Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397808.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_111.0, 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: 18664
ACGTcount: A:0.25, C:0.08, G:0.09, T:0.24
Warning! 6571 characters in sequence are not A, C, G, or T
Found at i:1769 original size:171 final size:170
Alignment explanation
Indices: 1014--3203 Score: 895
Period size: 171 Copynumber: 12.9 Consensus size: 170
1004 NNNNNNNNNN
* *
1014 TTTAACTAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATTAAAA-AATTTAAAA
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTA-TAAAACAATTTAAAG
* * * * * * **
1078 CGAGTAATAAGGTTTTTGAAGGAATGAGTGACTATAAATTGACTTTTCTTGCCAACGAATGTGTT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATGAATT
* **********
1143 TTTCTT-CACGTTTCTNNNNNNNNNNATTCAATTATAGTCTGT
129 TTT-TTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * * *
1185 TTTAGC-AAAAAGTGTAAAAAAATTTAACTTAAAATCAATTAAGAGATTATAAAACAATTTAAAG
1 TTTAACTAAAAA-TATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
* * * *** * * * * *
1249 CGAGTAATAAGGATTTAGAAGGAATCAATCACTATAAATGGAATTTTCTTGCAAATGAATGTATT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATGAATT
* * **
1314 TTTCTT-CACGTTTCTCCAA-GTAGAAATTCAATTATAGTCTGT
129 TTT-TTGCATGTTTCT-CAAGGCAGGCATTCAATTATAGTCTGT
* * * * * * ******
1356 TTTAGCTACAAATGTAAAAAAATTCATCTTCAAATCAATTATAAGATTATAAAACAATTNNNNNN
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
**** * * * * * * * *
1421 NNNNAATAAGGCTTTTGAAAGAATGAGTGACTGTAAATAGACTTTTTTTCTAAATGAGT-AGCTT
66 GAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATGA-ATT
* * * *
1485 TTTTTACACGTTTCTCAAGGAAAGCATTCAATTATAGTCTGT
129 TTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* *****************************
1527 TTTAA-TAAAAAATATAAAAAAATTTAACTTAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNAG
1 TTTAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
* * *
1591 TGAGTAATAAAGCTTTTGAAGGAATGAGTGACTATAAATGGACTTTTTTTCTTAATGAATGAATT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATGAATT
* * *
1656 TTTTTACATGTTTCTGAAGGCAGGCATTGAATTATAGTCTGT
129 TTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * * * * *
1698 TTTAACTATAAATGTCAAAAAATTCAACTCAAAATCAATTTTGGGATTATAAAAC-ATCTTAAAG
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAAT-TTAAAG
* * * * * **
1762 CGAGTAATAAGGCTTTTAAAGAAATGGGTGACTACAAATGGACTTTTCTTGCCAATGAATGTCTT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATG-AAT
* * ** * ********** *
1827 TTTTTTTCATATTTCTTGAGGTANNNNNNNNNNTATTGTCTGT
128 TTTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * *
1870 TTTAACCAAAAATAT-AAAAATTTCAACTTAAAATCAATTATGAAATTATAAAACAATTTAAAGC
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * *
1934 GAGTAAT-GAGACTTTTGAAGGAATGGGTGGCTATAAATGGA-TTTTTCTTCACAATGAAT-AGT
