Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018398786.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_207.0, 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: 13234
ACGTcount: A:0.24, C:0.09, G:0.08, T:0.24
Warning! 4679 characters in sequence are not A, C, G, or T
Found at i:342 original size:172 final size:171
Alignment explanation
Indices: 15--458 Score: 421
Period size: 171 Copynumber: 2.6 Consensus size: 171
5 ACATTATTGG
* * * * * * * * *
15 TTAAAATAGGCTATAATTGAATATCTACTTTAAGAAACATAAAGAAAGAGGCATTTATTGACAAG
1 TTAAAACAGACTATAATTGAATATCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGAGAAG
* * * * * *********
80 AAAAGTCCATTTATAGTCACCCATT-CTTCAAAAGCCTTATTACTTGC-TTNNNNNNNNNNTATA
66 AAAAGTCTATTTATAATCACACATTCCTTCAAAAGCCATATTACTAGCGTT-AAATTATTTTATA
** * *
143 AACTCATAATTGATTTTAAGCTGAATTTGTTTTCCATTTT-TGG
130 GTCTCATAATTGATTTTAAGCTGAATTT-TTTTACATTTTCT-A
* * ** * *
186 TTAAAACAGACTGTAATTG-AT-TGCTTGCCTTGAGAAACATGTGGAACAAGCCATTCATTGAGA
1 TTAAAACAGACTATAATTGAATAT-C-TACCTTGAGAAACATGAAGAAAAAGACATTCATTGAGA
* * *
249 GGAAAAGTTTATTTATAATCACTCATTCCTTCAAAAGCCATATTACTAGCGTTAAATTATTTTAT
64 AGAAAAGTCTATTTATAATCACACATTCCTTCAAAAGCCATATTACTAGCGTTAAATTATTTTAT
*
314 AGTCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTCTA
129 AGTCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTCTA
* * * * *
357 TTAAAGCAGGCTATAATTGAATATCTACCTTGAGAAACATGAAGAAAAAGATATTCATTTATAAG
1 TTAAAACAGACTATAATTGAATATCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGAGAAG
*
422 AAAAGTCTATTTATAGTCACACATTCCTTCAAAAGCC
66 AAAAGTCTATTTATAATCACACATTCCTTCAAAAGCC
459 TTATNNNNNN
Statistics
Matches: 216, Mismatches: 50, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
169 1 0.00
170 3 0.01
171 156 0.72
172 53 0.25
173 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.35
Consensus pattern (171 bp):
TTAAAACAGACTATAATTGAATATCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGAGAAG
AAAAGTCTATTTATAATCACACATTCCTTCAAAAGCCATATTACTAGCGTTAAATTATTTTATAG
TCTCATAATTGATTTTAAGCTGAATTTTTTTACATTTTCTA
Found at i:1441 original size:169 final size:170
Alignment explanation
Indices: 1145--1458 Score: 416
Period size: 169 Copynumber: 1.9 Consensus size: 170
1135 NNNNTTTGTA
*
1145 TAAAACAGACTATAATTGAATGTCTACTTGGAAAAACAAGAAGAAAAAAGTATTCATTGACAAGA
1 TAAAACAGACTATAATTGAATGTCTACTTGGAAAAACAAGAAGAAAAAAGCATTCATTGACAAGA
* * * *
1210 AAAATCCATTCATAGCCACCCATTCCTTGAAAAGCCTTATTACTCGCTTTAAATTGTTTTATAGT
66 AAAATCCATTCATAGCCACCCACTCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTTATAAT
*
1275 GTCATAATTGATTTTAAGTTAATTGTTTTATATTATTGGT
131 CTCATAATTGATTTTAAGTTAATTGTTTTATATTATTGGT
