Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold525
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: 92575
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 4326 characters in sequence are not A, C, G, or T
Found at i:5938 original size:44 final size:45
Alignment explanation
Indices: 5889--5973 Score: 106
Period size: 44 Copynumber: 1.9 Consensus size: 45
5879 TGCTTGTACG
5889 AATCTGCTATGAT-T-GTGAAGTTT-TTCTATGAATTT-GCATGTTTA
1 AATCTGCT-TGATCTAG-GAAGTTTCTTCTATG-ATTTCGCATGTTTA
*
5933 AATCTGCTTTATCTAGGAAGTTTCTTCTATGATTTCGCATG
1 AATCTGCTTGATCTAGGAAGTTTCTTCTATGATTTCGCATG
5974 AATGGACTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
43 3 0.08
44 20 0.56
45 13 0.36
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.46
Consensus pattern (45 bp):
AATCTGCTTGATCTAGGAAGTTTCTTCTATGATTTCGCATGTTTA
Found at i:8298 original size:45 final size:45
Alignment explanation
Indices: 8242--8338 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
8232 GCTTCAGAAG
* *
8242 TGGCTCCAATGGTGTTCTTTGAGTGTTTCCTTCGATCTTATCTGA
1 TGGCTCCAATGGTGTTCCTTGAGTGTTTCCTTCGATCTGATCTGA
* * * *
8287 TGGCTCTAATGGTGTTCCTTGAGTGTTTTCTTTGATCTGCTCTGA
1 TGGCTCCAATGGTGTTCCTTGAGTGTTTCCTTCGATCTGATCTGA
8332 TGGCTCC
1 TGGCTCC
8339 CCTGTCTCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.44
Consensus pattern (45 bp):
TGGCTCCAATGGTGTTCCTTGAGTGTTTCCTTCGATCTGATCTGA
Found at i:8500 original size:30 final size:30
Alignment explanation
Indices: 8449--8512 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
8439 CACGGGCTGG
* * *
8449 CACAGGGGCGTGTGTCCAGCCTATGTGTCT
1 CACAGGGGCATGTGCCCAGCCTATGTGGCT
*
8479 CACATGGGCATGTGCCCAGCCTATGTGGCT
1 CACAGGGGCATGTGCCCAGCCTATGTGGCT
8509 CACA
1 CACA
8513 AAATCTGCCG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (30 bp):
CACAGGGGCATGTGCCCAGCCTATGTGGCT
Found at i:10336 original size:6 final size:6
Alignment explanation
Indices: 10325--10393 Score: 66
Period size: 6 Copynumber: 11.0 Consensus size: 6
10315 CTTTAAGAAC
* *
10325 ATAAAA ATAAAA TAGCTAAAA ATAAAA ATAAAG ATAAAA ATAAAA CTAAAA
1 ATAAAA ATAAAA -A--TAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * *
10376 CTAAAA CTAAAA CTAAAA
1 ATAAAA ATAAAA ATAAAA
10394 GGAAAATAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
6 50 0.88
7 1 0.02
8 1 0.02
9 5 0.09
ACGTcount: A:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (6 bp):
ATAAAA
Found at i:10393 original size:18 final size:18
Alignment explanation
Indices: 10340--10393 Score: 74
Period size: 18 Copynumber: 3.0 Consensus size: 18
10330 AATAAAATAG
*
10340 CTAAAAATAAAAATAAAGA
1 CTAAAAATAAAACTAAA-A
10359 -TAAAAATAAAACTAAAA
1 CTAAAAATAAAACTAAAA
*
10376 CTAAAACTAAAACTAAAA
1 CTAAAAATAAAACTAAAA
10394 GGAAAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 1 0.03
18 31 0.97
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (18 bp):
CTAAAAATAAAACTAAAA
Found at i:10399 original size:18 final size:17
Alignment explanation
Indices: 10361--10403 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
10351 AATAAAGATA
*
10361 AAAATAAAACTAAAACT
1 AAAATAAAACTAAAACG
*
10378 AAAACTAAAACTAAAAGG
1 AAAA-TAAAACTAAAACG
10396 AAAATAAA
1 AAAATAAA
10404 TAAACTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAATAAAACTAAAACG
Found at i:11839 original size:50 final size:50
Alignment explanation
Indices: 11730--11827 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
11720 GAGATCCCAT
* * **
11730 GTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAACTCCCCC
* * *
11780 GTAAGACCATGTCTGGGACATGGCATGGGCCCCGATATGAGAACTCCC
1 GTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAACTCCC
11828 TTTTAAGACC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.24, C:0.27, G:0.31, T:0.18
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCACCAAGATGAGAACTCCCCC
Found at i:15817 original size:27 final size:27
Alignment explanation
Indices: 15787--15841 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
15777 GTCCAGGCCG
*
15787 TGTGGACCATTTTAGGACTTATAACCT
1 TGTGAACCATTTTAGGACTTATAACCT
* *
15814 TGTGAACCATTTTAGGCCTTGTAACCT
1 TGTGAACCATTTTAGGACTTATAACCT
15841 T
1 T
15842 CGAAAATTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (27 bp):
TGTGAACCATTTTAGGACTTATAACCT
Found at i:20919 original size:51 final size:51
Alignment explanation
Indices: 20831--21030 Score: 251
Period size: 51 Copynumber: 3.9 Consensus size: 51
20821 CCCTTATGAT
* *
20831 CAATGCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGAC
