Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2036
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: 93304
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:138 original size:15 final size:16
Alignment explanation
Indices: 106--140 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
96 CTGCAATTTG
*
106 TTTGAGCTTCTTTCAT
1 TTTGAGCTTCTCTCAT
122 TTTGAGCTTC-CTCAT
1 TTTGAGCTTCTCTCAT
137 TTTG
1 TTTG
141 GACATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.11, C:0.20, G:0.14, T:0.54
Consensus pattern (16 bp):
TTTGAGCTTCTCTCAT
Found at i:4222 original size:13 final size:13
Alignment explanation
Indices: 4204--4229 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4194 CAATTTTTTG
4204 TGTATCGATACAT
1 TGTATCGATACAT
4217 TGTATCGATACAT
1 TGTATCGATACAT
4230 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4241 original size:32 final size:33
Alignment explanation
Indices: 4184--4247 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
4174 TACAAGCCAA
**
4184 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
4217 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
4248 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:6556 original size:166 final size:165
Alignment explanation
Indices: 6320--6767 Score: 494
Period size: 166 Copynumber: 2.8 Consensus size: 165
6310 CAAATTATGG
* *
6320 AGTTTTCTTCTTCGTAAATTTTTTCGAGAGGATTTTCATGGGTTTAAAATTTTTAAAATTCATAA
1 AGTTTTCTTCTCCGTAAATTTTTTCGAGAGGATTTTCATGAGTTTAAAATTTTTAAAATTCATAA
* * * *
6385 AATATTATTATTTAATTT-ATATTAAATT-AGTTTTCAAAAATTCATTCATTTCCATGATTTTTT
66 AATATTATTATTT-ATTTCATATT-AATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTG
6448 AATTTTTCCTTGAAATTCTCTTGTTTTTTAAAAACGT
129 AATTTTTCCTTGAAATTCTCTTGTTTTTTAAAAACGT
* ** *
6485 AGTTTTCTTCTCCGTAAATTTTTTTCG-GAAGGATTTTCATTAGTTTTTAATTTTTAAAATTTAT
1 AGTTTTCTTCTCCGTAAA-TTTTTTCGAG-AGGATTTTCATGAGTTTAAAATTTTTAAAATTCAT
*
6549 CAAATATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTG
64 AAAATATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTG
* ** * *
6614 AATTTTTTTCTTG-AA---T-TT-TTTTCGAAATACGG
129 AA-TTTTTCCTTGAAATTCTCTTGTTTTTTAAAAACGT
* *
6646 AGTTTTCTACTCCGTAAATTTTTT-GAGAGG--------GA-TTT----TTTTT-AAATTCATCA
1 AGTTTTCTTCTCCGTAAATTTTTTCGAGAGGATTTTCATGAGTTTAAAATTTTTAAAATTCATAA
* * *
6696 AATATTATTATCTATTTCATATTAATTCAATTTTCAAAAATCCATTCATTTCCATGAATTTTGAA
66 AATATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAA
6761 TTTTTCC
131 TTTTTCC
6768 CTTAAGATTT
Statistics
Matches: 254, Mismatches: 23, Indels: 33
0.82 0.07 0.11
Matches are distributed among these distances:
144 6 0.02
145 71 0.28
146 5 0.02
150 3 0.01
151 1 0.00
159 4 0.02
160 7 0.03
161 27 0.11
162 2 0.01
163 1 0.00
165 26 0.10
166 92 0.36
167 9 0.04
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (165 bp):
AGTTTTCTTCTCCGTAAATTTTTTCGAGAGGATTTTCATGAGTTTAAAATTTTTAAAATTCATAA
AATATTATTATTTATTTCATATTAATTCAATTTTCAAAAATTCATTCATTTCCATAAATTTTGAA
TTTTTCCTTGAAATTCTCTTGTTTTTTAAAAACGT
Found at i:6634 original size:12 final size:13
Alignment explanation
Indices: 6611--6636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6601 TCCATAAATT
6611 TTGAATTTTTTTC
1 TTGAATTTTTTTC
6624 TTGAATTTTTTTC
1 TTGAATTTTTTTC
6637 GAAATACGGA
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:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TTGAATTTTTTTC
Found at i:15558 original size:20 final size:20
Alignment explanation
Indices: 15535--15607 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
15525 ACAATTCAAA
15535 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
15555 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
15576 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
15596 GTATCGATACAT
1 GTATCGATACAT
15608 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:15579 original size:21 final size:21
Alignment explanation