* * * * * * **
1315 TAAAATAGGCTATAATTGAATGTCTATCTT-GATAACCATGAAGAAAAAGGCATTCA-TGGTAAG
1 TAAAACAGACTATAATTGAATGTCTA-CTTGGAAAAACAAGAAGAAAAAAGCATTCATTGACAAG
* * * * * * *
1378 AAAAGTCTATTTATAGTCACCCACTCTTTCAAAAGCTTTATTACTTGCTTTAAATTATTTTATAA
65 AAAAATCCATTCATAGCCACCCACTCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTTATAA
1443 TCTCATAATTGATTTT
130 TCTCATAATTGATTTT
1459 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
169 74 0.61
170 45 0.37
171 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (170 bp):
TAAAACAGACTATAATTGAATGTCTACTTGGAAAAACAAGAAGAAAAAAGCATTCATTGACAAGA
AAAATCCATTCATAGCCACCCACTCCTTCAAAAGCCTTATTACTCGCTTTAAATTATTTTATAAT
CTCATAATTGATTTTAAGTTAATTGTTTTATATTATTGGT
Found at i:2170 original size:170 final size:168
Alignment explanation
Indices: 1709--2242 Score: 498
Period size: 171 Copynumber: 3.1 Consensus size: 168
1699 NNNNNNNNNN
** * *
1709 TTGAATGTCTACCTCGAGAAATATAAAGAAAAAGACATTCATTTGTAAGAAAAGTCTATTTATAG
1 TTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGACATTC-TTTG-AAAAAAAGTCTATTTATAG
* * * * * * * * **
1774 TCATCTAATATTTCAAAAGCCCTGTTACTCACTTTAAATTTTTTTATAATCTCATAATTGATTTT
64 TCACCCATTTTTTCAAAAGTCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTT
* *
1839 AAGTTGAATTGTTTTTACTGTTTTTGTTAAAACAGACTATAA
129 AAGTTGAATT-TTTTTAC-ATTTTAGTTAAAACAGACTATAA
* *** * * ** * *
1881 TTGAATATCTGTGTTGAGAAATGTGTGGAACAAG-CTATTCATTGAGAAAAAAGTCTATTTATAG
1 TTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGAC-ATTCTTTGA-AAAAAAGTCTATTTATAG
* ** * * ** ********** *
1945 TGACCCATTTCCTGAAAAGTTTTATTACTCGGGTTANNNNNNNNNNTAGTCTCATAATTGATTTT
64 TCACCCATTTTTTCAAAAGTCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTT
* * *
2010 AAGTTAAATTTTTTTACATTTTGGTTAAACCA-AGCTATAA
129 AAGTTGAATTTTTTTACATTTTAGTTAAAACAGA-CTATAA
*
2050 TTGAATGTCTACCTCAAGAAACGTGAAGAAAAAGACATTCTTTTTGAAAAAAAGTCTATTTATAG
1 TTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGACATTC--TTTGAAAAAAAGTCTATTTATAG
*
2115 TCACCCATTTTTTCAAAAGTCTTATTATTCGCTTTAAATAGTTTTATAATCTCATAATTGAGTTT
64 TCACCCATTTTTTCAAAAGTCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGA-TTT
*
2180 T-AGTTGAATTTTTTTGCATTTTTAGTTAAAACAGACTATAA
128 TAAGTTGAATTTTTTTACA-TTTTAGTTAAAACAGACTATAA
2221 TTGAATGTCTACCTCGAGAAAC
1 TTGAATGTCTACCTCGAGAAAC
2243 TTAAAGANNN
Statistics
Matches: 276, Mismatches: 77, Indels: 19
0.74 0.21 0.05
Matches are distributed among these distances:
168 1 0.00
169 46 0.17
170 84 0.30
171 116 0.42
172 29 0.11
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.39
Consensus pattern (168 bp):
TTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGACATTCTTTGAAAAAAAGTCTATTTATAGTC
ACCCATTTTTTCAAAAGTCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAA
GTTGAATTTTTTTACATTTTAGTTAAAACAGACTATAA
Found at i:2637 original size:22 final size:22
Alignment explanation
Indices: 2610--2657 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 22
2600 TCCTTGAAAA
2610 GTTTTAT-TGCTCATTTTAAATG
1 GTTTTATAT-CTCATTTTAAATG
2632 GTTTTATAATCTCATTTTAAATG
1 GTTTTAT-ATCTCATTTTAAATG
2655 GTT
1 GTT
2658 GAATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.29
23 16 0.67
24 1 0.04
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.54
Consensus pattern (22 bp):
GTTTTATATCTCATTTTAAATG
Found at i:4848 original size:171 final size:171
Alignment explanation
Indices: 4543--4857 Score: 418
Period size: 171 Copynumber: 1.8 Consensus size: 171
4533 NNNNNNNNNN
** *
4543 TTTCTCAAGGCAGACATTCAATTATAGCCTGTTTTAATAAAAATAGTAAAAAAATTCAACTTAAA
1 TTTCTCAAGGCAGACATTCAATTATAGCCTAATTTAATAAAAATAGCAAAAAAATTCAACTTAAA
* * ** * * *
4608 CTCAATTATAAGATTATTAAACCATTTAAAGCGAGTAATAAGACTTTTGAAGAAATGAGTCACTA
66 ATCAATTATAAGACTACAAAACAAGTTAAAGCGAGTAATAAGACTTTTAAAGAAATGAGTCACTA
*
4673 TAAATATACTTTTCAAATAAATGAATATCTTTTTCTTCACG
131 TAAATAGACTTTTCAAATAAATGAATATCTTTTTCTTCACG
* * *
4714 TTTCTTAAGGTAGACATTCAATTATAGTCTAATTTAATCAAAAATA-CAAAAAAATTCAACTTAA
1 TTTCTCAAGGCAGACATTCAATTATAGCCTAATTTAAT-AAAAATAGCAAAAAAATTCAACTTAA
* * * * *
4778 AATCAATTATAAGACTACAAAATAAGTTAACGCGAGTAATAAGGCTTTTAAA-AGAATGAGTGAT
65 AATCAATTATAAGACTACAAAACAAGTTAAAGCGAGTAATAAGACTTTTAAAGA-AATGAGTCAC
*
4842 TATAAATGGACTTTTC
129 TATAAATAGACTTTTC
4858 TTCTTGATGA
Statistics
Matches: 122, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
170 1 0.01
171 114 0.93
172 7 0.06
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (171 bp):
TTTCTCAAGGCAGACATTCAATTATAGCCTAATTTAATAAAAATAGCAAAAAAATTCAACTTAAA
ATCAATTATAAGACTACAAAACAAGTTAAAGCGAGTAATAAGACTTTTAAAGAAATGAGTCACTA
TAAATAGACTTTTCAAATAAATGAATATCTTTTTCTTCACG
Found at i:5160 original size:171 final size:171
Alignment explanation
Indices: 4983--5300 Score: 406
Period size: 171 Copynumber: 1.9 Consensus size: 171
4973 NNNTAAAGTG
* *
4983 AGTAATAAGGCTTTTGAAAGAATGGGTCACTATAAATAGACTTTTCTAAC-AAATGAAT-ACTTT
1 AGTAATAAGGCTTTTGAAAGAATGGGTCACTATAAATAGACTTTTCT-ACTAAATAAATGACTTG
* ** * * * *
5046 TTTCTTCACGTTTCTTGAGGTAGACATTCAATAATAGCCCGTTTTAACCAAAAATGTAAAAAAAT
65 TTTC-ACACGTTTCTCAAGGCAAACATTCAACAATAGCCCGTTTTAACCAAAAATATAAAAAAAT
5111 TCAACTTAAAATCAATTATAAGACTATAAAATAATTTCAGGTA
129 TCAACTTAAAATCAATTATAAGACTATAAAATAATTTCAGGTA
* * * * * * * * *
5154 AGTAATAAGGCTTTTGAAGGAATTGGTGATTCTAAGTAGACTTTTCTTCTCAATAAATGGCTTGT
1 AGTAATAAGGCTTTTGAAAGAATGGGTCACTATAAATAGACTTTTCTACTAAATAAATGACTTGT
