Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397494.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_3367.0, 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: 12402
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.31
Warning! 2095 characters in sequence are not A, C, G, or T
Found at i:785 original size:171 final size:169
Alignment explanation
Indices: 251--1374 Score: 848
Period size: 171 Copynumber: 6.6 Consensus size: 169
241 NNNNNNNAAT
* * * * * *
251 CATTCATTGGTAAAAAAAGTCCATTTCTAGTCACCCATTCCTTCAAAAGCCTTATTTCTCGCTTT
1 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTTT
* * * ** * *
316 AAATGGCTTTATAATCTCAAAATTGATTTTTTGTTCAATTGTTTTTACATTTTTGGTTAAAAC-A
66 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAA---TTTTTACATTTTTTGTTAAAACTA
* * * * * ** * *
380 GATTATCATTCAATGTTTACCTTTAGAAACATAAAG-AAAAGG
128 -ACTATAATTGAATGTCTAACTAGAGAAACATGAAGAAAAAAG
** * * * *
422 CATTCACAGGCAAGAAAAGTCGATTTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTT
1 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTTT
********** * *
487 AAATNNNNNNNNNNTCTCATAATTGATTTTAAGTTGAATTTTTTATATTTTTGGTTAAAACTAAC
66 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAA-TTTTTACATTTTTTGTTAAAACTAAC
* *
552 TATAATTGAATGTCTAACTTGAGAAACATGAAGAAAAATG
130 TATAATTGAATGTCTAACTAGAGAAACATGAAGAAAAAAG
* **********
592 GATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCNNNNNNNNNNGCTTT
1 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTTT
*
657 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGATTATTTTTTCATTTTTTGTTAAAAC-AG
66 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGA--ATTTTTACATTTTTTGTTAAAACTA-
* * *
721 A-TAATAATTGAATGTCTACCTAGTGAAACGTGAAGAAAAAAG
128 ACT-ATAATTGAATGTCTAACTAGAGAAACATGAAGAAAAAAG
* *
763 CATTCATTGGCAAGAGAAGTCCATTTATAGTCACCTATTCCTTCAAAGGCCGTATTACTCGCTTT
1 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTTT
********** *
828 AAATGNNNNNNNNNNCTCATAATTGATTTTAAGTTGAATTCTTTACATTTTTAGTTAAAACTAAC
66 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATT-TTTACATTTTTTGTTAAAACTAAC
893 TATAATTGAATGTCTAACTCA-AGAAACATGAAGAAAAATAG
130 TATAATTGAATGTCTAACT-AGAGAAACATGAAGAAAAA-AG
* * * * *
934 -ATTCATTGGCAAGAAAAATCCAATTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTT
1 CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTTT
* **********
998 AAATAGTTTTACNNNNNNNNNNTTGATTTTAAGTTGATTATTTTTACATTTTTTGTTAAAAC-AG
66 AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGA--ATTTTTACATTTTTTGTTAAAACTA-
* * * * *
1062 ACAATAATTGGATGTCTATCTTGAGAAACGTGAAG-AAAAAG
128 ACTATAATTGAATGTCTAACTAGAGAAACATGAAGAAAAAAG
*********** * * **
1103 ACATTCATTGGCAAGAAAAGTCCATTTATAGTNNNNNNNNNNNTCAAAAGCCTTATTTCTTACTT
1 -CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTT
* * * * *
1168 TAAATGGTTTTATAATCTCAAAATTGATTTTATGTTCAATTTCTTTTACATTTTTAGTTAAAAC-
65 TAAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAA--T-TTTTACATTTTTTGTTAAAACT
* * * * *
1232 ATATTATAATTCAATGT-TTACCATGAGAAACATGAAGAAAAAGG
127 A-ACTATAATTGAATGTCTAACTA-GAGAAACATGAAGAAAAAAG
* * * * * * *
1276 CATTCACTGACAAGAAAAGTCTATTTATAGTCAACC-ATTCTTTCAAAAGCCTTATCATTCGCTT
1 CATTCATTGGCAAGAAAAGTCCATTTATAGTC-ACCTATTCCTTCAAAAGCCGTATTACTCGCTT
* *
1340 TAAATGGTTTTATAATCTCATAATTAATTTTAAGT
65 TAAATGGTTTTACAATCTCATAATTGATTTTAAGT
1375 NNNNNNNNNN
Statistics
Matches: 745, Mismatches: 185, Indels: 45
0.76 0.19 0.05
Matches are distributed among these distances:
169 55 0.07
170 219 0.29
171 341 0.46
172 125 0.17
173 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.36
Consensus pattern (169 bp):
CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCGTATTACTCGCTTT
AAATGGTTTTACAATCTCATAATTGATTTTAAGTTGAATTTTTACATTTTTTGTTAAAACTAACT
ATAATTGAATGTCTAACTAGAGAAACATGAAGAAAAAAG
Found at i:831 original size:341 final size:330
Alignment explanation
Indices: 252--1374 Score: 951
Period size: 341 Copynumber: 3.3 Consensus size: 330
242 NNNNNNAATC
* * * *
252 ATTCATTGGTAA-AAAAAGTCCATTTCTAGTCACCCATTCCTTCAAAAGCCTTATTTCTCGCTTT
1 ATTCATTGGCAAGAAAAA-TCCAATTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
* * ** * * *
316 AAATGGCTTTATAATCTCAAAATTGATTTTTTGTTCAATTGTTTTTACATTTTTGGTTAAAACAG
65 AAATGGTTTTACAATCTCAAAATTGATTTTAAGTT-GATTATTTTTACATTTTTTGTTAAAACAG
* * * * * * * * ** *
381 ATTATCATTCAATGTTTACCTTTAGAAACATAAAGAAAAGGCATTCACAGGCAAGAAAAGTCGAT
129 ATAATAATTGAATGTCTACCTGT-GAAACGTGAAGAAAAAGCATTCATTGGCAAGAAAAGTCCAT
* * *
446 TTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATNNNNNNNNNNTCTCATAATT
193 TTATAGTCACCCATTCCTTCAAAAGCCGTATTACTCGCTTTAAAT---------GTCTCATAATT
* * * **
511 GATTTTAAGTTGAATTTTTTATATTTTTGGTTAAAACTAACTATAATTGAATGTCTAACTTGAGA
249 GATTTTAAGTTGAATTCTTTACATTTTTAGTTAAAACTAACTATAATTGAATGTCTAACTCAAGA
*
576 AACATGAAGAAAAATGG
314 AACATGAAGAAAAATAG
* * * **********
593 ATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCNNNNNNNNNNGCTTTA
1 ATTCATTGGCAAGAAAAATCCAATTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTA
* *
658 AATGGTTTTACAATCTCATAATTGATTTTAAGTTGATTATTTTTTCATTTTTTGTTAAAACAGAT
66 AATGGTTTTACAATCTCAAAATTGATTTTAAGTTGATTATTTTTACATTTTTTGTTAAAACAGAT
*