1 CAATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
* * * * *
20882 CAATACCATCCGGTACACATAGTAGCCTGCACATAGTACTACATACGTAAC
1 CAATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
* *
20933 CAA-AGCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGAC
1 CAATA-CTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
*** *
20984 C-ATAACTATCTTATACTCATAGTAGCCTACACATAGTACTACACATG
1 CAAT-ACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATG
21031 AGTTCTCATG
Statistics
Matches: 128, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.02
51 125 0.98
52 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.25
Consensus pattern (51 bp):
CAATACTATCCGGTACACATAGTAGCCTACACATAGTACTACACATGTGAC
Found at i:21011 original size:102 final size:102
Alignment explanation
Indices: 20835--21026 Score: 305
Period size: 102 Copynumber: 1.9 Consensus size: 102
20825 TATGATCAAT
*
20835 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGGTACAC
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGATACAC
*
20900 ATAGTAGCCTGCACATAGTACTACATACGTAACCAAA
66 ATAGTAGCCTACACATAGTACTACATACGTAACCAAA
* * ** *
20937 GCTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGTGACC-ATAACTATCTTATACT
1 GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAAT-ACCATCCGATACA
21001 CATAGTAGCCTACACATAGTACTACA
65 CATAGTAGCCTACACATAGTACTACA
21027 CATGAGTTCT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 2 0.02
102 80 0.98
ACGTcount: A:0.33, C:0.28, G:0.14, T:0.25
Consensus pattern (102 bp):
GCTATCCGGTACACATAGTAGCCTACACTTAGTACTACACATGTGACCAATACCATCCGATACAC
ATAGTAGCCTACACATAGTACTACATACGTAACCAAA
Found at i:26315 original size:25 final size:25
Alignment explanation
Indices: 26287--26334 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
26277 TCTCTCTCAC
* *
26287 GAGCCATATAACGGGAATCTCATGT
1 GAGCCATATAACAGGAAGCTCATGT
*
26312 GAGCCATGTAACAGGAAGCTCAT
1 GAGCCATATAACAGGAAGCTCAT
26335 AAAGGCTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACAGGAAGCTCATGT
Found at i:30022 original size:34 final size:34
Alignment explanation
Indices: 29976--30077 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 34
29966 CTCTGGATCA
* *
29976 ATTATCTCATACGAGCATTTGGTGTGCTAGATGG
1 ATTAGCTCATACGAGTATTTGGTGTGCTAGATGG
* * * * *
30010 ATTAGGTTATACGAGTATTTAGTGTGTTGGATGG
1 ATTAGCTCATACGAGTATTTGGTGTGCTAGATGG
* *
30044 ATTAGCTCATACGAGTATCTGGTGTGCTAAATGG
1 ATTAGCTCATACGAGTATTTGGTGTGCTAGATGG
30078 TTAATCGTGT
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
34 54 1.00
ACGTcount: A:0.25, C:0.11, G:0.28, T:0.36
Consensus pattern (34 bp):
ATTAGCTCATACGAGTATTTGGTGTGCTAGATGG
Found at i:34923 original size:28 final size:28
Alignment explanation
Indices: 34876--34932 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
34866 CCTTTCTCTG
* *
34876 GTTAGCACTTACTGATCTGTTAGTATTT
1 GTTAGCACTTAATGACCTGTTAGTATTT
34904 GTTAGCACTTAATGACCTGTTAGTATTT
1 GTTAGCACTTAATGACCTGTTAGTATTT
34932 G
1 G
34933 ATGCTAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (28 bp):
GTTAGCACTTAATGACCTGTTAGTATTT
Found at i:36161 original size:20 final size:20
Alignment explanation
Indices: 36136--36174 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
36126 AAATATTTTC
36136 GTAAATCATTTTCCAGAAAA
1 GTAAATCATTTTCCAGAAAA
36156 GTAAATCATTTTCCAGAAA
1 GTAAATCATTTTCCAGAAA
36175 TTATTTTACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
GTAAATCATTTTCCAGAAAA
Found at i:37037 original size:15 final size:14
Alignment explanation
Indices: 37011--37057 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
37001 TAATTAGGGA
*
37011 TTAATTAATTAAGT
1 TTAATTAATTAAGC
37025 TTAATTAACTTAAGC
1 TTAATTAA-TTAAGC
* *
37040 TTAACTAATTAACC
1 TTAATTAATTAAGC
37054 TTAA
1 TTAA
37058 GATAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (14 bp):
TTAATTAATTAAGC
Found at i:43790 original size:30 final size:28
Alignment explanation
Indices: 43718--43793 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 28
43708 AAAAGCATCT
* *
43718 AAAATAGTAGCAAAATGAACAATAAAAC
1 AAAATAGTAGCAATATAAACAATAAAAC
43746 AAAAGTTA-TA-CAATATCAAACAATAACAAC
1 AAAA--TAGTAGCAATAT-AAACAATAA-AAC
43776 AAAATAGTAGCAATATAA
1 AAAATAGTAGCAATATAA
43794 TAGCAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
28 11 0.28
29 14 0.35
30 15 0.38
ACGTcount: A:0.62, C:0.12, G:0.08, T:0.18
Consensus pattern (28 bp):
AAAATAGTAGCAATATAAACAATAAAAC
Found at i:54640 original size:17 final size:17
Alignment explanation