* * *
5219 TTCACACGTTTCTCAAGGCAAACATTCAACCATAGTCTGTTTTAACCAAAAATATAAAAAAATTC
66 TTCACACGTTTCTCAAGGCAAACATTCAACAATAGCCCGTTTTAACCAAAAATATAAAAAAATTC
*
5284 AACTTAAAATTAATTAT
131 AACTTAAAATCAATTAT
5301 GAGNNNNNNN
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
170 1 0.01
171 115 0.93
172 7 0.06
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (171 bp):
AGTAATAAGGCTTTTGAAAGAATGGGTCACTATAAATAGACTTTTCTACTAAATAAATGACTTGT
TTCACACGTTTCTCAAGGCAAACATTCAACAATAGCCCGTTTTAACCAAAAATATAAAAAAATTC
AACTTAAAATCAATTATAAGACTATAAAATAATTTCAGGTA
Found at i:11273 original size:171 final size:155
Alignment explanation
Indices: 11005--11322 Score: 289
Period size: 171 Copynumber: 1.9 Consensus size: 155
10995 TTTTAAGTTA
* * * *
11005 AATTTTTTTACATTTTTGGCTAAAATAGGCTATAATTGAATGTCTACCTCGAGAAACGTGAGGAA
1 AATTGTTTTACATTTTTAGCTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACGTGAGGAA
* * *
11070 AAAGATATTCATTGGCAAAAAAAGTCCATTTATAG-TCACCCATTACTTCAAAGGCCTTATTACT
66 AAAGACATTCATTGGCAAAAAAAGTCCATTTAT-GTTCACCCATTACTTCAAAAGCCTCATTACT
* *
11134 CGCTTTAAATAGTTTTATAATCTCAT
130 CACTTTAAATAGCTTTATAATCTCAT
*
11160 AATTGNNNNNNNNNNNNNNNNTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCTACCT
1 AATTG----------------TTTTACATTTTTAGCTAAAACAGACTATAATTGAATGTCTACCT
* * ** * * * *
11225 TGAGAAACTTGAGGAAACAAG-CATTCATTGGCATGAAAAGTTCATTTATGTTCTCCTATTCCTT
50 CGAGAAACGTGAGGAAA-AAGACATTCATTGGCAAAAAAAGTCCATTTATGTTCACCCATTACTT
*
11289 TAAAAGCCTCATTACTCACTTTAAATAGCTTTAT
114 CAAAAGCCTCATTACTCACTTTAAATAGCTTTAT
11323 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 19, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
155 4 0.03
170 1 0.01
171 118 0.94
172 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.35
Consensus pattern (155 bp):
AATTGTTTTACATTTTTAGCTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACGTGAGGAA
AAAGACATTCATTGGCAAAAAAAGTCCATTTATGTTCACCCATTACTTCAAAAGCCTCATTACTC
ACTTTAAATAGCTTTATAATCTCAT
Found at i:12374 original size:171 final size:171
Alignment explanation
Indices: 12083--13234 Score: 955
Period size: 171 Copynumber: 6.8 Consensus size: 171
12073 NNNNNNNNNG
* * * * * * *
12083 TTGAATGTCTGCCTTGAGAAACGTGTG-GAACAA-GCTATTTATTGAGAAGAAAAATCCT-TTTA
1 TTGAATGTCTACCTTAAGAAACATG-GAGAAAAAGGC-ATTCATTTAGAAGAAAAGT-CTATTTA
* * *
12145 TAAG-CACCCATTCCTTCAAAAACCTTATTACTCG-TATTAAATTA-TTTTATAGTCTCATAATT
63 T-AGTCACCCATTCTTTCAAAAGCCTTATTACTCGCT-TTAAA-TAGTTTTATAATCTCATAATT
* * *
12207 AATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGGCTATAT
125 AATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAA
* * * *