723 AATAATTGAATGTCTACCTAGTGAAACGTGAAGAAAAAAGCATTCATTGGCAAGAGAAGTCCATT
131 AATAATTGAATGTCTACCT-GTGAAACGTGAAG-AAAAAGCATTCATTGGCAAGAAAAGTCCATT
* * *
788 TATAGTCACCTATTCCTTCAAAGGCCGTATTACTCGCTTTAAATGNNNNNNNNNNCTCATAATTG
194 TATAGTCACCCATTCCTTCAAAAGCCGTATTACTCGCTTTAAATG---------TCTCATAATTG
853 ATTTTAAGTTGAATTCTTTACATTTTTAGTTAAAACTAACTATAATTGAATGTCTAACTCAAGAA
250 ATTTTAAGTTGAATTCTTTACATTTTTAGTTAAAACTAACTATAATTGAATGTCTAACTCAAGAA
918 ACATGAAGAAAAATAG
315 ACATGAAGAAAAATAG
*
934 ATTCATTGGCAAGAAAAATCCAATTATAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTA
1 ATTCATTGGCAAGAAAAATCCAATTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTA
* ********** *
999 AATAGTTTTACNNNNNNNNNNTTGATTTTAAGTTGATTATTTTTACATTTTTTGTTAAAACAGAC
66 AATGGTTTTACAATCTCAAAATTGATTTTAAGTTGATTATTTTTACATTTTTTGTTAAAACAGAT
* * *
1064 AATAATTGGATGTCTATCTTGAGAAACGTGAAGAAAAAGACATTCATTGGCAAGAAAAGTCCATT
131 AATAATTGAATGTCTA-CCTGTGAAACGTGAAGAAAAAG-CATTCATTGGCAAGAAAAGTCCATT
*********** * * ** *
1129 TATAGTNNNNNNNNNNNTCAAAAGCCTTATTTCTTACTTTAAATGGTTTTATAATCTCAAAATTG
194 TATAGTCACCCATTCCTTCAAAAGCCGTATTACTCGCTTTAAAT-G--------TCTCATAATTG
* * * * *
1194 ATTTTATGTTCAATTTCTTTTACATTTTTAGTTAAAAC-ATATTATAATTCAATGT-TTAC-CAT
250 ATTTTAAGTTGAA-TTC-TTTACATTTTTAGTTAAAACTA-ACTATAATTGAATGTCTAACTCA-
*
1256 GAGAAACATGAAGAAAAA-GG
311 -AGAAACATGAAGAAAAATAG
* * * * * * * * *
1276 CATTCACTGACAAGAAAAGTCTATTTATAGTCAACCATTCTTTCAAAAGCCTTATCATTCGCTTT
1 -ATTCATTGGCAAGAAAAATCCAATTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
* * *
1341 AAATGGTTTTATAATCTCATAATTAATTTTAAGT
65 AAATGGTTTTACAATCTCAAAATTGATTTTAAGT
1375 NNNNNNNNNN
Statistics
Matches: 630, Mismatches: 131, Indels: 40
0.79 0.16 0.05
Matches are distributed among these distances:
340 57 0.09
341 431 0.68
342 15 0.02
343 127 0.20
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.36
Consensus pattern (330 bp):
ATTCATTGGCAAGAAAAATCCAATTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTA
AATGGTTTTACAATCTCAAAATTGATTTTAAGTTGATTATTTTTACATTTTTTGTTAAAACAGAT
AATAATTGAATGTCTACCTGTGAAACGTGAAGAAAAAGCATTCATTGGCAAGAAAAGTCCATTTA
TAGTCACCCATTCCTTCAAAAGCCGTATTACTCGCTTTAAATGTCTCATAATTGATTTTAAGTTG
AATTCTTTACATTTTTAGTTAAAACTAACTATAATTGAATGTCTAACTCAAGAAACATGAAGAAA
AATAG
Found at i:2256 original size:158 final size:158
Alignment explanation
Indices: 2083--2371 Score: 350
Period size: 158 Copynumber: 1.8 Consensus size: 158
2073 ACATTTTGAT
* * * * * *
2083 TAAAACAAACTATAATTGAATGTCTA-CCTTAGGAAACGTGAA-GAAAAAACCATTCATTTGTAG
1 TAAAACAAACTATAATTGAATGTCTACCCTGA-CAAACAT-AAGGAAAAAACCATTCACTAGCA-
* * * *
2146 A-AAATGTCTATTTATAGTCACATATTCCTTCAAAAGTCTTATTACTCGCTATAAATGGTTTTAT
63 ATAAAAGTCTATTTATAGTCACACATTCCTTCAAAAGCCTTATTACTCGCTATAAAAGGTTTTAT
2210 AATCTCAAAATTGATTTTTTACATTTTTGGG
128 AATCTCAAAATTGATTTTTTACATTTTTGGG
* * * * **
2241 TAAAACAGATTATAATTTAATGTTTACCCTGACAAACATAAGGAAAAAGGCATTCACTAGCAATA
1 TAAAACAAACTATAATTGAATGTCTACCCTGACAAACATAAGGAAAAAACCATTCACTAGCAATA
* * * *
2306 AAAGTCTATTTTTAGTCACCCATTCTTTCAAAAGCCTTATTACTCGCTTTAAAAGGTTTTATAAT
66 AAAGTCTATTTATAGTCACACATTCCTTCAAAAGCCTTATTACTCGCTATAAAAGGTTTTATAAT
2371 C
131 C
2372 NNNNNNNNNN
Statistics
Matches: 108, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
157 3 0.03
158 101 0.94
159 4 0.04
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (158 bp):
TAAAACAAACTATAATTGAATGTCTACCCTGACAAACATAAGGAAAAAACCATTCACTAGCAATA
AAAGTCTATTTATAGTCACACATTCCTTCAAAAGCCTTATTACTCGCTATAAAAGGTTTTATAAT
CTCAAAATTGATTTTTTACATTTTTGGG
Found at i:4158 original size:171 final size:170
Alignment explanation
Indices: 3975--4337 Score: 404
Period size: 170 Copynumber: 2.1 Consensus size: 170
3965 GTCAACATAA
* * * * *
3975 ACATTGAATTATAATCTGTTTT-ACCTAAAAATGTAAAAAAATTGAACATAAAATCAATTTTGAG
1 ACATTCAATTATAGTCTGTTTTAACC--AAAATGTAAAAAAATTCAACACAAAATCAATTATGAG
**********
4039 ATTATAAAANNNNNNNNNNCGAGAAATAAGACTTTTGAAGGAATGGGTGACTATAAATAGACTTT
64 ATTATAAAACTATTTAAATCGAGAAATAAGACTTTTGAAGGAATGGGTGACTATAAATAGACTTT
*
4104 TTTTACAAATGAATGATTTTTTCTTCACATTTCCTAAGGTAG
129 TTTTACAAATGAATGATTTTGTCTTCACATTTCCTAAGGTAG
** * * **
4146 ATGTTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAAGTTCAACCCAAAATTGATTATGAGAT
1 ACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAAATTCAACACAAAATCAATTATGAGAT
* * *
4211 TATAAAACTATTTAAATCGAGTAATAAGACTTTTGAAGGAATGTGTGACTATAAATGGACTTTTT
66 TATAAAACTATTTAAATCGAGAAATAAGACTTTTGAAGGAATGGGTGACTATAAATAGACTTTTT
* * * * ** *
4276 TTGCCATTGAATGCTTTTGTCTTCATTTTTCTTAAGGTAG
131 TTACAAATGAATGATTTTGTCTTCACATTTCCTAAGGTAG
*
4316 ACATTCAATTATAGTCTATTTT
1 ACATTCAATTATAGTCTGTTTT
4338 TATGANNNNN
Statistics
Matches: 156, Mismatches: 35, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
170 135 0.87
171 18 0.12
172 3 0.02
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.37
Consensus pattern (170 bp):
ACATTCAATTATAGTCTGTTTTAACCAAAATGTAAAAAAATTCAACACAAAATCAATTATGAGAT
TATAAAACTATTTAAATCGAGAAATAAGACTTTTGAAGGAATGGGTGACTATAAATAGACTTTTT
TTACAAATGAATGATTTTGTCTTCACATTTCCTAAGGTAG
Found at i:5866 original size:171 final size:169
Alignment explanation
Indices: 5343--5885 Score: 556
Period size: 170 Copynumber: 3.2 Consensus size: 169
5333 NNNNNNNNNN
* * * * *