Indices: 54618--54653 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
54608 GAGACTGAAG
54618 GCCTTGTAAAACAATAT
1 GCCTTGTAAAACAATAT
54635 GCCTTGTAAAACAATAT
1 GCCTTGTAAAACAATAT
54652 GC
1 GC
54654 ACAGAAGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (17 bp):
GCCTTGTAAAACAATAT
Found at i:56831 original size:7 final size:7
Alignment explanation
Indices: 56819--56856 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
56809 GGATTTCAAA
56819 AAAAATG
1 AAAAATG
56826 AAAAATG
1 AAAAATG
*
56833 -AGAATG
1 AAAAATG
56839 AAAAAATG
1 -AAAAATG
56847 AAAAATG
1 AAAAATG
56854 AAA
1 AAA
56857 GAGTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 5 0.19
7 17 0.63
8 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:58231 original size:87 final size:87
Alignment explanation
Indices: 58085--58527 Score: 663
Period size: 87 Copynumber: 5.1 Consensus size: 87
58075 AGATCAGTGA
58085 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* *
58150 CTTTCTGCGTTAGCAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
58172 AGATC-AGAAACGAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCGA-AAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTG
58236 CCTTCCTGCGTTAACAGCGAAGC
65 CCTTCCTGCGTTAACAGCGAAGC
* * *
58259 AGATCGAAAACAAAGCCTTACCTCCACCGGTTGTAGTGGAGCTGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
58324 CTTCCTGTGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * * * *
58346 AGATCGAAAACAAAGCCTTGCCTCCATCGTTTGCAGTGGAACTGGTTAAAAAAAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
*
58411 CTTCCTGTGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * * * *
58433 AGATCGAAAACGAAGCCTTGCCTCTATCGTTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGT
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
* ** *
58498 CATCCTGCGTCGACAGTGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
*
58520 AAATCGAA
1 AGATCGAA
58528 GATTACAAGT
Statistics
Matches: 326, Mismatches: 28, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
86 1 0.00
87 324 0.99
88 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:58455 original size:43 final size:43
Alignment explanation
Indices: 58319--58455 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 43
58309 GATAGTAGAT
*
58319 CTTGCCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACGAAGC
* * * * ** * * *
58362 CTTGCC-TCCATCGT-TT-GCAGTGGAA-CTGGTTAAAAAAAGCAGAT
1 CTTGCCTTCC-T-GTGTTAACAG-CGAAGC-AGATCGAAAACGAAG-C
58406 CTTGCCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACGAAGC
1 CTTGCCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACGAAGC
58449 CTTGCCT
1 CTTGCCT
58456 CTATCGTTTG
Statistics
Matches: 66, Mismatches: 19, Indels: 18
0.64 0.18 0.17
Matches are distributed among these distances:
42 7 0.11
43 29 0.44
44 23 0.35
45 7 0.11
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (43 bp):
CTTGCCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACGAAGC
Found at i:58784 original size:44 final size:44
Alignment explanation
Indices: 58707--58821 Score: 142
Period size: 44 Copynumber: 2.6 Consensus size: 44
58697 ATCACATCGG
* * *
58707 GTCTTATCTCCCTGAAGTTGCAGCGGAGTAGACT-AAGAAAACAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAG-AAACAA
* ** *
58751 GTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAGCAA
1 GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGAAACAA
*
58795 ATCTTATCTCCCTGAAGTTGCAGTGGG
1 GTCTTATCTCCCTGAAGTTGCAGTGGG
58822 TAGATTGGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 56 0.95
45 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.23
Consensus pattern (44 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGGGCAGACTGAAGAAACAA
Found at i:59094 original size:22 final size:22
Alignment explanation
Indices: 59052--59096 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
59042 TTTCCCGGGC
59052 CCAAATCAAAAAAATAAATAAAA
1 CCAAATCAAAAAAAT-AATAAAA
*
59075 CCAAATGAAAAACAAT-ATAAAA
1 CCAAATCAAAAA-AATAATAAAA
59097 AATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 11 0.55
24 3 0.15
ACGTcount: A:0.71, C:0.13, G:0.02, T:0.13
Consensus pattern (22 bp):
CCAAATCAAAAAAATAATAAAA
Found at i:62381 original size:42 final size:42
Alignment explanation
Indices: 62319--62417 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
62309 GTTTACAAAC
* *
62319 AAAAACGCCGCTAAAGACCATTTTCTTTAGCGGCGCTTAGA-
1 AAAAACGCCGCTAAAAACCATGTTCTTTAGCGGCGCTTAGAG
62360 AAGAAACGCCGCTAAAAACCATGTTCTTTAGCGGCGCTTAGAG
