Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold506_ERROPOS21321947
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: 99999
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:246 original size:108 final size:108
Alignment explanation
Indices: 54--272 Score: 411
Period size: 108 Copynumber: 2.0 Consensus size: 108
44 TTCTCTTCCA
*
54 TTCATTTTCTTTCCTTTTTATTTTATCATCTTTGTTCATCTCGTTCTTCAATCTTATCTTTTTCT
1 TTCATTTTCTTTCCTTTTTATTTTATCATCTTTGTTCATCTCGTTCTTCAATCGTATCTTTTTCT
*
119 AGAAAACATCACAAACCCAACTGTTCATCTCTCTCATTTTTTT
66 AGAAAACATCACAAACCCAACTGTTCATCTCTCTCAATTTTTT
162 TTCATTTTCTTTCCTTTTTATTTTATCATCTTTGTTCATCTCGTTCTTCAATCGTATCTTTTTCT
1 TTCATTTTCTTTCCTTTTTATTTTATCATCTTTGTTCATCTCGTTCTTCAATCGTATCTTTTTCT
*
227 AGAAAACATCACAAGCCCAACTGTTCATCTCTCTCAATTTTTT
66 AGAAAACATCACAAACCCAACTGTTCATCTCTCTCAATTTTTT
270 TTC
1 TTC
273 TCTCTATAGG
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 108 1.00
ACGTcount: A:0.20, C:0.24, G:0.05, T:0.51
Consensus pattern (108 bp):
TTCATTTTCTTTCCTTTTTATTTTATCATCTTTGTTCATCTCGTTCTTCAATCGTATCTTTTTCT
AGAAAACATCACAAACCCAACTGTTCATCTCTCTCAATTTTTT
Found at i:992 original size:8 final size:8
Alignment explanation
Indices: 979--1005 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
969 TTATATATTA
979 TTTTTTAT
1 TTTTTTAT
987 TTTTTTAT
1 TTTTTTAT
995 TTTTTTAT
1 TTTTTTAT
1003 TTT
1 TTT
1006 CAGCTGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:5302 original size:22 final size:23
Alignment explanation
Indices: 5277--5322 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5267 CAACCAAATC
5277 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
5299 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
5322 A
1 A
5323 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:5328 original size:23 final size:23
Alignment explanation
Indices: 5284--5328 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5274 ATCAATTCAA
*
5284 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
5307 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
5329 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:15081 original size:7 final size:7
Alignment explanation
Indices: 15069--15101 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
15059 TTTCAATTTC
15069 ATATTGA
1 ATATTGA
15076 ATATTGA
1 ATATTGA
15083 ATATTGA
1 ATATTGA
15090 ATATTGA
1 ATATTGA
15097 ATATT
1 ATATT
15102 TCAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (7 bp):
ATATTGA
Found at i:28597 original size:31 final size:31
Alignment explanation
Indices: 28559--28617 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
28549 TAATAAAAGT
28559 CATAAACCAATGACTCTTGACCTTTCATTGC
1 CATAAACCAATGACTCTTGACCTTTCATTGC
