Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397961.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1268.0, 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: 11677
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.28
Warning! 2724 characters in sequence are not A, C, G, or T
Found at i:468 original size:171 final size:173
Alignment explanation
Indices: 236--592 Score: 422
Period size: 171 Copynumber: 2.1 Consensus size: 173
226 NNNNNNNNNN
* * * *
236 TCAAAATTGA-TTTTAATTTGAATTCTTTGTGCATTTTTAATTAAAACAGATTATAATTGAATGT
1 TCAAAATTGATTTTTAATTTGAATTCCTTCTACATTTTTAATAAAAACAGATTATAATTGAATGT
** * * * *
300 CTACCAT-AAGAAATGTGAAGGCAAAAGCATTCATTGATAAGAGAAGTCTATTTATAGTCACCCA
66 CTACC-TCAAGAAACATGAACGCAAAAGCAGTCATTGAGAAGAAAAGTCTATTTATAGTCACCCA
*
364 TTCCTTTAGAA-G-CCTTATTAC-CCATTGTAAATGGTTTTATAATC
130 TTCCTTTAAAAGGTCC-TATTACTCC-TT-TAAATGGTTTTATAATC
* *
408 TCAAAATTGATTTTTAA-TTGAATTCCTTCTATATTTTTAA-AAAAATAGATTATAATTGAATGT
1 TCAAAATTGATTTTTAATTTGAATTCCTTCTACATTTTTAATAAAAACAGATTATAATTGAATGT
* * * * * * *
471 CTTCCTCAAGAAACATGAACTCAAAGGCAGTCATTGGGAAGAAAAGTTTATTTATAGTCTCTCAT
66 CTACCTCAAGAAACATGAACGCAAAAGCAGTCATTGAGAAGAAAAGTCTATTTATAGTCACCCAT
*
536 TCCTTTAAAAGGTCCTATTACTTGCTTTAAATGGTTTTATAATC
131 TCCTTTAAAAGGTCCTATTAC-TCCTTTAAATGGTTTTATAATC
*
580 TCATAATTGATTT
1 TCAAAATTGATTT
593 CNNNNNNNNN
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
170 1 0.01
171 80 0.51
172 65 0.41
173 10 0.06
174 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (173 bp):
TCAAAATTGATTTTTAATTTGAATTCCTTCTACATTTTTAATAAAAACAGATTATAATTGAATGT
CTACCTCAAGAAACATGAACGCAAAAGCAGTCATTGAGAAGAAAAGTCTATTTATAGTCACCCAT
TCCTTTAAAAGGTCCTATTACTCCTTTAAATGGTTTTATAATC
Found at i:2319 original size:172 final size:171
Alignment explanation
Indices: 1920--2465 Score: 386
Period size: 172 Copynumber: 3.2 Consensus size: 171
1910 NNNNNNGAAT
* * * * *
1920 TTATAAAACCATTTAAAGCAAGTAATGAGACTTTCGAAGGCTTTAGTGACT-ATAAATGGACTTT
1 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCTTAAGTGA-TGATAAATGGACTCT
** ** * ** * * * * * * *
1984 TTGTATCAATGCATGGCTTTTGCTTCACGTTCCCCAAGGAAAACATTTAAATATAGCCTT-TTTT
65 TCATGCCAATGAATCCCTTTTGCTTCACCTTCCCTAAGGTAGACATTGAATTATA-ACTTGTTTT
* * * *
2048 AACCAAAATAT--AAAACAATTCAACTTAAAGTCAATTATAATA
129 AACCAAAA-ATGCAAAACAATTCAACTAAAAATCAATTATGAGA
** ********** * ** ** * *
2090 TTATAAAACCATTTAAAGTGAGTAATANNNNNNNNNNAGGAATGGGTGGCT-ATAAATGGACTTT
1 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCTTAAGT-GATGATAAATGGACTCT
* ** *** * * *
2154 TCTTGCCAATGAATCCCTATTT-CTTCATGTTTTTTGAGGTAGGCATTTAATTATAA-TCTGTTT
65 TCATGCCAATGAATCCCT-TTTGCTTCACCTTCCCTAAGGTAGACATTGAATTATAACT-TGTTT
* * * *
2217 TGACTAAAAATGCAAAACAAATTCAACTAAAAATTAATTATGAGT
128 TAACCAAAAATGCAAAAC-AATTCAACTAAAAATCAATTATGAGA
*
2262 TTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAAGCTTAAGTGATGATAAATGGACTCTT