66 GAGTAATAAAG-CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTT-TTC-CAATGAATGAAT
* **
1996 TTTTTTGCATGTTTCTCAAGACAAACATTCAATTATAGTCTGT
128 TTTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * * **********
2039 TTTAA-TGAGAAATGTAAAAAAAATCAACTTANNNNNNNNNNTGAGATTATAAAACAATTTAAAG
1 TTTAACT-AAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
* * * * * ** ** * **
2103 TGAGTAAGAAGGCTTTTGAAGGACTAGACGACTATAAATGGACTTTTCATACAATTGAATGCCTT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCAA-TGAATGAATT
* * * * *
2168 TTTTGGCATGTTTCTAAAGGTAGGCATTCAATTACAGTATGT
129 TTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
********* * *
2210 TTTAA-TAAAANNNNNNNNNNAATTCAACTTAAAATTAATTATAAGATTATAAAACAATTTAAAG
1 TTTAACTAAAA-ATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
* * * *
2274 CGGGTAAT-AAGATTTTTGATGGAATGGGTGACTATAAATGGAC-TTTTTTCTCAAT-AGT-AAC
65 CGAGTAATAAAG-CTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATGAA-
* * *
2335 TTTTTGTGCAT-TTTCTCAAGACAGGCATTCAATTATAGTCTAT
127 TTTTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * * * * **
2378 TTTAACAAAAAATAAAAAAAAATTCAACTTAAAATTAATTTTGAGATTATAAAACAATTTGAANN
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
******** * * * *
2443 NNNNNNNNAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTTTCCTCAATGAATG-GTTT
66 GAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATGAATTT
** * * * * *
2507 TTTTATACGTTTCTCGAGCCAAGCATTCGATTATAGTCT-T
130 TTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
*********** * *
2547 TTTNNNNNNNNNNGTAAAAAAATTCAACTTAAAATAAAATT-T-AGGATTGTAAAACAATTTAAA
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAAT-CAATTATGA-GATTATAAAACAATTTAAA
* ********** * * * * **
2610 GCGAGTAATAAGGCNNNNNNNNNNATAGGTGACTATAAATAGACTTTTCTTACAAATGAATGCCT
64 GCGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATGAAT
* * * ** * * *
2675 GTTTTTT-TATGTTTCTTAAGGTAAACATTCAATTATTGACTAT
128 -TTTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * ********** *
2718 TTTAACTAAAAATGTAAAAAAATTTANNNNNNNNNNAATTATGAGATTATAAAAGAATTTAAAGC
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
* * *****
2783 G-GATAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGAC-TTTTTTCTCAAT-AGTNNNNN
66 GAG-TAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTC-CAATGAATGAATT
*****
2845 NNNNNGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
129 TTTTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * * ***********
2887 TTTAACAAAAAAT-TAAAAAAAATTCAACTTCAAATTAATTATGAGATTATNNNNNNNNNNGAAG
1 TTTAACTAAAAATAT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAG
* * * **
2951 TGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGTAC-TTTTTTCCTTAATGAATGGGT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCC--AATGAATGAAT
