Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018403234.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_904.0, 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: 35713
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.25
Warning! 11502 characters in sequence are not A, C, G, or T
Found at i:409 original size:171 final size:170
Alignment explanation
Indices: 104--494 Score: 441
Period size: 171 Copynumber: 2.3 Consensus size: 170
94 NNNNNNNNNN
* * *
104 CATTCATTGGAAAGAAAAGTCCTTTATAATCACTCATTCCTTCAAAAGCCCTACTAATCGCTTTA
1 CATTCATTGGAAAGAAAAGTCATTTATAATCACTCATTCCTTCAAAAGCCATACTAATCGATTTA
* *
169 AATGGTTTTATAATCTCATAATTGATTTGCAAGTTGAATTTTTTATATTTTTGGTTAAAACATAC
66 AATGGTCTTATAATCTCATAATTGATTTGCAAGTTGAATTTTTTATATTTTTGGTTAAAACAAAC
* *
234 TATAATTGAATGTTTACTTTGAGAAACATAAAGAAAAAGG
131 TATAATTGAATGTCTACTTCGAGAAACATAAAGAAAAAGG
* *
274 CATTCATTGGAAAGAAAAGTCTATTTATAGTTACTCATTCCTTCAAAAGCCATA-TAACTCGATT
1 CATTCATTGGAAAGAAAAGTC-ATTTATAATCACTCATTCCTTCAAAAGCCATACTAA-TCGATT
* * * *******
338 TAAGTGGTCTTATAATCTCATATTTGATTT-TAAGTT-AATTTTTT-TNNNNNNNNNNGTTAAAA
64 TAAATGGTCTTATAATCTCATAATTGATTTGCAAGTTGAATTTTTTAT---ATTTTTGGTTAAAA
* * *
400 CAAACTATAATTGGATGTCTACTTCGAGAAACATGAAGAGAAAGG
126 CAAACTATAATTGAATGTCTACTTCGAGAAACATAAAGAAAAAGG
* * * * *
445 CATTC-TGTGGCAACAAAAGTCCATTTATAATCACCCATTCGTTTAAAAGC
1 CATTCAT-TGGAAAGAAAAGT-CATTTATAATCACTCATTCCTTCAAAAGC
495 TTTATTACTC
Statistics
Matches: 185, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
168 1 0.01
169 8 0.04
170 30 0.16
171 145 0.78
172 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.35
Consensus pattern (170 bp):
CATTCATTGGAAAGAAAAGTCATTTATAATCACTCATTCCTTCAAAAGCCATACTAATCGATTTA
AATGGTCTTATAATCTCATAATTGATTTGCAAGTTGAATTTTTTATATTTTTGGTTAAAACAAAC
TATAATTGAATGTCTACTTCGAGAAACATAAAGAAAAAGG
Found at i:3170 original size:171 final size:169
Alignment explanation
Indices: 2550--3320 Score: 633
Period size: 170 Copynumber: 4.5 Consensus size: 169
2540 NNNNNNNNNN
* * * * *
2550 CAATTTTGAGATTATAAAACCATTTAAAGCGAGTAAAAAGGCTTTTGAAGGAATAG-GAGACCAT
1 CAATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GCGTGACTAT
* * * * * ** ** *
2614 AAATGGA-TATTTCTTACCAATGAATGCTTTTTTCTTCACATTTC-CCTGGCTAGACATTTAATT
65 AAATAGACT-TTTCTTGCCAATGAATGCCTGTTTCTTTATGTTTCTCAAGG-TA-ACATTCAATT
* * * * * *
2677 ACAATCTGTTTGAA-C-AAAATGTAAAAAACTTCAACTTAAAAT
127 ATAGTCTGTTTTAACCAAAAATATAAAAAAATTCAA-TTAAAAC
*********** **
2719 CAATTATGAGATTATAAATNNNNNNNNNNCGAGTAATAAGGCTTTTGAAGGAAAACGTGACTATA
1 CAATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGGAATGCGTGACTATA
* **
2784 AATAGACTTTTCTTGCTAATGAATGCCTGTTTCTTTATGTTTCTTGAGGTTAACATTCAATTATA
66 AATAGACTTTTCTTGCCAATGAATGCCTGTTTCTTTATGTTTCTCAAGG-TAACATTCAATTATA
*
2849 GGCTGTTTTAACCAAAAATATAAAAAAATTCAATTAAAAC
130 GTCTGTTTTAACCAAAAATATAAAAAAATTCAATTAAAAC
* **
2889 CAATTATGAGATTATAAAACCATTCAAAGTGAGTAATAAGGCTTTTGAAAAAATAG-GTGACTAT
1 CAATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGGAAT-GCGTGACTAT
* * * *
2953 AAATGGACTTTTCTTGCCAATGAATTCATGTTTCTTTACGTTTCTCAAGGCTAACATTCAATTAT
65 AAATAGACTTTTCTTGCCAATGAATGCCTGTTTCTTTATGTTTCTCAAGG-TAACATTCAATTAT
* * *
3018 AGTCTGCTTTAACCAAAAATATAAAAAACTTCAACTTAAAAT
129 AGTCTGTTTTAACCAAAAATATAAAAAAATTCAA-TTAAAAC
********** * *
3060 NNNNNNNNNNATTATAAAACCATTTAAAGCGATTAATAAGGCTTTTGAAGGAATGCGTGACTATA
1 CAATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGGAATGCGTGACTATA
* * * * * *
3125 AATAGACTTCTCTTCCCAACGAATGCCT-TTTTTTTCATATTTCTCAAGGTAGACACTCAATTAT
66 AATAGACTTTTCTTGCCAATGAATGCCTGTTTCTTT-ATGTTTCTCAAGGTA-ACATTCAATTAT
* * * * * * *
3189 AATCTGTTTTGACCAAAAGTGTAAAAAAAAATGAGCA-TAAAAT
129 AGTCTGTTTTAACCAAAAATAT-AAAAAAATTCA--ATTAAAAC
* * * * *
3232 CAATTATTAGATAATAAAATCATTGACAA-CGAGTAATAAGGCTTTTGAAGGAATGCATGACTAT
1 CAATTATGAGATTATAAAACCATTCA-AAGCGAGTAATAAGGCTTTTGAAGGAATGCGTGACTAT
*
3296 AAATGGACTTTTCTTGCCAATGAAT
65 AAATAGACTTTTCTTGCCAATGAAT
3321 ACCTTNNNNN
Statistics
Matches: 471, Mismatches: 117, Indels: 25
0.77 0.19 0.04
Matches are distributed among these distances:
169 99 0.21
170 156 0.33
171 132 0.28
172 81 0.17
173 2 0.00