28590 CATAAACCAATGACTCTTGACCTTTCAT
1 CATAAACCAATGACTCTTGACCTTTCAT
28618 CCTCCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (31 bp):
CATAAACCAATGACTCTTGACCTTTCATTGC
Found at i:29899 original size:15 final size:15
Alignment explanation
Indices: 29879--29925 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
29869 CTTGAACAGG
*
29879 GAAGAAGAAGAAGAA
1 GAAGAAGAATAAGAA
*
29894 GAAGAAGAATAAGCA
1 GAAGAAGAATAAGAA
* *
29909 GCAGTAGAATAAGAA
1 GAAGAAGAATAAGAA
29924 GA
1 GA
29926 GATTGTAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.30, T:0.06
Consensus pattern (15 bp):
GAAGAAGAATAAGAA
Found at i:30924 original size:21 final size:20
Alignment explanation
Indices: 30898--30942 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
30888 CAATGTGGCA
30898 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
* *
30918 TAGTTAACTTGCCATATCAGC
1 -AGTTAACTGGCCACATCAGC
30939 AGTT
1 AGTT
30943 CTGTTAAGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:31037 original size:29 final size:31
Alignment explanation
Indices: 30973--31040 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
30963 ACTGTTAGTC
*
30973 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAACGTT
*
31004 AGTGACTGTTTTGTTA-TTTTTCA-AA-GTT
1 AGTGACTGTTTTGTCACTTTTTCATAACGTT
31032 AGGTGACTG
1 A-GTGACTG
31041 AAATAAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 4 0.12
29 9 0.26
30 6 0.18
31 15 0.44
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAACGTT
Found at i:37545 original size:556 final size:542
Alignment explanation
Indices: 36506--37577 Score: 1984
Period size: 556 Copynumber: 2.0 Consensus size: 542
36496 TCTTACAGTT
36506 TCAGCTTGGGCTTGCGTTGCCTTAAACTCTGCAGCTCTTGCAGCCAACTCAGCTTGCCTTGTCTC
1 TCAGCTTGGGCTTGCGTTGCCTTAAACTCTGCAGCTCTTGCAGCCAACTCAGCTTGCCTTGTCTC
36571 TTCTTGCTTCTTCATAAGTTCAAAGGCCTACAACAACAAGAAGAAGCCATTAGCATCACATAATG
66 TTCTTGCTTCTTCATAAGTTCAAAGGCCTACAACAACAAGAAGAAGCCATTAGCATCACATAATG
36636 AATAACCAAACAGTAAATATACAAAATATATAACTCAACCCTCCTCTAAAACAAGCAAAAATAAT
131 AATAACCAAACAGTAAATATACAAAATATATAACTCAACCCTCCTCTAAAACAAGCAAAAATAAT
36701 ATTAAAAAAAAAAAAGACATTCTGGTATGCAAATGTGAAGAAACCTTTTTGGCATTAGAGGAGCT
196 ATT-AAAAAAAAAAAGACATTCTGGTATGCAAATGTGAAGAAACCTTTTTGGCATTAGAGGAGCT
36766 GCTGATTTCCCTCAAGGCCTTGGCAATGTAATACCAAAAATCGATTGAACCAAGTGGTTGGACCA
260 GCTGATTTCCCTCAAGGCCTTGGCAATGTAATACCAAAAATCGATTGAACCAAGTGGTTGGACCA
36831 AATTGTTCAATTTATTTTTATCTTTCTAGTTTTTTAATAATTTTTTTATCAAACCAATTAAACCT
325 AATTGTTCAATTTATTTTTATCTTTCTAGTTTTTTAATAATTTTTTTATCAAACCAATTAAACCT
*
36896 TGCAAGTGGGTGCATGCATGCTTGATATTTTGGAAACTTGCTTTCATGTTAAGTTATACTGATAA
390 TGCAAGTGGGTGCATCCATGCTTGATATTTTGGAAACTTGCTTTCATGTTAAGTTATACTGATAA