1 AA-AAACGCCGCTAAAAACCATGTTCTTTAGCGGCGCTTAGAG
62403 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
62418 GATGCGCCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
41 2 0.04
42 50 0.93
43 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
AAAAACGCCGCTAAAAACCATGTTCTTTAGCGGCGCTTAGAG
Found at i:62842 original size:21 final size:20
Alignment explanation
Indices: 62816--62873 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 20
62806 TTTTGCTCTA
*
62816 CTCTGCTTCTCTCGCTGCAG
1 CTCTGCTTCCCTCGCTGCAG
*
62836 CCTCTGCTTCCCTTGCTGCAG
1 -CTCTGCTTCCCTCGCTGCAG
62857 CTGCTGCTTCCCTCGCT
1 CT-CTGCTTCCCTCGCT
62874 ACCGCCTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 2 0.06
21 31 0.94
ACGTcount: A:0.03, C:0.43, G:0.19, T:0.34
Consensus pattern (20 bp):
CTCTGCTTCCCTCGCTGCAG
Found at i:67834 original size:9 final size:9
Alignment explanation
Indices: 67807--67999 Score: 217
Period size: 9 Copynumber: 21.4 Consensus size: 9
67797 ATTTTAACTG
67807 TGTAAGTTA
1 TGTAAGTTA
* *
67816 TTTAATTTA
1 TGTAAGTTA
67825 TGTAAGTTA
1 TGTAAGTTA
67834 TGTAAGTTA
1 TGTAAGTTA
* *
67843 TTTAATTTA
1 TGTAAGTTA
67852 TGTAAGTTA
1 TGTAAGTTA
67861 TGTAAGTTA
1 TGTAAGTTA
* *
67870 TTTAATTTA
1 TGTAAGTTA
67879 TGTAAGTTA
1 TGTAAGTTA
67888 TGTAAGTTA
1 TGTAAGTTA
* *
67897 TTTAATTTA
1 TGTAAGTTA
67906 TGTAAGTTA
1 TGTAAGTTA
67915 TGTAAGTTA
1 TGTAAGTTA
* *
67924 TTTAATTTA
1 TGTAAGTTA
*
67933 TGTAGGTTA
1 TGTAAGTTA
67942 TGTAAGTTA
1 TGTAAGTTA
*
67951 TGTAACTTA
1 TGTAAGTTA
* *
67960 TTTAATTTA
1 TGTAAGTTA
67969 T-TCAAGTTA
1 TGT-AAGTTA
*
67978 TGTAAGTAA
1 TGTAAGTTA
* *
67987 TTTAATTTA
1 TGTAAGTTA
67996 TGTA
1 TGTA
68000 TAAGCTTGTA
Statistics
Matches: 151, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
8 1 0.01
9 149 0.99
10 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.51
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:67845 original size:27 final size:27
Alignment explanation
Indices: 67807--67978 Score: 283
Period size: 27 Copynumber: 6.4 Consensus size: 27
67797 ATTTTAACTG
67807 TGTAAGTTATTTAATTTATGTAAGTTA
1 TGTAAGTTATTTAATTTATGTAAGTTA
67834 TGTAAGTTATTTAATTTATGTAAGTTA
1 TGTAAGTTATTTAATTTATGTAAGTTA
67861 TGTAAGTTATTTAATTTATGTAAGTTA
1 TGTAAGTTATTTAATTTATGTAAGTTA
67888 TGTAAGTTATTTAATTTATGTAAGTTA
1 TGTAAGTTATTTAATTTATGTAAGTTA
*
67915 TGTAAGTTATTTAATTTATGTAGGTTA
1 TGTAAGTTATTTAATTTATGTAAGTTA
* * * *
67942 TGTAAGTTATGTAACTTATTTAATTTA
1 TGTAAGTTATTTAATTTATGTAAGTTA
67969 T-TCAAGTTAT
1 TGT-AAGTTAT
67979 GTAAGTAATT
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
26 1 0.01
27 137 0.99
ACGTcount: A:0.33, C:0.01, G:0.15, T:0.52
Consensus pattern (27 bp):
TGTAAGTTATTTAATTTATGTAAGTTA
Found at i:70515 original size:116 final size:113
Alignment explanation
Indices: 70354--70652 Score: 331
Period size: 116 Copynumber: 2.6 Consensus size: 113
70344 AAAATGCCAG
* * *
70354 ATAAATACGACACCGTTTAGCAAACACTTAAAACATATTTGCGGCGTTTATTGACAAAACGCCAC
1 ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATTGA-AAAACGCCAC
** *
70419 TAAAACAT-ACCTATTGC-G-GCATTTAACGA-AAAATGCCACTAATAACGCAAA
65 TAAAAC-TGAAATATTGCGGTGCA--TAA-GAGAAAACGCCACTAA-AACGC-AA
* * *
70470 ATAAAAACGACTGCGTTTAGCAAATACTTAAAACATAATTACGGCGTTTATCAT-AAAAACGCCA
1 ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTAT--TGAAAAACGCCA
* *
70534 CAAAAACTGAAATTTTGCGGTGCATAAGAGAAAACGCCACTAAAACGCAA
64 CTAAAACTGAAATATTGCGGTGCATAAGAGAAAACGCCACTAAAACGCAA
* * * *
70584 TTTAAAACGACAGTGTTTAGCAAAGACTTAAAACATAATTGCGGCGTTTA-TGAAGAAACGCCAC
1 ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATTGAA-AAACGCCAC
70648 TAAAA
65 TAAAA
70653 TGGAAACTAA
Statistics
Matches: 157, Mismatches: 18, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
111 1 0.01
112 2 0.01
113 13 0.08
114 46 0.29
115 8 0.05
116 81 0.52
117 2 0.01
118 4 0.03
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (113 bp):
ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATTGAAAAACGCCACT
AAAACTGAAATATTGCGGTGCATAAGAGAAAACGCCACTAAAACGCAA
Found at i:71001 original size:7 final size:7
Alignment explanation
Indices: 70991--71342 Score: 60
Period size: 7 Copynumber: 50.3 Consensus size: 7
70981 AAGCTACTAG
70991 CTAAACC
1 CTAAACC
*
70998 CTAAACA
1 CTAAACC
* *
71005 ATAAACA
1 CTAAACC
* *
71012 ATAAACA
1 CTAAACC
71019 CTAAACC
1 CTAAACC
*
71026 ATAAACC
1 CTAAACC
*
71033 C-ACACC
1 CTAAACC
* *
71039 CTACAGC
1 CTAAACC
71046 CTAAACC
1 CTAAACC
* *
71053 ATAAACA
1 CTAAACC
*
71060 CTAAATC
1 CTAAACC
* *
71067 ATAAACTG
1 CTAAAC-C
* *