174 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.33
Consensus pattern (169 bp):
CAATTATGAGATTATAAAACCATTCAAAGCGAGTAATAAGGCTTTTGAAGGAATGCGTGACTATA
AATAGACTTTTCTTGCCAATGAATGCCTGTTTCTTTATGTTTCTCAAGGTAACATTCAATTATAG
TCTGTTTTAACCAAAAATATAAAAAAATTCAATTAAAAC
Found at i:4386 original size:172 final size:163
Alignment explanation
Indices: 4121--4446 Score: 325
Period size: 172 Copynumber: 1.9 Consensus size: 163
4111 TAAAACCATT
* * *
4121 TAAAGCGAGTAATAAGGCTTTCGAAGGAATACGTGACTATAAATGGACTTCTCTTCCCAACGAAT
1 TAAAGCGAGTAATAAGGCTTTCGAACGAATACATGACTATAAATAGACTTCTCTTCCCAACGAAT
* * * * *
4186 GCCTTGTTCTTCGCCTTTCTCAAGGTAGACACTCAATTATAGTCTGTTTTGACCAA-AACTGTAA
66 ACCTTGTTCTTCACCTTTCTCAAGGTAGACACTCAACTATAATCTGTTTTAACCAATAA-TGTAA
* *
4250 AA-AAAATTGAGCTTATAATCAATTATGAGATAA
130 AACAAAATTGAACTTAAAATCAATTATGAGATAA
* * * *
4283 TAAANNNNNNNNNNGCGAGTAATAAGGCTTTTGAACGAATGCATGACTATAAATATACTTTTCTT
1 TAAA----------GCGAGTAATAAGGCTTTCGAACGAATACATGACTATAAATAGACTTCTCTT
* * * ** * * *
4348 GCCAATGAATACCTTTTTCTTCATGTTTCAT-GAGGTAGACATTCAACTATAATCTGTTTTAACT
56 CCCAACGAATACCTTGTTCTTCACCTTTC-TCAAGGTAGACACTCAACTATAATCTGTTTTAACC
4412 AATAATGTAAAACAAAATTGAACTTAAAATCAATT
120 AATAATGTAAAACAAAATTGAACTTAAAATCAATT
4447 NNNNNNNNNN
Statistics
Matches: 129, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
162 4 0.03
172 102 0.79
173 23 0.18
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.32
Consensus pattern (163 bp):
TAAAGCGAGTAATAAGGCTTTCGAACGAATACATGACTATAAATAGACTTCTCTTCCCAACGAAT
ACCTTGTTCTTCACCTTTCTCAAGGTAGACACTCAACTATAATCTGTTTTAACCAATAATGTAAA
ACAAAATTGAACTTAAAATCAATTATGAGATAA
Found at i:9081 original size:171 final size:170
Alignment explanation
Indices: 8648--9090 Score: 478
Period size: 172 Copynumber: 2.6 Consensus size: 170
8638 NNNNNNNNNN
* * *
8648 AGATTATAAAACCATTTAAAGCGAGTAATAAGGCTTTTGAAGGAATGCATAACTATAAATGGACT
1 AGATTATAAAACCA-TTAAAGCGAGTAATAAGGCTTTTGAAGGAATACGTGACTATAAATGGAC-
* * * ** **
8713 TTTCTTGTCAATGAATGAATTTTTCCTCATGTTTCTTAAAAAAGACATTCAAATACAGTCTGTTT
64 TTTCTTGCCAATGAATGCATTTTTCTTCACATTTCACAAAAAAGACATTCAAATACAGTCTGTTT
8778 TAACCAATAATATAAAAAGAATTAAACCTAAAATCAATTTAG
129 TAACCAATAATATAAAAAGAATTAAACCTAAAATCAATTTAG
* * * * * * *
8820 AGATTATAAAACCATTAAATGCGAGTGATAAGGCTGTTCAAGGAATAGGAGGCTATAAATAGACA
1 AGATTATAAAACCATTAAA-GCGAGTAATAAGGCTTTTGAAGGAATACGTGACTATAAATGGAC-
* * * ** *
8885 TTTCTTGCCAATGAACGCTTTTTTCTTCACATTTCACGAACTAGACATTCAATTACAGTCTGTTT
64 TTTCTTGCCAATGAATGCATTTTTCTTCACATTTCACAAAAAAGACATTCAAATACAGTCTGTTT
* ** * *
8950 TAACCAA-AATTATATAAA-CCTTCAACTTAAAATCAA-TTATG
129 TAACCAATAA-TATAAAAAGAATTAAACCTAAAATCAATTTA-G
* * *
8991 AGATTATAAAACCATCTAAAGTGAGTAATAATGCTTTTGAAGGAATATGTGACTATAAATGGACT
1 AGATTATAAAACCAT-TAAAGCGAGTAATAAGGCTTTTGAAGGAATACGTGACTATAAATGGACT
* ** *
9056 TCTCTTCCCAACAAATGCCTTTTTCTTCACATTTC
65 T-TCTTGCCAATGAATGCATTTTTCTTCACATTTC
9091 TCGNNNNNNN
Statistics
Matches: 223, Mismatches: 43, Indels: 11
0.81 0.16 0.04
Matches are distributed among these distances:
170 5 0.02
171 100 0.45
172 118 0.53
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (170 bp):
AGATTATAAAACCATTAAAGCGAGTAATAAGGCTTTTGAAGGAATACGTGACTATAAATGGACTT
TCTTGCCAATGAATGCATTTTTCTTCACATTTCACAAAAAAGACATTCAAATACAGTCTGTTTTA
ACCAATAATATAAAAAGAATTAAACCTAAAATCAATTTAG
Found at i:17319 original size:171 final size:169
Alignment explanation
Indices: 17134--18295 Score: 563
Period size: 171 Copynumber: 6.8 Consensus size: 169
17124 NNNAAGCCTT
* * * * * *
17134 ATTACTCACTTTAAATAGTTTTACAATCTTATAATTGATCTAAAGTTGAAGTTTTCTATATTTTT
1 ATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGAT-TTAAGTTGAAGTTTTTTATATTTTT
* *
17199 AGTTAAAACAGACTATAATTGAATGTCTAGTTAGAGAAACATGAAGAAAAAAGTATTCATTGGCA
65 AGTTAAAACAGACTATAATTGAATGTCTAGCTAGA-AAACATGAAGAAAAAAGCATTCATTGGCA
* **********
17264 AGAAATGTCCATTTATAGTCTCTTATTCCTTNNNNNNNNNN
129 AGAAATGTCCATTTATAGTCTCCTATTCCTTCAAAATCCTA
* * * * * * *
17305 ATTAGTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAGATTCAATTTTTGTTACATTAT
1 ATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAG-TTGAAGTTTT-TTATATTTT
* * * * *