36961 TACTTTTAAGAAGGTTAAATCGTACATAATAGAAATGAAAACAATAAAAATGAGTTTCCTCAAGG
455 TACTTTTAAGAAGGTTAAATCGTACATAATAGAAATGAAAACAATAAAAATGAGTTTCCTCAAGG
37026 CCTTGGCAATGTAATACCAAAAA
520 CCTTGGCAATGTAATACCAAAAA
37049 TCAGCTTGGGCTTGCGTTGCCTTAAACTCTGCAGCTCTTGCAGCCAACTCAGCTTGCCTTGTCTC
1 TCAGCTTGGGCTTGCGTTGCCTTAAACTCTGCAGCTCTTGCAGCCAACTCAGCTTGCCTTGTCTC
37114 TTCTTGCTTCTTCATCTCTTCTTGCCTTCAAAGTTCAAAGGCCTACAACAACAAGAAGAAGCCAT
66 TTCTTGCTTCTTCA-------------T--AAGTTCAAAGGCCTACAACAACAAGAAGAAGCCAT
37179 TAGCATCACATAATGAATAACCAAACAGTAAATATACAAAATATATAACTCAACCCTCCTCTAAA
116 TAGCATCACATAATGAATAACCAAACAGTAAATATACAAAATATATAACTCAACCCTCCTCTAAA
37244 ACAAGCAAAAATAATATT-AAAAAAAAAAGACATTCTGGTATGCAAATGTGAAGAAACCTTTTTG
181 ACAAGCAAAAATAATATTAAAAAAAAAAAGACATTCTGGTATGCAAATGTGAAGAAACCTTTTTG
37308 GCATTAGAGGAGCTGCTGATTTCCCTCAAGGCCTTGGCAATGTAATACCAAAAATCGATTGAACC
246 GCATTAGAGGAGCTGCTGATTTCCCTCAAGGCCTTGGCAATGTAATACCAAAAATCGATTGAACC
37373 AAGTGGTTGGACCAAATTGTTCAATTTATTTTTATCTTTCTAGTTTTTTAATAATTTTTTTATCA
311 AAGTGGTTGGACCAAATTGTTCAATTTATTTTTATCTTTCTAGTTTTTTAATAATTTTTTTATCA
37438 AACCAATTAAACCTTGCAAGTGGGTGCATCCATGCTTGATATTTTGGAAACTTGCTTTCATGTTA
376 AACCAATTAAACCTTGCAAGTGGGTGCATCCATGCTTGATATTTTGGAAACTTGCTTTCATGTTA
37503 AGTTATACTGATAATACTTTTAAGAAGGTTAAATCGTACATAATAGAAATGAAAACAATAAAAAT
441 AGTTATACTGATAATACTTTTAAGAAGGTTAAATCGTACATAATAGAAATGAAAACAATAAAAAT
37568 GAGTTTCCTC
506 GAGTTTCCTC
37578 CCGCCCAGGA
Statistics
Matches: 513, Mismatches: 1, Indels: 17
0.97 0.00 0.03
Matches are distributed among these distances:
543 79 0.15
556 316 0.62
558 118 0.23
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (542 bp):
TCAGCTTGGGCTTGCGTTGCCTTAAACTCTGCAGCTCTTGCAGCCAACTCAGCTTGCCTTGTCTC
TTCTTGCTTCTTCATAAGTTCAAAGGCCTACAACAACAAGAAGAAGCCATTAGCATCACATAATG
AATAACCAAACAGTAAATATACAAAATATATAACTCAACCCTCCTCTAAAACAAGCAAAAATAAT
ATTAAAAAAAAAAAGACATTCTGGTATGCAAATGTGAAGAAACCTTTTTGGCATTAGAGGAGCTG
CTGATTTCCCTCAAGGCCTTGGCAATGTAATACCAAAAATCGATTGAACCAAGTGGTTGGACCAA
ATTGTTCAATTTATTTTTATCTTTCTAGTTTTTTAATAATTTTTTTATCAAACCAATTAAACCTT
GCAAGTGGGTGCATCCATGCTTGATATTTTGGAAACTTGCTTTCATGTTAAGTTATACTGATAAT
ACTTTTAAGAAGGTTAAATCGTACATAATAGAAATGAAAACAATAAAAATGAGTTTCCTCAAGGC
CTTGGCAATGTAATACCAAAAA
Found at i:49612 original size:55 final size:55
Alignment explanation
Indices: 49520--49639 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 55
49510 CTGCCAAAAC
* * * *
49520 AACACGGGCGTGCGACACGCCCGTACTATGAACCCGTGGCTAAACCTGTCAAATT
1 AACACGGGCGTACGACACGCCCGTACCAAGAACCCGTGGCTAAACCTATCAAATT
* * * * *
49575 AACACCGGCGTACGACACGCCCGTGCCAAGCAA-CCGTGGTTGAACCTATTAAATT
1 AACACGGGCGTACGACACGCCCGTACCAAG-AACCCGTGGCTAAACCTATCAAATT
49630 AACACGGGCG
1 AACACGGGCG
49640 AGGGCCTACA
