Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_pilon, 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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 18
Found at i:1506372 original size:21 final size:21
Alignment explanation
Indices: 1506323--1506366 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1506313 TATATAGTTG
* *
1506323 TTAGGTATGTTTTGGAGCAGT
1 TTAGGGATATTTTGGAGCAGT
*
1506344 TTAGGGATATTTTGGAGCCGT
1 TTAGGGATATTTTGGAGCAGT
1506365 TT
1 TT
1506367 GAGGATGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.43
Consensus pattern (21 bp):
TTAGGGATATTTTGGAGCAGT
Found at i:1507444 original size:22 final size:22
Alignment explanation
Indices: 1507322--1507435 Score: 176
Period size: 22 Copynumber: 5.2 Consensus size: 22
1507312 GAAATGTTTA
*
1507322 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTAATTTATTTT
*
1507344 AAAATATGGATTTATTTATTTT
1 AAAATATGGATTAATTTATTTT
*
1507366 AAAATATGGA-AAATTTTATTTT
1 AAAATATGGATTAA-TTTATTTT
*
1507388 AAAATATGGATTGATTTATTTT
1 AAAATATGGATTAATTTATTTT
1507410 AAAATATGGATTAATTTATTTT
1 AAAATATGGATTAATTTATTTT
1507432 AAAA
1 AAAA
1507436 AATTTATTAT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
21 1 0.01
22 82 0.98
23 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
AAAATATGGATTAATTTATTTT
Found at i:1511558 original size:66 final size:66
Alignment explanation
Indices: 1511440--1511569 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 66
1511430 TAGGTCCGTA
* ***
1511440 AGGAATTACCAGTCGGTGTTGAACCTATAAAAGGAATTACTAACAGCAACTGAACCTGCCAGAGA
1 AGGAATTACCAATCGGTGCAAAACCTATAAAAGGAATTACTAACAGCAACTGAACCTGCCAGAGA
1511505 T
66 T
* * *
1511506 AGGAATTACCAATCGGTGCAAAACCTATAAAAGGAATTACCT-GCAGCGACTGAACCTTCCAGAG
1 AGGAATTACCAATCGGTGCAAAACCTATAAAAGGAATTA-CTAACAGCAACTGAACCTGCCAGAG
1511570 TCTTCATACC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 54 0.96
67 2 0.04
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (66 bp):
AGGAATTACCAATCGGTGCAAAACCTATAAAAGGAATTACTAACAGCAACTGAACCTGCCAGAGA
T
Found at i:1513549 original size:23 final size:23
Alignment explanation
Indices: 1513497--1513561 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1513487 AAAGTTAACG
* * *
1513497 GTCAACGGGTTGACTCGGTCTAT
1 GTCAACGGGTTGACTCAGTCAAA
*
1513520 GTTAACGGGTTGACTCAGTCAAA
1 GTCAACGGGTTGACTCAGTCAAA
* *
1513543 GTCAACGAGTTGACCCAGT
1 GTCAACGGGTTGACTCAGT
1513562 GAGTTGACTC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (23 bp):
GTCAACGGGTTGACTCAGTCAAA
Found at i:1524457 original size:32 final size:31
Alignment explanation
Indices: 1524417--1524516 Score: 112
Period size: 31 Copynumber: 3.2 Consensus size: 31
1524407 GTCGAGGGTT
* *
1524417 TACCTATGTTCTACGGAACATGTGGACAGAA
1 TACCTATGTTCTACGGAACATATGGACAGTA
* * *
1524448 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 -TACCTATGTTC-TACGGAACATATGGACAGTA
* *
1524480 TACCTATGTTCTAAGGAATATATGGACAGTA
1 TACCTATGTTCTACGGAACATATGGACAGTA
1524511 TACCTA
1 TACCTA
1524517 GGTTTTTGGG
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
31 31 0.55
32 25 0.45
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTA
Found at i:1529302 original size:32 final size:32
Alignment explanation
Indices: 1529261--1529350 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
1529251 AGTCGAGGGT
*
1529261 TTACCTATGTTCTACGGAACATGTGGAAAGAA
1 TTACCTATGTTCTACGGAACATATGGAAAGAA
* * * *
1529293 TTACCTATG-TCTTTCGGGACATATGGATAGTA
1 TTACCTATGTTC-TACGGAACATATGGAAAGAA
* *
1529325 -TACCTATGTTCTAAGGAATATATGGA
1 TTACCTATGTTCTACGGAACATATGGA
1529351 GAGTATACCT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
31 21 0.45
32 26 0.55
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGAAAGAA
Found at i:1543206 original size:22 final size:22
Alignment explanation
Indices: 1543163--1543207 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1543153 TGTCATAGCA
1543163 TTTTTATTTTACTTATTCATTT
1 TTTTTATTTTACTTATTCATTT
*
1543185 TTTTTAGTTTTACTTGTT-ATTT
1 TTTTTA-TTTTACTTATTCATTT
1543207 T
1 T
1543208 CATTATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.16, C:0.07, G:0.04, T:0.73
Consensus pattern (22 bp):
TTTTTATTTTACTTATTCATTT
Found at i:1553612 original size:194 final size:193
Alignment explanation
Indices: 1553256--1553613 Score: 448
Period size: 194 Copynumber: 1.8 Consensus size: 193
1553246 GTGTTTTGCT
* *
1553256 ACAATATCTCTTTCGTCACATATAAGGTGATTTAATGCATTATTTGTGACAATATAAATTATCAA
1 ACAATATCACTTTCGTCACATATAAGGTGATTTAATGCATTATTTGTGACAATATAAATCATCAA
**
1553321 TAACGAAATCTTATTTAATTTACTGAAATAACCAACTGTCATAGAATATAAATTATAAAGTGACG
66 TAACGAAATCTTACATAATTTACTGAAATAACCAACTGTCATAGAATATAAATTATAAAGTGACG
* * *
1553386 TTATGCATAAACGTCATTCATAATATTATTAGGTAACATTTATATTATGTCACTAAAAATGTG
131 TTATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTG
* * *
1553449 ACAATATCACTTTCGTCACATAT-AGGTTGATTTTAATGTATTATTTGTGACGATTTAAATCATC
1 ACAATATCACTTTCGTCACATATAAGG-TGA-TTTAATGCATTATTTGTGACAATATAAATCATC
* * * * ** ** * * * *
1553513 AATAACGAATTTTTACATAATTTAGTGACATAATTAGTTGTCTTTGAATATTAATTATATAGTGA
64 AATAACGAAATCTTACATAATTTACTGAAATAACCAACTGTCATAGAATATAAATTATAAAGTGA
* * * **
1553578 TGTTATATATAAATGTCATCCATGCTACTATTAGGT
129 CGTTATACATAAACGTCATCCATAATACTATTAGGT
1553614 GACGATATAC
Statistics
Matches: 136, Mismatches: 27, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
192 3 0.02
193 25 0.18
194 108 0.79
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (193 bp):
ACAATATCACTTTCGTCACATATAAGGTGATTTAATGCATTATTTGTGACAATATAAATCATCAA
TAACGAAATCTTACATAATTTACTGAAATAACCAACTGTCATAGAATATAAATTATAAAGTGACG
TTATACATAAACGTCATCCATAATACTATTAGGTAACATTTATATTATGTCACTAAAAATGTG
Found at i:1558240 original size:21 final size:21
Alignment explanation
Indices: 1558214--1558257 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1558204 TGTCATATCA
1558214 TTTTTA-TTTTACTTATTCATT
1 TTTTTAGTTTTACTTATT-ATT
*
1558235 TTTTTAGTTTTACTTGTTATT
1 TTTTTAGTTTTACTTATTATT
1558256 TT
1 TT
1558258 CATTATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTTAGTTTTACTTATTATT
Found at i:1563862 original size:20 final size:20
Alignment explanation
Indices: 1563837--1563875 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1563827 AAAGCTCATA
1563837 TAGGATCATATAGATGCATT
1 TAGGATCATATAGATGCATT
* *
1563857 TAGGATCATGTAGTTGCAT
1 TAGGATCATATAGATGCAT
1563876 CTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (20 bp):
TAGGATCATATAGATGCATT
Found at i:1568834 original size:14 final size:14
Alignment explanation
Indices: 1568815--1568849 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1568805 TGAGGGTGGC
1568815 TGATCAAAGCGTCA
1 TGATCAAAGCGTCA
1568829 TGATCAAAGCGTCA
1 TGATCAAAGCGTCA
1568843 TGATCAA
1 TGATCAA
1568850 CGTCTTCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (14 bp):
TGATCAAAGCGTCA
Found at i:1571672 original size:196 final size:202
Alignment explanation
Indices: 1571338--1571735 Score: 754
Period size: 196 Copynumber: 2.0 Consensus size: 202
1571328 ACCTTTATGG
1571338 TAAATGGTCGAAGACTGAAGGTGCACAATAGAGCACCCATCTTGTGTGATAAATCAATGTCATTA
1 TAAATGGTCGAAGACTGAAGGTGCACAATAGAGCACCCATCTTGTGTGATAAATCAATGTCATTA
1571403 CTTCATGATGCCCAAGAGTTTGCCCTTCTATTTCGAACAAATTTGGTTGCCTAGGCAACAAAAAC
66 CTTCATGATGCCCAAGAGTTTGCCCTTCTATTTCGAACAAATTTGGTTGCCTAGGCAACAAAAAC
1571468 TTACACA-T-TATATAAAT-ATATATTTTTATTTTA-TTTGTATG-ATTATTTA-TTCTATTTCT
131 TTACACATTATATATAAATAATATATTTTTATTTTATTTTGTATGAATTATTTATTTCTATTTCT
1571527 ATTTTTT
196 ATTTTTT
1571534 TAAATGGTCGAAGACTGAAGGTGCACAATAGAGCACCCATCTTGTGTGATAAATCAATGTCATTA
1 TAAATGGTCGAAGACTGAAGGTGCACAATAGAGCACCCATCTTGTGTGATAAATCAATGTCATTA
1571599 CTTCATGATGCCCAAGAGTTTGCCCTTCTATTTCGAACAAATTTGGTTGCCTAGGCAACAAAAAC
66 CTTCATGATGCCCAAGAGTTTGCCCTTCTATTTCGAACAAATTTGGTTGCCTAGGCAACAAAAAC
1571664 TTACACATTATATATAAATAATATATTTTTATTTTATTTTGTATGAATTATTTATTTCTATTTCT
131 TTACACATTATATATAAATAATATATTTTTATTTTATTTTGTATGAATTATTTATTTCTATTTCT
1571729 ATTTTTT
196 ATTTTTT
1571736 ATTTTTGTTT
Statistics
Matches: 196, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
196 137 0.70
197 1 0.01
198 9 0.05
199 16 0.08
200 8 0.04
201 8 0.04
202 17 0.09
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (202 bp):
TAAATGGTCGAAGACTGAAGGTGCACAATAGAGCACCCATCTTGTGTGATAAATCAATGTCATTA
CTTCATGATGCCCAAGAGTTTGCCCTTCTATTTCGAACAAATTTGGTTGCCTAGGCAACAAAAAC
TTACACATTATATATAAATAATATATTTTTATTTTATTTTGTATGAATTATTTATTTCTATTTCT
ATTTTTT
Found at i:1581406 original size:2 final size:2
Alignment explanation
Indices: 1581399--1581454 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1581389 TATTGTCATG
1581399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1581441 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1581455 CATAATTCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1583066 original size:2 final size:2
Alignment explanation
Indices: 1583059--1583111 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1583049 TCATATTGTC
1583059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1583101 AT AT AT AT AT A
1 AT AT AT AT AT A
1583112 ATTCTTATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1584224 original size:238 final size:239
Alignment explanation
Indices: 1583807--1584729 Score: 1068
Period size: 238 Copynumber: 3.9 Consensus size: 239
1583797 AAGTAAGTCT
* * * * ** *
1583807 GATTTCCAAAGTTTCTTACTTAGTAAGCCCTTCGAGCCATCAGTAAGTCTTTTGAGCACGATGAT
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCAATCAATAAGTCTTTCAAGCATGATGAT
* * * * * **
1583872 AAAATCCTTCAAGTCATCTATAAGCCTTTTGAGCAAGATAACAACTCCTTCGGGTGATCCATAAG
66 TAAATCCTTCAAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
* * * * * *
1583937 GCCTTCGAGCAGGATGTTTTCACATGA-TTTCTGAAAACTGAGAAAATGATTTCCAAAGTTTATG
131 ACCTTCGGGCAGGATGTTTTCACATTATTTTC-GAAAAATGAGAAAATGATTTCCAAAGTTTCTC
*
1584001 ATTTAAA-CTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAAT
195 ATTTAAATCTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAAC
* * * *
1584045 GATTTCCAAATTTTCTTACTTAGTAAGACCTTCGGGCAATCAGTAAGTCTTTCAAACATGATGAT
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCAATCAATAAGTCTTTCAAGCATGATGAT
*
1584110 TAAATCCTTCAAGTCATCTATAAGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCATAAG
66 TAAATCCTTCAAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
* * * * *
1584175 ACCTTTGGGCATGTTGTTTTCTCATTATTTTCGAAAAATGAGAAAATGATTTCTAAAGTTTCTCA
131 ACCTTCGGGCAGGATGTTTTCACATTATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCA
* * * **
1584240 TTTAAAACCTATTT-TGAAAATAATTTTTTTGAAAAGTAAGAAAAC
196 TTTAAATCTTTTTTCTGAAAAT--TGATTTTGAAAAGTAAGAAAAC
*
1584285 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTC-GGTACATCAATAAGTCTTTCAAGCATGATGA
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCA-ATCAATAAGTCTTTCAAGCATGATGA
** * ** * * ** **
1584349 TTAAATCCTTCGGGTCATCTATAAGTCTTTTAAGCAACATGATAAGT-ATTTTGGCCATATATAA
65 TTAAATCCTTCAAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
* * * * *
1584413 GACCTTCGGG-TGAGATGTTTTCACATTATTTTTGAAAAATGAGAAACTTATTTCCAAAGTTTCC
130 GACCTTCGGGCAG-GATGTTTTCACATTATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCT
