Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018399613.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2865.0, 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: 6595
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.30
Warning! 985 characters in sequence are not A, C, G, or T
Found at i:798 original size:174 final size:171
Alignment explanation
Indices: 124--1177 Score: 698
Period size: 171 Copynumber: 6.1 Consensus size: 171
114 TATTACTCAC
* * * * * *
124 TTTAAAATCTCATAATTGATTTTAAGCT-AACTTTTTTTACATTTTTA-ATTAAAACGGATTATG
1 TTTATAATCTCATAATTGATTTTAAGTTGAAATTTTTTTATATTTTTAGA-TAAAACAGATTATA
* * * * * ** *
187 ATTGACTATCTGCCTT-AAGAATCATGAAGAAAAA-GTCATTCATTGGTAAGAAAAGTCTATTTA
65 ATTGAATGTTTACCTTGAA-AA-CATGAAGAAAAACCT-ATTCATTGACAAGAAAAGTCCATTTA
* *
250 TAGTCACACATGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
127 TAGTCACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
* ** * * *
295 TTTATAATCTTATAATTGATTTTTGGTCG-AATTTTTTTATATTTTTAAATAAAACAGATTGTAA
1 TTTATAATCTCATAATTGATTTTAAGTTGAAATTTTTTTATATTTTTAGATAAAACAGATTATAA
* * * ** * * * *
359 TCGAATGTTTACCTTGAGAAACAAGAAAAAAAATTTATTCATTGGCAAAAAAAGCCCATTTATTG
66 TTGAATGTTTACCTTGA-AAACATGAAGAAAAACCTATTCATTGACAAGAAAAGTCCATTTATAG
*
424 TCACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAATGGT
130 TCACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
*
466 TTTATAATCTCATAATTGATTTTAAGTTGAACATTTTTTTACT-TTTTT-GAATAGAAA-ATATT
1 TTTATAATCTCATAATTGATTTTAAGTTGAA-ATTTTTTTA-TATTTTTAG-ATA-AAACAGATT
* * ** * * *
528 ATAATTGAATGTTTACTTTAGGAAATGTGAAGCAAAAACC-ATCCATTGATATGAAAAGTCCATT
62 ATAATTGAATGTTTACCTT-GAAAACATGAAG-AAAAACCTATTCATTGACAAGAAAAGTCCATT
* * * * *
592 TATAGTCACTCAAACCTTCAAAAGCGTTATTACTCGCTTTAAATCGT
125 TATAGTCACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
* * * *
639 TTTGTAAACTCATAATTGATTTTAAGTTGAATATTTTTTTTATATTTTTAGTTAAAACAGAGTAT
1 TTTATAATCTCATAATTGATTTTAAGTTGAA-A-TTTTTTTATATTTTTAGATAAAACAGATTAT
* * *
704 CATTGAATGTTTACCTTCGAAAACATGAAGAAACACCTGTTCATTGACAAGAAAAGTCCATTTAT
64 AATTGAATGTTTACCTT-GAAAACATGAAGAAAAACCTATTCATTGACAAGAAAAGTCCATTTAT
* * ** ********
769 AGTCACCCAGGCCTTCGAAAGCCTTATTACTTGCTTNNNNNNNN
128 AGTCACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
******************** * * * * *
813 NNNNNNNNNNNNNNNNNNNNTTTAAGTTG-AATTTCTTTACATTTTTGGTTAAAACAGACTATAA
1 TTTATAATCTCATAATTGATTTTAAGTTGAAATTTTTTTATATTTTTAGATAAAACAGATTATAA
* ** * * *
877 TTGAATGTTTGCCTCAAGAAACATGAGGAAAAA-CTCATTCATTGATAAGAAAAGCCCATTTATA
66 TTGAATGTTTACCTTGA-AAACATGAAGAAAAACCT-ATTCATTGACAAGAAAAGTCCATTTATA
* * * **
