Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397744.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_1041.0, 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: 17941
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.31
Warning! 3423 characters in sequence are not A, C, G, or T
Found at i:327 original size:171 final size:169
Alignment explanation
Indices: 93--628 Score: 639
Period size: 171 Copynumber: 3.1 Consensus size: 169
83 NNNNNNNNNN
* *
93 AACAGACTATAATCGAATGTCTACCTCGAGAAACATGAAGAAAAAAGCATTCA-TGGCCAAGAAA
1 AACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAA-CATTCATTGG-CAAGAAA
* * * *
157 AGTCCATTTATAGTCACTCATTCTTTCAAAAGCTTTATTACGT-GCTTTAAAT-GATTTTATACT
64 AGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTCTTAC-TCGTTTTAAATAG-TTTTATAAT
**********
220 CTCATAATTGATTTTAAGTTAAAATTTNNNNNNNNNNTGGTTAA
127 CTCATAATTGATTTTAAG-TAAAATTTTTTACATTTTTGGTTAA
*
264 AACAGACTATAATTGAATGTCTTCCTCAAGAAACATGAAGAAAAACACATTCATTGGCAAGAAAA
1 AACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAA-ACATTCATTGGCAAGAAAA
* * * *
329 ATTCATTTATAGTCGCTCATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAAACTC
65 GTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTC
*
394 ATAATTGATTTTAAGTAGAATTTTTTACATTTTTGGTTAA
130 ATAATTGATTTTAAGTAAAATTTTTTACATTTTTGGTTAA
* * * * * *
434 AATAGACTATAATTGAATGTCTACCTTGAA-AAATATGAAGAAAAAAAATTTATTGGCAGGAAAA
1 AACAGACTATAATTGAATGTCTACC-TCAAGAAACATGAAGAAAAAACATTCATTGGCAAGAAAA
* *
498 GTGCATTTATAGTCACTTATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTC
65 GTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTC
* * * * * *
563 ATAATTAATATTAATTTGAATTTTTTTACTTTTTTGGTTAA
130 ATAATTGATTTTAA-GTAAAATTTTTTACATTTTTGGTTAA
*
604 AACAGACTATAATTAAATGTCTACC
1 AACAGACTATAATTGAATGTCTACC
629 NNNNNNNNNN
Statistics
Matches: 316, Mismatches: 43, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
169 88 0.28
170 96 0.30
171 127 0.40
172 5 0.02
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
AACAGACTATAATTGAATGTCTACCTCAAGAAACATGAAGAAAAAACATTCATTGGCAAGAAAAG
TCCATTTATAGTCACTCATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTCA
TAATTGATTTTAAGTAAAATTTTTTACATTTTTGGTTAA
Found at i:590 original size:170 final size:169
Alignment explanation
Indices: 5--628 Score: 644
Period size: 170 Copynumber: 3.7 Consensus size: 169
1 CACC
* * ** * * *
5 CATTCTTTCAAAAGCCTTATTACCCACTTTAAATGGTTTTATAATCTCATCATTCATTTTAAGTT
1 CATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTT
* * ********** * * *
70 GAATATTTTATATNNNNNNNNNNAACAGACTATAATCGAATGTCTACCTCGAGAAACATGAAGAA
66 GAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAAAAACATGAAGAA
135 AAAAGCATTCA-TGGCCAAGAAAAGTCCATTTATAGTCACT
131 AAAA-CATTCATTGG-CAAGAAAAGTCCATTTATAGTCACT
* * * *
175 CATTCTTTCAAAAGCTTTATTACGT-GCTTTAAAT-GATTTTATACTCTCATAATTGATTTTAAG
1 CATTCTTTCAAAAGCCTTCTTAC-TCGTTTTAAATAG-TTTTATAATCTCATAATTGATTTTAAG
* ********** * *
238 TTAAAATTTNNNNNNNNNNTGGTTAAAACAGACTATAATTGAATGTCTTCC-TCAAGAAACATGA
64 TT-GAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAA-AAACATGA
* * *
302 AGAAAAACACATTCATTGGCAAGAAAAATTCATTTATAGTCGCT
127 AGAAAAA-ACATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
* *
346 CATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAAACTCATAATTGATTTTAAGTA
1 CATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTT
* *
411 GAATTTTTTACATTTTTGGTTAAAATAGACTATAATTGAATGTCTACCTTGAAAAATATGAAGAA
66 GAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAAAAACATGAAGAA
* * * *
476 AAAAAATTTATTGGCAGGAAAAGTGCATTTATAGTCACT
131 AAAACATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
* * * *
515 TATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTCATAATTAATATTAATTT
1 CATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTT
* *
580 GAATTTTTTTACTTTTTTGGTTAAAACAGACTATAATTAAATGTCTACC
66 GAA-TTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACC
629 NNNNNNNNNN
Statistics
Matches: 378, Mismatches: 66, Indels: 20
0.81 0.14 0.04
Matches are distributed among these distances:
169 93 0.25
170 149 0.39
171 131 0.35
172 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
CATTCTTTCAAAAGCCTTCTTACTCGTTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTT
GAATTTTTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTTGAAAAACATGAAGAA
AAAACATTCATTGGCAAGAAAAGTCCATTTATAGTCACT
Found at i:1025 original size:170 final size:160
Alignment explanation
Indices: 760--1077 Score: 295
Period size: 170 Copynumber: 1.9 Consensus size: 160
750 ATTTTTGGTT
** *
760 AAACAGACTATAATTGAAAGTTTACCTCAAGAAACGTGTAGAAAAAGGTATTCATTAGCGAAAAA
1 AAACAGACTATAATTGAAAGCCTACCTCAAGAAACGTGAAGAAAAAGGTATTCATTAGCGAAAAA
* * * *
825 AGTCCATTTATAGTTACCAATTCCTTC-AAAATCCTTATTAATCACT-TCAAATGCTTTTTTAAT
66 AGTCCATTTATACTCACCAATTCCTTCAAAAAT-CTTATTAATCACTGT-AAATGATTTTATAAT
*
888 CTCATAATTTATTTTAAGTTGAATTTTTTNNNNNNNNNNTTA
129 CTCATAATTGATTTTAAGTTGAATTTTTT----------TTA
* * * * *
930 AAACAGACTATAATTGAATGCCTGCCTC-TGAAAACGTGAAGAAAAATGTATTCATTGGC-AAGA
1 AAACAGACTATAATTGAAAGCCTACCTCAAG-AAACGTGAAGAAAAAGGTATTCATTAGCGAA-A
* * * * **
993 AATGTGCATTTATACTCACTC-ATTCTTTCAAAAATCTTATTATTTGCTGTAAATGATTTTATAA
64 AAAGTCCATTTATACTCAC-CAATTCCTTCAAAAATCTTATTAATCACTGTAAATGATTTTATAA
1057 TCTCATAATTGATTTTAAGTT
128 TCTCATAATTGATTTTAAGTT
1078 NNNNNNNNNN
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
169 3 0.02
170 114 0.92
171 7 0.06
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (160 bp):
AAACAGACTATAATTGAAAGCCTACCTCAAGAAACGTGAAGAAAAAGGTATTCATTAGCGAAAAA
AGTCCATTTATACTCACCAATTCCTTCAAAAATCTTATTAATCACTGTAAATGATTTTATAATCT
CATAATTGATTTTAAGTTGAATTTTTTTTA
Found at i:1488 original size:170 final size:169
Alignment explanation
Indices: 1138--2200 Score: 645
Period size: 170 Copynumber: 6.2 Consensus size: 169
1128 CAAAACACCT
* * *
1138 GAAGAAAAAGACATTCATTGGCAAGAAAAGTTCATTTATAG-TCCCATTTTTTCAAATGCCTTAT
1 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTTCCCATTCTTTCAAAAGCC-TAT
* * * * *
1202 TATTCGCTTTAAATGGTTTTATAATCTCAAAACTGATTTTGAGTTGAATTTTTTTTTGTATTTTT
65 TATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTT-AA-ATTTTTTTG-ATTTTT
** * *
1267 GGTT-AAACAGACTATTGTTTAATATCAACCTTGAGAAACCTA
127 GGTTAAAACAGACTATAATTGAATATCAACCTTGAGAAACCAA
* *
1309 -ATG-AAAAGGCATTCATTAGCAAGAAAAGTTCATTTATAGTTTCCCATTCTTTCAAAAGCCTAT
1 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAG-TTCCCATTCTTTCAAAAGCCTAT
* * *
1372 TACTCGCTTTAAGTAGTTTTATAATCTCATTATTGATTTTAAGTTAAATTTTTTTGCATTTTTGG
65 TATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTG-ATTTTTGG
* **********
1437 TTAAAACAGATTATAATTGAATNNNNNNNNNNAGAAA-CAA
129 TTAAAACAGACTATAATTGAATATCAACCTTGAGAAACCAA
* * * * * *
1477 GAAGAAAAAGGCATTCATTGGTAAGAAAAGTTTATTTATAG-TCACTCATTCCTTGAAAATCTTT
1 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTTC-C-CATTCTTTCAAAAGC-CT
* * *