* *
1584477 CATTTAAATCTTTTTTCTGGAAATTGATTTTGAAAAGTCAGAAAAC
194 CATTTAAATCTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAAC
* * * * * * *
1584523 AATTTCCAAAGTTTCTTACTTACTAAGTCATTTGGGCCATTAATATA-TCTTTTAAGCATGATGA
1 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCAATCAATA-AGTCTTTCAAGCATGATGA
* * * * *
1584587 TTAAATTCTTCAGGTCATCTATAAACCTTTCGAGCAAGAGGATAAGTCCTTCGGGCCATCTATAA
65 TTAAATCCTTCAAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAA
* * * * * * * *
1584652 GACATTCGGGTAGGATGTTTTTATATGATTTTTGAAAAATGAAAAAATGATTTCCAAAGCTTCTC
130 GACCTTCGGGCAGGATGTTTTCACATTATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTC
1584717 ATTTAAATCTTTT
195 ATTTAAATCTTTT
1584730 CTAGCATGAT
Statistics
Matches: 578, Mismatches: 96, Indels: 21
0.83 0.14 0.03
Matches are distributed among these distances:
238 285 0.49
239 172 0.30
240 121 0.21
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (239 bp):
GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCGGGCAATCAATAAGTCTTTCAAGCATGATGAT
TAAATCCTTCAAGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAG
ACCTTCGGGCAGGATGTTTTCACATTATTTTCGAAAAATGAGAAAATGATTTCCAAAGTTTCTCA
TTTAAATCTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAAC
Found at i:1584391 original size:42 final size:42
Alignment explanation
Indices: 1584312--1584391 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
1584302 ACTTAGTAAG
**
1584312 TCCTTCGGTACATCAATAAGTCTTTCAAGCATGATGATTAAA
1 TCCTTCGGTACATCAATAAGTCTTTCAAGCAACATGATTAAA
* *
1584354 TCCTTCGGGT-CATCTATAAGTCTTTTAAGCAACATGAT
1 TCCTTC-GGTACATCAATAAGTCTTTCAAGCAACATGAT
1584392 AAGTATTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 30 0.91
43 3 0.09
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (42 bp):
TCCTTCGGTACATCAATAAGTCTTTCAAGCAACATGATTAAA
Found at i:1584703 original size:478 final size:478
Alignment explanation
Indices: 1583807--1584723 Score: 1180
Period size: 478 Copynumber: 1.9 Consensus size: 478
1583797 AAGTAAGTCT
* * **
1583807 GATTTCCAAAGTTTCTTACTTAGTAAGCCCTTCGAGCCATCAGTAAGTCTTTTGAGCACGATGAT
1 GATTTCCAAAGTTTCTTACTTAGTAAGCCCTTCGAGACATCAATAAGTCTTTCAAGCACGATGAT
* * * ** *
1583872 AAAATCCTTCAAGTCATCTATAAGCCTTTTGAGCAAGATAACAACTCCTTCGGGTGATCCATAAG
66 AAAATCCTTCAAGTCATCTATAAGCCTTTTAAGCAACATAACAACTCATTCGGGCCATACATAAG
* * **
1583937 GCCTTCGAGCAGGATGTTTTCACATGATTTCTGAAAACTGAGAAAATGATTTCCAAAGTTTATGA
131 ACCTTCGAGCAGGATGTTTTCACATGATTTCTGAAAAATGAGAAAATGATTTCCAAAGTTTACCA
** *
1584002 TTTAAACTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAATGATTTCCAAATTTTCTTACTTA
196 TTTAAACTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTTA
* * *
1584067 GTAAGACCTTCGGGCAATCAGTAAGTCTTTCAAACATGATGATTAAATCCTTCAAGTCATCTATA
261 CTAAGACATTCGGGCAATCAATAAGTCTTTCAAACATGATGATTAAATCCTTCAAGTCATCTATA
* * * * * *
1584132 AGCCTTTCGAGAAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTTGGGCATGTTGTTTTCT
326 AACCTTTCGAGAAAGAGGATAAGTCCTTCGGGCCATCCATAAGACATTCGGGCAGGATGTTTTCT
* * *
1584197 CATTATTTTCGAAAAATGAGAAAATGATTTCTAAAGTTTCTCATTTAAAACCTATTTTGAAAATA
391 CATTATTTTCGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAAACCTATTTTGAAAATA
1584262 ATTTTTTTGAAAAGTAAGAAAAC
456 ATTTTTTTGAAAAGTAAGAAAAC
* *
1584285 GATTTCCAAAGTTTCTTACTTAGTAAGTCCTTCG-GTACATCAATAAGTCTTTCAAGCATGATGA
1 GATTTCCAAAGTTTCTTACTTAGTAAGCCCTTCGAG-ACATCAATAAGTCTTTCAAGCACGATGA
* ** * * * * ** *
1584349 TTAAATCCTTCGGGTCATCTATAAGTCTTTTAAGCAACATGATAAGT-ATTTTGGCCATATATAA
65 TAAAATCCTTCAAGTCATCTATAAGCCTTTTAAGCAACATAACAACTCATTCGGGCCATACATAA
** * * * * *
1584413 GACCTTCG-GGTGAGATGTTTTCACATTATTTTTGAAAAATGAGAAACTTATTTCCAAAGTTTCC
130 GACCTTCGAGCAG-GATGTTTTCACATGATTTCTGAAAAATGAGAAAATGATTTCCAAAGTTTAC
* *
1584477 CATTTAAATCTTTTTTCTGGAAATTGATTTTGAAAAGTCAGAAAACAATTTCCAAAGTTTCTTAC
194 CATTTAAA-CTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTAC
* * * * * * * *
1584542 TTACTAAGTCATTTGGGCCATTAATATA-TCTTTTAAGCATGATGATTAAATTCTTCAGGTCATC
258 TTACTAAGACATTCGGGCAATCAATA-AGTCTTTCAAACATGATGATTAAATCCTTCAAGTCATC
* * *
1584606 TATAAACCTTTCGAGCAAGAGGATAAGTCCTTCGGGCCATCTATAAGACATTCGGGTAGGATGTT
322 TATAAACCTTTCGAGAAAGAGGATAAGTCCTTCGGGCCATCCATAAGACATTCGGGCAGGATGTT
*
1584671 TT-T-ATATGATTTTTGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAA
387 TTCTCAT-T-ATTTTCGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAA
1584724 TCTTTTCTAG
Statistics
Matches: 371, Mismatches: 62, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
476 4 0.01
477 71 0.19
478 295 0.80
479 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (478 bp):
GATTTCCAAAGTTTCTTACTTAGTAAGCCCTTCGAGACATCAATAAGTCTTTCAAGCACGATGAT
AAAATCCTTCAAGTCATCTATAAGCCTTTTAAGCAACATAACAACTCATTCGGGCCATACATAAG
ACCTTCGAGCAGGATGTTTTCACATGATTTCTGAAAAATGAGAAAATGATTTCCAAAGTTTACCA
TTTAAACTTTTTTCTGAAAATTGATTTTGAAAAGTAAGAAAACAATTTCCAAAGTTTCTTACTTA
CTAAGACATTCGGGCAATCAATAAGTCTTTCAAACATGATGATTAAATCCTTCAAGTCATCTATA
AACCTTTCGAGAAAGAGGATAAGTCCTTCGGGCCATCCATAAGACATTCGGGCAGGATGTTTTCT
CATTATTTTCGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAAACCTATTTTGAAAATA
ATTTTTTTGAAAAGTAAGAAAAC
Found at i:1584859 original size:155 final size:156
Alignment explanation
Indices: 1584569--1584887 Score: 435
Period size: 155 Copynumber: 2.1 Consensus size: 156
1584559 CCATTAATAT
* *
1584569 ATCTTTT-AAGCATGATGATTAAATTCTTCAGGTCATCTATAAACCTTTCGAGCAAGAGGATAAG
1 ATCTTTTCTAGCATGATGATTAAATCCTTCAGGTCATCTATAAACCTTTCGAGCAAGAGGATAAG
* * * * * **
1584633 TCCTTCGGGCCATCTATAAGACATTCGGGTAGGATGTTTTTATATGATTTTTGAAAAATGAAAAA
66 TCATTCGGGCCATCTATAAGACATTCGCGAAGGATGTTTTCACATGATTTTCAAAAAATGAAAAA
*
1584698 ATGA-TTTCCAAAGCTTCTCATTTAA
131 ATGATTTTCAAAAGCTTCTCATTTAA
* * * *
1584723 ATCTTTTCTAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAG
1 ATCTTTTCTAGCATGATGATTAAATCCTTCAGGTCATCTATAAACCTTTCGAGCAAGAGGATAAG
* * *
1584788 TCATTCGGGCCATCTATAAGACCTTCGCGAAGGATGTTTTCCCATGATTTTCAAAAAATGAGAAA
66 TCATTCGGGCCATCTATAAGACATTCGCGAAGGATGTTTTCACATGATTTTCAAAAAATGAAAAA
** *
1584853 ATGATTTTCAAAATTTTCTTATTTAA
131 ATGATTTTCAAAAGCTTCTCATTTAA
*
1584879 ATCTCTTCT
1 ATCTTTTCT
1584888 GAAAATTGAT
Statistics
Matches: 142, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
154 7 0.05
155 110 0.77
156 25 0.18
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (156 bp):
ATCTTTTCTAGCATGATGATTAAATCCTTCAGGTCATCTATAAACCTTTCGAGCAAGAGGATAAG
TCATTCGGGCCATCTATAAGACATTCGCGAAGGATGTTTTCACATGATTTTCAAAAAATGAAAAA
ATGATTTTCAAAAGCTTCTCATTTAA
Found at i:1585064 original size:393 final size:392
Alignment explanation
Indices: 1584334--1585073 Score: 1002
Period size: 393 Copynumber: 1.9 Consensus size: 392
1584324 TCAATAAGTC
* *
1584334 TTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAAGTCTTTTAAGCAACATGATAAGTATT
1 TTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAAGCCTTTCAAGCAACATGATAAGTATT
** ** * ** * *
1584399 TTGGCCATATATAAGACCTTCGGGTGAGATGTTTTCACATTATTTTTGAAAAATGAGAAACTTAT
66 CGGGCCATATATAAGACCTTCGGAAGAGATGTTTTCACATGATTTTCAAAAAATGAGAAAATGAT
* * * *
1584464 TTCCAAAGTTTCCCATTTAAATCTTTTTTCTGGAAATTGATTTTGAAAAGTCAGAAAACAATTTC
131 TTCAAAAGTTTCCCATTTAAATC-TTCTTCTGAAAATTGATTTTGAAAAGTAAGAAAACAATTTC
* * * * *
1584529 CAAAGTTTCTTACTTACTAAGTCATTTGGGCCATTAATATATCTTTTAAGCATGATGATTAAATT
195 CAAAGTTTCTTACTTACTAAGTCATTTGAGACATCAATATATCTTTCAAGCATGATGATTAAATC
* * *
1584594 CTTCAGGTCATCTATAAACCTTTCGAGCAAGAGGATAAGTCCTTCGGGCCATCTATAAGACATTC
260 CTTCAGGTCATCTATAAACATTTCGAGCAAGAGGATAAGTCATTCAGGCCATCTATAAGACATTC
* *
1584659 GGGTAGGATGTTTTTATATGATTTTTGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAA
325 GGGCAGGATGTTTTGATATGATTTTTGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAA
1584724 TCT
390 TCT
* * * *
1584727 TTTCTAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCAT
1 TTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAAGCCTTTCAAGCAACATGATAAGT-AT
* *
1584792 TCGGGCCATCTATAAGACCTTCGCGAAG-GATGTTTTCCCATGATTTTCAAAAAATGAGAAAATG
65 TCGGGCCATATATAAGACCTTCG-GAAGAGATGTTTTCACATGATTTTCAAAAAATGAGAAAATG
* ** *
1584856 ATTTTCAAAATTTTCTTATTTAAATC-TCTTCTGAAAATTGATTTTGAAAAGTAAGAAAACGATT
129 A-TTTCAAAAGTTTCCCATTTAAATCTTCTTCTGAAAATTGATTTTGAAAAGTAAGAAAACAATT
* * *
1584920 TCCAAAGTTTCTTACTTAGTAAGTCCTTTGAGACATCAATA-AGTCTTTCAAGCATGATGCTTAA
193 TCCAAAGTTTCTTACTTACTAAGTCATTTGAGACATCAATATA-TCTTTCAAGCATGATGATTAA
** * * *
1584984 ATCCTTC-GAGTCATCTATAAGTATTTTGAGCAAGATGATAAGTCATTCAGGCCATCTGTAAGAC
257 ATCCTTCAG-GTCATCTATAAACATTTCGAGCAAGAGGATAAGTCATTCAGGCCATCTATAAGAC
*
1585048 CTTCGGGCAGGATGTTTTGATATGAT
321 ATTCGGGCAGGATGTTTTGATATGAT
1585074 ATTAAAAAAA
Statistics
Matches: 298, Mismatches: 44, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
392 2 0.01
393 221 0.74
394 53 0.18
395 22 0.07
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (392 bp):
TTTCAAGCATGATGATTAAATCCTTCGGGTCATCTATAAGCCTTTCAAGCAACATGATAAGTATT
CGGGCCATATATAAGACCTTCGGAAGAGATGTTTTCACATGATTTTCAAAAAATGAGAAAATGAT
TTCAAAAGTTTCCCATTTAAATCTTCTTCTGAAAATTGATTTTGAAAAGTAAGAAAACAATTTCC
AAAGTTTCTTACTTACTAAGTCATTTGAGACATCAATATATCTTTCAAGCATGATGATTAAATCC
TTCAGGTCATCTATAAACATTTCGAGCAAGAGGATAAGTCATTCAGGCCATCTATAAGACATTCG
GGCAGGATGTTTTGATATGATTTTTGAAAAATGAAAAAATGATTTCCAAAGCTTCTCATTTAAAT
CT
Found at i:1585573 original size:132 final size:132
Alignment explanation
Indices: 1585336--1585857 Score: 623
Period size: 132 Copynumber: 4.0 Consensus size: 132
1585326 TAATGTTTAA
* * * * * *
1585336 TTTCCAGATTTAATCTTCCCTGAAGAGCAATGGAACAAATATGCCTTGATTCAATCTTCCCTGGA
1 TTTCCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTTCCTTGATTCAATCTTCCCTGAA
* * * * * *
1585401 GAATAGTGGACTTAATC-ATCGTTTCGAGATTTGATCTACCCTAAAGAGCAGCGGAGCATATCCC
66 GAACAGTGGAATGAATCAAT-GTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATATCCC
1585465 CTT
130 CTT
* * *
1585468 TTTCCAGATTTGATCTTCCCTCAGGAGCAGTAGAACAAATCTTCCTCGATTCAATCTTCCCTGAA
1 TTTCCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTTCCTTGATTCAATCTTCCCTGAA
** * * *
1585533 GAACAGTATAATGAATCAATGTTTCCATATCTGGTCTACCCTGAAGAGCAGCGGATCATATCCCC
66 GAACAGTGGAATGAATCAATGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATATCCCC
1585598 TT
131 TT
* * * * *
1585600 TTTCCAAATTTGATCTTCCATAAGGAGCAGTGGAATAAATCTTCCTTGATTTAATCTTCCCTGAA
1 TTTCCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTTCCTTGATTCAATCTTCCCTGAA
* * * * **
1585665 TAATAGTGGAATGAATCAATGTTTCCAGATCTGATCTACCTTGAAGAGGAATGGAGCATATCCCC
66 GAACAGTGGAATGAATCAATGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATATCCCC
1585730 TT
131 TT
* ** * * * *
1585732 TTTCCAGATTTGATCTTCCCTGAGAAGCAGTGGAACAAATCTTCCAAGATTCAATATACTCTTAA
1 TTTCCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTTCCTTGATTCAATCTTCCCTGAA
* * * * * * *
1585797 GAACAGTGGAGTTAATCAACGTTTCCAAATCTAATCTACCCTGAAGAGAAGAGGAGCATAT
66 GAACAGTGGAATGAATCAATGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATAT
1585858 TTCTTTTCAA
Statistics
Matches: 328, Mismatches: 61, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
132 326 0.99
133 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.30
Consensus pattern (132 bp):