Indices: 15553--15628 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
15543 ACATGTTGCA
15553 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
15574 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
15594 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
15615 ATGTATCGATACAT
1 ATGTATCGATACAT
15629 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:15586 original size:41 final size:41
Alignment explanation
Indices: 15535--15628 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
15525 ACAATTCAAA
*
15535 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
15576 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
15617 GTATCGATACAT
1 GTATCGATACAT
15629 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:28634 original size:75 final size:71
Alignment explanation
Indices: 28546--28720 Score: 190
Period size: 71 Copynumber: 2.4 Consensus size: 71
28536 GTATTTGAAC
* **
28546 TCATTTATCTTTTTTAGTCCTTAAAAAGTAGGATGCATTTTCTGTTTTCTTCAAAGCCCATGCAA
1 TCATTTATCTTTTTTAGTCCTTAAAAAGT-GGATGC-CTTT-T-TTTTCTTCAAAGCCCACACAA
** *
28611 GCTGTTGGCA
62 GCTGGCGCCA
* * * * *
28621 TCATTTATCTTTTTCAGTTC-TCAAGAGCTGGATGCCTTTTTTTTCTTCAAAGTCCACACAAGCT
1 TCATTTATCTTTTTTAGTCCTTAAAAAG-TGGATGCCTTTTTTTTCTTCAAAGCCCACACAAGCT
28685 GGCGCCA
65 GGCGCCA
*
28692 TCATTTATCTTTTCTAGTCCTTAAAAAGT
1 TCATTTATCTTTTTTAGTCCTTAAAAAGT
28721 CTTCAAAGCC
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
71 43 0.52
72 6 0.07
73 3 0.04
74 11 0.13
75 19 0.23
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.41
Consensus pattern (71 bp):
TCATTTATCTTTTTTAGTCCTTAAAAAGTGGATGCCTTTTTTTTCTTCAAAGCCCACACAAGCTG
GCGCCA
Found at i:28750 original size:56 final size:56
Alignment explanation
Indices: 28664--28772 Score: 166
Period size: 56 Copynumber: 1.9 Consensus size: 56
28654 GCCTTTTTTT
*
28664 TCTTCAAAGTCCACACAAGCTGGCGCCATCATTTATC-TTTTCTAGTCCTTAAAAAG
1 TCTTCAAAGCCCACACAAGCTGGCGCCATCATTTATCTTTTTCTA-TCCTTAAAAAG
* * *
28720 TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTTTCTTTTTCTATCCTTAAA
1 TCTTCAAAGCCCACACAAGCTGGCGCCATCATTTATCTTTTTCTATCCTTAAA
28773 GAGCAAGACG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 41 0.85
57 7 0.15
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (56 bp):
TCTTCAAAGCCCACACAAGCTGGCGCCATCATTTATCTTTTTCTATCCTTAAAAAG
Found at i:28848 original size:74 final size:76
Alignment explanation
Indices: 28720--28925 Score: 251
Period size: 74 Copynumber: 2.7 Consensus size: 76
28710 CCTTAAAAAG
* *
28720 TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTTTCTTTTTCTATCCTTAAAGAGCAAGACG-C
1 TCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCTTTTTCTATCCTTAAAGAGCAAGACGCC
28784 TTTTTCTTT-T
66 TTTTTCTTTCT
* *
28794 TCTTCAAAACCCACACAAGCTAGTGGCATCATTTATC-TTTTCTAGT-CTTGAAAGAGCAAGATG
1 TCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCTTTTTCTA-TCCTT-AAAGAGCAAGACG
*
28857 CCTTTTTTTTTCT
64 CCTTTTTCTTTCT
* * *** *
28870 TCTTCAAAGCCCACACAAGTTGGTGGTGCCATTTA-CTTTTTCTAGTCCTCAAAGAG
1 TCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCTTTTTCTA-TCCTTAAAGAG
28926 TAGGACATTT
Statistics
Matches: 114, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
73 10 0.09
74 47 0.41
75 10 0.09
76 45 0.39
77 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.37
Consensus pattern (76 bp):
TCTTCAAAGCCCACACAAGCTAGTGGCATCATTTATCTTTTTCTATCCTTAAAGAGCAAGACGCC
TTTTTCTTTCT
Found at i:28903 original size:76 final size:74
Alignment explanation
Indices: 28720--28967 Score: 260
Period size: 76 Copynumber: 3.4 Consensus size: 74
28710 CCTTAAAAAG
*
28720 TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTTTCTTTTTCTA-TCCTTAAAGAGCAAGACGC
1 TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGT-CTTAAAGAGCAAGACGC
28784 TTTTTCTTTT
65 TTTTTCTTTT
* * *
28794 TCTTCAAAACCCACACAAGCTAGTGGCATCATTTATC-TTTTCTAGTCTTGAAAGAGCAAGATGC