17370 TGGCTAAAACAGATTATAATTGAATGTCTACCCT-GAACAACATGAAGGAAAAAGCATTCATTGG
64 TAGTTAAAACAGACTATAATTGAATGTCTA-GCTAGAA-AACATGAAGAAAAAAGCATTCATTGG
*
17434 CAAGAAAAGTCCATTTATAGT-TACGC-ATTCCTTCAAAATCCTA
127 CAAGAAATGTCCATTTATAGTCT-C-CTATTCCTTCAAAATCCTA
**********
17477 ATTACTCGCTTTAAATAGTTTTATAATCNNNNNNNNNNTTTTAAGTTGAAGTTTTTTATATTTTT
1 ATTACTCGCTTTAAATAGTTTTATAATC-TCAAAATTGATTTAAGTTGAAGTTTTTTATA-TTTT
* * * *
17542 TTGTTAAAACGGACTATAATTGAATGTCTAGCTAAAAAACATGAAGAAAAAAGCATTCATTGGTA
64 TAGTTAAAACAGACTATAATTGAATGTCTAGCTAGAAAACATGAAGAAAAAAGCATTCATTGGCA
* *
17607 GGAAATGTCCATTTATAGTCTCCTATTCCTTCAAAAGT-CTT
129 AGAAATGTCCATTTATAGTCTCCTATTCCTTCAAAA-TCCTA
********** * * * * * * *
17648 ATTACNNNNNNNNNNTGGTTTTATAATCTCAAAATTGATTTTAGGTTTAATTTTTTCTACAATAT
1 ATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGA-TTTAAGTTGAAGTTTTT-TATATTTT
* * * * * *
17713 TGGTTAAAACAGATTATAATTGAATGACTAGC-ATGAGAA-ATGTAGAGAAAAATGCATTCANNN
64 TAGTTAAAACAGACTATAATTGAATGTCTAGCTA-GAAAACATG-A-AGAAAAAAGCATTCA--T
******* * * * * * *
17776 NNNNNNNAAA--TCTATTTATAGTCACCCATTCCTTTAAAAGCCTT
124 TGGCAAGAAATGTCCATTTATAGTCTCCTATTCCTTCAAAATCCTA
** * * * * *
17820 ATTACTTACTTTCAGTGGTTTTATAATCTCAAAATTGATTTTAGGCTGAA-TGTTTTTATATTTT
1 ATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGA-TTTAAGTTGAAGT-TTTTTATATTTT
* * * * * * * *
17884 TCA-TTAAAACAAACTATAACTGAATG-CTTGCCTTGGGAAACATGTAG-AATAAGCCATTTATT
64 T-AGTTAAAACAGACTATAATTGAATGTCTAG-C-TAGAAAACATGAAGAAAAAAG-CATTCATT
* ** ** * * *
17946 AGG-AAAAAAAATCCATTTGCAGTCACCCATTCCTTC-AAATGCCTT
125 -GGCAAGAAATGTCCATTTATAGTCTCCTATTCCTTCAAAAT-CCTA
* * * * * * *
17991 ATTGCTCGGTTTAAAGT-GTTTTCTAATCTCATAATTAATTTGAAGTTGAATTTTTTTACATTTT
1 ATTACTCGCTTTAAA-TAGTTTTATAATCTCAAAATTGATTT-AAGTTGAAGTTTTTTATATTTT
* * * * * *
18055 TCA-TTAAAATAGACTATAATTTAATGACTACCTCA-AGAAACGTGTAG-AAAAAGCCATTCATT
64 T-AGTTAAAACAGACTATAATTGAATGTCTAGCT-AGA-AAACATGAAGAAAAAAG-CATTCATT
* * * * * * *
18117 GAG-AAAAAAAGTCTATTTATAGTCACAC-ATTCCTTCAGAAGCCTT
125 G-GCAAGAAATGTCCATTTATAGTCTC-CTATTCCTTCAAAATCCTA
* * *
18162 ATTACT-GACTTTAAATTGTTTTATAATCT-AATATTTGATTTTAAGTTGAATTTTTTTGA-ATT
1 ATTACTCG-CTTTAAATAGTTTTATAATCTCAA-AATTGA-TTTAAGTTGAAGTTTTTT-ATATT
* * * * * * * *
18224 TTTA-TTAAACCAAACTATAATTGAATGGCTACCTTGATAAATATGAAGAAAAATGTATTCATTG
62 TTTAGTTAAAACAGACTATAATTGAATGTCTAGCTAGA-AAACATGAAGAAAAAAGCATTCATTG
18288 GCAAGAAA
126 GCAAGAAA
18296 AGTCNNNNNN
Statistics
Matches: 749, Mismatches: 194, Indels: 97
0.72 0.19 0.09
Matches are distributed among these distances:
169 4 0.01
170 73 0.10
171 405 0.54
172 255 0.34
173 9 0.01
174 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.37
Consensus pattern (169 bp):
ATTACTCGCTTTAAATAGTTTTATAATCTCAAAATTGATTTAAGTTGAAGTTTTTTATATTTTTA
GTTAAAACAGACTATAATTGAATGTCTAGCTAGAAAACATGAAGAAAAAAGCATTCATTGGCAAG
AAATGTCCATTTATAGTCTCCTATTCCTTCAAAATCCTA
Found at i:21527 original size:170 final size:168
Alignment explanation
Indices: 20892--21534 Score: 582
Period size: 171 Copynumber: 3.8 Consensus size: 168
20882 ATGGGTGACT
*
20892 TTTTTCTTTATGTTTCTC-AAGCTGGACATTCAATTATAGCCTGTTTTAACCAAAAATGTAAAAA
1 TTTTTCTTTATGTTTCTCAAAG-T--ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAA
* * * * *
20956 TATTGAACTTGAAATCAAATT-TAAGATTATAAAA-CAATTTACAGCGAGTAATAAGGCTTTTG-
63 AATTTAACTTAAAATC-AATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGA
*
21018 AAGAAATGGGTGACTATGAAAGGACTTTTCTTGCCAATGAATG-C
126 AAG-AATGGGTGACTAT-AAATGACTTTTCTTGCCAATGAATGCC
* * * * **
21062 TTCTTTTTTTATGTTTCTTGAGACTGACATTCAATTATAGTCTGTTTTAATTAAAAATGTAAAAA
1 TT-TTTCTTTATGTTTC-TCAAAGT-ACATTCAATTATAGTCTGTTTTAACCAAAAATGT-AAAA
* * * *
21127 AACATTTAACTTAAAATCAATTAGGAGATTATAAAATCATTTAAAGCAAGAAATAAGGTTTTTGA
62 AA-ATTTAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGA
* * * *
21192 AGGAATGGGTAACTATAAATGTACTTTTGTTGCCAAAGAATGCC
126 AAGAATGGGTGACTATAAATG-ACTTTTCTTGCCAATGAATGCC
* * ** * * **********
21236 TTTCTCTTCATGTTTCTTGAAGTAGACATTCAATTATAGTTTGCTTNNNNNNNNNNTGTAAAAAA
1 TTTTTCTTTATGTTTCTCAAAGT--ACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
* * * *
21301 ATTCAACTTAAAATCAAATATGAGATTATAAAATCACTTAAACCGAGTAATAAGGCTTTTGAAAG
