Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018400979.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_414.0, whole genome shotgun sequence
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: 12299
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.24
Warning! 3799 characters in sequence are not A, C, G, or T
Found at i:1646 original size:172 final size:170
Alignment explanation
Indices: 1050--1699 Score: 648
Period size: 171 Copynumber: 3.8 Consensus size: 170
1040 TTCTTGAGGC
* * * *
1050 AAACACTCGATTATAATTTGTTTTAACAAAAAGTGTAAAACA-ATTCAACTTAAAATCAATTATG
1 AAACACTCAATTATAATCTGTTTTAATAAAAAATGTAAAA-AGATTCAACTTAAAATCAATTATG
* ** **
1114 AGATTGTAAAACCATTCCAAGCAAGTAATAAGGCTTTCGAAGGCATGGGTGACTATGAATGG--A
65 AGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT-GAAGGCATGGGTGACTACAAATGGACA
* * *
1177 TTCTCTTGCCAATGAATAGATTTTTCTTCATGTTTCCCAAGGC
129 TT-TCTTGCCAATGAATAGCTTTTTCCTCATGTTTCCCAAGGA
* * * * * *** *
1220 AGACATTCAAATATAATCTGTTTTAATAAAAAAATATAAAAAAATTTGGCTGAAAATCAATTATG
1 AAACACTCAATTATAATCTGTTTTAAT-AAAAAATGTAAAAAGATTCAACTTAAAATCAATTATG
* ** * * * *
1285 AGATTATAAAACCATTTAAA-TATAGCGATACGGCTTCTAAAGGTATGGGTGGCTACAAATGGAC
65 AGATTATAAAACCATTTAAAGCA-AGTAATAAGGCTT-TGAAGGCATGGGTGACTACAAATGGAC
* **** *
1349 TTTTCTTGCCAATGAATCA-CTTTTTCAC-CATGTTTGTTGAGGT
128 ATTTCTTGCCAATGAAT-AGCTTTTTC-CTCATGTTTCCCAAGGA
* * * * * * *
1392 AGACATTGAATTTTAATATGTTTTAATCAAAAATGTAAAAAGATTCAACTAAAAATCAATTATGA
1 AAACACTCAATTATAATCTGTTTTAATAAAAAATGTAAAAAGATTCAACTTAAAATCAATTATGA
* * * *
1457 GATAATAAAACCATTTAAAGCGAGTAATAAGGCTTTGGAATGCATGGGTGACTATAAATGGACAT
66 GATTATAAAACCATTTAAAGCAAGTAATAAGGCTTT-GAAGGCATGGGTGACTACAAATGGACAT
* * *
1522 TTCTTGTCAATGAATGGCTTTTTCCTCAAGTTTCCCAAGGA
130 TTCTTGCCAATGAATAGCTTTTTCCTCATGTTTCCCAAGGA
* * *
1563 AAACACTCAATTATAATCTGTTTTGAGTAAAAATTGTAAAAAGA-TCTAGCTTAAAATCAATTAT
1 AAACACTCAATTATAATCTGTTTT-AATAAAAAATGTAAAAAGATTC-AACTTAAAATCAATTAT
* * *
1627 GAGATTGTAAAACCATTTAAAGCAAGTAGTAAGGCTTTTGAAGCCATGGGTGACTACAAATGGAC
64 GAGATTATAAAACCATTTAAAGCAAGTAATAAGGC-TTTGAAGGCATGGGTGACTACAAATGGAC
*
1692 TTTTCTTG
128 ATTTCTTG
1700 NNNNNNNNNN
Statistics
Matches: 384, Mismatches: 81, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
170 25 0.07
171 207 0.54
172 146 0.38
173 6 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (170 bp):
