Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2555
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: 31754
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:12786 original size:28 final size:28
Alignment explanation
Indices: 12746--12815 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
12736 ATAGTAAGTC
*
12746 CGCACACTTAGTGCT-TAATAATCAAACT
1 CGCACACTTAGTGCTAT-ACAATCAAACT
*
12774 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
12802 CGCACACTTAGTGC
1 CGCACACTTAGTGC
12816 CAATCTCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 38 0.97
29 1 0.03
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:16078 original size:47 final size:47
Alignment explanation
Indices: 15938--16211 Score: 467
Period size: 47 Copynumber: 5.7 Consensus size: 47
15928 TTAGGATTCT
15938 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
15987 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
16036 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
16083 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
16130 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
16177 ATGTGATGAATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
16212 TCTCGAAGGG
Statistics
Matches: 218, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
47 149 0.68
49 69 0.32
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:16380 original size:37 final size:37
Alignment explanation
Indices: 16330--16445 Score: 187
Period size: 37 Copynumber: 3.1 Consensus size: 37
16320 CCGAGCTCTA
*
16330 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
16367 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
16404 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
16441 AAGAC
1 AAGAC
16446 TTCGTAATAA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:18691 original size:40 final size:40
Alignment explanation
Indices: 18337--18688 Score: 515
Period size: 40 Copynumber: 8.8 Consensus size: 40
18327 GAGTTACTAA
* * *
18337 ATCCGGGTTAAGTCCCAAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
18377 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* * *
18417 ATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* *
18457 GTCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
18497 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
18537 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* *
18577 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* *** * * * *
18617 ATCCGTGCTAAACCCCGAAGAGCATTCGTGCTGGTGTTAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* * *
18657 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCT
18689 GGTACGTGTA
Statistics
Matches: 287, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 287 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
Found at i:22333 original size:47 final size:47
Alignment explanation
Indices: 22193--22464 Score: 449
Period size: 47 Copynumber: 5.7 Consensus size: 47
22183 TTAGGATTCT
22193 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
22242 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
22291 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
22338 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
22385 ATGTGATGAATGTGAAAGTGTATATATGTGA-CAGGGCGAGTGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
22431 ATGTGATG-ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
22465 TCCGAAGGGC
Statistics
Matches: 216, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
45 21 0.10
46 21 0.10
47 105 0.49
49 69 0.32
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:22628 original size:36 final size:36
Alignment explanation
Indices: 22581--22694 Score: 167
Period size: 36 Copynumber: 3.1 Consensus size: 36
22571 CCGAGCTCTA
*
22581 AAGACCCGATGACTACATGTGGGGATTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTGTCCGGGT
22617 AAGACCCGATGACTACGTGT-GGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGA-TTTGTCCGGGT
* * *
22653 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATT-TGTCCGGGT
22690 AAGAC
1 AAGAC
22695 TTCGTAATAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 4 0.06
36 50 0.70
37 17 0.24
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (36 bp):
AAGACCCGATGACTACGTGTGGGGATTTGTCCGGGT