TTTCCAGATTTGATCTTCCCTGAGGAGCAGTGGAACAAATCTTCCTTGATTCAATCTTCCCTGAA
GAACAGTGGAATGAATCAATGTTTCCAGATCTGATCTACCCTGAAGAGCAGCGGAGCATATCCCC
TT
Found at i:1586081 original size:16 final size:16
Alignment explanation
Indices: 1586060--1586125 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
1586050 TCTTGTTAAC
1586060 ATTATT-TTAATTATT
1 ATTATTATTAATTATT
1586075 AATTATTATT-ATTATTT
1 -ATTATTATTAATTA-TT
* *
1586092 AGTTATCATT-ATTTTT
1 A-TTATTATTAATTATT
1586108 ATTATTATTAATT-TT
1 ATTATTATTAATTATT
1586123 ATT
1 ATT
1586126 TTACAAACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
15 12 0.28
16 17 0.40
17 14 0.33
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
ATTATTATTAATTATT
Found at i:1586082 original size:3 final size:3
Alignment explanation
Indices: 1586060--1586117 Score: 55
Period size: 3 Copynumber: 18.3 Consensus size: 3
1586050 TCTTGTTAAC
* *
1586060 ATT ATT -TT AATT ATT AATT ATT ATT ATT ATTT AGTT ATC ATT ATT TTT
1 ATT ATT ATT -ATT ATT -ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT
1586108 ATT ATT ATT A
1 ATT ATT ATT A
1586118 ATTTTATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 2 0.04
3 33 0.72
4 11 0.24
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:1586241 original size:22 final size:22
Alignment explanation
Indices: 1586216--1586284 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
1586206 TAATTACAAA
1586216 AACCTTAACCTAAATTTAACCT
1 AACCTTAACCTAAATTTAACCT
* * *
1586238 AACCCTCATCCT--TTTTAACCT
1 AA-CCTTAACCTAAATTTAACCT
*
1586259 AAACCCTAA-CTAAATTTAACCT
1 -AACCTTAACCTAAATTTAACCT
1586281 AACC
1 AACC
1586285 CTCATCCTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 12 0.33
23 7 0.19
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (22 bp):
AACCTTAACCTAAATTTAACCT
Found at i:1586254 original size:21 final size:21
Alignment explanation
Indices: 1586230--1586295 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
1586220 TTAACCTAAA
1586230 TTTAACCTAACCCTCATCCTT
1 TTTAACCTAACCCTCATCCTT
* *
1586251 TTTAACCTAAACCCT-A-ACTAAA
1 TTTAACCT-AACCCTCATCCT--T
1586273 TTTAACCTAACCCTCATCCTT
1 TTTAACCTAACCCTCATCCTT
1586294 TT
1 TT
1586296 ACAATAAGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
20 2 0.06
21 17 0.47
22 15 0.42
23 2 0.06
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTAACCTAACCCTCATCCTT
Found at i:1604613 original size:19 final size:19
Alignment explanation
Indices: 1604547--1604616 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
1604537 TTTCTTTGAA
1604547 TTTTT-TTTCTTTTCT--T
1 TTTTTATTTCTTTTCTGAT
1604563 TTTTTAATTTCTTCTTCTAGTAT
1 TTTTT-ATTTCTT-TTCT-G-AT
***
1604586 TTGCAATTTCTTTTCTGAT
1 TTTTTATTTCTTTTCTGAT
1604605 TTTTTATTTCTT
1 TTTTTATTTCTT
1604617 CACTTGCACT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
16 5 0.12
18 6 0.15
19 15 0.37
20 1 0.02
21 4 0.10
22 7 0.17
23 3 0.07
ACGTcount: A:0.11, C:0.13, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTTTATTTCTTTTCTGAT
Found at i:1604630 original size:11 final size:11
Alignment explanation
Indices: 1604614--1604638 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1604604 TTTTTTATTT
1604614 CTTCACTTGCA
1 CTTCACTTGCA
1604625 CTTCACTTGCA
1 CTTCACTTGCA
1604636 CTT
1 CTT
1604639 TGTTGTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
CTTCACTTGCA
Found at i:1617043 original size:28 final size:28
Alignment explanation
Indices: 1617003--1617056 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1616993 CGTTAATGCA
*
1617003 TATGGATCAAGATAAGCCCAGGACTTCT
1 TATGGATCAAGATAAGCCCAAGACTTCT
1617031 TATGGATCAAGATAAGCCCAAGACTT
1 TATGGATCAAGATAAGCCCAAGACTT
1617057 ATCAAGAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (28 bp):
TATGGATCAAGATAAGCCCAAGACTTCT
Found at i:1622793 original size:165 final size:165
Alignment explanation
Indices: 1622535--1622831 Score: 378
Period size: 165 Copynumber: 1.8 Consensus size: 165
1622525 AAGTACAAGC
* * * **
1622535 GATCGACCCTCTCAAGCTAATAAGGGCAAGGCCCCGATAAATGACTCCTCTACTGTAGCTGAAAA
1 GATCGACCCTCTCAAGCTAATAAGGGCAAGGCCCCGATAAATGAATCCCCTACTATAGCCCAAAA
* * * * * * * *
1622600 AGATAACCTCTTCACTATTGAGAGTGACAATGGTGAATTTACTGATGATGATGTTGAGCCTACTC
66 AGATAACCCCATAACTATTAAAAGTGACAATGATGAATTTACTAATGATGATGATGAGCCTACTC
1622665 CTACCGAACCAACCCACACAAGGGAAAATGCTGGA
131 CTACCGAACCAACCCACACAAGGGAAAATGCTGGA
* * ** ** * *
1622700 GATCTACCCTCTCAAGCTGATAAGGGCAAGGCGTCGATGGATGAATCCCCTATTATAGCCCAAGA
1 GATCGACCCTCTCAAGCTAATAAGGGCAAGGCCCCGATAAATGAATCCCCTACTATAGCCCAAAA
* * *
1622765 AGATGACCCCATAACTATTAAAAGTGACACTGATGAATTTATTAATGATGATGATGAGCCTACTC
66 AGATAACCCCATAACTATTAAAAGTGACAATGATGAATTTACTAATGATGATGATGAGCCTACTC
1622830 CT
131 CT
1622832 GCACCAGCCC
Statistics
Matches: 108, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
165 108 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (165 bp):
GATCGACCCTCTCAAGCTAATAAGGGCAAGGCCCCGATAAATGAATCCCCTACTATAGCCCAAAA
AGATAACCCCATAACTATTAAAAGTGACAATGATGAATTTACTAATGATGATGATGAGCCTACTC
CTACCGAACCAACCCACACAAGGGAAAATGCTGGA
Found at i:1626196 original size:24 final size:23
Alignment explanation
Indices: 1626144--1626197 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1626134 TCAAAAATAA
*
1626144 ATAAATAGAATTCAACTTAATTTG
1 ATAAATAGAACTCAAC-TAATTTG
1626168 A-AAATAGAAACTCAA-TAATTTG
1 ATAAATAG-AACTCAACTAATTTG
1626190 CATAAATA
1 -ATAAATA
1626198 TAATAGTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.27
23 7 0.27
24 12 0.46
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.31
Consensus pattern (23 bp):
ATAAATAGAACTCAACTAATTTG
Found at i:1626711 original size:24 final size:24
Alignment explanation
Indices: 1626679--1626748 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
1626669 TTGTATAAAT
* *
1626679 TGCACCGAAGTGTCGCGTAGAATA
1 TGCACCGAAGTGCCACGTAGAATA
1626703 TGCACCGAAGTGCCACGTAGAATA
1 TGCACCGAAGTGCCACGTAGAATA
* *
1626727 TGCACCGAACTGCCACATAGAA
1 TGCACCGAAGTGCCACGTAGAA
1626749 ATGTCCTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (24 bp):
TGCACCGAAGTGCCACGTAGAATA
Found at i:1626815 original size:23 final size:23
Alignment explanation
Indices: 1626789--1626840 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
1626779 GATAGAACGC
*
1626789 GTAGAAATGTCTCGAATGACCAT
1 GTAGAAATGTCTCGAAGGACCAT
* *
1626812 GTAGAATTGTCTCGAAGGACCGT
1 GTAGAAATGTCTCGAAGGACCAT
1626835 GTAGAA
1 GTAGAA
1626841 CCCTCGACTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (23 bp):
GTAGAAATGTCTCGAAGGACCAT
Found at i:1630653 original size:22 final size:22
Alignment explanation
Indices: 1630625--1630669 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1630615 ATTGGCAATG
1630625 AAAGTTTGGCATCCTTGTCACA
1 AAAGTTTGGCATCCTTGTCACA
1630647 AAAGTTTGGCATCCTTGTCACA
1 AAAGTTTGGCATCCTTGTCACA
1630669 A
1 A
1630670 TAACTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (22 bp):
AAAGTTTGGCATCCTTGTCACA
Found at i:1631171 original size:12 final size:12
Alignment explanation
Indices: 1631154--1631179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1631144 GACTGATTCA
1631154 TTCCTCTACCTC
1 TTCCTCTACCTC
1631166 TTCCTCTACCTC
1 TTCCTCTACCTC
1631178 TT
1 TT
1631180 TGAGATACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.46, G:0.00, T:0.46
Consensus pattern (12 bp):
TTCCTCTACCTC
Found at i:1633077 original size:24 final size:24
Alignment explanation
Indices: 1633044--1633089 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1633034 TAGTATAAAT
* *
1633044 TGCACTGAAGTGCCTCGTAGAATA
1 TGCACCGAAGTGCCACGTAGAATA
1633068 TGCACCGAAGTGCCACGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
1633090 ATGTCCTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (24 bp):
TGCACCGAAGTGCCACGTAGAATA
Found at i:1633106 original size:23 final size:23
Alignment explanation
Indices: 1633072--1633181 Score: 105
Period size: 23 Copynumber: 4.8 Consensus size: 23
1633062 AGAATATGCA
*
1633072 CCGAAGTG-CCACGTAGAAATGTC
1 CCGAAG-GACCACATAGAAATGTC
* *
1633095 CTGAAGGACCACATAGATATGTC
1 CCGAAGGACCACATAGAAATGTC
* * * *
1633118 CCGAATGAACGCGTAGAAATGTC
1 CCGAAGGACCACATAGAAATGTC
* * *
1633141 TCGAATGACCACATAGAATTGTC
1 CCGAAGGACCACATAGAAATGTC
*
1633164 CCGAAGGACCGCATAGAA
1 CCGAAGGACCACATAGAA
1633182 CCGTCGACTC
Statistics
Matches: 69, Mismatches: 17, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
22 1 0.01
23 68 0.99
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACATAGAAATGTC
Found at i:1633122 original size:46 final size:47
Alignment explanation
Indices: 1633072--1633169 Score: 123
Period size: 46 Copynumber: 2.1 Consensus size: 47
1633062 AGAATATGCA
*
1633072 CCGAAGTG-CCACGTAGAAATGTC-CTGAAGGACCACATAG-ATATGTC
1 CCGAAGTGAACACGTAGAAATGTCTC-GAAGGACCACATAGAAT-TGTC
* *
1633118 CCGAA-TGAACGCGTAGAAATGTCTCGAATGACCACATAGAATTGTC
1 CCGAAGTGAACACGTAGAAATGTCTCGAAGGACCACATAGAATTGTC
1633164 CCGAAG
1 CCGAAG
1633170 GACCGCATAG
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
45 2 0.04
46 40 0.89
47 3 0.07
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.19
Consensus pattern (47 bp):
CCGAAGTGAACACGTAGAAATGTCTCGAAGGACCACATAGAATTGTC
Found at i:1633181 original size:46 final size:46
Alignment explanation
Indices: 1633085--1633181 Score: 126
Period size: 46 Copynumber: 2.1 Consensus size: 46
1633075 AAGTGCCACG
* *
1633085 TAGAAATGTCCTGAAGGACCACATAGATATGTCCCGAATGAACGCG
1 TAGAAATGTCCTGAAGGACCACATAGATATGTCCCGAAGGAACGCA
* *
1633131 TAGAAATGT-CTCGAATGACCACATAGA-ATTGTCCCGAAGGACCGCA
1 TAGAAATGTCCT-GAAGGACCACATAGATA-TGTCCCGAAGGAACGCA
1633177 TAGAA
1 TAGAA
1633182 CCGTCGACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 3 0.07
46 42 0.93
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (46 bp):
TAGAAATGTCCTGAAGGACCACATAGATATGTCCCGAAGGAACGCA
Found at i:1633292 original size:16 final size:16
Alignment explanation
Indices: 1633258--1633311 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
1633248 TTATACCATT
*
1633258 TCACATAG-CTTAT-A
1 TCACATAGACATATAA
1633272 TCACATAGACATATAA
1 TCACATAGACATATAA
*
1633288 TCACATAGATCATGTAA
1 TCACATAGA-CATATAA
1633305 -CACATAG
1 TCACATAG
1633312 GATGAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 8 0.23
15 4 0.11
16 17 0.49
17 6 0.17
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (16 bp):
TCACATAGACATATAA
Found at i:1640033 original size:135 final size:135
Alignment explanation
Indices: 1639811--1640111 Score: 370
Period size: 135 Copynumber: 2.2 Consensus size: 135
1639801 TAATGATCTT
* * * * *
1639811 TCTACTAGAAATGTTGATCCCTCAAGTGAGGCGTTACTATTTCAGAATGTCGTGAATCGAGCAAA
1 TCTACTGGAAATGTTGATCCCTCAAGTGAGGCATCACTATTTCAAAATGTAGTGAATCGAGCAAA
* **
1639876 GGTTGAACAAGTTCTTCTCATTACAAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCAATATA
66 GGTTAAACAAGTTCTTCTCATTACAAACTTCTTCAACCTCTATCAGATGAGTTCTTCTCAATATA
*
1639941 AATTC
131 AACTC
* * *
1639946 TCTACTGGAAATGTTGGTCCCTCAAGTGCGGCATCGCTGA-TTCAAAATGTAGTGAATCGAGCAA
1 TCTACTGGAAATGTTGATCCCTCAAGTGAGGCATCACT-ATTTCAAAATGTAGTGAATCGAGCAA
** ** * *
1640010 AGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCAACCTCTATTGGATGAGTTTTTCTCATTAT
