Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398347.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1647.0, 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: 3572
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.32
Warning! 572 characters in sequence are not A, C, G, or T
Found at i:618 original size:171 final size:170
Alignment explanation
Indices: 1--803 Score: 516
Period size: 171 Copynumber: 4.7 Consensus size: 170
* * * * * *
1 TTTTTTACATTTTT-AGTTAAAACAGACTATAATTGAATGTCTAACTCGAGAAAC-TAGAAGGAA
1 TTTTTTAAATTTTTCA-TTAAAACAGACTATAGTTGAATGCCTACCTCAAAAAACAT-GAA-GAA
* * ** * **
64 AAA-ACATTCATTGGTAAGAAATGTCCATTTATAGTCACTCATTCTTTCAAAAGCCATATTACTC
63 AAAGGCATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTGTTC
* **********
128 GCTTTAAATGGCTTTANNNNNNNNNNATTGATTTTAAGTTGAAT
128 GC-TTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * * * * * * **
172 TTTTTTACATTTTT-AGTTAAAA-AAACTATAATTAAATGTCTACATTAGGAAAC-TAGAAGAAA
1 TTTTTTAAATTTTTCA-TTAAAACAGACTATAGTTGAATGCCTACCTCAAAAAACAT-GAAGAAA
* ** * * * *
234 AAGACAATT-ATTGAAAAGAAAAGTCCATTTATAGACATTCATTCTTTCAAAAGCCTTATTGCTC
64 AAGGC-ATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTGTTC
** **********
298 ATTTTAANNNNNNNNNNAATCTCATAATTGATTTTAAGTTGAAT
128 -GCTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * ** * * *
342 ATTTTAAAATTTTTGGTTAAAACAGA-TAATAGTTGAATGTCTACCTCAAGAAACTTGAAGAAAA
1 TTTTTTAAATTTTTCATTAAAACAGACT-ATAGTTGAATGCCTACCTCAAAAAACATGAAGAAAA
* *
406 AGACATTCATTGGCAAG-AAAAGCACA-TTATACG-CAACTCATTCTTTCAAAAGCCTTATTGTT
65 AGGCATTCATTGGCAAGAAAAATC-CATTTATA-GTC-ACTCATTCTTTCAAAAGCCTTATTGTT
*
468 CGCTGTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGTAT
127 CGCT-TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * * * *
513 TTGTTTTATATTTTTCATTAAAACAGACTATTGTTGAATGCCCACGTCAAAAAAAATGAAG-AAA
1 TT-TTTTAAATTTTTCATTAAAACAGACTATAGTTGAATGCCTACCTCAAAAAACATGAAGAAAA
* *************
577 AGGCATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCCTTCAAAANNNNNNNNNNNNNN
65 AGGCATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCTTTCAAAA-GCCTTATTGTTCG
*
642 NTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
129 CTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
* * * * * * *** *
684 TTTCTTACA-TTTTCAATTAAAATAGACAATAATTAAATGCCTACCTTGGAAAACGTGAAGAAAA
1 TTTTTTAAATTTTTC-ATTAAAACAGACTATAGTTGAATGCCTACCTCAAAAAACATGAAGAAAA
* * *
748 AGGCATTCATTGGCAAGAAAAGTCCATTTATACTTACTCATTCTTTCAAAAGCCTT