1 TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGTCTT-AAAGAGCAAGACG-
*
28858 CTTTTTTTTTCT
64 CTTTTTCTTT-T
* *** * * *
28870 TCTTCAAAGCCCACACAAGTTGGTGGTGCCATTTA-CTTTTTCTAGTCCTCAAAGAGTAGGA--C
1 TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGT-CTTAAAGAGCAAGACGC
*
28932 ATTTTC---T
65 TTTTTCTTTT
* *
28939 TCTTCAAAACCCGCACAAGCTGGTGGCAT
1 TCTTCAAAGCCCACACAAGCTGGTGGCAT
28968 TTACCTACTT
Statistics
Matches: 146, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
69 24 0.16
73 15 0.10
74 47 0.32
75 10 0.07
76 48 0.33
77 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (74 bp):
TCTTCAAAGCCCACACAAGCTGGTGGCATCATTTATCTTTTTCTAGTCTTAAAGAGCAAGACGCT
TTTTCTTTT
Found at i:28997 original size:66 final size:69
Alignment explanation
Indices: 28864--28997 Score: 150
Period size: 69 Copynumber: 2.0 Consensus size: 69
28854 ATGCCTTTTT
* * ** * * **
28864 TTTTCTTCTTCAAAGCCCACACAAGTTGGTGGTGCCATTTACTTTTTCTAGTCCTCAAAGAGTAG
1 TTTTCTTCTTCAAAACCCACACAAGCTGGTGGTGCCATTTACTACTTCAAGTCCTCAAAAAACAG
28929 GACA
66 GACA
*
28933 TTTTCTTCTTCAAAACCCGCACAAGCTGGT-G-G-CATTTACCTACTT-AAGTCCTCAAAAAACA
1 TTTTCTTCTTCAAAACCCACACAAGCTGGTGGTGCCATTTA-CTACTTCAAGTCCTCAAAAAACA
28994 GGAC
65 GGAC
28998 GCTTACCCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
66 22 0.40
67 5 0.09
68 1 0.02
69 27 0.49
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (69 bp):
TTTTCTTCTTCAAAACCCACACAAGCTGGTGGTGCCATTTACTACTTCAAGTCCTCAAAAAACAG
GACA
Found at i:42425 original size:16 final size:16
Alignment explanation
Indices: 42404--42435 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42394 AGCTACTGAT
42404 TCCATTTTTTTATTTA
1 TCCATTTTTTTATTTA
42420 TCCATTTTTTTATTTA
1 TCCATTTTTTTATTTA
42436 AAGAAAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (16 bp):
TCCATTTTTTTATTTA
Found at i:48082 original size:20 final size:20
Alignment explanation
Indices: 48057--48129 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
48047 TTTTAACTAG
48057 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAAGA
*
48077 ATGTATCGATACA-T-CAGA
1 ATGTATCGATACATTGAAGA
* *
48095 ATGTATCGATGCATTGAAAA
1 ATGTATCGATACATTGAAGA
48115 ATGTATCGATACATT
1 ATGTATCGATACATT
48130 TAGGTACTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 15 0.33
19 2 0.04
20 29 0.63
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAGA
Found at i:49101 original size:28 final size:28
Alignment explanation
Indices: 49007--49492 Score: 434
Period size: 28 Copynumber: 16.8 Consensus size: 28
48997 AAAAAAGTGT
* *
49007 CACTAACTTGTGTAGGCTTTGAAAAGAGTTGC
1 CACTGACTTGTG--GGCTTTG-AAAG-GGTGC
* *
49039 CACCGACTCGTGTGGGCTTTGAAAAGAGTGC
1 CACTGACT--TGTGGGCTTTG-AAAGGGTGC
* *
49070 TACTGACTTGTGGGCCTTGAAAGGGTGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
* * * *
49098 TACTGACTTATGGGCTTTGAAATGATGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
* * **
49126 CACTAACTTATGGGCTTTGAAAAGAATGC
1 CACTGACTTGTGGGCTTTG-AAAGGGTGC
49155 CACTGACTTGTGGGCTTTGAAAGGGTGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
*
49183 CACTGACTTGTGGGCTTTGAAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
*
49211 CACTGACTTGTGGGCTTTGAAAAGAGTTGC
1 CACTGACTTGTGGGCTTTG-AAAG-GGTGC
* * * * *
49241 CACCGACTCGTGGTCTTTGAAAAGATGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
* * * * *
49269 CATTGACTTGTGAGCTTTAAAAAAAGTTGC
1 CACTGACTTGTGGGCTTT--GAAAGGGTGC
* **
49299 CACTGACTCGTGTGGGCTTCGAAAATAGTGC
1 CACTGACT--TGTGGGCTTTG-AAAGGGTGC
* *
49330 CA-TTAGCTTATGGGCTTTGAAAGGGTGC
1 CACTGA-CTTGTGGGCTTTGAAAGGGTGC
* *
49358 CACTAACTTGTGGGCTTTGAAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
* * *
49386 CACTGACTTGTGGGATTTGAAAAGAGTTAC
1 CACTGACTTGTGGGCTTTG-AAAG-GGTGC
* *
49416 CACTGGCTTATGGGCTTTGAAAGGGTGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
* *
49444 CACTAACTTGTGGTCTTTGAAAGGGTGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGC
*
