Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018401321.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_446.0, 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: 14510
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.30
Warning! 2740 characters in sequence are not A, C, G, or T
Found at i:604 original size:156 final size:156
Alignment explanation
Indices: 428--717 Score: 409
Period size: 156 Copynumber: 1.9 Consensus size: 156
418 ACCAAAAATA
* * * *
428 AAAAAAATTCAACTTAAAATCAATTATTACATTATAAAATAATTTGAAGCGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAATAATTTAAAGAGAGTAATAAGGCTTT
* * * * * *
493 TGAAGGGATGGGTGACTATAAACGGACTCTTCTTCTCAATAAATGGCTTTTTTTACATGTTTCTT
66 AGAAGAGATGGGTGACTATAAACAGACTCTTCTTCTCAACAAATGGCTTTTCTTACACGTTTCTT
558 GAGGCAAGCATTTTAATGAAAAATGT
131 GAGGCAAGCATTTTAATGAAAAATGT
** *
584 AAAAAAATTTTACTTAAAATCAATTATGAAATTATAAAATCATTTAAAGAGAGTAATAAGGCTTT
1 AAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAATAATTTAAAGAGAGTAATAAGGCTTT
* * * * * *
649 AGAAGATATGGGTGACTATAAATAGACTTTTTTTCTCAACGAATGGCTTTTCTTACACGTTTTTT
66 AGAAGAGATGGGTGACTATAAACAGACTCTTCTTCTCAACAAATGGCTTTTCTTACACGTTTCTT
714 GAGG
131 GAGG
718 AAAACATTCA
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
156 115 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (156 bp):
AAAAAAATTCAACTTAAAATCAATTATGAAATTATAAAATAATTTAAAGAGAGTAATAAGGCTTT
AGAAGAGATGGGTGACTATAAACAGACTCTTCTTCTCAACAAATGGCTTTTCTTACACGTTTCTT
GAGGCAAGCATTTTAATGAAAAATGT
Found at i:885 original size:171 final size:171
Alignment explanation
Indices: 568--1284 Score: 734
Period size: 172 Copynumber: 4.2 Consensus size: 171
558 GAGGCAAGCA
** *
568 TTTTAATGAAAAATGTAAAAAAATTTTACTTAAAATCAATTATGAAATTATAAAATCATTTAAAG
1 TTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAG
* * * * * * * * **
633 AGAGTAATAAGGCTTTAGAAGATA-TGGGTGACTATAAATAGACTTTT-TTTCTCAACGAATGGC
66 CGAGTAATAAGGCTTTTGAAAAAAGT-AGTGACTATAAATGGACTTTTCTTTC-AAATGAATACC
* * *
696 -TTTTCTTACACGTTTTTTGAGGAAAAC-ATTCAATTATAGTTTG
129 TTTTTCTT-CACATTTTTTGAGGTAAACAATT-AATTATAGTCTG
* *
739 TTTTAATGAAAAATGTAAACAAATTCAACTTAAAATCAATTATGAGATTCTAAAATCATTTAAAG
1 TTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAG
* * * *
804 TGAGTACTAAGGCTTTTGAAACAAGTAGTGACTATAAATGGACTTCTCTTTCAAATGAATACCTT
66 CGAGTAATAAGGCTTTTGAAAAAAGTAGTGACTATAAATGGACTTTTCTTTCAAATGAATACCTT
* * *
869 TTTCTTCACATTTTTTGAGGTAGACAATTAATTGTAGTCTT
131 TTTCTTCACATTTTTTGAGGTAAACAATTAATTATAGTCTG
*** * * * *
910 TTTTAACCCAAAATGTAAAAGAAATTCAAATGAAAATCAATTATGAGATTTTAAAACCATTTAAA
1 TTTTAATGAAAAATGTAAAA-AAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAA
* * **
975 GCGAGTAATAAGGCTTTTGAAAAAAGTGGTGACTGTAAATGGACTTTTCATAGC-AATGAATACC
65 GCGAGTAATAAGGCTTTTGAAAAAAGTAGTGACTATAAATGGACTTTTC-TTTCAAATGAATACC
** * * * *
1039 TTTTTCTGAACGTTTCTTGAGGTAAAC-ATCCAATTATTA-TCTA
129 TTTTTCTTCACATTTTTTGAGGTAAACAAT-TAATTA-TAGTCTG
* * * * *
1082 TTTTTATGAAAAAAGAAAAAAAATTCGACTTAAAAATCAATTATGAGAATATAAAA-CTATTTAA
1 TTTTAATGAAAAATGTAAAAAAATTCAACTT-AAAATCAATTATGAGATTATAAAATC-ATTTAA
* * * * *
1146 AACGAGTAATAAGGCTTTTGAAAGAAGTAGTAACTATAAACGGACTTTTCTTTAAAATGAAT-CT
64 AGCGAGTAATAAGGCTTTTGAAAAAAGTAGTGACTATAAATGGACTTTTCTTTCAAATGAATAC-
* *
1210 CTTTTTCTTCACATTTCTCT-AGGTAAACAATTAATTATAGTCAG
128 CTTTTTCTTCACATTT-TTTGAGGTAAACAATTAATTATAGTCTG
**
1254 TTTTAACCAAAAATGTAAAAAACAATTCAAC
1 TTTTAATGAAAAATGT-AAAAA-AATTCAAC
1285 NNNNNNNNNN
Statistics
Matches: 447, Mismatches: 82, Indels: 31
0.80 0.15 0.06
Matches are distributed among these distances:
171 159 0.36
172 269 0.60
173 12 0.03
174 7 0.02
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (171 bp):
TTTTAATGAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAG
CGAGTAATAAGGCTTTTGAAAAAAGTAGTGACTATAAATGGACTTTTCTTTCAAATGAATACCTT
TTTCTTCACATTTTTTGAGGTAAACAATTAATTATAGTCTG
Found at i:1225 original size:344 final size:342
Alignment explanation
Indices: 576--1275 Score: 863
