Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398113.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1416.0, 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: 8114
ACGTcount: A:0.31, C:0.10, G:0.11, T:0.30
Warning! 1364 characters in sequence are not A, C, G, or T
Found at i:715 original size:343 final size:323
Alignment explanation
Indices: 1--769 Score: 705
Period size: 343 Copynumber: 2.3 Consensus size: 323
* * *
1 CTAAATTTTTTTATATTTTTCATTACAATAGAGTATAATTGAATGCCTGCCTCAGGAAACATATC
1 CTAAATTTTTTTATATTTTTCATTAAAATAAAGTATAATTGAATGCCTGCCTCAGGAAACATATA
* **
66 GAAAAAGCCATTCATTGGTAAGAAAAGTCTATTTATAGTCNNNNNNNNNNTCAAAAGCCTTACTA
66 GAAAAAGCCATTCATTGGTAAGAAAAGTCCATTTATAGTC--------CTTCAAAAGCCTTACTA
* * *
131 CTCACTTTAAATGGTTTTATAATCCCAAAAATGATTTTAAGTTTTATTTTTTTTTTACTTTTTTG
123 CTCACTTTAAATGGTTTTATAATCCCAAAAATGATTTTAAGATTTAATTTTTTTTCACTTTTTTG
****** **
196 GTTAAAATAGATTATAATNNNNNNNNNNCATTGGGGAATATGAAGAAAAAGGCATTTGTTGCAAG
188 GTTAAAATAGATTATAAT----TGTCTACATTGGGGAATATGAAGAAAAAGGCATTCATTGCAAG
* * * **
261 AAAAGTCTATTTATTGTCATCCATTCCTTCAAAAGCCTTATTACTCGCTNNNNNNNNNNNTATAA
249 AAAAGTCTATGTATTGTCACCCATTCCTTCAAAAGCCTTATTACTCACT---------TTTATAA
326 TCTCACAATTAATTTTAAG
305 TCTCACAATTAATTTTAAG
*
345 CTAAATTTTTTTATATTTTTCATTAAAATAAAGTATAATTGAATGCCTGTCTCAGGAAACATATA
1 CTAAATTTTTTTATATTTTTCATTAAAATAAAGTATAATTGAATGCCTGCCTCAGGAAACATATA
* ** *
410 GAAAAAGGCATTCATTGGTAAGAAAAGTCCATTTATAGNNNNNNNNNNCTTCAAAAGCTTTACTA
66 GAAAAAGCCATTCATTGGTAAGAAAAGTCCATTTATAG--------TCCTTCAAAAGCCTTACTA
*
475 CTCACTTTAAATGGTTTTATAATCTCAAAAATGATTTTAA-ATTTAATTTTTTTTCACTTTTTTG
123 CTCACTTTAAATGGTTTTATAATCCCAAAAATGATTTTAAGATTTAATTTTTTTTCACTTTTTTG
******
539 GTTAAAATAGATNNNNNNNNNNTGTCTACATTGGGGAATATGAAGAAAAAGGCATTCATTGCAAG
188 GTTAAAATAGAT----TATAATTGTCTACATTGGGGAATATGAAGAAAAAGGCATTCATTGCAAG
*
604 AAAAGTCTATGTATTGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTNNNNNNNNNNATAA
249 AAAAGTCTATGTATTGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTT---------TATAA
* *
669 TCTCATAATTGATTTTAAG
305 TCTCACAATTAATTTTAAG
* * * * * * * * * * *
688 TTGAATTTCTTTACATTTTTAATTAAAACAAACTATAATTGAATACCTACCTC-GAGAAATATGT
1 CTAAATTTTTTTATATTTTTCATTAAAATAAAGTATAATTGAATGCCTGCCTCAG-GAAACATAT
752 AGAAAAAGCCATTCATTG
65 AGAAAAAGCCATTCATTG
770 AGAAGAANNN
Statistics
Matches: 353, Mismatches: 50, Indels: 45
0.79 0.11 0.10
Matches are distributed among these distances:
342 1 0.00
343 202 0.57
344 150 0.42
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.36
Consensus pattern (323 bp):
CTAAATTTTTTTATATTTTTCATTAAAATAAAGTATAATTGAATGCCTGCCTCAGGAAACATATA
GAAAAAGCCATTCATTGGTAAGAAAAGTCCATTTATAGTCCTTCAAAAGCCTTACTACTCACTTT
AAATGGTTTTATAATCCCAAAAATGATTTTAAGATTTAATTTTTTTTCACTTTTTTGGTTAAAAT
AGATTATAATTGTCTACATTGGGGAATATGAAGAAAAAGGCATTCATTGCAAGAAAAGTCTATGT
ATTGTCACCCATTCCTTCAAAAGCCTTATTACTCACTTTTATAATCTCACAATTAATTTTAAG