941 GTCACCTAAGCTTTCAAAAGCCTTATTGCTCGTTTTAAATAAGT
129 GTCACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAAT-AGT
* * * * * *
985 TTTATAACCTCATAATTAATTTTAAATCG-AATTTTTTTACATTTTTAGTTAAAACATG-TTATA
1 TTTATAATCTCATAATTGATTTTAAGTTGAAATTTTTTTATATTTTTAGATAAAACA-GATTATA
* *** ** * * * *
1048 ATTGAATGTTTGCCCTTGGGGATGTGAAGAAAAA-GTCATTCATTGATAAGAAAAGTCTAATTAT
65 ATTGAATGTTT-ACCTTGAAAACATGAAGAAAAACCT-ATTCATTGACAAGAAAAGTCCATTTAT
* * * * * * *
1112 AATCGCTCATTG-CTTTAAAAGCCTTACTACTGACTTTAAATAGT
128 AGTCACCCA-AGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
*
1156 TTTGTAATCTCATAATTGATTT
1 TTTATAATCTCATAATTGATTT
1178 NNNNNNNNNN
Statistics
Matches: 673, Mismatches: 187, Indels: 46
0.74 0.21 0.05
Matches are distributed among these distances:
170 3 0.00
171 287 0.43
172 117 0.17
173 149 0.22
174 116 0.17
175 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.37
Consensus pattern (171 bp):
TTTATAATCTCATAATTGATTTTAAGTTGAAATTTTTTTATATTTTTAGATAAAACAGATTATAA
TTGAATGTTTACCTTGAAAACATGAAGAAAAACCTATTCATTGACAAGAAAAGTCCATTTATAGT
CACCCAAGCCTTCAAAAGCCTTATTACTCACTTTAAATAGT
Found at i:2574 original size:172 final size:159
Alignment explanation
Indices: 2320--2758 Score: 522
Period size: 172 Copynumber: 2.7 Consensus size: 159
2310 ATGTTTATTG
* *
2320 AGGCATACATTCAATTATAGTCTGTTTTAACTAAAAATGTAAAAAATATTCAACTTAAAATCAAT
1 AGGCAAACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAA-ATTCAACTTAAAATCAAT
* * * **
2385 TATGAGATTACAAAACCATTTAAAGTC-AGTAGTAAGGCTTTT-AAAGCAATAGGCGACTATAGT
65 TATGAGATTATAAAACCATTTAAAG-CGAGTAATAAGGCTTTTGAAAGC-ATAGGCGACAATAAA
* *
2448 TAGGCTTTTTTTGTCAATGAATGACTTTTTCTTCACGTCTCTAA
128 TAGGCTTTTTTTGCCAATGAA--A----ATCTT----TCT-T-A
* * *
2492 AGGCAAACATTCAATTATAATATGTTTTAACGAAAAATGTAAAAAAAATCAACTTAAAATCAATT
1 AGGCAAACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATT
* * * * * *
2557 ATGAGGTTATAAAAACCATTTAAAGCGAGTAATAAGCCTTTTGAAGGCTTAGGTGACAATAAATG
66 ATGAGATTAT-AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGCGACAATAAATA
*
2622 GGCTTTTTTTGCCAATGAAAATGTTTCTTA
130 GGCTTTTTTTGCCAATGAAAATCTTTCTTA
* *
2652 AGGCAAACATTCAAATATAGTATGTTTTAACTAAAAATGTAAAGAAATTCAACTTTAAAATCAAT
1 AGGCAAACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAAATTCAAC-TTAAAATCAAT
2717 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
65 TATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTT
2759 NNNNNNNNNN
Statistics
Matches: 237, Mismatches: 26, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
160 79 0.33
161 22 0.09
162 3 0.01
166 3 0.01
170 1 0.00
171 27 0.11
172 98 0.41