65 AGGCATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCTTTCAAAAGCCTT
804 NNNNNNNNNN
Statistics
Matches: 496, Mismatches: 116, Indels: 41
0.76 0.18 0.06
Matches are distributed among these distances:
169 11 0.02
170 172 0.35
171 254 0.51
172 58 0.12
173 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.34
Consensus pattern (170 bp):
TTTTTTAAATTTTTCATTAAAACAGACTATAGTTGAATGCCTACCTCAAAAAACATGAAGAAAAA
GGCATTCATTGGCAAGAAAAATCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTGTTCGCT
TAAATGGTTTTATAATCTCATAATTGATTTTAAGTTGAAT
Found at i:1519 original size:21 final size:21
Alignment explanation
Indices: 1485--1524 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1475 GAGAAACATG
* *
1485 AAGAAAATTGCATTCATTAGT
1 AAGAAAAGTCCATTCATTAGT
*
1506 AAGAAAAGTCCATTTATTA
1 AAGAAAAGTCCATTCATTA
1525 TCACNNNNNN
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (21 bp):
AAGAAAAGTCCATTCATTAGT
Found at i:1920 original size:171 final size:169
Alignment explanation
Indices: 1243--3484 Score: 841
Period size: 171 Copynumber: 13.2 Consensus size: 169
1233 NNNNNNNNNN
* * * * * * *
1243 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACATACTATAATTGAACGTTTATCTT-GAG
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTATAATTGAATGCTTACCTTAGA-
** * * * **
1307 AAACCAGAAGAACA-AGACATTCAATGCCAAGAAAAGTTCATTTATAGTCACTTATTCTTTTC-A
64 AAACGTGAAGAA-AGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTC-TTTCAA
* * **********
1370 AAGCCTTATTGCTCGCTTTAAATGGTTTTATNNNNNNNNNNTTG
127 AAGCCTTATTACTCG-TTTAAATAGTTTTATAATCTCATAATTG
* * * * * * *
1414 ATTTTAAGTTCAATTTTTTTACT-TTTTTATTTAAAACATATTATAACTGAATG-TCGACATT-G
1 ATTTTAAGTTGAATTTTTTTA-TATTTTT-TTTAAAATAGACTATAATTGAATGCT-TACCTTAG
* * * *********
1476 AGAAACATGAAGAAA-ATTG-CATTCATTAGTAAGAAAAGTCCATTTATTA-TCACNNNNNNNNN
63 A-AAACGTGAAGAAAGA--GACATTCATTGGCAAGAAAAGTCCATTTA-TAGTCACCCATTCTTT
* ** *
1538 NAAAAGCCTTATTACTCGCTTTAAATTTTTTTATAATCTCAAAATTG
124 CAAAAGCCTTATTACTCG-TTTAAATAGTTTTATAATCTCATAATTG
** * * * * *
1585 ATTTTAAGTTTTATTTTTTT-TACTTCTTTGATTAAAACAGATTATAATTGAATG-TCTA-CATC
1 ATTTTAAGTTGAATTTTTTTATA-TT-TTT-TTTAAAATAGACTATAATTGAATGCT-TACCTTA
* * *** * * * *
1647 GAAAAACGTGAAAAAAAAAAGTTTTTCATTGGCAAGTAAAGTCTATTTATTGTCACCCATTCCTT
62 G-AAAACGTG--AAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTT
* * * *
1712 CAAAAACCTTATTACTCGTTTTAAATGGCTTTATAATCTCATAACTG
124 CAAAAGCCTTATTACTCG-TTTAAATAGTTTTATAATCTCATAATTG
*
1759 ATTATAAGTTGAATTTTTTTATATTTTTCTTTAAAATAGACTATAATTGAATGCTTACCTTAGAA