Found at i:1313 original size:172 final size:161
Alignment explanation
Indices: 988--1318 Score: 376
Period size: 172 Copynumber: 2.0 Consensus size: 161
978 AAAGCTTTAA
* * **
988 TACTCGCTTTAAATGGTTTTATTATCTCATTATTGATTTTAAGTTAAATGTTTTTATATTTTTCA
1 TACTAGCTTTAAATAGTTTTATTATCTCACAATTGATTTTAAGTTAAATGTTTTTATATTTTTCA
* * ** * *
1053 TTAAAACATACTATAATTGAATACTTACCTCCAGAAATGTGTAGAAAAAGCCATTCGTTTATAAA
66 TTAAAACAGACTATAATTGAATACCTACCTCCAGAAACATGTAGAAAAAGCCATTCGCTGATAAA
1118 AAAAGTCTATTTATAGTCACCCATTNNNNNNNNNNCCTTAT
131 AAAAGTCTATTTATAGTCACCCATT----------CCTTAT
* * *
1159 TACTAGCTTTAAATAGTTTTATTATCTCACAATTGATTTTCAGTTAAATTTTTTTATATTTTTTT
1 TACTAGCTTTAAATAGTTTTATTATCTCACAATTGATTTTAAGTTAAATGTTTTTATA-TTTTTC
* * * *
1224 ATTAAAACAGACTATAATTGAATACCTGCCT-TAGGAAACATGTAGAAAAATCCATTTGCTGATA
65 ATTAAAACAGACTATAATTGAATACCTACCTCCA-GAAACATGTAGAAAAAGCCATTCGCTGATA
* *
1288 AGAAAAGTCTATTTATTGTCACCCATTCCTT
129 AAAAAAGTCTATTTATAGTCACCCATTCCTT
1319 TAAAAGCCTT
Statistics
Matches: 139, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
162 4 0.03
171 53 0.38
172 82 0.59
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.41
Consensus pattern (161 bp):
TACTAGCTTTAAATAGTTTTATTATCTCACAATTGATTTTAAGTTAAATGTTTTTATATTTTTCA
TTAAAACAGACTATAATTGAATACCTACCTCCAGAAACATGTAGAAAAAGCCATTCGCTGATAAA
AAAAGTCTATTTATAGTCACCCATTCCTTAT
Found at i:1635 original size:171 final size:169
Alignment explanation
Indices: 582--1643 Score: 693
Period size: 171 Copynumber: 6.2 Consensus size: 169
572 GGGAATATGA
* * *
582 AGAAAAAGGCATTCATTG-CAAGAAAAGTCTATGTATTGTCACCCATTCCTTCAAAAGCCTTATT
1 AGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTTATT
********** * * * *
646 ACTCACTTTNNNNNNNNNNATAATCTCATAATTGATTTTAAGTTGAATTTCTTTACATTTTTAAT
66 ACTCACTTTAAATGTTTTTA-AATCTCACAATTGATTTTAAGTTGAATTTTTTTATATTTTTTAT
* * *
711 TAAAACAAACTATAATTGAATACCTACCTCGAGAAATATGT
130 TAAAACAGACTATAATTGAATACCTACCT-TAGAAACATGT
********** * * *
752 AGAAAAAGCCATTCATTGAGAAGAANNNNNNNNNNATAGTCACTCATTTCTTCAAAAGCCTTATT
1 AGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTTATT
* * ** * * *
817 ACACGCTTTAAAT-TGTTTTATAATCTCGTAATTAATTTTAAGTTTAATTTTTTTTATATTTTTG
66 ACTCACTTTAAATGT-TTTTA-AATCTCACAATTGATTTTAAGTTGAA-TTTTTTTATATTTTTT
* * * * *
881 GTTAAAACAGACTATAATAGAA-AGTCTACCCCTAGAAACATGA
128 ATTAAAACAGACTATAATTGAATA-CCTA-CCTTAGAAACATGT
********** * *
924 AGAANNNNNNNNNNATTG-GCAAGAAAACAG-C-ATTTATAGTCACCCATTCCTTCAAAAGCTTT
1 AGAAAAAGCCATTCATTGAG-AAG-AAA-AGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTT
* * * * ** * *
986 AATACTCGCTTTAAATGGTTTTATTATCTCATTATTGATTTTAAGTTAAATGTTTTTATATTTTT
63 ATTACTCACTTTAAATGTTTTTA-AATCTCACAATTGATTTTAAGTTGAATTTTTTTATATTTTT
* * * * **
1051 CATTAAAACATACTATAATTGAATACTTACCTCCAGAAATGTGT
127 TATTAAAACAGACTATAATTGAATACCTACCT-TAGAAACATGT
* * * * * **********
1095 AGAAAAAGCCATTCGTTTATAAAAAAAGTCTATTTATAGTCACCCATTNNNNNNNNNNCCTTATT