49472 CACTAACTTGTGGGCTTTGAA
1 CACTGACTTGTGGGCTTTGAA
49493 GAGATGAACA
Statistics
Matches: 377, Mismatches: 63, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
28 212 0.56
29 60 0.16
30 56 0.15
31 19 0.05
32 26 0.07
34 4 0.01
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
CACTGACTTGTGGGCTTTGAAAGGGTGC
Found at i:49270 original size:58 final size:58
Alignment explanation
Indices: 49007--49498 Score: 473
Period size: 58 Copynumber: 8.5 Consensus size: 58
48997 AAAAAAGTGT
* *
49007 CACTAACTTGTGTAGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAG-TGC
1 CACTGACTTGTG--GGCTTTGAAAAGA--TGCCACTGACT--TGTGGGCTTTGAAAAGAGTTGC
* * * * * * *
49070 TACTGACTTGTGGGCCTTGAAAGGGTGCTACTGACTTATGGGCTTTGAAATGA--TGC
1 CACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
* * *
49126 CACTAACTTATGGGCTTTGAAAAGAATGCCACTGACTTGTGGGCTTTG-AAAG-GGTGC
1 CACTGACTTGTGGGCTTTGAAAAG-ATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
*
49183 CACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
1 CACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
* * * * * * *
49241 CACCGACTCGTGGTCTTTGAAAAGATGCCATTGACTTGTGAGCTTTAAAAAAAGTTGC
1 CACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
* * * * *
49299 CACTGACTCGTGTGGGCTTCGAAAATAGTGCCA-TTAGCTTATGGGCTTTG-AAAG-GGTGC
1 CACTGACT--TGTGGGCTTTGAAAAGA-TGCCACTGA-CTTGTGGGCTTTGAAAAGAGTTGC
* * * *
49358 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGATTTGAAAAGAGTTAC
1 CACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
* * * * * * *
49416 CACTGGCTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGTCTTTG-AAAG-GGTGC
1 CACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
* *
49472 CACTAACTTGTGGGCTTTGAAGAGATG
1 CACTGACTTGTGGGCTTTGAAAAGATG
49499 AACATTCTAG
Statistics
Matches: 352, Mismatches: 65, Indels: 31
0.79 0.15 0.07
Matches are distributed among these distances:
56 88 0.25
57 87 0.25
58 104 0.30
59 20 0.06
60 18 0.05
61 25 0.07
63 10 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (58 bp):
CACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGC
Found at i:49440 original size:86 final size:85
Alignment explanation
Indices: 49007--49492 Score: 542
Period size: 86 Copynumber: 5.6 Consensus size: 85
48997 AAAAAAGTGT
* * *
49007 CACTAACTTGTGTAGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTGCTA
1 CACTAACTTGTG--GGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCA
*
49072 CTGACTTGTGGGCCTTGAAAGGGTGC
60 CTGACTTGTGGGCTTTGAAAGGGTGC
* * * * * * *
49098 TACTGACTTATGGGCTTTGAAATGATGCCACTAACTTATGGGCTTTGAAAAGAATGCCACTGACT
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
49163 TGTGGGCTTTGAAAGGGTGC
66 TGTGGGCTTTGAAAGGGTGC
* *
49183 CACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGAC
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGAC
* * * *
49248 TCGTGGTCTTTGAAAAGATGC
65 TTGTGGGCTTTGAAAGGGTGC
* * * * * * * *
49269 CATTGACTTGTGAGCTTTAAAAAAAGTTGCCACTGACTCGTGTGGGCTTCGAAAATAGTGCCA-T
1 CACTAACTTGTGGGCTTT--GAAAGGATGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACT
* *
49333 TAGCTTATGGGCTTTGAAAGGGTGC
62 GA-CTTGTGGGCTTTGAAAGGGTGC
* * *
49358 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGATTTGAAAAGAGTTACCACTGGC
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGAC
*
49423 TTATGGGCTTTGAAAGGGTGC
65 TTGTGGGCTTTGAAAGGGTGC
* * *
49444 CACTAACTTGTGGTCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAA
1 CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
49493 GAGATGAACA
Statistics
Matches: 335, Mismatches: 52, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
85 108 0.32
86 113 0.34
87 26 0.08
88 19 0.06
89 44 0.13
90 16 0.05
91 9 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (85 bp):
CACTAACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACT
TGTGGGCTTTGAAAGGGTGC
Found at i:50744 original size:8 final size:8