12254 TTGAATGTCTACCTCAAGCAACATGGATAAAAAGGCATTCATTTATAAGAAAAGTCTATTTATAG
1 TTGAATGTCTACCTTAAGAAACATGGAGAAAAAGGCATTCATTTAGAAGAAAAGTCTATTTATAG
* * * *
12319 TGACCCATTCTTTCAAAAGCATTATTACTCGCTTTAAATGGTTTAATAATCTCATAATTAATTTT
66 TCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTTT
* * * *
12384 AAGTTGAATTTTTCTACTACTTTT-GTTCAAACAGGCTACT-A
131 AAGTTGAATTTTTTTAC-ATTTTTGGTTAAAACAGACTA-TAA
* * * ** * *
12425 TTGAATGTCTGCCTTGAGAAACGTGTG-GAGCAAGTCATTCATTGAGAAGAAAAGTCTATTTATA
1 TTGAATGTCTACCTTAAGAAACATG-GAGAAAAAGGCATTCATTTAGAAGAAAAGTCTATTTATA
* * * * * *
12489 ATCACCCATTCCTTT-AAAAGCCTTATTACTCACGTTAAATTGTTTTATAGTCTCATAATTGATT
65 GTCACCCATT-CTTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATT
* * * * *
12553 TCAAGTTAAATTTTTTTCCATTTGTGGTTAAAACAGGCTATAA
129 TTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAA
* * * * * *
12596 TTGAATGTCTACCTCAAGAAACTTGAAGAAAAATGTATTCATTTATAAGAAAAGTCTATTTATAG
1 TTGAATGTCTACCTTAAGAAACATGGAGAAAAAGGCATTCATTTAGAAGAAAAGTCTATTTATAG
* * * * * * * * *
12661 -CGACTCATTCCTTCAAAAGTCTTATTACTCGTTTTAAATAGTTTAATAATTTTATAATTGAGTT
66 TC-ACCCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTT
*
12725 TAAGTTGAATTTTTTTACTATTTTT-CTTAAAACAGACTATAA
130 TAAGTTGAATTTTTTTAC-ATTTTTGGTTAAAACAGACTATAA
* * * * * * * *
12767 TTGAATGTCTCCCTTGAGGAACGTGTGA-AACAAGCCATTC-TTTGAGAAAAAAAGTCCATTTAT
1 TTGAATGTCTACCTTAAGAAACATG-GAGAAAAAGGCATTCATTT-AGAAGAAAAGTCTATTTAT
* * * * * ** *
12830 AGTCATCTATT-TCTTAAAAAACTTTATTACTCGCGATAAATAGTTTTATAGTCTCATAATTAAT
64 AGTCACCCATTCT-TTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAAT
* * * ** *
12894 TTTAAATTGAAATGTTTTACATTTTTACTCAAAACAGACTATAA
128 TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAA
** * *
12938 TTGAATGTC-AGCCTTAAGAAACATAAAGAAACAA-GCATTCA-TTGGCAAGAAAAGTCCATTTA
1 TTGAATGTCTA-CCTTAAGAAACATGGAGAAA-AAGGCATTCATTTAG-AAGAAAAGTCTATTTA
* * * *
13000 TAGTCACCTATTCCTTT--AAAGCCTTATGACTCGCTTTAAAT-GATTTTATAATCGCATAATTG
63 TAGTCACCCATT-CTTTCAAAAGCCTTATTACTCGCTTTAAATAG-TTTTATAATCTCATAATTA
*
13062 ATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGAC--T-A
126 ATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAA
* * * *
13105 -T-AATGTCTA-CTTGGAA-AAACGT-GAGGAAAAAAGCATTCA-TTGGCAAGAAAAGTCCATTT
1 TTGAATGTCTACCTT--AAGAAACATGGA-GAAAAAGGCATTCATTTAG-AAGAAAAGTCTATTT
* * * *
13164 ATAGTCACCGATT-TCTCCAAAAGCCTTATTACTCGTTTTAAATTA-TTTTATAATATCATAATT
62 ATAGTCACCCATTCT-TTCAAAAGCCTTATTACTCGCTTTAAA-TAGTTTTATAATCTCATAATT
*
13227 GATTTTAA
125 AATTTTAA
Statistics
Matches: 794, Mismatches: 148, Indels: 83
0.77 0.14 0.08
Matches are distributed among these distances:
163 1 0.00
164 7 0.01
165 54 0.07
166 49 0.06
167 2 0.00