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
55 52 0.96
56 2 0.04
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.17
Consensus pattern (55 bp):
AACACGGGCGTACGACACGCCCGTACCAAGAACCCGTGGCTAAACCTATCAAATT
Found at i:55178 original size:12 final size:13
Alignment explanation
Indices: 55163--55191 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55153 GTTTATTATT
55163 TTTTATTTTT-GG
1 TTTTATTTTTGGG
55175 TTTTATTTTTGGG
1 TTTTATTTTTGGG
55188 TTTT
1 TTTT
55192 TATGGGCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTGGG
Found at i:64556 original size:19 final size:19
Alignment explanation
Indices: 64520--64556 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64510 TAATTAGGCT
* *
64520 TTAATTAGGTGAATTTAAC
1 TTAATTAGGAGAAATTAAC
64539 TTAATTAGGAGAAATTAA
1 TTAATTAGGAGAAATTAA
64557 GAAAAAAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.16, T:0.38
Consensus pattern (19 bp):
TTAATTAGGAGAAATTAAC
Found at i:71913 original size:39 final size:39
Alignment explanation
Indices: 71889--72017 Score: 213
Period size: 39 Copynumber: 3.3 Consensus size: 39
71879 GACTTTAGCT
* *
71889 CGGACGTAATTCCACCATATAGCCTGCGGACCTTAAGTC
1 CGGACATAATTCCAACATATAGCCTGCGGACCTTAAGTC
71928 CGGACATAATTCCAACATATAGCCTGCGGACCTTAAGTC
1 CGGACATAATTCCAACATATAGCCTGCGGACCTTAAGTC
*
71967 CGGACATAATTCCAGCATATAGCCTGCGGACCTTAAGTC
1 CGGACATAATTCCAACATATAGCCTGCGGACCTTAAGTC
* *
72006 CGAATATAATTC
1 CGGACATAATTC
72018 ATCACTGAGT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (39 bp):
CGGACATAATTCCAACATATAGCCTGCGGACCTTAAGTC
Found at i:76669 original size:40 final size:42
Alignment explanation
Indices: 76574--76673 Score: 116
Period size: 40 Copynumber: 2.4 Consensus size: 42
76564 ATACTATATT
* *
76574 TGAGATAGGCTAAGGCCCTACTATATATGCCTGATTCTGTATT
1 TGAG-TAGGCTAAGGCCCTACTATATATGCCTGATTCTGCATC
* * *
76617 TGA-TTGGACTAAGGCCCTAGTATAT-T-TCTGATTCTGCATC
1 TGAGTAGG-CTAAGGCCCTACTATATATGCCTGATTCTGCATC
76657 TGAGTAGGCTAAGGCCC
1 TGAGTAGGCTAAGGCCC
76674 ACACTGATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
40 23 0.47
41 7 0.14
42 16 0.33
43 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (42 bp):
TGAGTAGGCTAAGGCCCTACTATATATGCCTGATTCTGCATC
Found at i:80411 original size:11 final size:11
Alignment explanation
Indices: 80397--80438 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
80387 TAAAGATTAC
80397 TTTATTAATAT
1 TTTATTAATAT
*
80408 TTTAATGAGATAT
1 TTT-ATTA-ATAT
80421 TTTATTAATAT
1 TTTATTAATAT
80432 TTTATTA
1 TTTATTA
80439 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:84113 original size:71 final size:71
Alignment explanation
Indices: 83990--84139 Score: 248
Period size: 71 Copynumber: 2.1 Consensus size: 71
83980 TTTTGGGGTG
* *