Found at i:24602 original size:77 final size:76
Alignment explanation
Indices: 24540--24876 Score: 352
Period size: 75 Copynumber: 4.4 Consensus size: 76
24530 CGAGTTACTA
*
24540 ATCCGGGTTAAGTCCCAAAGAGCATTCATGC-AGTGATGTATCCGGGCTAAGTTCG-AGAGCATT
1 ATCCGGG-TAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAAGAGCATT
*
24603 CATGCTAGTGAT
65 CGTGCTAGTGAT
* * *
24615 GTACCGGGTAAGTCCCGAAGAGCATTCGTGCTAGTGA-GTGTCCGGGCTAAGTTCCGAAGAGCAT
1 AT-CCGGGTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTT-CGAAGAGCAT
24679 TCGTGCTAGTGATGT
64 TCGTGCTAGTGA--T
24694 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTAT-C-GGCTAAGTTCGAAGAGCATT
1 ATCCGGG-TAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAAGAGCATT
24756 C-TGCTAGTGATGT
65 CGTGCTAGTGA--T
* * * * * ***
24769 ATCCGGCTAAGTTCCGAAGAGCATTCGTGCTAG-GATATATCCGTGCTAAACCCCGAAGAGCATT
1 ATCCGGGTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCT-AAGTTCGAAGAGCATT
*
24833 C-TGCTGGTGTTAT
65 CGTGCTAGTG--AT
* *
24846 ATCCGGGCTAGGT-CCGAAGAGCAATCATGCT
1 ATCCGGG-TAAGTCCCGAAGAGCATTCATGCT
24877 GGTACGTGTA
Statistics
Matches: 227, Mismatches: 20, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
74 11 0.05
75 75 0.33
76 27 0.12
77 71 0.31
78 32 0.14
79 11 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (76 bp):
ATCCGGGTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAAGAGCATTC
GTGCTAGTGAT
Found at i:24636 original size:75 final size:78
Alignment explanation
Indices: 24540--24876 Score: 417
Period size: 77 Copynumber: 4.4 Consensus size: 78
24530 CGAGTTACTA
* *
24540 ATCCGGGTTAAGTCCCAAAGAGCATTCATGC-AGTGATGTATCCGGGCTAAGTTCG-AGAGCATT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAAGAGCATT
24603 CATGCTAGTGATGT
66 C-TGCTAGTGATGT
* *
24617 A-CCGGG-TAAGTCCCGAAGAGCATTCGTGCTAGTGA-GTGTCCGGGCTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTT-CGAAGAGCAT
24679 TCGTGCTAGTGATGT
65 TC-TGCTAGTGATGT
24694 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTAT-C-GGCTAAGTTCGAAGAGCATT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAAGAGCATT
24756 CTGCTAGTGATGT
66 CTGCTAGTGATGT
* * * * ***
24769 ATCC-GGCTAAGTTCCGAAGAGCATTCGTGCTAG-GATATATCCGTGCTAAACCCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCT-AAGTTCGAAGAGCAT
* * *
24832 TCTGCTGGTGTTAT
65 TCTGCTAGTGATGT
* *
24846 ATCCGGGCTAGGT-CCGAAGAGCAATCATGCT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
24877 GGTACGTGTA
Statistics
Matches: 231, Mismatches: 18, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
74 14 0.06
75 72 0.31
76 27 0.12
77 75 0.32
78 35 0.15
79 8 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (78 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAAGAGCATT
CTGCTAGTGATGT
Found at i:24786 original size:153 final size:153
Alignment explanation
Indices: 24540--24876 Score: 459
Period size: 153 Copynumber: 2.2 Consensus size: 153
24530 CGAGTTACTA
* *
24540 ATCCGGGTTAAGTCCCAAAGAGCATTCATGC-AGTGATGTATCCGGGCTAAGTTCGAGAGCATTC
1 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAGAGCATTC
* * * ***
24604 ATGCTAGTGATGTACCGGGTAAGTCCCGAAGAGCATTCGTGCTAGTGA-GTGTCCGGGCTAAGTT
65 ATGCTAGTGATGTACCGGCTAAGTCCCGAAGAGCATTCGTGCTAG-GATATATCCGGGCTAAACC
*
24668 CCGAAGAGCATTCGTGCTAGTGATGT
129 CCGAAGAGCATTC-TGCTAGTGATAT
24694 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTAT-C-GGCTAAGTTCGAAGAGCATTC
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCG-AGAGCATTC
* *
24757 -TGCTAGTGATGTATCCGGCTAAGTTCCGAAGAGCATTCGTGCTAGGATATATCCGTGCTAAACC
65 ATGCTAGTGATGTA-CCGGCTAAGTCCCGAAGAGCATTCGTGCTAGGATATATCCGGGCTAAACC
* *
24821 CCGAAGAGCATTCTGCTGGTGTTAT
129 CCGAAGAGCATTCTGCTAGTGATAT
* *
24846 ATCCGGGCTAGGTCCGAAGAGCAATCATGCT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCT
24877 GGTACGTGTA
Statistics
Matches: 164, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
152 64 0.39
153 78 0.48
154 22 0.13
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (153 bp):
ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCGAGAGCATTCA
TGCTAGTGATGTACCGGCTAAGTCCCGAAGAGCATTCGTGCTAGGATATATCCGGGCTAAACCCC
GAAGAGCATTCTGCTAGTGATAT
Found at i:24879 original size:39 final size:39
Alignment explanation
Indices: 24540--24876 Score: 399
Period size: 39 Copynumber: 8.8 Consensus size: 39