1 AGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTTATT
* * *
1160 ACT-AGCTTTAAATAG-TTTTATTATCTCACAATTGATTTTCAGTTAAATTTTTTTATATTTTTT
66 ACTCA-CTTTAAAT-GTTTTTA-AATCTCACAATTGATTTTAAGTTGAATTTTTTTATA-TTTTT
*
1223 TATTAAAACAGACTATAATTGAATACCTGCCTTAGGAAACATGT
127 TATTAAAACAGACTATAATTGAATACCTACCTTA-GAAACATGT
* *** * *
1267 AGAAAAATCCATTTGCTGATAAGAAAAGTCTATTTATTGTCACCCATTCCTTTAAAAGCCTTATT
1 AGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTTATT
* * * **
1332 ACTCATTTTAAATGTTTTTAAATCTCACAATTGATTTTAAGTTGAATTCTTTTACATTTTTTGGT
66 ACTCACTTTAAATGTTTTTAAATCTCACAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATT
* * ********* *
1397 AAAACAAACTATAACTGAATNNNNNNNNNNAGAAACATTT
131 AAAACAGACTATAATTGAAT-ACCTACCTTAGAAACATGT
*
1437 AGAAAAAGCCATTCATTAAGAAGAAAAGTGC-ATTTATTGTCACCCATTCCTTCAAAAGCCTTAT
1 AGAAAAAGCCATTCATTGAGAAGAAAAGT-CTATTTATTGTCACCCATTCCTTCAAAAGCCTTAT
* ********** **
1501 TACTCGCTTNNNNNNNNNNTATAATCTCACAATTGATTTTAAGTTGAATTTTTTTATATTTTACA
65 TACTCACTTTAAATGTTTTTA-AATCTCACAATTGATTTTAAGTTGAATTTTTTTATATTTTTTA
* * *
1566 TTAAAATAGACTATAGTTGAATGCCTACCTTGAGAAACATGT
129 TTAAAACAGACTATAATTGAATACCTACCTT-AGAAACATGT
*
1608 AGAAAAAGCCATTCATTGGGAAGAAAAGTCTATTTA
1 AGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTA
1644 NNNNNNNNNN
Statistics
Matches: 671, Mismatches: 196, Indels: 49
0.73 0.21 0.05
Matches are distributed among these distances:
169 2 0.00
170 121 0.18
171 318 0.47
172 225 0.34
173 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.36
Consensus pattern (169 bp):
AGAAAAAGCCATTCATTGAGAAGAAAAGTCTATTTATTGTCACCCATTCCTTCAAAAGCCTTATT
ACTCACTTTAAATGTTTTTAAATCTCACAATTGATTTTAAGTTGAATTTTTTTATATTTTTTATT
AAAACAGACTATAATTGAATACCTACCTTAGAAACATGT
Found at i:2532 original size:171 final size:170
Alignment explanation
Indices: 1744--3879 Score: 1056
Period size: 171 Copynumber: 12.5 Consensus size: 170
1734 NNNNNNNNNN
* * * *
1744 ATTCAACTTAAAATCAATTATGAGATTATAAAACCTTTTAAAGAGAGTAATATGACTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * **
1809 AAATG-GTGACTATAAAT-GCACTTTTCTTGCCAGA-GAAT-ACTTTTTTCTTCATGTTTCTTGA
66 -AATGAGTGACTATAAATAG-ACTTTTCTTCCCA-ATGAATGGC-TTTTTCTACATGTTTCTCAA
********** * **
1870 GGTANNNNNNNNNNTATAATCTGTTTTGACCAAAAATGTGAAAAAAA
127 GGTAGGCATTCAATTATAGTCTGTTTT-AATAAAAATGT--AAAAAA
* * * * * *
1917 ATTGAACTTAAAATCAATTTTGAGATTATAAAACCATTTAGAGCGAGTTATATGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
*** *
1982 AAT-AGGTGACTATAAAT-GTACTTTTCTTCTTGATGAATGGCTTTTCTTGTAC--GTTTCT-AG
66 AATGA-GTGACTATAAATAG-ACTTTTCTTCCCAATGAATGGC-TTT-TTCTACATGTTTCTCA-
* * * * * *
2042 AGATAGACATGCAATTATAGTCTATTTTAATGAAGAATATAAAAAA
126 AGGTAGGCATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAA
********** *
2088 ATTCAACTTAAAATCAATTATGAGANNNNNNNNNNATTTAAAGTAAGTAATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * * ** **