Period size: 344 Copynumber: 2.0 Consensus size: 342
566 CATTTTAATG
** * * *
576 AAAAATGTAAAAAAATTTTACTTAAAATCAATTATGAAATTATAAAATCATTTAAAGAGAGTAAT
1 AAAAATGTAAAAAAATTCAAATGAAAATCAATTATGAAATTATAAAACCATTTAAAGAGAGTAAT
* * ** ** ** *
641 AAGGCTTTAGAAGATATGGGTGACTATAAATAGACTTTTTTTCTCAACGAATGGCTTTTCTTACA
66 AAGGCTTTAGAAAAAATGGGTGACTATAAATAGACTTTTCATAGCAACGAATACCTTTTCTGACA
* * * * * * *
706 CGTTTTTTGAGGAAAACATTCAATTATAGTTTGTTTTAATGAAAAATGTAAACAAATTCAACTTA
131 CGTTTCTTGAGGAAAACATCCAATTATAGTCTATTTTAATGAAAAAAGAAAAAAAATTCAACTTA
* * ** * *
771 AAATCAATTATGAGATTCTAAAATCATTTAAAGTGAGTACTAAGGCTTTTGAAACAAGTAGTGAC
196 AAATCAATTATGAGAATATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAACAAGTAGTAAC
* * * *
836 TATAAATGGACTTCTCTTTCAAATGAATACCTTTTTCTTCACATTT-TTTGAGGTAGACAATTAA
261 TATAAACGGACTTCTCTTTAAAATGAATACCTTTTTCTTCACATTTCTCT-AGGTAAACAATTAA
* **
900 TTGTAGTCTTTTTTAACC
325 TTATAGTCAGTTTTAACC
* * * *
918 CAAAATGTAAAAGAAATTCAAATGAAAATCAATTATGAGATTTTAAAACCATTTAAAGCGAGTAA
1 AAAAATGTAAAA-AAATTCAAATGAAAATCAATTATGAAATTATAAAACCATTTAAAGAGAGTAA
* * * *
983 TAAGGCTTTTGAAAAAA-GTGGTGACTGTAAATGGACTTTTCATAGCAATGAATACCTTTTTCTG
65 TAAGGCTTTAGAAAAAATG-GGTGACTATAAATAGACTTTTCATAGCAACGAATACC-TTTTCTG
* * *
1047 A-ACGTTTCTTGAGGTAAACATCCAATTATTA-TCTATTTTTATGAAAAAAGAAAAAAAATTCGA
128 ACACGTTTCTTGAGGAAAACATCCAATTA-TAGTCTATTTTAATGAAAAAAGAAAAAAAATTCAA
*
1110 CTTAAAAATCAATTATGAGAATATAAAA-CTATTTAAAACGAGTAATAAGGCTTTTGAAAGAAGT
192 CTT-AAAATCAATTATGAGAATATAAAATC-ATTTAAAACGAGTAATAAGGCTTTTGAAACAAGT
*
1174 AGTAACTATAAACGGACTTTTCTTTAAAATGAAT-CTCTTTTTCTTCACATTTCTCTAGGTAAAC
255 AGTAACTATAAACGGACTTCTCTTTAAAATGAATAC-CTTTTTCTTCACATTTCTCTAGGTAAAC
1238 AATTAATTATAGTCAGTTTTAACC
319 AATTAATTATAGTCAGTTTTAACC
1262 AAAAATGTAAAAAA
1 AAAAATGTAAAAAA
1276 CAATTCAACN
Statistics
Matches: 302, Mismatches: 48, Indels: 15
0.83 0.13 0.04
Matches are distributed among these distances:
342 12 0.04
343 142 0.47
344 146 0.48
345 2 0.01
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (342 bp):
AAAAATGTAAAAAAATTCAAATGAAAATCAATTATGAAATTATAAAACCATTTAAAGAGAGTAAT
AAGGCTTTAGAAAAAATGGGTGACTATAAATAGACTTTTCATAGCAACGAATACCTTTTCTGACA
CGTTTCTTGAGGAAAACATCCAATTATAGTCTATTTTAATGAAAAAAGAAAAAAAATTCAACTTA
AAATCAATTATGAGAATATAAAATCATTTAAAACGAGTAATAAGGCTTTTGAAACAAGTAGTAAC
TATAAACGGACTTCTCTTTAAAATGAATACCTTTTTCTTCACATTTCTCTAGGTAAACAATTAAT
TATAGTCAGTTTTAACC
Found at i:3705 original size:341 final size:331
Alignment explanation
Indices: 3098--3728 Score: 639
Period size: 341 Copynumber: 1.9 Consensus size: 331
3088 NNNNNNNNNA
* * * * *
3098 TAAAAAAATTTAACTTAAAATCAATTATTGGATTATTAAACAATTTGAAGCAAATAATAAGGCTT
1 TAAAAAAATTCAACTTAAAATCAATTATTGGATTATAAAACAATTTAAAACAAATAACAAGGCTT
* *
3163 CTAAAGGAATGGTGACTATAAATGGACTATTCTTCTCAATAAATGGCATTTTTTACACATTTTTT
66 CTAAAGAAATGGTGACTATAAATGGACTATTCGTCTCAATAAATGGCATTTTTTACACATTTTTT
* *
3228 GAGACAGATATTCAATTATAATTTGTTTTAATAAAAAATATAAAAAAATTCAATTTAAAATCAAT
131 GAGACAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAATTTAAAATCAAT
* * ********** * *
3293 TATGAGATTAGAAAACCATCTTAAGTGAGTAANNNNNNNNNNGAAGGAATGGGTGAGTATAAACA
196 TATGAGATTAGAAAACAATCTTAAGTGAATAATAAGGCTTTAGAAAGAATGGGTGACTATAAACA
*
3358 GACTTTT-TTTGTCAATGAATACCTTTTTCTTTATGTTTCTCANNNNNNNNNNTCAATTATAGTC
261 GACTTTTCTTT-TCAATGAATAACTTTTTCTTTATGTTTCTCA----------TCAATTATAGTC
3422 TTTTTTAATGAAAAATG
315 TTTTTTAATGAAAAATG
* * *
3439 TAAAAACAATTCACCTTAAAATCAATTA-TGAGATTATAAAACCATTTAAAACAAGTAACAAGGC
1 TAAAAA-AATTCAACTTAAAATCAATTATTG-GATTATAAAACAATTTAAAACAAATAACAAGGC
* * * * * * * *
3503 TTTTGAAGAAATGGTTGACTATAAATGGACTTTTCGTGTCAATGAAT-GCCTTTTTT-TACGTTT
64 TTCTAAAGAAATGG-TGACTATAAATGGACTATTCGTCTCAATAAATGGCATTTTTTACACATTT
* * *
3566 TTCT-ACG-TAGACATTCAATTATAGTCTGTTTT-ATAAAAAAATATAAAAAAATTTAATTTAAA
128 TT-TGA-GACAGACATTCAATTATAATCTGTTTTAAT-AAAAAATATAAAAAAATTCAATTTAAA
** * *
3628 ATCAATTATTCGATTATAAAATAAT-TTGAAGTGAATAATAAGGCTTTAGAAAGAATGGGTGACT
