG
48389 TATGATAACTAACCTAAGAATGAAAATTAAATGATAGGCATTGGCATGGTAATAG
66 TATGATAACTAACCTAAGAATGAAAATTAAATGATAGGCATTGGCATGGTAATAG
*
48444 CATGAGAAT-AAACATAGTAATGTCATGGGTATGAGG-TTTCTCTAATAACTCAATTTAACACGA
1 CATGAGAATGAAA-ATAGTAATGTAATGGGTATGAGGTTTTC-CTAAT--CTCAATTTAACACGA
* *
48507 AATGTATGATAACTAACCTAAGAATGCAAATTAAATGATAG
62 AACGTATGATAACTAACCTAAGAATGAAAATTAAATGATAG
48548 AATAATGAGG
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
119 6 0.06
120 36 0.38
122 52 0.55
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (120 bp):
CATGAGAATGAAAATAGTAATGTAATGGGTATGAGGTTTTCCTAATCTCAATTTAACACGAAACG
TATGATAACTAACCTAAGAATGAAAATTAAATGATAGGCATTGGCATGGTAATAG
Found at i:49076 original size:55 final size:55
Alignment explanation
Indices: 48991--49101 Score: 125
Period size: 55 Copynumber: 2.0 Consensus size: 55
48981 CGTGTCAATC
* * * *
48991 TAACAGGTTCGACCACGGGTGCTAGCCACGGGCGTGTCGCACGCCGGTGCTGTTT
1 TAACAGGTTCGACCACGGGTGCTACCCACGGGCATGTCACACGCCCGTGCTGTTT
* * * * *
49046 TAACAGGTTCGCCCAC-GGTTCTTCCACACGGGCATGTCACATGCCCGTGTTGTTT
1 TAACAGGTTCGACCACGGGTGCTACC-CACGGGCATGTCACACGCCCGTGCTGTTT
49101 T
1 T
49102 GGCAAGCTCG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
54 6 0.13
55 40 0.87
ACGTcount: A:0.15, C:0.30, G:0.29, T:0.26
Consensus pattern (55 bp):
TAACAGGTTCGACCACGGGTGCTACCCACGGGCATGTCACACGCCCGTGCTGTTT
Found at i:53407 original size:27 final size:27
Alignment explanation
Indices: 53377--53554 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
53367 ATATTGAGTC
* * * *
53377 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
53404 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53431 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
53459 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
53486 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
53513 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
53540 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
53555 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:53516 original size:82 final size:81
Alignment explanation
Indices: 53398--53553 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
53388 TGCTATATAA
* *
53398 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
53463 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
53480 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
53544 CACTTAGTGC
65 CACTTAGTGC
53554 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:62424 original size:74 final size:73
Alignment explanation
Indices: 62303--62448 Score: 238
Period size: 74 Copynumber: 2.0 Consensus size: 73
62293 AGACACGCTT
*
62303 TTATTCAGAGGAGAAATAGACCTTATCTAAGAGTACATTTGCCATAATTAAGCAGAGTTGATTGC
1 TTATTCAGAGGAGAAATAGACCCTATCTAAGAGTACATTTGCCATAATTAAGCAGAGTTGATTGC
62368 GCGCCTAGC
66 G-GCCTAGC
* * **
62377 TTATTCAGAGGAGGAATAGACCCTGTCTAAGAGTACATTTGCCATAATTAAGTGGAGTTGATTGC
1 TTATTCAGAGGAGAAATAGACCCTATCTAAGAGTACATTTGCCATAATTAAGCAGAGTTGATTGC
62442 GGCCTAG
66 GGCCTAG
62449 AAATAGGGTG
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 6 0.09
74 61 0.91
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (73 bp):
TTATTCAGAGGAGAAATAGACCCTATCTAAGAGTACATTTGCCATAATTAAGCAGAGTTGATTGC
GGCCTAGC
Found at i:63069 original size:5 final size:5
Alignment explanation
Indices: 63059--63088 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
63049 TTTTTCTTAC
63059 AATTT AATTT AATTT AATTT AATTT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
63089 TACTATTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
AATTT
Found at i:68223 original size:5 final size:5
Alignment explanation
Indices: 68213--68238 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