* * * **
3015 TTTTTAT--ACGTTTCTCGAGGCAAGCATTTGATTATAGTCT-T
128 TTTTT-TGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
* * * * *********
3056 TTGAACCATAAATGTAAAAAAATTCAACTTAAAAT-ANNNNNNNNNNTTATAAAACAATTTAAAG
1 TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCA-ATTATGAGATTATAAAACAATTTAAAG
* ** * * * *
3120 CGAGTAATAAGGCTTTCAAAGCAATGGGTGACTATAAATGGACTTTTCTTACAAATGAAT-ACCT
65 CGAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTT-TTTCCAATGAATGA-AT
3184 TTTTTT-CATGTTTCTCAAGG
128 TTTTTTGCATGTTTCTCAAGG
3204 TAAACATTCA
Statistics
Matches: 1459, Mismatches: 503, Indels: 116
0.70 0.24 0.06
Matches are distributed among these distances:
168 104 0.07
169 369 0.25
170 216 0.15
171 718 0.49
172 52 0.04
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.34
Consensus pattern (170 bp):
TTTAACTAAAAATATAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACAATTTAAAGC
GAGTAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTTCCAATGAATGAATTTT
TTTGCATGTTTCTCAAGGCAGGCATTCAATTATAGTCTGT
Found at i:3075 original size:509 final size:497
Alignment explanation
Indices: 1864--3213 Score: 1087
Period size: 509 Copynumber: 2.7 Consensus size: 497
1854 NNNNNNTATT
* * * * * *
1864 GTCTGTTTTAACCAAAAAT-ATAAAAATTTCAACTTAAAATCAATTATGAAATTATAAAACAATT
1 GTCTATTTTAACAAAAAATAAAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACAATT
* * * * * * * *
1928 TAAAGCGAGTAATGAGACTTTTGAAGGAATGGGTGGCTATAAATGGA-TTTTTCTTCACAATGAA
66 TGAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTT-TCCTCAATGAA
* * ** * * * * * * ** *
1992 TAGTTTTTTTGCATGTTTCTCAAGACAAACATTCAATTATAGTCTGTTTTAATGAGAAATGTAAA
130 TGGGTTTTTTATACGTTTCTCGAGCCAAGCATTCGATTATAGTCT-TTTGAACCATAAATGTAAA
* ********** * * **
2057 AAAAATCAACTTANNNNNNNNNNT-GAGATTATAAAACAATTTAAAGTGAGTAAGAAGGCTTTTG
194 AAAATTCAACTTAAAATAAAATTTAG-GATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCA
* * ** * * * * * *
2121 AAGGACTAGACGACTATAAATGGACTTTTCATACAATTGAATGCCTTTTTTGGCATGTTTCTAAA
258 AAGCAATAGGTGACTATAAATAGACTTTTCTTACAAATGAATACCTTTTTT-TCATGTTTCTCAA
** ** * *
2186 GGTAGGCATTCAATTACAGTA-TGTTTTAA-TAAAANNNNNNNNNNAAT-TCAACTTAAAA-TT-
322 GGTAAACATTCAATTATTG-ACTATTTTAACT-AAA----------AATGT-AA--AAAAATTTA
* * *
2246 AATTATAAGATTATAAAACAATTTAAAGCGGGTAATAAGATTTTTGATGGAATGGGTGACTATAA
372 AATTATAAGATTATAAAACAATTTAAAGCGGATAATAAGACTTTTGAAGGAATGGGTGACTATAA
2311 ATGGACTTTTTTCTCAATAGTAACTTTTTGTGCATTTTCTCAAGACAGGCATTCAATTATA
437 ATGGACTTTTTTCTCAATAGTAACTTTTTGTGCATTTTCTCAAGACAGGCATTCAATTATA
*
2372 GTCTATTTTAACAAAAAATAAAAAAAAATTCAACTTAAAATTAATTTTGAGATTATAAAACAATT
1 GTCTATTTTAACAAAAAATAAAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACAATT
**********
2437 TGAANNNNNNNNNNAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTTTCCTCAATGAAT
66 TGAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTTTCCTCAATGAAT
* ***********
2502 GGTTTTTTTATACGTTTCTCGAGCCAAGCATTCGATTATAGTCTTTTTNNNNNNNNNNGTAAAAA
131 GGGTTTTTTATACGTTTCTCGAGCCAAGCATTCGATTATAGTCTTTTGAACCATAAATGTAAAAA
* ********
2567 AATTCAACTTAAAATAAAATTTAGGATTGTAAAACAATTTAAAGCGAGTAATAAGGCNNNNNNNN
196 AATTCAACTTAAAATAAAATTTAGGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCAAAG
** * * *
2632 NNATAGGTGACTATAAATAGACTTTTCTTACAAATGAATGCCTGTTTTTTTATGTTTCTTAAGGT
261 CAATAGGTGACTATAAATAGACTTTTCTTACAAATGAATACCT-TTTTTTCATGTTTCTCAAGGT
*
2697 AAACATTCAATTATTGACTATTTTAACTAAAAATGTAAAAAAATTTANNNNNNNNNNAATTATGA
325 AAACATTCAATTATTGACTATTTTAACTAAAAATGTAAAAAAATTTA----------AATTATAA
* *
2762 GATTATAAAAGAATTTAAAGCGGATAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT
380 GATTATAAAACAATTTAAAGCGGATAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTT
********** *
2827 TTTTCTCAATAGTNNNNNNNNNNGCATGTTTCTCAAGGCAGGCATTCAATTATA
445 TTTTCTCAATAGTAACTTTTTGTGCAT-TTTCTCAAGACAGGCATTCAATTATA
* * * *********
2881 GTCTGTTTTAACAAAAAATTAAAAAAAATTCAACTTCAAATTAATTATGAGATTATNNNNNNNNN
1 GTCTATTTTAACAAAAAATAAAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACAATT
* * * *
2946 NGAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGTACTTTTTTCCTTAATGAAT
66 TGAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTTTCCTCAATGAAT
* *
3011 GGGTTTTTTATACGTTTCTCGAGGCAAGCATTTGATTATAGTCTTTTGAACCATAAATGTAAAAA
131 GGGTTTTTTATACGTTTCTCGAGCCAAGCATTCGATTATAGTCTTTTGAACCATAAATGTAAAAA
**********
3076 AATTCAACTTAAAATANNNNNNNNNNTTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCAAAG
196 AATTCAACTTAAAATAAAATTTAGGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCAAAG
* *
3141 CAATGGGTGACTATAAATGGACTTTTCTTACAAATGAATACCTTTTTTTCATGTTTCTCAAGGTA
261 CAATAGGTGACTATAAATAGACTTTTCTTACAAATGAATACCTTTTTTTCATGTTTCTCAAGGTA
3206 AACATTCA
326 AACATTCA
3214 NNNNNNNNNN
Statistics
Matches: 658, Mismatches: 164, Indels: 40
0.76 0.19 0.05
Matches are distributed among these distances:
496 4 0.01
497 2 0.00
498 5 0.01
499 1 0.00
507 1 0.00
508 251 0.38
509 389 0.59
510 5 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.33
Consensus pattern (497 bp):
GTCTATTTTAACAAAAAATAAAAAAAAATTCAACTTAAAATTAATTATGAGATTATAAAACAATT
TGAAGTGAGTAATAAGGCTTTTGAAGGAATGGGTGACAATAAATGGACTTTTTTCCTCAATGAAT
GGGTTTTTTATACGTTTCTCGAGCCAAGCATTCGATTATAGTCTTTTGAACCATAAATGTAAAAA
AATTCAACTTAAAATAAAATTTAGGATTATAAAACAATTTAAAGCGAGTAATAAGGCTTTCAAAG
CAATAGGTGACTATAAATAGACTTTTCTTACAAATGAATACCTTTTTTTCATGTTTCTCAAGGTA
AACATTCAATTATTGACTATTTTAACTAAAAATGTAAAAAAATTTAAATTATAAGATTATAAAAC
AATTTAAAGCGGATAATAAGACTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTCTCAATA
GTAACTTTTTGTGCATTTTCTCAAGACAGGCATTCAATTATA
Found at i:4741 original size:170 final size:169
Alignment explanation
Indices: 4440--4881 Score: 495