173 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (159 bp):
AGGCAAACATTCAATTATAGTATGTTTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATT
ATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAAGCATAGGCGACAATAAATAG
GCTTTTTTTGCCAATGAAAATCTTTCTTA
Found at i:3468 original size:171 final size:170
Alignment explanation
Indices: 3060--4412 Score: 1239
Period size: 170 Copynumber: 8.0 Consensus size: 170
3050 NNNNNNNNNN
* * * *
3060 TAAAATTAATTATGAGATTACAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAATGCTTGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * * * * ** *
3125 ACCATAAATGGACTTTTCTTATCAATGAATGCCTCTTTCTTCAAT-TTCTT--AAACCAAATATT
66 ACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTC-ATGTT-TTCCAAGGCAAACATT
*
3187 CAATTATAATCTATTTTAACAAAACATGTAAAACAATTCAACT
129 CAATTATAATCTATTTTAACAAAA-ATGTAAAAAAATTCAACT
* * * ** * *
3230 AAAAATCAATTATGAGATTATAAAGCTATTTAAAGCAAGTAAAAAGGCTTTTAAAGGCTTGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * * *
3295 ACTATAAATGGGCTTTTCTTACCAATGACTTG-TTTTTCTTAATGTTTTCCAAGGCAAACATTTA
66 ACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCA
*
3359 ATTATAATCTGTTTTAATCAAAAATGTAAAACAAATTCAACT
131 ATTATAATCTATTTTAA-CAAAAATGTAAAA-AAATTCAACT
* * *
3401 TAAAATCAATTATGAGATTATAAAACCATTTATAGTGAGTAGTAAGGCTTTTGAAGGAATT-GGT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG-CTTGGGT
* *** * * *
3465 GACTATAATTAAACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTC
65 GACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTC
* * * * **
3530 AATTCTCATATGTTTTAACCAAAAATGT-AAAAAATTTGACT
130 AATTATAATCTATTTTAA-CAAAAATGTAAAAAAATTCAACT
* ** * * * *
3571 T-AAATCAATTATGAGGTTATAAAACCATTTAAAACGAGTAATAAGGCTTTTAAAAGCTTAGGTA
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
** * * ** *
3635 ACTATAAATGGGCTTTTCTTGTCAATAAATAGG-TTTTTCTTCACG-TTTCTTGAGGAAAACATT
66 ACTATAAATGGGCTTTTCTTACCAATGAAT-GGCTTTTTCTTCATGTTTTC-CAAGGCAAACATT
* * * **
3698 CAGTTATTATCTATTTTACCTAAAAATGTAAAAATGTTCAACT
129 CAATTATAATCTATTTTAAC-AAAAATGTAAAAAAATTCAACT
* * * *
3741 TAAAATCAATTATGCGATCATAAAATC-TTTAAAAGTGAGTAATAAGGCTTTTGAAGGCTTAGGT
1 TAAAATCAATTATGAGATTATAAAACCATTT-AAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGT
* * * *
3805 GAATATAAATGGGCTCTTT-TTACCAATGAATGGGTTTTTCTTCATG-GTTCCTAAGGCATACAT
65 GACTATAAATGGGCT-TTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCC-AAGGCAAACAT
* * *
3868 TTAATTATAATCTATTTTAACCAAAATGTAAAAGAATTCAACT
128 TCAATTATAATCTATTTTAACAAAAATGTAAAAAAATTCAACT
* * * **
3911 TACAATGAATTATGAGGTTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGGGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * * ** * * **