64 ATTTAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAG
21366 AATGGGTGACTATAAATAGA-TTTTCTTGCCAATGAATGCC
129 AATGGGTGACTATAAAT-GACTTTTCTTGCCAATGAATGCC
* ********
21406 TTTTTCTTTACGTTTCTCAAAGTANNNNNNNNNNTATAGTCTGTTTTAACCAAAAATGTAAAAAA
1 TTTTTCTTTATGTTTCTCAAAGTA--CATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAA
** *
21471 ATTTAACTTGCAATCAATTATGAGATTATAAAA-CTATTTAAAGCGAGTAGTAAGGCTTTT-AAA
64 ATTTAACTTAAAATCAATTATGAGATTATAAAATC-ATTTAAAGCGAGTAATAAGGCTTTTGAAA
21534 G
128 G
21535 GNNNNNNNNN
Statistics
Matches: 374, Mismatches: 84, Indels: 31
0.76 0.17 0.06
Matches are distributed among these distances:
168 1 0.00
169 5 0.01
170 108 0.29
171 118 0.32
172 25 0.07
173 111 0.30
174 6 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.35
Consensus pattern (168 bp):
TTTTTCTTTATGTTTCTCAAAGTACATTCAATTATAGTCTGTTTTAACCAAAAATGTAAAAAAAT
TTAACTTAAAATCAATTATGAGATTATAAAATCATTTAAAGCGAGTAATAAGGCTTTTGAAAGAA
TGGGTGACTATAAATGACTTTTCTTGCCAATGAATGCC
Found at i:22218 original size:168 final size:169
Alignment explanation
Indices: 21780--22239 Score: 466
Period size: 172 Copynumber: 2.7 Consensus size: 169
21770 NNNNNNNNNG
* * * *
21780 TTTTACATTATTAGTTAAAACAGATTATAGTCGAATGTCTACCTCAAGAAACATGAAGAAAAAGG
1 TTTTACATTTTTAGTTAAAACAGATTATAATTGAATATCTACCTCAAGAAACATGAAGAAAAA-G
* * * * *
21845 TATTCATTTGCAAGAAAAGTCCATTTATAGCCATGCATTCCTTTAAAAGCCTTATTACTCGCAGT
65 AATTCATTGGCAAGAAAAGTCCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCGCAGT
* *
21910 AAATGATTTTATTATCTCATAATTGATTTGAAGCTTAATTTT
130 AAATGATTTTATAATATCATAA-T-ATTTGAAGCTTAATTTT
* * * * * ** * **
21952 TTTTACAATTTT-GATCAAAACATATTATAATTGAGTCTCTACCTTGAGAGATGTGAAGAAAAAG
1 TTTTACATTTTTAG-TTAAAACAGATTATAATTGAATATCTACCTCAAGAAACATGAAGAAAAAG
** * * *
22016 ACATTTGTTGAG-AAGAGAAGTCCATTTATAGTCACGCATTCCTTCAAAAACCTTATTACTCGCT
65 A-ATTCATTG-GCAAGAAAAGTCCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCGCA
* *
22080 TTAAATGGTTTTATAATATCAT-A-ATTT-AAG-TTAATTATTT
128 GTAAATGATTTTATAATATCATAATATTTGAAGCTTAA-T-TTT
** * *
22120 TTTTACATTTTTAGTTAAAACAGGCTATAATTGAATAT-TAGTCTCAAGAAACATAAAGAAAGAA
1 TTTTACATTTTTAGTTAAAACAGATTATAATTGAATATCTA-CCTCAAGAAACATGAAGAAA-AA
* * *
22184 GAATTCATTGGCAAGAAAAGTCCTTTTATAGTCACCCATTCCATCAAAAGCCTTAT
64 GAATTCATTGGCAAGAAAAGTCCATTTATAGTCACGCATTCCTTCAAAAGCCTTAT
22240 AAAACTATTT
Statistics
Matches: 231, Mismatches: 48, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
166 4 0.02
167 7 0.03
168 94 0.41
169 5 0.02
171 3 0.01
172 117 0.51
173 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (169 bp):
TTTTACATTTTTAGTTAAAACAGATTATAATTGAATATCTACCTCAAGAAACATGAAGAAAAAGA
ATTCATTGGCAAGAAAAGTCCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCGCAGTA
AATGATTTTATAATATCATAATATTTGAAGCTTAATTTT
Found at i:22957 original size:172 final size:171
Alignment explanation
Indices: 22484--22956 Score: 540
Period size: 172 Copynumber: 2.8 Consensus size: 171
22474 TGTCAGCCTC
** * * ***
22484 GAGAAACAT-AAGGAAACAAGCATTCATTGGCAAGAAAAGTATTTTTATAGTCACCCATTCCTTC
1 GAGAAACATAAAAAAAAAAAGCATTCATTGGCAACAAAAGTCCATTTATAGTCACCCATTCCTTC
* * * **
22548 AAAAACTTTATTATTCGCTTTAAATAGTTTTATAATCTCATAATTGATTGCAAGTTGAATTTTTT
66 AAAAGCCTTATTACTCGCTTT-AATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTT
* * *
22613 TACTTTTTTAGTTAAAACACATAATAATTGAATGTTTACTTT
130 TACATTTTTAGTTAAAACAAATAATAATTGAATGTCTACTTT
**********
22655 GAGAAACATAAAAAAAAAAAGCATTCATTGGCAANNNNNNNNNNTTTATAGTCACCCATTCCTTC
1 GAGAAACATAAAAAAAAAAAGCATTCATTGGCAACAAAAGTCCATTTATAGTCACCCATTCCTTC
* * * *
22720 AAAAGCCTTATAACTCGCTTTAAGTGGTTTTATAATCTCATATTTGATTTTAAGTTAAATTTTTT
66 AAAAGCCTTATTACTCGCTTTAA-TAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTT
* *
22785 TACATTTTTAGTTCAAACAAACT-ATAATTGGATGTCTACTTT
130 TACATTTTTAGTTAAAACAAA-TAATAATTGAATGTCTACTTT
* * * *
22827 GAGAAACAT-GAAGAGAAAGGCATTC-TCTGGCAACAAAAGTCCATTTATAGTCACCCATTCCTT
1 GAGAAACATAAAAAAAAAAAGCATTCAT-TGGCAACAAAAGTCCATTTATAGTCACCCATTCCTT
* *
22890 CAAAAGCCTTATTACGCGATTTGAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