5343 ACTCGCTTTAAATAGTTTTATAATCTCATAATTGATTTTAAGTTGAA-TTCTTTACATTTGTGGT
1 ACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTT-AATTTTTTTACATTTTTTGT
* * * * * *
5407 TAAAACTA-ACTATAATTGAATGTCTAACTCGAGAAACGTGAAGAAAAATAG-ATTCATTGACAA
65 TAAAAC-AGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAA-GGCATTCATAG-CAA
* * * * *
5470 GAAAAGTCCCTTTATAGTCACCCATTCCTTCAAAAACTTTATT
127 GAAAAGTCCATTTATAGTCAACCATTCCTTTAAAAGCCTTATT
* * * *
5513 ACTCACTTTAAATGGTTTTACAATCTCATAATTGATTTTAAGTTGATTAGTTTTACTTTTTTTGT
1 ACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATT-TTTTTACATTTTTTGT
* * * *
5578 TAAAACAGATAATAATTGAATG-TCACCTTGAGAAACGTGAAGAAAAAGACATTCATTGGCAAGA
65 TAAAACAGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGGCATTCA-TAGCAAGA
*************
5642 AAAGTCCATTTATANNNNNNNNNNNNNTTAAAAGCCTTATT
129 AAAGTCCATTTATAGTCAACCATTCCTTTAAAAGCCTTATT
* *
5683 TCTCACTTTAAATGGTTTTATAATCTCAAAATTGATTTTATA-TTCAATTTTTTTACATTTTTTG
1 ACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTA-AGTT-AATTTTTTTACATTTTTTG
* * * * *
5747 TTAAAACAGATTATAATTTAATGTTTACCTTGATAAACATGAAGAAGAAGGCATTCGCTAGCAAG
64 TTAAAACAGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGGCATTC-ATAGCAAG
*
5812 AAAAGTCCATTTATAGTCAACCATTCCTTTAAAAGCCTTATC
128 AAAAGTCCATTTATAGTCAACCATTCCTTTAAAAGCCTTATT
*
5854 ACTCGCTTTAAATGGTTTTATAATCTCATAAT
1 ACTCACTTTAAATGGTTTTATAATCTCATAAT
5886 NNNNNNNNNN
Statistics
Matches: 297, Mismatches: 67, Indels: 17
0.78 0.18 0.04
Matches are distributed among these distances:
169 1 0.00
170 171 0.58
171 125 0.42
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.37
Consensus pattern (169 bp):
ACTCACTTTAAATGGTTTTATAATCTCATAATTGATTTTAAGTTAATTTTTTTACATTTTTTGTT
AAAACAGATTATAATTGAATGTTTACCTTGAGAAACGTGAAGAAAAAGGCATTCATAGCAAGAAA
AGTCCATTTATAGTCAACCATTCCTTTAAAAGCCTTATT
Found at i:6678 original size:171 final size:168
Alignment explanation
Indices: 6473--7363 Score: 601
Period size: 170 Copynumber: 5.2 Consensus size: 168
6463 AAAAACGGAT
* * * * *
6473 AGAAAAAGGCATTCATTGACAAGAAAAGTCCATTTAAAATCACCAATTCTTTCAAAAGCCTTGTT
1 AGAAAAAAGCATTCATTG-CAAAAAAAGTCCATTTATAGTCACC-ATTCTTTCAAAAGCCTTATT
* * * *
6538 ACTCGCTTTAAATAGTTTTATAATGTTATAATTAATTTTACATTAAATTTTTTTACATTTTTGGT
64 ACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTACGTTAAATTTTTTTACATTTTTGGT
* *
6603 TAAAACAGACTATAATTGGATCTCTACCATAAGAAACATGA
129 TAAAACAGACTATAATTGAATATCTACC-TAAGAAACATGA
* * * * * *
6644 AGACAAAGGCATTCATTGCCAAAAAAAATCCATTTACAGTCATGCATTCATTCAAAAGCCTTATT
1 AGAAAAAAGCATTCATTG-CAAAAAAAGTCCATTTATAGTCA-CCATTCTTTCAAAAGCCTTATT
* ********** * * *
6709 ACTCACTTTAAATAGTTTTATAATCTCANNNNNNNNNNTAGGTTGAACTTTTTTACA-TTTTGGT
64 ACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTACGTTAAATTTTTTTACATTTTTGGT
* * * *
6773 TAAAACAGACTATAATTGAATGTCCACCTTAGAAAACGTGA
129 TAAAACAGACTATAATTGAATATCTACCTAAG-AAACATGA
* * * * *
6814 AGAAAAAATCAGTCATTGGTAAAAAAGGTCCATTTATAGTCACCCATT-TCTTCAAAAGCCTTCT
1 AGAAAAAAGCATTCATT-GCAAAAAAAGTCCATTTATAGTCA-CCATTCT-TTCAAAAGCCTTAT
* * * * *
6878 TTCTCGCTTTAAAT-GATTTTGTAATCTCAAAATTAATTTTATGTTCAATTTTTTTTATATTTTT
63 TACTCGCTTTAAATAG-TTTTATAATCTCAAAATTAATTTTACGTT-AAATTTTTTTACATTTTT
* * * * * *
6942 GGTTAAAATAGATTATAATTCAATATTTACCTTGAGAAACATAA
126 GGTTAAAACAGACTATAATTGAATATCTACC-TAAGAAACATGA
* * * *
6986 AGAAAAAAGCATTCACTAGTAAGAAAAGTCCATTTATAGTCACTCATTCTTCCAAAAGCCTTATT
1 AGAAAAAAGCATTCA-TTGCAAAAAAAGTCCATTTATAGTCAC-CATTCTTTCAAAAGCCTTATT
********** * * * *
7051 ACTCGCTTTAAANNNNNNNNNNATCTCATAATTGATTTTAAGTTGAA-TTTTTTACATTTTTGGT
64 ACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTACGTTAAATTTTTTTACATTTTTGGT
* * * *
7115 TAAAACTA-ACTATAATAGAATGTCTAACTTGAGAAACATGA
129 TAAAAC-AGACTATAATTGAATATCT-ACCTAAGAAACATGA
* * ** * * * ***
7156 AGAAAAATTG-ATTCATTGGTAGGAAAAGTCTATTTATTGTCACCTATTCCTTCAAAAGCCTNNN
1 AGAAAAA-AGCATTCATT-GCAAAAAAAGTCCATTTATAGTCACC-ATTCTTTCAAAAGCCTTAT
******* * * * * * *
7220 NNNNNNNTTTAAATAGTTTTACAATCTCATAATTGATTTTAAGTT-AATTATTTTTATATTTTTT
63 TACTCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTACGTTAAATT-TTTTTACATTTTTG
* * * *
7284 ATTAAAACAGA-TAATAATTGAATGTTTACCTTAAGAAACGTGA
127 GTTAAAACAGACT-ATAATTGAATATCTACC-TAAGAAACATGA
* *
7327 AGAAAAAGGCATTCATTGGCAAGAAAAGTCCATTTAT
1 AGAAAAAAGCATTCATT-GCAAAAAAAGTCCATTTAT
7364 NNNNNNNNNN
Statistics
Matches: 557, Mismatches: 140, Indels: 46
0.75 0.19 0.06
Matches are distributed among these distances:
169 8 0.01
170 243 0.44
171 183 0.33
172 118 0.21
173 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.36
Consensus pattern (168 bp):
AGAAAAAAGCATTCATTGCAAAAAAAGTCCATTTATAGTCACCATTCTTTCAAAAGCCTTATTAC
TCGCTTTAAATAGTTTTATAATCTCAAAATTAATTTTACGTTAAATTTTTTTACATTTTTGGTTA
AAACAGACTATAATTGAATATCTACCTAAGAAACATGA
Found at i:8301 original size:174 final size:171
Alignment explanation
Indices: 8031--8365 Score: 390
Period size: 174 Copynumber: 1.9 Consensus size: 171
8021 NNNNNNNNAT
*
8031 TTTAAGTTAAATTTTTTTACATTTGTTATTAAAACAGACTATAATCGAATGCTTACCTTAGAAAA
1 TTTAAGTTAAATTTTTTTACATTTGTTATCAAAACAGACTATAATCGAATGCTTACCTTAGAAAA
** * * * * * *
8096 CATGTAGAAAAAGCTACTCATTGACAAGAAAATTCCATTTATAGCCTCTCATTCTTTT-AAAAGC
66 CATAAAGAAAAAGCTACTCACTGACAAGAAAAGTCCATTTACAGCCACCCATT-TTTTCAAAACC
*