3976 ACTATAAATGGGCTTTTTTTGCAAATGAACAGATTTCTCTTCATG-TTTCTGAGGCAAACATTCA
66 ACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCA
* * *
4040 ATTTTAATTTATTTTAACTAAAAATATAAAAAATATTCAACT
131 ATTATAATCTATTTTAAC-AAAAATGTAAAAAA-ATTCAACT
* * * * **
4082 TAAAATTAATTATGAGATTACAAAACCATTTAAACTGAGTAATAAGGCTTTTG-AGGGTATGAAT
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCT-TGGGT
* * ** * * * * * *
4146 GACTATAAAT-GGATTTTTTTGTCAATAAATGCCTTTTTCTACACGTTTT-CAAGCCGAACA-TC
65 GACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTC
* * * * * *
4208 AACTACAATATGTTTTAACCGAAAATAT-AAAAAATTCAACT
130 AATTATAATCTATTTTAA-CAAAAATGTAAAAAAATTCAACT
* * * * * *
4249 TGAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTACTAAGGCTTTCGAAGGCTTGAGTG
1 TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
* * * * * ** * * * * * *
4314 ACTATAAGTGGACTTTTCATACTAATGGATAACTTTTGCTTCATATTTTCTAAGGTAGACATTTA
66 ACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCA
* *
4379 ATTATAATATATTTTAATCAAAAATATAAAAAAA
131 ATTATAATCTATTTTAA-CAAAAATGTAAAAAAA
4413 NNNNNNNNNN
Statistics
Matches: 952, Mismatches: 202, Indels: 57
0.79 0.17 0.05
Matches are distributed among these distances:
167 66 0.07
168 43 0.05
169 185 0.19
170 318 0.33
171 284 0.30
172 56 0.06
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (170 bp):
TAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGCTTGGGTG
ACTATAAATGGGCTTTTCTTACCAATGAATGGCTTTTTCTTCATGTTTTCCAAGGCAAACATTCA
ATTATAATCTATTTTAACAAAAATGTAAAAAAATTCAACT
Found at i:3697 original size:341 final size:340
Alignment explanation
Indices: 3060--4412 Score: 1338
Period size: 341 Copynumber: 4.0 Consensus size: 340
3050 NNNNNNNNNN
* * * * *
3060 TAAAATTAATTATGAGATTACAAAATCATTTAAAGTGAGTAATAAGGCTTTTGAATGCTTGGGTG
1 TAAAATCAATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGATTAGGTG
* * * * ** * *
3125 ACCATAAATGGACTTTTCTTATCAATGAATGCCTCTTTCTTCA-ATTTCTTAAACCAAATATTCA
66 ACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCCCAAGCCAAACATTCA
* *
3189 ATTATAATCTATTTTAA-CAAAACATGTAAAACAATTCAACTAAAAATCAATTATGAGATTATAA
131 ATTATAATATATTTTAACCAAAA-ATGTAAAACAATTCAACT-TAAATCAATTATGAGATTATAA
* * * * *
3253 AGCTATTTAAAGCAAGTAAAAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTACC
194 AACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTT-GC
* * * ** * *
3318 AATGACT-TGTTTTTCTTAATGTTT-TCCAAGGCAAACATTTAATTATAATCTGTTTTAA-TCAA
258 AATGAATAGGTTTTTCTTCATGTTTCT-TGAGGCAAACATTCAATTATAATCTATTTTAACT-AA
3380 AAATGTAAAACAAATTCAACT
321 AAATGTAAAA-AAATTCAACT