24530 CGAGTTACTA
* *
24540 ATCCGGGTTAAGTCCCAAAGAGCATTCATGC-AGTGATGT
1 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGT
*
24579 ATCCGGGCTAAGTTCG-AGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGT
*
24617 A-CCGGG-TAAGTCCCGAAGAGCATTCGTGCTAGTGA-GT
1 ATCCGGGCTAAGT-CCGAAGAGCATTCATGCTAGTGATGT
* *
24654 GTCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAG-TCCGAAGAGCATTCATGCTAGTGATGT
24694 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGT
*
24733 AT-C-GGCTAAGTTCGAAGAGCATTC-TGCTAGTGATGT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGT
* *
24769 ATCC-GGCTAAGTTCCGAAGAGCATTCGTGCTAG-GATAT
1 ATCCGGGCTAAG-TCCGAAGAGCATTCATGCTAGTGATGT
* ** * * *
24807 ATCCGTGCTAAACCCCGAAGAGCATTC-TGCTGGTGTTAT
1 ATCCGGGCT-AAGTCCGAAGAGCATTCATGCTAGTGATGT
* *
24846 ATCCGGGCTAGGTCCGAAGAGCAATCATGCT
1 ATCCGGGCTAAGTCCGAAGAGCATTCATGCT
24877 GGTACGTGTA
Statistics
Matches: 263, Mismatches: 21, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
36 19 0.07
37 50 0.19
38 73 0.28
39 105 0.40
40 16 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
ATCCGGGCTAAGTCCGAAGAGCATTCATGCTAGTGATGT
Found at i:28478 original size:47 final size:47
Alignment explanation
Indices: 28332--28604 Score: 442
Period size: 47 Copynumber: 5.7 Consensus size: 47
28322 TTAGGATTCT
28332 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
28381 ATGTGATG-ATGTGAAAGTGTATATATAGTGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATA-TGTGATAAGGCCTAATGGCCG
28430 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
28477 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
28524 ATGTGATGAATGTGAAAGTGT-TATATGTGACAGGGCCGAGTGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
28570 ATGTGATGAATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
28605 TCCGAAGGGC
Statistics
Matches: 214, Mismatches: 7, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
46 42 0.20
47 99 0.46
48 25 0.12
49 37 0.17
50 11 0.05
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:28589 original size:140 final size:143
Alignment explanation
Indices: 28332--28604 Score: 446
Period size: 140 Copynumber: 1.9 Consensus size: 143
28322 TTAGGATTCT
28332 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAA
1 ATGTGATGAATGTGAAAGTG-ATATATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAA
* * *
28397 GTGTATATATAGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
65 GTG-ATATATAGTGTGACAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGAT
28462 AAGGCCTAATGGCCG
129 AAGGCCTAATGGCCG
28477 ATGTGATGAATGTGAAAGTG-TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATG-ATGTGAAA
* *
28541 GTG-T-TATA-TGTGACAGGGCCGAGTGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATA
65 GTGATATATAGTGTGACAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATA
28603 AG
130 AG
28605 TCCGAAGGGC
Statistics
Matches: 122, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
140 51 0.42
141 4 0.03
142 1 0.01
143 35 0.29
144 11 0.09
145 20 0.16
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGATATATATGTGATAAGGCCTAATGGCCGATGTGATGATGTGAAAG
TGATATATAGTGTGACAAGGCCGAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGATAA
GGCCTAATGGCCG
Found at i:28599 original size:93 final size:94
Alignment explanation
Indices: 28332--28604 Score: 442
Period size: 93 Copynumber: 2.9 Consensus size: 94
28322 TTAGGATTCT
28332 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG-ATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
28396 AGTGTATATATAGTGTGATAAGGCCTAATGGCCG
64 AGTGTATA-A-A-TGTGATAAGGCCTAATGGCCG
28430 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
28495 TGTATATATGTGATAAGGCCTAATGGCCG
66 TGTATAAATGTGATAAGGCCTAATGGCCG
* * * *
28524 ATGTGATGAATGTGAAAGTGT-TATATGTGACAGGGCCGAGTGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
28588 TGTATAAATGTGATAAG
66 TGTATAAATGTGATAAG
28605 TCCGAAGGGC
Statistics
Matches: 168, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
93 55 0.33
94 42 0.25
95 1 0.01
96 35 0.21
97 15 0.09
98 20 0.12
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.30
Consensus pattern (94 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATAAATGTGATAAGGCCTAATGGCCG
Found at i:28810 original size:37 final size:37