2153 AATGAGTGACTATAAATGGTCTTTTTTTCTGAATGAATGGCTTTTTCTACACCTTTCTCAAGGTA
66 AATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGTA
* * **
2218 GGCAATCAATTATAGTTTGTTTTAATGAAAAATGTAAAANN
131 GGCATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAA
******** * * * *
2259 NNNNNNNNTAAAATCAATTATGAGGTTATAAAACCTTTTAAAGGGAGTAATAAAGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* ********* ** * *
2324 AATGGGTGACTATNNNNNNNNNNTTT-TTCTTAATGAATGGCTTTTTCAATATGTTTCTCAAGGT
66 AATGAGTGACTAT-AAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGT
*
2388 AGGCATTCAATTATAGTATGTTTTAATAAAAATTGTAAAAAA
130 AGGCATTCAATTATAGTCTGTTTTAATAAAAA-TGTAAAAAA
* **********
2430 ATTCCACTTAAAATCAATTATGAGATTATAAAACCATTTANNNNNNNNNNTAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
** ** ** *
2495 AATGAGTGA-TAATAAATAGACTTTTCTTCCCAATGAATCCCTTTTTCTTTATGTTTCTTGATGT
66 AATGAGTGACT-ATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGT
* * * *
2559 AGACATTCAATTAAAATCTGTTTTAACTAAAAAAGTAAAAAA
130 AGGCATTCAATTATAGTCTGTTTTAA-TAAAAATGTAAAAAA
* * * **********
2601 ATTGAACTTAAAACCAATTTTGAGATTATNNNNNNNNNNAAAGTGAGTAATAAGGCTTTTGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* **
2666 AATG-GATGACTATAAAT-GCACTTTT-TTCCTCAATCAATGGCTTTTTCTACACCTTTCT-AAG
66 AATGAG-TGACTATAAATAG-ACTTTTCTTCC-CAATGAATGGCTTTTTCTACATGTTTCTCAAG
* * *
2727 GCAGGCATTCAATTATAGTTTGTTTTAATGAAAAGTGTAAAAAA
128 GTAGGCATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAA
* * * ********** * *
2771 ATTCAACTTAACATTAATTATGAGATTATAAAACTATTTAAAGTGANNNNNNNNNNTTTTAAAGA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
*
2836 AATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGATTTTTCTACATGTTTCTCAAGGTA
66 AATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGTA
* * * *
2901 GGCATTCAACTATAGCCTGTTTTAATGTAAAATAT-AAAAA
131 GGCATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAA
* ********* *
2941 ATTCAACTTAAAATCAATTGTGAGATTATAAANNNNNNNNNNA-CGAGTAATAAGGCTTTTGAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAA-ACCATTTAAAGTGAGTAATAAGGCTTTTGAAG
* * * ** * *******
3005 GAATGGGTGACAATAAATGGAC-TTTCTTCTTAATGAATGGCTTTTTCTAAATGTTTCNNNNNNN
65 GAATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGT
*** * * **
3069 NNNCATTCAGTTATAGTTTGTTTTACCA-AAAAATGTAAAGGA
130 AGGCATTCAATTATAGTCTGTTTTA--ATAAAAATGTAAAAAA
* * *******
3111 ATTCAACTTAAAATCAATTGTGAGATT-TAAAACCATTTAAAATGAGTAATAAGGCTTNNNNNNN
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
*** * * ** * * * *
3175 NNNGGGTGA-TAATAAATAGACTTTTCTTGCCAGCGAATGCCTTTTTCTTGACA--TTCCTTAAC
66 AATGAGTGACT-ATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTC-T-ACATGTTTCTCAAG
* * * * * *
3237 ATAGACTTTCAATTATAATCTGTTTTAACCAAAAAAGTAAAAAAAAA
128 GTAGGCATTCAATTATAGTCTGTTTTAA-TAAAAATGT---AAAAAA
* *
3284 ATT-ATACTTAAAATCAATTTTGAGATTATAAAACCATTTAATGTGAG-AAGTAAGGCTTTTGAA
1 ATTCA-ACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAA-TAAGGCTTTTGAA