71075 C-ATACT
1 CTAAACC
*
71081 TTAAACC
1 CTAAACC
*
71088 ATAAA-C
1 CTAAACC
*
71094 CTACACC
1 CTAAACC
71101 CTAAACC
1 CTAAACC
* *
71108 GTAAACA
1 CTAAACC
*
71115 CTAAACT
1 CTAAACC
*
71122 ATAAA-C
1 CTAAACC
*
71128 C-AATAAC
1 CTAA-ACC
*
71135 CTAAGCC
1 CTAAACC
*
71142 CTACACC
1 CTAAACC
*
71149 CTACACC
1 CTAAACC
71156 CTAAACC
1 CTAAACC
* *
71163 ATAAACA
1 CTAAACC
*
71170 CTAAACT
1 CTAAACC
* *
71177 CTTAACA
1 CTAAACC
*
71184 CTAAATC
1 CTAAACC
* *
71191 ATAAACTG
1 CTAAAC-C
*
71199 C-ATA-C
1 CTAAACC
*
71204 TTAAAACC
1 CT-AAACC
*
71212 ATAAA-C
1 CTAAACC
*
71218 CTACACC
1 CTAAACC
*
71225 CTAAACA
1 CTAAACC
* *
71232 GTAAACA
1 CTAAACC
*
71239 CTAAATC
1 CTAAACC
*
71246 GTAAA-C
1 CTAAACC
*
71252 CAATAACC
1 CTA-AACC
71260 CTTAAACC
1 C-TAAACC
*
71268 CTAAGACG
1 CTAA-ACC
*
71276 AT-AA-C
1 CTAAACC
71281 CTAAACCC
1 CTAAA-CC
71289 CTAAACC
1 CTAAACC
*
71296 TTAAACC
1 CTAAACC
*
71303 TTTAAACC
1 -CTAAACC
*
71311 TTAAACC
1 CTAAACC
*
71318 TCTAAAGC
1 -CTAAACC
*
71326 ATAAACCC
1 CTAAA-CC
71334 CTAAACC
1 CTAAACC
71341 CT
1 CT
71343 TAAATCATAA
Statistics
Matches: 243, Mismatches: 80, Indels: 44
0.66 0.22 0.12
Matches are distributed among these distances:
5 3 0.01
6 19 0.08
7 183 0.75
8 37 0.15
9 1 0.00
ACGTcount: A:0.46, C:0.32, G:0.03, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:71041 original size:41 final size:41
Alignment explanation
Indices: 70995--71072 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
70985 TACTAGCTAA
70995 ACCCTA-AACAATAAACAATAAACACTAAACCATAAACCCAC
1 ACCCTACAAC-ATAAACAATAAACACTAAACCATAAACCCAC
* * * *
71036 ACCCTACAGCCTAAACCATAAACACTAAATCATAAAC
1 ACCCTACAACATAAACAATAAACACTAAACCATAAAC
71073 TGCATACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
41 30 0.94
42 2 0.06
ACGTcount: A:0.53, C:0.32, G:0.01, T:0.14
Consensus pattern (41 bp):
ACCCTACAACATAAACAATAAACACTAAACCATAAACCCAC
Found at i:71058 original size:55 final size:55
Alignment explanation
Indices: 70991--71196 Score: 188
Period size: 55 Copynumber: 3.7 Consensus size: 55
70981 AAGCTACTAG
* * * *
70991 CTAAACCCTAAACAATAAACAATAAACACTAAACCATAAACCCACACCCTACAGC
1 CTAAACCATAAACACTAAACTATAAACACTAAACCATAAACCCACACCCTACACC
* * ** * *
71046 CTAAACCATAAACACTAAA-TCATAAACTGC-ATACTTTAAA-CCATAAACCTACACC
1 CTAAACCATAAACACTAAACT-ATAAAC-ACTAAACCATAAACCCA-CACCCTACACC
* * *
71101 CTAAACCGTAAACACTAAACTATAAAC-CAATAACC-TAAGCCCTACACCCTACACC
1 CTAAACCATAAACACTAAACTATAAACACTA-AACCATAAACCC-ACACCCTACACC
* * *
71156 CTAAACCATAAACACTAAACTCTTAACACTAAATCATAAAC
1 CTAAACCATAAACACTAAACTATAAACACTAAACCATAAAC
71197 TGCATACTTA
Statistics
Matches: 119, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
53 1 0.01
54 7 0.06
55 102 0.86
56 9 0.08
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (55 bp):
CTAAACCATAAACACTAAACTATAAACACTAAACCATAAACCCACACCCTACACC
Found at i:71069 original size:14 final size:14
Alignment explanation
Indices: 70991--71196 Score: 86
Period size: 14 Copynumber: 14.9 Consensus size: 14
70981 AAGCTACTAG
*
70991 CTAAACCCTAAACA
1 CTAAACCATAAACA
* *
71005 ATAAACAATAAACA
1 CTAAACCATAAACA
71019 CTAAACCATAAAC-
1 CTAAACCATAAACA
* * * *
71032 CCACACCCTACAGC-
1 CTAAACCATA-AACA
71046 CTAAACCATAAACA
1 CTAAACCATAAACA
* *
71060 CTAAATCATAAACTG
1 CTAAACCATAAAC-A
* **
71075 C-ATACTTTAAAC-
1 CTAAACCATAAACA
* *
71087 CATAAACC-TACACC
1 C-TAAACCATAAACA
*
71101 CTAAACCGTAAACA
1 CTAAACCATAAACA
*
71115 CTAAACTATAAAC-
1 CTAAACCATAAACA
* * *
71128 CAATAACC-TAAGCC
1 CTA-AACCATAAACA
* * * *
71142 CTACACCCTACACC
1 CTAAACCATAAACA
71156 CTAAACCATAAACA
1 CTAAACCATAAACA
*
71170 CTAAACTC-TTAACA
1 CTAAAC-CATAAACA
*
71184 CTAAATCATAAAC
1 CTAAACCATAAAC
71197 TGCATACTTA
Statistics
Matches: 140, Mismatches: 40, Indels: 24
0.69 0.20 0.12
Matches are distributed among these distances:
12 1 0.01
13 29 0.21
14 108 0.77
15 2 0.01
ACGTcount: A:0.48, C:0.32, G:0.02, T:0.18
Consensus pattern (14 bp):
CTAAACCATAAACA
Found at i:71105 original size:41 final size:40
Alignment explanation
Indices: 71060--71243 Score: 101
Period size: 41 Copynumber: 4.5 Consensus size: 40
71050 ACCATAAACA
* * *
71060 CTAAATCATAAACTGC-ATACTTTAAACCATAAACCTACACC
1 CTAAACCATAAAC-GCTAAACTATAAACCATAAACCTA-ACC
* *
71101 CTAAACCGTAAACACTAAACTATAAACCA-ATAACCTAAGCC
1 CTAAACCATAAACGCTAAACTATAAACCATA-AACCTAA-CC
* * * * * *
71142 CTACACCCTACACCCTAAACCATAAA-CACTAAACTCTTAACA
1 CTAAACCATAAACGCTAAACTATAAACCA-TAAAC-C-TAACC
* *
71184 CTAAATCATAAACTGC-ATACT-TAAAACCATAAACCTACACC
1 CTAAACCATAAAC-GCTAAACTAT-AAACCATAAACCTA-ACC