190 ATCAATTATGAGATTAGAAAACAATCTT-AAGTGAATAATAAGGCTTTAGAAAGAATGGGTGACT
** *
3692 ATAAATGGACTTTTCTTTTTAATGAATAACTTTTTCT
254 ATAAACAGACTTTTCTTTTCAATGAATAACTTTTTCT
3729 ACACGTTTTT
Statistics
Matches: 237, Mismatches: 45, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
340 4 0.02
341 135 0.57
342 70 0.30
343 28 0.12
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.36
Consensus pattern (331 bp):
TAAAAAAATTCAACTTAAAATCAATTATTGGATTATAAAACAATTTAAAACAAATAACAAGGCTT
CTAAAGAAATGGTGACTATAAATGGACTATTCGTCTCAATAAATGGCATTTTTTACACATTTTTT
GAGACAGACATTCAATTATAATCTGTTTTAATAAAAAATATAAAAAAATTCAATTTAAAATCAAT
TATGAGATTAGAAAACAATCTTAAGTGAATAATAAGGCTTTAGAAAGAATGGGTGACTATAAACA
GACTTTTCTTTTCAATGAATAACTTTTTCTTTATGTTTCTCATCAATTATAGTCTTTTTTAATGA
AAAATG
Found at i:4283 original size:171 final size:170
Alignment explanation
Indices: 4027--4443 Score: 409
Period size: 171 Copynumber: 2.4 Consensus size: 170
4017 TTTTTTCACG
* * * * * *
4027 TTTCTTGAGGTAGACATTCAATTATAGTATGTTTCAACT-AAAAATATAAAAAAATTTAACTTAA
1 TTTCTAGAGATAGACATTCAATTATAGTATGTTT-TACTGAAAAACATAAAACAATTCAACTTAA
* * *
4091 AACCAATTATTGGATTATAAAATAATTTGAAATGAGTAAAAAGG-TTGTTGAAGGAATAGG-TGA
65 AATCAATTA-TGGATTATAAAACAATTTGAAATGAGTAAAAAGGCTT-TCGAAGGAAT-GGATGA
*
4154 CTATAAATGAACTTTTCTTATCAATGAATGGCTTTTTCCACATA
127 CTATAAATGAACTTTTCCTATCAATGAATGGCTTTTTCCACATA
*
4198 TTTCTAGAGGCA-AG-CATTCAATTATAGTTTGTTTTACTGAAAAACATAAAACAATTCAACTTA
1 TTTCTAGA-G-ATAGACATTCAATTATAGTATGTTTTACTGAAAAACATAAAACAATTCAACTTA
********** *
4261 AAATCAATTATGAGATTATAAAACAATNNNNNNNNNNTAATAAGGCTTTCGAAGGAATGGATGAC
64 AAATCAATTATG-GATTATAAAACAATTTGAAATGAGTAAAAAGGCTTTCGAAGGAATGGATGAC
* * ** *
4326 TATAAATGGACTTTTCCTCTCAATGAATGGCTTTTTTTACATG
128 TATAAATGAACTTTTCCTATCAATGAATGGCTTTTTCCACATA
* * * *
4369 TTTCTCGAGATAGACATTTAATTATAGTCTGTTTTAATGAAAAATGCA-AAAAC-ATTCAA-TTG
1 TTTCTAGAGATAGACATTCAATTATAGTATGTTTTACTGAAAAA--CATAAAACAATTCAACTT-
4431 AAAATCAATTATG
63 AAAATCAATTATG
4444 TNNNNNNNNN
Statistics
Matches: 204, Mismatches: 31, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
169 1 0.00
170 12 0.06
171 179 0.88
172 10 0.05
173 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.35
Consensus pattern (170 bp):
TTTCTAGAGATAGACATTCAATTATAGTATGTTTTACTGAAAAACATAAAACAATTCAACTTAAA
ATCAATTATGGATTATAAAACAATTTGAAATGAGTAAAAAGGCTTTCGAAGGAATGGATGACTAT
AAATGAACTTTTCCTATCAATGAATGGCTTTTTCCACATA
Found at i:6646 original size:171 final size:173
Alignment explanation
Indices: 5980--8361 Score: 2251
Period size: 171 Copynumber: 14.0 Consensus size: 173
5970 NNNNNNNNNN
* * ** ** *
5980 AAATTAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAATAAAT-AGGTTA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * * *
6044 CCATAAATGGACTTTTCTTGCT-AATGAAAT--CTTTTTCTACACGTTTCTTAAGGTAA-ACATT
66 CTATAAATGGACTTTTCTTGCTCAATG-AATGCCTTTTTCTTCATGTTTCTCAAGG-AAGACATT
* * ** **
6105 CATTTATAATCTATTTTAACCAAAAATACAAAAAAA-TCAAACTTA
129 CAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTC-AACTTA
* * * * *
6150 AAATGAATTATGAGATTATAAAACTATTTAAAGGGAGTAATAAGGCTTTTGTAGGAATG-GGTAA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * * * * *
6214 CTATTAATAGACTTTTCTTAC-CAATGAATACCCTTTTCTTCATGTTTC-CAA-GACAGGCATTC
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGA-AGACATTC
* * * * *
6276 AATTATTGTCAATTTTAATGAAAAATGTGAAAAAATTCTACTTG
130 AATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
* * * *
6320 AAATCAATTATAAGATTATAAAACTATTTTAAGCGAGTTATAAGGCTTTTGAAGGAAT-AGGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * *** * * * *
6384 CGAT-AATAGACTTTTCTTGC-CAATGAATATATTTTTC-TCTACGTTTTTCAAGGTAGACATTT
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTC-ATGTTTCTCAAGGAAGACATTC
* * ** *
6446 AATTATTGTCTCTTTTAACCAAAAATGTAAAACAATTCAACTTA
130 AATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
* ** *
6490 AAATCAATTATGGGATTATAAAACCATTTAAAGTAAGTAATAAGG-TATTTGAAGGAACGA-GTG
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCT-TTTGAAGGAATGAGGTG