* * ** *** * * *
3347 GGAATGGGGGACTATAAATAGACTTTTCTTATCAGCAAATGGATTTTTCTATATGTTTC-CTGAG
64 GGAATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTC-AAG
* * *
3411 GCAGGTATTCAATTATAGTCTGTTTTAATAAAAAATATAAAAAA
128 GTAGGCATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAA
**************** * * *
3455 ATTCAACTTAAANNNNNNNNNNNNNNNNTAAAACTATTTAAAGCT-AGTAATAAAGCTTTTAAAG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAG-TGAGTAATAAGGCTTTTGAAG
* * ** * * **
3519 GAATGGGTGACTATAAATAGACTTTTTTTATCAACGAATGGCTTTTTCTACACGTTTCTGGAGGT
65 GAATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGT
* * * ********* *
3584 AAGTATTCAATTATAGTATGTTTTAATNNNNNNNNNNAAACA
130 AGGCATTCAATTATAGTCTGTTTTAAT-AAAAATGTAAAAAA
* * * * *
3626 ATTTAACTTAAAATCAATAATGAGATTATAAAACCATTTAAAGTGAGTATTAAAGCTTTCGAAGG
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
* * ********** * *
3691 AATGGGTGACTATAAAT-G-CTGTTTTCTTGCCAANNNNNNNNNNTTTCTTCATGTTTCT-AGGG
66 AATGAGTGACTATAAATAGAC--TTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCA-AG
* * * * *
3753 GTAGACTTTCTATTATAGTCAGTTTTAACCAAAAATGTAAAAAAA
128 GTAGGCATTCAATTATAGTCTGTTTTAA-TAAAAATGT-AAAAAA
* * * * *
3798 ATTAAACTTAAAATCAATTACGAGATTATAAAACAATTTAAAGTGTGTAATAAGGCTTTTGAAGA
1 ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
*
3863 AATGGGTGACTATAAAT
66 AATGAGTGACTATAAAT
3880 GGGTGACGAG
Statistics
Matches: 1437, Mismatches: 468, Indels: 117
0.71 0.23 0.06
Matches are distributed among these distances:
168 2 0.00
169 95 0.07
170 277 0.19
171 714 0.50
172 104 0.07
173 142 0.10
174 98 0.07
175 5 0.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.34
Consensus pattern (170 bp):
ATTCAACTTAAAATCAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTTGAAGG
AATGAGTGACTATAAATAGACTTTTCTTCCCAATGAATGGCTTTTTCTACATGTTTCTCAAGGTA
GGCATTCAATTATAGTCTGTTTTAATAAAAATGTAAAAAA
Found at i:3057 original size:18 final size:20
Alignment explanation
Indices: 3020--3057 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
3010 GGTGACAATA
*
3020 AATGGACTTTCTTCTTAATG
1 AATGGACTTTCTTCTAAATG
3040 AATGG-CTTT-TTCTAAATG
1 AATGGACTTTCTTCTAAATG
3058 TTTCNNNNNN
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (20 bp):
AATGGACTTTCTTCTAAATG
Found at i:4417 original size:172 final size:172
Alignment explanation
Indices: 3887--4418 Score: 453
Period size: 172 Copynumber: 3.1 Consensus size: 172
3877 AATGGGTGAC
* * *
3887 GAGTAATAAGGCTTTTGAAGGAATGGATGACAATACATAGACTTTTCTTGCAACGAATGCCTTTT
1 GAGTAGTAAGGCTTTTGAAGGAATGGATGATAATAAATAGACTTTTCTTGCAACGAATGCCTTTT
* ********** *
3952 TCTTCATATTCCCCAATGTAGACANNNNNNNNNNATCTATTTTAACCAAAAAAGTGAAAAAAAAT
66 TCTTCATATTTCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAAT
*
4017 TAAACTTAAAATCATTTTTGAGATTATAAAATCATTTAAAGT
131 TAAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGT
* ********** * * * *