8160 CTTATTACTCACTTTATATGGTTTTATAATCTCAAAAATGAC
130 CTTATTACTCACTTTAAATGGTTTTATAATCTCAAAAATGAC
* * * *
8202 TTTAAGTTCAATATTTTTTTTACATTT-TTAGTCAAAACAGATTGTAATTGAATGTTTACCTT-G
1 TTTAAGTT-AA-A-TTTTTTTACATTTGTTA-TCAAAACAGACTATAATCGAATGCTTACCTTAG
* * ** * *
8265 ACAAATATAAAGAAAAAGGC-ATTCACTGGTAAGAAAAGTCCATTTACAGTCACCCATTTTTTCG
62 A-AAACATAAAGAAAAA-GCTACTCACTGACAAGAAAAGTCCATTTACAGCCACCCATTTTTTCA
*
8329 AAACCCTTATTACTCGCTTTAAATGGTTTTATAATCT
125 AAACCCTTATTACTCACTTTAAATGGTTTTATAATCT
8366 TATAATTGAT
Statistics
Matches: 136, Mismatches: 21, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
171 8 0.06
172 2 0.01
173 10 0.07
174 114 0.84
175 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.39
Consensus pattern (171 bp):
TTTAAGTTAAATTTTTTTACATTTGTTATCAAAACAGACTATAATCGAATGCTTACCTTAGAAAA
CATAAAGAAAAAGCTACTCACTGACAAGAAAAGTCCATTTACAGCCACCCATTTTTTCAAAACCC
TTATTACTCACTTTAAATGGTTTTATAATCTCAAAAATGAC
Found at i:8586 original size:170 final size:160
Alignment explanation
Indices: 8391--8699 Score: 307
Period size: 169 Copynumber: 1.9 Consensus size: 160
8381 NNNNNNTTTC
* *
8391 TTACATTTTTCATAAAAATAGACTATAATTGAATGTCTACCTTAAGCAAA-ATGAAGACAAAAGC
1 TTACATTTTTCATAAAAACAGACTATAATTGAATGTCTACCTT-AGCAAATATGAAGAAAAAAGC
**
8455 ATTCATTGGCAAAAAAAATCTATTTACAGTCATGCATTCCTTCAAAAGCCTTATTACTCGCTTTA
65 ATT-ATTGGCAAAAAAAATCTATTTACAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTA
8520 AATAGTTTTATNNNNNNNNNNTTGATTTTAGGTTGAACTTTT
129 AATAGTTTTAT----------TTGATTTTAGGTTGAACTTTT
* * * * * * *
8562 TTACA-TTTTGATTAAAACAGACTATAATTGAATGTCTGCCTTTGGAAATGTGAAGAAAAAATCA
1 TTACATTTTTCATAAAAACAGACTATAATTGAATGTCTACCTTAGCAAATATGAAGAAAAAAGCA
* * * ** * * * *
8626 TTGTTGGTAGAAAAGGTCTATTTATAGTCACCCATTCCTTCAAAAGTCTTATTTCTCGCTTTTAA
66 TTATTGGCAAAAAAAATCTATTTACAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA
*
8691 TGGTTTTAT
131 TAGTTTTAT
8700 AATCTCAAAA
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
169 64 0.55
170 47 0.41
171 5 0.04
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.37
Consensus pattern (160 bp):
TTACATTTTTCATAAAAACAGACTATAATTGAATGTCTACCTTAGCAAATATGAAGAAAAAAGCA
TTATTGGCAAAAAAAATCTATTTACAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAA
TAGTTTTATTTGATTTTAGGTTGAACTTTT
Found at i:8961 original size:170 final size:169
Alignment explanation
Indices: 7703--9019 Score: 834
Period size: 170 Copynumber: 7.7 Consensus size: 169
7693 TGTTCAATTG
* * * * *
7703 TTTTTACATTTTTGGTTAAAACAGATTATAATTCAATGTTTACCTTGAGAAACATGAAGAAAAAG
1 TTTTTACATTTTTAGTTAAAA-AAACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* * * * * * *******
7768 -CATTCACTAGCAACAAAAGTCCATTTATAGTCAACCATTCCTTCAAAAGCCTTATCANNNNNNN
65 ACATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTT
*** * * * *
7832 NNNATAGTTTTATAATCTCATAATTGATTTTAAATTGAACC
130 TAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAA-T
* * *
7873 TTTTTACATTTATTAG-TAAAACAGACTATAATTGAATGTTTGA-CTTGAGAAACGTGAA-AAAC
1 TTTTTACATTT-TTAGTTAAAA-AAACTATAATTGAATGTCT-ACCTTGAGAAACATGAAGAAA-
** * ** * * *
7935 AA-ACCATTCATTGACAAGAAAAGTCTATTTATAGTCTTCAATTCCTTCAAAAGCCTTAGTACTA
62 AAGA-CATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* ********** *
7999 GCTTTAAATAGTTTTATAATNNNNNNNNNNATTTTAAGTTAAATT
126 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAA-T
* * *
8044 TTTTTACATTTGTTA-TTAAAACAGACTATAATCGAATG-CTTACCTT-AGAAAACATGTAGAAA
1 TTTTTACATTT-TTAGTTAAAA-AAACTATAATTGAATGTC-TACCTTGAG-AAACATGAAGAAA
* ** * * * * * *
8106 AAG-CTACTCATTGACAAGAAAATTCCATTTATAGCCTCTCATTCTTTTAAAAGCCTTATTACTC
62 AAGAC-ATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* * * * *
8170 ACTTTATATGGTTTTATAATCTCAAAAATGACTTTAAGTTCAATATTT
126 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-GA-A--T
* * * * * * * *
8218 TTTTTACATTTTTAGTCAAAACAGATTGTAATTGAATGTTTACCTTGACAAATATAAAGAAAAAG
1 TTTTTACATTTTTAGTTAAAA-AAACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* * * ** * *
8283 GCATTCACTGGTAAGAAAAGTCCATTTACAGTCACCCATTTTTTCGAAACCCTTATTACTCGCTT
65 ACATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTT
* * **********
8348 TAAATGGTTTTATAATCTTATAATTGATTNNNNNNNNNNT
130 TAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAAT
* *
8388 TTCTTACATTTTTCA--TAAAAATAGACTATAATTGAATGTCTACCTTAAGCAAA-ATGAAGACA
1 TTTTTACATTTTT-AGTTAAAAA-A-ACTATAATTGAATGTCTACCTTGAG-AAACATGAAGA-A
* * * * * **
8450 AAAG-CATTCATTGGCAAAAAAAATCTATTTACAGTCATGCATTCCTTCAAAAGCCTTATTACTC
61 AAAGACATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTC
* ********** *
8514 GCTTTAAATAGTTTTATNNNNNNNNNNTTGATTTTAGGTTGAACT
126 GCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAA-T
* * * **
8559 TTTTTACATTTTGA-TTAAAACAGACTATAATTGAATGTCTGCCTTTG-GAAATGTGAAGAAAAA
1 TTTTTACATTTTTAGTTAAAA-AAACTATAATTGAATGTCTACC-TTGAGAAACATGAAGAAAAA
* * * *
8622 -ATCATT-GTTGGT-AGAAAAGGTCTATTTATAGTCACCCATTCCTTCAAAAGTCTTATTTCTCG
64 GA-CATTCATTGGTAAGAAAA-GTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCG
* **********
8684 CTTTTAATGGTTTTATAATCTCAAAATTGATTNNNNNNNNNNTTT
127 CTTTAAATGGTTTTATAATCTCAAAATTGATT--TTAAGTTGAAT
* ** * * *
8729 TTTTTACATTTTTAGTTAAAAAAGATTATAATCCAATGTTTACCTTGAAAAACATAAAGAAAAAG