AAACACTCAATTATAATCTGTTTTAATAAAAAATGTAAAAAGATTCAACTTAAAATCAATTATGA
GATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTGAAGGCATGGGTGACTACAAATGGACATT
TCTTGCCAATGAATAGCTTTTTCCTCATGTTTCCCAAGGA
Found at i:3425 original size:171 final size:167
Alignment explanation
Indices: 3248--4324 Score: 532
Period size: 171 Copynumber: 6.3 Consensus size: 167
3238 NCTTCCAAAA
* * *
3248 CCTTATTACTCGCTTTAAATGGTTTTATAAGCTCGTATTTGATTTTAAGTTGAATTTTTTTTCCT
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTCCT
* *
3313 TTTTTTGTTAAACAGATTATAATTGAGTTTTTGCCTCAACAAACATGAAGAAAAAGCCATTCATT
66 TTTTTGGTTAAACAGATTATAATTGAGTTTTTGCCTCAAGAAACATGAAGAAAAAGCCATTCATT
3378 GGCACAAAATATCCATTTATAGTAACCTATGCATTCCGAAG
131 GGCA-AAAATATCCATTTATAGTAACC-ATGC-TT-CGAAG
* * ** * * *
3419 CCTTATTACTCACTTTAAATGGTCTTATACCCTCATTATTGATTATAAGTTGAATTTTTTTAT-A
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT-TCC
* * * * * ** * * * *
3483 TTTGTT-ATTAAAACAGATTAAAATTCAATTCCTACCTCAATAAACA-CAACAAAAAAGCCATTC
65 TTTTTTGGTT-AAACAGATTATAATTGAGTTTTTGCCTCAAGAAACATGAA-GAAAAAGCCATTC
* ** ** *
3546 ATTGATCAGAAAAGTA--CATTTGCAGTCGTCCATGCCTTTGGAAG
128 ATTG-GCA-AAAA-TATCCATTTATAGT-AACCATG-C-TTCGAAG
* ** * * *
3590 CCTTTAAGTCAATTTCTATCTTTAAATAGTTTTATAATCTCATAATTGACTTTAAG-TCAATTTT
1 CC--T---T--ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTT
** * * * * * *** * *
3654 TTTTTATATTTTTAGTTAAAACAGATTATATTTGTA-TGTCTACCTTGGGAAATATAAAGAAAAA
59 TTTTCCT-TTTTTGGTT-AAACAGATTATAATTG-AGTTTTTGCCTCAAGAAACATGAAGAAAAA
* * *
3718 GCTATTCATTGGCAAGAAA-AGTCTATTTATAGTGAACCATGCCTTTGAAAG
121 GCCATTCATTGGCAA-AAATA-TCCATTTATAGT-AACCATG-CTTCG-AAG
* * * ** * *
3769 CCTTACTACTCGCGTTAAATAGTTTTACGATCTCATAATTGATTTTAAGTTGAA-TTGTTTTCCA
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTCCT
* * * * * * * *
3833 TTATTGGTTAAAGTAAATTATAATTGAGTGTTTGACTCAAGAAACATGAAGAGAATGCAATTCAT
66 TTTTTGGTTAAA-CAGATTATAATTGAGTTTTTGCCTCAAGAAACATGAAGAAAAAGCCATTCAT
* * * * *
3898 TAGCAAGAAA-GTCCATTTATGGTCACCTATGGCTTTCAAAG
130 TGGCAA-AAATATCCATTTATAGTAACC-AT-GC-TTCGAAG
********** * * *
3939 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATNNNNNNNNNNAAGTTGAA-TCTTTTTACA
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTCCT
* * * * *
4003 TTTTTGGTCAAAACAGATTATAATTTAGTGTTTAG-CTCAA-AAACATGAAGAGAAAGCCACTCA
66 TTTTTGGT-TAAACAGATTATAATTGAGT-TTTTGCCTCAAGAAACATGAAGAAAAAGCCATTCA
