Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1341
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: 34448
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:932 original size:55 final size:54
Alignment explanation
Indices: 806--971 Score: 234
Period size: 52 Copynumber: 3.1 Consensus size: 54
796 CTGTTGGTGG
* *
806 AAAACATGTCATGAAACATGTTCTATTAATGGAAAAATAAAAT-AGAAGCAT-GG-
1 AAAACATGTCATG-AACATGTT-TGTTAATGGAAGAATAAAATAAGAAGCATGGGA
*
859 CAAACATGTCATGAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGCATGGGA
1 AAAACATGTCATGAACATGTT-TGTTAATGGAAGAATAAAATAAGAAGCATGGGA
914 AAAACATGTCATGAACATG-TTG-TAATGGAAGAATAAAATAAGAAGCATGGGA
1 AAAACATGTCATGAACATGTTTGTTAATGGAAGAATAAAATAAGAAGCATGGGA
966 ATAAAC
1 A-AAAC
972 TAATAAGAAA
Statistics
Matches: 104, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
52 57 0.55
53 26 0.25
54 3 0.03
55 18 0.17
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (54 bp):
AAAACATGTCATGAACATGTTTGTTAATGGAAGAATAAAATAAGAAGCATGGGA
Found at i:2007 original size:38 final size:39
Alignment explanation
Indices: 1818--2000 Score: 214
Period size: 40 Copynumber: 4.7 Consensus size: 39
1808 TCGAATGATG
* * *
1818 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
*
1858 TCCGGAG-TAAGAT-TCGAAGGCATTTGTGCGAGTTACTAA
1 TCCGG-GCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
1897 TTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
*
1937 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
*
1975 TCCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
2001 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 18
0.82 0.07 0.12
Matches are distributed among these distances:
38 25 0.20
39 34 0.27
40 57 0.46
41 9 0.07
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:8480 original size:48 final size:48
Alignment explanation
Indices: 8409--8501 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
8399 GGCCATGAAT
8409 GCATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAAGAA
1 GCATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAAGAA
8457 GCATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAA
1 GCATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAA
8502 TAAAATAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.11, G:0.27, T:0.24
Consensus pattern (48 bp):
GCATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAAGAA
Found at i:9784 original size:79 final size:81
Alignment explanation
Indices: 9648--9830 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
9638 TCGAATGATG
* *
9648 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
9712 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
9727 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
9789 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
9807 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
9831 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:9846 original size:40 final size:40
Alignment explanation
Indices: 9649--9832 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
9639 CGAATGATGT
* * * *
9649 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
9689 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
9729 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9767 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
9808 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
9833 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:9854 original size:79 final size:79
Alignment explanation
Indices: 9701--9865 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
9691 GGACTAAGAT
* **
9701 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
9766 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
9780 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
9843 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
9859 CCGAAGG
1 CCGAAGG
9866 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:14292 original size:43 final size:43
Alignment explanation
Indices: 14247--14611 Score: 556
Period size: 43 Copynumber: 8.5 Consensus size: 43