1 TTTTTACATTTTTAGTTAAAAAA-ACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* * * * * * *
8794 ACATTCACTAGTAAGAAAAGTCCATTTTTAGTCACACATTCTTTCAGAAGCCTTATTACTCACTT
65 ACATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTT
* *
8859 TAAATGGTTTTATAATCTGAAAATTTATTTTAAGTTGAAT
130 TAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAAT
* * *
8899 TTTTTATATTTTTAGTTAAAAATAACTATAATTGAATGTCTAACTCGAGAAACATGAAGAAAAAG
1 TTTTTACATTTTTAGTTAAAAA-AACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAG
* * *
8964 AGATTCATTGGTAAGAACAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTTAT
65 ACATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTAT
9020 NNNNNNNNNN
Statistics
Matches: 869, Mismatches: 237, Indels: 82
0.73 0.20 0.07
Matches are distributed among these distances:
168 6 0.01
169 75 0.09
170 315 0.36
171 263 0.30
172 74 0.09
173 10 0.01
174 124 0.14
175 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.36
Consensus pattern (169 bp):
TTTTTACATTTTTAGTTAAAAAAACTATAATTGAATGTCTACCTTGAGAAACATGAAGAAAAAGA
CATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTCAAAAGCCTTATTACTCGCTTT
AAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGAAT
Found at i:9479 original size:170 final size:171
Alignment explanation
Indices: 9154--11365 Score: 1199
Period size: 171 Copynumber: 13.1 Consensus size: 171
9144 NNNNNNNNNN
* ** * * *
9154 TAAGTTG-ATTATTTTTACATTTTTT-ATTAAAACAGACAATAATTGAATGTGTACATCAAGAAC
1 TAAGTTGAATT-TTTTTAC-TTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAA
* * * * * ********
9217 CGTGAAGAAATAGGCATTCATTGGTAAGAAAAGTCCATTTATAGTCACCCATTCCTTNNNNNNNN
64 CATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCC
** * *
9282 NNATTACTCGCTTTAAATGGTTTTATAATTTCATAATTAATTT
129 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* ** * *
9325 TAAGTTGAATTTTCTTACTTTTTTCCTT-AAATAGATTATAAATGAATGTCTACCTCAAGAAACA
1 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACA
* ** *
9389 TGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATTATTTGAAAAGCCTT
66 TGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTT
* *
9454 ATTTCTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTT
131 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * * *
9495 TACGTTCATTCTTTTTTACATTTTTGGTTAAAACAGATTATAATTCAATGTTTACCTTGAA-AAA
1 TAAGTTGAAT-TTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACC-TCAAGAAA
* * * * *
9559 CATGAAG-AAAAGGCATTTACTAGCAAGAAAAGTTCATTTATAGTCAACC-ATTCCTTCAAAAGC
64 CATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTC-ACCTATTCCTTCAAAAGC
* * *
9622 CTTATCACTTGCTTTAAATGG-TTT-T-A--T-A-GA-TGATTT
128 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * *
9658 TAACTTTG-ATTTTTTTA-TTTTTTAG-T-AAACAAGACATATAATTG--T-TGTAGCCT-GAGA
1 TAA-GTTGAATTTTTTTACTTTTTTGGTTAAAAC-AGA-TTATAATTGAATGTCTA-CCTCAAGA
* * * * **
9715 AACGTGTAGACAAAAGCATTCATT-GCAAGAAAAGTCTATTTATAGTCAACC-ATAACTTCAAAA
62 AACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTC-ACCTATTCCTTCAAAA
* *
9778 GCCTTATCACTCGCTTTAAATGGTTTTATAATTTCATAATTGATTT
126 GCCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * *
9824 TAAGCTGAACTTTTTTATAGC--TTTTAG-TAAAACAGATTATAATTAAATGTTTAGCTCGAGAA
1 TAAGTTGAA-TTTTTT-TA-CTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAA
* * * * * * * *
9886 ACATGAGGAACAAAGTATTCATTAGCAAGAAAAGTCTATTTATAGTCTCCAATTCATTCAAAAGC
63 ACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGC
* * ********** *
9951 CTTATTACTAGCTTTAAATTGTTTTNNNNNNNNNNAATTAATTT
128 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * ** * * *
9995 TAAGTTGAATTTTTTTACATTTGTCATTAAAACAGACTATAATTGAATG-CTTGCCT-TAGAAA-
1 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTC-TACCTCAAGAAAC
* * * * * * ** *
10057 ACG-GGTAGAAAAGTCATTTATTGACAAGAAAAGTCCATTTATAGTC-TCTCATTATTTTAAAAG
65 ATGAAG-AAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCT-ATTCCTTCAAAAG
* ********** * *
10120 CCTTATTACTCACTTTAAANNNNNNNNNNATCTCAAAATTGACTT
127 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * *
10165 TAAGTTCAATTTTTTTCTTACATTTTTT-GTCAAAACAGATTATAATTGAATGTTTAACTTAAAA
1 TAAGTTGAA--TTTTT-TTAC-TTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGA
* * ** * * * * *
10229 AACATAAAGAAAAAGGCATTCATTAACAAGAAAAGCCCATTTAAAATCACCAATTCTTTCAAAAG
62 AACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAG
********** * * *
10294 CCTTATNNNNNNNNNNAAATAGTTTTATAACCTCATAATT-AATT
127 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * * *
10338 TAAGTTGAATTTTTTTACGTTTTTGGTTAAAATATACTATAATTGGATCTCTACCTTAAGAAACA
1 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACA
* ** *
10403 TGAAGACAAAAGCATTCATTACCAAAAAAAGTCCATTTA-AG---------CCTT----A---TT
66 TGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTT
** *
10451 A---CTCATTTTAAATAGTTTTATAATCTCATAATTGA-TT
131 ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * * * *
10488 TCAGATTGAACTTTTCTAC-ATTTTGGTTAAAACAGACTATAATTGAATGTCTATCTTAGGAAAC
1 TAAG-TTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAAC
* * * * *
10552 GTGAAGAAAAAATCATTTATTGGTAAAAAAAGGTCCATTTAT-GCTCA-CTCATTCCTTCAAAAG
65 ATGAAGAAAAAAGCATTCATTGGCAAGAAAA-GTCCATTTATAG-TCACCT-ATTCCTTCAAAAG