Period size: 170 Copynumber: 2.6 Consensus size: 169
4430 NNNNNNNNAT
* * *
4440 TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATGGATGG-CTATAACT
1 TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAATGG-GGGACTATAAAT
* * * *
4504 AGACTTTTCTTGCT-AATGAATGCCTTTTTTTCATGTTTCTCAAGGTAAAAATTTAATTATTGTC
65 GGACTTTTCTTGCTCAATGAATG-CTTTTTTTCATGTTTCTCAAAGTAAAAATTCAATTATAGTC
** *
4568 TGTTTTCACCAAAAATAT-AAAAACAT-TCAA-TTCAAAATCAA
129 TGTTTGAACCAAAAAT-TCAAAAAAATCT-AACTT-AAAATCAA
* * * * *
4609 TTATGAGTTTATAAAACAATTTAAAGTAAGTAATAAAGCTTTTGAAGAAATGGGGGACCATAAAT
1 TT-TGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAATGGGGGACTATAAAT
* * **
4674 GGACTTTT-TTTCTCAATGAATAGCTTTTTTTGCATGTTTCTCAAAG-CAGGATTCAATTATAGT
65 GGACTTTTCTTGCTCAATGAAT-GCTTTTTTT-CATGTTTCTCAAAGTAAAAATTCAATTATAGT
*
4737 CTGTTTGAACCAAAAGTTCAAAAAAATCTAACTTAAAATCAA
128 CTGTTTGAACCAAAAATTCAAAAAAATCTAACTTAAAATCAA
* * * * ** *
4779 TTTGAGATTATAAAATAATTTAAAGCGAGTAATAACGCTTTTAAAGGAATAGGTAACTATAAACG
1 TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAATGGGGGACTATAAATG
* *
4844 GACTTTTCTTGC-CAATGAATGATTTTTTTCACGTTTCT
66 GACTTTTCTTGCTCAATGAATGCTTTTTTTCATGTTTCT
4882 TGAGGTANNN
Statistics
Matches: 229, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
167 8 0.03
168 8 0.03
169 75 0.33
170 121 0.53
171 17 0.07
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (169 bp):
TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAATGGGGGACTATAAATG
GACTTTTCTTGCTCAATGAATGCTTTTTTTCATGTTTCTCAAAGTAAAAATTCAATTATAGTCTG
TTTGAACCAAAAATTCAAAAAAATCTAACTTAAAATCAA
Found at i:4862 original size:169 final size:167
Alignment explanation
Indices: 4440--5007 Score: 484
Period size: 169 Copynumber: 3.4 Consensus size: 167
4430 NNNNNNNNAT
* *
4440 TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAGGCTTTTAAAGGAATGGATGGCTAT-AACT
1 TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAATGG-TGACTATAAAC-
* * * * *
4504 AGACTTTTCTTGCTAATGAATGCCTTTTTTTCATGTTTCTCAAGGTAAAAATTTAATTATTGTCT
64 GGACTTTTCTTGCCAATGAATG-CTTTTTTTCATGTTTCTCAAAGTAAAAATTCAATTATAGTCT
** *
4569 GTTTTCACCAAAAATATAAAAACATTCAATTCAAAATCAA
128 GTTTGAACCAAAAATATAAAAAAATTCAATTCAAAATCAA
* * * * * * *
4609 TTATGAGTTTATAAAACAATTTAAAGTAAGTAATAAAGCTTTTGAAGAAATGGGGGACCATAAAT
1 TT-TGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAAT-GGTGACTATAAAC
* * **
4674 GGACTTTT-TTTCTCAATGAATAGCTTTTTTTGCATGTTTCTCAAAG-CAGGATTCAATTATAGT
64 GGACTTTTCTTGC-CAATGAAT-GCTTTTTTT-CATGTTTCTCAAAGTAAAAATTCAATTATAGT
*
4737 CTGTTTGAACCAAAAGT-TCAAAAAAA-TCTAACTT-AAAATCAA
126 CTGTTTGAACCAAAAATAT-AAAAAAATTC-AA-TTCAAAATCAA
* * * *
4779 TTTGAGATTATAAAATAATTTAAAGCGAGTAATAACGCTTTTAAAGGAATAGGTAACTATAAACG
1 TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAAT-GGTGACTATAAACG
* * ** * **********
4844 GACTTTTCTTGCCAATGAATGATTTTTTTCACGTTTCTTGAGGTANNNNNNNNNNTATAGTCTGT