Alignment explanation
Indices: 50731--50822 Score: 75
Period size: 8 Copynumber: 11.6 Consensus size: 8
50721 TTTGGACCCC
50731 TTTTTGTT
1 TTTTTGTT
50739 TTTTTGTT
1 TTTTTGTT
*
50747 ATTTT-TT
1 TTTTTGTT
** *
50754 CCTTGGTT
1 TTTTTGTT
50762 TTTTTGTTTT
1 TTTTTG--TT
50772 TTTTTGTT
1 TTTTTGTT
50780 TTTTTGTT
1 TTTTTGTT
50788 TTTTT-TGT
1 TTTTTGT-T
50796 TTTTT-TT
1 TTTTTGTT
**
50803 TGGTT-TT
1 TTTTTGTT
50810 TTTTTGTT
1 TTTTTGTT
50818 TTTTT
1 TTTTT
50823 TGTATGAAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
7 14 0.21
8 46 0.68
10 8 0.12
ACGTcount: A:0.01, C:0.02, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTGTT
Found at i:50753 original size:11 final size:10
Alignment explanation
Indices: 50731--50823 Score: 104
Period size: 10 Copynumber: 9.4 Consensus size: 10
50721 TTTGGACCCC
50731 TTTTTGTTTT
1 TTTTTGTTTT
*
50741 TTTGTTATTTT
1 TTT-TTGTTTT
* *
50752 TTCCTTG-GTT
1 TT-TTTGTTTT
50762 TTTTTGTTTT
1 TTTTTGTTTT
50772 TTTTTG--TT
1 TTTTTGTTTT
50780 TTTTTG-TTT
1 TTTTTGTTTT
50789 TTTTTGTTTT
1 TTTTTGTTTT
50799 TTTTTGGTTTT
1 TTTTT-GTTTT
50810 TTTTTGTTTT
1 TTTTTGTTTT
50820 TTTT
1 TTTT
50824 GTATGAAGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
8 8 0.11
9 11 0.15
10 32 0.45
11 20 0.28
ACGTcount: A:0.01, C:0.02, G:0.12, T:0.85
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:50762 original size:23 final size:19
Alignment explanation
Indices: 50731--50822 Score: 116
Period size: 19 Copynumber: 4.7 Consensus size: 19
50721 TTTGGACCCC
50731 TTTTTGTTTTTTTGTTATTT
1 TTTTTGTTTTTTTGTT-TTT
50751 TTTCCTTGGTTTTTTTG-TTTT
1 TTT--TT-GTTTTTTTGTTTTT
50772 TTTTTGTTTTTTTGTTTTT
1 TTTTTGTTTTTTTGTTTTT
*
50791 TTTGTT-TTTTTTTGGTTTT
1 TTT-TTGTTTTTTTGTTTTT
50810 TTTTTGTTTTTTT
1 TTTTTGTTTTTTT
50823 TGTATGAAGG
Statistics
Matches: 65, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
18 11 0.17
19 31 0.48
20 5 0.08
21 6 0.09
22 3 0.05
23 9 0.14
ACGTcount: A:0.01, C:0.02, G:0.12, T:0.85
Consensus pattern (19 bp):
TTTTTGTTTTTTTGTTTTT
Found at i:50764 original size:1 final size:1
Alignment explanation
Indices: 50760--50823 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
50750 TTTTCCTTGG
* * * * ** *
50760 TTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTTTGGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
50824 GTATGAAGGA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:50774 original size:9 final size:9
Alignment explanation
Indices: 50731--50825 Score: 93
Period size: 9 Copynumber: 9.8 Consensus size: 9
50721 TTTGGACCCC
50731 TTTTTGTTTT
1 TTTTTG-TTT
*
50741 TTTGTTATTT
1 TTT-TTGTTT
*
50751 TTTCCTTGGTT
1 TTT--TTGTTT
50762 TTTTTGTTT
1 TTTTTGTTT
50771 TTTTT-TGTT
1 TTTTTGT-TT
50780 TTTTTGTTT
1 TTTTTGTTT
50789 TTTTTGTTTT
1 TTTTTG-TTT
50799 TTTTTGGTTTT
1 TTTTT-G-TTT
50810 TTTTTGTTT
1 TTTTTGTTT
50819 TTTTTGT
1 TTTTTGT
50826 ATGAAGGACG
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
8 1 0.01
9 35 0.47
10 19 0.26
11 19 0.26
ACGTcount: A:0.01, C:0.02, G:0.13, T:0.84
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:56748 original size:28 final size:28
Alignment explanation
Indices: 56687--56768 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
56677 TTTTGGAGAT
*
56687 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
56715 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
56743 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
56769 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:56910 original size:51 final size:51
Alignment explanation
Indices: 56748--56920 Score: 195
Period size: 52 Copynumber: 3.4 Consensus size: 51
56738 GATGAAATAA
* *
56748 CGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGGAAATAAAAT
* * * * *
56800 CG-GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCCGATT-ATGAAAAATTGGTATTTTGGAAATAAAAT
* *** *
56852 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