65 AGGTTAAACAAGTTCTTCTCATTACAAACTTCTTCAACCTCTATCAGATGAGTTCTTCTCAATAT
*
1640075 GAACTC
130 AAACTC
* * * * *
1640081 TCCATTGGAAATGTTAATCCATTAAGTGAGG
1 TCTACTGGAAATGTTGATCCCTCAAGTGAGG
1640112 TTTCACTGTA
Statistics
Matches: 139, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
135 138 0.99
136 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (135 bp):
TCTACTGGAAATGTTGATCCCTCAAGTGAGGCATCACTATTTCAAAATGTAGTGAATCGAGCAAA
GGTTAAACAAGTTCTTCTCATTACAAACTTCTTCAACCTCTATCAGATGAGTTCTTCTCAATATA
AACTC
Found at i:1640738 original size:55 final size:55
Alignment explanation
Indices: 1640668--1641102 Score: 549
Period size: 55 Copynumber: 7.9 Consensus size: 55
1640658 CCCACTCCCA
** *
1640668 ATACGAAAGCTCACACACTTAGTATGAATTTCTT-AGTTTTGCACAC-AGTGCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACACTAGTGCCC
* *
1640721 ATACGTAAATTCACACACTTAGTATGAATTTCTTAA-TTTTGTACACATAGTGCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACAC-TAGTGCCC
* * *
1640776 ATACGGAAATTCGCACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTTCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACAC-TAGTGCCC
* *
1640832 TTACAAAAATTCACACACTTAGTATGAATTTCTTAATTTTCTGCACACGTAGTGCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTT-TGCACAC-TAGTGCCC
* *
1640889 ATACGGAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACACATATTGCCC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACAC-TAGTGCCC
* * * * *
1640945 ATCCGAAAATTCATACACTTTGTATAAATTTCTTAA-TTTTGCACACATAGTGCAC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACAC-TAGTGCCC
* *
1641000 ATAC-ATAAATTCATACACTTAGTATGAATTTCTTAA-TTTTGCACATATAGTGCCC
1 ATACGA-AAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACA-CTAGTGCCC
* * *
1641055 ATACGGAATTTCATACACTTAGTATGAATTTCTTAACTTTTTGCACAC
1 ATACGAAAATTCACACACTTAGTATGAATTTCTTAA-TTTTTGCACAC
1641103 AAGGTGCCAT
Statistics
Matches: 338, Mismatches: 34, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
53 40 0.12
54 2 0.01
55 138 0.41
56 98 0.29
57 60 0.18
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (55 bp):
ATACGAAAATTCACACACTTAGTATGAATTTCTTAATTTTTGCACACTAGTGCCC
Found at i:1640864 original size:111 final size:112
Alignment explanation
Indices: 1640678--1641103 Score: 594
Period size: 113 Copynumber: 3.8 Consensus size: 112
1640668 ATACGAAAGC
* *
1640678 TCACACACTTAGTATGAATTTCTT-AGTTTTGCACAC--AGTGCCCATACGTAAATTCACACACT
1 TCACACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACT
*
1640740 TAGTATGAATTTCTTAA-TTTTGTACACATAGTGCCCATACGGAAAT
66 TAGTATGAATTTCTTAACTTTTGCACACATAGTGCCCATACGGAAAT
* * * *
1640786 TCGCACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTTCCCTTACAAAAATTCACACACT
1 TCACACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACT
* *
1640851 TAGTATGAATTTCTTAATTTTCTGCACACGTAGTGCCCATACGGAAAT
66 TAGTATGAATTTCTTAACTTT-TGCACACATAGTGCCCATACGGAAAT
* * *
1640899 TCACACACTTAGTATGAATTTCTTAATTTTTGCACACATATTGCCCATCCGAAAATTCATACACT
1 TCACACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACT
* * * **
1640964 TTGTATAAATTTCTTAA-TTTTGCACACATAGTGCACATACATAAAT
66 TAGTATGAATTTCTTAACTTTTGCACACATAGTGCCCATACGGAAAT
* * * * *
1641010 TCATACACTTAGTATGAATTTCTTAA-TTTTGCACATATAGTGCCCATACGGAATTTCATACACT
1 TCACACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACT
1641074 TAGTATGAATTTCTTAACTTTTTGCACACA
66 TAGTATGAATTTCTTAAC-TTTTGCACACA
1641104 AGGTGCCATT
Statistics
Matches: 282, Mismatches: 29, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
108 23 0.08
109 11 0.04
110 48 0.17
111 86 0.30
112 17 0.06
113 97 0.34
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (112 bp):
TCACACACTTAGTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACT
TAGTATGAATTTCTTAACTTTTGCACACATAGTGCCCATACGGAAAT
Found at i:1640987 original size:168 final size:166
Alignment explanation
Indices: 1640678--1641103 Score: 624
Period size: 168 Copynumber: 2.6 Consensus size: 166
1640668 ATACGAAAGC
* *
1640678 TCACACACTTAGTATGAATTTCTTAGTTTTGCACAC-AGTGCCCATACGTAAATTCACACACTTA
1 TCACACACTTAGTATGAATTTCTTAATTTTGCACACTAGTGCCCATACGGAAATTCACACACTTA
* * * *
1640742 GTATGAATTTCTTAA-TTTTGTACACATAGTGCCCATACGGAAATTCGCACACTTAGTATGAATT
66 GTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACTTAGTATAAATT
* * *
1640806 TCTTAATTTTTGCACACATAGTTCCCTTACAAAAAT
131 TCTTAATTTTTGCACACATAGTGCACATACAAAAAT
1640842 TCACACACTTAGTATGAATTTCTTAATTTTCTGCACACGTAGTGCCCATACGGAAATTCACACAC
1 TCACACACTTAGTATGAATTTCTTAA-TTT-TGCACAC-TAGTGCCCATACGGAAATTCACACAC
* * * *
1640907 TTAGTATGAATTTCTTAATTTTTGCACACATATTGCCCATCCGAAAATTCATACACTTTGTATAA
63 TTAGTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACTTAGTATAA
*
1640972 ATTTCTTAA-TTTTGCACACATAGTGCACATACATAAAT
128 ATTTCTTAATTTTTGCACACATAGTGCACATACAAAAAT
* * * *
1641010 TCATACACTTAGTATGAATTTCTTAATTTTGCACATATAGTGCCCATACGGAATTTCATACACTT
1 TCACACACTTAGTATGAATTTCTTAATTTTGCACA-CTAGTGCCCATACGGAAATTCACACACTT
1641075 AGTATGAATTTCTTAACTTTTTGCACACA
65 AGTATGAATTTCTTAA-TTTTTGCACACA
1641104 AGGTGCCATT
Statistics
Matches: 237, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
164 25 0.11
165 3 0.01
166 55 0.23
167 15 0.06
168 92 0.39
169 47 0.20
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (166 bp):
TCACACACTTAGTATGAATTTCTTAATTTTGCACACTAGTGCCCATACGGAAATTCACACACTTA
GTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGAAAATTCACACACTTAGTATAAATT
TCTTAATTTTTGCACACATAGTGCACATACAAAAAT
Found at i:1643722 original size:32 final size:31
Alignment explanation
Indices: 1643573--1643722 Score: 84
Period size: 32 Copynumber: 4.6 Consensus size: 31
1643563 TTTTTATAAC
* * * *
1643573 TTTTTTACTGTGACTAAATAATTTTGTTACAA
1 TTTTTTATTGTGA-AAAATAAATTTGTCACAA
* * *
1643605 TTTGTTATTGTGAAAGAATATTATTTGTCAAAA
1 TTTTTTATTGTGAAA-AATA-AATTTGTCACAA
* ** * *
1643638 TCTTTTATAATGAAAAATTAATATTTGTTATAA
1 TTTTTTATTGTGAAAAA-TAA-ATTTGTCACAA
* * * *
1643671 ATTGTTATTTTGATTAAATAAATTTGTCACAA
1 TTTTTTATTGTGA-AAAATAAATTTGTCACAA
*
1643703 TTTTTTATTTTGACAAAATA
1 TTTTTTATTGTGA-AAAATA
1643723 TTGGGACGAA
Statistics
Matches: 87, Mismatches: 26, Indels: 10
0.71 0.21 0.08
Matches are distributed among these distances:
31 1 0.01
32 42 0.48
33 41 0.47
34 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (31 bp):
TTTTTTATTGTGAAAAATAAATTTGTCACAA
Found at i:1646401 original size:3 final size:3
Alignment explanation
Indices: 1646395--1646420 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1646385 ATCTTCTTAA
1646395 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1646421 AAGTATAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1647189 original size:2 final size:2
Alignment explanation
Indices: 1647182--1647219 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1647172 TCCCAATTCA
1647182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1647220 CAATTTTTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1647361 original size:13 final size:13
Alignment explanation
Indices: 1647345--1647395 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
1647335 TTTTTGATAA
1647345 TATATTTTGTTAT
1 TATATTTTGTTAT
*
1647358 TATATTTTATTTGAT
1 TATATTTT-GTT-AT
1647373 AATATATTTTGTTAT
1 --TATATTTTGTTAT
1647388 TATATTTT
1 TATATTTT
1647396 ATTTGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
13 16 0.50
14 2 0.06
15 4 0.12
16 2 0.06
17 8 0.25
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (13 bp):
TATATTTTGTTAT
Found at i:1647373 original size:30 final size:30
Alignment explanation
Indices: 1647337--1647401 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
1647327 CCTTGAACTT
1647337 TTTGATAATATATTTTGTTATTATATTTTA
1 TTTGATAATATATTTTGTTATTATATTTTA
1647367 TTTGATAATATATTTTGTTATTATATTTTA
1 TTTGATAATATATTTTGTTATTATATTTTA
1647397 TTTGA
1 TTTGA
1647402 AAATGCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTGATAATATATTTTGTTATTATATTTTA
Found at i:1654791 original size:19 final size:19
Alignment explanation
Indices: 1654767--1654804 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1654757 TGCCTTAGAG
*
1654767 ATAAGGAGAGGGTTTTATT
1 ATAAGGAGAGCGTTTTATT
1654786 ATAAGGAGAGCGTTTTATT
1 ATAAGGAGAGCGTTTTATT
1654805 CGACTAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.37
Consensus pattern (19 bp):
ATAAGGAGAGCGTTTTATT
Found at i:1657408 original size:118 final size:118
Alignment explanation
Indices: 1657200--1657437 Score: 476
Period size: 118 Copynumber: 2.0 Consensus size: 118
1657190 GGGTTCCATC
1657200 GAATTCCCTGACTTCATTATGATAAGCTCTCATCTGTGTGTTGTCTACGGGAATCCTTTGCAACG
1 GAATTCCCTGACTTCATTATGATAAGCTCTCATCTGTGTGTTGTCTACGGGAATCCTTTGCAACG
1657265 TATCCAAAGATATCATGTTTAACACATACACGTTATCTTTAGAACCCCTGCAA
66 TATCCAAAGATATCATGTTTAACACATACACGTTATCTTTAGAACCCCTGCAA
1657318 GAATTCCCTGACTTCATTATGATAAGCTCTCATCTGTGTGTTGTCTACGGGAATCCTTTGCAACG
1 GAATTCCCTGACTTCATTATGATAAGCTCTCATCTGTGTGTTGTCTACGGGAATCCTTTGCAACG
1657383 TATCCAAAGATATCATGTTTAACACATACACGTTATCTTTAGAACCCCTGCAA
66 TATCCAAAGATATCATGTTTAACACATACACGTTATCTTTAGAACCCCTGCAA
1657436 GA
1 GA
1657438 CATGGTTGTC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 120 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (118 bp):
GAATTCCCTGACTTCATTATGATAAGCTCTCATCTGTGTGTTGTCTACGGGAATCCTTTGCAACG
TATCCAAAGATATCATGTTTAACACATACACGTTATCTTTAGAACCCCTGCAA
Found at i:1661838 original size:107 final size:107
Alignment explanation
Indices: 1661652--1661865 Score: 428
Period size: 107 Copynumber: 2.0 Consensus size: 107
1661642 TTCTTTTCTG
1661652 ATATGATCTTTGGAAATGAGGAATTGACCTGTCTTGCATAACTTTTATCAATCTTCCTCTTCTCG
1 ATATGATCTTTGGAAATGAGGAATTGACCTGTCTTGCATAACTTTTATCAATCTTCCTCTTCTCG
1661717 AAACCTACATGTGAAACAATCACACGCTAAGTCATAGACTTC
66 AAACCTACATGTGAAACAATCACACGCTAAGTCATAGACTTC
1661759 ATATGATCTTTGGAAATGAGGAATTGACCTGTCTTGCATAACTTTTATCAATCTTCCTCTTCTCG
1 ATATGATCTTTGGAAATGAGGAATTGACCTGTCTTGCATAACTTTTATCAATCTTCCTCTTCTCG
1661824 AAACCTACATGTGAAACAATCACACGCTAAGTCATAGACTTC
66 AAACCTACATGTGAAACAATCACACGCTAAGTCATAGACTTC
1661866 GTGAGGTATG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (107 bp):
ATATGATCTTTGGAAATGAGGAATTGACCTGTCTTGCATAACTTTTATCAATCTTCCTCTTCTCG
AAACCTACATGTGAAACAATCACACGCTAAGTCATAGACTTC
Found at i:1666303 original size:11 final size:11
Alignment explanation
Indices: 1666274--1666362 Score: 90
Period size: 11 Copynumber: 7.9 Consensus size: 11
1666264 TTCAGCTTTG
1666274 GGTTGGGTATTT
1 GGTTGGGT-TTT
1666286 AGGTTGGGTTTT
1 -GGTTGGGTTTT
**
1666298 GGTTGGGCCTT
1 GGTTGGGTTTT
*
1666309 AGTTGGGTTTT
1 GGTTGGGTTTT
* *
1666320 GGCTGGGTTTA
1 GGTTGGGTTTT
1666331 GGTTGGGTTTT
1 GGTTGGGTTTT
*
1666342 AGG-TGGGTTTC
1 -GGTTGGGTTTT
1666353 GGTTGGGTTT
1 GGTTGGGTTT
1666363 AAATCTGGGA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
10 2 0.03
11 48 0.76
12 5 0.08
13 8 0.13
ACGTcount: A:0.06, C:0.04, G:0.44, T:0.46
Consensus pattern (11 bp):
GGTTGGGTTTT
Found at i:1666335 original size:33 final size:33
Alignment explanation
Indices: 1666275--1666363 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
1666265 TCAGCTTTGG
*
1666275 GTTGGGTATTTAGGTTGGGTTTTGGTTGGGCCTTA
1 GTTGGGT-TTT-GGTTGGGTTTAGGTTGGGCCTTA