* * * * *
4066 TTGCCATGATATGTCCATTTATAGTCACCCATGGCTTCGAAAG
129 TTGGCA-AAAATATCCATTTATAGT-AACCAT-GCTTCG-AAG
* * * ********** * * *
4109 CCTTACTACTTGCTTTAAATGGTTTTATAATCTCGTNNNNNNNNNNAAGTTGAA-TTGTTTTACA
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTCCT
* * * * * *
4173 TTTTTGGTCAAAACAAATTAGAATTGAGTTTTGGCCTC-GGAAAACATGAAAAAAAAGCCATTCA
66 TTTTTGGT-TAAACAGATTATAATTGAGTTTTTGCCTCAAG-AAACATGAAGAAAAAGCCATTCA
* *
4237 TTGAG-AAGAAA-AGTCCATTTGTAGTCACCCATGGCTTCGAAAG
129 TTG-GCAA-AAATA-TCCATTTATAGT-AACCAT-GCTTCG-AAG
* * *
4280 CCTTACTACTTGCTTTAAATAGTTTTATAATCTCATAATTGATTT
1 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
4325 NNNNNNNNNN
Statistics
Matches: 701, Mismatches: 163, Indels: 84
0.74 0.17 0.09
Matches are distributed among these distances:
169 36 0.05
170 203 0.29
171 272 0.39
172 55 0.08
173 6 0.01
174 1 0.00
176 3 0.00
177 14 0.02
178 47 0.07
179 61 0.09
180 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.37
Consensus pattern (167 bp):
CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTTCCT
TTTTTGGTTAAACAGATTATAATTGAGTTTTTGCCTCAAGAAACATGAAGAAAAAGCCATTCATT
GGCAAAAATATCCATTTATAGTAACCATGCTTCGAAG
Found at i:4084 original size:170 final size:158
Alignment explanation
Indices: 3814--4321 Score: 477
Period size: 170 Copynumber: 3.1 Consensus size: 158
3804 TAATTGATTT
* * * **
3814 TAAGTTGAATTGTTTTCCATTATTGGTTAAAGTAAATTATAATTGAGTGTTTGACTCAAGAAACA
1 TAAGTTGAATTGTTTTACATTTTTGGTCAAAACAAATTATAATTGAGTGTTTGACTCAA-AAACA
* * * *
3879 TGAAGAGAATGCAATTCATTAGCAAGAAAGTCCATTTATGGTCACCTATGGCTTTC-AAAGCCTT
65 TGAAGAGAAAGCCATTCATT-GCAAGAAAGTCCATTTATAGTCACCCATGGC-TTCGAAAGCCTT
* *
3943 ATTACTCGCTTTAAATGGTTTTATAATCTCA
128 ACTACTTGCTTTAAATGGTTTTATAATCTCA
* *
3974 TNNNNNNNNNNAAGTTGAATCT-TTTTACATTTTTGGTCAAAACAGATTATAATTTAGTGTTT-A
1 T----------AAGTTGAAT-TGTTTTACATTTTTGGTCAAAACAAATTATAATTGAGTGTTTGA
* * *
4037 GCTCAAAAACATGAAGAGAAAGCCACTCATTGCCATGATATGTCCATTTATAGTCACCCATGGCT
55 -CTCAAAAACATGAAGAGAAAGCCATTCATTG-CAAGA-AAGTCCATTTATAGTCACCCATGGCT
*
4102 TCGAAAGCCTTACTACTTGCTTTAAATGGTTTTATAATCTCG
117 TCGAAAGCCTTACTACTTGCTTTAAATGGTTTTATAATCTCA
* *
4144 TNNNNNNNNNNAAGTTGAATTGTTTTACATTTTTGGTCAAAACAAATTAGAATTGAGT-TTTGGC
1 T----------AAGTTGAATTGTTTTACATTTTTGGTCAAAACAAATTATAATTGAGTGTTT-GA
* * * * *
4208 CTCGGAAAACATGAAAAAAAAGCCATTCATTGAGAAGAAAAGTCCATTTGTAGTCACCCATGGCT