1 TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCTTAAGTGATGATAAATGGACTCTT
* ** *
2327 CATGCCAATGGATGGCTTTTGCTTCACCTTCCCTAAGGTAGACATTGAATTATAACTTTTTTTAA
66 CATGCCAATGAATCCCTTTTGCTTCACCTTCCCTAAGGTAGACATTGAATTATAACTTGTTTTAA
* ** *
2392 CCAAAAATGTAAAACAATTCAACTTGAAGTCAATTATGAGA
131 CCAAAAATGCAAAACAATTCAACTAAAAATCAATTATGAGA
* *
2433 TTATTAAACCATTTAAAGCGAGTAATAAGGCTT
1 TTATAAAACCATTTAAAGCAAGTAATAAGGCTT
2466 CTAAAGGAAT
Statistics
Matches: 280, Mismatches: 86, Indels: 19
0.73 0.22 0.05
Matches are distributed among these distances:
168 1 0.00
169 3 0.01
170 88 0.31
171 65 0.23
172 122 0.44
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (171 bp):
TTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGCTTAAGTGATGATAAATGGACTCTT
CATGCCAATGAATCCCTTTTGCTTCACCTTCCCTAAGGTAGACATTGAATTATAACTTGTTTTAA
CCAAAAATGCAAAACAATTCAACTAAAAATCAATTATGAGA
Found at i:2515 original size:171 final size:171
Alignment explanation
Indices: 2190--2521 Score: 373
Period size: 171 Copynumber: 1.9 Consensus size: 171
2180 ATGTTTTTTG
* * * * *
2190 AGGTAGGCATTTAATTATAATCTGTTTTGACTAAAAATGCAAAACAAATTCAACTAAAAATTAAT
1 AGGTAGACATTGAATTATAATCTGTTTTAACCAAAAATGCAAAACAAATTCAACTAAAAATCAAT
* * ** * ** *
2255 TATGAGTTTATAAAACCATTTAAAGTAAGTAATAAGGCTTTCGAAAGCTTAAGTGATGATAAATG
66 TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATAAGAGACCATAAATA
*
2320 GACTCTTCATGCCAATGGATGGCTTTTGCTTCACCTTCCCTA
131 GACTCTTCATGCCAATGAATGGCTTTT-CTTCACCTTCCCTA
* * ** *
2362 AGGTAGACATTGAATTATAA-CTTTTTTTAACCAAAAATGTAAAAC-AATTCAACTTGAAGTCAA
1 AGGTAGACATTGAATTATAATC-TGTTTTAACCAAAAATGCAAAACAAATTCAACTAAAAATCAA
* * * *
2425 TTATGAGATTATTAAACCATTTAAAGCGAGTAATAAGGC-TTCTAAAGGAATGAGAGACCATAAA
65 TTATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAA-GAATAAGAGACCATAAA
* ***
2489 TAGACTTTTCATTTTAATGAATGGCTTTTCTTC
129 TAGACTCTTCATGCCAATGAATGGCTTTTCTTC
2522 TACNNNNNNN
Statistics
Matches: 131, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
170 10 0.08
171 84 0.64
172 37 0.28
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (171 bp):
AGGTAGACATTGAATTATAATCTGTTTTAACCAAAAATGCAAAACAAATTCAACTAAAAATCAAT
TATGAGATTATAAAACCATTTAAAGCAAGTAATAAGGCTTTCGAAAGAATAAGAGACCATAAATA
GACTCTTCATGCCAATGAATGGCTTTTCTTCACCTTCCCTA
Found at i:5379 original size:171 final size:170
Alignment explanation
Indices: 4879--5855 Score: 771
Period size: 171 Copynumber: 5.7 Consensus size: 170
4869 NNNNNNNTTC
* * **
4879 CTTCAAAAGCCTTATTACTCACTTTAAAT-GATTTTATAATCTCATAATT-AGCTACAAGTTGAA
1 CTTCAAAAGCCTTATTACTCACTTTAAATAG-TTTTATAATCTCAAAATTGA-TTTTAAGTTGAA
* * * ** * *** *
4942 TTGTTTTACATTTTTGGTTAAAAAAGGCTATAATTAAATGTCTACCTTGGGCAACGTGAAGTAAA
64 TTTTTTTACATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAG-AAA
* * * * * *
5007 AA-CCATCCATTGGTACGAAAAGTCTATTTATAGTCA-CTAAAG