*
56903 TGAGGTTGGAGTATCCCC
1 CGAGGTTGGAGTATCCCC
56921 TCGGAAATAA
Statistics
Matches: 100, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
51 37 0.37
52 52 0.52
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGGAAATAAAAT
Found at i:56930 original size:31 final size:28
Alignment explanation
Indices: 56892--56948 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 28
56882 TCAATATTTT
56892 GGAAATAAAGTTGAGGTTGGAGTATCCCCTC
1 GGAAATAAAG--G-GGTTGGAGTATCCCCTC
*
56923 GGAAATAACGGGGTTGGAGTATCCCC
1 GGAAATAAAGGGGTTGGAGTATCCCC
56949 GATGATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 15 0.60
29 1 0.04
31 9 0.36
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.23
Consensus pattern (28 bp):
GGAAATAAAGGGGTTGGAGTATCCCCTC
Found at i:56941 original size:28 final size:27
Alignment explanation
Indices: 56906--56977 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
56896 ATAAAGTTGA
**
56906 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCGAGG-AATAACGG
* *
56934 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGAGGAATAACGG
*
56961 GGTTGGAGTGTCCCCGA
1 GGTTGGAGTATCCCCGA
56978 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGG
Found at i:59448 original size:13 final size:13
Alignment explanation
Indices: 59430--59455 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
59420 ACAAAGATCC
59430 ATGTATCGATACA
1 ATGTATCGATACA
59443 ATGTATCGATACA
1 ATGTATCGATACA
59456 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:59451 original size:33 final size:33
Alignment explanation
Indices: 59409--59475 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
59399 AAAATTTCCA
***
59409 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
59442 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
59475 A
1 A
59476 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:59535 original size:13 final size:13
Alignment explanation
Indices: 59517--59541 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59507 ACAATACTTA
59517 TGTATCGATACAT
1 TGTATCGATACAT
59530 TGTATCGATACA
1 TGTATCGATACA
59542 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:59541 original size:32 final size:32
Alignment explanation
Indices: 59498--59560 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
59488 TAGCTAATTA
*
59498 TGTAACGATACAATACTTATGTATCGATACAT
1 TGTAACGATACAAAACTTATGTATCGATACAT
*
59530 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTAACGATACAAAACTTATGTATCGATACA
59561 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (32 bp):
TGTAACGATACAAAACTTATGTATCGATACAT
Found at i:59554 original size:19 final size:19
Alignment explanation
Indices: 59495--59562 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
59485 CAGTAGCTAA
* *
59495 TTATGTAACGATACAATAC
1 TTATGTATCGATACAAAAC
59514 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
59529 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
59546 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
59563 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 1 0.02
19 27 0.64
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:69759 original size:20 final size:21
Alignment explanation
Indices: 69734--69773 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
69724 TGAGAAGCTG
*
69734 AACAT-ATTAAAAATGCATGA
1 AACATAATAAAAAATGCATGA
69754 AACATAATAAAAAATGCATG
1 AACATAATAAAAAATGCATG
69774 GTCAAAGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (21 bp):
AACATAATAAAAAATGCATGA
Found at i:70201 original size:13 final size:14
Alignment explanation
Indices: 70183--70211 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
70173 GGGAATGGAC
70183 TTTTTGTTGA-GTT
1 TTTTTGTTGATGTT
70196 TTTTTGTTGATGTT
1 TTTTTGTTGATGTT
70210 TT
1 TT
70212 GCTAAGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.72
Consensus pattern (14 bp):
TTTTTGTTGATGTT