1541 ATTATTCGTTTTAAATAGCTTTATAATCTCATAATTGATTTTAAGTTCAA-TTTTTT-ATATTTT
63 ATTATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTGAT-TTTT
** ** * *
1604 CATTAAAACAGACTATAATTGAATAGT-TGCCTTGGGAAA-CAT
127 GGTTAAAACAGACTATAATTGAATA-TCAACCTTGAGAAACCAA
** *** * * * ** *
1646 GTTGAAAAAAATATAT-ATTCGAAAGAAAAGTCCATTTATAGTCTCTTATTCTTTAAAAAGCCTT
1 GAAGAAAAAGGCAT-TCATTGGCAAGAAAAGTTCATTTATAGT-TCCCATTCTTTCAAAAGCC-T
* * ********** * * **
1710 ATTATTCACTTTAAATGGTTTTATAATCTNNNNNNNNNNTTTAAATTGAATTTTTTT-ACAGTTT
63 ATTATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTGA-TTTTT
* * * *
1774 GGTTAAAACATATTATAATTGAATGTCTACCTTGAGAAA-CAA
127 GGTTAAAACAGACTATAATTGAATATCAACCTTGAGAAACCAA
* * * * *
1816 GAAGAAAATGACATTCATTGGCAGGAAAAG-TCTATTTAT-GATCACCGATTCCTTCAAAAGCCT
1 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTC-ATTTATAGTTC-CC-ATTCTTTCAAAAGCC-
* * * * *********
1879 TATTAGTCGCTTTAAATGGTTTTGTAAGCTCATAATTGATTTNNNNNNNNNNTTTTTTAT-ATTT
62 TATTATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTT-TAAGTTAAATTTTTT-TGATTT
* * * * *
1943 TTGATTAAAACAGACTATAATTGAGT-GCTGACCTTGAGAAA-CAT
125 TTGGTTAAAACAGACTATAATTGAATATC-AACCTTGAGAAACCAA
* * * *
1987 GAAGAAAAATGCATTCATTAGCAA-AGAAAGGTCTATTTATAGTTATCCATTCTTTCAAAAGCCT
1 GAAGAAAAAGGCATTCATTGGCAAGA-AAAGTTC-ATTTATAGTT-CCCATTCTTTCAAAAGCC-
* * * * * * *
2051 TATTAGTCGCTTTAAATGGTTTCATAATCTCATAATTAATTTTAAGCTGAATTTTTTTATATTTT
62 TATTATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTT-GATTTT
** * * * * * ** **
2116 TTATTAATAGAGACTATAGTTGAATGTCTACCTCAAGAAA-CGT
126 TGGTTAAAACAGACTATAATTGAATATCAACCTTGAGAAACCAA
* * *
2159 GAAGAAAAAGGAATTCATTGGTAAGAAAAGTCCATTTATAGT
1 GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGT
2201 CACCCATNNN
Statistics
Matches: 679, Mismatches: 181, Indels: 64
0.73 0.20 0.07
Matches are distributed among these distances:
168 26 0.04
169 170 0.25
170 208 0.31
171 144 0.21
172 125 0.18
173 6 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.38
Consensus pattern (169 bp):
GAAGAAAAAGGCATTCATTGGCAAGAAAAGTTCATTTATAGTTCCCATTCTTTCAAAAGCCTATT
ATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTAAATTTTTTTGATTTTTGGTT
AAAACAGACTATAATTGAATATCAACCTTGAGAAACCAA
Found at i:2754 original size:172 final size:169
Alignment explanation
Indices: 2294--4120 Score: 845
Period size: 171 Copynumber: 10.7 Consensus size: 169
2284 NNNNNNNACA
* * *
2294 TTTTTGGTTAAAACAAACTATAATTGAATG-CTTACCTTG-GAAA-ATGTGAAGAAAAAGGCATT
1 TTTTTGGTTAAAACATATTATAATTGAATGTC-TACATTGAGAAACA--TGAAGAAAAA-GCATT
* * * * * * * * *
2356 CATTGACAAGAAATGTCCATTTACACTCACTCATTCTTTCAAAAGCCTTATTACTCGCTGTAAAT
62 CATTGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTCACTTTAAAT
* * * *
2421 AGTTTTATAATATCATATTTGATTTTAAGTTGTATTTTTT-TAT
126 AGTTTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT
* * * ********** * **
2464 ATTTTTAGTTAAAACAGACTATNNNNNNNNNNCTACCTCAAGAAAC-TAGAAGAAAAAGACATTC
1 -TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACAT-GAAGAAAAAG-CATTC
* * * * *
2528 ATTGGTAAGAAAAG-TCTATTTATACTCACCCATTCTTTTAAAAGCCTCATTACTCACTTTAAAT
63 ATTGGCAAGAAAAGTTC-ATTTATAGTCACCCATTC-CTTCAAAGCCTTATTACTCACTTTAAAT
*
2592 AGTTTCATAATCTCATAATTGATTTTAAGTTGAATTTTCTTGTAT
126 AGTTTCATAATCTCATAATTGATTTTAAGTTGAATTTT-TTATAT
* *
2637 TTTTTGGTTAAAACATATTATAGTTGAATGTCTACATTGAGAAACATGAAGAAAAAGTTATTCAT
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAGAAAAAG-CATTCAT
**********
2702 TGGCANNNNNNNNNNATTTATAGTCACCCATTCCTTCAAAGTCCTTATTACTCACTTTAAA-AGG
65 TGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAG-CCTTATTACTCACTTTAAATA-G
* * * *
2766 TTTTATAATGTCATAATTGATTTTAAGTTGACTTGTTTTACAT
128 TTTCATAATCTCATAATTGATTTTAAGTTGAATT-TTTTATAT
* * * * * *
2809 TTATT-GTCAAAACAGT-TTATAATTAAATGTTTACCTTAAGAAACATGAAGAAAGAAGCATTCA
1 TTTTTGGTTAAAACA-TATTATAATTGAATGTCTACATTGAGAAACATGAAGAAA-AAGCATTCA
* * * *
2872 TTGGCAAGAAAAGTTCATTTGTAGTCTCCCTTTCCTTCAAAAACCTTATTACTCGA-TTTAAATA
64 TTGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTC-ACTTTAAATA
* * * * *
2936 GTTTCATAATCTCAAAATTGATTTTCAGTTCAATTTTTTTTAC
127 GTTTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT
* * * *
2979 TTTTTGATTAAAACATATTATAACTGAATTTCTACAGTGAGAAACATGAAGAAAAATGCATTCAT
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAGAAAAA-GCATTCAT
* * * * * ********** *
3044 TAGTAAGAAAAGTCCATTTCTTA-TCACTCATTCCTTCAAAAGCCTTATTANNNNNNNNNNATGG
65 TGGCAAGAAAAGTTCATTT-ATAGTCACCCATTCCTTC-AAAGCCTTATTACTCACTTTAAATAG
* * * * * *
3108 TTTTATATTCTCAAAATTGACTTTAAGTTCAATTTTTTTTAACT
128 TTTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTAT-A-T
* * * * ** * * *
3152 TGTTTGGCTAAAATAGATTATAATTGAATGTCTATGTTGAGAAACGTTAAGAAAACGGCATTCAT
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAGAAAA-AGCATTCAT
* * * * * * * *
3217 TAGAAACAAAAGTTCATTTATTGACACTCATTTCTTCAAAAGCCTTATTACTCGCTTTAAATTA-
65 TGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTCACTTTAAA-TAG
** * * *
3281 TTTTGTTATCTCATAATTGATTATAAGTTGAATTTTTT-TACA
128 TTTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTATA-T
** * * * * * * * * * *
3323 TTTTTGGTTAAATTAGACTATAATTCAATATCTACCTTGGGAAACGTGTAA-AAATACCATTTAT
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATG-AAGAAAAAGCATTCAT
** * * * ********* * * *
3387 T-AAAAAAAAAGTCCATTTATAGTCACCCATTCTTTCAANNNNNNNNNNACCCGCTTTAAATGGT
65 TGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAA-AGCCTTATTACTCACTTTAAATAGT
* * * * *
3451 TTTATAATTTCATAATTCATTTTAAGTCGAATTTTTT-TACA
129 TTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTATA-T
* * * * * * * * * * **
3492 TTTTTAGTT-AGACAGACTATAATTAAAAGTCTACCTCGAGAAACGTTAAGAAAAAAATTATTCA
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAG--AAAAAGCATTCA
** * * * * *
3556 CGGGCAAGAAAAGTCCATTTATAGTCACTCATTCTTTCAAAAGCCTTATTACGCGCTTTAAAT-G
64 TTGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTCACTTTAAATAG
********** *
3620 ATNNNNNNNNNNCATAATTGATTTTAAGCTGAATTTTTTTATAT
128 -TTTCATAATCTCATAATTGATTTTAAGTTGAA-TTTTTTATAT
* * * * * * * * * *
3664 TTTTT-GTTATAACAGACTATAATTAAATATCTTCCTTGAGAAATATGAAGAAAAACACATCCAT
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAGAAAAA-GCATTCAT
* * * * ** * *
3728 TGTCAAGAAAAATCCATTTATCGTCACCCATTATTTCAAAAGCCTTATTACTCGCTTTAAATGGT
65 TGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTCACTTTAAATAGT
** * * * * *
3793 TTTGTAATGTTAGAATCGATTTTAAGTTAAATTTTTTATA-
129 TTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT
** * * ** * * * * *
3833 TTGCTCGTTAAAACAAAAAATAATTGAATGTCTACCTCGAGAAACGTAAAGAAAAAAACATTCA-
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAG-AAAAAGCATTCAT
* * * * * * *********** *
3897 TGGATAAGAAATGTCCATTTATAGTCACTCATTCTTGTAAAAGCNNNNNNNNNNGCTTTAAATGG
65 TGG-CAAGAAAAGTTCATTTATAGTCACCCATTCCT-TCAAAGCCTTATTACTCACTTTAAATAG
** *
3962 TTTTGTAATCTCATAATTGATTTTAAGTTGAATATTTTATA-
128 TTTCATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT
** * * * * ** *
4003 TTTTTCATTAAAACAGACTATAATCGAATGTCTACCTTGAGAAATGTGAAGAAAAAAGCATTTAT
1 TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAG-AAAAAGCATTCAT
* * * **
4068 GGGCAAGAAAAGTCCATTTATAGTCACTCATTTTTTCAAAAGCCTTATTACTC
65 TGGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTC-AAAGCCTTATTACTC
4121 GCTTNNNNNN
Statistics
Matches: 1257, Mismatches: 350, Indels: 99
0.74 0.21 0.06
Matches are distributed among these distances:
167 2 0.00
168 32 0.03
169 88 0.07
170 248 0.20
171 558 0.44
172 196 0.16
173 132 0.11
174 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
TTTTTGGTTAAAACATATTATAATTGAATGTCTACATTGAGAAACATGAAGAAAAAGCATTCATT
GGCAAGAAAAGTTCATTTATAGTCACCCATTCCTTCAAAGCCTTATTACTCACTTTAAATAGTTT
CATAATCTCATAATTGATTTTAAGTTGAATTTTTTATAT
Found at i:4631 original size:171 final size:170
Alignment explanation
Indices: 4304--4641 Score: 437
Period size: 171 Copynumber: 2.0 Consensus size: 170
4294 NNNAAAAGTC
* * *
4304 CATTTATAGTCACCCATTCTTTCGAAAGCCTTATTACTTGCTTTAAATGATTTTATAAACTCGTA
1 CATTTATAGTCACCCATTCTTTCGAAAGCATTATTACTTGCTTTAAAAGATTTTATAAACTCATA
* * * * * *
4369 ATTGATTTTAAGTTGAATTTTTTAAAGTTTTGGTTAAAACAAACTATAATTGATTGTTTACCTTG
66 ATTAATATTAAGTTAAATTTTTTAAAGTTTTGGTTAAAACAAACAATAATTGAATGTCTACCTTG
*
4434 AGAAACGTGAAGAAAAAAACATTCATTGGCAAGAAAATTA
131 AGAAACATGAAGAAAAAAACATTCATTGGCAAGAAAATTA
* * *
4474 CATTTATAGTCACTCATTCTTT-GAAAAGCATTTTTACTTGCTTTAAAAGGTTTTATAATA-TCA
1 CATTTATAGTCACCCATTCTTTCG-AAAGCATTATTACTTGCTTTAAAAGATTTTATAA-ACTCA
* * * * * *
4537 TAATTAATATTAATTTAAATATTTTTACATTTTTGGTTAAAATAGACAATAATTGAATGTCTAGC
64 TAATTAATATTAAGTTAAAT-TTTTTAAAGTTTTGGTTAAAACAAACAATAATTGAATGTCTACC
***
4602 TTGAGAAACATGAAGAAAAAGGTATTCATTGGCAAGAAAA
128 TTGAGAAACATGAAGAAAAAAACATTCATTGGCAAGAAAA
4642 GNNNNNNNNN
Statistics
Matches: 143, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
169 1 0.01
170 69 0.48
171 73 0.51
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (170 bp):
CATTTATAGTCACCCATTCTTTCGAAAGCATTATTACTTGCTTTAAAAGATTTTATAAACTCATA
ATTAATATTAAGTTAAATTTTTTAAAGTTTTGGTTAAAACAAACAATAATTGAATGTCTACCTTG
AGAAACATGAAGAAAAAAACATTCATTGGCAAGAAAATTA
Found at i:4981 original size:171 final size:170
Alignment explanation
Indices: 4708--5287 Score: 488
Period size: 171 Copynumber: 3.4 Consensus size: 170
4698 NNNNNNNNNN
* **
4708 TATAATCTCATTATTGATTTTAAGTTAAATTTTTTTATATTTTTTATTAAACAGACTATAGTTGA
1 TATAATCTCATTATTGATTTTAAGTTAAATTTTGTTATATTTTTGGTTAAACAGACTATAGTTGA
* * * * * * * * *
4773 TTATCTACC-TCAGAAAATATAAAGAAAAAGGCATTCATTGGTAAGAAATGTCCATTAATACTTA
66 ATGTCTACCTTGAG-AAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTAATACTCA
**
4837 -CTCATTCTTTCCGAAGCCTTATTACTC-ATTGTAAACAGTTT
130 TC-CATTCTTTCAAAAGCCTTATTACTCGATT-TAAACAGTTT
* * * * * *
4878 TATAATCTCATAATTAATTTTAATTTGAATTTTGTTATATTTTTGGTTATAACAGACTATAATTA
1 TATAATCTCATTATTGATTTTAAGTTAAATTTTGTTATATTTTTGGTTA-AACAGACTATAGTTG
* * * *
4943 AATGTCTACCTTGAGAAACATGAAGAAAACGACATTCATTGGGAAGAAAAGTCCATTTATAGTCA
65 AATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTAATACTCA
** * *
5008 TCCATTCTTTCAAAAGGGTTATTACTCGCTTTAAATAGTTT
130 TCCATTCTTTCAAAAGCCTTATTACTCGATTTAAACAGTTT
********** * *
5049 TATAATCTCATTATTGATTTTAAGTTNNNNNNNNNNACATTTTTGGTTAAAACAAACTATAGTTG
1 TATAATCTCATTATTGATTTTAAGTTAAATTTTGTTATATTTTTGGTT-AAACAGACTATAGTTG
* * * * ****
5114 AATGTCTACCTCGAGAAACATGAATAAAAAGACATTCATTAGCAAGAAAAGTCCATTTATANNNN
65 AATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTAATACTCA
****** * * *
5179 NNNNNNCTTTCAAAATCCTTATTACTCGCTTTAAATAGTTT
130 TCCATTCTTTCAAAAGCCTTATTACTCGATTTAAACAGTTT
* * * * *
5220 T-TAAATCTCATAATTGATTTTAAGTTGAATTTT-TTACATTTTTAGTTCAAACAGA-TGATAAT
1 TAT-AATCTCATTATTGATTTTAAGTTAAATTTTGTTATATTTTTGGTT-AAACAGACT-ATAGT
5282 TGAATG
63 TGAATG
5288 CATGTCTTAG
Statistics
Matches: 327, Mismatches: 76, Indels: 14
0.78 0.18 0.03
Matches are distributed among these distances:
169 1 0.00
170 70 0.21
171 249 0.76
172 7 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.39
Consensus pattern (170 bp):
TATAATCTCATTATTGATTTTAAGTTAAATTTTGTTATATTTTTGGTTAAACAGACTATAGTTGA
ATGTCTACCTTGAGAAACATGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATTAATACTCAT
CCATTCTTTCAAAAGCCTTATTACTCGATTTAAACAGTTT
Found at i:5833 original size:18 final size:20
Alignment explanation
Indices: 5810--5846 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
5800 AAAAATGTGA
5810 AAAAAAAG-T-ATTTATTGG
1 AAAAAAAGCTCATTTATTGG
5828 AAAAAAAGCTCATTTATTG
1 AAAAAAAGCTCATTTATTG
5847 TCACCCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (20 bp):
AAAAAAAGCTCATTTATTGG
Found at i:6810 original size:170 final size:168
Alignment explanation
Indices: 5775--6872 Score: 547
Period size: 170 Copynumber: 6.5 Consensus size: 168
5765 NNNNNNNNNN
* * * *
5775 AGATTATAATTGAATGTCTACCTCGAA-AAATGTGAAA-AAAAA-GTATTTATTG-GAAAAAAAG
1 AGATTATAATTGAATGTCTACCTC-AAGAAATAT-AAAGAAAAAGGCATTCATTGATAAAAAAAG
* * * * * * * ***
5836 -CTCATTTATTGTCACCCATTTCTTCAAAAGCCTAATTAGTCACTTTAAATAGTTTTATAATNNN
64 TC-CATTTATAGTCACCCATTCCTTTAAAAGCCTTATTATTCGCTTTAAATGGTTTTATAATCCT
******* * * *
5900 NNNNNNNATTTTAAGTTGAATTTTTTATATTGTTAGTTAAAAT
128 AAAATTGATTTTAAGTTCAATTTTTTATATT-TT-TTTAAAAC
* * * * * * ** *
5943 AG-TCTATAGTTGAATGTCTACC-AAAGAAACACAAAGAAAAAAGCATTCATGGGCAAGAAAAGT
1 AGAT-TATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTCATTGATAAAAAAAGT
* ** * * * * * *
6006 GCATTTATAGTCAGTCAAT-CTTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTGTAA-GCTC
65 CCATTTATAGTCACCCATTCCTTT-AAAAGCCTTATTATTCGCTTTAAATGGTTTTATAATCCT-
* * * **********
6069 ATAATTGATTTTAGGTTGANNNNNNNNNNTTTTTAGTTAAAAC
128 AAAATTGATTTTAAGTTCAATTTTTTATATTTTT--TTAAAAC
* * * * * * * * * **
6112 AGACTATAAATGAGTGCCTACTTCAAGAAACATGAAGCAAAATGCATTCATTGGCAAAGAAAAGT
1 AGATTATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTCATTGATAAA-AAAAGT
* * * ** *
6177 CCGTTTATAGTTACCCATGCCTAAAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAAT-CTCA
65 CCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTATTCGCTTTAAATGGTTTTATAATCCT-A
* * *
6241 TAATTAATTTTCAA-TTGAATTTTTTATATTTTTAATTAAAAC
129 AAATTGATTTT-AAGTTCAATTTTTTATATTTTT--TTAAAAC
* ********** ** * ** * * **
6283 AGACTATAATTGANNNNNNNNNNCAAGAAACGTGAAGAAAAAAACATTCATGGGTAGGAAAAGTC
1 AGATTATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTCATTGATAAAAAAAGTC
* * * * * * *
6348 CATTCATAGTCTCCTATTCCTTTAAAAGCCTTATTACTCGCTTCAAATTGTTTTATAATCTTAAA
66 CATTTATAGTCACCCATTCCTTTAAAAGCCTTATTATTCGCTTTAAATGGTTTTATAATCCTAAA
* * **
6413 ATTGATTTTAGGTTCAATTTTTTTTCCATTAGTAGTTAAAAC
131 ATTGATTTTAAGTTCAATTTTTTAT--ATT--TTTTTAAAAC
* * * *
6455 AGATTATAATTGAATGTCTACCTTGAA-AAATATTAAGAGAAAGGCATTCATTGGA-AAAACAAG
1 AGATTATAATTGAATGTCTACC-TCAAGAAATATAAAGAAAAAGGCATTCATT-GATAAAAAAAG
* * *
6518 TCCATTTATTGTCACCCATTCCTTTAAAAGCCTTATTACTT-GCTTTAAATGCTTTAATAAT-CT