*
71225 CTAAA-CAGTAAACACTAAA
1 CTAAACCA-TAAACGCTAAA
71244 TCGTAAACCA
Statistics
Matches: 109, Mismatches: 21, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
40 10 0.09
41 70 0.64
42 23 0.21
43 6 0.06
ACGTcount: A:0.47, C:0.30, G:0.03, T:0.20
Consensus pattern (40 bp):
CTAAACCATAAACGCTAAACTATAAACCATAAACCTAACC
Found at i:71113 original size:62 final size:61
Alignment explanation
Indices: 71020--71230 Score: 182
Period size: 62 Copynumber: 3.4 Consensus size: 61
71010 CAATAAACAC
* *
71020 TAAACCATAAACCCACACCCTACAGCCTAAACCATAAACACTAAATCATAAACTGCATACTT
1 TAAACCATAAACCTACACCCTA-AACCTAAACCATAAACACTAAATCATAAACTGCATACTT
* * *
71082 TAAACCATAAACCTACACCCTAAACCGTAAA-CACTAAACTA-TAAACCAATAACCT--A-AGCC
1 TAAACCATAAACCTACACCCTAAACC-TAAACCA-TAAAC-ACTAAATC-ATAAACTGCATA-CT
*
71142 C
61 T
* * * * * *
71143 TACACCCTACACCCTAAACCATAAACACTAAACTC-TTAACACTAAATCATAAACTGCATACTT
1 TAAACCATA-AACCTACACCCTAAAC-CTAAAC-CATAAACACTAAATCATAAACTGCATACTT
*
71206 AAAACCATAAACCTACACCCTAAAC
1 TAAACCATAAACCTACACCCTAAAC
71231 AGTAAACACT
Statistics
Matches: 114, Mismatches: 22, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
60 1 0.01
61 21 0.18
62 74 0.65
63 16 0.14
64 2 0.02
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (61 bp):
TAAACCATAAACCTACACCCTAAACCTAAACCATAAACACTAAATCATAAACTGCATACTT
Found at i:71175 original size:69 final size:68
Alignment explanation
Indices: 71101--71251 Score: 150
Period size: 69 Copynumber: 2.2 Consensus size: 68
71091 AACCTACACC
* * *
71101 CTAAACCGTAAACACTAAA-CTATAAAC-CAATAACCT-AAGCCCTACACCCTACACCCTAAACC
1 CTAAACCGTAAACACTAAATC-ATAAACGC-AT-ACCTAAAACCATA-AACCTACACCCTAAA-C
71163 A-TAAACA
61 AGTAAACA
* *
71170 CTAAACTC-TTAACACTAAATCATAAACTGCATACTTAAAACCATAAACCTACACCCTAAACAGT
1 CTAAAC-CGTAAACACTAAATCATAAAC-GCATACCTAAAACCATAAACCTACACCCTAAACAGT
71234 AAACA
64 AAACA
*
71239 CTAAATCGTAAAC
1 CTAAACCGTAAAC
71252 CAATAACCCT
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
68 3 0.04
69 54 0.79
70 10 0.15
71 1 0.01
ACGTcount: A:0.47, C:0.30, G:0.03, T:0.19
Consensus pattern (68 bp):
CTAAACCGTAAACACTAAATCATAAACGCATACCTAAAACCATAAACCTACACCCTAAACAGTAA
ACA
Found at i:71302 original size:15 final size:15
Alignment explanation
Indices: 71278--71346 Score: 77
Period size: 15 Copynumber: 4.6 Consensus size: 15
71268 CTAAGACGAT
71278 AACC-TAAACCCCTA
1 AACCTTAAACCCCTA
**
71292 AACCTTAAACCTTTA
1 AACCTTAAACCCCTA
*
71307 AACCTTAAACCTCTA
1 AACCTTAAACCCCTA
* *
71322 AAGCATAAACCCCTA
1 AACCTTAAACCCCTA
71337 AACCCTTAAA
1 AA-CCTTAAA
71347 TCATAAACTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
14 4 0.09
15 36 0.80
16 5 0.11
ACGTcount: A:0.43, C:0.33, G:0.01, T:0.22
Consensus pattern (15 bp):
AACCTTAAACCCCTA
Found at i:71431 original size:22 final size:21
Alignment explanation
Indices: 71366--71433 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
71356 CTTGATTAAA
*
71366 CCCTAAACCATAAGCCATTAAC
1 CCCTAAACCATAAGCC-CTAAC
* * *
71388 CCATAGACCCTAAGCCCATAAC
1 CCCTAAACCATAAGCCC-TAAC
71410 CCCTAAACCATAAGCTCCTAAC
1 CCCTAAACCATAAGC-CCTAAC
71432 CC
1 CC
71434 TTACACTAGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 35 0.95
23 2 0.05
ACGTcount: A:0.37, C:0.41, G:0.06, T:0.16
Consensus pattern (21 bp):
CCCTAAACCATAAGCCCTAAC
Found at i:71619 original size:12 final size:12
Alignment explanation
Indices: 71602--71631 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
71592 ATTTTTTCAT
71602 TTTTAACAAATA
1 TTTTAACAAATA
71614 TTTTAACAAATA
1 TTTTAACAAATA
71626 TTTTAA
1 TTTTAA
71632 ACTATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (12 bp):
TTTTAACAAATA
Found at i:71963 original size:73 final size:73
Alignment explanation
Indices: 71771--72013 Score: 301
Period size: 73 Copynumber: 3.4 Consensus size: 73
71761 CTGAGCATTA
* * **
71771 GCGGCGCTTTCCTAAAAACGCCGCTGTATCCACGAAAGCTCAAAAAACGACATCGTTTCGTTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAG
*
71836 G-TTTTTA
66 GTTTTTTT
* * * * * * *
71843 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTAGTTGGGTTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAG
71908 GTTTTTTT
66 GTTTTTTT
** * * * *
71916 GCGGCGCTTTCTTAAAAACACCACTATATCCACGAAAGCTCAAAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAG
71981 GTTTTTTT
66 GTTTTTTT
*
71989 GCGGCGCTTTCTC-AAAACGCCGCTA
1 GCGGCGCTTTCCCAAAAACGCCGCTA
72014 AAGCCCTCGC
Statistics
Matches: 142, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
72 65 0.46
73 77 0.54