14237 ATTATAATTA
* **
14247 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGGTGTGTATTTA
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
*
14290 GGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
* * *
14333 GGCCTTCGTGCCTAGCAGGCTTCT-TGCCAGTGATGTGAACTCG
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCG
14376 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
14419 GGCCTTCGTGCCTAGCAGGCTTCT-TGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCG
* *
14462 GGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
* *
14505 GGCCTTCGTGCCTAGCAGGCTTCT-TACCGGTGATGTGTATTTG
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTCG
* *
14548 GGCCTTCGTGCCTAGAAGGCTTCGTGCCGGTGATGTGTATTCG
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
*
14591 AGCCTTCGTGCCTAGCAGGCT
1 GGCCTTCGTGCCTAGCAGGCT
14612 ATTATGCTGG
Statistics
Matches: 293, Mismatches: 23, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.00
43 291 0.99
44 1 0.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (43 bp):
GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCG
Found at i:14477 original size:129 final size:129
Alignment explanation
Indices: 14247--14611 Score: 624
Period size: 129 Copynumber: 2.8 Consensus size: 129
14237 ATTATAATTA
* *
14247 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGGTGTGTATTTAGGCCTTCGTGCCTAGCAGGCTT
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTT
*
14312 CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCTTGCCAGTGATGTGAACTCG
66 CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGAACTCG
*
14376 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTT
1 GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTT
* * *
14441 CTTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGTATTCG
66 CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGAACTCG
* *
14505 GGCCTTCGTGCCTAGCAGGCTTCT-TACCGGTGATGTGTATTTGGGCCTTCGTGCCTAGAAGGCT
1 GGCCTTCGTGCCTAGCAGGCTT-TGTGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCT
*
14569 TCGTGCCGGTGATGTGTATTCGAGCCTTCGTGCCTAGCAGGCT
65 TCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCT
14612 ATTATGCTGG
Statistics
Matches: 223, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
129 222 1.00
130 1 0.00
ACGTcount: A:0.11, C:0.25, G:0.33, T:0.31
Consensus pattern (129 bp):
GGCCTTCGTGCCTAGCAGGCTTTGTGCCGGTGATGTGTATTTGGGCCTTCGTGCCTAGCAGGCTT
CGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCAGTGATGTGAACTCG
Found at i:14658 original size:45 final size:45
Alignment explanation
Indices: 14585--14679 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
14575 CGGTGATGTG
* * *
14585 TATTCGAGCCTTCGTGCCTAGCAGGCTATTATGCTGGTG-GAATAC
1 TATTCGAGCCTTCGAGCCAAGCAGGCTATAATGCTGGTGAG-ATAC
* * *
14630 TATTCGGGCCTTTGAGCCAAGCATGCTATAATGCTGGTGAGATAC
1 TATTCGAGCCTTCGAGCCAAGCAGGCTATAATGCTGGTGAGATAC
14675 TATTC
1 TATTC
14680 AGGCTTTCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (45 bp):
TATTCGAGCCTTCGAGCCAAGCAGGCTATAATGCTGGTGAGATAC
Found at i:18798 original size:204 final size:205
Alignment explanation
Indices: 18448--18851 Score: 765
Period size: 204 Copynumber: 2.0 Consensus size: 205
18438 AAATGCACTT
18448 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
1 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
* *
18513 CCAATCAAAAATTTGAAAAAAATTATAAATCAATTTAGTGTCTACAAGAATAAATTAGTCTTTCT
66 CCAATCAAAAATTTGAAAAAAATTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
18578 CTACTTTTTCTGTAAAACAAATTAATTATAT-AAAATAAATTAATTTTTCTCTCCTCGTTATGTA
131 CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCCTCGTTATGTA
18642 ACAACCAGTG
196 ACAACCAGTG
*
18652 CATAAAAAAGTATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
1 CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
*
18717 CCAATCAAAAATTTGAAAAAATTTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
66 CCAATCAAAAATTTGAAAAAAATTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
18782 CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCCTCGTTATGTA
131 CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCCTCGTTATGTA
18847 ACAAC
196 ACAAC
18852 TCATACCCGT
Statistics
Matches: 195, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
204 157 0.81
205 38 0.19
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (205 bp):
CATAAAAAAATATATTGTATATAATTGCTAATTGATACTAAAAATAAAAATAATAAAAAAAGTGA
CCAATCAAAAATTTGAAAAAAATTATAAATCAAATTAGTGTCTACAAGAATAAATTAATCTTTCT
CTACTTTTTCTGTAAAACAAATTAATTATATAAAAATAAATTAATTTTTCTCTCCTCGTTATGTA
ACAACCAGTG
Found at i:20263 original size:50 final size:47
Alignment explanation
Indices: 20188--20372 Score: 176
Period size: 50 Copynumber: 3.9 Consensus size: 47
20178 TGGGGTAAGA
20188 TGCCGATGCCATGTCCTAGACATGGTCTTACATAGGCTCTAGCATATCTG
1 TGCCGATG-CATGTCCTAGACATGGTCTTACATAGGCTCTA-CA-ATCTG
*
20238 TGCCGATGCCATGTCCTAGACATGGTCTTAC--A--CT-GACACATCTCG
1 TGCCGATG-CATGTCCTAGACATGGTCTTACATAGGCTCTACA-ATCT-G
*
20283 TAGCCGATGCATGTCCCT-GACATGGTCTTACACT-GGCTCTCACAATGTG
1 T-GCCGATGCATGT-CCTAGACATGGTCTTACA-TAGGCTCT-ACAATCTG
20332 -GCCGATGCATGTCCTAGACAT-GTCTTACACTA-GCTC-ACAAT
1 TGCCGATGCATGTCCTAGACATGGTCTTACA-TAGGCTCTACAAT
20373 AACCCATATG
Statistics
Matches: 119, Mismatches: 4, Indels: 30
0.78 0.03 0.20
Matches are distributed among these distances:
44 11 0.09
45 21 0.18
46 29 0.24
47 17 0.14
48 1 0.01
49 3 0.03
50 34 0.29
51 3 0.03
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (47 bp):
TGCCGATGCATGTCCTAGACATGGTCTTACATAGGCTCTACAATCTG
Found at i:21690 original size:28 final size:29
Alignment explanation
Indices: 21659--21716 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
21649 CTCACATATG
21659 TTAGAA-TTTTTTCTAAATAAGTAATCAA
1 TTAGAATTTTTTTCTAAATAAGTAATCAA
21687 TTAGAATTTTTTTCTAAATAAGTAATCAA
1 TTAGAATTTTTTTCTAAATAAGTAATCAA
21716 T
1 T
21717 CTTTCAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (29 bp):
TTAGAATTTTTTTCTAAATAAGTAATCAA
Found at i:22384 original size:20 final size:19
Alignment explanation
Indices: 22346--22384 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
22336 ATTATAACTG
*
22346 TTTTATAAAATATAGAAAA
1 TTTTATAAAAAATAGAAAA
*
22365 TTTTATTAAAAAATATAAAA
1 TTTTA-TAAAAAATAGAAAA
22385 AGTATAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TTTTATAAAAAATAGAAAA
Found at i:22412 original size:91 final size:87
Alignment explanation
Indices: 22273--22445 Score: 197
Period size: 91 Copynumber: 1.9 Consensus size: 87
22263 CATAAATTAT
* ** *
22273 AAATTTCATAAAAAATAGAAAAATATATAAAAGTTTTAAATGATAT-AAATTTTTAAGAAAAATA
1 AAATTTCATAAAAAATAGAAAAATATAGAAAAAATTTAAATGATATAAAAATTTT-AGAAAAATA
22337 T-TATAACTGTTTTATAAAATATAGA
65 TATATAA-T-TTTTA-AAAATATAGA
* * * * *
22362 AAATTTTATTAAAAAATATAAAAAGTATAGAAAAAATTTGAATGTTATAAAAATTTTAGAATAAT
1 AAATTTCA-TAAAAAATAGAAAAA-TATAGAAAAAATTTAAATGATATAAAAATTTTAGAAAAAT
22427 ATATATAATTTTTAAAAAT
64 ATATATAATTTTTAAAAAT
22446 TTTCAAAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
89 12 0.17
90 19 0.27
91 28 0.39
92 12 0.17
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.37
Consensus pattern (87 bp):
AAATTTCATAAAAAATAGAAAAATATAGAAAAAATTTAAATGATATAAAAATTTTAGAAAAATAT
ATATAATTTTTAAAAATATAGA
Found at i:22490 original size:21 final size:20
Alignment explanation
Indices: 22433--22492 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
22423 TAATATATAT
* *
22433 AATTTTTAAAAATTTTCAAAA
1 AATTTATAAAAA-TTTAAAAA
*
22454 AATATATAAAAA-TTAAAGAA
1 AATTTATAAAAATTTAAA-AA
22474 AATTTATAAAAATTTAAAA
1 AATTTATAAAAATTTAAAA
22493 TTATGACACA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 4 0.12
20 14 0.42
21 15 0.45
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AATTTATAAAAATTTAAAAA
Found at i:30270 original size:17 final size:17
Alignment explanation
Indices: 30232--30264 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
30222 ACATACGAAA
30232 CATATGCACAATTTTTT
1 CATATGCACAATTTTTT
30249 CATATGCACAATTTTT
1 CATATGCACAATTTTT
30265 CAATATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (17 bp):
CATATGCACAATTTTTT
Found at i:30606 original size:39 final size:40
Alignment explanation