4059 GAGTAGTAAAGCTTTTGAAGNNNNNNNNNNCT-ATAAATGGACTTTTCTTACCAATGAATGGCTT
1 GAGTAGTAAGGCTTTTGAAG-GAATGGATGATAATAAATAGACTTTTCTT-GCAACGAATGCCTT
* * * * * * * ** *
4123 TTTCTAT-ATGTTTCCTAA-GACAGGCATTCAATTATACTTTATTTTAA-TGAAAAA-TATAAAA
64 TTTCT-TCATATTTCCCAATG-TAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAA
* * * * * * *
4184 ACATTTAGCTTAAAATTAATTGTGAGATTATAAAACCATTTAAAGN
127 AAATTAAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGT
*********
4230 NNNNNNNNNGGCTTTTGAAGGAATGGATGATAATAAATAGACTTTTCTTGCAACGAATGCCTTTT
1 GAGTAGTAAGGCTTTTGAAGGAATGGATGATAATAAATAGACTTTTCTTGCAACGAATGCCTTTT
4295 TCTTCATATTTCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAAT
66 TCTTCATATTTCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAAT
* * *
4360 AAAACTTAAAATCGTTTTTGGGATTATAAAACCATTTAAAGT
131 TAAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGT
4402 GAGTAGTAAGGCTTTTG
1 GAGTAGTAAGGCTTTTG
4419 NNNNNNNNNN
Statistics
Matches: 251, Mismatches: 100, Indels: 18
0.68 0.27 0.05
Matches are distributed among these distances:
169 1 0.00
170 48 0.19
171 75 0.30
172 89 0.35
173 37 0.15
174 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.33
Consensus pattern (172 bp):
GAGTAGTAAGGCTTTTGAAGGAATGGATGATAATAAATAGACTTTTCTTGCAACGAATGCCTTTT
TCTTCATATTTCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAAT
TAAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGT
Found at i:4596 original size:343 final size:336
Alignment explanation
Indices: 3888--4598 Score: 767
Period size: 343 Copynumber: 2.1 Consensus size: 336
3878 ATGGGTGACG
*
3888 AGTAATAAGGCTTTTGAAGGAATGGATGACAATACATAGACTTTTCTTGCAACGAATGCCTTTTT
1 AGTAATAAGGCTTTTGAAGGAATGGATGACAATAAATAGACTTTTCTTGCAACGAATGCCTTTTT
********** * *
3953 CTTCATATTCCCCAATGTAGACANNNNNNNNNNATCTATTTTAACCAAAAAAGTGAAAAAAAATT
66 CTTCATATTCCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAATA
*
4018 AAACTTAAAATCATTTTTGAGATTATAAAATCATTTAAAGTGAGTAGTAAAGCTTTTGAAGNNNN
131 AAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTTTGAAG----
*** * * *
4083 NNNNNNCTATAAATGGACTTTTCTTACCAATGAATGGCTTTTTCTATATGTTTCCTAAGACAGGC
192 ---GGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCGATATATTTCCTAAGACAGGC
* * *
4148 ATTCAATTATACTTTATTTTAATGAAAAATATAAAAACATTTAGCTTAAAATTAATTGTGAGATT
254 ATTCAATTATACTCTATTGTAATGAAAAATATAAAAACATTTAGCTTAAAATCAATTGTGAGATT
**
4213 ATAAAACCATTTAAAGNN
319 ATAAAACCATTTAAAGCA
******** *
4231 NNNNNNNNGGCTTTTGAAGGAATGGATGATAATAAATAGACTTTTCTTGCAACGAATGCCTTTTT
1 AGTAATAAGGCTTTTGAAGGAATGGATGACAATAAATAGACTTTTCTTGCAACGAATGCCTTTTT
*
4296 CTTCATATTTCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAATA
66 CTTCATATTCCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAATA
* * *
4361 AAACTTAAAATCGTTTTTGGGATTATAAAACCATTTAAAGTGAGTAGTAAGGCTTTTGNNNNNNN
131 AAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTTTG-------