********** * *
10615 CCTTATTNNNNNNNNNNAATGGTTTTATAATCTCAAAATTAATTT
127 CCTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * * * * * * *
10660 TATGTTCAATTTTTTTACATTTTTAGTTAAAACATATTATAATTCAGTGTTTAACTTGAA-AAAC
1 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCT-ACCTCAAGAAAC
* * * * *
10724 ATAAAG-AAAAAGACATTCACTGGAAAGAAAAGTCCATTTATAGACA-CTCATTCTTTCAAAAGC
65 ATGAAGAAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCT-ATTCCTTCAAAAGC
**********
10787 CTTATTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTGATTT
128 CTTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * * *
10831 TAAGTTGAA-TGTTTTACATTTTTGGTTAAAA-ATAACTATAATTGAATGTCTAACTCAAGAAAC
1 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACA-GATTATAATTGAATGTCTACCTCAAGAAAC
* * * * * *
10894 ATGAAGAAAAAGGGATTCATTGGTAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAGAATCCT
65 ATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCT
* *
10959 TATTACTCGCTTTCAATGATTTTATAATCTCATAATTGATTT
130 TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
*********** * * **
11001 NNNNNNNNNNATTTTTACATTTTTT-GTTAAAACAGATAATAATTGAATGTGTACCTTGAGAAAC
1 TAAGTTGAATTTTTTTAC-TTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAAC
* * * * * *
11065 GTGAAG-AACAAGACATTCAATGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAACGCC
65 ATGAAGAAAAAAG-CATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCC
* **********
11129 TTGTTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTGATTT
129 TTATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * ** * * *
11172 TAAGTTAAATTTTCTTACTTTTTTCCTTAAAATAGACTATAAGTGAATGTCTA-CTGCAAGAAAC
1 TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCT-CAAGAAAC
* * * * *
11236 GTGAAGAAAAAAGAATTCATTAGCAAGAAAAGTCCATTTATAGTCACCTAGTCCTTTAAAAGCCT
65 ATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCT
* * * *
11301 TATTTCTCACTTTAAATGGTTTTATAATCCCAAAATTGATTT
130 TATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
* * * *
11343 TACGTTCATTTTTTTTACATTTT
1 TAAGTTGAATTTTTTTACTTTTT
11366 NNNNNNNNNN
Statistics
Matches: 1529, Mismatches: 423, Indels: 178
0.72 0.20 0.08
Matches are distributed among these distances:
150 90 0.06
151 23 0.02
153 3 0.00
156 1 0.00
157 1 0.00
158 69 0.05
159 20 0.01
160 8 0.01
161 18 0.01
162 7 0.00
163 10 0.01
164 4 0.00
165 5 0.00
166 11 0.01
167 13 0.01
168 19 0.01
169 29 0.02
170 435 0.28
171 539 0.35
172 107 0.07
173 45 0.03
174 64 0.04
175 7 0.00
176 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.37
Consensus pattern (171 bp):
TAAGTTGAATTTTTTTACTTTTTTGGTTAAAACAGATTATAATTGAATGTCTACCTCAAGAAACA
TGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCCATTTATAGTCACCTATTCCTTCAAAAGCCTT
ATTACTCGCTTTAAATGGTTTTATAATCTCATAATTGATTT
Found at i:9622 original size:171 final size:169
Alignment explanation
Indices: 9284--10441 Score: 720
Period size: 170 Copynumber: 6.8 Consensus size: 169
9274 NNNNNNNNNN
* * * * *
9284 ATTACTCGCTTTAAATGGTTTTATAATTTCATAATTAATTTTAAGTTGAATTTTCTTACTTTTTT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTG-ATTTTTTTACATTTTT
** * * * * *
9349 CCTT-AAATAGATTATAAATGAATGTCTACC-TCAAGAAACATGAAGAAAAAAGCATTCATTGGC
65 AGTTAAAACAGATTATAATTGAATGTTTACCTTGAA-AAACATGAAG-AAAAAGCATTCATTAGC
* *
9412 AAGAAAAGTCTATTTATAGTCACCTATTATTTGAAAAGCCTT
128 AAGAAAAGTCTATTTATAGTCACCAATTATTTCAAAAGCCTT
* * *
9454 ATTTCTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCATTCTTTTTTACATTTT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGA-T-TTTTTTACATTTT
* * * * *
9519 TGGTTAAAACAGATTATAATTCAATGTTTACCTTGAAAAACATGAAGAAAAGGCATTTACTAGCA
64 TAGTTAAAACAGATTATAATTGAATGTTTACCTTGAAAAACATGAAGAAAAAGCATTCATTAGCA
**
9584 AGAAAAGT-TCATTTATAGTCAACC-ATTCCTTCAAAAGCCTT
129 AGAAAAGTCT-ATTTATAGTC-ACCAATTATTTCAAAAGCCTT
* * * * *
9625 ATCACTTGCTTTAAATGG-TTT-T-A--T--AGA-TGATTTTAACTTTGATTTTTTTA-TTTTTT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAA-GTTGATTTTTTTACATTTTT
* * * * *
9681 AG-T-AAACAAGACATATAATTG--T-TGTAGCC-TGAGAAACGTGTAGACAAAAGCATTCATT-
65 AGTTAAAAC-AGA-TTATAATTGAATGTTTA-CCTTGAAAAACATGAAGA-AAAAGCATTCATTA
* *
9739 GCAAGAAAAGTCTATTTATAGTCAACC-ATAACTTCAAAAGCCTT
126 GCAAGAAAAGTCTATTTATAGTC-ACCAATTATTTCAAAAGCCTT
* * * * * * *
9783 ATCACTCGCTTTAAATGGTTTTATAATTTCATAATTGATTTTAAGCTGAACTTTTTTATAGCTTT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTG-ATTTTTTTACA-TTTT
* * * * * *
9848 TAG-TAAAACAGATTATAATTAAATGTTTAGCTCGAGAAACATGAGGAACAAAGTATTCATTAGC
64 TAGTTAAAACAGATTATAATTGAATGTTTACCTTGAAAAACATGAAGAA-AAAGCATTCATTAGC
*
9912 AAGAAAAGTCTATTTATAGTCTCCAATTCA-TTCAAAAGCCTT
128 AAGAAAAGTCTATTTATAGTCACCAATT-ATTTCAAAAGCCTT
* * ********** *
9954 ATTACTAGCTTTAAATTGTTTTNNNNNNNNNNAATTAATTTTAAGTTGAATTTTTTTACATTTGT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTG-ATTTTTTTACATTT-T
* * * * ** * *
10019 CA-TTAAAACAGACTATAATTGAATGCTTGCCTT-AGAAAACGGGTAG-AAAAGTCATTTATT-G
64 TAGTTAAAACAGATTATAATTGAATGTTTACCTTGA-AAAACATGAAGAAAAAG-CATTCATTAG
* * *
10080 ACAAGAAAAGTCCATTTATAGTCTCTC-ATTATTTTAAAAGCCTT
127 -CAAGAAAAGTCTATTTATAGTCAC-CAATTATTTCAAAAGCCTT
* ********** * *
10124 ATTACTCACTTTAAANNNNNNNNNNATCTCAAAATTGACTTTAAGTTCAATTTTTTTCTTACATT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTT-GA--TTTTT-TTACATT