* **
1666310 GTTGGGTTTTGGCTGGGTTTAGGTTGGGTTTTA
1 GTTGGGTTTTGGTTGGGTTTAGGTTGGGCCTTA
* *
1666343 GGTGGGTTTCGGTTGGGTTTA
1 GTTGGGTTTTGGTTGGGTTTA
1666364 AATCTGGGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 37 0.79
34 3 0.06
35 7 0.15
ACGTcount: A:0.07, C:0.04, G:0.43, T:0.46
Consensus pattern (33 bp):
GTTGGGTTTTGGTTGGGTTTAGGTTGGGCCTTA
Found at i:1668264 original size:22 final size:22
Alignment explanation
Indices: 1668223--1668265 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1668213 CGTATAATTT
*
1668223 TTGTTATATTTTTTTACTTATA
1 TTGTTATATTTATTTACTTATA
1668245 TTGTTATATATTATTT-CTTAT
1 TTGTTATAT-TTATTTACTTAT
1668266 TAAATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (22 bp):
TTGTTATATTTATTTACTTATA
Found at i:1668564 original size:45 final size:45
Alignment explanation
Indices: 1668510--1668603 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
1668500 TTTAATTTTA
* *
1668510 TGTTTGAACTCATTTTATGTG-GACTTATGATTTCAATCATCCTTG
1 TGTTCGAACTCATTTTATATGAG-CTTATGATTTCAATCATCCTTG
* * * *
1668555 TGTTCGAACTCGTTTTATATGAGCTTGTGATTTTAATCATCTTTG
1 TGTTCGAACTCATTTTATATGAGCTTATGATTTCAATCATCCTTG
1668600 TGTT
1 TGTT
1668604 TGAATCACTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.17, T:0.49
Consensus pattern (45 bp):
TGTTCGAACTCATTTTATATGAGCTTATGATTTCAATCATCCTTG
Found at i:1669628 original size:20 final size:20
Alignment explanation
Indices: 1669603--1669658 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
1669593 TGGTTCACGA
*
1669603 AATGTAAGATTATCAGTGGG
1 AATGTAAGATTACCAGTGGG
1669623 AATGTAAGATTACCAGTGGG
1 AATGTAAGATTACCAGTGGG
1669643 AATGTAAGATTACCAG
1 AATGTAAGATTACCAG
1669659 GGAATAAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.27
Consensus pattern (20 bp):
AATGTAAGATTACCAGTGGG
Found at i:1669668 original size:16 final size:18
Alignment explanation
Indices: 1669606--1669671 Score: 73
Period size: 20 Copynumber: 3.6 Consensus size: 18
1669596 TTCACGAAAT
*
1669606 GTAAGATTATCAGTGGGAA
1 GTAAGATTACCAG-GGGAA
1669625 TGTAAGATTACCAGTGGGAA
1 -GTAAGATTACCAG-GGGAA
1669645 TGTAAGATTACCA-GGGAA
1 -GTAAGATTACCAGGGGAA
1669663 -TAAGATTAC
1 GTAAGATTAC
1669672 TGAGAATGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
16 9 0.20
18 5 0.11
20 31 0.69
ACGTcount: A:0.38, C:0.09, G:0.27, T:0.26
Consensus pattern (18 bp):
GTAAGATTACCAGGGGAA
Found at i:1670645 original size:2 final size:2
Alignment explanation
Indices: 1670632--1670690 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
1670622 TTTGAGCTTA
* *
1670632 AT AT AC AT AT AT AT GT A- AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1670673 AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT
1670691 TTACTAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1680922 original size:67 final size:67
Alignment explanation
Indices: 1680837--1680993 Score: 244
Period size: 66 Copynumber: 2.4 Consensus size: 67
1680827 CTCGCTTGAG
*
1680837 ACAATTTCTTTTGAGAAAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 ACAATTTCTTTTGAGAAAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1680902 AA
66 AA
* * *
1680904 ACAATTTCTTTTGTG-AAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTG
1 ACAATTTCTTTTGAGAAAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
*
1680968 AG
66 AA
* *
1680970 ACAATTTATTTTGGGAAAAAAATC
1 ACAATTTCTTTTGAGAAAAAAATC
1680994 ATCTTTGAGT
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 60 0.73
67 22 0.27
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (67 bp):
ACAATTTCTTTTGAGAAAAAAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
AA
Found at i:1681412 original size:130 final size:129
Alignment explanation
Indices: 1681147--1681582 Score: 426
Period size: 130 Copynumber: 3.4 Consensus size: 129
1681137 TATTACACCT
* * ** * * * *
1681147 AGATAACCAGTCGTCCTTATCACGTAGGAATTGTGTTATCATCCCCAAATATGGCTTGTCATCAT
1 AGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATGTCATCCT
* * * * * * *
1681212 CATCGCGTAGGAACCGTCTCATCCCCCGAACATACCTCCTCATAACATAGGAGCCATATTACCCC
66 CATCGCGTAGGAACCGTGTCAT-CCCCGACCAGACCTCCTCATAACGTAGGAGCCATGTCACCCA
* * * * *
1681277 TGATAACCAGCCATCCTCATCATGTAGGAACCGTGTTATCATCCCTAAAGATGACATATCATCCT
1 AGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATGTCATCCT
* * * * *
1681342 CATCGCGTAGAAACAGTGTCATCCCTCG-CCAGACCTCCTCATCATGTAGGAGCCACGTCAGCCC
66 CATCGCGTAGGAACCGTGTCATCCC-CGACCAGACCTCCTCATAACGTAGGAGCCATGTCA-CCC
1681406 A
129 A
* * * * * * **
1681407 AGATAACCAGTCGTCCTCATCATGTAAGAACCATGTTATTATTCCTAAAGATGGCATGTGGTCCT
1 AGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATGTCATCCT
** ** * *
1681472 CATCATGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATTGCGTAGGAACCGTGTCACCCC
66 CATCGCGTAGGAACCGTGTCATCC-CCGACCAGACCTCCTCATAACGTAGGAGCCATGTCA-CCC
*
1681537 T
129 A
* **
1681538 AGATAACCAGTCATCCTCATCGCGTAGGAATTGTGTTATCA-CCCT
1 AGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCT
1681583 TCCTAAAGAT
Statistics
Matches: 245, Mismatches: 57, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
129 27 0.11
130 155 0.63
131 63 0.26
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (129 bp):
AGATAACCAGTCATCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGGCATGTCATCCT
CATCGCGTAGGAACCGTGTCATCCCCGACCAGACCTCCTCATAACGTAGGAGCCATGTCACCCA
Found at i:1681656 original size:134 final size:131
Alignment explanation
Indices: 1681144--1681697 Score: 393
Period size: 130 Copynumber: 4.2 Consensus size: 131
1681134 AACTATTACA
* * * *** * * * * *
1681144 CCTAGATAACCAGTCGTCCTTATCACGTAGGAATTGTGTTATCATCCCCAAATATGGCTTG-TCA
1 CCTAGATAACCAGTCATCCTCATCACGTAAGAACCATGTTATCATTCCTAAAGATGGCATGAAC-
* ** * * * * * ** * * *
1681208 TCATCATCGCGTAGGAACCGTCTCATCCCCCGAACATACCTCCTCATAACATAGGAGCCATATTA
65 TCCTCATCATGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCCGTGTCA
1681273 CC
130 CC
* * * * * * *
1681275 CCT-GATAACCAGCCATCCTCATCATGTAGGAACCGTGTTATCATCCCTAAAGATGACAT-ATCA
1 CCTAGATAACCAGTCATCCTCATCACGTAAGAACCATGTTATCATTCCTAAAGATGGCATGAAC-
** * * **
1681338 TCCTCATCGCGTAGAAACAGTGTCATCC-CTCG-CCAGACCTCCTCATCATGTAGGAGCCACGTC
65 TCCTCATCATGTAGGAACCGTGTCATCCAC-CGACCAGACCTCCTCATCATGTAGGAGCCGTGTC
*
1681401 AGC
129 ACC
* * * * ***
1681404 CCAAGATAACCAGTCGTCCTCATCATGTAAGAACCATGTTATTATTCCTAAAGATGGCATGTGGT
1 CCTAGATAACCAGTCATCCTCATCACGTAAGAACCATGTTATCATTCCTAAAGATGGCATGAACT
*** *
1681469 CCTCATCATGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATTGCGTAGGAACCGTGTCAC
66 CCTCATCATGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCCGTGTCAC
1681534 C
131 C
* * ***
1681535 CCTAGATAACCAGTCATCCTCATCGCGTAGGAATTGTGTTATCACCCTTCCTAAAGATGGCCA-G
1 CCTAGATAACCAGTCATCCTCATCACGTAAGAACCATGTTATCA---TTCCTAAAGATGG-CATG
* * ** * * * *
1681599 AACTCTTCATCATGTATGAGTCGTGTCATCCACCGACCATATCTCCTCATCATGTAGGAGTCGTA
62 AACTCCTCATCATGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCCGTG
1681664 TCACC
127 TCACC
* * * *
1681669 CTTAGATGACCA-TACCTCTTCATCACGTA
1 CCTAGATAACCAGT-CATCCTCATCACGTA
1681698 TGAGTCGTGT
Statistics
Matches: 338, Mismatches: 74, Indels: 19
0.78 0.17 0.04
Matches are distributed among these distances:
129 28 0.08
130 150 0.44
131 66 0.20
133 1 0.00
134 91 0.27
135 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (131 bp):
CCTAGATAACCAGTCATCCTCATCACGTAAGAACCATGTTATCATTCCTAAAGATGGCATGAACT
CCTCATCATGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCATGTAGGAGCCGTGTCAC
C
Found at i:1681886 original size:3 final size:3
Alignment explanation
Indices: 1681860--1681913 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
1681850 TCTACAAAAA
* * * *
1681860 TAT TAAT TAT ATAT TAT TAC TAT TAT TAT TAT TGT TAT TTT TAT TAA
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1681907 TAT TAT T
1 TAT TAT T
1681914 TACATATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1684607 original size:54 final size:55
Alignment explanation
Indices: 1684538--1684642 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 55
1684528 CGAAATGGAA
* *
1684538 ATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTC-AAAATCGTT
1 ATTCACAAACACATTATGAATACCATGGATTGCACACATAGTGTCGAAAATCGTT
* * **
1684592 ATTCATAAACACATTATGAATACCATGGGTTGCACATTTAGTGTCGAAAAT
1 ATTCACAAACACATTATGAATACCATGGATTGCACACATAGTGTCGAAAAT
1684643 GCACCGTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
54 39 0.89
55 5 0.11
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (55 bp):
ATTCACAAACACATTATGAATACCATGGATTGCACACATAGTGTCGAAAATCGTT
Found at i:1685182 original size:12 final size:12
Alignment explanation
Indices: 1685162--1685209 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
1685152 TATTCGATAA
*
1685162 CCTTATTCTTGC
1 CCTTTTTCTTGC
1685174 CCTTTTTCTTGC
1 CCTTTTTCTTGC
*
1685186 CCTTTTTCTTTC
1 CCTTTTTCTTGC
1685198 CCTTTTTCTTGC
1 CCTTTTTCTTGC
1685210 TTGACTCTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.02, C:0.33, G:0.06, T:0.58
Consensus pattern (12 bp):
CCTTTTTCTTGC
Found at i:1688623 original size:110 final size:111
Alignment explanation
Indices: 1688413--1688636 Score: 432
Period size: 110 Copynumber: 2.0 Consensus size: 111
1688403 GGTTTCCCCT
1688413 ACCCCTTCTCTTTATTATGCTTAATCCGAATGGATGCAAAATGTTTTAAAAAAAATAAATAAAAA
1 ACCCCTTCTCTTTATTATGCTTAATCCGAATGGATGCAAAATGTTTTAAAAAAAATAAATAAAAA
1688478 TAAATACATGTTGTTTTGTGTGATTGTATTACTGAAAAATGAACGA
66 TAAATACATGTTGTTTTGTGTGATTGTATTACTGAAAAATGAACGA
*
1688524 ACCCCTTCTCTTTATTATGCTTAATCCGAATGGATGTAAAATGTTTT-AAAAAAATAAATAAAAA
1 ACCCCTTCTCTTTATTATGCTTAATCCGAATGGATGCAAAATGTTTTAAAAAAAATAAATAAAAA
1688588 TAAATACATGTTGTTTTGTGTGATTGTATTACTGAAAAATGAACGA
66 TAAATACATGTTGTTTTGTGTGATTGTATTACTGAAAAATGAACGA
1688634 ACC
1 ACC
1688637 AGGAAGAAAA
Statistics
Matches: 112, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
110 66 0.59
111 46 0.41
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (111 bp):
ACCCCTTCTCTTTATTATGCTTAATCCGAATGGATGCAAAATGTTTTAAAAAAAATAAATAAAAA
TAAATACATGTTGTTTTGTGTGATTGTATTACTGAAAAATGAACGA
Found at i:1689348 original size:38 final size:37
Alignment explanation
Indices: 1689298--1689371 Score: 139
Period size: 38 Copynumber: 2.0 Consensus size: 37
1689288 CGAACTCGAG
1689298 ATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAA
1 ATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAA
1689335 ATTGATTTTGCTTCACTACTCTTTGGTGAAGGCTTAA
1 ATTGA-TTTGCTTCACTACTCTTTGGTGAAGGCTTAA
1689372 GATGGCCCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 5 0.14
38 31 0.86
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (37 bp):
ATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAA
Found at i:1689455 original size:79 final size:79
Alignment explanation
Indices: 1689324--1689533 Score: 334
Period size: 79 Copynumber: 2.7 Consensus size: 79
1689314 ACTCTTTGGT
* *
1689324 GAAGGCTTA-AAATTGATTTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACT
1 GAAGGCTTACTAA-TGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACT
1689388 TAATCATCATGCTCG
65 TAATCATCATGCTCG
1689403 GAAGGCTTACTAATGAATTTGCTTCACTACTCTTTGGTGAAGG-TGTAAGATGGCCCGGAGGACT