128 AAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCT-AAT
** * ** * * * * **
5049 CTTTCGGAAGCCTTACTACTTGCTTTAAATAGTTTTATAAACTCATAATTAATTTTTAGTTGAGG
1 C-TTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAAT
* * * *
5114 TTTTTTACATTTTTCGTT-AAA-A-A--AGAATTAAATGTCTACCTCAAGAAACGTGAAGAAAAT
65 TTTTTTACATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAA
* * * * *
5174 GGCATTGATTGACAAGAAAAGCCCATTTATAGTCACCTATT
130 GACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTAAT
* * *
5215 CGTTCATAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTGAAAATTGGTTTTAAGTTGAAT
1 C-TTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAAT
** * *
5280 TTTTTTGTATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAGCGTAAAGAAAAA
65 TTTTTTACATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAA
* * *
5345 GACATTTATTGGTAAGAAAAGTCCATTCATAGTCACCTATAT
130 GACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTA-AT
* * ********* * *
5387 CTTTAGAAGCCTTATTACTCA-TNNNNNNNNNNTTTATAATCTCATAATTGATTTT-TGATTGAA
1 CTTCAAAAGCCTTATTACTCACT-TTAAATAGTTTTATAATCTCAAAATTGATTTTAAG-TTGAA
* * * * * *
5450 TGTTTTTATATTTTTTGTTAGAATAGATTATAATTGAATGTCTACCT-AGGAAACGTGAAGAAAA
64 TTTTTTTACATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAG-AAA
** ********** *
5514 AAGA-GGTCATTGGCAAGAAAAGNNNNNNNNNNGTCACCCAAT
128 AAGACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTAAT
* * * * *
5556 CCTTCAAAAGCCTTATTACTCACTATAAATGGTTTTACAATCTCAAAACTGGTTTTAAGTT-AAT
1 -CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAA-
*
5620 TTTTTTTTGCATTTTTAGTT-AAAGAAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAGAA
64 -TTTTTTTACATTTTTAGTTAAAAG-AGATTATAATTGAATGTCTACCTCAAGAAACGTGAAGAA
* * *
5684 AAATG-CAATCATTGGCAAGAAAAGTCCATTTATAGTCACCCACAA
127 AAA-GACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTA-AT
* * * * *
5729 CTTCAAAAGCCTTATTACTAACTTTAAATAGTTCTATGATCTCAACATTGATTTTAAGTTCAATT
1 CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATT
* * * * * *
5794 GTTTTTACATTTCTAGTTAAAACATATCATAATTGAATGTCTACCTTAAGAAACATGAAGAA
66 -TTTTTACATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAGAA
5856 NNNNNNNNNN
Statistics
Matches: 630, Mismatches: 150, Indels: 52
0.76 0.18 0.06
Matches are distributed among these distances:
165 4 0.01
166 120 0.19
167 5 0.01
168 1 0.00
169 6 0.01
170 79 0.13
171 267 0.42
172 142 0.23
173 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.36
Consensus pattern (170 bp):
CTTCAAAAGCCTTATTACTCACTTTAAATAGTTTTATAATCTCAAAATTGATTTTAAGTTGAATT
TTTTTACATTTTTAGTTAAAAGAGATTATAATTGAATGTCTACCTCAAGAAACGTGAAGAAAAAG
ACATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTAAT
Found at i:7231 original size:172 final size:169
Alignment explanation
Indices: 6255--8776 Score: 2116
Period size: 171 Copynumber: 14.7 Consensus size: 169