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTATAATTGAATGCTTACCTTAGAA
* * * * *
1824 AACGTGAAGAAAGAGGCATTCATTGACAAGAAAAGTCCATTTCTACTCACTCATTCTTTCAAAAG
65 AACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAG
* * *
1889 CCTTATTGCGCGTTGTAAATAGTTTTATAATCTTATAATTG
130 CCTTATTACTCGTT-TAAATAGTTTTATAATCTCATAATTG
* * * * * *
1930 ATTTTAAGTTGTATCTTTTTATATTTTTATTTAAAACATACTACAATTGAATG-TCTACCTCA-A
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTATAATTGAATGCT-TACCTTAGA
* * * * * *
1993 AAAC-TAGAAGAAAAAGACATTCATTGGTAAGAAATGTTCATTTAGAGTCACTCATTCTTTCAAA
64 AAACGT-GAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
* ********** *
2057 AGCCTTATTGCTCGCTTNNNNNNNNNNTATAATCTAATAATTG
128 AGCCTTATTACTCG-TTTAAATAGTTTTATAATCTCATAATTG
* * * *
2100 ATTTTAAATTGAATTGTTTTATATTTTTGGTTAAAATAGACTATTAA-TGAATGCCTACCTT-GA
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTA-TAATTGAATGCTTACCTTAGA
* * * ** * *
2163 GAAATGTCAAGTAA-AGTTATTCATTGGCAAGAAAAATCCATTTATAGTCACCCATTCCTTCAAA
64 -AAACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
********** * *
2227 AGCCTTANNNNNNNNNNNAAATACTTTTATAATCTTATAATTG
128 AGCCTTA-TTACTCGTTTAAATAGTTTTATAATCTCATAATTG
* * * *
2270 ATTTTAAGTTGAATTTGTTTACATTTTTTATTAAAATAGACTATAATTAAATGTCTGA-CTCTAG
1 ATTTTAAGTTGAATTTTTTTATATTTTTT-TTAAAATAGACTATAATTGAATG-CTTACCT-TAG
* ** *
2334 -AAACGTGAAGAAAGATACATTCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTATTTCAAA
63 AAAACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
* * * *
2398 AACTTTATTACACAATTTAAATAGTTTTATAATCTCAAATCTCAAATATG
128 AGCCTTATTACTC-GTTTAAATAGTTTTATAATCTC--A--T--AAT-TG
* ** * * * * *
2448 ATTTTAAGTTTAATTTTTTT-TACTTTTGGTTAAAACATA-TAATAACTGAATG-TCGACATT-G
1 ATTTTAAGTTGAATTTTTTTATA-TTTTTTTTAAAATAGACT-ATAATTGAATGCT-TACCTTAG
* * * * * * ** *
2509 AAAAACATGAAGAAAAATATATTCATTAGCAAGAAAAGTCTATTTATTA-TCACCTGTTCCTTCA
63 -AAAACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTA-TAGTCACCCATTCTTTCA
* * *
2573 AAAGCCTGATTACTCGCTTTAAATTGTTTTATAATCTCAAAATTG
126 AAAGCCTTATTACTCG-TTTAAATAGTTTTATAATCTCATAATTG
* * * * * * *
2618 ATATTAAGTTTACTTTTTTGT-TACTTGTTTACTTAAAACAGATTATAATTGAATG-TCCACACT
1 ATTTTAAGTTGAATTTTTT-TATA-TT-TTT-TTTAAAATAGACTATAATTGAATGCT-TAC-CT
* * * * * * *
2681 AAG-AAACTTGAATAAA-AAACCATTCATTGGTAAGAAAAGTCTATTTATTGTCA--C---C---
60 TAGAAAACGTGAAGAAAGAGA-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTT
*************************** *
2736 C---A----TNNNNNNNNNNNNNNNNNNNNNNNNNNNTCATAACTG