Alignment explanation
Indices: 28718--28832 Score: 178
Period size: 37 Copynumber: 3.1 Consensus size: 37
28708 CCGAGCTCTA
*
28718 AAGACCCGATGACTACATGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
28755 AAGA-CCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
* * * *
28791 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
28828 AAGAC
1 AAGAC
28833 TTCGTAATAA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 35 0.49
37 37 0.51
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.26
Consensus pattern (37 bp):
AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
Found at i:30918 original size:79 final size:80
Alignment explanation
Indices: 30713--31063 Score: 494
Period size: 79 Copynumber: 4.4 Consensus size: 80
30703 GAGTTACTAA
* *
30713 ATCCGGGTTAAGTCCCAAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCA-
30778 TATC-TGCTAGTGATGT
65 T-TCGTGCTAGTGATGT
* * *
30794 ATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGTGTCCGGGCTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
30859 TCGTGCTAGTGATGT
66 TCGTGCTAGTGATGT
*
30874 ATCC-GGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
*
30938 TCATGCTAGTGATGT
66 TCGTGCTAGTGATGT
* * * * **
30953 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAA-CCCCGAAGAGCAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
* * *
31017 TCGTTGCTGGTGTTAT
66 TCG-TGCTAGTGATGT
*
31033 ATCCGGGCT-AGTCCCGAAGAGCAATCATGCT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
31064 GGTACGTGTA
Statistics
Matches: 247, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
79 108 0.44
80 78 0.32
81 61 0.25
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
TCGTGCTAGTGATGT
Found at i:30945 original size:119 final size:119
Alignment explanation
Indices: 30713--31063 Score: 492
Period size: 119 Copynumber: 2.9 Consensus size: 119
30703 GAGTTACTAA
* * * *
30713 ATCCGGGTTAAGTCCCAAAGAGCATTCATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCC-GGCTAAGTTCCGAAGAGCAT
* *
30778 T-ATCTGCTAGTGATGTATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
65 TCA--TGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
*
30834 GTCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGCTAAGTTCCGAAGAGCATT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGCTAAGTTCCGAAGAGCATT
*
30899 CATGCTAGTGATGTATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
66 CATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
* **
30953 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATATATCCGTGCTAA-CCCCGAAGAGCAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCG-GCTAAGTTCCGAAGAGCAT
* * * * *
31017 TCGTTGCTGGTGTTATATCCGGGCT-AGTCCCGAAGAGCAATCATGCT
65 TC-ATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCT
31064 GGTACGTGTA
Statistics
Matches: 209, Mismatches: 18, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
119 125 0.60
120 44 0.21
121 40 0.19
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (119 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGCTAAGTTCCGAAGAGCATT
CATGCTAGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
Found at i:31080 original size:40 final size:40
Alignment explanation
Indices: 30713--31063 Score: 476
Period size: 40 Copynumber: 8.8 Consensus size: 40
30703 GAGTTACTAA
* * *
30713 ATCCGGGTTAAGTCCCAAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
30753 ATCCGGGCTAAGTTCCGAAGAGCATT-ATCTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCA--TGCTAGTGATGT
* * *
30794 ATCCGGGTTAAGTCCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* *
30834 GTCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
30874 ATCC-GGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
30913 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* *
30953 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
* ** * * * *
30993 ATCCGTGCTAA-CCCCGAAGAGCATTCGTTGCTGGTGTTAT
1 ATCCGGGCTAAGTTCCGAAGAGCATTC-ATGCTAGTGATGT
* *
31033 ATCCGGGCT-AGTCCCGAAGAGCAATCATGCT
1 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCT
31064 GGTACGTGTA
Statistics
Matches: 282, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
39 57 0.20
40 189 0.67
41 36 0.13
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
Done.