65 CAAAAGCCTTATTACTCGCTTT-AATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTT
22955 TT
129 TT
22957 TTNNNNNNNN
Statistics
Matches: 250, Mismatches: 47, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
170 1 0.00
171 107 0.43
172 141 0.56
173 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.37
Consensus pattern (171 bp):
GAGAAACATAAAAAAAAAAAGCATTCATTGGCAACAAAAGTCCATTTATAGTCACCCATTCCTTC
AAAAGCCTTATTACTCGCTTTAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTT
ACATTTTTAGTTAAAACAAATAATAATTGAATGTCTACTTT
Found at i:23932 original size:171 final size:169
Alignment explanation
Indices: 23525--24294 Score: 720
Period size: 171 Copynumber: 4.5 Consensus size: 169
23515 NNNNNNNNNN
* **
23525 ATTCATTGGCAAGAAAAGTCCTTTTATAGTCACCAATTCTTTCAAAAGTTTTATTACTCGCTTTA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACC-ATTCTTTC-AAAGCCTTATTACTCGCTTTA
* ** ** ** *
23590 AATGGTTTTATAATCTCATAATTGATTGCAAGTTGAATTTTTTTGTATTTTTTATTAAAACATAC
64 AATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* *
23655 TATAATTGAATGTCTACTTTGAGAAACATAAAGAAAAAGGC
129 TATAATTGAATGTCTACTTAGAGAAACATGAAGAAAAAGGC
* ** ********* * *
23696 ATTCATTAGCAAGAAAAGTTTATTTANNNNNNNNNNTTCCTTCAAAAGCCTTATTACTCGCTTTG
1 ATTCATTGGCAAGAAAAGTCCATTTA-TAGTCACCATTCTTTC-AAAGCCTTATTACTCGCTTTA
** * * *
23761 AGCAGTTTTATAATCTCATATTTGATTTTAAATTGAATTTTTTTACATTTTTGGTTAAAACAGAG
64 AATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
*
23826 TATAATTGATTGTCTACTTCAG-GAAACATGAAGAAAAAGGC
129 TATAATTGAATGTCTACTT-AGAGAAACATGAAGAAAAAGGC
* * * * * *
23867 ATTCTTTGGCAACAAAAGTCCATTTATAGTCACTCATTCGTTCACAAGCCTAATTACTTGCTTTG
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCAC-CATTCTTTCA-AAGCCTTATTACTCGCTTTA
* * * * ********** *
23932 AATGGTTTTCTAATCTCATAATTTATTTTAAGTTAAATTTTTTTACATNNNNNNNNNNAACAGGC
64 AATAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGAC
* * * *
23997 TATAATTGAATGTCTACTTTGAGAAATATGAAGCAAAAGGT
129 TATAATTGAATGTCTACTTAGAGAAACATGAAGAAAAAGGC
* * * ** *
24038 ATTTATTGGCTATAAAAGTCCATTTACGGTCACCAATTAC-TTCAAATGCCTTATTACTCCCTTT
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACC-ATT-CTTTCAAA-GCCTTATTACTCGCTTT
** *
24102 AAATAGTTTTATAATCAT-ATAATTGATTTTAAGTTGACGTTTTTTATATTTTTGGTTAAAACAG
63 AAATAGTTTTATAATC-TCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAG
* * * *
24166 ACTATAATTAAATGTCTGGCTCA-AGAAACATGAAGAAAAAAGC
127 ACTATAATTGAATGTCT-ACTTAGAGAAACATGAAGAAAAAGGC
** *
24209 ATTCATTGGCGTGAAAAGTCCATTTATAGTCACCCATTTTTTCGAAAGCCTTATTACTCGCTTTA
1 ATTCATTGGCAAGAAAAGTCCATTTATAGTCA-CCATTCTTTC-AAAGCCTTATTACTCGCTTTA
24274 AATAGTTTTATAATCTCATAA
64 AATAGTTTTATAATCTCATAA
24295 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 119, Indels: 28
0.76 0.19 0.05
Matches are distributed among these distances:
170 6 0.01
171 450 0.97
172 10 0.02
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.38
Consensus pattern (169 bp):
ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCATTCTTTCAAAGCCTTATTACTCGCTTTAAA
TAGTTTTATAATCTCATAATTGATTTTAAGTTGAATTTTTTTACATTTTTGGTTAAAACAGACTA
TAATTGAATGTCTACTTAGAGAAACATGAAGAAAAAGGC
Found at i:26899 original size:171 final size:171
Alignment explanation
Indices: 26523--26948 Score: 428
Period size: 171 Copynumber: 2.5 Consensus size: 171
26513 NNNNNNNNNN
* ** *
26523 GCCTTATTACTCGCTTTAAATTATTTTATAATCTCAAAATTGATTTTAGGTTCAATTTTTTATAC
1 GCCTTATTACTAGCTTTAAAAGATTTTATAATCTCAAAATTGATTTTAGATTCAATTTTTTATA-
**
26588 ATTATTGGCTAAAACAGATTATAATTGAATGTCTACCCTAAGAAACATGAAGGAAAAGGCATTCA
65 ATTATTGGCTAAAACAGACAATAATTGAATGTCTACCCTAAGAAACATGAAGGAAAAGGCATTCA
*
26653 TTAGTAAGAAAAGTCCATTTGTAGTCACGCATTTCTTCAAAA
130 TTAGTAAGAAAAGTCCATTTGTAGTCACGCATTCCTTCAAAA
* ********** * * * *
26695 GCCTTATTACTTGCTNNNNNNNNNNTGATAATCTCATAATTGATTTTATATTGAAGTTTTTTAT-
1 GCCTTATTACTAGCTTTAAAAGATTTTATAATCTCAAAATTGATTTTAGATTCAA-TTTTTTATA
* * * * * * *
26759 ATTTTTTGTTAGAACAGACAATAATTGAATGTCTAGCTTGAGAAACATGAA-GAAAAGAGCATTC
65 ATTATTGGCTAAAACAGACAATAATTGAATGTCTACCCTAAGAAACATGAAGGAAAAG-GCATTC
* **
26823 ATT-G-ATAGAAAATGTCCATTTGTAGTCTCTTATTCCTTCAAAA
129 ATTAGTA-AGAAAA-GTCCATTTGTAGTCACGCATTCCTTCAAAA
* * * * *