55 CTC-AAAAACATGAAGAGAAAGCCATTCATTG-CAAG-AAAGTCCATTTATAGTCACCCATGGCT
*
4273 TCGAAAGCCTTACTACTTGCTTTAAATAGTTTTATAATCTCA
117 TCGAAAGCCTTACTACTTGCTTTAAATGGTTTTATAATCTCA
4315 TAA-TTGA
1 TAAGTTGA
4322 TTTNNNNNNN
Statistics
Matches: 296, Mismatches: 32, Indels: 40
0.80 0.09 0.11
Matches are distributed among these distances:
160 5 0.02
161 2 0.01
168 1 0.00
169 34 0.11
170 161 0.54
171 92 0.31
172 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.34
Consensus pattern (158 bp):
TAAGTTGAATTGTTTTACATTTTTGGTCAAAACAAATTATAATTGAGTGTTTGACTCAAAAACAT
GAAGAGAAAGCCATTCATTGCAAGAAAGTCCATTTATAGTCACCCATGGCTTCGAAAGCCTTACT
ACTTGCTTTAAATGGTTTTATAATCTCA
Found at i:5847 original size:171 final size:170
Alignment explanation
Indices: 5670--6256 Score: 545
Period size: 171 Copynumber: 3.4 Consensus size: 170
5660 NNNNNNNNNN
* * * * *
5670 AAGTTGAATCTTTTTACATTTTTGGTCAAAAGAGATTATAATTTATTTTTTAGCTCCAAAAACAT
1 AAGTTGAATCTTTTTACATTTTTGGTCAAAACAGATTATAATTAATGTTTT-GCTCGAGAAACAT
* * * *
5735 GGAGAAAAAGCTACTCATTGGCAAGAAAAGTCGATTTATAGCCACCCATGCCTTCCAAAGCTTTA
65 GGAGAAAAAGCAATTCATTGGCAAGAAAAGTCCATTTATAGCCACCCATGCCTTCCAAAGCCTTA
* **********
5800 TTACACGCTTTAAATGGTNNNNNNNNNNCATAATTAATTTT
130 TTACATGCTTTAAATGGTTTTATAATCTCATAATTAATTTT
* * * *
5841 AAGTTGAAT-TGTTTTACATTTTTGGTCAAAACAAATTGA-AATTGA-GTGTTGGCCTCGGGAAA
1 AAGTTGAATCT-TTTTACATTTTTGGTCAAAACAGATT-ATAATTAATGT-TTTG-CTCGAGAAA
* * * * * **
5903 CATGGAGAAAAAGAAATTCATTGCCAAGAAAAGTCCATTTCTAGTCACCCATGGCTTTGAAAGCC
62 CATGGAGAAAAAGCAATTCATTGGCAAGAAAAGTCCATTTATAGCCACCCATGCCTTCCAAAGCC
* *** *
5968 TTACTGTTTGCTTTAAATGGTTTTATAATCTCATAATTGATTTT
127 TTATTACATGCTTTAAATGGTTTTATAATCTCATAATTAATTTT
* * * * *
6012 AAGCTAAATCTTTTTACATTTTTGCTCAAAACAGATTATAATTAAGTGTTTTCCTTGAGAAACAT
1 AAGTTGAATCTTTTTACATTTTTGGTCAAAACAGATTATAATTAA-TGTTTTGCTCGAGAAACAT
* * * *
6077 GAAGAAAAAGCCATTCATTTGCAAGAAATGTCCATTTATA-CTCACCCATGCCTTCCAAAGCCTT
65 GGAGAAAAAGCAATTCATTGGCAAGAAAAGTCCATTTATAGC-CACCCATGCCTTCCAAAGCCTT
* *
6141 ATTACATGCTTTAAATGGTTTTATTATCTCATAATTGATTTT
129 ATTACATGCTTTAAATGGTTTTATAATCTCATAATTAATTTT
* * * ** * * * * *
6183 TAGTTAAATCTTTTT-CTTTTTTTATTAAAACAGATTAAAATTCAATGTCTTCCTCAAGAAACAT
1 AAGTTGAATCTTTTTACATTTTTGGTCAAAACAGATTATAATT-AATGTTTTGCTCGAGAAACAT
*
6247 GGTGAAAAAG
65 GGAGAAAAAG
6257 TGANNNNNNN
Statistics
Matches: 334, Mismatches: 72, Indels: 21