64 TCCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTA-TTCGCTTTAAATGGTTTTATAATCCT
* * * *
6581 CATAATTGATTTTAAGTTGTATTTTTTTATATTTTTGGTT-AAAN
128 -AAAATTGATTTTAAGTT-CAATTTTTTATATTTTT--TTAAAAC
********* * * *
6625 NNNNNNNNNTTGAATGTCTACCTCAAGAAACACAAAGAAAAAGGTATTCATTGATAAAAAAAGAT
1 AGATTATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTCATTGATAAAAAAAG-T
* * *
6690 -CATTTATAGTCACCCATTTCTTCAAAAGCCTTATTATTCGCTTTATATGGTTTTATAATCCTAA
65 CCATTTATAGTCACCCATTCCTTTAAAAGCCTTATTATTCGCTTTAAATGGTTTTATAATCCTAA
*
6754 AATGGATTTTAAGTTCAATTTCTTTATATTTTTTCTAAAAC
130 AATTGATTTTAAGTTCAATTT-TTTATATTTTTT-TAAAAC
* ** * * * * *
6795 AGATTATAATTGAATGTTTACCTTGAGAAATGTGAAGCAAAAGGCATTCACTGATAAGAAAAGTC
1 AGATTATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTCATTGATAAAAAAAGTC
6860 CATTTATAGTCAC
66 CATTTATAGTCAC
6873 TTATTCCNNN
Statistics
Matches: 683, Mismatches: 209, Indels: 74
0.71 0.22 0.08
Matches are distributed among these distances:
166 5 0.01
167 9 0.01
168 32 0.05
169 98 0.14
170 283 0.41
171 130 0.19
172 113 0.17
173 12 0.02
174 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.36
Consensus pattern (168 bp):
AGATTATAATTGAATGTCTACCTCAAGAAATATAAAGAAAAAGGCATTCATTGATAAAAAAAGTC
CATTTATAGTCACCCATTCCTTTAAAAGCCTTATTATTCGCTTTAAATGGTTTTATAATCCTAAA
ATTGATTTTAAGTTCAATTTTTTATATTTTTTTAAAAC
Found at i:7490 original size:171 final size:173
Alignment explanation
Indices: 7093--7947 Score: 679
Period size: 171 Copynumber: 5.0 Consensus size: 173
7083 NNNNNNNNNN
* * * * *
7093 ATTGATTTTAGGTTGA-ACTTTTT-TACA-TTTTGGTTAAAACAGACT-CTAATTGAATGTCAAC
1 ATTGATTTTAAGTTGATA-TTTTTATACATTTTTGATTAAAAAAGACTAATAATTGAATGTCTAC
* * * * * * * * * * * *
7154 CTTAAAAAACATAGAGAAAAAGACACTCCTTTGCCAAAAAAAAGTTCGTTTATAGTCACCCATTC
65 CTTGAGAAACGTAAAGAAAAAGGCA-TTCATTGGC-AAGAAAAGTCCATTTATAGTCACACATTC
* * * *****
7219 CTTCACAAGCCTTATTACTCGTTTTAAATGATTTTATAATCNNNNN
128 CTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATA
***** * * * * * **
7265 NNNNNTTTTAGGTTGA-ATTTTTTTACATTTTTGATTAGAACAGATTAA-AATTGAATGTCTGTC
1 ATTGATTTTAAGTTGATATTTTTATACATTTTTGATTAAAAAAGACTAATAATTGAATGTCTACC
* * * * ** * *
7328 TTGGGAAACGTGAAGAAAAAGGTATTCATTGGCATGAAAAGTTTATTTATAGTCACCCATTCTTT
66 TTGAGAAACGTAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACACATTCCTT
* * * *
7393 TAAAAGTCTTATTACTCGCTTTAAATGGTTTTACAAACTCATA
131 CAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATA
7436 ATTGATTTTAAGTTGATTATTTTTATA-ATTTTT-ATTAAAAAAGA-TAATAATTGAATGTCTAC
1 ATTGATTTTAAGTTGA-TATTTTTATACATTTTTGATTAAAAAAGACTAATAATTGAATGTCTAC
* **********
7498 CTTGAGAAACGTAAAGAAAAAGGCATTCATTGGGAAGAAAAGTCCATTTATANNNNNNNNNNCCT
65 CTTGAGAAACGTAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACACATTCCT
* * * *
7563 TCAAAGGCCTTATTACTCGTTTTAAATGATTTTATAATGTCATA
130 TCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATA
* * * *
7607 ATTGATTTTAAGTTTA-ATGTTTT-TACATTTTTGGA-TAAAACAGACT-ATAATTGAATTTCAA
1 ATTGATTTTAAGTTGATAT-TTTTATACATTTTT-GATTAAAAAAGACTAATAATTGAATGTCTA
* * ** * *
7668 CCTTGAGAAACATAAAGAAAAAGACATTCATTGATAAAAAAAAAGTCCATTTATAGTCACATATT
64 CCTTGAGAAACGTAAAGAAAAAGGCATTCATTG--GCAAGAAAAGTCCATTTATAGTCACACATT
* *
7733 CCTTCACAAGCCGTATTACTCGCTTTAAATGGTTTTATAATCTCATA
127 CCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATA
* * * *
7780 ACTGATTTT-AGATTGA-ATTTTT-TACATTTTT-AGTTAGAACAA-A-TTATAATTAAATGTCT
1 ATTGATTTTAAG-TTGATATTTTTATACATTTTTGA-TTA-AAAAAGACTAATAATTGAATGTCT
* * * * * * *
7839 ACCTTGGGAAACGTGACGAAAAAGGTATTC-TTGGCAAGAAAAGTTCATTTATAGTCGCTCATTC
63 ACCTTGAGAAACGTAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACACATTC
*
7903 CTTCAAAAGCCTTATTACTCGCTTCAAATGGTTTTATAATCTCAT
128 CTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAT
7948 NNNNNNNNNN
Statistics
Matches: 540, Mismatches: 125, Indels: 39
0.77 0.18 0.06
Matches are distributed among these distances:
169 70 0.13
170 14 0.03
171 248 0.46
172 83 0.15
173 125 0.23
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.37
Consensus pattern (173 bp):
ATTGATTTTAAGTTGATATTTTTATACATTTTTGATTAAAAAAGACTAATAATTGAATGTCTACC
TTGAGAAACGTAAAGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACACATTCCTT
CAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATA
Found at i:7990 original size:342 final size:343
Alignment explanation
Indices: 7402--8051 Score: 749
Period size: 342 Copynumber: 1.9 Consensus size: 343
7392 TTAAAAGTCT
*
7402 TATTACTCGCTTTAAATGGTTTTACAAACTCATAATTGATTTTAAGTTGATTATTTTTATAATTT
1 TATTACTCGCTTTAAATGGTTTTACAAACTCATAACTGATTTTAAGTTGA-TATTTTTATAATTT
* *
7467 TTATTAAAAAAGATAATAATTGAATGTCTACCTTGAGAAACGTAAAGAAAAAGGCATTCATTGGG
65 TTATTAAAAAAGATAATAATTAAATGTCTACCTTGAGAAACGTAAAGAAAAAGGCATTCATTGGC
********** * * *
7532 AAGAAAAGTCCATTTATANNNNNNNNNNCCTTCAAAGGCCTTATTACTCGTTTTAAATGATTTTA
130 AAGAAAAGTCCATTTATAGTCGCTCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATGATTTTA
* * * *
7597 TAATGTCATAATTGATTTTAAGTTTAATGTTTTTACATTTTTGGATAAAACAGACTATAATTGAA
195 TAATCTCATAATTGATTTTAAGTTAAATGTTTTTACATTTTTGAATAAAACAGACTATAATTAAA
*
7662 TTTCAACCTTGAGAAACATAAAGAAAA-AGACATTCATT-GATAAAAAAAAAGTCCATTTATAGT
260 TATCAACCTTGAGAAACATAAA-AAAAGAGACATTCATTCG-TAAAAAAAAAGTCCATTTATAGT
7725 CACATATTCCTTCACAAGCCG
323 CACATATTCCTTCACAAGCCG
* *
7746 TATTACTCGCTTTAAATGGTTTTATAATCTCATAACTGATTTT-AGATTGA-ATTTTT-TACATT
1 TATTACTCGCTTTAAATGGTTTTACAAACTCATAACTGATTTTAAG-TTGATATTTTTATA-ATT
* * * * * *
7808 TTTAGTTAGAACAA-ATTATAATTAAATGTCTACCTTGGGAAACGTGACGAAAAAGGTATTC-TT
64 TTTA-TTA-AAAAAGATAATAATTAAATGTCTACCTTGAGAAACGTAAAGAAAAAGGCATTCATT
* *
7871 GGCAAGAAAAGTTCATTTATAGTCGCTCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATGGTT
127 GGCAAGAAAAGTCCATTTATAGTCGCTCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATGATT
********** * *
7936 TTATAATCTCATNNNNNNNNNNAAGTTAAATTTTTTTATATTTTT-AATTAAAACAGACTATAAT
192 TTATAATCTCATAATTGATTTTAAGTTAAATGTTTTTACATTTTTGAA-TAAAACAGACTATAAT
* * * *
8000 TAAATATCTATCTTGAGAAACATAAAAAAAGAGATATTCTTTCGTAAAAAAA
256 TAAATATCAACCTTGAGAAACATAAAAAAAGAGACATTCATTCGTAAAAAAA
8052 GAGATATTCT
Statistics
Matches: 252, Mismatches: 47, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
341 7 0.03
342 150 0.60
343 47 0.19
344 48 0.19
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.37
Consensus pattern (343 bp):
TATTACTCGCTTTAAATGGTTTTACAAACTCATAACTGATTTTAAGTTGATATTTTTATAATTTT
TATTAAAAAAGATAATAATTAAATGTCTACCTTGAGAAACGTAAAGAAAAAGGCATTCATTGGCA
AGAAAAGTCCATTTATAGTCGCTCATTCCTTCAAAAGCCTTATTACTCGCTTCAAATGATTTTAT
AATCTCATAATTGATTTTAAGTTAAATGTTTTTACATTTTTGAATAAAACAGACTATAATTAAAT
ATCAACCTTGAGAAACATAAAAAAAGAGACATTCATTCGTAAAAAAAAAGTCCATTTATAGTCAC
ATATTCCTTCACAAGCCG
Found at i:8050 original size:22 final size:22
Alignment explanation
Indices: 8022--8074 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
8012 TTGAGAAACA
8022 TAAAAAAAGAGATATTCTTTCG
1 TAAAAAAAGAGATATTCTTTCG
*
8044 TAAAAAAAGAGATATTCTTTGG