1 GAAGGCTTACTAATGAATTTGCTTCACTACTCTTTGGTGAAGGCT-TAAGATGGCCCGGAGGACT
1689467 TAATCATCATGCTCG
65 TAATCATCATGCTCG
* ** *
1689482 GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTATGATG
1 GAAGGCTTACTAATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATG
1689534 AATTTCTTCA
Statistics
Matches: 122, Mismatches: 6, Indels: 6
0.91 0.04 0.04
Matches are distributed among these distances:
78 1 0.01
79 118 0.97
80 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (79 bp):
GAAGGCTTACTAATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGACTT
AATCATCATGCTCG
Found at i:1689548 original size:36 final size:38
Alignment explanation
Indices: 1689482--1689564 Score: 143
Period size: 36 Copynumber: 2.2 Consensus size: 38
1689472 ATCATGCTCG
*
1689482 GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGT
1 GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCAGT
1689520 GAAGGCTTA-TGATGAATTT-CTTCACTACTCTTCAGT
1 GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCAGT
1689556 GAAGGCTTA
1 GAAGGCTTA
1689565 AGATTGCCCG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
36 25 0.57
37 10 0.23
38 9 0.20
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.36
Consensus pattern (38 bp):
GAAGGCTTACTGATGAATTTGCTTCACTACTCTTCAGT
Found at i:1689679 original size:41 final size:41
Alignment explanation
Indices: 1689617--1689765 Score: 140
Period size: 41 Copynumber: 3.6 Consensus size: 41
1689607 ATCCTACCCG
* * * * *
1689617 AAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGATCAA
1 AAGG-CTTATAGATGACCCGAAGGACTTATCATCTTGCTCGA
* * *
1689659 AAGGCTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTATAGATGACCCGAAGGACTT-ATCATCTTGCTCGA
* * *
1689701 AAGACTTACT-GATGGCCCGAAGGACTTATCATCTTCCTCTGA
1 AAGGCTTA-TAGATGACCCGAAGGACTTATCATCTTGCTC-GA
*
1689743 AA-GCTTACAGATGACCCGAAGGA
1 AAGGCTTATAGATGACCCGAAGGA
1689766 TTTAAGCATG
Statistics
Matches: 86, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
41 45 0.52
42 40 0.47
43 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (41 bp):
AAGGCTTATAGATGACCCGAAGGACTTATCATCTTGCTCGA
Found at i:1689721 original size:42 final size:42
Alignment explanation
Indices: 1689669--1689802 Score: 147
Period size: 41 Copynumber: 3.3 Consensus size: 42
1689659 AAGGCTTATA
1689669 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
* * * * * *
1689711 GATGGCCCGAAGGACTT-ATCATCTTCCTCTGAAAG-CTTACA
1 GATGACCCGAAGGATTTAAGCATCATGCTC-GAAAGACTTACT
1689752 GATGACCCGAAGGATTTAAG---CATGCTCG-AAGACTTACT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
*
1689790 GATG-GCCGAAGGA
1 GATGACCCGAAGGA
1689803 CTTATAAATT
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
37 11 0.14
38 10 0.13
39 5 0.07
41 29 0.38
42 21 0.28
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
Found at i:1689767 original size:83 final size:79
Alignment explanation
Indices: 1689628--1689807 Score: 256
Period size: 83 Copynumber: 2.2 Consensus size: 79
1689618 AGGTCTTATG
* * *
1689628 GATGGCCCGAAAGACTTATCATCTTGATCAAAAGGCTTATAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTCATCAAAAGGCTTACAGATGACCCGAAGGATTTAAG---C
1689693 ATGCTCGAAAGACTTACT
63 ATGCTCG-AAGACTTACT
* *
1689711 GATGGCCCGAAGGACTTATCATCTTCCTCTGAAA-GCTTACAGATGACCCGAAGGATTTAAGCAT
1 GATGGCCCGAAGGACTTATCATCTTCATC-AAAAGGCTTACAGATGACCCGAAGGATTTAAGCAT
1689775 GCTCGAAGACTTACT
65 GCTCGAAGACTTACT
1689790 GATGG-CCGAAGGACTTAT
1 GATGGCCCGAAGGACTTAT
1689808 AAATTGTGAA
Statistics
Matches: 91, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
78 13 0.14
79 15 0.16
80 8 0.09
83 52 0.57
84 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (79 bp):
GATGGCCCGAAGGACTTATCATCTTCATCAAAAGGCTTACAGATGACCCGAAGGATTTAAGCATG
CTCGAAGACTTACT
Found at i:1690054 original size:41 final size:41
Alignment explanation
Indices: 1689921--1690105 Score: 176
Period size: 42 Copynumber: 4.5 Consensus size: 41
1689911 AGGTCTTATG
* * * *
1689921 GATGGCCCGAAGGACTTATCATCTTGCTCTAAGGGCTTACA
1 GATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACA
* * *
1689962 GATGACCCGAAGGATTTAAGCATCATT-CTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATC-TTGCTCGAAAGACTTACA
* * *
1690004 GATTG-CCCGAAGGACTTATCATCTTACTCTAAAGGCTTACA
1 GA-TGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACA
* * * *
1690045 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-ATCATCTTGCTCGAAAGACTTACA
* *
1690087 GATGGCCCGAATGACTTAT
1 GATGACCCGAAGGACTTAT
1690106 AAATTGTGAA
Statistics
Matches: 115, Mismatches: 23, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
40 4 0.03
41 46 0.40
42 61 0.53
43 4 0.03
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (41 bp):
GATGACCCGAAGGACTTATCATCTTGCTCGAAAGACTTACA
Found at i:1690064 original size:83 final size:83
Alignment explanation
Indices: 1689921--1690105 Score: 325
Period size: 83 Copynumber: 2.2 Consensus size: 83
1689911 AGGTCTTATG
* *
1689921 GATGGCCCGAAGGACTTATCATCTTGCTCTAAGGGCTTACAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTACTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
*
1689986 ATTCTCGAAAGACTTACT
66 ATGCTCGAAAGACTTACT
*
1690004 GATTGCCCGAAGGACTTATCATCTTACTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
1 GATGGCCCGAAGGACTTATCATCTTACTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
1690069 ATGCTCGAAAGACTTACT
66 ATGCTCGAAAGACTTACT
*
1690087 GATGGCCCGAATGACTTAT
1 GATGGCCCGAAGGACTTAT
1690106 AAATTGTGAA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 96 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (83 bp):
GATGGCCCGAAGGACTTATCATCTTACTCTAAAGGCTTACAGATGACCCGAAGGATTTAAGCATC
ATGCTCGAAAGACTTACT
Found at i:1690354 original size:36 final size:36
Alignment explanation
Indices: 1690251--1690479 Score: 229
Period size: 36 Copynumber: 6.4 Consensus size: 36
1690241 TCTTGCTCTA
* *
1690251 AAGGCTTACAGATGGATTTGCTTTACTACTCTTC-GATG
1 AAGGCTTA-AGATTG-TTTGCTTCACTACTCTTCTG-TG
*
1690289 AAGGCTTAAGA-TG-GTGCTTCACTACTCTTCTGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCTGTG
* * *
1690323 AAGGCTTAAGATTGTTTGCTTCACCATTCTTCGGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCTGTG
*
1690359 AAGGCTTAAGA-TGATTGCTTCACTACTCTT-TGGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCT-GTG
* * * * * *
1690394 AAGGCTTCAA-ATGGATCGCTTCATTACTCTCCAGTG
1 AAGGCTT-AAGATTGTTTGCTTCACTACTCTTCTGTG
*
1690430 AAGGCTTAAGATTATTTGCTTCACTACTC-TCTAGTG
1 AAGGCTTAAGATTGTTTGCTTCACTACTCTTCT-GTG
1690466 AAGGCTTAAGATTG
1 AAGGCTTAAGATTG
1690480 ACTTGCCCCA
Statistics
Matches: 158, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
34 28 0.18
35 33 0.21
36 86 0.54
37 3 0.02
38 8 0.05
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (36 bp):
AAGGCTTAAGATTGTTTGCTTCACTACTCTTCTGTG
Found at i:1690415 original size:71 final size:70
Alignment explanation
Indices: 1690251--1690477 Score: 242
Period size: 71 Copynumber: 3.2 Consensus size: 70
1690241 TCTTGCTCTA
* * * * *
1690251 AAGGCTTACAGATGGATTTGCTTTACTACTCTTCGATGAAGGCTTAAGATG-GTGCTTCACTACT
1 AAGGCTTA-AGATGGA-TCGCTTCACCACTCTTCGGTGAAGGCTTAAGATGATTGCTTCACTACT
1690315 CTTCTGTG
64 CTT-TGTG
* * * *
1690323 AAGGCTTAAGATTGTTTGCTTCACCATTCTTCGGTGAAGGCTTAAGATGATTGCTTCACTACTCT
1 AAGGCTTAAGATGGATCGCTTCACCACTCTTCGGTGAAGGCTTAAGATGATTGCTTCACTACTCT
1690388 TTGGTG
66 TT-GTG
** * * *
1690394 AAGGCTTCAA-ATGGATCGCTTCATTACTCTCCAGTGAAGGCTTAAGATTATTTGCTTCACTACT
1 AAGGCTT-AAGATGGATCGCTTCACCACTCTTCGGTGAAGGCTTAAGATGA-TTGCTTCACTACT
*
1690458 CTCTAGTG
64 CT-TTGTG
1690466 AAGGCTTAAGAT
1 AAGGCTTAAGAT
1690478 TGACTTGCCC
Statistics
Matches: 132, Mismatches: 17, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
70 31 0.23
71 63 0.48
72 37 0.28
73 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (70 bp):
AAGGCTTAAGATGGATCGCTTCACCACTCTTCGGTGAAGGCTTAAGATGATTGCTTCACTACTCT
TTGTG
Found at i:1690448 original size:107 final size:107
Alignment explanation
Indices: 1690251--1690477 Score: 291
Period size: 107 Copynumber: 2.1 Consensus size: 107
1690241 TCTTGCTCTA
*
1690251 AAGGCTTACAGATGGATTTGCTTTACTACTCTTCGATGAAGGCTTAAGATGGTGCTTCACTACTC
1 AAGGCTTA-AGATGGATTTGCTTCACTACTCTTCGATGAAGGCTTAAGATGGTGCTTCACTACTC
* * * * *
1690316 TTCTGTGAAGGCTTAAGATTGTTTGCTTCACCATTCT-TCGGTG
65 TCCAGTGAAGGCTTAAGATTATTTGCTTCACCACTCTCT-AGTG
* * *
1690359 AAGGCTTAAGAT-GA-TTGCTTCACTACTCTTTGGTGAAGGCTTCAA-ATGGATCGCTTCATTAC
1 AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGATGAAGGCTT-AAGATGG-T-GCTTCACTAC
*
1690421 TCTCCAGTGAAGGCTTAAGATTATTTGCTTCACTACTCTCTAGTG
63 TCTCCAGTGAAGGCTTAAGATTATTTGCTTCACCACTCTCTAGTG
1690466 AAGGCTTAAGAT
1 AAGGCTTAAGAT
1690478 TGACTTGCCC
Statistics
Matches: 105, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
105 29 0.28
106 5 0.05
107 62 0.59
108 9 0.09
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (107 bp):
AAGGCTTAAGATGGATTTGCTTCACTACTCTTCGATGAAGGCTTAAGATGGTGCTTCACTACTCT
CCAGTGAAGGCTTAAGATTATTTGCTTCACCACTCTCTAGTG
Found at i:1691428 original size:125 final size:125
Alignment explanation
Indices: 1691221--1691525 Score: 430
Period size: 125 Copynumber: 2.4 Consensus size: 125
1691211 TCAATGACTT
* ** * * *
1691221 CTTGGTCTGAATCTTATTTTCTCATCATGACGTGGGTTCAGTCGTGCCCCAACCTTATCTTATAC
1 CTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTATAC
* * *
1691286 TGGTATAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAGGCCCATTCTTCATGCCTC
66 TAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAAGCCCATTCTTCATGCCTC
* * * * *
1691346 CTTGGTCCGAATCTTGTCATCTCAACATGATGTGGGTTTAGTTGTTCCCCCACATTATCTTATAC
1 CTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTATAC
* *
1691411 TAGTACAGGCCTTCAAAATGCCCCATCACCTCAAATTGTAAAGCTCATTCTTCATGCCTC
66 TAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAAGCCCATTCTTCATGCCTC
* ** *
1691471 ATTGGTCTGAAAGTTGTCATCTCAACATAATGTGGGTTCAGTCGTGCCCCAACAT
1 CTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACAT
1691526 ATCCTAACTT
Statistics
Matches: 155, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
125 155 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (125 bp):
CTTGGTCTGAATCTTGTCATCTCAACATGATGTGGGTTCAGTCGTGCCCCAACATTATCTTATAC
TAGTACAAGCCTTCAAAATGCCCCATCACCTCAAATTGTAAAGCCCATTCTTCATGCCTC
Found at i:1692603 original size:361 final size:366
Alignment explanation
Indices: 1691932--1692664 Score: 1388
Period size: 361 Copynumber: 2.0 Consensus size: 366
1691922 TTCAAAGATC
1691932 AAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCGCAATCAAATCAAATCATA
1 AAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCGCAATCAAATCAAATCATA
*
1691997 GATATGAGTTCACAGAATATCAAAAGAATCAATAGCTCTTTAATGTTTTTAGGGTTATAGTTATT
66 GATATGAGTTCACAGAATATC-AAAGAATCAATA-CACTTTAATGTTTTTAGGGTTATAGTTATT
1692062 TGACAGGTGTTAAAATTAAGGGGTTTGCTTCAGGTTGGCTTCCTATTTTCTAAGGTTTCGACCAC
129 TGACAGGTGTTAAAATTAAGGGGTTTGCTTCAGGTTGGCTTCCTATTTTCTAAGGTTTCGACCAC
1692127 CAGAATGTCATTTTTTTCTTGATCATTGTGAATATCGCAACTTGTCTTTCTTTCTTGGCTTGGTA
194 CAGAATGTCATTTTTTTCTTGATCATTGTGAATATCGCAACTTGTCTTTCTTTCTTGGCTTGGTA
1692192 TTTTAATCGGATGCGGACAAAATGACGCAACTAGGATAATCAATTACTAGACTTTCTAGAACACT