124 CAAAAGCCTTATTACTCGTTTAAATAGTTTTATAATCTCATAATTG
* * * * * * **
2775 ATTATAAGTTAAATTTTTTTATATTTTTCTTTAAAACAGACTATACTTCAATGCCTGTCTTAGAA
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTATAATTGAATGCTTACCTTAGAA
* * * **
2840 AACGTGAAGAAA-AAAGCATTCATTGGCAAGAAAAGTCTATTTATACTCACTTATTCTTTCAAAA
65 AACGTGAAGAAAGAGA-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAA
* * * *
2904 GCCTTATTACTCACTGTAAATGGTTTTACAATCTCATAATTG
129 GCCTTATTACTC-GTTTAAATAGTTTTATAATCTCATAATTG
* * * * * *
2946 ATTTTAAGTTGTATTTTTTTACATTTTTGATTAAAACAGACTATATTTGAATG-TATACCTCA-A
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTATAATTGAATGCT-TACCTTAGA
* ** * * * * *
3009 GAAGCCAGAAGAAAAAGACAATCATTGGCAAGAGAAGTCCATTTATAGTCTCTCATTCTTTCAAA
64 -AAACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
* * *
3074 AGCCTTATTGCTTAC-TTTGAATGGTTTTATAATCTCATAATT-
128 AGCCTTATTAC-T-CGTTTAAATAGTTTTATAATCTCATAATTG
* ********** * * **
3116 AATTTNNNNNNNNNNTTTTTATATTTTTGGTTAAAACAGACTATTGTTGAATGGC-TACCTT-GA
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGACTATAATTGAAT-GCTTACCTTAG-
* * * * ** * * * *
3179 AAAACTTAAAGAAA-AGGCATTCATTAGTGAGAAAAATCTATTTATAGTCATCCATTCCTTCAAA
63 AAAACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
* * * * *
3243 GGCCTTATTACTCATTTTAAAT-GATTTTATAACCTTATAACTG
128 AGCCTTATTACTC-GTTTAAATAG-TTTTATAATCTCATAATTG
* * * * ** *
3286 ATTTTAAGTTGAATTTATTTATATTTTTAGTTAAAACAG-CTTATAACTGAATGCGCACCTCAGA
1 ATTTTAAGTTGAATTTTTTTATATTTTT-TTTAAAATAGAC-TATAATTGAATGCTTACCTTAGA
* * * * ******
3350 AAACAT-AAGGAAAAAGACATTCATTGGCAAGAAAAGTCCATTTATATTCACTCATTCTNNNNNN
64 AAACGTGAA-GAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAA
**** * * *
3414 NNNNTTATTACTCACTTTAAATGGTTTTATAATCTCATAACTG
128 AGCCTTATTACTC-GTTTAAATAGTTTTATAATCTCATAATTG
* **
3457 ATTTTAGGTTCTATTTTTTTATATTTTT
1 ATTTTAAGTTGAATTTTTTTATATTTTT
3485 AGTTAANNNN
Statistics
Matches: 1534, Mismatches: 440, Indels: 194
0.71 0.20 0.09
Matches are distributed among these distances:
154 4 0.00
155 67 0.04
156 3 0.00
157 24 0.02
160 1 0.00
162 1 0.00
163 1 0.00
165 1 0.00
166 1 0.00
167 1 0.00
168 3 0.00
169 78 0.05
170 373 0.24
171 593 0.39
172 48 0.03
173 100 0.07
174 94 0.06
175 8 0.01
176 4 0.00
177 103 0.07
178 26 0.02
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.38
Consensus pattern (169 bp):
ATTTTAAGTTGAATTTTTTTATATTTTTTTTAAAATAGACTATAATTGAATGCTTACCTTAGAAA
ACGTGAAGAAAGAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCCATTCTTTCAAAAGC
CTTATTACTCGTTTAAATAGTTTTATAATCTCATAATTG