65 GACTTTTCTTGCCAATGAATGCTTTTTTTCATGTTTCTCAAAGTAAAAATTCAATTATAGTCTGT
* * * * * *
4909 TTTAGCAAAAAACT-TAACAAAATTCAACTCAAAATTAA
130 TTGAACCAAAAA-TATAAAAAAATTCAATTCAAAATCAA
* * * * *
4947 TTATGCGATTATAAAACAAATTAAAGCGAGTAATAAGGCTTTTGAAGGAATGGGTGACTAT
1 TT-TGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAAT-GGTGACTAT
5008 NNNNNNNNNN
Statistics
Matches: 319, Mismatches: 65, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
167 11 0.03
168 43 0.13
169 129 0.40
170 116 0.36
171 20 0.06
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.34
Consensus pattern (167 bp):
TTTGAGATTATAAAACAATTTAAAGCAAGTAATAAAGCTTTTAAAGGAATGGTGACTATAAACGG
ACTTTTCTTGCCAATGAATGCTTTTTTTCATGTTTCTCAAAGTAAAAATTCAATTATAGTCTGTT
TGAACCAAAAATATAAAAAAATTCAATTCAAAATCAA
Found at i:5658 original size:171 final size:159
Alignment explanation
Indices: 5457--5773 Score: 305
Period size: 169 Copynumber: 1.9 Consensus size: 159
5447 TTATAGTGAG
* * * * *
5457 TAATAAGGCTTTTGAAGGAATAGGTGACTATAAATGGGCTTTTGTT-CTCAATGAATGACTTTTT
1 TAATAAGGCTTTTAAAGGAATAGGTGACTATAAATAGACTTTTCTTGCT-AATGAATG-CCTTTT
** * * *
5521 TTACACATTTCTAAAGGCATGCATTCAATTATAGTCCGTTTTTACCATAAATGTAAAAAAATTTA
64 TT-CACATTTCTAAAGGCAAACATTCAATTATAGTCCGTTTTAACCAAAAATATAAAAAAATTTA
*
5586 ACTTAAAACCAATTTTGAGATTGTAAAATAAT
128 ACTTAAAACCAATTATGAGATTGTAAAATAAT
*
5618 TNNNNNNNNNNAATAAGGCTTTTAAAGGAAT-GGATGACTATAACTAGACTTTTCTTGCTAATGA
1 T----------AATAAGGCTTTTAAAGGAATAGG-TGACTATAAATAGACTTTTCTTGCTAATGA
* * * * * * *
5682 ATGCCTTTTTTCATATTTCTCAAGGTAAACATTTAATTATTGTCTGTTTTAACTAAAAATATAAA
55 ATGCCTTTTTTCACATTTCTAAAGGCAAACATTCAATTATAGTCCGTTTTAACCAAAAATATAAA
* *
5747 ACAATTTAACTTAAAATCAATTATGAG
120 AAAATTTAACTTAAAACCAATTATGAG
5774 TTNNNNNNNN
Statistics
Matches: 123, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
161 1 0.01
169 66 0.54
170 9 0.07
171 45 0.37
172 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.37
Consensus pattern (159 bp):
TAATAAGGCTTTTAAAGGAATAGGTGACTATAAATAGACTTTTCTTGCTAATGAATGCCTTTTTT
CACATTTCTAAAGGCAAACATTCAATTATAGTCCGTTTTAACCAAAAATATAAAAAAATTTAACT
TAAAACCAATTATGAGATTGTAAAATAAT
Found at i:6873 original size:170 final size:169
Alignment explanation
Indices: 6446--6875 Score: 407
Period size: 170 Copynumber: 2.5 Consensus size: 169
6436 AAAATTTAAT
* * * * * *
6446 TATAGTCTGTTTTAGCCAAAAATTTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAT
1 TATAGTCTGTTATA-ACAAAAAATAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAAC
********** * *
6511 AANNNNNNNNNNGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTCTCAAGG
65 AATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTTTCTCAAGG
* * * **
6576 AATAGCTTTTTGTGCATGTTTCTCAAGGCAGGCATTCAAC
130 AATAGCTTTTTGTACACGTTTCCCAAGGCAACCATTCAAC
* * *