68203 TTTTAGAAAG
68213 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
68239 ATTAATTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:71418 original size:292 final size:292
Alignment explanation
Indices: 70889--71473 Score: 1125
Period size: 292 Copynumber: 2.0 Consensus size: 292
70879 TCCCAAAAGC
* * *
70889 AATTCCCCAATTTTTTTCTCTGTGCATTCTTAGTTTAGATAATTAGTTAATTAAAATAAACCCTT
1 AATTCCCCAATTCTTTTCTCTATGCATTCTTAGTTTAGATAATTAGTTAATTAAAACAAACCCTT
70954 TTATTCTTAGGCTAGATAATAAAGAGATAGTTATTACTAGTACTTTTGGTTCCCTTGGGTACGAT
66 TTATTCTTAGGCTAGATAATAAAGAGATAGTTATTACTAGTACTTTTGGTTCCCTTGGGTACGAT
*
71019 ATCCCGGTCTTGCCATTACTATACTATTGTTCGATAGGTGCGCTTGCTTTTTCGTCGTGATAATA
131 ATCACGGTCTTGCCATTACTATACTATTGTTCGATAGGTGCGCTTGCTTTTTCGTCGTGATAATA
71084 GTTAGTCTAGGTTTGATCTTCAATATAAATATTTATTACTTGTTACGAATCACGAGATCATCGTA
196 GTTAGTCTAGGTTTGATCTTCAATATAAATATTTATTACTTGTTACGAATCACGAGATCATCGTA
71149 ATAGTGATCTTCTCAAGTACGCACTCCCGCGA
261 ATAGTGATCTTCTCAAGTACGCACTCCCGCGA
*
71181 AATTTCCCAATTCTTTTCTCTATGCATTCTTAGTTTAGATAATTAGTTAATTAAAACAAACCCTT
1 AATTCCCCAATTCTTTTCTCTATGCATTCTTAGTTTAGATAATTAGTTAATTAAAACAAACCCTT
71246 TTATTCTTAGGCTAGATAATAAAGAGATAGTTATTACTAGTACTTTTGGTTCCCTTGGGTACGAT
66 TTATTCTTAGGCTAGATAATAAAGAGATAGTTATTACTAGTACTTTTGGTTCCCTTGGGTACGAT
71311 ATCACGGTCTTGCCATTACTATACTATTGTTCGATAGGTGCGCTTGCTTTTTCGTCGTGATAATA
131 ATCACGGTCTTGCCATTACTATACTATTGTTCGATAGGTGCGCTTGCTTTTTCGTCGTGATAATA
71376 GTTAGTCTAGGTTTGATCTTCAATATAAATATTTATTACTTGTTACGAATCACGAGATCATCGTA
196 GTTAGTCTAGGTTTGATCTTCAATATAAATATTTATTACTTGTTACGAATCACGAGATCATCGTA
71441 ATAGTGATCTTCTCAAGTACGCACTCCCGCGA
261 ATAGTGATCTTCTCAAGTACGCACTCCCGCGA
71473 A
1 A
71474 CCTCACATCT
Statistics
Matches: 288, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
292 288 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (292 bp):
AATTCCCCAATTCTTTTCTCTATGCATTCTTAGTTTAGATAATTAGTTAATTAAAACAAACCCTT
TTATTCTTAGGCTAGATAATAAAGAGATAGTTATTACTAGTACTTTTGGTTCCCTTGGGTACGAT
ATCACGGTCTTGCCATTACTATACTATTGTTCGATAGGTGCGCTTGCTTTTTCGTCGTGATAATA
GTTAGTCTAGGTTTGATCTTCAATATAAATATTTATTACTTGTTACGAATCACGAGATCATCGTA
ATAGTGATCTTCTCAAGTACGCACTCCCGCGA
Found at i:86796 original size:79 final size:79
Alignment explanation
Indices: 86674--86830 Score: 287
Period size: 79 Copynumber: 2.0 Consensus size: 79
86664 CAACGAGCTC
* *
86674 GGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
1 GGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
86739 TCAAACTCGGACTT
66 TCAAACTCGGACTT
86753 GGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
1 GGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
*
86818 TCGAACTCGGACT
66 TCAAACTCGGACT
86831 CAACTCAACG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (79 bp):
GGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
TCAAACTCGGACTT
Found at i:88565 original size:152 final size:152
Alignment explanation
Indices: 88289--88591 Score: 597
Period size: 152 Copynumber: 2.0 Consensus size: 152
88279 CTGAAAGCTT
*
88289 ATAGTCTCAACTCTCAACTGTTCTTAAATTTTCAACCCTTCTCAGTTTCCCATTATATCATGACA
1 ATAGTCTCAACTCTCAACTATTCTTAAATTTTCAACCCTTCTCAGTTTCCCATTATATCATGACA
88354 TAAAACCCGGATCTTAACTTGATTAATGGAGAACGGAATTCCAAGAAATCCAACAATCAAAGAGA
66 TAAAACCCGGATCTTAACTTGATTAATGGAGAACGGAATTCCAAGAAATCCAACAATCAAAGAGA
88419 CCTGAAATTCCGTGAATCTGAG
131 CCTGAAATTCCGTGAATCTGAG
88441 ATAGTCTCAACTCTCAACTATTCTTAAATTTTCAACCCTTCTCAGTTTCCCATTATATCATGACA
1 ATAGTCTCAACTCTCAACTATTCTTAAATTTTCAACCCTTCTCAGTTTCCCATTATATCATGACA
88506 TAAAACCCGGATCTTAACTTGATTAATGGAGAACGGAATTCCAAGAAATCCAACAATCAAAGAGA
66 TAAAACCCGGATCTTAACTTGATTAATGGAGAACGGAATTCCAAGAAATCCAACAATCAAAGAGA
88571 CCTGAAATTCCGTGAATCTGA
131 CCTGAAATTCCGTGAATCTGA
88592 TAAGTAGGAA