Found at i:2122 original size:170 final size:170
Alignment explanation
Indices: 1539--2672 Score: 507
Period size: 170 Copynumber: 6.6 Consensus size: 170
1529 NNNNNNNNNN
* * ** **
1539 AAAAGCCTTATTACTCGCTT-TAAATTTTTTTATAATCTCAA-AATTGATTTTAAGTTTTATTTT
1 AAAAGCCTTATTGCGCG-TTGTAAATAGTTTTATAATCT-AATAATTGATTTTAAGTTGAATTTT
* * * * *
1602 TTTTACTTCTTTGA-TTAAAACAGATTATAATTGAATG-TCTACATC-GAAAAACGTGAAAAAAA
64 TTATA-TT-TTT-ATTTAAAACAGACTACAATTGAATGCT-TACCTCAG-AAAACGTG--AAGAA
*** * * * *** * *
1664 AAAGTTTTTCATTGGCAAGTAAAGTCTATTTATTGTCACCCATTCCTTC
122 AAAGACATTCATTGACAAGAAAAGTCCATTTAGACTCACTCATTCTTTC
* * * * * * * * *
1713 AAAAACCTTATTACTCGTTTTAAATGGCTTTATAATCTCATAACTGATTATAAGTTGAATTTTTT
1 AAAAGCCTTATTGCGCGTTGTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTGAA-TTTTT
* * * * * *
1778 TATATTTTTCTTTAAAATAGACTATAATTGAATGCTTACCTTAGAAAACGTGAAGAAAGAGGCAT
65 TATATTTTTATTTAAAACAGACTACAATTGAATGCTTACCTCAGAAAACGTGAAGAAAAAGACAT
**
1843 TCATTGACAAGAAAAGTCCATTTCTACTCACTCATTCTTTC
130 TCATTGACAAGAAAAGTCCATTTAGACTCACTCATTCTTTC
* *
1884 AAAAGCCTTATTGCGCGTTGTAAATAGTTTTATAATCTTATAATTGATTTTAAGTTGTATCTTTT
1 AAAAGCCTTATTGCGCGTTGTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTGAAT-TTTT
*
1949 TATATTTTTATTTAAAACATACTACAATTGAATG-TCTACCTCA-AAAAC-TAGAAGAAAAAGAC
65 TATATTTTTATTTAAAACAGACTACAATTGAATGCT-TACCTCAGAAAACGT-GAAGAAAAAGAC
** * * *
2011 ATTCATTGGTAAGAAATGTTCATTTAGAGTCACTCATTCTTTC
128 ATTCATTGACAAGAAAAGTCCATTTAGACTCACTCATTCTTTC
* ********** *
2054 AAAAGCCTTATTGCTCGCTT-NNNNNNNNNNTATAATCTAATAATTGATTTTAAATTGAATTGTT
1 AAAAGCCTTATTGCGCG-TTGTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTGAATT-TT
** * * * * * * * *
2118 TTATATTTTTGGTTAAAATAGACTATTAA-TGAATGCCTACCT-TGAGAAATGTCAAG-TAAAGT
64 TTATATTTTTATTTAAAACAGACTA-CAATTGAATGCTTACCTCAGA-AAACGTGAAGAAAAAGA
* * * * * * *
2180 TATTCATTGGCAAGAAAAATCCATTTATAGTCACCCATTCCTTC
127 CATTCATTGACAAGAAAAGTCCATTTAGACTCACTCATTCTTTC
*********** * *
2224 AAAAGCCTTANNNNNNNNNNNAAATACTTTTATAATCTTATAATTGATTTTAAGTTGAATTTGTT
1 AAAAGCCTTATTGCGCGTTGTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTGAATTT-TT
* * * * * * *
2289 TACATTTTT-TATTAAAATAGACTATAATTAAATGTCTGA-CTCTAG-AAACGTGAAGAAAGATA
65 TATATTTTTAT-TTAAAACAGACTACAATTGAATG-CTTACCTC-AGAAAACGTGAAGAAAAAGA
* ** * * * *
2351 CATTCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTATTTC
127 CATTCATTGACAAGAAAAGTCCATTTAGACTCACTCATTCTTTC
* * * * * *
2395 AAAAACTTTATTACACAATT-TAAATAGTTTTATAATCTCAAATCTCAAATATGATTTTAAGTTT