Found at i:70665 original size:20 final size:20
Alignment explanation
Indices: 70632--70745 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
70622 TTTTAACTAG
*
70632 ATGTATCAATACATTGAAAA
1 ATGTATCGATACATTGAAAA
* * *
70652 ATGCATTGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* *
70672 ATGTATCGATACGTTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
70692 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
70712 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
70732 ATGTATCGATACAT
1 ATGTATCGATACAT
70746 CTGGGTACTT
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 79 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:73162 original size:22 final size:22
Alignment explanation
Indices: 73134--73175 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
73124 GGGTCTCAAG
73134 CTGACTATAGCTAAGAGAGCAA
1 CTGACTATAGCTAAGAGAGCAA
*
73156 CTGACTATTGCTAAGAGAGC
1 CTGACTATAGCTAAGAGAGC
73176 CTGAGTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.21
Consensus pattern (22 bp):
CTGACTATAGCTAAGAGAGCAA
Found at i:84163 original size:33 final size:33
Alignment explanation
Indices: 84126--84192 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
84116 AGTAGCTTAA
84126 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
84159 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
84192 A
1 A
84193 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:84166 original size:13 final size:13
Alignment explanation
Indices: 84148--84172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
84138 CAAAAAAATA
84148 TGTATCGATACAT
1 TGTATCGATACAT
84161 TGTATCGATACA
1 TGTATCGATACA
84173 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:85081 original size:49 final size:49
Alignment explanation
Indices: 84897--85218 Score: 292
Period size: 52 Copynumber: 6.4 Consensus size: 49
84887 AAAAGGATGT
* * * *
84897 CAATGTGCTGATTCATGG-TCAGCGACATTAGACTTGAAA-ATGAGAAGAATGC
1 CAATATGCTGATTCAAGGCT-AGCGACATTGGACTT-AAAGAT--GAAG-GTGC
* ** *
84949 CAATGTGCTGATTCAAGGCTAGCGACATTGGGTTTTAAAGATGACTAAGGCGC
1 CAATATGCTGATTCAAGGCTAGCGACATT-GGACTTAAAGATG---AAGGTGC
* *
85002 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGGTGC
* * * * *
85051 CAATGTGCTGGTTCAAGGCTAGTGACATTGGACTTAAAGGTGCCAAAGGCGC
1 CAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATG---AAGGTGC
* * *
85103 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAA-GTGC
1 CAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGGTGC
** * * *
85151 CAATGCGCTGATTCAAGGCTAGCTACATTGGACTTAAAAGA-CAAGATGC
1 CAATATGCTGATTCAAGGCTAGCGACATTGGACTT-AAAGATGAAGGTGC
85200 CAATATGCTGATTCAAGGC
1 CAATATGCTGATTCAAGGC
85219 CAGCTATATT
Statistics
Matches: 222, Mismatches: 37, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
48 34 0.15
49 69 0.31
51 1 0.00
52 81 0.36
53 34 0.15
54 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCTAGCGACATTGGACTTAAAGATGAAGGTGC
Found at i:85121 original size:101 final size:99
Alignment explanation
Indices: 84897--85228 Score: 393
Period size: 101 Copynumber: 3.3 Consensus size: 99
84887 AAAAGGATGT
* * * * * *
84897 CAATGTGCTGATTCATGGTCAGCGACATTAGACTTGAAA-ATGAGAAGAATGCCAATGTGCTGAT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGAT--GAAG-GTGCCAATGTGCTGAT
* **
84961 TCAAGGCTAGCGACATTGGGTTTTAAAGATGACTAAGGCGC
62 TCAAGGCTAGTGACATT-GGACTTAAAG-TGAC-AAGGCGC
*
85002 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGGTTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
*
85067 GGCTAGTGACATTGGACTTAAAGGTGCCAAAGGCGC
66 GGCTAGTGACATTGGACTTAAA-GTGAC-AAGGCGC
* *
85103 CAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAA-GTGCCAATGCGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* **
85167 GGCTAGCT-ACATTGGACTTAAA-AGACAAGATGC
66 GGCTAG-TGACATTGGACTTAAAGTGACAAGGCGC
*
85200 CAATATGCTGATTCAAGGCCAGCTATATT
1 CAATATGCTGATTCAAGGCCAGCGATATT
85229 TTAGTAGTCT
Statistics