* * * *
6553 ACTATGAATGGATTTTTCTT-CTCAATGAATGCCTTTTTCTACATGTTTCCCAAGGCAAG-CATT
65 ACTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGG-AAGACATT
* * *
6616 CAATTATAGTCTATTTTAATGAAAAATGTAAAACAATTTAACATA
129 CAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
* *
6661 AAATCAATTATGAGATTATGAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAAT-AGGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * * *
6725 CTATAAATAGACTTTT-TTG-ACAATGAATGCCATTTTCCTCATGTTTCTCAAGGTAA-ACATTC
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGG-AAGACATTC
* * *
6787 AATTATAGTTTGTTTTAATGAAAAATAT-AAAAAATTCAACTTA
130 AATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
* * * *
6830 AAATCAATTATGAGATTATAAAGCTATTTAAAGCGAGTAATAAGGCTTTAGAAGAAAT-AGGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
*** * * *
6894 CTATAAATGGACTTTTCTTGCT-AATGAATG-CTTTTTCCTTTGCGTTTCTTAAGGTAGACATTT
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTT-CTTCATGTTTCTCAAGGAAGACATTC
* * * *
6957 ATTTATAATCTGTTTTAACT-AAAAATGTAAAAAAAATT-AATTTA
130 AATTATAGTCTATTTTAA-TGAAAAATGT-AAAAAAATTCAACTTA
* * * * * *
7001 AAATGAATTATGAGATGATAAAACCATTTAAAGGGAGTAATATGGCTTTTGTAGGAATG-GGTAA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * * * * * * *
7065 CTATTAATAGACTTTTATTAC-CAATGAATACCCTTTTCTTCACGTTTC-CAAGGTATG-CATTC
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGG-AAGACATTC
* *
7127 AATTATAGTCAATTTTAATGAAAAATGTAAAAAAATTCATCTTA
130 AATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
* * * * *
7171 AAATCAATTATGAGATTATAAAATCATTTAAAGCGGGTTATAAAGCCTTTGAAGGAAT-AGGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * * * * *
7235 CTCA-AAATGGACTTTTCTT-TTTAATGAATGGCTTTTTCTAT-ATGTTTCCCAAGGTAGGCATT
66 CT-ATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCT-TCATGTTTCTCAAGGAAGACATT
*
7297 CAATTATAGTCTATTTTAATGAAAAATATATAAAAAAAATT-AACTTA
129 CAATTATAGTCTATTTTAATG-AAAA-ATGT-AAAAAAATTCAACTTA
* * **
7344 AAATCAATTATGCGATTATAAAACTATGAAAAGCGAGTAATAAGGCTTTTGATA-GAAT-AGGTG
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATGAGGTG
* * * * * * *
7407 ACTATAAATAGACTTTTCTTGC-CAATGAATGCTTTTTTTTTTAT-TTTCTTAAGGTAGACAGTC
65 ACTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGAAGACATTC
** *
7470 AATTATAGTCTATTTTAACCAAAAATGTAAAAAAATTTAACTTA
130 AATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
* * * *
7514 AAATCAATTATTG-GATTATTAAACAATTTGAAGCGAGTAATAAGGCTTTTGAAAGAAT--GGTG
1 AAATCAATTA-TGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTG
* * * * * * * *
7576 ACAATAAATAGACTTTTATTTCT-AATGAATCCCTTTTTCTTCATATTTCTCAATGTAGACATTC
65 ACTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGAAGACATTC
* * ** * *
7640 AATTATAATCTGTTTTAACCAAAAAAGTAAAAAAAATTGAACTTA
130 AATTATAGTCTATTTTAATGAAAAATGT-AAAAAAATTCAACTTA
* * * * * * *
7685 AAATTAATTTTGAGAGTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGTAATGA-GAGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * * *
7749 CTATAAATGGACTTTTCTTGC-CAATGAATG-CTTTGTCTTCACGTTTCTC-ATGATAGACAATC
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGA-AGACATTC
* * *
7811 AATTATAGTCTGTTTTAATGAAAGATGTAAAAAAAAATCAACTTA
130 AATTATAGTCTATTTTAATGAAAAATGT-AAAAAAATTCAACTTA
* * * * * *
7856 AAATCAATTATGAGATTACAAAACCATTTAAAACAAGTAATAAAGCTTTCGAAGAAATG-GGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* *** *
7920 CTATCAATGGACTTTTCTTGCT-AATGAATTATTTTTTCTTCATATTTCTCAAGGTAA-ACATTC
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGG-AAGACATTC
* * **
7983 ATTTATAGTCAATTTTGAA-GAAAAATGTAAAAACTTTCAACTTA
130 AATTATAGTCTATTTT-AATGAAAAATGTAAAAAAATTCAACTTA
*
8027 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTTATAAGGCTTTTGAAGGAAT-AGGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
* * ** * * * * *
8091 TTATAAATGGACTTTTCTT-TTTGATGAATGACTTTTTCTAT-ACG-TTCTCGATGTAGACATTC
66 CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCT-TCATGTTTCTCAAGGAAGACATTC