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTCCCAAAAACGCCGCTATATCCACGAAAGCTCAAAAAACGACATCGTTGGGTTTAG
GTTTTTTT
Found at i:72113 original size:112 final size:111
Alignment explanation
Indices: 71916--72240 Score: 390
Period size: 112 Copynumber: 2.9 Consensus size: 111
71906 AGGTTTTTTT
* * * * *
71916 GCGGCGCTTTCTTAAAAACACCACTATATCCACGAAAGCTCAAAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
71981 GTTTTTTTGCGGCGCTTTCTCAAAACGCCGCTAAAGCCCTCG-CATTA
66 G-TTTTTTGCGGCGCTTTCTCAAAACGCCGCTAAAGCCCT-GACATTA
*
72028 GCGGCGCTTTAC-TAAAAACACCGCTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTTT-CTTAAAAACACCACTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTA
* * *
72092 GGTTTGTTTGTGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTGATCTTTT
65 GGTTT-TTTGCGGCGCTTTCTC-AAAACGCCGCTAAAGCCCTGA-CATTA
* * * * *
72142 GGGGCGCTTTCTTGAAAACGCAACTAAAAT-CCCAGAAA-CTCCGAAAACGGCGTCGTTGGGCTT
1 GCGGCGCTTTCTTAAAAACACCACT-AAATCCCCA-AAAGCTCAGAAAACGGCGTCGTTGGGCTT
*
72205 AGGTTTTTAGCGGCGCTTTCT-AGAAATCGCCGCTAA
64 AGGTTTTTTGCGGCGCTTTCTCA-AAA-CGCCGCTAA
72241 TGTTTATTTT
Statistics
Matches: 186, Mismatches: 17, Indels: 19
0.84 0.08 0.09
Matches are distributed among these distances:
111 4 0.02
112 77 0.41
113 43 0.23
114 55 0.30
115 7 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (111 bp):
GCGGCGCTTTCTTAAAAACACCACTAAATCCCCAAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG
GTTTTTTGCGGCGCTTTCTCAAAACGCCGCTAAAGCCCTGACATTA
Found at i:72326 original size:12 final size:12
Alignment explanation
Indices: 72309--72334 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
72299 TTTGGAAAAT
72309 AAACGCCGCTAA
1 AAACGCCGCTAA
72321 AAACGCCGCTAA
1 AAACGCCGCTAA
72333 AA
1 AA
72335 GCCTGTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:74408 original size:51 final size:50
Alignment explanation
Indices: 74353--74450 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 50
74343 AAATTTCCTC
* *
74353 TCAATTTGCTGTCAAATTCATTC-AAATTTTCTCTTAAATCCTTATTTAATT
1 TCAATTTGCTCTCAAATTC-TTCTAAA-TTTCTCTTAAATCCCTATTTAATT
*
74404 TCAATTTGCTCTCAAGTTCTTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCTTC-TAAATTTCTCTTAAATCCCTATTT
74451 TTAAATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
50 3 0.07
51 36 0.86
52 3 0.07
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (50 bp):
TCAATTTGCTCTCAAATTCTTCTAAATTTCTCTTAAATCCCTATTTAATT
Found at i:75056 original size:23 final size:23
Alignment explanation
Indices: 75026--75070 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
75016 CAGTATAAAT
75026 AACAAAAA-AATAGCAAAAATAAC
1 AACAAAAACAATAG-AAAAATAAC
*
75049 AACAAAAACAGTAGAAAAATAA
1 AACAAAAACAATAGAAAAATAA
75071 GAGCACCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.73, C:0.11, G:0.07, T:0.09
Consensus pattern (23 bp):
AACAAAAACAATAGAAAAATAAC
Found at i:75610 original size:25 final size:26
Alignment explanation
Indices: 75576--75626 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
75566 TTTGACTCTA
*
75576 ATTTTTTTTAAATTTCTC-TCAATTT
1 ATTTTTTTTAAATTTATCGTCAATTT
*
75601 ATTTTTTTTAACTTTATCGTCAATTT
1 ATTTTTTTTAAATTTATCGTCAATTT
75627 GCTTTAGTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.24, C:0.12, G:0.02, T:0.63
Consensus pattern (26 bp):
ATTTTTTTTAAATTTATCGTCAATTT
Found at i:75719 original size:11 final size:11
Alignment explanation
Indices: 75699--75736 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
75689 CTCAACACCA
75699 AAATTGAGAGG
1 AAATTGAGAGG
*
75710 AAATTTAGAGG
1 AAATTGAGAGG
*
75721 AAACTGAGAGG
1 AAATTGAGAGG
75732 AAATT
1 AAATT
75737 AAATTTGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.03, G:0.29, T:0.21
Consensus pattern (11 bp):
AAATTGAGAGG
Found at i:79466 original size:4 final size:4
Alignment explanation
Indices: 79457--79482 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
79447 GAAGGATGGG
79457 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
79483 ACACTAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:81317 original size:13 final size:13
Alignment explanation
Indices: 81299--81364 Score: 55
Period size: 13 Copynumber: 5.1 Consensus size: 13
81289 AGTTTGGCAA
*
81299 TACTTTTGATAAG
1 TACTTTTGAAAAG
81312 TACTTTTGAAAAG
1 TACTTTTGAAAAG
* *
81325 T-GTTGTGGAAAAG
1 TACTT-TTGAAAAG
*
81338 TGA-TTTTGAGAAG
1 T-ACTTTTGAAAAG
*
81351 TGCTTTTGAAAAG
1 TACTTTTGAAAAG
81364 T
1 T
81365 TTGGTTTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
12 2 0.05
13 38 0.90
14 2 0.05