Matches: 203, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
97 32 0.16
98 2 0.01
100 38 0.19
101 61 0.30
102 31 0.15
103 4 0.02
104 3 0.01
105 32 0.16
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (99 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
GGCTAGTGACATTGGACTTAAAGTGACAAGGCGC
Found at i:86697 original size:19 final size:19
Alignment explanation
Indices: 86673--86740 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
86663 AATTTAACAA
86673 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
86692 TTTGTATTGATAC--AA--
1 TTTGTATCGATACATAAGT
86707 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
86724 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
86741 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:86716 original size:32 final size:32
Alignment explanation
Indices: 86675--86737 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
86665 TTTAACAATT
* *
86675 TGTATCGATACATAAGTTTTGTATTGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
86707 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
86738 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:86798 original size:13 final size:13
Alignment explanation
Indices: 86780--86805 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
86770 CATTTTTCTG
86780 TGTATCGATACAT
1 TGTATCGATACAT
86793 TGTATCGATACAT
1 TGTATCGATACAT
86806 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:86802 original size:33 final size:33
Alignment explanation
Indices: 86760--86826 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
86750 GCCAAGGAAA
***
86760 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
86793 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
86826 T
1 T
86827 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:89416 original size:52 final size:53
Alignment explanation
Indices: 89331--89500 Score: 181
Period size: 52 Copynumber: 3.3 Consensus size: 53
89321 TTATTTCCGA
* *
89331 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTC-CAAAAACACCAATTTTTCCACAATC
* * **
89383 GGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATC
* *
89435 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
* *
89487 GAGGATGCTCCAAC
1 GGGGATACTCCAAC
89501 CTCGTTATTT
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
51 9 0.09
52 71 0.72
53 13 0.13
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
Found at i:89543 original size:212 final size:212
Alignment explanation
Indices: 89160--89567 Score: 579
Period size: 212 Copynumber: 1.9 Consensus size: 212
89150 TTATCAATTC
* * *
89160 TCCACAATCAAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGTGA
1 TCCACAATCAAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
89225 TACTCTAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAAC
66 TACTCCAACTCCGATTTTATTTCC--AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * *
89290 CCCGTTAATCATCGGAGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTA
129 CCCGTTAATCATCGGAGATACTCCAACCCCGTTACTTCCGAGCGGATACTCCAACCCCGGCTTTA
89355 TCGCTAAAACACTAATTTT
194 TCGCTAAAACACTAATTTT
** * * *
89374 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCAAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
89438 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATGCTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
89501 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGCGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGAGATACTCCAACCCCGTTACTTCCGAGCGGATACTCCAACCCCGGCTTT
89566 AT
193 AT
89568 TCCCAAAATA
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
211 27 0.16
212 66 0.38
213 3 0.02
214 42 0.24
215 34 0.20
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCAAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGAGATACTCCAACCCCGTTACTTCCGAGCGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Done.