Indices: 30511--30733 Score: 260
Period size: 39 Copynumber: 5.7 Consensus size: 40
30501 GCTACTCGTT
* *
30511 CAAATGCCTTCGGGACATAGCCCGG-TTATAGAAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
30551 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCG-A
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
30590 AAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
30630 CAAATGCCTTC-GGATCTTAGTCC-GAATTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
30669 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
30709 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
30734 CATCATTCAA
Statistics
Matches: 162, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
39 94 0.58
40 66 0.41
41 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:30626 original size:79 final size:80
Alignment explanation
Indices: 30512--30733 Score: 267
Period size: 79 Copynumber: 2.8 Consensus size: 80
30502 CTACTCGTTC
* * *
30512 AAATGCCTTCGGGACATAGCCCGG-TTATAGAAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 AAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
30576 ATTTAGTAACTCG-AA
65 AATTAGTAACTCGTAA
* *
30591 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC-G
1 AAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCGG
*
30654 AATTAGTAACTCGTAC
65 AATTAGTAACTCGTAA
* * * * *
30670 AAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
1 AAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
30733 A
65 A
30734 CATCATTCAA
Statistics
Matches: 123, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 32 0.26
79 89 0.72
80 2 0.02
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.25
Consensus pattern (80 bp):
AAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGTAA
Found at i:33765 original size:37 final size:38
Alignment explanation
Indices: 33715--33848 Score: 164
Period size: 38 Copynumber: 3.5 Consensus size: 38
33705 GGATTATATC
33715 GGTTAAGTCCCGAAGGCATTCGTGC-GGTTGTTATCCG
1 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATCCG
* *
33752 GGTTAAGTCCCGAAGGCATTCGTCCTGGTTGTTATATCG
1 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTAT-CCG
* *
33791 AGTTAAG-CCCGAAGGCATTTGTGCTGGTTGTTATATCCG
1 GGTTAAGTCCCGAAGGCATTCGTGCTGGTTG-T-TATCCG
* *
33830 GGCTAAAATCCCGAAGGCA
1 GG-TTAAGTCCCGAAGGCA
33849 ATTGGGTTGG
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
37 24 0.29
38 30 0.37
39 12 0.15
40 6 0.07
41 10 0.12
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (38 bp):
GGTTAAGTCCCGAAGGCATTCGTGCTGGTTGTTATCCG
Found at i:33802 original size:38 final size:38
Alignment explanation
Indices: 33708--33827 Score: 174
Period size: 38 Copynumber: 3.2 Consensus size: 38
33698 CAATTGAGGA
33708 TTATATCGGTTAAGTCCCGAAGGCATTCGTGC-GGTTG
1 TTATATCGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
33745 TTAT-CCGGGTTAAGTCCCGAAGGCATTCGTCCTGGTTG
1 TTATATC-GGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
33783 TTATATCGAGTTAAG-CCCGAAGGCATTTGTGCTGGTTG
1 TTATATCG-GTTAAGTCCCGAAGGCATTCGTGCTGGTTG
33821 TTATATC
1 TTATATC
33828 CGGGCTAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
36 1 0.01
37 28 0.38
38 38 0.51
39 7 0.09
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (38 bp):
TTATATCGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:33857 original size:75 final size:72
Alignment explanation
Indices: 33708--33848 Score: 176
Period size: 75 Copynumber: 1.9 Consensus size: 72
33698 CAATTGAGGA
* *
33708 TTATATCGGTTAAGTCCCGAAGGCATTCGTGCGGTTGTTATCCGGGTTAAGTCCCGAAGGCATTC
1 TTATATCGGTTAAGTCCCGAAGGCATTCGTGCGGTTGTTATCCGGGTAAAATCCCGAAGGCATTC
33773 GTCCTGGTTG
66 G--C-GGTTG
*
33783 TTATATCGAGTTAAG-CCCGAAGGCATTTGTGCTGGTTGTTATATCCGGGCTAAAATCCCGAAGG
1 TTATATCG-GTTAAGTCCCGAAGGCATTCGTGC-GGTTG-T-TATCCGGG-TAAAATCCCGAAGG
33847 CA
61 CA
33849 ATTGGGTTGG
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
75 24 0.41
76 11 0.19
77 1 0.02
78 8 0.14
79 14 0.24
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (72 bp):
TTATATCGGTTAAGTCCCGAAGGCATTCGTGCGGTTGTTATCCGGGTAAAATCCCGAAGGCATTC
GCGGTTG
Done.