* * *
3401 TAAAATCAATTATGAGATTATAAAACCATTTATAGTGAGTAGTAAGGCTTTTGAAGGAATT-GGT
1 TAAAATCAATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG-ATTAGGT
* ** * * **
3465 GACTATAATTAAACTTTTCTTGCCAATGAATGGCTTTTTCTTCATGTTTCCCAAGGAAAACATTC
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCCCAAGCCAAACATTC
* * * ** *
3530 AATTCTCATATGTTTTAACCAAAAATGTAAAA-AATTTGACTTAAATCAATTATGAGGTTATAAA
130 AATTATAATATATTTTAACCAAAAATGTAAAACAATTCAACTTAAATCAATTATGAGATTATAAA
* * * *
3594 ACCATTTAAAACGAGTAATAAGGCTTTTAAAAGCTTAGGTAACTATAAATGGGCTTTTCTTGTCA
195 ACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTG-CA
* * * * * *
3659 ATAAATAGGTTTTTCTTCACGTTTCTTGAGGAAAACATTCAGTTATTATCTATTTTACCTAAAAA
259 ATGAATAGGTTTTTCTTCATGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTAACTAAAAA
**
3724 TGTAAAAATGTTCAACT
324 TGTAAAAAAATTCAACT
* * * * *
3741 TAAAATCAATTATGCGATCATAAAATC-TTTAAAAGTGAGTAATAAGGCTTTTGAAGGCTTAGGT
1 TAAAATCAATTATGAGATTACAAAACCATTT-AAAGTGAGTAATAAGGCTTTTGAAGGATTAGGT
* * ** * * * *
3805 GAATATAAATGGGCTCTTT-TTACCAATGAATGGGTTTTTCTTCATGGTTCCTAAGGCATACATT
65 GACTATAAATGGACT-TTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCCCAAGCCAAACATT
* * * * *
3869 TAATTATAATCTATTTTAACC-AAAATGTAAAAGAATTCAACTTACAATGAATTATGAGGTTATA
129 CAATTATAATATATTTTAACCAAAAATGTAAAACAATTCAACTTA-AATCAATTATGAGATTATA
* * *
3933 AAACCATTTAAAGTGAGTAATAAGGCTTTCAAAGGCTTGGGTGACTATAAATGGGCTTTTTTTGC
193 AAACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC
* * * * *
3998 AAATGAACAGATTTCTCTTCATGTTTC-TGAGGCAAACATTCAATTTTAATTTATTTTAACTAAA
258 -AATGAATAGGTTTTTCTTCATGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTAACTAAA
*
4062 AATATAAAAAATATTCAACT
322 AATGTAAAAAA-ATTCAACT
* * * * *
4082 TAAAATTAATTATGAGATTACAAAACCATTTAAACTGAGTAATAAGGCTTTTGAGGGTATGA-AT
1 TAAAATCAATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG-ATTAGGT
* ** * * * * *
4146 GACTATAAATGGA-TTTTTTTGTCAATAAATGCCTTTTTCTACACGTTT-TCAAGCCGAACA-TC
65 GACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCCCAAGCCAAACATTC
* * * * *
4208 AACTACAATATGTTTTAACCGAAAATATAAAA-AATTCAACTTGAAATCAATTATGAGATTATAA
130 AATTATAATATATTTTAACCAAAAATGTAAAACAATTCAACTT-AAATCAATTATGAGATTATAA
* * ** * * * * *
4272 AATCATTTAAAGCGAGTACTAAGGCTTTCGAAGGCTTGAGTGACTATAAGTGGACTTTTCATACT
194 AACCATTTAAAGCGAGTAATAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGC-
* ** * * * * * * *
4337 AATGGATAACTTTTGCTTCATATTT-TCTAAGGTAGACATTTAATTATAATATATTTTAA-TCAA
258 AATGAATAGGTTTTTCTTCATGTTTCT-TGAGGCAAACATTCAATTATAATCTATTTTAACT-AA
*
4400 AAATATAAAAAAA
321 AAATGTAAAAAAA
4413 NNNNNNNNNN
Statistics