168 1 0.00
169 1 0.00
170 96 0.12
171 557 0.70
172 25 0.03
173 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (171 bp):
TTGAATGTCTACCTTAAGAAACATGGAGAAAAAGGCATTCATTTAGAAGAAAAGTCTATTTATAG
TCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATAGTTTTATAATCTCATAATTAATTTT
AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTATAA
Found at i:12431 original size:342 final size:340
Alignment explanation
Indices: 12083--13234 Score: 1287
Period size: 342 Copynumber: 3.4 Consensus size: 340
12073 NNNNNNNNNG
* *
12083 TTGAATGTCTGCCTTGAGAAACGTGTGGAACAAGCTATTTATTGAGAAGAAAAATCCTTTTATAA
1 TTGAATGTCTGCCTTGAGAAACGTGTGGAACAAGCTATTCATTGAGAAGAAAAATCCATTTAT-A
12148 G-CACCCATTCCTTCAAAAACCTTATTACTCGTATTAAATTATTTTATAGTCTCATAATTAATTT
65 GTCACCCATTCCTTCAAAAACCTTATTACTCGTATTAAATTATTTTATAGTCTCATAATTAATTT
* * *
12212 TAAGTTGAATTTTTTTACATTTTTGGTTAAAATAGGCTATATTTGAATGTCTACCTCAAGCAACA
130 TAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGGCTATAATTGAATGTCTACCTCAAGAAACA
* *
12277 TGGATAAAAAGGCATTCATTTATAAGAAAAGTCTATTTATAGTGACCCATTCTTTCAAAAGCATT
195 TGAAGAAAAA-GCATTCATTTATAAGAAAAGTCTATTTATAGTGACCCATTCTTTCAAAAGC-TT
* * *
12342 ATTACTCGCTTTAAATGGTTTAATAATCTCATAATTAATTTTAAGTTGAATTTTTCTACTACTTT
258 ATTACTCGCTTTAAATGGTTTAATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTATTTT
*
12407 TGTTCAAACAGGCTACTA
323 TGTTAAAACAGGCTACTA
* * *
12425 TTGAATGTCTGCCTTGAGAAACGTGTGGAGCAAG-TCATTCATTGAGAAGAAAAGTCTATTTATA
1 TTGAATGTCTGCCTTGAGAAACGTGTGGAACAAGCT-ATTCATTGAGAAGAAAAATCCATTTATA
* * * *** * *
12489 ATCACCCATTCCTTTAAAAGCCTTATTACTCACGTTAAATTGTTTTATAGTCTCATAATTGATTT
65 GTCACCCATTCCTTCAAAAACCTTATTACTCGTATTAAATTATTTTATAGTCTCATAATTAATTT
* * * * *
12554 CAAGTTAAATTTTTTTCCATTTGTGGTTAAAACAGGCTATAATTGAATGTCTACCTCAAGAAACT
130 TAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGGCTATAATTGAATGTCTACCTCAAGAAACA
* * * *
12619 TGAAGAAAAATGTATTCATTTATAAGAAAAGTCTATTTATAGCGACTCATTCCTTCAAAAGTCTT
195 TGAAGAAAAA-GCATTCATTTATAAGAAAAGTCTATTTATAGTGACCCATTCTTTCAAAAG-CTT
* * * * *
12684 ATTACTCGTTTTAAATAGTTTAATAATTTTATAATTGAGTTTAAGTTGAATTTTTTTACTATTTT
258 ATTACTCGCTTTAAATGGTTTAATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTATTTT
* *
12749 TCTTAAAACAGACTA-TAA
323 TGTTAAAACAGGCTACT-A
* * * * *
12767 TTGAATGTCTCCCTTGAGGAACGTGTGAAACAAGCCATTCTTTGAGAA-AAAAAGTCCATTTATA
1 TTGAATGTCTGCCTTGAGAAACGTGTGGAACAAGCTATTCATTGAGAAGAAAAA-TCCATTTATA
* * * * * *
12831 GTCATCTATTTCTTAAAAAACTTTATTACTCGCGA-TAAA-TAGTTTTATAGTCTCATAATTAAT
65 GTCACCCATTCCTTCAAAAACCTTATTACTCG-TATTAAATTA-TTTTATAGTCTCATAATTAAT
* * * ** * * *
12894 TTTAAATTGAAATGTTTTACATTTTTACTCAAAACAGACTATAATTGAATGTC-AGCCTTAAGAA