26866 GCCTTATTACTAGCTTTAAAAGGTTTTATAATCTCAAAATTAATTTTAGGTTCCATTTTTTCTAC
1 GCCTTATTACTAGCTTTAAAAGATTTTATAATCTCAAAATTGATTTTAGATTCAATTTTTTATA-
*
26931 ATTATTGGTTAAAACAGA
65 ATTATTGGCTAAAACAGA
26949 TTATAATTNN
Statistics
Matches: 197, Mismatches: 51, Indels: 12
0.76 0.20 0.05
Matches are distributed among these distances:
169 1 0.01
170 20 0.10
171 114 0.58
172 54 0.27
173 8 0.04
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.38
Consensus pattern (171 bp):
GCCTTATTACTAGCTTTAAAAGATTTTATAATCTCAAAATTGATTTTAGATTCAATTTTTTATAA
TTATTGGCTAAAACAGACAATAATTGAATGTCTACCCTAAGAAACATGAAGGAAAAGGCATTCAT
TAGTAAGAAAAGTCCATTTGTAGTCACGCATTCCTTCAAAA
Found at i:28539 original size:170 final size:170
Alignment explanation
Indices: 28363--28700 Score: 398
Period size: 171 Copynumber: 2.0 Consensus size: 170
28353 NNNNNNNNNN
28363 ATCTCATAATTGATTGTAAGTT-AATTTTTTTTAC-TTTCTTGGTAAAAACAAACTATAATCGAA
1 ATCTCATAATTGATTGTAAGTTGAA-TTTTTTTACATTT-TTGGTAAAAACAAACTATAATCGAA
*
28426 TGTCTACTTTGAGAAACATGAAGAAAACA-CATTCATTGGAAACAAAAG-TCCATTTATAGTTAC
64 TGTCTACTTTGAAAAACATGAAGAAAA-AGCATTCATTGGAAACAAAAGCT-CATTTATAGTTAC
* **
28489 -CTATTCCTTCGAAAGCCTTATTACTCGCTTTACGTGGTTTTTTA
127 TC-ATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTTTA
* * * ********** *
28533 ATCTCATATTTGATTTTAGGTTGAATTTTTTTACATTTTTGNNNNNNNNNNACTATAATTGAATG
1 ATCTCATAATTGATTGTAAGTTGAATTTTTTTACATTTTTGGTAAAAACAAACTATAATCGAATG
* * *
28598 TCTACTTTGAAAAACATGAAGAAAAAGGCATTCATTGGCAAGAAACGCTCATTTATAGTTACTCA
66 TCTACTTTGAAAAACATGAAGAAAAA-GCATTCATTGGAAACAAAAGCTCATTTATAGTTACTCA
28663 TTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT
130 TTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT
28701 NNNNNNNNNN
Statistics
Matches: 141, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
169 1 0.01
170 68 0.48
171 70 0.50
172 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.38
Consensus pattern (170 bp):
ATCTCATAATTGATTGTAAGTTGAATTTTTTTACATTTTTGGTAAAAACAAACTATAATCGAATG
TCTACTTTGAAAAACATGAAGAAAAAGCATTCATTGGAAACAAAAGCTCATTTATAGTTACTCAT
TCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTTTA
Found at i:29473 original size:172 final size:159
Alignment explanation
Indices: 29351--29680 Score: 141
Period size: 168 Copynumber: 2.0 Consensus size: 159
29341 NNNNNNNNNN
* *
29351 TCTCATAATTGATTTTAAGTTGAATTGTTTTCACATTTTTCATTAAAACAGGCTATAATTGA-AT
1 TCTCATAATTGATTTTAAGTTGAATT-TTTTAACA-TTTTCATTAAAACAGACTATAATTGAGAT
** **
29415 GCATGTCTCAAGAAACATGTAGAAA-AAGCCATTCATTGAGCAA-AAATA-TCCATTTATAGTCA
64 -CA-ACCTCAAGAAACATAAAGAAACAAG-CATTCATTGA-CAAGAAA-AGTCCATTTATAGTCA
* * * * * * *
29477 CTTATTCCTTCAAAAGCCTTATTAAGTTTAAATTATTTTATT
124 CCTATCCCTTCAAAAGCCTTATT-A--CT-CA--CTTTAAAT
* * * ** * *
29519 ATCTAATATTTGATTTTAAGTTTAATTGTTTT-GTATTTTTATTAAAACCAAACTATAATTGA-A
1 -TCTCATAATTGATTTTAAGTTGAATT-TTTTAACATTTTCATTAAAA-CAGACTATAATTGAGA
* * * * * * ** * * **
29582 TGTCTATCTTAAGAAACATGAAGAAAAAAGAATTCATTGGTAAGAAAAGTTCATTCATAGTTGCC
63 --TCAACCTCAAGAAACATAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACC
* * *
29647 CATTCCTTCAAAAGCCTTATTACTCGCTTTAAAT
126 TATCCCTTCAAAAGCCTTATTACTCACTTTAAAT
29681 AGNNNNNNNN
Statistics
Matches: 128, Mismatches: 27, Indels: 19
0.74 0.16 0.11
Matches are distributed among these distances:
162 5 0.04
165 1 0.01
167 15 0.12
168 74 0.58
169 32 0.25
170 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (159 bp):
TCTCATAATTGATTTTAAGTTGAATTTTTTAACATTTTCATTAAAACAGACTATAATTGAGATCA
ACCTCAAGAAACATAAAGAAACAAGCATTCATTGACAAGAAAAGTCCATTTATAGTCACCTATCC
CTTCAAAAGCCTTATTACTCACTTTAAAT
Found at i:29619 original size:168 final size:169
Alignment explanation
Indices: 29173--29807 Score: 402
Period size: 171 Copynumber: 3.7 Consensus size: 169
29163 NNNNNNNNGG
* * * * ** *
29173 TTTTATAATCTCATAATTGATTTTAAGTTGAATT-TTTTAACA-TTTTGGTTAAAACAGACTATA
1 TTTTATTATCTAATATTTGATTTTAAGTTGAATTGTTTTCACATTTTTCATTAAAACAAACTATA
* * * * * * * *
29236 ATTGAGTAT-CA-ACCTGAAGAAACGTAAAGAAACAAGC-TTTCATTGACAAGAAAAGTCCTTTT
66 ATTGA--ATGCATATCTCAAGAAACATGAAGAAA-AAGCAATTCATTGGCAAGAAAAGTCCATTC
* * * **
29298 ATAGTCACCTATCCCTTCAAAAGCCTTATTACTCACTTTAAATNN