*** * * *
4426 NNNGGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCGATATATTTCTTGAGGCAGGC
189 AAGGGACTATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCGATATATTTCCTAAGACAGGC
*********
4491 ATTCAATTATACTCTATTGTAATGANNNNNNNNNNAAA-ATTTAGCTTAAAATCAATTGTGAGAT
254 ATTCAATTATACTCTATTGTAATGA-AAAATATAAAAACATTTAGCTTAAAATCAATTGTGAGAT
* *
4555 TATAAATCCATTTAAGGCA
318 TATAAAACCATTTAAAGCA
* *
4574 AGTAATAAAGCTTTTAAAGGAATGG
1 AGTAATAAGGCTTTTGAAGGAATGG
4599 GTGANNNNNN
Statistics
Matches: 295, Mismatches: 65, Indels: 16
0.78 0.17 0.04
Matches are distributed among these distances:
343 292 0.99
344 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.33
Consensus pattern (336 bp):
AGTAATAAGGCTTTTGAAGGAATGGATGACAATAAATAGACTTTTCTTGCAACGAATGCCTTTTT
CTTCATATTCCCCAATGTAGACATGCAATTATAATCTATTTTAACCAAAAAAGTAAAAAAAAATA
AAACTTAAAATCATTTTTGAGATTATAAAACCATTTAAAGTGAGTAGTAAAGCTTTTGAAGGGAC
TATAAATAGACTTTTCTTACCAATGAATGGCTTTTTCGATATATTTCCTAAGACAGGCATTCAAT
TATACTCTATTGTAATGAAAAATATAAAAACATTTAGCTTAAAATCAATTGTGAGATTATAAAAC
CATTTAAAGCA
Found at i:7341 original size:170 final size:160
Alignment explanation
Indices: 7165--7475 Score: 329
Period size: 170 Copynumber: 1.9 Consensus size: 160
7155 TGAAATTGTA
* * *
7165 AAACCATTTAAAGTGAATAATAAGGCTTTTAAAGGAATGGG-AGACTATAAATTGACTTTTCTTA
1 AAACCATTTAAAGCGAATAATAAGGCTTTTAAAGGAAAGGGTA-ACTATAAATGGACTTTTCTTA
** * * * *
7229 TCAATGAATGTTTTTTTCTTCACATTTC-CTAATGTAGACATTCAATTATAGCCTATTTTAACCA
65 TCAATGAATGGCTTTTTCTACACATTTCTC-AAGGTAAACATTCAATTATAGCCTATTTTAACAA
*
7293 AAAATGTAAAAAAATTCAANNNNNNNNNNATTATGAGATTAT
129 AAAATATAAAAAAATTCAA----------ATTATGAGATTAT
* * * *
7335 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAAAGGGTAACTATAAATGGGCTTTTCTTCT
1 AAACCATTTAAAGCGAATAATAAGGCTTTTAAAGGAAAGGGTAACTATAAATGGACTTTTCTTAT
* * * * *
7400 TAATGAATGGCTTTTTCTACACGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAAGAAAA
66 CAATGAATGGCTTTTTCTACACATTTCTCAAGGTAAACATTCAATTATAGCCTATTTTAACAAAA
7465 AATATAAAAAA
131 AATATAAAAAA
7476 NNNNNNNNNN
Statistics
Matches: 120, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
170 118 0.98
171 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (160 bp):
AAACCATTTAAAGCGAATAATAAGGCTTTTAAAGGAAAGGGTAACTATAAATGGACTTTTCTTAT
CAATGAATGGCTTTTTCTACACATTTCTCAAGGTAAACATTCAATTATAGCCTATTTTAACAAAA
AATATAAAAAAATTCAAATTATGAGATTAT
Found at i:7889 original size:171 final size:171
Alignment explanation
Indices: 7012--8104 Score: 728
Period size: 171 Copynumber: 6.4 Consensus size: 171
7002 NNNNNNNNNN
* ** * * * *
7012 TAATAAGGCTTTTGAAGGAATGAGTGACAATAAATAGACTTTTCTTACCAATGACTCCCTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC
** ** * * * * *
7077 TTCATGTTTCTTGACATAAACATTCAATT-TCAATCTATTTTAATAAAAAA-GTAAAAAAATTGA
66 TTCACATTTCTTGAGGTAAACATTCAATTAT-AGTCTGTTTTAACAAAAAATATAAAAAAATTCA
* * *
7140 ACTTAAAATCAATTTTGAAATTGTAAAACCATTTAAAGTGAA