0.78 0.17 0.05
Matches are distributed among these distances:
170 50 0.15
171 278 0.83
172 4 0.01
173 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.36
Consensus pattern (170 bp):
AAGTTGAATCTTTTTACATTTTTGGTCAAAACAGATTATAATTAATGTTTTGCTCGAGAAACATG
GAGAAAAAGCAATTCATTGGCAAGAAAAGTCCATTTATAGCCACCCATGCCTTCCAAAGCCTTAT
TACATGCTTTAAATGGTTTTATAATCTCATAATTAATTTT
Found at i:7005 original size:170 final size:170
Alignment explanation
Indices: 6476--7994 Score: 875
Period size: 171 Copynumber: 8.9 Consensus size: 170
6466 NNNNNNNNNN
* * * *** * * **
6476 AATGGCTTTATAATTTCATAATTGATTTTAAGCCAAATTTTTTTAGATTTTTTTTTAAAACAGAT
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAGAT
* * * *** * * ** * *
6541 TATATTTGAATGTCTACTTTGGGAAACATGAAGAAAAAGCTGTTCATTGGCAAGAAAATTTCATT
66 TATA-TTGAATGTTTGCCTCAAGAAACATGAGGAAAAAACCATTCATTGGCAAGAAAAGTCCATT
* * * * * *
6606 CATAGTCACCCATTCCTTCGAAAGCCTTATTATTTGCTTGA
130 TATAGACACCCATGCCTTCGAAAGCCTTATTACTCGCTTTA
* *
6647 AATGGTTTTACAATCTCATAAGTGATTTTAAGTTGAATTCTTTTATA-TTTTGGTT-TAA-A-A-
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAGAT
* * * * * * * **** * ** * *
6707 T-CA---AATTTTTGCCCCAAGAAACGTAAAGAGAACGTGATTCATTGGGAAGTGAAGTCTATAT
66 TATATTGAATGTTTGCCTCAAGAAACATGAGGAAAAAACCATTCATTGGCAAGAAAAGTCCATTT
* * * * *
6768 ATAGTCATCCATACCTTTC-AAAACCTTATTAC-CTACTTTA
131 ATAGACACCCATGCC-TTCGAAAGCCTTATTACTC-GCTTTA
* * * * * *
6808 ACTAGTTTTATAAGCTCATATTTGATTTTAACTTGAATTCTTTTATA-TTTTGGTTAAAACAGAT
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAGAT
*** * *
6872 TATATTCGAATGTTTGCCTTGGGAATCGA-GAGGAAAAAACCATTCATTAGCAAGAAAAGTCCAT
66 TATATT-GAATGTTTGCCTCAAGAAAC-ATGAGGAAAAAACCATTCATTGGCAAGAAAAGTCCAT
* * * *
6936 TTATAGACACCCATGCATTCGTAAGCCTTATTACTTGCTTGA
129 TTATAGACACCCATGCCTTCGAAAGCCTTATTACTCGCTTTA
* ** * * **
6978 AATGGTTTTACAATCTCATAATTGATTTTAAGCTGAATTGGTTTACATTTTTTGTTCAACTCA-A
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTCTTTTATATTTTTGGTT-AAAACAGA
* * * ** * * ** * *
7042 TTATAATAGAGTGTTTGCCTAAAGAAATGTGAAGG-GAACATGATTCATTGGCAAGAGAAGACCA
65 TTAT-ATTGAATGTTTGCCTCAAGAAACATG-AGGAAAAAACCATTCATTGGCAAGAAAAGTCCA
* * * *
7106 TTTAGAGTAATCCATACCTTCCAAAGCCTTCTAAAGACTTATTACTCGCTTTA
128 TTTATAG--A--C--A-C--CC-ATGCCTTCGAAAGCCTTATTACTCGCTTTA
* * * * *
7159 AATGGTTTTACAATCTCATAATTGATTTTAAGTTAAAATT-TTCTACATTTTTAGTT-AAATAGA