Matches: 833, Mismatches: 157, Indels: 47
0.80 0.15 0.05
Matches are distributed among these distances:
338 119 0.14
339 77 0.09
340 277 0.33
341 311 0.37
342 44 0.05
343 5 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (340 bp):
TAAAATCAATTATGAGATTACAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGGATTAGGTG
ACTATAAATGGACTTTTCTTACCAATGAATGCCTTTTTCTTCATGTTTCCCAAGCCAAACATTCA
ATTATAATATATTTTAACCAAAAATGTAAAACAATTCAACTTAAATCAATTATGAGATTATAAAA
CCATTTAAAGCGAGTAATAAGGCTTTTAAAGGCTTGGGTGACTATAAATGGGCTTTTCTTGCAAT
GAATAGGTTTTTCTTCATGTTTCTTGAGGCAAACATTCAATTATAATCTATTTTAACTAAAAATG
TAAAAAAATTCAACT
Found at i:4881 original size:172 final size:161
Alignment explanation
Indices: 4684--5015 Score: 326
Period size: 172 Copynumber: 2.0 Consensus size: 161
4674 NNNNNNNNNN
* * * *
4684 TAAAGTGAGTAATAAGGCTTTTGAAGGCTTAAGTGAATATAAATGGGCTTTTCTTATCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGCATAAGTGAATATAAATAGACTTTTCTTATCAATGAAT
* * * * *
4749 GGGTTTTTCTTCACGTTTCCT-AAGGTAAACATTCGATTACAATATGCTTTAACTAAAAAA-GTA
66 AGCTTTTTCTTCACG-TTCCTCAAGGCAAACAGTCAATTACAATATGCTTTAA-TAAAAAATGTA
4812 AAAAAAACTCAACGTAAAATCAATTATGAGATTNNNNNNNNNNT
129 AAAAAAA-TCAACGTAAAATCAATTATGAGATT----------T
* ** * *
4856 TAAAGCGAGTAATACGGCTTTTGAAGGCATGGGTGACTATAAATAGACTTTTCTTGTCAATGAAT
1 TAAAGCGAGTAATAAGGCTTTTGAAGGCATAAGTGAATATAAATAGACTTTTCTTATCAATGAAT
* * * * * *
4921 AGCTTTTTCTTTATGTTCCTCATGGCAGACAGTCAATTACAATTTGTTTTAATAAAAAATGTAAA
66 AGCTTTTTCTTCACGTTCCTCAAGGCAAACAGTCAATTACAATATGCTTTAATAAAAAATGTAAA
* * *
4986 GATAATCAACGTAAAATTAATTATGAGATT
131 AAAAATCAACGTAAAATCAATTATGAGATT
5016 ACAAAACCAT
Statistics
Matches: 135, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
171 36 0.27
172 99 0.73
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.34
Consensus pattern (161 bp):
TAAAGCGAGTAATAAGGCTTTTGAAGGCATAAGTGAATATAAATAGACTTTTCTTATCAATGAAT
AGCTTTTTCTTCACGTTCCTCAAGGCAAACAGTCAATTACAATATGCTTTAATAAAAAATGTAAA
AAAAATCAACGTAAAATCAATTATGAGATTT
Found at i:5710 original size:170 final size:170
Alignment explanation
Indices: 5204--6087 Score: 818
Period size: 171 Copynumber: 5.2 Consensus size: 170
5194 NNCGAGTAAT
* * * * * **
5204 AAGGCTTGAGTGTCTATAAATGGACTTTTCATA-CTAATGGATGACTTTTGCTTCACATTTC-CT
1 AAGGCTTGAGTGACTAGAAGTGGACTTTTCATATC-AATAGATGGCTTTTGCTTCATGTTTCTC-
* * * * * * **
5267 AAGATAGACATTCAATTATAATATATCTTAATAAAAAATATTAAAAAAATTTAACTTAAAATCAA
64 AAGGTAAACATTCAATCATATTATATTTTAATAAAAAA-AGT-AAAAAATACAACTTAAAATCAA
* * *
5332 TTA-GAAGATTATAAAACCAATTTAAAGCGAGTAATAAAGCTTTCG
127 TTATG-AGATTATAAAACC-ATTCAAAGAGAGTAATAAGGCTTTCG