128 ATAGTCACCCATTCCTTCAAAAGCCTTATTA---AGTTTAAATTA
******** * * **
29343 NNNNNNNNTCTCATAATTGATTTTAAGTTGAATTGTTTTCACATTTTTCATTAAAACAGGCTATA
1 TTTTATTATCTAATATTTGATTTTAAGTTGAATTGTTTTCACATTTTTCATTAAAACAAACTATA
* * * *
29408 ATTGAATGCATGTCTCAAGAAACATGTAGAAAAAGCCATTCATTGAGCAA-AAATA-TCCATTTA
66 ATTGAATGCATATCTCAAGAAACATGAAGAAAAAGCAATTCATTG-GCAAGAAA-AGTCCATTCA
**
29471 TAGTCACTTATTCCTTCAAAAGCCTTATTAAGTTTAAATTA
129 TAGTCACCCATTCCTTCAAAAGCCTTATTAAGTTTAAATTA
* **
29512 TTTTATTATCTAATATTTGATTTTAAGTTTAATTGTTTT-GTATTTTT-ATTAAAACCAAACTAT
1 TTTTATTATCTAATATTTGATTTTAAGTTGAATTGTTTTCACATTTTTCATTAAAA-CAAACTAT
* * *
29575 AATTGAATGTC-TATCTTAAGAAACATGAAGAAAAAAG-AATTCATTGGTAAGAAAAGTTCATTC
65 AATTGAATG-CATATCTCAAGAAACATGAAG-AAAAAGCAATTCATTGGCAAGAAAAGTCCATTC
** *
29638 ATAGTTGCCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA-TA
128 ATAGTCACCCATTCCTTCAAAAGCCTTATTA--AG-TTTAAATTA
********** * * * * *
29682 GNNNNNNNNNNTCATAATTAATTTGAAGTTGAATTGTTTT-ACATTTTT-AGTTAAAACAGACTA
1 -TTTTATTATCTAATATTTGATTTTAAGTTGAATTGTTTTCACATTTTTCA-TTAAAACAAACTA
* * **
29745 TAAGTGAATGCCTA-CTTTGAGAAACATGAAGAAAAAG-ACATTCATTGGCAAGAAAAGTCCATT
64 TAATTGAATGCATATC-TCAAGAAACATGAAGAAAAAGCA-ATTCATTGGCAAGAAAAGTCCATT
29808 TANNNNNNNN
Statistics
Matches: 370, Mismatches: 75, Indels: 39
0.76 0.15 0.08
Matches are distributed among these distances:
167 11 0.03
168 80 0.22
169 43 0.12
170 40 0.11
171 103 0.28
172 89 0.24
173 4 0.01
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.36
Consensus pattern (169 bp):
TTTTATTATCTAATATTTGATTTTAAGTTGAATTGTTTTCACATTTTTCATTAAAACAAACTATA
ATTGAATGCATATCTCAAGAAACATGAAGAAAAAGCAATTCATTGGCAAGAAAAGTCCATTCATA
GTCACCCATTCCTTCAAAAGCCTTATTAAGTTTAAATTA
Found at i:30370 original size:173 final size:171
Alignment explanation
Indices: 29829--30392 Score: 410
Period size: 171 Copynumber: 3.3 Consensus size: 171
29819 NNNNNNNNNN
* * *
29829 AAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTAAAAATTGATTTTAAGTTTAA-TGCTTTT
1 AAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTCAAGT-TTTTT
* * * * ** * * *
29893 ACATT-TTGCATTAAAATAGACTATAATTAAAT-T-TATGCCTTGGGAAACGT-ATAGAAAAAGG
65 AAATTATTG-ATTAAAATAGACTAGAATTGAATGTCTA-G-CATGAAAAATGTGA-GGAAAAAAG
** * * * * *
29954 CATTCATTTAGAAAAAAAGTCCACTTGTAG-CCACGCATTCCTTTAA
126 CATTCATTGGGAAGAAAAGTCCATTTATAGTCTAC-CATTCCTTCAA
********** * * * *
30000 AANNNNNNNNNNTCGCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAAGTTTTTTA
1 AAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTCAAGTTTTTTA
* * * * *
30065 TATTTTTGGTTAAAATAGACTAGAATTGAATGTCTAGCTTGAGAAATGTGAGGAAAAAAGCATTC
66 AATTATTGATTAAAATAGACTAGAATTGAATGTCTAGCATGAAAAATGTGAGGAAAAAAGCATTC
* * * *
30130 ATTGGTAGGAAATGTCCATTTATAGTCTACTATTCCTTCAA
131 ATTGGGAAGAAAAGTCCATTTATAGTCTACCATTCCTTCAA
********** * * *
30171 AAGCCTTANNNNNNNNNNTAAATGGTTTTACAATCTCAAAATTGATTTTAGGTTCAATTTTTTTT
1 AAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTCAA--GTTTTT
*
30236 TAAATTATTGATTAAAATAGATTTA-AATTGAATGTCTAGCATGAAAAACATG-GA-GAAAAAAG
64 TAAATTATTGATTAAAATAGA-CTAGAATTGAATGTCTAGCATG-AAAA-ATGTGAGGAAAAAAG
*
30298 CATTCATTGGGAAGAAAAGTTCATTTATAGTC-ACCCATTCCTTCAA
126 CATTCATTGGGAAGAAAAGTCCATTTATAGTCTA-CCATTCCTTCAA
* * *
30344 AAGCTTTATTACTTGCTTTGAATGGTTTTATAACCTCAAAATTGATTTT
1 AAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCAAAATTGATTTT
30393 GACTTGAATG
Statistics
Matches: 303, Mismatches: 78, Indels: 22
0.75 0.19 0.05
Matches are distributed among these distances:
171 158 0.52
172 11 0.04
173 124 0.41
174 7 0.02
175 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.37
Consensus pattern (171 bp):
AAGCCTTATTACTTGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTCAAGTTTTTTA
AATTATTGATTAAAATAGACTAGAATTGAATGTCTAGCATGAAAAATGTGAGGAAAAAAGCATTC
ATTGGGAAGAAAAGTCCATTTATAGTCTACCATTCCTTCAA
Found at i:30409 original size:173 final size:172
Alignment explanation
Indices: 30014--30410 Score: 419
Period size: 173 Copynumber: 2.3 Consensus size: 172
30004 NNNNNNNNTC
* * * * *
30014 GCTTTAAATGGTTTTATAATCTCATAATTCATTTTAAGTTGAA-G-TTTTTTATATTTTTGGTTA