* * * * *
10189 TTTTGTCAAAACAGATTATAATTGAATGTTTAACTTAAAAAACATAAAGAAAAAGGCATTCATTA
62 TTTAGTTAAAACAGATTATAATTGAATGTTTACCTTGAAAAACATGAAGAAAAA-GCATTCATTA
* * * * * *
10254 ACAAGAAAAGCCCATTTAAAATCACCAATTCTTTCAAAAGCCTT
126 GCAAGAAAAGTCTATTTATAGTCACCAATTATTTCAAAAGCCTT
********** * * * * *
10298 ATNNNNNNNNNNAAATAGTTTTATAACCTCATAATT-AATTTAAGTTGAATTTTTTTACGTTTTT
1 ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTG-ATTTTTTTACATTTTT
* * * * * * * *
10362 GGTTAAAATATACTATAATTGGATCTCTACCTT-AAGAAACATGAAGACAAAAGCATTCATTACC
65 AGTTAAAACAGATTATAATTGAATGTTTACCTTGAA-AAACATGAAGA-AAAAGCATTCATTAGC
* *
10426 AAAAAAAGTCCATTTA
128 AAGAAAAGTCTATTTA
10442 AGCCTTATTA
Statistics
Matches: 765, Mismatches: 171, Indels: 104
0.74 0.16 0.10
Matches are distributed among these distances:
158 72 0.09
159 21 0.03
160 5 0.01
161 14 0.02
162 7 0.01
163 10 0.01
164 5 0.01
165 3 0.00
166 18 0.02
167 7 0.01
168 11 0.01
169 17 0.02
170 219 0.29
171 197 0.26
172 42 0.05
173 55 0.07
174 61 0.08
175 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.37
Consensus pattern (169 bp):
ATTACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGTTGATTTTTTTACATTTTTA
GTTAAAACAGATTATAATTGAATGTTTACCTTGAAAAACATGAAGAAAAAGCATTCATTAGCAAG
AAAAGTCTATTTATAGTCACCAATTATTTCAAAAGCCTT
Found at i:10009 original size:329 final size:330
Alignment explanation
Indices: 9382--9975 Score: 822
Period size: 329 Copynumber: 1.8 Consensus size: 330
9372 GTCTACCTCA
* * *
9382 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATTATTTGAA
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATAACTTCAA
** * * *
9447 AAGCCTTATTTCTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTACGTTCATTCTTTTTT
66 AAGCCTTATCACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGCTCATACTTTTTT
* * * * * *
9512 ACATTTTTGGTTAAAACAGATTATAATTCAATGTTTACCTTGAAAAACATGAAGAAAAGGCATTT
131 ACACTTTTAGTTAAAACAGATTATAATTAAATGTTTACCTCGAAAAACATGAAGAAAAAGCATTC
* *
9577 ACTAGCAAGAAAAGTTCATTTATAGTCAACCATTCCTTCAAAAGCCTTATCACTTGCTTTAAATG
196 ACTAGCAAGAAAAGTTCATTTATAGTCAACCATTCATTCAAAAGCCTTATCACTAGCTTTAAATG
9642 GTTTTATAGATGATTTTAACTTTGATTTTTTTATTTTTTAGTAAACAAGACATATAATTGTTGTA
261 GTTTTATAGATGATTTTAACTTTGATTTTTTTATTTTTTAGTAAACAAGACATATAATTGTTGTA
9707 GCCTG
326 GCCTG
* * *
9712 AGAAACGTGTAGACAAAAGCATTCATT-GCAAGAAAAGTCTATTTATAGTCAACC-ATAACTTCA
1 AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTC-ACCTATAACTTCA
* * *
9775 AAAGCCTTATCACTCGCTTTAAATGGTTTTATAATTTCATAATTGATTTTAAGCTGA-ACTTTTT
65 AAAGCCTTATCACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGCTCATACTTTTT
* * * * *
9839 TATAGCTTTTAG-TAAAACAGATTATAATTAAATGTTTAGCTCGAGAAACATGAGGAACAAAGTA
130 TACA-CTTTTAGTTAAAACAGATTATAATTAAATGTTTACCTCGAAAAACATGAAGAA-AAAGCA
* * *
9903 TTCATTAGCAAGAAAAG-TCTATTTATAGTC-TCCAATTCATTCAAAAGCCTTATTACTAGCTTT
193 TTCACTAGCAAGAAAAGTTC-ATTTATAGTCAACC-ATTCATTCAAAAGCCTTATCACTAGCTTT
*
9966 AAATTGTTTT
256 AAATGGTTTT
9976 NNNNNNNNNN
Statistics
Matches: 228, Mismatches: 31, Indels: 11
0.84 0.11 0.04
Matches are distributed among these distances:
328 53 0.23
329 148 0.65
330 27 0.12
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.38
Consensus pattern (330 bp):
AGAAACATGAAGAAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCTATAACTTCAA
AAGCCTTATCACTCGCTTTAAATGGTTTTATAATCTCAAAATTGATTTTAAGCTCATACTTTTTT
ACACTTTTAGTTAAAACAGATTATAATTAAATGTTTACCTCGAAAAACATGAAGAAAAAGCATTC
ACTAGCAAGAAAAGTTCATTTATAGTCAACCATTCATTCAAAAGCCTTATCACTAGCTTTAAATG
GTTTTATAGATGATTTTAACTTTGATTTTTTTATTTTTTAGTAAACAAGACATATAATTGTTGTA
GCCTG
Found at i:10580 original size:150 final size:151
Alignment explanation
Indices: 10310--10592 Score: 372
Period size: 150 Copynumber: 1.9 Consensus size: 151
10300 NNNNNNNNNN
* * * * *
10310 AAATAGTTTTATAACCTCATAATTAATTTAAGTTGAATTTTTTTACGTTTTTGGTTAAAATATAC
1 AAATAGTTTTATAACCTCATAATTAATTTAAGTTGAACTTTTCTACGATTTTGGTTAAAACAGAC
* *
10375 TATAATTGGATCTCTACCTTAAGAAACATGAAGACAAAAGCATTCATTACCAAAAAAA-GTCCAT
66 TATAATTGAATCTCTACCTTAAGAAACATGAAGAAAAAAGCATTCATTACCAAAAAAAGGTCCAT
10439 TTAAGCCTTATTACTCATTTT
131 TTAAGCCTTATTACTCATTTT
* * *
10460 AAATAGTTTTATAATCTCATAATTGATTTCAGATTGAACTTTTCTAC-ATTTTGGTTAAAACAGA
1 AAATAGTTTTATAACCTCATAATTAATTTAAG-TTGAACTTTTCTACGATTTTGGTTAAAACAGA
* * * * * * ***
10524 CTATAATTGAATGTCTATCTTAGGAAACGTGAAGAAAAAATCATTTATTGGTAAAAAAAGGTCCA
65 CTATAATTGAATCTCTACCTTAAGAAACATGAAGAAAAAAGCATTCATTACCAAAAAAAGGTCCA
10589 TTTA
130 TTTA
10593 TGCTCACTCA
Statistics
Matches: 112, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
150 91 0.81
151 21 0.19
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (151 bp):
AAATAGTTTTATAACCTCATAATTAATTTAAGTTGAACTTTTCTACGATTTTGGTTAAAACAGAC
TATAATTGAATCTCTACCTTAAGAAACATGAAGAAAAAAGCATTCATTACCAAAAAAAGGTCCAT
TTAAGCCTTATTACTCATTTT
Found at i:11360 original size:342 final size:331
Alignment explanation
Indices: 10632--11365 Score: 752
Period size: 341 Copynumber: 2.2 Consensus size: 331
10622 NNNNNNNNNN
* * *
10632 AATGGTTTTATAATCTCAAAATTAATTTTATGTTCAATTTTTTTACATTTTTAGTTAAAACATAT
1 AATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTTTTTTACATTTTTAGTTAAAACAGAT
* * * *