259 TTTTAATCGGATGCGGACAAAATGACGCAACTAGGATAATCAATTACTAGACTTTCTAGAACACT
1692257 TCCATTTCAGTTCTCTGAAATCTTTCATTTTTTCAAGCTTCAT
324 TCCATTTCAGTTCTCTGAAATCTTTCATTTTTTCAAGCTTCAT
1692300 AAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCGCAATCAAATCAAATCATA
1 AAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCGCAATCAAATCAAATCATA
1692365 GATATGAGTTCACAGAATATC-AA-AATC-ATA-ACTTTAATGTTTTTAGGGTTATAGTTATTTG
66 GATATGAGTTCACAGAATATCAAAGAATCAATACACTTTAATGTTTTTAGGGTTATAGTTATTTG
1692426 -CAGGTGTTAAAATTAAGGGGTTTGCTTCAGGTTGGCTTCCTA-TTTCTAAGGTTTCGACCACCA
131 ACAGGTGTTAAAATTAAGGGGTTTGCTTCAGGTTGGCTTCCTATTTTCTAAGGTTTCGACCACCA
1692489 GAATGTCATTTTTTTTCTTGATCATTGTGAATATCGCAACTTGTCTTTCTTTCTTGGCTTGGTAT
196 GAATGTCA-TTTTTTTCTTGATCATTGTGAATATCGCAACTTGTCTTTCTTTCTTGGCTTGGTAT
1692554 TTTAATCGGATGCGGACAAAATGACGCAACTAGGATAATCAATTACTAGACTTTCTAGAACACTT
260 TTTAATCGGATGCGGACAAAATGACGCAACTAGGATAATCAATTACTAGACTTTCTAGAACACTT
1692619 CCATTTCAGTTCTCTGAAATCTTTCATTTTTTCAAGCTTCAT
325 CCATTTCAGTTCTCTGAAATCTTTCATTTTTTCAAGCTTCAT
1692661 AAAG
1 AAAG
1692665 CTCCTCTAAC
Statistics
Matches: 363, Mismatches: 1, Indels: 9
0.97 0.00 0.02
Matches are distributed among these distances:
360 29 0.08
361 209 0.58
362 30 0.08
364 3 0.01
365 4 0.01
366 2 0.01
368 86 0.24
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (366 bp):
AAAGAATGAAAGAATTTTATAAAACATTGCCCCTTAATTCAGGCTCGCAATCAAATCAAATCATA
GATATGAGTTCACAGAATATCAAAGAATCAATACACTTTAATGTTTTTAGGGTTATAGTTATTTG
ACAGGTGTTAAAATTAAGGGGTTTGCTTCAGGTTGGCTTCCTATTTTCTAAGGTTTCGACCACCA
GAATGTCATTTTTTTCTTGATCATTGTGAATATCGCAACTTGTCTTTCTTTCTTGGCTTGGTATT
TTAATCGGATGCGGACAAAATGACGCAACTAGGATAATCAATTACTAGACTTTCTAGAACACTTC
CATTTCAGTTCTCTGAAATCTTTCATTTTTTCAAGCTTCAT
Found at i:1709944 original size:51 final size:51
Alignment explanation
Indices: 1709868--1709971 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 51
1709858 ATCGCACATC
* *
1709868 ATTCAAGACACCGCTGTGAATGTCCCCGTTCAAACTGGTCTATGAAAAAGA
1 ATTCAAGACACCGCTGTGAATGTCCCCATTCAAACTGGTCTACGAAAAAGA
* *
1709919 ATTCAAGACACCGCTGTGAGTGTCCCCATTCAAATTGGTCTACGAAAAAGA
1 ATTCAAGACACCGCTGTGAATGTCCCCATTCAAACTGGTCTACGAAAAAGA
1709970 AT
1 AT
1709972 GCCAGCTGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (51 bp):
ATTCAAGACACCGCTGTGAATGTCCCCATTCAAACTGGTCTACGAAAAAGA
Found at i:1718690 original size:20 final size:20
Alignment explanation
Indices: 1718665--1718716 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1718655 CTAGAATTCA
1718665 TAGTATTGATACGTTCATTT
1 TAGTATTGATACGTTCATTT
*
1718685 TAGTATTGATACTTTCATTT
1 TAGTATTGATACGTTCATTT
*
1718705 TAGTATCGATAC
1 TAGTATTGATAC
1718717 CTACAGAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (20 bp):
TAGTATTGATACGTTCATTT
Found at i:1722976 original size:17 final size:18
Alignment explanation
Indices: 1722937--1722980 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1722927 CTTTAGATTA
*
1722937 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
1722955 TTTATTTAATTCTTAT-T
1 TTTATTTAATTATTATCT
1722972 TTTATTTAA
1 TTTATTTAA
1722981 AAAACAACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:1723103 original size:10 final size:10
Alignment explanation
Indices: 1723088--1723116 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1723078 TCCTACTGTT
1723088 TTTTATTTTG
1 TTTTATTTTG
1723098 TTTTATTTTG
1 TTTTATTTTG
1723108 TTTTATTTT
1 TTTTATTTT
1723117 TATTTTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTATTTTG
Found at i:1724265 original size:30 final size:31
Alignment explanation
Indices: 1724197--1724265 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 31
1724187 AAATTATACA
* *
1724197 TTTGGTAAAGTTTGGTGACCAAAGTATAAAC
1 TTTGGAAAAGTTTGGTGACCAAAATATAAAC
* *
1724228 TTT-GAAAAGTTTAGG-GACCAAAATGT-AAT
1 TTTGGAAAAGTTT-GGTGACCAAAATATAAAC
1724257 TTTGGAAAA
1 TTTGGAAAA
1724266 CTTACAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.16
30 22 0.69
31 5 0.16
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (31 bp):
TTTGGAAAAGTTTGGTGACCAAAATATAAAC
Found at i:1725859 original size:40 final size:39
Alignment explanation
Indices: 1725806--1725951 Score: 213
Period size: 40 Copynumber: 3.7 Consensus size: 39
1725796 AGGACACTAA
* * * *
1725806 GTGTACATAGTGGGCACAACCTTATGTGTAATACA-TTT
1 GTGTATATGGTGGGCACGACCTTATGCGTAATACACTTT
1725844 CGATGTATATGGTGGGCACGACCTTATGCGTAAATACACTTT
1 -G-TGTATATGGTGGGCACGACCTTATGCGT-AATACACTTT
1725886 GTGTATATGGTGGGCACGACCTTATGCGTAATACACTTT
1 GTGTATATGGTGGGCACGACCTTATGCGTAATACACTTT
1725925 GGTGTATATGGTGGGCACGACCTTATG
1 -GTGTATATGGTGGGCACGACCTTATG
1725952 TGTAGCACTA
Statistics
Matches: 99, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
39 11 0.11
40 78 0.79
41 7 0.07
42 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (39 bp):
GTGTATATGGTGGGCACGACCTTATGCGTAATACACTTT
Found at i:1730284 original size:32 final size:31
Alignment explanation
Indices: 1730231--1730315 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
1730221 AGGAAGAGTG
* *
1730231 GGGGCATCTTTGAAGACTCAACATCAAATGTT
1 GGGGCATCTTTG-AGATTCAACATCAAATATT
* *
1730263 GGGGCATTTTTAGAGATTCAACATCGAATATT
1 GGGGCATCTTT-GAGATTCAACATCAAATATT
* *
1730295 GGTGCATCTTTGGGGATTCAA
1 GGGGCATCTTT-GAGATTCAA
1730316 AATCCTGATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (31 bp):
GGGGCATCTTTGAGATTCAACATCAAATATT
Found at i:1731398 original size:201 final size:199
Alignment explanation
Indices: 1731048--1731442 Score: 479
Period size: 201 Copynumber: 2.0 Consensus size: 199
1731038 CAATGGGGGT
* ** * * * * *
1731048 TATCTCCCAGCCTATTACAGTATAGCTCAAGGCGAGAAGGGTTATCTGTCAACGAAAACTTTCGA
1 TATCTCCCAGCCAATTACAACATAGCTCAAGGCGAGAAGGGCTATATATCAACGAAAACCTTAGA
* * * * * *
1731113 GTTCGATTCCATTCATCTCGAGGGAACATCAATCGTATAGTAGCAATGAAGAACTACTTTTTGGT
66 GTTCGATTCCATTCAGCTCGAGGGAACATAAACCATATAGTAGCAATGAAGAACTACTTTCTAGT
* ** * * * *
1731178 TGAAGTTTAAACGGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAACAAG
131 TGAAGTTTAAACCGAGGTCTTTAAACCAAGAAAAAGACCAAGGTTGACTACGATTTAGCAACAAG
1731243 GAAC
196 GAAC
1731247 TATCTCCCAGCCGAATTTACAACATAGCTCAAGGCGAGAAGGGCTATATATCAAC-AAAACCTTA
1 TATCTCCCAGCC-AA-TTACAACATAGCTCAAGGCGAGAAGGGCTATATATCAACGAAAACCTTA
* * * * * *
1731311 GATTTCGATTTCATTCAGCTCGAGGGCATATAAACCATATGGTAGC-ATCGAGGAACTACTTTCT
64 GAGTTCGATTCCATTCAGCTCGAGGGAACATAAACCATATAGTAGCAAT-GAAGAACTACTTTCT
* *
1731375 AGTTGAATTTTCAAACCGAGGTCTTTAAACCAAGAAAAAGACCAAGGTTGACTACGATTTGGCAA
128 AGTTGAAGTTT-AAACCGAGGTCTTTAAACCAAGAAAAAGACCAAGGTTGACTACGATTTAGCAA
1731440 CAA
192 CAA
1731443 TAAGCCAATT
Statistics
Matches: 163, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
199 14 0.09
200 67 0.41
201 82 0.50
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (199 bp):
TATCTCCCAGCCAATTACAACATAGCTCAAGGCGAGAAGGGCTATATATCAACGAAAACCTTAGA
GTTCGATTCCATTCAGCTCGAGGGAACATAAACCATATAGTAGCAATGAAGAACTACTTTCTAGT
TGAAGTTTAAACCGAGGTCTTTAAACCAAGAAAAAGACCAAGGTTGACTACGATTTAGCAACAAG
GAAC
Found at i:1732292 original size:22 final size:19
Alignment explanation
Indices: 1732245--1732294 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
1732235 TCTCTTTAAA
1732245 TTATTTATTTATTTAATTC
1 TTATTTATTTATTTAATTC
1732264 TTA-TTATTTATTTAATTC
1 TTATTTATTTATTTAATTC
*
1732282 TTATAT-TTTATTT
1 TTATTTATTTATTT
1732295 TAAAAACTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 25 0.86
19 4 0.14
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTATTTATTTAATTC
Found at i:1732369 original size:15 final size:15
Alignment explanation
Indices: 1732349--1732396 Score: 87
Period size: 15 Copynumber: 3.1 Consensus size: 15
1732339 TATATTTTCC
1732349 TTGTTTTATCTTATT
1 TTGTTTTATCTTATT
1732364 TTGTTTTATCTTATT
1 TTGTTTTATCTTATT
1732379 TTGTTTTATCTTTATT
1 TTGTTTTATC-TTATT
1732395 TT
1 TT
1732397 CATACTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 25 0.78
16 7 0.22
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (15 bp):
TTGTTTTATCTTATT
Found at i:1732385 original size:5 final size:5
Alignment explanation
Indices: 1732330--1732432 Score: 50
Period size: 5 Copynumber: 20.4 Consensus size: 5
1732320 CTATTATTTA
* ** * * * *
1732330 TTATT TTATT ATATT TT-CC TTGTT TTATC TTATT TTGTT TTATC TTATT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
* * * *
1732379 TTGTT TTATCT TTATT TTCATAC TT-TT TTA-T TTGTT TTGTT TTACTT
1 TTATT TTAT-T TTATT TT-AT-T TTATT TTATT TTATT TTATT TTA-TT
1732426 TTATT TT
1 TTATT TT
1732433 CTCTTTTAAC
Statistics
Matches: 72, Mismatches: 19, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
4 7 0.10
5 51 0.71
6 12 0.17
7 2 0.03
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:1738441 original size:27 final size:27
Alignment explanation
Indices: 1738403--1738481 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
1738393 TAGAATCATG
1738403 TCATGCACGAGCATGCATGGAACTATC
1 TCATGCACGAGCATGCATGGAACTATC
*
1738430 TCATGCACGAGCATGCATGGAATTATC
1 TCATGCACGAGCATGCATGGAACTATC
* *
1738457 TCATGCATGAGCATGCAAGGAACTA
1 TCATGCACGAGCATGCATGGAACTA
1738482 CTGCACGAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (27 bp):
TCATGCACGAGCATGCATGGAACTATC
Found at i:1751148 original size:15 final size:15
Alignment explanation
Indices: 1751128--1751157 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1751118 CCAACTTGGG
*
1751128 AAAAATAATGAGAAT
1 AAAAATAAAGAGAAT
1751143 AAAAATAAAGAGAAT
1 AAAAATAAAGAGAAT
1751158 GAGGAATGGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (15 bp):
AAAAATAAAGAGAAT
Found at i:1753498 original size:24 final size:24
Alignment explanation
Indices: 1753466--1753518 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
1753456 GGTACATTCG
1753466 TGTGC-ATTCTACGTGACAC-ATT
1 TGTGCAATTCTACGTGACACTATT
* *
1753488 ATGTGCAATTCTATGTGGCACTATT
1 -TGTGCAATTCTACGTGACACTATT
1753513 TGTGCA
1 TGTGCA
1753519 TTGAAGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.19
24 18 0.69
25 3 0.12
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TGTGCAATTCTACGTGACACTATT
Found at i:1755043 original size:25 final size:25
Alignment explanation
Indices: 1755015--1755063 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1755005 AACCCTAATT
1755015 TAGTTTATAAATCACCCACTAAACA
1 TAGTTTATAAATCACCCACTAAACA
*
1755040 TAGTTTATAAATCATCCACTAAAC
1 TAGTTTATAAATCACCCACTAAAC
1755064 TGCCAAAAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.04, T:0.31
Consensus pattern (25 bp):
TAGTTTATAAATCACCCACTAAACA
Found at i:1755170 original size:23 final size:23
Alignment explanation
Indices: 1755140--1755188 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1755130 GATTATGCTA
1755140 GTGGAGGTTCACTTGTTTTTAGG
1 GTGGAGGTTCACTTGTTTTTAGG
1755163 GTGGAGGTTCACTTGTTTTTAGG
1 GTGGAGGTTCACTTGTTTTTAGG
1755186 GTG
1 GTG
1755189 AATGTGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.12, C:0.08, G:0.37, T:0.43
Consensus pattern (23 bp):
GTGGAGGTTCACTTGTTTTTAGG
Found at i:1756061 original size:42 final size:42
Alignment explanation
Indices: 1756013--1756097 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1756003 TTATTAGAGA
1756013 GCCGCTTTTGATGATTTTGAATTAAAAGTGTATCCCATTAGT