1 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTT-AGTTGAATGTTTTTTTAAATTATTGATTA
* * * *
30077 AAATAGACTAGAATTGAATGTCTAGCTTGAGAAATGTGAGGAAAAAAGCATTCATTGGTAGGAAA
65 AAATAGACTAGAATTGAATGTCTAGCATGAAAAATGTGAGGAAAAAAGCATTCATTGGGAAGAAA
* * ******
30142 TGTCCATTTATAGTCTACTATTCCTTCAAAAGCCTTANNNNNN
130 AGTCCATTTATAGTCTACCATTCCTTCAAAAGCCTTATTACTT
**** * * *
30185 NNNNTAAATGGTTTTACAATCTCAAAATTGATTTTAGGTTCAATTTTTTTTTAAATTATTGATTA
1 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTA-GTTGAATGTTTTTTTAAATTATTGATTA
*
30250 AAATAGATTTA-AATTGAATGTCTAGCATGAAAAACATG-GA-GAAAAAAGCATTCATTGGGAAG
65 AAATAGA-CTAGAATTGAATGTCTAGCATG-AAAA-ATGTGAGGAAAAAAGCATTCATTGGGAAG
* *
30312 AAAAGTTCATTTATAGTC-ACCCATTCCTTCAAAAGCTTTATTACTT
127 AAAAGTCCATTTATAGTCTA-CCATTCCTTCAAAAGCCTTATTACTT
* * *
30358 GCTTTGAATGGTTTTATAACCTCAAAATTGATTTTGACTTGAATGTTTTTTTA
1 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTT-AGTTGAATGTTTTTTTA
30411 GTTTCCATTA
Statistics
Matches: 181, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
170 1 0.01
171 33 0.18
172 1 0.01
173 135 0.75
174 8 0.04
175 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.39
Consensus pattern (172 bp):
GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAGTTGAATGTTTTTTTAAATTATTGATTAA
AATAGACTAGAATTGAATGTCTAGCATGAAAAATGTGAGGAAAAAAGCATTCATTGGGAAGAAAA
GTCCATTTATAGTCTACCATTCCTTCAAAAGCCTTATTACTT
Found at i:34844 original size:171 final size:171
Alignment explanation
Indices: 34165--34963 Score: 616
Period size: 171 Copynumber: 4.7 Consensus size: 171
34155 NNNNNNCTCG
* * * * *
34165 CTTTAAATTATTTTCTACTCTCATAATTGATTTTAAGTTGAATTTTTTTAAATTTTTCATTAAAA
1 CTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTGAATTGTTTTACATTTTTCATTAAAA
* * * *
34230 CAGGCTACAATTTAATGCTTGCCTCAAGAAACATGTAGAAAAAGCCATTCATTGA-AAAAAATAA
66 CAGACTATAATTAAATGCTTGCTTCAAGAAACATGTAGAAAAAGCCATTCATTGAGAAAAAA-AA
* *
34294 TCCATTTATAGTCACGCATTCCTTCAAAATCCTTATTACACA
130 TCCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCA
* * * * **
34336 CTTTAAATTGTTTTATAATCTAATATTTAATTTTAAGTGGAATT-TGTTTACATTTTTGGTTAAA
1 CTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTGAATTGT-TTTACATTTTTCATTAAA
* * * * * * * ** *
34400 CCAGACTATAATTAAAT-CTCTACCTT-GATAAATATGAATAAAAAGGTATTCATTG-GCAAGAA
65 ACAGACTATAATTAAATGCT-T-GCTTCAAGAAACATGTAGAAAAAGCCATTCATTGAG-AAAAA
* * ** **
34462 AAGTCCATTCATAGTTGTC-CATTCCTTCAAAAGCCTTATTACTTG
127 AAATCCATTTATAG-TCACGCATTCCTTCAAAAGCCTTATTACTCA
* ** * *********
34507 CTTTCAATGGTTTTATAATCTTAA-AATTGATTTTAGGTTGAA-TGTTTTNNNNNNNNNNATTAA
1 CTTTAAATTATTTTATAATC-TAATAATTGATTTTAAGTTGAATTGTTTT-ACATTTTTCATTAA
* ** *
34570 AACAGACTATAATTGAATGC-TGACCTTGGA-AAACATGTAGAACAAGCCATTCATTGAGAAAAA
64 AACAGACTATAATTAAATGCTTG--CTTCAAGAAACATGTAGAAAAAGCCATTCATTGAGAAAAA
* * * ********* *
34633 AAGTCCATTTCTAGTCACCCA-TCCNNNNNNNNNNCTTATTACTCC
127 AAATCCATTTATAGTCACGCATTCC-TTCAAAAGCCTTATTACTCA
* * * * * *
34678 CTTTATATTATTTTCTAATCTCATAATTGATTTTAAGTTGAATTGTTTTAGATTTTTTATTGAAA
1 CTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTGAATTGTTTTACATTTTTCATTAAAA
* * * *
34743 CAGGCTATAA-TATAATGCTTGCTTCAAGAAACATGTTGAAAGAGCTATTCATTGAGAAAAAAAA
66 CAGACTATAATTA-AATGCTTGCTTCAAGAAACATGTAGAAAAAGCCATTCATTGAGAAAAAAAA
34807 TCCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCA
130 TCCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCA
* * * **
34849 CTTTAAATTACTTTATAGTCTAATATTTGATTTTAAGTTGAATTTGTTTTACATTTTTGGTTAAA
1 CTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTGAA-TTGTTTTACATTTTTCATTAAA
* * * * * * *
34914 CCAGACTATAATTGAATG-TCTACCTCAAGAAATATGGAGAAAAAGACATT
65 ACAGACTATAATTAAATGCT-TGCTTCAAGAAACATGTAGAAAAAGCCATT
34964 NNNNNNNNNN
Statistics
Matches: 471, Mismatches: 132, Indels: 49
0.72 0.20 0.08
Matches are distributed among these distances:
170 20 0.04
171 370 0.79
172 80 0.17
173 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.38
Consensus pattern (171 bp):
CTTTAAATTATTTTATAATCTAATAATTGATTTTAAGTTGAATTGTTTTACATTTTTCATTAAAA
CAGACTATAATTAAATGCTTGCTTCAAGAAACATGTAGAAAAAGCCATTCATTGAGAAAAAAAAT
CCATTTATAGTCACGCATTCCTTCAAAAGCCTTATTACTCA
Done.