1 AAAAGCCTTATTGCGC-GTTGTAAATAGTTTTATAATCT--AA--T--AAT-TGATTTTAAGTTG
* * ** * * * * * * *
2459 AATTTTTTTTACTTTTGGTTAAAACATA-TAATAACTGAATG-TCGACAT-TGAAAAACATGAAG
58 AATTTTTTATATTTTTATTTAAAACAGACT-ACAATTGAATGCT-TACCTCAG-AAAACGTGAAG
* * * * * *
2521 AAAAATATATTCATT-AGCAAGAAAAGTCTATTTATTA-TCAC-CTGTTCCTTC
120 AAAAAGACATTCATTGA-CAAGAAAAGTCCATTTA-GACTCACTC-ATTCTTTC
* * * * * * *
2572 AAAAGCCTGATTACTCGCTT-TAAATTGTTTTATAATCTCAA-AATTGATATTAAGTTTACTTTT
1 AAAAGCCTTATTGCGCG-TTGTAAATAGTTTTATAATCT-AATAATTGATTTTAAGTTGAATTTT
* * * *
2635 TTGTTACTTGTTTACTTAAAACAGATTATAATTGAATG
64 TT-ATA-TT-TTTATTTAAAACAGACTACAATTGAATG
2673 TCCACACTAA
Statistics
Matches: 744, Mismatches: 170, Indels: 93
0.74 0.17 0.09
Matches are distributed among these distances:
169 6 0.01
170 268 0.36
171 212 0.28
172 3 0.00
173 62 0.08
174 50 0.07
175 11 0.01
176 6 0.01
177 107 0.14
178 19 0.03
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.39
Consensus pattern (170 bp):
AAAAGCCTTATTGCGCGTTGTAAATAGTTTTATAATCTAATAATTGATTTTAAGTTGAATTTTTT
ATATTTTTATTTAAAACAGACTACAATTGAATGCTTACCTCAGAAAACGTGAAGAAAAAGACATT
CATTGACAAGAAAAGTCCATTTAGACTCACTCATTCTTTC
Found at i:2431 original size:341 final size:340
Alignment explanation
Indices: 1539--2738 Score: 864
Period size: 341 Copynumber: 3.5 Consensus size: 340
1529 NNNNNNNNNN
* * ** * * * *
1539 AAAAGCCTTATTACTCGCTT-TAAATTTTTTTATAATCTCAAAATTGATTTTAAGTTTTATTTTT
1 AAAAGCCTTATTGCGCG-TTGTAAATACTTTTATAATCTTATAATTGATTTTAAG-TTGA-ATTT
* * * *
1603 TTTAC-TTCTTTGATTAAAACAGATTATAATTGAATGTCTACATCGAAAAACGTGAAAAAAAAAA
63 TTTACATT-TTTTATTAAAACAGACTATAATTGAATGTCTAC-TCTAAAAACGTGAAGAAAAAAA
** * * * * *
1667 GTTTTTCATTGGCAAGTAAAGTCTATTTATTGTCACCCATTCCTTCAAAAACCTTATTACTCGTT
126 --CATTCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCGAT
* * * * *
1732 TTAAATGGCTTTATAATCTCATAACTGATTATAAGTTGAATTTTTTTATATTTTTCTTTAAAATA
189 TTAAATAGCTTTATAATCTAATAACTGATTATAAATTGAATTGTTTTATATTTTTCGTTAAAATA
* * *
1797 GACTATAATTGAATGCTTACCTTAGAAAACGTGAAGAAAGAGGCATTCATTGACAAGAAAAGTCC
254 GACTATAATTGAATGCCTACCTTAGAAAACGTCAAGAAAGAGGCATTCATTGACAAGAAAAATCC
* * *
1862 ATTTCTACTCACTCATTCTTTC
319 ATTTATACTCACCCATTCCTTC
* *
1884 AAAAGCCTTATTGCGCGTTGTAAATAGTTTTATAATCTTATAATTGATTTTAAGTTGTATCTTTT
1 AAAAGCCTTATTGCGCGTTGTAAATACTTTTATAATCTTATAATTGATTTTAAGTTGAAT-TTTT
* * * *
1949 TATA-TTTTTATTTAAAACATACTACAATTGAATGTCTAC-CTCAAAAAC-TAGAAGAAAAAGAC
65 TACATTTTTTA-TTAAAACAGACTATAATTGAATGTCTACTCT-AAAAACGT-GAAGAAAAAAAC
* * * * * * * * **