6616 TATAGTCTGTTATAACAAAAAATAAAAAAAATTTAACTTAAAATTAATTATGAGATTATAAAAGA
1 TATAGTCTGTTATAACAAAAAATAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACA
* ** * *
6681 ATTTGAAGTGAGTAATAAGGCTTTTGAAGGAATGAGTGATTATAAATGAACTTTTTTCCTCAATG
66 ATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTTT-CTCAAGG
* * * * * * *
6746 AATGGTTTTTTTTATACGTTTCCCGAGGCAACCATTCGAT
130 AATAGCTTTTTGTACACGTTTCCCAAGGCAACCATTCAAC
* * * *
6786 TATAGTCT-TTTTAACGATAAATGTAAAAAAATTCAACTTAAAATCAAATT-T-AGGATTATAAA
1 TATAGTCTGTTATAACAAAAAAT-AAAAAAAATTCAACTTAAAAT-AAATTATGA-GATTATAAA
*
6848 ACAATTTAAAGCAAGTAACAAGGCTTTT
63 ACAATTTAAAGCAAGTAATAAGGCTTTT
6876 NNNNNNNNNN
Statistics
Matches: 212, Mismatches: 44, Indels: 8
0.80 0.17 0.03
Matches are distributed among these distances:
169 101 0.48
170 107 0.50
171 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.34
Consensus pattern (169 bp):
TATAGTCTGTTATAACAAAAAATAAAAAAAATTCAACTTAAAATAAATTATGAGATTATAAAACA
ATTTAAAGCAAGTAATAAGGCTTTTGAAGGAATGAGTGACTATAAATGAACTTTTTTCTCAAGGA
ATAGCTTTTTGTACACGTTTCCCAAGGCAACCATTCAAC
Found at i:8613 original size:172 final size:170
Alignment explanation
Indices: 8203--8650 Score: 391
Period size: 172 Copynumber: 2.6 Consensus size: 170
8193 NNNNNNNNNN
* * * * * ** *
8203 TAATAAGGCTTTTAAAGGAATGAGTGATTATAAATGGACTTTTCTTGCCAATGATTGCCCTTTTC
1 TAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGA-AACCTTTTTC
* * * * * * **
8268 TTCATGTTTCCTGAGGTAGACATTCAATTATTGTCTGTTTTCATTAAAAATATAAAAAAATTCAA
65 TTCATGTTTCCTGAAGTAAAAATTCAATTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAA
* *
8333 CTTAACAACAATTATGAGATTATAAAATAATTTAAAATGAG
130 CTTAAAAACAATTATGAGATTATAAAATAATTTAAAACGAG
********** * * * **
8374 TANNNNNNNNNNTGAAGGAATGGGTGACTTTAAATAGACTTTTCTTGCTAA-CAAATGTGTGTTT
1 TAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGAAACCT-T-TTT
* *
8438 CTTCATGTTTCTCT-AAGTAAAAATTTAATTATAGTATGTTTTAACCAAAAATGTAAAAACAATT
64 CTTCATGTTTC-CTGAAGTAAAAATTCAATTATAGTATGTTTTAACCAAAAATATAAAAA-AATT
* * *
8502 CAAC-TAAAAATCAATTATGATATTATAAAATAATTTACAGCGAG
127 CAACTTAAAAA-CAATTATGAGATTATAAAATAATTTAAAACGAG
* *
8546 TAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTACTAATGACCACCTTTTTC
1 TAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGA-AACCTTTTTC
* * * * *
8611 TTCACT-TTTCTTGAGGTAGACATTCAATTATAGTCTGTTT
65 TTCA-TGTTTCCTGAAGTAAAAATTCAATTATAGTATGTTT
8651 CANNNNNNNN
Statistics
Matches: 208, Mismatches: 60, Indels: 17
0.73 0.21 0.06
Matches are distributed among these distances:
170 2 0.01
171 90 0.43
172 111 0.53
173 3 0.01
174 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.37
Consensus pattern (170 bp):
TAATAAAGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTCTTGCTAATGAAACCTTTTTCT
TCATGTTTCCTGAAGTAAAAATTCAATTATAGTATGTTTTAACCAAAAATATAAAAAAATTCAAC
TTAAAAACAATTATGAGATTATAAAATAATTTAAAACGAG
Done.