6245 NNNNNNNNNN
* * * *
6255 AATCTCATAATTGATTTCAAGTTGAATTTTTTTTACATTTTTTGTTAAAACAGATTATAATTTAA
1 AATCTCAAAATTGATTTTAAGTTGAA-TTTTTTTACA-TTTTTATTAAAACAGATTATAATTAAA
* * * * * ** * * *
6320 TGTCTACCTCGAGAAACGTAAAGAAAAAAGCATTTATTAGTTAGAGAAGTTCATTTATAGTCACC
64 TGTCTACCTTGAGAAACGTGAAG-AAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
* * * * * *
6385 CTTTTCTTTAAAAGTCTTATTAGTCACTTTAAATAGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * ** *
6427 AATCT-AAAATTAATTTTAAATTGAATTTCTTGCACATTTTCTGTTAAAACAGATTATAATTAAA
1 AATCTCAAAATTGATTTTAAGTTGAATTT-TTTTACATTTT-TATTAAAACAGATTATAATTAAA
* * ** * * * *
6491 TCTCTACCTCGAGAAATATGAAGGAAAGGTATTCATTGGTAAG-AAAGTCTATTTATAGTCA-TC
64 TGTCTACCTTGAGAAACGTGAAGAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACTC
* * * * *
6554 TATTCTTTCAAAAGTCATATTACTTAATTTAAATGGTTTTAT
129 -ATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * ** * * * *
6596 AATCTCATAATTGATTTCAGGTTGAATTTTTTTGTATTTTTGGTT-AGACAAGGTTATAATTTAA
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTT-ATTAAAAC-AGATTATAATTAAA
* * * * ********** *
6660 TGTCTACCTTGGGAAACATGAAGAAAAAGGTATTCATTGCCAAGAAAAGNNNNNNNNNNGTCACC
64 TGTCTACCTTGAGAAACGTGAAG-AAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
*
6725 CATTCCTTCAAAAGCCTTATTACTCACTTTAAAGGGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * *
6767 AATCCCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTCAGTTAAAACAGATAATAATTGAAT
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTA-TTAAAACAGATTATAATTAAAT
*** * * * * * * * *
6832 GTCTACCACAAGAAACATATAAGAAAAGCCATTCATTTAG-AAGAAAAGTCTATTTATGGTCTCC
65 GTCTACCTTGAGAAACGT-GAAGAAAAGGCATTCA-TTGGCAAGAAAAGTCCATTTATAGTCACT
* * * * **
6896 CATTCCTTTAGAAGCCTTTTTACTCCCTTTAAATGGTTCAAT
128 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * * * * * *
6938 AATGTCATAATTGACTTCAAGTTGAATTATTTTACATTTTTGGTTAAAA-AAAGTTATAATTCAA
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTT-ATTAAAACAGA-TTATAATTAAA
* * * * * * *
7002 TGTCTACCTTGGGGAAGGTGAAGCAAAAGCCATCCATTGGCACGAAAAGTCCATTTATCGTCACT
64 TGTCTACCTTGAGAAACGTGAAG-AAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
* ** * *
7067 TAAGCCTTCGAAAGCCTTATTACTTACTTTAAATGGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * * ** ** *
7109 AAACTTATAATTAATTTTTGGTTGAATTTGTTTTGTATTTTTATTCAAAACAGATTATAGTTAAA
1 AATCTCAAAATTGATTTTAAGTTGAATTT-TTTTACATTTTTATT-AAAACAGATTATAATTAAA
* * * *
7174 TGTCTACCTTAAGAAACGTGAAGAACCAGGCATTCATTAGCAAGAAAAGTCCATTTATAGTCACC
64 TGTCTACCTTGAGAAACGTGAAGAA-AAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
*
7239 CATTCCTTCAAAAGTCTTATTACTCACTTTAAATGGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * * * * * * ** *
7281 AATATTATAATTGACTTCAAGTTGAATTGTTTTATATTTTGT-TTAAAAAAGGCTATATTTAAAT
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTT-TATTAAAACAGATTATAATTAAAT