10697 TATAATTCAGTGTTTAACTTGAAAAACATAAAGAAAAAGACATTCACTGGAAAGAAAAGTCCATT
66 AATAATTCAATGTGTAACTTGAAAAACATAAAGAAAAAGACATTCAATGGAAAGAAAAGTCCATT
* *
10762 TATAGACACTCATTCTTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTG
131 TATAGACACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT----------AATTG
* ** *
10827 ATTTTAAGTTGAATGTTTTACATTTTTGGTTAAAAATAACTATAATTGAATGTCTAACTCAAGAA
186 ATTTTAAGTTAAATGTTTTACATTTTTCCTTAAAAATAACTATAAGTGAATGTCTAACTCAAGAA
* * * * * * * *
10892 ACATGAAGAAAAAGGGATTCATTGGTAAGAAAAGTCTATTTATAGTCACCTATTCCTTCAGAATC
251 ACATGAAGAAAAAAGAATTCATTAGCAAGAAAAGTCCATTTATAGTCACCTAGTCCTTCAAAAGC
* *
10957 CTTATTACTCGCTTTC
316 CTTATTACTCACTTTA
* * *********** *
10973 AATGATTTTATAATCTCATAATTGATTTNNNNNNNNNNATTTTTACATTTTTTGTTAAAACAGAT
1 AATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTTTTTTACATTTTTAGTTAAAACAGAT
* * * * * * * *
11038 AATAATTGAATGTGTACCTTGAGAAACGTGAAGAACAAGACATTCAATGGCAAGAAAAGTCTATT
66 AATAATTCAATGTGTAACTTGAAAAACATAAAGAAAAAGACATTCAATGGAAAGAAAAGTCCATT
* * *
11103 TATAGTCACCCATTCCTTCAAACGCCTTGTTACTCGCTTTAAATGGTTTTNNNNNNNNNNAATTG
131 TATAGACACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTT----------AATTG
* *
11168 ATTTTAAGTTAAATTTTCTTACTTTTTTCCTT-AAAATAGACTATAAGTGAATGTCT-ACTGCAA
186 ATTTTAAGTTAAATGTT-TTACATTTTTCCTTAAAAATA-ACTATAAGTGAATGTCTAACT-CAA
* *
11231 GAAACGTGAAGAAAAAAGAATTCATTAGCAAGAAAAGTCCATTTATAGTCACCTAGTCCTTTAAA
248 GAAACATGAAGAAAAAAGAATTCATTAGCAAGAAAAGTCCATTTATAGTCACCTAGTCCTTCAAA
*
11296 AGCCTTATTTCTCACTTTA
313 AGCCTTATTACTCACTTTA
* *
11315 AATGGTTTTATAATCCCAAAATTGATTTTACGTTCATTTTTTTTACATTTT
1 AATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTTTTTTACATTTT
11366 NNNNNNNNNN
Statistics
Matches: 324, Mismatches: 66, Indels: 5
0.82 0.17 0.01
Matches are distributed among these distances:
341 186 0.57
342 138 0.43
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.37
Consensus pattern (331 bp):
AATGGTTTTATAATCTCAAAATTGATTTTACGTTCAATTTTTTTACATTTTTAGTTAAAACAGAT
AATAATTCAATGTGTAACTTGAAAAACATAAAGAAAAAGACATTCAATGGAAAGAAAAGTCCATT
TATAGACACCCATTCCTTCAAAAGCCTTATTACTCGCTTTAAATGGTTTTAATTGATTTTAAGTT
AAATGTTTTACATTTTTCCTTAAAAATAACTATAAGTGAATGTCTAACTCAAGAAACATGAAGAA
AAAAGAATTCATTAGCAAGAAAAGTCCATTTATAGTCACCTAGTCCTTCAAAAGCCTTATTACTC
ACTTTA
Found at i:11774 original size:171 final size:171
Alignment explanation
Indices: 11470--11889 Score: 477
Period size: 171 Copynumber: 2.5 Consensus size: 171
11460 NNNNNNNNNN
* * *
11470 AAAAAGGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACTCATTCCTTCAAAGGCCTTATTAC
1 AAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAC
* * * * * *
11535 TCGCGTTAAATGGTTTTATAATCTCATAACTGATTTTAAGTTAAATTGTTTTATATTTTTCCTTA
66 TTGCTTTAAATGGTTTTATAATCTCAAAACTGATTTTAAGTTAAATTGTTTTATAATTCTACTTA
* * *
11600 AAATAG-ACTATAAATGAATGCCTACCTCAAAAAACGTGAAG
131 AAAT-GTACTATAAATCAATGCCTACCTCAAAAAACATAAAG
** * * * *
11641 AAAAAAGCATTTGTTGGCAAGAAAAGTCTATTTATTGTCACCCATCCCTTCAAAAGTCTTATTTC
1 AAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAC
* * * * *
11706 TTGCTTTAAATGGTTTTATAATCTCAAAATTGA-TTTATGTTCAATTTTTTTTATAATTCTAGTT
66 TTGCTTTAAATGGTTTTATAATCTCAAAACTGATTTTAAGTT-AAATTGTTTTATAATTCTACTT
* * ** * *
11770 AAAATGTATTATAATTCAATGTTTACCTTAAGAAACATAAAG
130 AAAATGTACTATAAATCAATGCCTACCTCAAAAAACATAAAG
* * * * * *
11812 AAAAAGGCATTCACTAGCATGAAAAGTCCATTTATAGTCAACCATTCCTTCAAAAGCCTTATTAC
1 AAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAC
11877 TCT-CTTTAAATGG
66 T-TGCTTTAAATGG
11890 NNNNNNNNNN
Statistics
Matches: 205, Mismatches: 41, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
170 8 0.04
171 196 0.96
172 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (171 bp):
AAAAAAGCATTCATTGGCAAGAAAAGTCTATTTATAGTCACCCATTCCTTCAAAAGCCTTATTAC
TTGCTTTAAATGGTTTTATAATCTCAAAACTGATTTTAAGTTAAATTGTTTTATAATTCTACTTA
AAATGTACTATAAATCAATGCCTACCTCAAAAAACATAAAG
Found at i:12080 original size:171 final size:162
Alignment explanation
Indices: 11903--12220 Score: 331
Period size: 172 Copynumber: 1.9 Consensus size: 162
11893 NNNNNNNTCA
* * * * * *
11903 TAATTGATTTTAAGTTGAACTT-TTTTACTTTTTTTAGTAAAACAGACTATAATTGAATGTTTAG
1 TAATTGATTTTAAGTTGAACTTGTTTTACATTTATCAGTAAAACAGACTATAATCGAATGCTTAC
* * *
11967 CTT-GAGAAATATGAAGAACAAAG-CATTCATT-GCTAA-AAAATATCTATTTATAGTCTCTAAT
66 CTTAG-GAAACATGAAGAA-AAAGTCATTCATTAAC-AAGAAAA-ATCCATTTATAGTCTCTAAT
12028 TCCTTCAAAAGCCTTATTACTAGCTTTAAATAGTTT
127 TCCTTCAAAAGCCTTATTACTAGCTTTAAATAGTTT
* *
12064 NNNNNNNNNNTAATTGATTTTAAGTTGAATTTGTTTTACATTTATCATTAAAACAGACTATAATC
1 ----------TAATTGATTTTAAGTTGAACTTGTTTTACATTTATCAGTAAAACAGACTATAATC
* *
12129 GAATGCTTACCTTAGGAAACATGTAGAAAAAGTCATTCATTAACAAGTAAAATCCATTTATAGTC
56 GAATGCTTACCTTAGGAAACATGAAGAAAAAGTCATTCATTAACAAGAAAAATCCATTTATAGTC
* * *
12194 TCTCATTCTTTTAAAAGCCTTATTACT
121 TCTAATTCCTTCAAAAGCCTTATTACT
12221 NNNNNNNNNN
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
171 25 0.20
172 96 0.76
173 5 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.39
Consensus pattern (162 bp):
TAATTGATTTTAAGTTGAACTTGTTTTACATTTATCAGTAAAACAGACTATAATCGAATGCTTAC
CTTAGGAAACATGAAGAAAAAGTCATTCATTAACAAGAAAAATCCATTTATAGTCTCTAATTCCT
TCAAAAGCCTTATTACTAGCTTTAAATAGTTT
Done.