128 TTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGGCTATAATTGAATGTCTA-CCTCAAGAA
* *** * * *
12958 ACATAAAGAAACAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTT--AAAG
192 ACATGAAGAAA-AAGCATTCATTTATAAGAAAAGTCTATTTATAGTGACCCATT-CTTTCAAAAG
* * * *
13021 CCTTATGACTCGCTTTAAATGATTTTATAATCGCATAATTGATTTTAAGTTGAATTTTTTTAC-A
255 -CTTATTACTCGCTTTAAATGGTTTAATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTA
13085 TTTTTGATTAAAACA-G--ACTA
319 TTTTTG-TTAAAACAGGCTACTA
* * * * *
13105 -T-AATGTCT-ACTTGGAAAAACGTGAGGAAAAAAGC-ATTCATTG-GCAAGAAAAGTCCATTTA
1 TTGAATGTCTGCCTT-GAGAAACGTGTGG-AACAAGCTATTCATTGAG-AAGAAAAATCCATTTA
* * * * * * * *
13165 TAGTCACCGATTTCTCCAAAAGCCTTATTACTCGTTTTAAATTATTTTATAATATCATAATTGAT
63 TAGTCACCCATTCCTTCAAAAACCTTATTACTCGTATTAAATTATTTTATAGTCTCATAATTAAT
13230 TTTAA
128 TTTAA
Statistics
Matches: 677, Mismatches: 114, Indels: 44
0.81 0.14 0.05
Matches are distributed among these distances:
335 4 0.01
336 88 0.13
337 13 0.02
338 2 0.00
339 1 0.00
340 6 0.01
341 74 0.11
342 483 0.71
343 6 0.01
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.38
Consensus pattern (340 bp):
TTGAATGTCTGCCTTGAGAAACGTGTGGAACAAGCTATTCATTGAGAAGAAAAATCCATTTATAG
TCACCCATTCCTTCAAAAACCTTATTACTCGTATTAAATTATTTTATAGTCTCATAATTAATTTT
AAGTTGAATTTTTTTACATTTTTGGTTAAAACAGGCTATAATTGAATGTCTACCTCAAGAAACAT
GAAGAAAAAGCATTCATTTATAAGAAAAGTCTATTTATAGTGACCCATTCTTTCAAAAGCTTATT
ACTCGCTTTAAATGGTTTAATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACTATTTTTGT
TAAAACAGGCTACTA
Found at i:12690 original size:513 final size:506
Alignment explanation
Indices: 12114--13234 Score: 1226
Period size: 513 Copynumber: 2.2 Consensus size: 506
12104 CGTGTGGAAC
* * * * *
12114 AAGCTATTTATTGAGAAGAAAAATCCTTTTATAAG-CACCCATTCCTTCAAAAACCTTATTACTC
1 AAGC-ATTCATTGACAAGAAAAGTCCATTTAT-AGTCA-CCATTCCTTCAAAAGCCTTATTACTC
* * * * *
12178 GTATTAAATTATTTTATAGTCTCATAATTAATTTTAAGTTGAATTTTTTTAC-ATTTTTGGTTAA
63 GTTTTAAATTATTTTATAATATCATAATTGATTTTAAGTTGAATTTTTTTACTATTTTT-CTTAA
* * * * * *
12242 AATAGGCTATATTTGAATGTCTACCTCAAGCAACATG-GATAAAAAGGCATTCATTT-ATAAGAA
127 AACAGACTATAATTGAATGTCTACCTCAAGCAACATGTGA-AAAAAGCCATTC-TTTGAGAAAAA
* * * * ** *
12305 AAGTCTATTTATAGTGACCCA-TTCTTTCAAAAGCATTATTACTCGCTTTAAATGGTTTAATAAT
190 AAGTCCATTTATAGTCACCCATTTC-TTAAAAAACATTATTACTCGCGATAAATAGTTTAATAAT
* * ** *
12369 CTCATAATTAATTTTAAGTTG-AATTTTTCTACTACTTTTGTTC-AAACAGGCTACT-ATTGAAT
254 CTCATAATTAATTTTAAATTGAAATGTTT-TAC-ACTTTTACTCAAAACAGACTA-TAATTGAAT
* * * ** * * *
12431 GTCTGCCTTGAGAAACGT-GTGGAGCAAGTCATTCATTGAG-AAGAAAAGTCTATTTATAATCAC
316 GTCAGCCTTAAGAAACATAAAGAAACAAG-CATTCATTG-GCAAGAAAAGTCCATTTATAATCAC
* * *