* * * * * *
7345 GTTTACCTTGGGGAACGTGAAGCAAAAGCCATGCATTGGTACA-AAAAGTCCATTTATAGTCACT
65 GTCTACCTTGAGAAACGTGAAG-AAAAGGCATTCATTGGCA-AGAAAAGTCCATTTATAGTCACT
* ** * * **
7409 AAAGCCTTCGAAAGCCTCATTACTTGCTTTAAATGGTTTTAT
128 CATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * * * * *
7451 AAAT-TCATAATTAATTTTTAGTTGAATTGTTTTACATTTTTGGTCAAAACAGATTATAATTTAA
1 -AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTT-ATTAAAACAGATTATAATTAAA
* ** *
7515 TGTCTACCTTGAGAAACGTAAAGAAAAAGGCATTCATTGATAAGAAAAGTCCATTTATAGTCAGT
64 TGTCTACCTTGAGAAACGTGAAG-AAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
* * *
7580 CATTGCTTCAAAAGCTTTATTAC-CAACTTTAAATGATTTTAT
128 CATTCCTTCAAAAGCCTTATTACTC-ACTTTAAATGGTTTTAT
* * * * * * * * *
7622 TATCTCAAAATTAATTTTAAATTGAATTCCTTGTGCATTTTCAATTAAAACGGATTATAATTGAA
1 AATCTCAAAATTGATTTTAAGTTGAATT-TTTTTACATTTT-TATTAAAACAGATTATAATTAAA
* * * * * *
7687 TGTCTACCTCGAGAAACGTGAAAAAAAAAAGCATTTATTGTCAAAAAAAGTCCATTTATAGTCAC
64 TGTCTACCTTGAGAAACGTG--AAGAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCAC
* * * *
7752 TCATTCCTTCAAAAACCTTATCAGTCTCTTTAAATGGTTTTAT
127 TCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * ** * * * *
7795 AATCTCACAATTGATTTTAAGCTAAATAATTTTATATTTTTCATTAAAACAGATTGTTATTGAAT
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTT-ATTAAAACAGATTATAATTAAAT
* * * * *
7860 G-CTTACCTAG-GAAAACTTGTAA-AGAAA-GCTAGTCATTTGAAAGAAAAGTCCATTTATAGTC
65 GTC-TACCTTGAG-AAACGTG-AAGA-AAAGGC-ATTCATTGGCAAGAAAAGTCCATTTATAGTC
* * * * *
7921 TCTCATTCTTTCAAAAGCCTTATTACTTATTTTAAACGGTTTTAT
125 ACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * * *
7966 AATCTCATAATTGATTTTGAGTTGAATATTTTTACATTTTTTGTTAAAACATATTATAA-TAGAA
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACA-TTTTTATTAAAACAGATTATAATTA-AA
8030 TG-CTTACCTTGAGAAACATGTAGAA-AAAAGG-ATTCATTGGCAAGAAAAGTCCATTTATAGTC
64 TGTC-TACCTTGAGAAAC--GT-GAAGAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTC
* * * * *
8092 ACCCATTCTTTCAAAAGTCTTATTACTCGCTTTAAAAGGTTTTAT
125 ACTCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
** * * * *
8137 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACAATTTTCGTTAAAATAGACTAGAATTGAAT
1 AATCTCAAAATTGATTTTAAGTTGAATTTTTTTAC-ATTTTTATTAAAACAGATTATAATTAAAT
* * * ** * *
8202 GTCTACCATGAGAAATGTGAAGACAAAAGCATTCATTGATAAGAGAAGTCCATTTATAGTCACCC
65 GTCTACCTTGAGAAACGTGAAGA-AAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACTC
* *
8267 ATTCCTTTAAAATCCTTATTACTCACTTTAAATGGTTTTAT
129 ATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
** * ** *
8308 AATCTCAAAATTGATTTTAAAATGAATTCTTTGTACATTTTCGGTTAAAATAGATTATAATTAAA
1 AATCTCAAAATTGATTTTAAGTTGAATT-TTTTTACATTTT-TATTAAAACAGATTATAATTAAA
* ** * *
8373 TATCTACCTCAAGAAATGTGAAGGAAAAGGCATTCATTGACAAG-AAAGTCCATTTATAGTCACG