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 150 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (152 bp):
ATAGTCTCAACTCTCAACTATTCTTAAATTTTCAACCCTTCTCAGTTTCCCATTATATCATGACA
TAAAACCCGGATCTTAACTTGATTAATGGAGAACGGAATTCCAAGAAATCCAACAATCAAAGAGA
CCTGAAATTCCGTGAATCTGAG
Found at i:89431 original size:30 final size:30
Alignment explanation
Indices: 89387--89475 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
89377 CAAAGATAAT
89387 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
89416 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
89446 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
89476 CGACATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:89435 original size:15 final size:15
Alignment explanation
Indices: 89387--89466 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
89377 CAAAGATAAT
*
89387 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
89401 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
89416 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
89431 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
89446 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
89461 AAGAAA
1 AAGAAA
89467 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:89475 original size:15 final size:15
Alignment explanation
Indices: 89398--89475 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
89388 AGAAAACCGA
89398 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
89413 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
89427 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
89442 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
89458 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
89473 ATA
1 ATA
89476 CGACATTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:95186 original size:30 final size:30
Alignment explanation
Indices: 95142--95230 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
95132 CAAAGATAAT
95142 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
95171 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
95201 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
95231 CGATATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:95190 original size:15 final size:15
Alignment explanation
Indices: 95142--95221 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
95132 CAAAGATAAT
*
95142 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
95156 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
95171 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
95186 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
95201 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
95216 AAGAAA
1 AAGAAA
95222 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:95230 original size:15 final size:15
Alignment explanation
Indices: 95153--95230 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
95143 AGAAAACCGA
95153 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
95168 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
95182 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
95197 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
95213 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
95228 ATA
1 ATA
95231 CGATATTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:97360 original size:20 final size:20
Alignment explanation
Indices: 97313--97360 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
97303 AGTAAGCTCG
97313 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
97333 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
97353 GTTGAGCT
1 GTTGAGCT
97361 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Done.