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:81361 original size:26 final size:26
Alignment explanation
Indices: 81301--81364 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
81291 TTTGGCAATA
*
81301 CTTTTGATAAGTACTTTTGAAAAGTG
1 CTTTTGAAAAGTACTTTTGAAAAGTG
* *
81327 -TTGTGGAAAAGTGA-TTTTGAGAAGTG
1 CTT-TTGAAAAGT-ACTTTTGAAAAGTG
81353 CTTTTGAAAAGT
1 CTTTTGAAAAGT
81365 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 2 0.06
26 26 0.84
27 3 0.10
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.39
Consensus pattern (26 bp):
CTTTTGAAAAGTACTTTTGAAAAGTG
Found at i:88917 original size:9 final size:9
Alignment explanation
Indices: 88903--88933 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
88893 GTTAAACGAA
88903 TCGAGTTAT
1 TCGAGTTAT
*
88912 TCGAGTTAA
1 TCGAGTTAT
88921 TCGAGTTAT
1 TCGAGTTAT
88930 TCGA
1 TCGA
88934 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:89001 original size:9 final size:9
Alignment explanation
Indices: 88984--89020 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
88974 TGAGTTTTCG
88984 AATTCGAAT
1 AATTCGAAT
*
88993 AACTCGAAT
1 AATTCGAAT
*
89002 AATTCAAAT
1 AATTCGAAT
89011 AATTCGAAT
1 AATTCGAAT
89020 A
1 A
89021 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.49, C:0.14, G:0.08, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:89501 original size:22 final size:22
Alignment explanation
Indices: 89471--89513 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
89461 ACACCAAAAC
*
89471 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
89493 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
89514 AGCGCCACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:89705 original size:43 final size:42
Alignment explanation
Indices: 89652--89875 Score: 170
Period size: 43 Copynumber: 5.2 Consensus size: 42
89642 TTTGGAAAAG
*
89652 CGCCGCTAAAGGCCATGACCTATAGCGGCGC-TTCTCTAACAAA
1 CGCCGCTAAA-GCCATGACCTTTAGCGGCGCTTTCTC-AACAAA
* * * *
89695 TGCCGCTAAAGACATTGACCTTTAGCGGCGCTTTTTCCACAAA
1 CGCCGCTAAAGCCA-TGACCTTTAGCGGCGCTTTCTCAACAAA
* * * *
89738 CGCCGCTATAGCTCATGAGCTTTAGCGGCGCTTTTTCCACAAA
1 CGCCGCTAAAGC-CATGACCTTTAGCGGCGCTTTCTCAACAAA
* * * * *
89781 CGTCGCTATAGCTCAT-ACCTTTAGTGGTGCTTT-TCCCACAAA
1 CGCCGCTAAAGC-CATGACCTTTAGCGGCGCTTTCT-CAACAAA
* * *
89823 CGTCGCTATAGCTCGAT-ACCTTTAGCGGCGC-TTCTCACAAAAA
1 CGCCGCTAAAGC-C-ATGACCTTTAGCGGCGCTTTCTCA-ACAAA
*
89866 CGCCACTAAA
1 CGCCGCTAAA
89876 AATATAACAT
Statistics
Matches: 154, Mismatches: 20, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 41 0.27
43 106 0.69
44 6 0.04
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (42 bp):
CGCCGCTAAAGCCATGACCTTTAGCGGCGCTTTCTCAACAAA
Found at i:89820 original size:42 final size:42
Alignment explanation
Indices: 89712--89855 Score: 225
Period size: 43 Copynumber: 3.4 Consensus size: 42
89702 AAAGACATTG
*
89712 ACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTATAGCTCAT
1 ACCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTCAT
*
89754 GAGCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTCAT
1 -ACCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTCAT
* * *
89797 ACCTTTAGTGGTGCTTTTCCCACAAACGTCGCTATAGCTCGAT
1 ACCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTC-AT
89840 ACCTTTAGCGGCGCTT
1 ACCTTTAGCGGCGCTT
89856 CTCACAAAAA
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 36 0.39
43 56 0.61
ACGTcount: A:0.20, C:0.30, G:0.19, T:0.31
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTCAT
Found at i:89867 original size:85 final size:85
Alignment explanation
Indices: 89652--89867 Score: 217
Period size: 85 Copynumber: 2.5 Consensus size: 85
89642 TTTGGAAAAG
* * * * * * *
89652 CGCCGCTAAAGGC-CATGACCTATAGCGGCGC-TTCTCTAACAAATGCCGCTAAAG-ACATTGAC
1 CGCCGCTATA-GCTCATGACCTTTAGCGGCGCTTTCTCCAA-AAACGTCGCTATAGCTCA-T-AC
*
89714 CTTTAGCGGCGCTTTTTCCACAAA
62 CTTTAGCGGCGCTTTTCCCACAAA
* * *
89738 CGCCGCTATAGCTCATGAGCTTTAGCGGCGCTTTTTCCACAAACGTCGCTATAGCTCATACCTTT
1 CGCCGCTATAGCTCATGACCTTTAGCGGCGCTTTCTCCAAAAACGTCGCTATAGCTCATACCTTT
* *
89803 AGTGGTGCTTTTCCCACAAA
66 AGCGGCGCTTTTCCCACAAA
*
89823 CGTCGCTATAGCTCGAT-ACCTTTAGCGGCGC-TTCTCACAAAAACG
1 CGCCGCTATAGCTC-ATGACCTTTAGCGGCGCTTTCTC-CAAAAACG
89868 CCACTAAAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
84 4 0.04
85 58 0.54
86 39 0.36
87 7 0.06
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (85 bp):
CGCCGCTATAGCTCATGACCTTTAGCGGCGCTTTCTCCAAAAACGTCGCTATAGCTCATACCTTT
AGCGGCGCTTTTCCCACAAA
Done.