83990 TGATCGAGGGGCGGAGAGGTGTGTTGGCTGGATGAGTGAGTTTTTACTACTTGACTGCACTCATA
1 TGATTGAGGGGCGGAGAGGTGTGTTGGCTGGATGAGTGAGTTTTTACGACTTGACTGCACTCATA
84055 CACATC
66 CACATC
*
84061 TGATTGAGGGGCGGAGAGGTGTGTTGGCTGGAT-AGGTGAGTTTTTACGACTTGACTGCATTCAT
1 TGATTGAGGGGCGGAGAGGTGTGTTGGCTGGATGA-GTGAGTTTTTACGACTTGACTGCACTCAT
*
84125 ACGCATC
65 ACACATC
84132 TGATTGAG
1 TGATTGAG
84140 TGGCTGGGTG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
70 1 0.01
71 73 0.99
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.31
Consensus pattern (71 bp):
TGATTGAGGGGCGGAGAGGTGTGTTGGCTGGATGAGTGAGTTTTTACGACTTGACTGCACTCATA
CACATC
Found at i:90264 original size:30 final size:30
Alignment explanation
Indices: 90228--90284 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
90218 ACAAAACATG
90228 TAAACCCAACATCAAGCTTCCATAATCATA
1 TAAACCCAACATCAAGCTTCCATAATCATA
90258 TAAACCCAACATCAAGCTTCCATAATC
1 TAAACCCAACATCAAGCTTCCATAATC
90285 CATCAACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.32, G:0.04, T:0.23
Consensus pattern (30 bp):
TAAACCCAACATCAAGCTTCCATAATCATA
Found at i:93123 original size:30 final size:30
Alignment explanation
Indices: 93082--93139 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
93072 ATTTCAACAA
* * *
93082 TAGGGGTAAAATGGTCATTTTGCCAAAGCC
1 TAGGGGCAAAATAGTCATTTTACCAAAGCC
*
93112 TAGGGGCAAAATAGTTATTTTACCAAAG
1 TAGGGGCAAAATAGTCATTTTACCAAAG
93140 ATGTGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAATAGTCATTTTACCAAAGCC
Found at i:93682 original size:93 final size:93
Alignment explanation
Indices: 93481--93700 Score: 236
Period size: 93 Copynumber: 2.4 Consensus size: 93
93471 TTCTTGTGTG
* * * *
93481 CCAGTGTAAGACATGTCTGGGACATGCATCGGCACATTATTAGTGCCAGTGTAAGACCATGTCTG
1 CCAGTATAAAACATGTCTGGGACATGCATCGGCACATGATTAGTGCCAGTGTAAGACCATGTCCG
*
93546 GGACATGGCATCGGCGTAGAGATGAGTA
66 GGACATGGCATCGACGTAGAGATGAGTA
* * *
93574 CCAGTATAAGACATGTCAGGGACATGCATCGGCTA-A-GAGTT-GTGCTAGTGTAAGA-CATGTC
1 CCAGTATAAAACATGTCTGGGACATGCATCGGC-ACATGA-TTAGTGCCAGTGTAAGACCATGTC
* *
93635 CGGGACAT-GCATCAGCACGTATATATGAG-A
64 CGGGACATGGCATC-G-ACGTAGAGATGAGTA
*
93665 GCTAGTATAAAACCATGTCTGGGACATGGCATCGGC
1 -CCAGTATAAAA-CATGTCTGGGACAT-GCATCGGC
93701 CACTTATCCC
Statistics
Matches: 109, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
90 5 0.05
91 15 0.14
92 33 0.30
93 47 0.43
94 9 0.08
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (93 bp):
CCAGTATAAAACATGTCTGGGACATGCATCGGCACATGATTAGTGCCAGTGTAAGACCATGTCCG
GGACATGGCATCGACGTAGAGATGAGTA
Found at i:94512 original size:55 final size:55
Alignment explanation
Indices: 94446--94575 Score: 179
Period size: 55 Copynumber: 2.4 Consensus size: 55
94436 CACTTAAAAT
* * * *