* * ** * * *
8153 AATTATAATCTGTTTTAACCCATAAA-GTAAAAAAAATTGAACCTA
130 AATTATAGTCTATTTTAA-TGAAAAATGT-AAAAAAATTCAACTTA
* * * *
8198 AAATCAATTTTGAGAGTATAAAACCATTTAAA-CTGAGTAATAACGCTTTTGAAGGAATGA-GAG
1 AAATCAATTATGAGATTATAAAACCATTTAAAGC-GAGTAATAAGGCTTTTGAAGGAATGAGGTG
* * * * *
8261 ACTATAAATGGACTTTTCTTG-ACAATGAATGCATTTTTCTTCATATTGT-TCAAAGTAGACATT
65 ACTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTT-TCTCAAGGAAGACATT
**
8324 CAATTATAGTCTATTTTAACCAAAAATGTAAAAAAATT
129 CAATTATAGTCTATTTTAATGAAAAATGTAAAAAAATT
8362 TANNNNNNNN
Statistics
Matches: 1818, Mismatches: 316, Indels: 155
0.79 0.14 0.07
Matches are distributed among these distances:
168 3 0.00
169 194 0.11
170 640 0.35
171 713 0.39
172 158 0.09
173 99 0.05
174 11 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.36
Consensus pattern (173 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGAGGTGA
CTATAAATGGACTTTTCTTGCTCAATGAATGCCTTTTTCTTCATGTTTCTCAAGGAAGACATTCA
ATTATAGTCTATTTTAATGAAAAATGTAAAAAAATTCAACTTA
Found at i:6778 original size:341 final size:338
Alignment explanation
Indices: 5980--8363 Score: 2335
Period size: 340 Copynumber: 7.0 Consensus size: 338
5970 NNNNNNNNNN
* * ** ** *
5980 AAATTAATTATGAGATTATAAAACCATTTAAAGTGAGTAATAAGGCTTTCAAATAAATAGGTTAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* * * * * *
6045 CATAAATGGACTTTTCTTGCTAATGAAAT--CTTTTTCTACACGTTTCTTAAGGTAAACATTCAT
66 TATAAATAGACTTTTCTTGCCAATG-AATGCCTTTTTCT-CACGTTTCTCAAGGTAGACATTCAA
* ** *
6108 TTATAATCTATTTTAACCAAAAATACAAAAAAA-TCAAACTTAAAATGAATTATGAGATTATAAA
129 TTATAGTCTATTTTAACCAAAAATGTAAAAAAATTC-AACTTAAAATCAATTATGAGATTATAAA
* * * * * * * *
6172 ACTATTTAAAGGGAGTAATAAGGCTTTTGTAGGAATGGGTAACTATTAATAGACTTTTCTTACCA
193 ACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT-CTA
* * * *
6237 ATGAATACCCTTTTCTTCATGTTTC-CAA-GACAGGCATTCAATTATTGTCAATTTTAATGAAAA
256 ATGAATGCCTTTTTCTTCATGTTTCTCAAGGA-A-GCATTCAATTATAGTCTATTTTAATGAAAA
* *
6300 ATGTGAAAAAATTCT-ACTTG
319 ATGTAAAAAAATT-TAACTTA
* * * *
6320 AAATCAATTATAAGATTATAAAACTATTTTAAGCGAGTTATAAGGCTTTTGAAGGAATAGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* *** * *
6385 GAT-AATAGACTTTTCTTGCCAATGAATATATTTTTCTCTACGTTTTTCAAGGTAGACATTTAAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTC-ACGTTTCTCAAGGTAGACATTCAAT
* * * *
6449 TATTGTCTCTTTTAACCAAAAATGTAAAACAATTCAACTTAAAATCAATTATGGGATTATAAAAC
130 TATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
** * * *
6514 CATTTAAAGTAAGTAATAAGGTATTTGAAGGAACGAGTGACTATGAATGGATTTTTCTTCTCAAT
195 CATTTAAAGCGAGTAATAAGGT-TTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCT-AAT
* *
6579 GAATGCCTTTTTCTACATGTTTCCCAAGGCAAGCATTCAATTATAGTCTATTTTAATGAAAAATG
258 GAATGCCTTTTTCTTCATGTTTCTCAAGG-AAGCATTCAATTATAGTCTATTTTAATGAAAAATG
* *
6644 TAAAACAATTTAACATA
322 TAAAAAAATTTAACTTA
* *
6661 AAATCAATTATGAGATTATGAAACCATTTAAAACGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* * * *
6726 TATAAATAGACTTTT-TTGACAATGAATGCCATTTTCCTCATGTTTCTCAAGGTAAACATTCAAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCC-TTTTTCTCACGTTTCTCAAGGTAGACATTCAAT
* * ** * *
6790 TATAGTTTGTTTTAATGAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTATAAAGC
130 TATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAAC
* * *
6854 TATTTAAAGCGAGTAATAAGGCTTTAGAAGAAAT-AGGTGACTATAAATGGACTTTTCTTGCTAA
195 CATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGA-GTGACTATAAATGGACTTTTCTT-CTAA
*** * * * * * *
6918 TGAATG-CTTTTTCCTTTGCGTTTCTTAAGGTAGACATTTATTTATAATCTGTTTTAACT-AAAA
257 TGAATGCCTTTTT-CTTCATGTTTCTCAAGGAAG-CATTCAATTATAGTCTATTTTAA-TGAAAA
* *
6981 ATGTAAAAAAAATTAATTTA
319 ATGTAAAAAAATTTAACTTA
* * * * * * *
7001 AAATGAATTATGAGATGATAAAACCATTTAAAGGGAGTAATATGGCTTTTGTAGGAATGGGTAAC
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* * * * *
7066 TATTAATAGACTTTTATTACCAATGAATACCCTTTTCTTCACGTTTC-CAAGGTATG-CATTCAA