1 TAAAAAAAGAGATATTCTTTCG
8066 TAAAAAAAG
1 TAAAAAAAG
8075 TCCATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (22 bp):
TAAAAAAAGAGATATTCTTTCG
Found at i:8711 original size:170 final size:169
Alignment explanation
Indices: 8426--9542 Score: 623
Period size: 170 Copynumber: 6.5 Consensus size: 169
8416 AAAATCTTAT
* ** * *
8426 AATTGATTTTAAGTTGATTTTTTTTGTATTTTTGTTTAAAACAGACTATAATTGAATGTCTAACT
1 AATTGATTTTAAGTTGA-ATTTTTTACA-TTTTGTTTAAAACAGATTATAATTGAATGTCTACCT
** * ** * * ********** *
8491 CAAAAAATATGAAGAAAAAGGTATTCATTGACAANNNNNNNNNNTTTATAGTCACCCATTTCTTC
64 TGAGAAACGTGAAGAAAAAGGCATTCATTGAAAAGAAAAGTCCATTTATAGTCACCCATTCCTTC
* *
8556 AAAAGTCTTATTATTCGCTTTAAATGGTTTTATAATCCCAA
129 AAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCCCAA
* ** * *
8597 AA-TGTATTTTAAGTTCAATTTCTTTTTATTTT-TTCTAAAACAGATTATAATTGAATGTTTAGC
1 AATTG-ATTTTAAGTTGAATTT-TTTACATTTTGTT-TAAAACAGATTATAATTGAATGTCTACC
* * * *********
8660 TTGAGAAACGTGAAGCAAAAGGCATTCACTGATAAGAAAAGTCCATTTATAGTCACTTNNNNNNN
63 TTGAGAAACGTGAAGAAAAAGGCATTCATTGAAAAGAAAAGTCCATTTATAGTCACCCATTCCTT
*** ** * *
8725 NNNAAGGGTTATTACTCGCTTTAAAT-AGTTTTATAATCTCAT
128 CAAAAGTCTTATTACTCGCTTTAAATGA-TTTTATAATCCCAA
* * * ** * *
8767 AACTGATTTTAGGTTGAACTTTTTTACATTTTGGTTAAAACA-AACAGTAATTAAAATGTCAACC
1 AATTGATTTTAAGTTGAA-TTTTTTACATTTTGTTTAAAACAGATTA-TAATT-GAATGTCTACC
* * * * *
8831 TTGAAAAACATAAAGAAAAAGACATTCATTGGCAAAAAAAAAAGTCCATTTATAGTCACCCATTC
63 TTGAGAAACGTGAAGAAAAAGGCATTCATT-G--AAAAGAAAAGTCCATTTATAGTCACCCATTC
* * * ********** * *
8896 CTTTACAAGCCTTATTACTCGNNNNNNNNNNTTTTATAATCTCAT
125 CTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCCCAA
* * * *
8941 AATTGATTTTAGGTTGAATTTTTTTACATTTTGATTAGAACAGATTATAATTGAATGTCTGCCTT
1 AATTGATTTTAAGTTGAA-TTTTTTACATTTTGTTTAAAACAGATTATAATTGAATGTCTACCTT
* * * * ** ** ** *
9006 GGGAAACGTGAAAAAAAAAGTATTCATTGGCAAGAAAAGTTTATTTATAGTCACCCATTTTTTTA
65 GAGAAACGTGAAGAAAAAGGCATTCATTGAAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCA
* *
9071 AAAGTCTTATTACTCGCTTTAAATGATTTTACAA-CCTCAT
130 AAAGTCTTATTACTCGCTTTAAATGATTTTATAATCC-CAA
* * * * *
9111 AATTGATTTTAAGTTG-ATTATCTTTATATTTTTTATTAAAAAAGATAATAATTGAATGTTTACC
1 AATTGATTTTAAGTTGAATT-T-TTTACATTTTGT-TTAAAACAGATTATAATTGAATGTCTACC
* * ** *
9175 TCGAGAAATGTGAA-AAAAAGGCATTCATTGGGAAGAAAAGTCCATTTATAGTCACCGATTCCTT
63 TTGAGAAACGTGAAGAAAAAGGCATTCATTGAAAAGAAAAGTCCATTTATAGTCACCCATTCCTT
* * * *
9239 CAAAGGTCTTATTACTCGTTTTAAATGATTTTATAATCTCAT
128 CAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCCCAA
*********** * * *
9281 AATTGATNNNNNNNNNNTTTTTTTTACATTTTTGGTTAAAACAGAGTATAATTGAATGTCAACCT
1 AATTGAT-TTTAAGTTGAATTTTTTACA-TTTTGTTTAAAACAGATTATAATTGAATGTCTACCT
* * ** **********
9346 TGAGAAACATAAAGAAAAAGATATTCATTGACAANNNNNNNNNNATTTATAGTCACCCATTCCTT
64 TGAGAAACGTGAAGAAAAAGGCATTCATTGA-AAAGAAAAGTCCATTTATAGTCACCCATTCCTT
* * * * **
9411 CACAAG-CTGTATTACTTGCTTTAAATGGTTTTATAATCTCGT
128 CAAAAGTCT-TATTACTCGCTTTAAATGATTTTATAATCCCAA
* * * * * *
9453 AACTGTTTTTAGGTTGAATTTTTTACATTTT-TAGTTAGAACATATTATAATTAAATGTCTACCT
1 AATTGATTTTAAGTTGAATTTTTTACATTTTGT--TTAAAACAGATTATAATTGAATGTCTACCT
* *
9517 TGGGAAACGTGAAGAAAAAGGTATTC
64 TGAGAAACGTGAAGAAAAAGGCATTC
9543 TTGGCAANNN
Statistics
Matches: 705, Mismatches: 214, Indels: 54
0.72 0.22 0.06
Matches are distributed among these distances:
168 2 0.00
169 7 0.01
170 340 0.48
171 168 0.24
172 63 0.09
173 30 0.04
174 93 0.13
175 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.37
Consensus pattern (169 bp):
AATTGATTTTAAGTTGAATTTTTTACATTTTGTTTAAAACAGATTATAATTGAATGTCTACCTTG
AGAAACGTGAAGAAAAAGGCATTCATTGAAAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAA
AAGTCTTATTACTCGCTTTAAATGATTTTATAATCCCAA
Found at i:9192 original size:171 final size:169
Alignment explanation
Indices: 8535--9661 Score: 617
Period size: 170 Copynumber: 6.6 Consensus size: 169
8525 NNNNNNNNNN
* * * * *
8535 TTTATAGTCACCCATTTCTTCAAAAGTCTTATTATTCGCTTTAAATGGTTTTATAATCCCA-AAA
1 TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAT
* ** * * * * * *
8599 TGTATTTTAAGTTCAATTTCTTTTTATTTT-TTCTAAAACAGATTATAATTGAATGTTTAGCTTG
66 TG-ATTTTAAGTTGAATTTCTTTACATTTTGAT-TAAAAAAGATAATAATTGAATGTCTACCTCG
* * * **
8663 AGAAACGTGAAGCAAAAGGCATTCACTGATAAGAAAAGTCCA
129 AGAAACGTGAA-AAAAAAGCATTCATTGGCAAGAAAAGTCCA
************ **
8705 TTTATAGTCACTTNNNNNNNNNNAAGGGTTATTACTCGCTTTAAAT-AGTTTTATAATCTCATAA
1 TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGA-TTTTATAATCTCATAA
* * * * * * *
8769 CTGATTTTAGGTTGAACTTT-TTTACATTTTGGTTAAAACAA-ACAGTAATTAAAATGTCAACCT
65 TTGATTTTAAGTTGAA-TTTCTTTACATTTTGATTAAAA-AAGATAATAATT-GAATGTCTACCT
* * * *
8832 TGAAAAACAT-AAAGAAAAAGACATTCATTGGCAAAAAAAAAAGTCCA
127 CGAGAAACGTGAAA-AAAAAG-CATTCATTGGC---AAGAAAAGTCCA
* * * **********
8879 TTTATAGTCACCCATTCCTTTACAAGCCTTATTACTCGNNNNNNNNNNTTTTATAATCTCATAAT
1 TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAT
* * * * * * * *
8944 TGATTTTAGGTTGAATTTTTTTACATTTTGATTAGAACAGATTATAATTGAATGTCTGCCTTGGG
66 TGATTTTAAGTTGAATTTCTTTACATTTTGATTAAAAAAGATAATAATTGAATGTCTACCTCGAG
* **
9009 AAACGTGAAAAAAAAAGTATTCATTGGCAAGAAAAGTTTA
131 AAACGTG-AAAAAAAAGCATTCATTGGCAAGAAAAGTCCA
** * * *
9049 TTTATAGTCACCCATTTTTTTAAAAGTCTTATTACTCGCTTTAAATGATTTTACAACCTCATAAT
1 TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAT
* * *
9114 TGATTTTAAGTTG-ATTATCTTTATATTTTTTATTAAAAAAGATAATAATTGAATGTTTACCTCG
66 TGATTTTAAGTTGAATT-TCTTTACA-TTTTGATTAAAAAAGATAATAATTGAATGTCTACCTCG
* * *
9178 AGAAATGTGAAAAAAAGGCATTCATTGGGAAGAAAAGTCCA
129 AGAAACGTGAAAAAAAAGCATTCATTGGCAAGAAAAGTCCA
* * *
9219 TTTATAGTCACCGATTCCTTCAAAGGTCTTATTACTCGTTTTAAATGATTTTATAATCTCATAAT
1 TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAT
*********** * * * * *
9284 TGATNNNNNNNNNNTTTTTTTTACATTTTTGGTTAAAACAGAGT-ATAATTGAATGTCAACCTTG
66 TGATTTTAAGTTGAATTTCTTTACA-TTTTGATTAAAAAAGA-TAATAATTGAATGTCTACCTCG
* * * *********
9348 AGAAACAT-AAAGAAAAAGATATTCATTGACAANNNNNNNNNNA
129 AGAAACGTGAAA-AAAAAG-CATTCATTGGCAA-GAAAAGTCCA
* * * *
9391 TTTATAGTCACCCATTCCTTCACAAG-CTGTATTACTTGCTTTAAATGGTTTTATAATCTCGTAA
1 TTTATAGTCACCCATTCCTTCAAAAGTCT-TATTACTCGCTTTAAATGATTTTATAATCTCATAA
* * * * * * * * * *
9455 CTGTTTTTAGGTTGAATTT-TTTACATTTTTAGTTAGAACATATTATAATTAAATGTCTACCTTG
65 TTGATTTTAAGTTGAATTTCTTTACATTTTGA-TTAAAAAAGATAATAATTGAATGTCTACCTCG
* * * **********
9519 GGAAACGTGAAGAAAAAGGTATTC-TTGGCAANNNNNNNNNN
129 AGAAACGTGAA-AAAAAAGCATTCATTGGCAAGAAAAGTCCA
* * *
9560 TTTATAGTCGCCCATTCCTTCAAAAGCCTTATTACTCGCTTCAAAT-AGTTTT-TAATCTCATAA
1 TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGA-TTTTATAATCTCATAA
* * * * * *
9623 TCGAGTTTAAGTTAAATTTTTTTATATTTTTAATTAAAA
65 TTGATTTTAAGTTGAATTTCTTTACA-TTTTGATTAAAA
9662 NNNNNNNNNN
Statistics
Matches: 726, Mismatches: 199, Indels: 65
0.73 0.20 0.07
Matches are distributed among these distances:
168 23 0.03
169 68 0.09
170 310 0.43
171 129 0.18
172 68 0.09
173 31 0.04