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTT-GAATTCTTTTATATTTTTGGTTAAAACAGA
* * * * *
7222 TTATAATTGACTTTTTGCCTCAAGAAACATGA--AAAAAACATGATTCATTGGCAAGAGATGTCC
65 TTAT-ATTGAATGTTTGCCTCAAGAAACATGAGGAAAAAAC--CATTCATTGGCAAGAAAAGTCC
* * * *
7285 ATCTATAGCCATCCATGCCTTCCAAAGCCTTATTACTCGCTTTA
127 ATTTATAGACACCCATGCCTTCGAAAGCCTTATTACTCGCTTTA
* * * *
7329 AATGGTTTTACGATCTCATAATTGATTTTAAGTTAAATAT-TTTTATATTTTTAGTTAAAATAGA
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAAT-TCTTTTATATTTTTGGTTAAAACAGA
* * * * * **
7393 TTATAATTTAGTGTTTACCTTAAAAAACATGA--AAAGAACATGATTCATTTGGCAAGAAAAGTC
65 TTAT-ATTGAATGTTTGCCTCAAGAAACATGAGGAAA-AA-ACCATTCA-TTGGCAAGAAAAGTC
* * * *
7456 CATTTATAGCCACCCATGCCTTCCAAAACCTTATTACTTGCTTTA
126 CATTTATAGACACCCATGCCTTCGAAAGCCTTATTACTCGCTTTA
* * * * * *
7501 AATGGTTTTA-TATGCTCAT-ATTCGATTGTAAGTTGAATTTTTTTCTTTTTTTGGTTAAAACAT
1 AATGGTTTTACAAT-CTCATAATT-GATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAG
* * * * * * * *
7564 ATTATAATTGAGTTTTTGCCTCGAGAAACATGAAGAAAAAGCCATTTATTGGCACGAAATGTCCA
64 ATTAT-ATTGAATGTTTGCCTCAAGAAACATGAGGAAAAAACCATTCATTGGCAAGAAAAGTCCA
* *
7629 TTTATAGTA-ACCTATGCCTTCCG-AAGCCTTATTACTCACTTTA
128 TTTATAG-ACACCCATGCCTT-CGAAAGCCTTATTACTCGCTTTA
* * * * * **
7672 AATGGTTTTATACTCCCATTATTGATTTTAAGTTGAA-TCTTTTTACATTTTTTCTTAAAACAGA
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTC-TTTTATATTTTTGGTTAAAACAGA
* * ** * ** * * * *
7736 TTAAAATTCAATGCCTACCTCAAGAAACATGACCAAAAAGCCATTCATTTGCAAGAGAAGTCTAT
65 TT-ATATTGAATGTTTGCCTCAAGAAACATGAGGAAAAAACCATTCATTGGCAAGAAAAGTCCAT
* * * *
7801 TTATAGTCATCCATACCTTTC-AAAGCCTTATTACTCGCTTTG
129 TTATAGACACCCATGCC-TTCGAAAGCCTTATTACTCGCTTTA
*********** * *
7843 AATANNNNNNNNNNCTCATATTTGATTTTAAGTTGAATTCTGTTATA-TTTTGGTTAAAACAGAT
1 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAGAT
* * *** ** * * * *
7907 TATGTTCGAATGCTTGCCTTTTGACTC-TGGAGGTAAAAGCCATTCATTAGTAAGAAAAGTCCAT
66 TATATT-GAATGTTTGCCTCAAGAAACAT-GAGGAAAAAACCATTCATTGGCAAGAAAAGTCCAT
*
7971 TTATAGTCACCCATGCCTTCGAAA
129 TTATAGACACCCATGCCTTCGAAA
7995 NNNNNNNNNN
Statistics
Matches: 1036, Mismatches: 255, Indels: 115
0.74 0.18 0.08
Matches are distributed among these distances:
161 111 0.11
162 5 0.00
163 1 0.00
164 1 0.00
165 2 0.00
166 2 0.00
167 1 0.00
168 1 0.00
169 16 0.02
170 256 0.25
171 343 0.33
172 152 0.15
173 4 0.00
174 4 0.00
175 1 0.00