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC-TCACGTTTCTCAAGGTA-GACATTCAA
* ** *
7129 TTATAGTCAATTTTAATGAAAAATGTAAAAAAATTCATCTTAAAATCAATTATGAGATTATAAAA
129 TTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAA
* * * ** *
7194 TCATTTAAAGCGGGTTATAAAGCCTTTGAAGGAAT-AGGTGACTCA-AAATGGACTTTTCTTTTT
194 CCATTTAAAGCGAGTAAT-AAGGTTTTGAAGGAATGA-GTGACT-ATAAATGGACTTTTC-TTCT
* * *
7257 AATGAATGGCTTTTTCTAT-ATGTTTCCCAAGGTAGGCATTCAATTATAGTCTATTTTAATGAAA
255 AATGAATGCCTTTTTCT-TCATGTTTCTCAAGG-AAGCATTCAATTATAGTCTATTTTAATG-AA
* *
7321 AATATATAAAAAAAATTAACTTA
317 AA-ATGTAAAAAAATTTAACTTA
* * **
7344 AAATCAATTATGCGATTATAAAACTATGAAAAGCGAGTAATAAGGCTTTTGATA-GAATAGGTGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGA-AGGAATAGGTGA
* * * * * *
7408 CTATAAATAGACTTTTCTTGCCAATGAATGCTTTTTTTTTTA-TTTTCTTAAGGTAGACAGTCAA
65 CTATAAATAGACTTTTCTTGCCAATGAATGC-CTTTTTCTCACGTTTCTCAAGGTAGACATTCAA
* *
7472 TTATAGTCTATTTTAACCAAAAATGTAAAAAAATTTAACTTAAAATCAATTATTG-GATTATTAA
129 TTATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTA-TGAGATTATAAA
* * * * * *
7536 ACAATTTGAAGCGAGTAATAAGGCTTTTGAAAGAATG-GTGACAATAAATAGACTTTTATTTCTA
193 ACCATTTAAAGCGAGTAATAAGG-TTTTGAAGGAATGAGTGACTATAAATGGACTTTT-CTTCTA
* * * * * * **
7600 ATGAATCCCTTTTTCTTCATATTTCTCAATGTAGACATTCAATTATAATCTGTTTTAACCAAAAA
256 ATGAATGCCTTTTTCTTCATGTTTCTCAAGGAAG-CATTCAATTATAGTCTATTTTAATGAAAAA
* *
7665 AGTAAAAAAAATTGAACTTA
320 TGT-AAAAAAATTTAACTTA
* * * * * * *
7685 AAATTAATTTTGAGAGTATAAAACTATTTAAAGTGAGTAATAAGGCTTTTGAAGTAAT-GAGAGA
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAG-GTGA
* * * * *
7749 CTATAAATGGACTTTTCTTGCCAATGAATG-CTTTGTCTTCACGTTTCTCATGATAGACAATCAA
65 CTATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTC-TCACGTTTCTCAAGGTAGACATTCAA
* ** * * *
7813 TTATAGTCTGTTTTAATGAAAGATGTAAAAAAAAATCAACTTAAAATCAATTATGAGATTACAAA
129 TTATAGTCTATTTTAACCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* * * * * * *
7878 ACCATTTAAAACAAGTAATAAAGCTTTCGAAGAAATGGGTGACTATCAATGGACTTTTCTTGCTA
193 ACCATTTAAAGCGAGTAAT-AAGGTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT-CTA
*** * * * *
7943 ATGAATTATTTTTTCTTCATATTTCTCAAGGTAAACATTCATTTATAGTCAATTTTGAA-GAAAA
256 ATGAATGCCTTTTTCTTCATGTTTCTCAAGG-AAGCATTCAATTATAGTCTATTTT-AATGAAAA
*
8007 ATGT-AAAAACTTTCAACTTA
319 ATGTAAAAAAATTT-AACTTA
* *
8027 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTTATAAGGCTTTTGAAGGAATAGGTGAT
1 AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
* **** * * * *
8092 TATAAATGGACTTTTCTTTTTGATGAATGACTTTTTCTATACG-TTCTCGATGTAGACATTCAAT
66 TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCT-CACGTTTCTCAAGGTAGACATTCAAT
* * * * * * *
8156 TATAATCTGTTTTAACCCATAAA-GTAAAAAAAATTGAACCTAAAATCAATTTTGAGAGTATAAA
130 TATAGTCTATTTTAA-CCAAAAATGT-AAAAAAATTCAACTTAAAATCAATTATGAGATTATAAA
* *
8220 ACCATTTAAA-CTGAGTAATAACGCTTTTGAAGGAATGAGAGACTATAAATGGACTTTTCTTGAC
193 ACCATTTAAAGC-GAGTAATAA-GGTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTT--C
* * * * **
8284 -AATGAATGCATTTTTCTTCATATTGT-TCAAAGTAGACATTCAATTATAGTCTATTTTAACCAA
254 TAATGAATGCCTTTTTCTTCATGTT-TCTCAAGGAAG-CATTCAATTATAGTCTATTTTAATGAA
8347 AAATGTAAAAAAATTTA
317 AAATGTAAAAAAATTTA
8364 NNNNNNNNNN
Statistics
Matches: 1682, Mismatches: 296, Indels: 130
0.80 0.14 0.06
Matches are distributed among these distances:
338 3 0.00
339 35 0.02
340 466 0.28
341 457 0.27
342 424 0.25
343 287 0.17
344 10 0.01
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (338 bp):
AAATCAATTATGAGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATAGGTGAC
TATAAATAGACTTTTCTTGCCAATGAATGCCTTTTTCTCACGTTTCTCAAGGTAGACATTCAATT
ATAGTCTATTTTAACCAAAAATGTAAAAAAATTCAACTTAAAATCAATTATGAGATTATAAAACC
ATTTAAAGCGAGTAATAAGGTTTTGAAGGAATGAGTGACTATAAATGGACTTTTCTTCTAATGAA
TGCCTTTTTCTTCATGTTTCTCAAGGAAGCATTCAATTATAGTCTATTTTAATGAAAAATGTAAA
AAAATTTAACTTA
Found at i:8797 original size:170 final size:161
Alignment explanation
Indices: 8611--8933 Score: 327