174 94 0.13
175 3 0.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.38
Consensus pattern (169 bp):
TTTATAGTCACCCATTCCTTCAAAAGTCTTATTACTCGCTTTAAATGATTTTATAATCTCATAAT
TGATTTTAAGTTGAATTTCTTTACATTTTGATTAAAAAAGATAATAATTGAATGTCTACCTCGAG
AAACGTGAAAAAAAAGCATTCATTGGCAAGAAAAGTCCA
Found at i:10533 original size:171 final size:171
Alignment explanation
Indices: 10019--11486 Score: 1295
Period size: 171 Copynumber: 8.6 Consensus size: 171
10009 NNNNNNNNNN
* * * * * * * * **
10019 TTTTATAGTCTCAAAATTAATTTTATGTTCAATTTCTTTATATTTTT--TGTAAAATAGGTTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGAT-TAAAACAGACTATA
* ** * * * * * * *
10082 ATTGAATGTTTACCTAAAGAAACGTGATGCAAAAGGCATTTACTT-A-TAAGAAAGTCCATTTAT
65 ATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCA-TTGACAAAAAAAGTCCATTTAT
** * * *
10145 AGTCACTTATTCCTTCAAAAGGCTTATTACTCGTTTTAAATAG
129 AGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * * *
10188 TTTTATAATCTCATAATTGATTTTAGGTTGAACTTTTTTACA-TGTTGGTTAAAACAAACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAA
* * * * ** *
10252 TTGAATGTCAACCATGAAAAACATAAAGAAAAAGACATTCATTGGCAAAAAAAAAGTCCATTTAT
66 TTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATT-G-ACAAAAAAAGTCCATTTAT
* *
10317 AGTCACCCATTCCTTCACAAGCCTTATTACTTGCTTTAAATGG
129 AGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * *
10360 TTTTATAATCTTATAATTGATTTTAGGTTGAATTTTTTTACATTTTTGATTAGAACAGATTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAA
* * * *
10425 TTGAATGTCTGCCTTGGGAAACATGAAGAAAAAGGTATTCATTGACAAGAAAAGTTCATTTATAG
66 TTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATTGACAAAAAAAGTCCATTTATAG
*
10490 TCACCCATTCTCTT-AAAAGTCTTATTACTCGCTTTAAATGG
131 TCACCCATTC-CTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * *
10531 TTTTATAACCTCATAATTAATTTTAAGTTG-ATTATTTTTATATTTTTTATTAGAAAC-GA-TAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTTACATTTTTGATTA-AAACAGACT-A
* * ** *
10593 TAATTGAATGTCTACCTCGAGAAACATGAAGAAAAAGGCATTCATTGGGAAGAAAAGTCCATTTA
63 TAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATTGACAAAAAAAGTCCATTTA
* *
10658 TAGTCACCCATTCCTTCAAAAGCCTTATTACTCGTTTTAAATGA
128 TAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * ** *
10702 TTTTACAATCTCATAATTGATTTTAAGTTAAATTTTTTTACATTTTTGGTTAAATTATACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAA
* * ** * *
10767 TTGAATGTCAACCTTGAGAAACATAAAGAAAAAGACATTCATTGATAAAAAAAATTCCATTTATA
66 TTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATTGA-CAAAAAAAGTCCATTTATA
* *
10832 GTCACCCATTCCTTCACAAGCCGTATTACTCGCTTTAAATGG
130 GTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * * *
10874 TTTTATAACCTCATAACTGATTTTAGGTTGAA-TTTTTTACATTTTT-AGTTATAACAGATTATA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGA-TTAAAACAGACTATA
********************* * * *
10937 ATTGAATGNNNNNNNNNNNNNNNNNNNNNAAAAAGGTATTC-TTGGCAAGAAAAGTTCATTTATA
65 ATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATTGACAAAAAAAGTCCATTTATA
* * * *
11001 GTCGCCCATTCCTTCAAAATCCCTATTACTCGCTTCAAATGG
130 GTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * * * * * * *
11043 -TTTATGATATCATAATCGAGTTTAACTTAAATTTTTTTATATTTTTAATTAAAA-AAACTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAA
* **
11106 TTGAATGTCTATCTTGAG-AA-ATGTAA-AAAAAGTGATATTCATTGGTAAAAAAAGTCCATTTA
66 TTGAATGTCTACCTTGAGAAACATG-AAGAAAAAG-G-TATTCATTGACAAAAAAAGTCCATTTA
* * * ** * *
11168 TACTCACCCATTCTTTCGAAAGCCTTATTACAGGTTTTAAATAG
128 TAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * * *
11212 TTTTATAATCTCATAGTTGATTTTAAGTTGAATTTTTTTGCATATTTGGTTAAAACAGGCTATAA
1 TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAA
**
11277 TTGAATGTCTACCTCAAGAAACATGAAG-AAAAGGTATTCATTGACAAAAAAAGAT-CATTTATA
66 TTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATTGACAAAAAAAG-TCCATTTATA
* *
11340 GTCACCCATTTCTTCAAAGGCCTTATTACTCGCTTTAAATGG
130 GTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
* * * * * * * * * **
11382 TTTTATAGTC-CTAAAATTGATTTTATGTTCAATTTCTTTATATTTATCA-TAAAATAGGTTATA
1 TTTTATAATCTC-ATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATA
* * * * * *
11445 ATTGAATGTTTACCTTAAGAAACGTGATGCAAAAGGCATTCA
65 ATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCA
11487 CNNNNNNNNN
Statistics
Matches: 1038, Mismatches: 230, Indels: 61
0.78 0.17 0.05
Matches are distributed among these distances:
166 6 0.01
167 1 0.00
168 46 0.04
169 233 0.22
170 160 0.15
171 345 0.33
172 192 0.18
173 55 0.05
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.38
Consensus pattern (171 bp):
TTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGATTAAAACAGACTATAA
TTGAATGTCTACCTTGAGAAACATGAAGAAAAAGGTATTCATTGACAAAAAAAGTCCATTTATAG
TCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGG
Found at i:12553 original size:169 final size:171
Alignment explanation
Indices: 12199--12578 Score: 388
Period size: 169 Copynumber: 2.2 Consensus size: 171
12189 NNNNNNNTTG
* * *
12199 TAAGTTGAATTTTTTTACATTTTTGGTTAAAACAAACTATAATTGAATGTCAACCTTGAGAAACA
1 TAAGTT-AAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCAACCTTGAGAAACA
*
12264 TAAAGAAAAAGACATTCATTGACAAAAAAAAGTCCATTTATAGTCACCCATTCCTTCACAAGCCG
65 TAAAGAAAAAGACATTCATTGACAAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCG
* * *****
12329 TATTACTTGCTTTAAATGGTTTTATAATCTCATAACTNNNNN
130 TATTACTCGCTTCAAATGGTTTTATAATCTCATAACTGAGTT
***** * * * * * **
12371 NNNNNTGAATTTTTTACATTTTTAGTTAGAACAGATTATAATTGAATGTCTACCTTGGGAAAGGT
1 TAAGTTAAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCAACCTTGAGAAACAT
* ** * * * ** * *
12436 GAAGAAAAAGGTATTC-TTGGC-AAGAAAAGTTCATTTATAGTTGCCCATTCCTTCAAAAGTCTT
66 AAAGAAAAAGACATTCATTGACAAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCGT
*
12499 ATTACTCGCTTCAAATGGTTTTATATTCTCATAA-TCGAGTT
131 ATTACTCGCTTCAAATGGTTTTATAATCTCATAACT-GAGTT
* *
12540 TAAGTTAAATTTTTTTATATTTTTAATTAAAACAGACTA
1 TAAGTTAAA-TTTTTTACATTTTTAGTTAAAACAGACTA
12579 NNNNNNNNNN
Statistics
Matches: 162, Mismatches: 44, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
168 1 0.01
169 69 0.43
170 29 0.18
171 62 0.38
172 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.37
Consensus pattern (171 bp):
TAAGTTAAATTTTTTACATTTTTAGTTAAAACAGACTATAATTGAATGTCAACCTTGAGAAACAT
AAAGAAAAAGACATTCATTGACAAAAAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCGT
ATTACTCGCTTCAAATGGTTTTATAATCTCATAACTGAGTT
Found at i:14423 original size:170 final size:169
Alignment explanation
Indices: 13928--15228 Score: 719
Period size: 171 Copynumber: 7.6 Consensus size: 169
13918 NNNNNNNNNN
* ** * * * ** *
13928 GTGACTATAAATGAACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCAAGGCATTCTT
1 GTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACAT
* * *
13993 TCAATTATAATCTGTTCTAACCAAAAATATAAAAAAATTCAA-TCTGAAATCAATTATGAGTTTA
66 TCAATTATAATCTGTTTTAA-CAAAAATAT-AAAAAATTCAACT-TAAAATCAATTATGAGATTA