2011 ATTCATTGGTAAGAAATGTTCATTTAGAGTCACTCATTCTTTCAAAAGCCTTATTGCTCGCTTNN
127 ATTCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCGATTTA
******** * * *
2076 NNNNNNNNTATAATCTAATAATTGATTTTAAATTGAATTGTTTTATATTTTTGGTTAAAATAGAC
192 AATAGCTTTATAATCTAATAACTGATTATAAATTGAATTGTTTTATATTTTTCGTTAAAATAGAC
* * ** *
2141 TATTAA-TGAATGCCTACCTT-GAGAAATGTCAAGTAA-AGTTATTCATTGGCAAGAAAAATCCA
257 TA-TAATTGAATGCCTACCTTAGA-AAACGTCAAGAAAGAGGCATTCATTGACAAGAAAAATCCA
*
2203 TTTATAGTCACCCATTCCTTC
320 TTTATACTCACCCATTCCTTC
***********
2224 AAAAGCCTTANNNNNNNNNNNAAATACTTTTATAATCTTATAATTGATTTTAAGTTGAATTTGTT
1 AAAAGCCTTATTGCGCGTTGTAAATACTTTTATAATCTTATAATTGATTTTAAGTTGAATTT-TT
* * * * *
2289 TACATTTTTTATTAAAATAGACTATAATTAAATGTCTGACTCTAGAAACGTGAAGAAAGATACAT
65 TACATTTTTTATTAAAACAGACTATAATTGAATGTCT-ACTCTAAAAACGTGAAGAAAAAAACAT
* * * *
2354 TCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTATTTCAAAAACTTTATTACACAATTTAAA
129 TCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCGATTTAAA
* * * * * * * *
2419 TAGTTTTATAATCTCAAATCTCAAATATGATTTTAAGTTTAATT-TTTTTTACTTTTGGTTAAAA
194 TAGCTTTATAATCT--AA--T--AA-CTGATTATAAATTGAATTGTTTTATATTTTTCGTTAAAA
* * * * * * * * * ***
2483 CATA-TAATAACTGAATGTCGACATT-GAAAAACATGAAGAAAAATATATTCATT-AGCAAGAAA
252 TAGACT-ATAATTGAATGCCTACCTTAG-AAAACGTCAAGAAAGAGGCATTCATTGA-CAAGAAA
* * **
2545 AGTCTATTTATTA-TCACCTGTTCCTTC
314 AATCCATTTA-TACTCACCCATTCCTTC
* * * ** * * * * *
2572 AAAAGCCTGATTACTCGCTT-TAAATTGTTTTATAATCTCAAAATTGATATTAAGTTTACTTTTT
1 AAAAGCCTTATTGCGCG-TTGTAAATACTTTTATAATCTTATAATTGATTTTAAGTTGA--ATTT
* * * * * *
2636 TGTTAC-TTGTTTACTTAAAACAGATTATAATTGAATGTCCACACTAAGAAACTTGAATAAAAAA
63 T-TTACATTTTTTA-TTAAAACAGACTATAATTGAATGTCTACTCTAA-AAACGTGAAGAAAAAA
* * * *
2700 CCATTCATTGGTAAGAAAAGTCTATTTATTGTCACCCAT
125 ACATTCATTGGCAAGAAAAGTTTATTTATAGTCACCCAT
2739 NNNNNNNNNN
Statistics
Matches: 666, Mismatches: 157, Indels: 59
0.76 0.18 0.07
Matches are distributed among these distances:
339 2 0.00
340 115 0.17
341 207 0.31
342 8 0.01
343 22 0.03
344 36 0.05
345 46 0.07
346 4 0.01
347 44 0.07
348 92 0.14
349 14 0.02
350 76 0.11
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (340 bp):
AAAAGCCTTATTGCGCGTTGTAAATACTTTTATAATCTTATAATTGATTTTAAGTTGAATTTTTT
ACATTTTTTATTAAAACAGACTATAATTGAATGTCTACTCTAAAAACGTGAAGAAAAAAACATTC
ATTGGCAAGAAAAGTTTATTTATAGTCACCCATTCTTTCAAAAACCTTATTACTCGATTTAAATA
GCTTTATAATCTAATAACTGATTATAAATTGAATTGTTTTATATTTTTCGTTAAAATAGACTATA
ATTGAATGCCTACCTTAGAAAACGTCAAGAAAGAGGCATTCATTGACAAGAAAAATCCATTTATA
CTCACCCATTCCTTC
Done.