Period size: 170 Copynumber: 2.0 Consensus size: 161
8601 TAAAACCATT
* * *
8611 TAAAATGAGTAATAAGGCTTTTGCAGGAATGGGTA-ACTATTAATA-GAA-TTTTCTTACCAATG
1 TAAAACGAGTAATAAGGCTTTTGAAGGAATGAG-AGACTA-TAA-ACGAACTTTTCTTACCAATG
* * *
8673 AATACCCTTTTCTTCATGTTTCT--AAGACAGGCATTCAATTATAGT-TAATTTTAATAAAAAAT
63 AATACCCTTTTCTTCATCTTTCTCAAAG-CAGACATTCAATTATAGTCT-ATTTTAACAAAAAAT
*
8735 AGT-AAAAAATTCAACTTAATATCAATTATAAGATTA
126 -GTAAAAAAATTCAACTTAAAATCAATTATAAGATTA
8771 TAAAACNNNNNNNNNNGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAACGAACTTTTCTT
1 TAAAAC----------GAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAACGAACTTTTCTT
* * * * * **
8836 GCCAGTGAATGCCTTTTTCTTCATCTTTCTCAAAGTAGACATTCAATTATAGTCTATTTTAACCC
56 ACCAATGAATACCCTTTTCTTCATCTTTCTCAAAGCAGACATTCAATTATAGTCTATTTTAACAA
8901 AAAATGTAAAAAAATTCAACTTAAAATCAATTA
121 AAAATGTAAAAAAATTCAACTTAAAATCAATTA
8934 NNNNNNNNNN
Statistics
Matches: 132, Mismatches: 14, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
160 5 0.04
168 1 0.01
169 7 0.05
170 63 0.48
171 52 0.39
172 4 0.03
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.34
Consensus pattern (161 bp):
TAAAACGAGTAATAAGGCTTTTGAAGGAATGAGAGACTATAAACGAACTTTTCTTACCAATGAAT
ACCCTTTTCTTCATCTTTCTCAAAGCAGACATTCAATTATAGTCTATTTTAACAAAAAATGTAAA
AAAATTCAACTTAAAATCAATTATAAGATTA
Found at i:11008 original size:171 final size:167
Alignment explanation
Indices: 10572--11022 Score: 428
Period size: 171 Copynumber: 2.6 Consensus size: 167
10562 TTTATAATCT
10572 CATAATTGATTTTAAGTTGAAGTTTTTTACATTTTT-GTTAAAACAAACTATAATTGAATGTCTA
1 CATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTAGTTAAAACAAACTATAATTGAATGTCTA
* * * * *
10636 CCTTGAGAAACGTAAAGCAAAAGGCATTCATTGGCCAA-AAAAGTCTATTAATAGTCACCCATTC
65 CC-TAAGAAACATGAAG-AAAAAGCATTCATTGG-CAAGAAAAGTCCATTAATAGTCACCCATTC
* *********
10700 TTTCAAAAGCCTTATTACTCGCTTAAATGGTTNNNNNNNNN
127 TTTCAAAAGCCTTATTACTCGCTTAAATAGTTTTGTAATTC
* * * *
10741 NATAATTGATTTTATGTTGAATTATTTTACATTTTTCA-TTAAAATAAACTATAATTGAATGCCT
1 CATAATTGATTTTAAGTTGAATT-TTTTACATTTTT-AGTTAAAACAAACTATAATTGAATGTCT
* * * **
10805 GA-CTTAGAAAATATGAAGAAAAAGCTATTCATTGAG-AAGAAAAGTCCATTTATAGTCAATC-T
64 -ACCTAAG-AAACATGAAGAAAAAGC-ATTCATTG-GCAAGAAAAGTCCATTAATAGTCACCCAT
* *
10867 TTTCTTCAAAAGCCTTGTTACTCGCTTTAAATAGTTTTGTAATTC
125 TCT-TTCAAAAGCCTTATTACTCGC-TTAAATAGTTTTGTAATTC
* * * * *
10912 CATAATTGATTTTAAGTTGAATTGTTTTATATTTTTAGTTAAAAGAGACAATAATTAAATGTCTA
1 CATAATTGATTTTAAGTTGAATT-TTTTACATTTTTAGTTAAAACAAACTATAATTGAATGTCTA
* *
10977 CCTCAAGAAACATGAAGAAAAATACATTCATTGGTAAGAAAAGTCC
65 CCT-AAGAAACATGAAGAAAAA-GCATTCATTGGCAAGAAAAGTCC
11023 NNNNNNNNNN
Statistics
Matches: 230, Mismatches: 37, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
168 2 0.01
169 45 0.20
170 81 0.35
171 99 0.43
172 3 0.01
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.36
Consensus pattern (167 bp):
CATAATTGATTTTAAGTTGAATTTTTTACATTTTTAGTTAAAACAAACTATAATTGAATGTCTAC
CTAAGAAACATGAAGAAAAAGCATTCATTGGCAAGAAAAGTCCATTAATAGTCACCCATTCTTTC
AAAAGCCTTATTACTCGCTTAAATAGTTTTGTAATTC
Found at i:11994 original size:171 final size:169
Alignment explanation
Indices: 11505--12056 Score: 489
Period size: 171 Copynumber: 3.2 Consensus size: 169
11495 NNNNNNNAAT
*** * * *
11505 TTTTTTACATTTTTCATTAAAATTGACTATAATTGAATGCCTACCTTG-GAAACCTGAATAAAAG
1 TTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTACCTTGAGAAACATGAACAAAAA
* * * * *
11569 GGCATTCATTGGTAAGAAAAGTCTATTAAAAGTCACCTATTCCTAT-AAAAGCCTTATTACTCCC
66 AGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATTCCT-TCAAAAGCCTTATTACTCGC
* * ***********
11633 TTTAAATGGTTTTATAATCTCATAATTCATNNNNNNNNNNTT
130 TTTAAAT-GATTTATAATCTCATAATTGAT-TTTATATTGAA
** * * * ** * * *
11675 TTTTTTACATTTTTTGTTAAAACAGATTATAAATGAATATCTACATGGAGAAACGTGAACAAAAA
1 TTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTACCTTGAGAAACATGAACAAAAA
* * * ** *
11740 AGCTTTCATTAGCAAGAAAAGTCTATTTATAGTCACTTATTTTTTCGAAAGCCTTATTACTCGCT