** *
14057 TAAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGAAATAG
128 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAA
* * * ** * **
14099 GTGACTATAAATGGACTTTT-TTTTGCAAATGAATGTCTTTTTCTTTATATTTTTCATGGTTCAC
1 GTGACTATAAATGGACTTTTCTTAT-C-AATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAAC
* * * * * * *
14163 ATACAATTATAGTCTATTTTAACTAAAATGTACAAAAGTTCAACCTAAAATCAATTATGAGATTA
64 ATTCAATTATAATCTGTTTTAACAAAAATATA-AAAAATTCAACTTAAAATCAATTATGAGATTA
** *
14228 TAAAATTATTTAAAGCGAGTAATAA-GCTTGTTGAAGGAATAA
128 TAAAACCATTTAAAGCGAGTAATAAGGCTT-TTGAAGAAATAA
* *
14270 GTGACTATAAATGGACTTTTCTTATCAGTGAATGCCTTTTACTTCACGTTTTTCAAGGTAAACAT
1 GTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACAT
** * * * *
14335 TCAATTATAATCTGTTTTAGGAAAAATATAAAGAAATTGAACTTAAAATTAATTTTGAAATTATA
66 TCAATTATAATCTGTTTTAACAAAAATATAAA-AAATTCAACTTAAAATCAATTATGAGATTATA
* ****
14400 AAACCATTTAAAGCGAATAATAAGGCTTTTGAAGAANNNN
130 AAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAA
****** * * * * * * *
14440 NNNNNNATAAATGGTCTTTTTTTGTCAATGAATACCTTTTTCTTCATGTTTCTT-AAAGTAGACA
1 GTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTT-TTCAAGGTAAACA
* * * *
14504 TTCAATTATAGTCTGTTTTAAACAAAAATGTAAAAAAATCAACTTAAAATCAATTATAAGATTAT
65 TTCAATTATAATCTGTTTT-AACAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTAT
* * * * **
14569 AAAACCATTGAAAACGTGTAATAAGGCTTTCGAA-AGAATGG
129 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGA-AATAA
* * ** * * * * * *
14610 GTGACTATAAATTGACATTTT-TTACCAATGAATATCTTTTT-TTTAAGCTTTTCGAGATAGACA
1 GTGACTATAAATGGAC-TTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACA
* * * *********************
14673 TTCAATTATAGTCTGTTTTAATTAAAAATATAAAAAAATTTAACNNNNNNNNNNNNNNNNNNNNN
65 TTCAATTATAATCTGTTTTAA-CAAAAATAT-AAAAAATTCAACTTAAAATCAATTATGAGATTA
*********** * *
14738 NNNNNNNNNNNAAAGCGAGTAATAAGGCTTTTGAAGGAATAG
128 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAA
* * ** * * ** *
14780 GTAACTATAAATGAACTTTTCTTCCCAATGAATGCCTTTTTCTTTACATTTTTTGAGGTAGACAT
1 GTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACAT
* * * * * * ** *
14845 TCAATTATTATCTTTTTTAGCAAAAATTGTAAAAATAATCAACTTAAAATTAATTATGAGGCTGT
66 TCAATTATAATCTGTTTTAACAAAAA-TATAAAAA-ATTCAACTTAAAATCAATTATGAGATTAT
* * * *
14910 AAAACCGTTTAAAGCGAGTAATAAGGCTTTTAAAGGAATAG
129 AAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAA
********** * ** *
14951 GTGACTATAAAT-GANNNNNNNNNNCCAATGAATACCTTTTTCTTCACGTTTCCCAAGGTAGACA
1 GTGACTATAAATGGA-CTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACA
* * * * * * *
15015 TTCAATTGTACTCTGTTCTAACCAAAAATGTAAAACAATTCAACCTAAAATTAATTATAAGATTA
65 TTCAATTATAATCTGTTTTAA-CAAAAATATAAAA-AATTCAACTTAAAATCAATTATGAGATTA
* * * **********
15080 TAAAATCATTTAAAGTGAGTAATAAGGCTTGTNNNNNNNNNN
128 TAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAA
* * * * * * **
15122 GTGACTATAAATGGACTTTTTTTTTCAATAAATGTCTTTTTCTTTATGTTTTTCAAGGTTGACAT
1 GTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACAT
* * *
15187 TCAATTATAGTCTGTTTTAACTAAAATGTAAAAAAGTTCAAC
66 TCAATTATAATCTGTTTTAACAAAAATATAAAAAA-TTCAAC
15229 CTANNNNNNN
Statistics
Matches: 833, Mismatches: 272, Indels: 51
0.72 0.24 0.04
Matches are distributed among these distances:
168 4 0.00
169 48 0.06
170 351 0.42
171 375 0.45
172 55 0.07
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.35
Consensus pattern (169 bp):
GTGACTATAAATGGACTTTTCTTATCAATGAATGCCTTTTTCTTCACGTTTTTCAAGGTAAACAT
TCAATTATAATCTGTTTTAACAAAAATATAAAAAATTCAACTTAAAATCAATTATGAGATTATAA
AACCATTTAAAGCGAGTAATAAGGCTTTTGAAGAAATAA
Found at i:14593 original size:340 final size:340
Alignment explanation
Indices: 13928--14712 Score: 801
Period size: 340 Copynumber: 2.3 Consensus size: 340
13918 NNNNNNNNNN
* * * * ** *
13928 GTGACTATAAATGAACTTTTCTTGCCAATGAATACCTTTTTCTTCACGTTTCTCAAGGCATTCTT
1 GTGACTATAAATGGACTTTTCTTACCAATGAATACC-TTTTCTTCACGTTTTTCAAGGTAAACAT
* * **
13993 TCAATTATAATCTGTTCTAACCAAAAATATAAAAAAATTCAATCTGAAATCAATTATGAGTTTAT
65 TCAATTATAATCTGTT-TTACCAAAAATATAAAAAAATTCAATCTAAAATCAATTATGAAATTAT
*
14058 AAAACCATTTAAAGCGAGTAATAAGGCTTTCAAAGAAATAGGTGACTATAAATGGACTTTTTTTT
129 AAAACCATTTAAAGCGAATAATAAGGCTTTCAAAGAAATAGGTGACTATAAATGGACTTTTTTTT
** * ** * *
14123 GCAAATGAATGTCTTTTTCTTTATATTTTTCATGGTTCACATACAATTATAGTCTATTTTAACTA
194 GCAAATGAATACCTTTTTCTTCATATTTTTCAAAGTACACATACAATTATAGTCTATTTTAACAA
** * ** * *
14188 AAATGTACAAAAGTTCAACCTAAAATCAATTATGAGATTATAAAATTATTTAAAGCGAGTAATAA
259 AAATGTACAAAAAATCAACCTAAAATCAATTATAAGATTATAAAACCATTGAAAACGAGTAATAA
* *
14253 -GCTTGTTGAAGGAATAA
324 GGCTT-TCGAAAGAATAA
* * *
14270 GTGACTATAAATGGACTTTTCTTATCAGTGAATGCCTTTTACTTCACGTTTTTCAAGGTAAACAT
1 GTGACTATAAATGGACTTTTCTTACCAATGAATACCTTTT-CTTCACGTTTTTCAAGGTAAACAT
** * * * *
14335 TCAATTATAATCTGTTTTAGGAAAAATATAAAGAAATTGAA-CTTAAAATTAATTTTGAAATTAT
65 TCAATTATAATCTGTTTTACCAAAAATATAAAAAAATTCAATC-TAAAATCAATTATGAAATTAT
** ********** *
14399 AAAACCATTTAAAGCGAATAATAAGGCTTTTGAAGAANNNNNNNNNNATAAATGGTC-TTTTTTT
129 AAAACCATTTAAAGCGAATAATAAGGCTTTCAAAGAAATAGGTGACTATAAATGGACTTTTTTTT
* * * *
14463 GTC-AATGAATACCTTTTTCTTCATGTTTCTT-AAAGTAGACATTCAATTATAGTCTGTTTTAAA
194 G-CAAATGAATACCTTTTTCTTCATATTT-TTCAAAGTACACATACAATTATAGTCTATTTT-AA
* *
14526 CAAAAATGTA-AAAAAATCAACTTAAAATCAATTATAAGATTATAAAACCATTGAAAACGTGTAA
256 CAAAAATGTACAAAAAATCAACCTAAAATCAATTATAAGATTATAAAACCATTGAAAACGAGTAA
**
14590 TAAGGCTTTCGAAAGAATGG
321 TAAGGCTTTCGAAAGAATAA
* * * * * * * * *
14610 GTGACTATAAATTGACATTTT-TTACCAATGAATATCTTTTTTTTAAGCTTTTCGAGATAGACAT
1 GTGACTATAAATGGAC-TTTTCTTACCAATGAATACCTTTTCTTCACGTTTTTCAAGGTAAACAT
* **
14674 TCAATTATAGTCTGTTTTAATTAAAAATATAAAAAAATT
65 TCAATTATAATCTGTTTT-ACCAAAAATATAAAAAAATT
14713 TAACNNNNNN
Statistics
Matches: 361, Mismatches: 74, Indels: 18
0.80 0.16 0.04
Matches are distributed among these distances:
339 34 0.09
340 156 0.43
341 105 0.29
342 66 0.18
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.37
Consensus pattern (340 bp):
GTGACTATAAATGGACTTTTCTTACCAATGAATACCTTTTCTTCACGTTTTTCAAGGTAAACATT
CAATTATAATCTGTTTTACCAAAAATATAAAAAAATTCAATCTAAAATCAATTATGAAATTATAA
AACCATTTAAAGCGAATAATAAGGCTTTCAAAGAAATAGGTGACTATAAATGGACTTTTTTTTGC
AAATGAATACCTTTTTCTTCATATTTTTCAAAGTACACATACAATTATAGTCTATTTTAACAAAA
ATGTACAAAAAATCAACCTAAAATCAATTATAAGATTATAAAACCATTGAAAACGAGTAATAAGG
CTTTCGAAAGAATAA
Found at i:15845 original size:171 final size:169
Alignment explanation
Indices: 15332--15924 Score: 554
Period size: 171 Copynumber: 3.5 Consensus size: 169
15322 NNNNNNNNNN
* * * * * *
15332 TTTATAATCTCATAATTGATTTTAGGTTAAATTGTTTTACATTTTTAGTTAGAACAGAGTATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTTATATTTTTAGTTAAAACAGACTATAAT
* * *
15397 TGAATGTCTACCTTGGGAA-ATGTGAAGAAAAAGGTATTCATTGGCAAAAAAAGTTCATTTATAG
66 TGAATGTCTACCTCGAGAACAT-T-AAAAAAAAGGTATTCATTGG-AAAAAAAGTTCATTTATAG
* * ** * *