* * * * * * * * * *
5377 AAAG-TTTAGGTGACTATAAATGGACTTTTCTTGTTAATAAATGGCTTTTTCTTCATGTTTCCCA
1 AAGGCTTGA-GTGACTAGAAGTGGACTTTTCATATCAATAGATGGCTTTTGCTTCATGTTTCTCA
** * * * * ***********
5441 AGACAAACATTCAATTATAATCTGTTTTAACTAGAAATNNNNNNNNNNT-CAACTTAAAATCAAT
65 AGGTAAACATTCAATCATATTATATTTTAA-TA-AAAAAAGTAAAAAATACAACTTAAAATCAAT
* *
5505 TATGTGATTATAAAACCATGT-AAAGCGAGTAATAAGGCTTTCG
128 TATGAGATTATAAAACCAT-TCAAAGAGAGTAATAAGGCTTTCG
* * *
5548 AAGGCTTGAGTGACTAGAAATGGACTTTTCATATCAATAGATGGTTTTTGCTTCAGGTTTCTCAA
1 AAGGCTTGAGTGACTAGAAGTGGACTTTTCATATCAATAGATGGCTTTTGCTTCATGTTTCTCAA
* ** * * * * *
5613 GTTTGACACTAAATCATAATATATTTTAATTAAAAAAGTAAAAAATGCAACTTAAAATCAATTAT
66 GGTAAACATTCAATCATATTATATTTTAATAAAAAAAGTAAAAAATACAACTTAAAATCAATTAT
** *
5678 GAGATTATAAAAATATTCAGAGAGAGTAATAAGGCTTTCG
131 GAGATTATAAAACCATTCAAAGAGAGTAATAAGGCTTTCG
*
5718 AAGGCTTGAGTGACT-GTAAGTGGACTTTTCATATAAATAGATGGCTTTTGCTTCATGTTTCTCA
1 AAGGCTTGAGTGACTAG-AAGTGGACTTTTCATATCAATAGATGGCTTTTGCTTCATGTTTCTCA
** *
5782 AGGCCAACATTCAATCATATTATATTTTAATCAAAAAAGTAAAACAATACAACTTAAAATCAATT
65 AGGTAAACATTCAATCATATTATATTTTAATAAAAAAAGTAAAA-AATACAACTTAAAATCAATT
* * * *
5847 ATGATATTATAAAACCATTCAAAGTGAGTAACAACGCTTTCG
129 ATGAGATTATAAAACCATTCAAAGAGAGTAATAAGGCTTTCG
* * * * *
5889 GAGGCTAGAGTG--TATAAGTGGACTTTTCATATCAATAGATGCCTTTTGCTTCATGTTTGTCAA
1 AAGGCTTGAGTGACTAGAAGTGGACTTTTCATATCAATAGATGGCTTTTGCTTCATGTTTCTCAA
* *
5952 GGTAAACATTCAATCATATTATATTCTAATAAAAAAAGTAAAAAAATACAACTTAAACTCAATTA
66 GGTAAACATTCAATCATATTATATTTTAATAAAAAAAGT-AAAAAATACAACTTAAAATCAATTA
* * *
6017 TGAGATTATAAAGCCATTTAAAGCA-AGTAATAAGGCTTTCA
130 TGAGATTATAAAACCATTCAAAG-AGAGTAATAAGGCTTTCG
** *
6058 AAGGCTTG-GATGACTTTAAGTGGGCTTTTC
1 AAGGCTTGAG-TGACTAGAAGTGGACTTTTC
6088 TTCATATTTC
Statistics
Matches: 583, Mismatches: 110, Indels: 38
0.80 0.15 0.05
Matches are distributed among these distances:
168 1 0.00
169 148 0.25
170 150 0.26
171 171 0.29
172 35 0.06
173 72 0.12
174 3 0.01
175 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (170 bp):
AAGGCTTGAGTGACTAGAAGTGGACTTTTCATATCAATAGATGGCTTTTGCTTCATGTTTCTCAA
GGTAAACATTCAATCATATTATATTTTAATAAAAAAAGTAAAAAATACAACTTAAAATCAATTAT
GAGATTATAAAACCATTCAAAGAGAGTAATAAGGCTTTCG
Found at i:5837 original size:341 final size:338
Alignment explanation
Indices: 5204--6087 Score: 917
Period size: 341 Copynumber: 2.6 Consensus size: 338
5194 NNCGAGTAAT
* *
5204 AAGGCTTGAGTGTCTATAAATGGACTTTTCATA-CTAATGGATGACTTTTGCTTCACATTTC-CT
1 AAGGCTTGAGTG-CTATAAATGGACTTTTCATATC-AATAGATGACTTTTGCTTCACGTTTCTC-
* * * **
5267 AAGATAGACATTCAATTATAATATATCTTAATAAAAAATATTAAAAAAATTTAACTTAAAATCAA