64 TGTCTACCTTGAGAAACGTGAA-GAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCAC-
* **
8437 T-AATCCTTCAAAAGCCTTATTACTCACTTTAAATTATTTTAT
127 TCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * ** *
8479 AATCTCAAAATTGATTTTAAATTGTATTCCTTGCACATTTTTAATTAAAACAGATTATAATCAAA
1 AATCTCAAAATTGATTTTAAGTTGAATT-TTTTTACATTTTT-ATTAAAACAGATTATAATTAAA
* * * *
8544 TGTCTACCTCGAGAAACGTGAAAGAAAAAGCATTCATTGGCAAAAAAAGTCTATTTATAGTCAGC
64 TGTCTACCTTGAGAAACGTG-AAGAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCA-C
* * * *
8609 -CATTCATTCAAAAGTCTTATTAATCATTTTAAATGGTTTTAT
127 TCATTCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
* * * **
8651 AATCTCAAAATTGATTTTAAATTGTATTCCTTGCACATTTTTAGTTAAAACAGATTATAATTAAA
1 AATCTCAAAATTGATTTTAAGTTGAATT-TTTTTACATTTTTA-TTAAAACAGATTATAATTAAA
* * *
8716 TGTCTAACTTGAGAAATGTGAAGGAAAAGGCATTCATTGGTAAGAAAAGTCCATTTATAGT
64 TGTCTACCTTGAGAAACGTGAA-GAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGT
8777 NNNNNNNNNN
Statistics
Matches: 1895, Mismatches: 391, Indels: 128
0.79 0.16 0.05
Matches are distributed among these distances:
168 8 0.00
169 97 0.05
170 204 0.11
171 1013 0.53
172 470 0.25
173 99 0.05
174 4 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (169 bp):
AATCTCAAAATTGATTTTAAGTTGAATTTTTTTACATTTTTATTAAAACAGATTATAATTAAATG
TCTACCTTGAGAAACGTGAAGAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACTCAT
TCCTTCAAAAGCCTTATTACTCACTTTAAATGGTTTTAT
Found at i:7734 original size:19 final size:20
Alignment explanation
Indices: 7710--7750 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
7700 AAACGTGAAA
*
7710 AAAAAAAG-CATTTATTGTC
1 AAAAAAAGCCATTTATAGTC
7729 AAAAAAAGTCCATTTATAGTC
1 AAAAAAAG-CCATTTATAGTC
7750 A
1 A
7751 CTCATTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
21 11 0.58
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAAAAAGCCATTTATAGTC
Found at i:10477 original size:172 final size:169
Alignment explanation
Indices: 10081--10647 Score: 490
Period size: 172 Copynumber: 3.3 Consensus size: 169
10071 NNNNNNNNNN
* * * *
10081 TAAAACCATTTAAAGTGAGTAATACGGCTTTTGAAGGAATAGGTGACTATAAATAGACTTTTTTA
1 TAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTA
* * * * * *
10146 CCAATGAATGCCTTTTCTTTCACATTTCTTGAGGTAGATATTTAATTATAATATATTTTAACAGA
66 TCAATGAATGCTTTTTC-TTCACATTTC-TCAGGTAGACATTTAATTATAATATATTTTAATAAA
** *
10211 AAATGCACAAGGAATTCAATTTAAAATCAATTTTGAGATTA
129 AAATGCACAAAAAATTCAAATTAAAATCAATTTTGAGATTA
** * * *
10252 TAAAAGTATTTAAAATGAGTAATAAGGCTTTTAAAGGAATGGGTGATTATAAATGGACTTCTCTT
1 TAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTT-TTTT
* * * *
10317 GTCAATGAATGCTTTTGTCTTCACATTTCTCATGGTAGACATTCAATTATAATTTGTTTTAATAA
65 ATCAATGAATGCTTTT-TCTTCACATTTCTCA-GGTAGACATTTAATTATAATATATTTTAATAA
10382 AAAATGCACAAAAAATTCAAATTAAAATCAATTTTGAGATTA
128 AAAATGCACAAAAAATTCAAATTAAAATCAATTTTGAGATTA