15461 TCACCTATTCTTTTAAGCGCCTTATTCCTCGCTTTAAATGGT
128 TCACCCATTCTTTCAAAAGCCTTATTACACGCTTTAAATGGT
* ** * * * *
15503 TTTACAGCCTCATAATTGATTTTAAGTTGATTATTTTTATATTTTT-GCTAAAAAAGA-TAATAA
1 TTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTTATATTTTTAGTTAAAACAGACT-ATAA
* *
15566 TTGAATGTCTACCTCGA-AAAACGT--AAAAAAGGTATTCATTGGAAATAAAAGTTCATTTATAG
65 TTGAATGTCTACCTCGAGAACA-TTAAAAAAAAGGTATTCATTGGAAA-AAAAGTTCATTTATAG
* * ********** *
15628 TGACCCATTCCTTCAAAAGCCTNNNNNNNNNNTTTAAATAGT
128 TCACCCATTCTTTCAAAAGCCTTATTACACGCTTTAAATGGT
** * *
15670 TTTATAATCTCATAATCAATTTTAAGTTAATTTTTTTTATATTTTTAATTAAAATAGACTATAAT
1 TTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTTATATTTTTAGTTAAAACAGACTATAAT
* * * * *
15735 TGAATGTCTATCTCGTGAAGCATTAAAAAAAAGTTATTCATTGGTAAAAAATGTCCATTTATAGT
66 TGAATGTCTACCTCGAGAA-CATTAAAAAAAAGGTATTCATTGG-AAAAAAAGTTCATTTATAGT
* * **
15800 CACCCATTCTTTCGAAAGCCTTATTACACGTTTTCCATGGT
129 CACCCATTCTTTCAAAAGCCTTATTACACGCTTTAAATGGT
* **
15841 TTTATAATCTTATAATTGATTTTAAGTTGAATTTTTTTGCT-TTTTT-GTTTAAAACAGACTATA
1 TTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTTATATTTTTAG-TTAAAACAGACTATA
*
15904 ATTGAATGTCTACCTCAAGAA
64 ATTGAATGTCTACCTCGAGAA
15925 ACATGAAGAA
Statistics
Matches: 333, Mismatches: 76, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
166 3 0.01
167 97 0.29
168 27 0.08
169 7 0.02
170 30 0.09
171 156 0.47
172 13 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.40
Consensus pattern (169 bp):
TTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTTATATTTTTAGTTAAAACAGACTATAAT
TGAATGTCTACCTCGAGAACATTAAAAAAAAGGTATTCATTGGAAAAAAAGTTCATTTATAGTCA
CCCATTCTTTCAAAAGCCTTATTACACGCTTTAAATGGT
Found at i:17411 original size:172 final size:170
Alignment explanation
Indices: 17206--17941 Score: 534
Period size: 171 Copynumber: 4.3 Consensus size: 170
17196 AGAAAAATGT
** * *
17206 ATTTATAGTCACTTAGTTC-TTCAAAAGCCTTATTTCTTGCTTTAAATGGTTTTATAATCTCAAA
1 ATTTATAGTCACCCA-TTCGTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTC-AA
* * * * * * * *
17270 AATTAATTTTATGTTCAATTTTTTTTACATTTTTCGTTAAAAC-AGATTATCATTCAATGTTTAC
64 AATTAATTTTAAGTT-AA-ATTTTTTACATTTTTAGTTAAAACTA-ACTATAATTCAATATCTAA
* *
17334 CTTGAGAAATATAAAGAAAAAG-CATTCATTGGCAAGAAAAGTCC
126 CTCGAGAAACATAAAGAAAAAGACATTCATTGGCAAGAAAAGTCC
* * * * * *
17378 ATTTGTAGTCGCCCATTCTTTCAAAAACCTTATTACTCACTTTAAATGGTTTTATAATCTCATAA
1 ATTTATAGTCACCCATTCGTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAA
** *
17443 TTTGTTTTAAGTTAAATTTTTTACATTTTTAGTTAAAACTAACTATAATTGAATATCTAACTCGA
66 TTAATTTTAAGTTAAATTTTTTACATTTTTAGTTAAAACTAACTATAATTCAATATCTAACTCGA
* * * *
17508 GAAACGTGAAGAAAAAGAGATTCATTGGCAAGAAAAGTCT
131 GAAACATAAAGAAAAAGACATTCATTGGCAAGAAAAGTCC
* **********
17548 ATTTATAGTCACCCATTCGTTCAAAAGCCTTATCACTCGCTTTAAATGGTTTTNNNNNNNNNNAA
1 ATTTATAGTCACCCATTCGTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAA
* * * * * * * *
17613 TTGATTTTAAGTT-GATTATATTTACATTTTTTGTTAAAAC-AGACAATAATTTATTGTCTACCT
66 TTAATTTTAAGTTAAATT-T-TTTACATTTTTAGTTAAAACTA-ACTATAATTCAATATCTAACT
* * * ********** *
17676 CAAGAAACGTGAAGAAAAAGACATTCATNNNNNNNNNNAGTCT
128 CGAGAAACATAAAGAAAAAGACATTCATTGGCAAGAAAAGTCC
* * * *
17719 ATTTATAGTCACCCATTCCTTTAAAGGCCTTATTACTCGCTTT-AATGGTTTTATAATCTCATAA
1 ATTTATAGTCACCCATTCGTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAA
* ********* * * * *
17783 TTGATTTNNNNNNNNNNTTTTTTACATTTTTGGTTAAAAC-AGACTATATTTGAATGTC-AATCT
66 TTAATTT-TAAGTTAAATTTTTTACATTTTTAGTTAAAACTA-ACTATAATTCAATATCTAA-CT
* * * * *
17846 CGAGAAACATGAAGAAAAAGGCATTCATTGACAAAAAAAAGACC
128 CGAGAAACATAAAGAAAAAGACATTCATTGGC-AAGAAAAGTCC
* * *
17890 ATTTATAGTCACCCATTCCTTCACAAGGCTTATTACTCGCTTTAAATGGTTT
1 ATTTATAGTCACCCATTCGTTCAAAAGCCTTATTACTCGCTTTAAATGGTTT
Statistics
Matches: 443, Mismatches: 110, Indels: 22
0.77 0.19 0.04
Matches are distributed among these distances:
169 57 0.13
170 163 0.37
171 164 0.37
172 59 0.13
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.37
Consensus pattern (170 bp):
ATTTATAGTCACCCATTCGTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTATAATCTCAAAA
TTAATTTTAAGTTAAATTTTTTACATTTTTAGTTAAAACTAACTATAATTCAATATCTAACTCGA
GAAACATAAAGAAAAAGACATTCATTGGCAAGAAAAGTCC
Found at i:17593 original size:170 final size:170
Alignment explanation
Indices: 17118--17941 Score: 712
Period size: 170 Copynumber: 4.8 Consensus size: 170
17108 NNNNNNNNNN
* *
17118 TTTACA-TTTTGGTTAAAACAGACTATAATTGAATGTCTACCT-TAGGAAACGTGAGGAAAAA-A
1 TTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTCGA-GAAACGTGAAGAAAAAGA
* * * ** * *
17180 TCATTCATTGGTAAAAAGAAAAATGTATTTATAGTCACTTAGTT-CTTCAAAAGCCTTATTTCTT
65 -CATTCATTGG---CAAGAAAAGTCTATTTATAGTCACCCA-TTCCTTCAAAAGCCTTATTACTC
* * * *
17244 GCTTTAAATGGTTTTATAATCTCAAAAATTAATTTTATGTTCAATTTTT
125 GCTTTAAATGGTTTTATAATCTC-ATAATTGATTTTAAGTT-AA-ATTT
* * * * * * ** *
17293 TTTACATTTTTCGTTAAAACAGATTATCATTCAATGTTTACCTTGAGAAATATAAAGAAAAAG-C
1 TTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGAC
* * * * * *
17357 ATTCATTGGCAAGAAAAGTCCATTTGTAGTCGCCCATTCTTTCAAAAACCTTATTACTCACTTTA
66 ATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTA
17422 AATGGTTTTATAATCTCATAATTTG-TTTTAAGTTAAATTT
131 AATGGTTTTATAATCTCATAA-TTGATTTTAAGTTAAATTT
* * *
17462 TTTACATTTTTAGTTAAAACTA-ACTATAATTGAATATCTAACTCGAGAAACGTGAAGAAAAAGA
1 TTTACATTTTTGGTTAAAAC-AGACTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGA
* * *
17526 GATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCGTTCAAAAGCCTTATCACTCGCTTT
65 CATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
********** *
17591 AAATGGTTTTNNNNNNNNNNAATTGATTTTAAGTT-GATTAT
130 AAATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATT-T
* * * * *
17632 ATTTACATTTTTTGTTAAAACAGACAATAATTTATTGTCTACCTCAAGAAACGTGAAGAAAAAGA
1 -TTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGA
********** * *
17697 CATTCATNNNNNNNNNNAGTCTATTTATAGTCACCCATTCCTTTAAAGGCCTTATTACTCGCTTT
65 CATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
*********
17762 -AATGGTTTTATAATCTCATAATTGATTTNNNNNNNNNNTTT
130 AAATGGTTTTATAATCTCATAATTGATTT-TAAGTTAAATTT
* * * * *
17803 TTTACATTTTTGGTTAAAACAGACTATATTTGAATGTCAATCTCGAGAAACATGAAGAAAAAGGC
1 TTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGAC
* * * * * *
17868 ATTCATTGACAAAAAAAAGACCATTTATAGTCACCCATTCCTTCACAAGGCTTATTACTCGCTTT
66 ATTCATTGGC-AAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
17933 AAATGGTTT
130 AAATGGTTT
Statistics
Matches: 511, Mismatches: 123, Indels: 33
0.77 0.18 0.05
Matches are distributed among these distances:
169 59 0.12
170 162 0.32
171 161 0.32
172 69 0.14
175 16 0.03
176 43 0.08
177 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.37
Consensus pattern (170 bp):
TTTACATTTTTGGTTAAAACAGACTATAATTGAATGTCTACCTCGAGAAACGTGAAGAAAAAGAC
ATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTA
AATGGTTTTATAATCTCATAATTGATTTTAAGTTAAATTT
Done.