94446 TTTAAGTCAGTATTGTGCACGGGTAGGCCACACGGGCGTGTGCCATGGCCGTGTC
1 TTTAAGTCAGTATTGTACACGAGTAGGCCACACGGGCGTGTGCCATGACCATGTC
* *
94501 TTTAAGTCAGTATTGTACACGAGTAGGTCACACGGGCGTGTGTCATGACCATGTC
1 TTTAAGTCAGTATTGTACACGAGTAGGCCACACGGGCGTGTGCCATGACCATGTC
* * *
94556 TTAAAGTCAGTGTTGCACAC
1 TTTAAGTCAGTATTGTACAC
94576 AGGCTAAGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (55 bp):
TTTAAGTCAGTATTGTACACGAGTAGGCCACACGGGCGTGTGCCATGACCATGTC
Found at i:94929 original size:34 final size:34
Alignment explanation
Indices: 94886--94953 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
94876 ATAGTCAAAT
*
94886 GCAGTTCGGGCCTTAGCCTATTTCAGTTTCAGTA
1 GCAGTTCGGGCCTTAGCCCATTTCAGTTTCAGTA
*
94920 GCAGTTCGGGCCTTAGCCCATTTCAGTTTTAGTA
1 GCAGTTCGGGCCTTAGCCCATTTCAGTTTCAGTA
94954 TCAGACATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (34 bp):
GCAGTTCGGGCCTTAGCCCATTTCAGTTTCAGTA
Found at i:96013 original size:38 final size:39
Alignment explanation
Indices: 95928--96112 Score: 225
Period size: 38 Copynumber: 4.7 Consensus size: 39
95918 TAATCCAGTC
* * * *
95928 ACCAGCACAAAACCTGCGGGACTTTAAACTCGAATATAAA
1 ACCAGCACAAAGCCTGCGGGACTTT-AACCCGGATATAAT
* *
95968 ACTAGCACTAAGCCTGCGGGA-TTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGACTTTAACCCGGATATAAT
*
96006 ACCAGCACGAAGCCTGCGGGA-TTTAACCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGACTTTAACCCGGATATAAT
*
96044 ACTAGCACAAAGCCTGC-GGACCTTTAAGCCCGGATATAAT
1 ACCAGCACAAAGCCTGCGGGA-CTTTAA-CCCGGATATAAT
*
96084 ACCAGCACGAAGCCTGC-GGACCTTTAACC
1 ACCAGCACAAAGCCTGCGGGA-CTTTAACC
96113 ACAGATACAC
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
37 3 0.02
38 62 0.48
39 10 0.08
40 55 0.42
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (39 bp):
ACCAGCACAAAGCCTGCGGGACTTTAACCCGGATATAAT
Found at i:96078 original size:78 final size:78
Alignment explanation
Indices: 95928--96110 Score: 248
Period size: 78 Copynumber: 2.3 Consensus size: 78
95918 TAATCCAGTC
* * * *
95928 ACCAGCACAAAACCTGCGGGACTTTAAACTCGAATATAAAACTAGCACTAAGCCTGCGGGATTTA
1 ACCAGCACGAAGCCTGCGGGACTTTAAACCCGAATATAAAACTAGCACAAAGCCTGCGGGATTTA
95993 ACCCGGATATAAT
66 ACCCGGATATAAT
* *
96006 ACCAGCACGAAGCCTGCGGGA-TTT-AACCCGGATATAATACTAGCACAAAGCCTGC-GGACCTT
1 ACCAGCACGAAGCCTGCGGGACTTTAAACCCGAATATAAAACTAGCACAAAGCCTGCGGGA--TT
96068 TAAGCCCGGATATAAT
64 TAA-CCCGGATATAAT
96084 ACCAGCACGAAGCCTGC-GGACCTTTAA
1 ACCAGCACGAAGCCTGCGGGA-CTTTAA
96111 CCACAGATAC
Statistics
Matches: 93, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
75 3 0.03
76 27 0.29
77 11 0.12
78 48 0.52
79 3 0.03
80 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (78 bp):
ACCAGCACGAAGCCTGCGGGACTTTAAACCCGAATATAAAACTAGCACAAAGCCTGCGGGATTTA
ACCCGGATATAAT
Done.