176 1 0.00
177 1 0.00
178 4 0.00
179 3 0.00
180 54 0.05
181 69 0.07
182 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (170 bp):
AATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTCTTTTATATTTTTGGTTAAAACAGAT
TATATTGAATGTTTGCCTCAAGAAACATGAGGAAAAAACCATTCATTGGCAAGAAAAGTCCATTT
ATAGACACCCATGCCTTCGAAAGCCTTATTACTCGCTTTA
Found at i:9637 original size:171 final size:169
Alignment explanation
Indices: 9457--10015 Score: 575
Period size: 171 Copynumber: 3.3 Consensus size: 169
9447 AAAGATTTAG
* * * * *
9457 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCAAGCAGTGAGGCTTTCAAAACCATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGC-TTCAAAACCATGGG
* * * *
9522 TGACTATAAATGGACTTTTCTTGGCAATGAATGGCTTTTTCTCCATGTTTCCCGAGGCCAACACT
65 TGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTCATGTTT-CCGAGGCAAACACT
* ** * *
9587 CAATTCCAATTTGTTTTGACAAAAAATGTAAAAAAATTCAA
129 AAATTATAATCTATTTTGACAAAAAATGTAAAAAAATTCAA
* * * * * **
9628 ATGAAAATCAATTATGAGATTATAAAATCATTTAAAGCGTGTAATAAAGCTTCGGAAGGCATGGG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTC-AAAACCATGGG
* * * * ** *
9693 TGGCTATAAATGGACTTTTCTTGCCAATGAGTAGCTTTTTGTTCAAGTTTTTG-GAGCTAAACAA
65 TGACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTCATGTTTCCGAG-GC-AAACAC
* * * *
9757 TAAATTATAATCTCTTTTGACCAAAAATATAAAAAGATTCAA
128 TAAATTATAATCTATTTTGACAAAAAATGTAAAAAAATTCAA
* * * * *
9799 CTTAAAATCAATAATGAGGTTATAAAACCATTTAAAGTGAGTATTAAAGCTTCAAAAGCCATGAG
1 CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTCAAAA-CCATGGG
* * * * **
9864 TGACCATAAATGGAC-TTTCTTGCCAATGAATCG-TGTTCTCTTAATGTTTCTTATGGCAAACAC
65 TGACTATAAATGGACTTTTCTTGCCAATGAATAGCT-TTTTCTTCATGTTTCCGA-GGCAAACAC
* * * *
9927 TGAATTATAATCTATTTTAACTAAAAATGGAAAAAAATTCAA
128 TAAATTATAATCTATTTTGACAAAAAATGTAAAAAAATTCAA
**
9969 CTTAAAATCAAATTATGAGATCGTAAAACCATTTAAAGCGAGTAATA
1 CTTAAAATC-AATTATGAGATTATAAAACCATTTAAAGCGAGTAATA
10016 NNNNNNNNNN
Statistics
Matches: 313, Mismatches: 67, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
169 2 0.01
170 84 0.27
171 226 0.72
172 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.32
Consensus pattern (169 bp):
CTTAAAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAAGCTTCAAAACCATGGGT
GACTATAAATGGACTTTTCTTGCCAATGAATAGCTTTTTCTTCATGTTTCCGAGGCAAACACTAA
ATTATAATCTATTTTGACAAAAAATGTAAAAAAATTCAA
Done.