63 AAGATAGACATTCAATCATAATATATTTTAATAAAAAA-AGTAAAAAAATACAACTTAAAATCAA
* * * *
5332 TTA-GAAGATTATAAAACCAATTTAAAGCGAGTAATAAAGCTTTCGAAAG-TTTAGGTGACTATA
127 TTATG-AGATTATAAAA--AATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGA-GTGACTATA
* * * * * *
5395 AATGGACTTTTCTTGTTAATAAATGGCTTTTTCTTCATGTTTCCCAAGACAAACATTCAATTATA
188 AGTGGACTTTTCATATAAATAAATGGCTTTTGCTTCATGTTTCCCAAGACAAACATTCAATCATA
* * * * ********
5460 ATCTGTTTTAACTAGAAATNNNNNNNNNNTCAACTTAAAATCAATTATG-TGATTATAAAACCAT
253 ATATATTTTAACAAAAAAT--AAAAACAATCAACTTAAAATCAATTATGAT-ATTATAAAACCAT
* *
5524 GT-AAAGCGAGTAATAAGGCTTTCG
315 -TCAAAGCGAGTAACAACGCTTTCG
* ** *
5548 AAGGCTTGAGTGACTAGAAATGGACTTTTCATATCAATAGATGGTTTTTGCTTCAGGTTTCTCAA
1 AAGGCTTGAGTG-CTATAAATGGACTTTTCATATCAATAGATGACTTTTGCTTCACGTTTCTCAA
* * * * * *
5613 GTTTGACACTAAATCATAATATATTTTAATTAAAAAAGT-AAAAAATGCAACTTAAAATCAATTA
65 GATAGACATTCAATCATAATATATTTTAATAAAAAAAGTAAAAAAATACAACTTAAAATCAATTA
* * *
5677 TGAGATTATAAAAATATTCAGAGAGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTGTAAGTGGA
130 TGAGATTATAAAAA-ATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAGTGGA
* * * * *
5742 CTTTTCATATAAATAGATGGCTTTTGCTTCATGTTTCTCAAGGCCAACATTCAATCATATTATAT
194 CTTTTCATATAAATAAATGGCTTTTGCTTCATGTTTCCCAAGACAAACATTCAATCATAATATAT
5807 TTTAATCAAAAAAGT-AAAACAATACAACTTAAAATCAATTATGATATTATAAAACCATTCAAAG
259 TTTAA-CAAAAAA-TAAAAACAAT-CAACTTAAAATCAATTATGATATTATAAAACCATTCAAAG
*
5871 TGAGTAACAACGCTTTCG
321 CGAGTAACAACGCTTTCG
* * * * * *
5889 GAGGCTAGAGTG-TATAAGTGGACTTTTCATATCAATAGATGCCTTTTGCTTCATGTTTGTCAAG
1 AAGGCTTGAGTGCTATAAATGGACTTTTCATATCAATAGATGACTTTTGCTTCACGTTTCTCAAG
* * * * *
5953 GTAAACATTCAATCATATTATATTCTAATAAAAAAAGTAAAAAAATACAACTTAAACTCAATTAT
66 ATAGACATTCAATCATAATATATTTTAATAAAAAAAGTAAAAAAATACAACTTAAAATCAATTAT
** * *
6018 GAGATTATAAAGCCATTTAAAGCA-AGTAATAAGGCTTTCAAAGGCTTG-GATGACTTTAAGTGG
131 GAGATTATAAA-AAATTTAAAG-AGAGTAATAAGGCTTTCGAAGGCTTGAG-TGACTATAAGTGG
*
6081 GCTTTTC
193 ACTTTTC
6088 TTCATATTTC
Statistics
Matches: 452, Mismatches: 74, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
339 77 0.17
340 85 0.19
341 158 0.35
342 43 0.10
343 4 0.01
344 83 0.18
345 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.34
Consensus pattern (338 bp):
AAGGCTTGAGTGCTATAAATGGACTTTTCATATCAATAGATGACTTTTGCTTCACGTTTCTCAAG
ATAGACATTCAATCATAATATATTTTAATAAAAAAAGTAAAAAAATACAACTTAAAATCAATTAT
GAGATTATAAAAAATTTAAAGAGAGTAATAAGGCTTTCGAAGGCTTGAGTGACTATAAGTGGACT
TTTCATATAAATAAATGGCTTTTGCTTCATGTTTCCCAAGACAAACATTCAATCATAATATATTT
TAACAAAAAATAAAAACAATCAACTTAAAATCAATTATGATATTATAAAACCATTCAAAGCGAGT
AACAACGCTTTCG
Done.