130 ACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAG
* * * ** **
7182 TAATAAGGCTTTTAAAGGAATGGGAGACTATAAATTGACTTTTCTTATCAATGAATGTTTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC
* * * * * * * *
7247 TTCACATTTCCTAATGTAGACATTCAATTATAGCCTATTTTAACCAAAAATGTAAAAAAATTCAA
66 TTCACATTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAA
********** * *
7312 NNNNNNNNNNATTATGAGATTAT-AAACCATTTAAAGCGAG
131 CTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAG
* * * * * *
7352 TAATAAGGCTTTTGAAGGAAAGGGTAACTATAAATGGGCTTTTCTT-CTTAATGAATGGCTTTTT
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGC-CAATGAATGCCTTTTT
* * ** * *****
7416 CTACACGTTTCTCAAGGTAAACATTCAATTATAGTCTGTTTTAAGAAAAAATATAAAAAANNNNN
65 CTTCACATTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCA
**************** *
7481 NNNNNNNNNNNNNNNNGAAATTATAAAATCATTTAAAGTGAG
130 ACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAG
* * ** * * *
7523 TAATAAGGCTTTTGAAAGAATGAGTGACAAGAAATAGACTTTTCTTGCCAATGAATCCCTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC
* * ** * * * *
7588 TTCACACTCCTTGACATAAACATTCAATTACAATATGTTTTAATCAAAAAAGTA-AAAAAAATTA
66 TTCACATTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAA-CAAAAAA-TATAAAAAAATTC
* **********
7652 AACTTAAAATCAATTTTGANNNNNNNNNNCCATTTAAAGTGAG
129 AACTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAG
* * * ** *
7695 TAATAAGGCTTTTGAAAGAATGGGAAATTATAAATAAACTTTTCTTGCCAACAAATGCTTTTTTC
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC
* * * *
7760 TTCACATTTCTTGAGGTAGACATTCAATTATAGCCCGTTTTAACTAAAAATATAAAAAAATTCAA
66 TTCACATTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAA
* *
7825 CTTAAAGTCAATTATGAAATTATAAAACCATTTAAGGTGAG
131 CTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAG
* ** * * * *
7866 TAATAAGACTTTTGAAGGAATGGGTGATTATAAATTA-ACTTTTCTGGTCAATGAATACCTTTTT
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAA-TAGACTTTTCTTGCCAATGAATGCCTTTTT
** * *
7930 CTTCATGTTTCTCGAGGTAAACATTCAATTATTA-TCTGTTTTAACCAAAAATATAAAAAAATTC
65 CTTCACATTTCTTGAGGTAAACATTCAATTA-TAGTCTGTTTTAACAAAAAATATAAAAAAATTC
********** * *
7994 AACNNNNNNNNNNTTATGAGATTATAAAACCATTTAGAGCT-AG
129 AACTTAAAATCAATTATGAAATTATAAAACCATTTAAAG-TGAG
* * *** * **
8037 TAATAAGGCTTTCGAAGGAATAGCTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTT-
1 TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC
8101 TTCA
66 TTCA
8105 TGTTTCTCAA
Statistics
Matches: 709, Mismatches: 202, Indels: 24
0.76 0.22 0.03
Matches are distributed among these distances:
170 233 0.33
171 354 0.50
172 120 0.17
173 2 0.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.34
Consensus pattern (171 bp):
TAATAAGGCTTTTGAAGGAATGGGAAACTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC
TTCACATTTCTTGAGGTAAACATTCAATTATAGTCTGTTTTAACAAAAAATATAAAAAAATTCAA
CTTAAAATCAATTATGAAATTATAAAACCATTTAAAGTGAG
Done.