* * ********** * *
10424 TGAAACCATTTAAAGTGANNNNNNNNNNTTTTGAAGTAATGGGAGACTATAAATGGACTTTTTT-
1 TAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTA
* ** * * * *
10488 TCTTAATGAATGACTTTTTCTACATGTTTCCCAAGGCAGACATTTAATTATAATCTATTTTAATG
66 TC--AATGAATG-CTTTTTCTTCACATTTCTC-AGGTAGACATTTAATTATAATATATTTTAATA
* ********** *
10553 AAAAATGTA-AAAAANNNNNNNNNNAAATCAATTTTGAAATTA
127 AAAAATGCACAAAAAATTCAAATTAAAATCAATTTTGAGATTA
*** * * *
10595 TAAAACCATTTAAAGCAAATAATAAGGTTTTTGAAAGAATGGGTGACTATAAA
1 TAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAA
10648 NNNNNNNNNN
Statistics
Matches: 311, Mismatches: 78, Indels: 14
0.77 0.19 0.03
Matches are distributed among these distances:
170 2 0.01
171 116 0.37
172 185 0.59
173 8 0.03
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.35
Consensus pattern (169 bp):
TAAAACCATTTAAAATGAGTAATAAGGCTTTTGAAGGAATGGGTGACTATAAATGGACTTTTTTA
TCAATGAATGCTTTTTCTTCACATTTCTCAGGTAGACATTTAATTATAATATATTTTAATAAAAA
ATGCACAAAAAATTCAAATTAAAATCAATTTTGAGATTA
Found at i:11674 original size:171 final size:168
Alignment explanation
Indices: 11182--11677 Score: 464
Period size: 171 Copynumber: 2.9 Consensus size: 168
11172 NNNNNNNNNN
* * ** *
11182 ATAAGGCTTTTGAA-GAAATGGGTGACTATAAATAGACTTTTCTTGGCAATGAATACCGTTTTCT
1 ATAAGGCTTTTGAAGGAAA-AGGTGACTATAAATGGACTTTTCTTACCAATAAAT-CCGTTTTCT
* ** * *
11246 TCATATTTCCCAAGGTAGACATTCAATTATAGCCTTG-TCTAACCAATAAA-GTAAAAAAATTCA
64 TCACATTTCTTAAGGTAGACATTCAATTATAG--TTGTTTTAA-CAAAAAATGT-AAAAAATTCA
* * * * *
11309 ACCTGAGATCAATTATGAGATTATAAAACTATTTAAATTGAGTA
125 ACTTGAAATCAATTATGAGATTATAAAACCAATTAAAGTGAGTA
* * * *********
11353 ATAGGGCTTTTGAAGGAATAGATGACTATAAATGGACTTTTCTTACCAATNNNNNNNNNNTTCTT
1 ATAAGGCTTTTGAAGGAAAAGGTGACTATAAATGGACTTTTCTTACCAAT-AAATCCGTTTTCTT
* * * ** *
11418 CACATTTCTTAAGGTAGACATTCAATTATAATCTGTTTTAATAGAAAATGTGCAAGGAATTCAAT
65 CACATTTCTTAAGGTAGACATTCAATTATAGT-TGTTTTAACAAAAAATGT--AAAAAATTCAAC
*
11483 TTAAAATCAAGTT-T-AGATTATAAAACCAATTAAAGTGAGTA
127 TTGAAATCAA-TTATGAGATTATAAAACCAATTAAAGTGAGTA
* * * *
11524 ATAAGGCTTTTAAAGGAAAAGGTGACTATAAATGGACTTCTCTTACCAATAAATGCTTTTCTCTT
1 ATAAGGCTTTTGAAGGAAAAGGTGACTATAAATGGACTTTTCTTACCAATAAATCCGTTT-TCTT
*
11589 CA-AGTTTCTTAAGGTAGATATTCAATTATAGTATGTTTTAACAAAAAATGTAAAAATATTCAAC
65 CACA-TTTCTTAAGGTAGACATTCAATTATAGT-TGTTTTAACAAAAAATGTAAAAA-ATTCAAC
11653 TTGAAATCAATTATGAGATTATAAA
127 TTGAAATCAATTATGAGATTATAAA
Statistics
Matches: 256, Mismatches: 57, Indels: 24
0.76 0.17 0.07
Matches are distributed among these distances:
169 6 0.02
170 24 0.09
171 204 0.80
172 20 0.08
173 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.34
Consensus pattern (168 bp):
ATAAGGCTTTTGAAGGAAAAGGTGACTATAAATGGACTTTTCTTACCAATAAATCCGTTTTCTTC
ACATTTCTTAAGGTAGACATTCAATTATAGTTGTTTTAACAAAAAATGTAAAAAATTCAACTTGA
AATCAATTATGAGATTATAAAACCAATTAAAGTGAGTA
Done.