66 AGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCT
********* *
11805 TNNNNNNNNNNTATAATCTCATAATTGATTTTATGTTGAA
131 T-TAAATGATTTATAATCTCATAATTGATTTTATATTGAA
*
11845 CTTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTACCTTGAGAAACAT-AAGGAAA
1 -TTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTACCTTGAGAAACATGAA-CAAA
* * * *
11909 AATGCATTCATTGGCAAAAAAAGTCTGTTTATAGTTACCTATTCCTTCAAAAGCCTTATTACTCG
64 AAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCG
*
11974 CTTTAAATGATTTCATAATCTCTTAATTGATTTTATATTGAA
129 CTTTAAATGATTT-ATAATCTCATAATTGATTTTATATTGAA
* *
12016 TTGTTTTACATTTTTCATTAAAATAAACTGTAATTGAATGC
1 TT-TTTTACATTTTTCATTAAAACAAACTATAATTGAATGC
12057 TATTCATTGA
Statistics
Matches: 296, Mismatches: 79, Indels: 13
0.76 0.20 0.03
Matches are distributed among these distances:
170 44 0.15
171 252 0.85
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.38
Consensus pattern (169 bp):
TTTTTTACATTTTTCATTAAAACAAACTATAATTGAATGCCTACCTTGAGAAACATGAACAAAAA
AGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAAAAGCCTTATTACTCGCT
TTAAATGATTTATAATCTCATAATTGATTTTATATTGAA
Found at i:12577 original size:171 final size:162
Alignment explanation
Indices: 12312--12645 Score: 300
Period size: 171 Copynumber: 2.0 Consensus size: 162
12302 ATAATCTCAA
* * * *
12312 AATTGATTTTAAGTTTAATTTTTTTGAGATTTTTAGTCAAAACAGATTATAATTGAATGTGTATC
1 AATTGATTTTAAGTTAAATTCTTTTGACATTTTTAGTCAAAACAGATTATAATTGAATGTCTATC
* * * ** *
12377 TTGAGAAACGTGTAGAAAAAGGCATTCATTGGTAAA-AAAAGCCCATTTATAGTCACCTACTCAT
66 TCGAGAAACGTATAGAAAAAAGCATTCATT-AAAAAGAAAAGCCCATTTAGAGTCACCTACTC-T
* **
12441 -TCAAAAGCCTTATTATTTGCTTTAAATAGTTTT
129 GTCAAAAGCCTTATTACTCACTTTAAATAGTTTT
* *
12474 NNNNNNNNNNAATTGATTTTAAGTTAAATTCTTTT-ACATTTTTCA-TTAAAATAGATTATAATT
1 ----------AATTGATTTTAAGTTAAATTCTTTTGACATTTTT-AGTCAAAACAGATTATAATT
* * * *
12537 GAATGTCTGTCTCGGGGAACGTATA-AAAAAAGCAATTCATTAAAAAGAAAAGTCCATTTAGAGT
55 GAATGTCTATCTCGAGAAACGTATAGAAAAAAGC-ATTCATTAAAAAGAAAAGCCCATTTAGAGT
** * *
12601 CATGTATTCTGTCAAAAGCCTTATTACTCACTTTAAATGGTTTT
119 CACCTACTCTGTCAAAAGCCTTATTACTCACTTTAAATAGTTTT
12645 A
1 A
12646 TAATCNNNNN
Statistics
Matches: 135, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
161 1 0.01
170 11 0.08
171 99 0.73
172 24 0.18
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.38
Consensus pattern (162 bp):
AATTGATTTTAAGTTAAATTCTTTTGACATTTTTAGTCAAAACAGATTATAATTGAATGTCTATC
TCGAGAAACGTATAGAAAAAAGCATTCATTAAAAAGAAAAGCCCATTTAGAGTCACCTACTCTGT
CAAAAGCCTTATTACTCACTTTAAATAGTTTT
Found at i:12703 original size:171 final size:161
Alignment explanation
Indices: 12661--12993 Score: 242
Period size: 171 Copynumber: 2.0 Consensus size: 161
12651 NNNNNNNNNN
* * * ** *
12661 TTTTAAGTTGAATTTTTTTATATTTTTGGTCAAAACAGATTATAAATGAATGTCTACCTTAAGAA
1 TTTTAAGTTAAATTCTTTTACATTTTTCATCAAAACAGATTATAAATGAATGTCTACCTCAAGAA
*** * *
12726 ACATGAAGAAAAAAGAATTCATTGGTAAGAAAAGTCTATTTATAGTCAACCATTTCTTCAAAAGC
66 ACATGAAGAAAAAAGAATTCATTAAAAAGAAAAGTCCATTTAGAGTCAACCATTTCTTCAAAAGC
12791 CTTATTACAAGCTTTAAATGGTTTTATAATC
131 CTTATTACAAGCTTTAAATGGTTTTATAATC
* * ** * * *
12822 TCNNNNNNNNNNTTAAGTTGAATAT-TTTTACATTTTTGGTTAAAACAGATTATAACTGAATGTT
1 T----------TTTAAGTTAAAT-TCTTTTACATTTTTCATCAAAACAGATTATAAATGAATGTC
* * * ** ** *
12886 TACCTCAAGAAAGATGAAGAAAAAAGCATTCATTGATGAGAAAAGTCTGTTTATG-G-CCACCTA
55 TACCTCAAGAAACATGAAGAAAAAAGAATTCATTAAAAAGAAAAGTCCATTTA-GAGTCAACC-A
* * * *
12949 TTCCTTCAAAACCCTTATAACTCA-CTTTAAATGGTTTTATAATC
118 TTTCTTCAAAAGCCTTATTAC-AAGCTTTAAATGGTTTTATAATC
12993 T
1 T
12994 CATAATTGAT
Statistics
Matches: 141, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
161 1 0.01
170 4 0.03
171 134 0.95
172 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.36
Consensus pattern (161 bp):
TTTTAAGTTAAATTCTTTTACATTTTTCATCAAAACAGATTATAAATGAATGTCTACCTCAAGAA
ACATGAAGAAAAAAGAATTCATTAAAAAGAAAAGTCCATTTAGAGTCAACCATTTCTTCAAAAGC
CTTATTACAAGCTTTAAATGGTTTTATAATC
Done.