12494 CCATTCCTTTAAAAGCCTTATTACTCACGTTAAATTG-TTTTATAGTCTCATAATTGATTTCAAG
379 CCATTCCTTT-AAAGCCTTATGACTCACGTTAAA-TGATTTTATAATCGCATAATTGATTTCAAG
* * * *
12558 TTAAATTTTTTTCCATTTGTGGTTAAAACAGGCTATAATTGAATGTCTACCT-CAAGAAACTTGA
442 TTAAATTTTTTTACATTTGTGATTAAAACAGAC--T-A-T-AATGTCTACCTGCAA-AAACGTGA
12622 AGAAAA
501 AGAAAA
* * * * * *
12628 ATGTATTCATTTATAAGAAAAGTCTATTTATAG-CGACTCATTCCTTCAAAAGTCTTATTACTCG
1 AAGCATTCATTGACAAGAAAAGTCCATTTATAGTC-AC-CATTCCTTCAAAAGCCTTATTACTCG
* * * *
12692 TTTTAAA-TAGTTTAATAATTTTATAATTGAGTTTAAGTTGAATTTTTTTACTATTTTTCTTAAA
64 TTTTAAATTA-TTTTATAATATCATAATTGATTTTAAGTTGAATTTTTTTACTATTTTTCTTAAA
* ** * * *
12756 ACAGACTATAATTGAATGTCTCCCTTGAGGAACGTGTGAAACAAGCCATTCTTTGAGAAAAAAAG
128 ACAGACTATAATTGAATGTCTACCTCAAGCAACATGTGAAAAAAGCCATTCTTTGAGAAAAAAAG
* * * * *
12821 TCCATTTATAGTCATCTATTTCTTAAAAAACTTTATTACTCGCGATAAATAGTTTTATAGTCTCA
193 TCCATTTATAGTCACCCATTTCTTAAAAAACATTATTACTCGCGATAAATAGTTTAATAATCTCA
*
12886 TAATTAATTTTAAATTGAAATGTTTTACATTTTTACTCAAAACAGACTATAATTGAATGTCAGCC
258 TAATTAATTTTAAATTGAAATGTTTTACACTTTTACTCAAAACAGACTATAATTGAATGTCAGCC
* *
12951 TTAAGAAACATAAAGAAACAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTT
323 TTAAGAAACATAAAGAAACAAGCATTCATTGGCAAGAAAAGTCCATTTATAATCACCCATTCCTT
* * * *
13016 TAAAGCCTTATGACTCGCTTTAAATGATTTTATAATCGCATAATTGATTTTAAGTTGAATTTTTT
388 TAAAGCCTTATGACTCACGTTAAATGATTTTATAATCGCATAATTGATTTCAAGTTAAATTTTTT
* * * *
13081 TACATTTTTGATTAAAACAGACTATAATGTCTACTTGGAAAAACGTGAGGAAAA
453 TACATTTGTGATTAAAACAGACTATAATGTCTACCTGCAAAAACGTGAAGAAAA
* * *
13135 AAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCGATTTCTCCAAAAGCCTTATTACTCGT
1 AAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACC-ATTCCTTCAAAAGCCTTATTACTCGT
13200 TTTAAATTATTTTATAATATCATAATTGATTTTAA
65 TTTAAATTATTTTATAATATCATAATTGATTTTAA
Statistics
Matches: 504, Mismatches: 86, Indels: 41
0.80 0.14 0.06
Matches are distributed among these distances:
506 1 0.00
507 102 0.20
508 6 0.01
509 1 0.00
510 1 0.00
511 2 0.00
512 90 0.18
513 276 0.55
514 25 0.05
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (506 bp):
AAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCATTCCTTCAAAAGCCTTATTACTCGTT
TTAAATTATTTTATAATATCATAATTGATTTTAAGTTGAATTTTTTTACTATTTTTCTTAAAACA
GACTATAATTGAATGTCTACCTCAAGCAACATGTGAAAAAAGCCATTCTTTGAGAAAAAAAGTCC
ATTTATAGTCACCCATTTCTTAAAAAACATTATTACTCGCGATAAATAGTTTAATAATCTCATAA
TTAATTTTAAATTGAAATGTTTTACACTTTTACTCAAAACAGACTATAATTGAATGTCAGCCTTA
AGAAACATAAAGAAACAAGCATTCATTGGCAAGAAAAGTCCATTTATAATCACCCATTCCTTTAA
AGCCTTATGACTCACGTTAAATGATTTTATAATCGCATAATTGATTTCAAGTTAAATTTTTTTAC
ATTTGTGATTAAAACAGACTATAATGTCTACCTGCAAAAACGTGAAGAAAA
Done.