1 GCCGCTTTTGATGATTTTGAATTAAAAGTGTATCCCATTAGT
1756055 GCCGCTTTTGATGATTTTGAATTAAAAGTGTATCCCATTAGT
1 GCCGCTTTTGATGATTTTGAATTAAAAGTGTATCCCATTAGT
1756097 G
1 G
1756098 ACACCTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (42 bp):
GCCGCTTTTGATGATTTTGAATTAAAAGTGTATCCCATTAGT
Found at i:1763476 original size:20 final size:20
Alignment explanation
Indices: 1763453--1763520 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
1763443 AAACAGAAAA
1763453 TTTCATCTCGCTTGAGATAG
1 TTTCATCTCGCTTGAGATAG
* **
1763473 TTTCAT-TTGAAAT-AGA-AG
1 TTTCATCTCG-CTTGAGATAG
*
1763491 ATTTTATCTCGCTTGAGATAG
1 -TTTCATCTCGCTTGAGATAG
1763512 TTTCA-CTCG
1 TTTCATCTCG
1763521 AAACAAAAGA
Statistics
Matches: 35, Mismatches: 8, Indels: 11
0.65 0.15 0.20
Matches are distributed among these distances:
18 2 0.06
19 15 0.43
20 16 0.46
21 2 0.06
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (20 bp):
TTTCATCTCGCTTGAGATAG
Found at i:1763637 original size:194 final size:193
Alignment explanation
Indices: 1763404--1763858 Score: 655
Period size: 194 Copynumber: 2.4 Consensus size: 193
1763394 AAAATTGTTT
* *
1763404 TTAAAAC-AAGATTTATCTCGCTTGAGATTCTTTCACTCGAAACAGAAAATTTCATCTCGCTTGA
1 TTAAAACAAAGATTTATCTCGCTTGAGATACTTTCACTCGAAACAGAAGATTTCATCTCGCTTGA
* *
1763468 GATAGTTTCATTTGAAATAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATT
66 GATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATT
* *
1763533 TTATCTCGCTTGAGATTGTTTCACTCGAAACAGAAGATTTTATCTTGCTAGAGATTGTTTCAC
131 TTATCTCGCTTGAGATTGTTTCACTCGAAAAAGAAGATTTTATCTCGCTAGAGATTGTTTCAC
* *
1763596 TTAAAACAAAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTCATATCGCTTG
1 TTAAAAC-AAAGATTTATCTCGCTTGAGATACTTTCACTCGAAACAGAAGATTTCATCTCGCTTG
* * *
1763661 GGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTTAGATAGTTTCACTCGAAACAGAAGAT
65 AGATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGAT
* * * * * *
1763726 TTTATCTCTCTTGAGATTGTTTCACTCGAAAAAGAATATTTTTTCTCGCTTGATATTGTTTCCC
130 TTTATCTCGCTTGAGATTGTTTCACTCGAAAAAGAAGATTTTATCTCGCTAGAGATTGTTTCAC
** * * *
1763790 TCGAAACAGAAGATTTTATCTCACTTGAGATATTTTCACTCGAAACCA-AAGATTT-ATCTCACT
1 TTAAAACA-AAGA-TTTATCTCGCTTGAGATACTTTCACTCGAAA-CAGAAGATTTCATCTCGCT
1763853 TGAGAT
63 TGAGAT
1763859 TATTTTTCTT
Statistics
Matches: 234, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
192 7 0.03
193 1 0.00
194 188 0.80
195 36 0.15
196 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (193 bp):
TTAAAACAAAGATTTATCTCGCTTGAGATACTTTCACTCGAAACAGAAGATTTCATCTCGCTTGA
GATAGTTTCACTTGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATT
TTATCTCGCTTGAGATTGTTTCACTCGAAAAAGAAGATTTTATCTCGCTAGAGATTGTTTCAC
Found at i:1763864 original size:39 final size:39
Alignment explanation
Indices: 1763411--1763858 Score: 580
Period size: 39 Copynumber: 11.6 Consensus size: 39
1763401 TTTTTAAAAC
**
1763411 AAGA-TTTATCTCGCTTGAGATTCTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * * *
1763449 AAAATTTCATCTCGCTTGAGATAGTTTCATTTGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
1763488 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
1763527 AAGATTTTATCTCGCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * ** *
1763566 AAGATTTTATCTTGCTAGAGATTGTTTCACTTAAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1763605 AAGA-TTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
1763643 AAGATTTCATATCGCTTGGGATAGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
1763682 AAGATTTTATCTCGCTTTAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
1763721 AAGATTTTATCTCTCTTGAGATTGTTTCACTCGAAAAAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * * *
1763760 AATATTTTTTCTCGCTTGATATTGTTTCCCTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
1763799 AAGATTTTATCTCACTTGAGATATTTTCACTCGAAACCA-
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAA-CAG
*
1763838 AAGA-TTTATCTCACTTGAGAT
1 AAGATTTTATCTCGCTTGAGAT
1763859 TATTTTTCTT
Statistics
Matches: 355, Mismatches: 52, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
38 52 0.15
39 301 0.85
40 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
Found at i:1764189 original size:63 final size:63
Alignment explanation
Indices: 1764077--1764197 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
1764067 CCAATAAGAG
* * * * * *
1764077 AGAATAAGTTCATAATTAGAAGAACTTGTTCAATCTTTGTCTGATTCCATCATAGAAGAAGGA
1 AGAAGAAGTTAATAATGAGAAGAACTTGTTCAATCTTTGTCTAAATCCATCACAGAAGAAGGA
*
1764140 AGAAGAAGTTAATAATGAGAAGAATTTGTTCAA-CTTT-TGCTTAAATCCATCACAGAAG
1 AGAAGAAGTTAATAATGAGAAGAACTTGTTCAATCTTTGT-C-TAAATCCATCACAGAAG
1764198 GAGATGGATC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
61 1 0.02
62 5 0.10
63 43 0.88
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (63 bp):
AGAAGAAGTTAATAATGAGAAGAACTTGTTCAATCTTTGTCTAAATCCATCACAGAAGAAGGA
Found at i:1764270 original size:115 final size:116
Alignment explanation
Indices: 1764138--1764400 Score: 334
Period size: 115 Copynumber: 2.2 Consensus size: 116
1764128 ATAGAAGAAG
* * * * * *
1764138 GAAGAAGAAGTTAATAATGAGAAGAATTTGTTCAACTTTTGCTTAAATCCATCACAGAAGGAGAT
1 GAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTGCTCAAATCCATCACAGAAAGAGAT
** *
1764203 GGATCTTCATTTCCAAT-GGAAGAGTTAATAATGAGAAGAACTCA-TCCAA-A
66 GGATCAACATTT-CAATAGAAAG-GTTAATAATGAGAAGAACTCATTCCAACA
* *
1764253 GAAGAAGAAGTTCATAATGAGAAAAACTTATTCAACCTTTGCTCAAATCCATCACAGAAAGAGGT
1 GAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTGCTCAAATCCATCACAGAAAGAGAT
* *
1764318 GGATCAACATTTCAATAGAAAGGTTCATAATGAGAAGAACTCATTCGAACA
66 GGATCAACATTTCAATAGAAAGGTTAATAATGAGAAGAACTCATTCCAACA
*
1764369 GAAGAGTGGAAAGTTCATAATGAGAAGAACTT
1 GAAGA--AG-AAGTTCATAATGAGAAGAACTT
1764401 GGAACTCAAA
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
114 24 0.19
115 75 0.59
116 6 0.05
118 1 0.01
119 21 0.17
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (116 bp):
GAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTGCTCAAATCCATCACAGAAAGAGAT
GGATCAACATTTCAATAGAAAGGTTAATAATGAGAAGAACTCATTCCAACA
Found at i:1765621 original size:29 final size:29
Alignment explanation
Indices: 1765567--1765664 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
1765557 TATTTTTGTA
* *
1765567 TTTAATTTTATTTACATTTAAATTTATGCCT
1 TTTATTTTTATTT--ATTTAATTTTATGCCT
1765598 TTTATTTTTATTTATTTAATTTTA-GTCCT
1 TTTATTTTTATTTATTTAATTTTATG-CCT
* * * **
1765627 TATA-TTTTATTTACTTTATTTTTTTATCT
1 TTTATTTTTATTTA-TTTAATTTTATGCCT
1765656 TTTATTTTT
1 TTTATTTTT
1765665 GTCCCTTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
28 10 0.18
29 29 0.53
30 4 0.07
31 12 0.22
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.68
Consensus pattern (29 bp):
TTTATTTTTATTTATTTAATTTTATGCCT
Found at i:1765920 original size:28 final size:28
Alignment explanation
Indices: 1765885--1765941 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1765875 TTTTTGGTCT
*
1765885 TTGCTTTTTATTGTATATATATTTTTGC
1 TTGCTTTTTATTGCATATATATTTTTGC
1765913 TTGCTTTTTATTGCATATATATTTTTGC
1 TTGCTTTTTATTGCATATATATTTTTGC
1765941 T
1 T
1765942 ATTAAAGTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.18, C:0.09, G:0.11, T:0.63
Consensus pattern (28 bp):
TTGCTTTTTATTGCATATATATTTTTGC
Found at i:1766171 original size:2 final size:2
Alignment explanation
Indices: 1766164--1766189 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1766154 TGAGGCTTTC
1766164 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1766190 GAAAGCCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1766624 original size:8 final size:8
Alignment explanation
Indices: 1766611--1766639 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1766601 CTGCAATGGT
1766611 CGATCAAA
1 CGATCAAA
1766619 CGATCAAA
1 CGATCAAA
1766627 CGATCAAA
1 CGATCAAA
1766635 CGATC
1 CGATC
1766640 GACTGTCACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.45, C:0.28, G:0.14, T:0.14
Consensus pattern (8 bp):
CGATCAAA
Found at i:1767442 original size:18 final size:18
Alignment explanation
Indices: 1767419--1767468 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
1767409 TAAAAAATAT
1767419 AAATATGAATTTCTTTTA
1 AAATATGAATTTCTTTTA
1767437 AAATATGAATTTCTTTTA
1 AAATATGAATTTCTTTTA
1767455 AAATATGAATTTCT
1 AAATATGAATTTCT
1767469 GTTATAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (18 bp):
AAATATGAATTTCTTTTA
Found at i:1767567 original size:16 final size:15
Alignment explanation
Indices: 1767548--1767577 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1767538 TTTTTTATTG
1767548 GTTTTTATTTTAAATT
1 GTTTTTA-TTTAAATT
1767564 GTTTTTATTTAAAT
1 GTTTTTATTTAAAT
1767578 CATGGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (15 bp):
GTTTTTATTTAAATT
Found at i:1768618 original size:21 final size:20
Alignment explanation
Indices: 1768541--1768626 Score: 86
Period size: 21 Copynumber: 4.2 Consensus size: 20
1768531 CTAAAATATA
1768541 TTTAAAATATTTATTTAATT
1 TTTAAAATATTTATTTAATT
1768561 TTTAAAATTATATTATTT-ATT
1 TTTAAAA-TAT-TTATTTAATT
** *
1768582 TGAAATAATA-CTATTTAACTT
1 TTTAA-AATATTTATTTAA-TT
1768603 TTTAAAATATTTATTTAATAT
1 TTTAAAATATTTATTTAAT-T
1768624 TTT
1 TTT
1768627 TATTATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
19 5 0.09
20 13 0.25
21 27 0.51
22 8 0.15
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (20 bp):
TTTAAAATATTTATTTAATT
Found at i:1769902 original size:28 final size:27
Alignment explanation
Indices: 1769834--1769902 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 27
1769824 GTCATTAGAT
* * *
1769834 TTTTAAAAATTATAAAATATATATTAA
1 TTTTAAATATTAAAAAATATATATTGA
*
1769861 TTTTAGACTTTATTAAAAAATATATATTGA
1 TTTTA-A--ATATTAAAAAATATATATTGA
1769891 TTGTTAAATATT
1 TT-TTAAATATT
1769903 GTTAAGGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
27 5 0.15
28 5 0.15
30 20 0.61
31 3 0.09
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
TTTTAAATATTAAAAAATATATATTGA
Found at i:1770118 original size:19 final size:19
Alignment explanation
Indices: 1770080--1770116 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1770070 TTACTTTTAA
*
1770080 AATTTAAAAATATTTATTT
1 AATTAAAAAATATTTATTT
1770099 AATTAAAAAATA-TTATTT
1 AATTAAAAAATATTTATTT
1770117 TATGAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTAAAAAATATTTATTT
Found at i:1771976 original size:32 final size:31
Alignment explanation
Indices: 1771935--1772035 Score: 94
Period size: 32 Copynumber: 3.2 Consensus size: 31
1771925 AGAAACCAAC
* * *
1771935 CTAAGGGAGTATATTGGGGTCTGAGAGCCTA
1 CTAAAGGAGTATATTGGGGCCTAAGAGCCTA
* *
1771966 CTAAATGGAGTATATTAGGGCCTAAGATCCTA
1 CTAAA-GGAGTATATTGGGGCCTAAGAGCCTA
* ** *
1771998 CTCAAGAGAGTACCTTGGGGCCTTAGAGCCTA
1 CTAAAG-GAGTATATTGGGGCCTAAGAGCCTA
*
1772030 CCAAAG
1 CTAAAG
1772036 TAAATGCCTT
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
31 5 0.09
32 50 0.91
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (31 bp):
CTAAAGGAGTATATTGGGGCCTAAGAGCCTA
Found at i:1772046 original size:32 final size:32
Alignment explanation
Indices: 1772010--1772095 Score: 172
Period size: 32 Copynumber: 2.7 Consensus size: 32
1772000 CAAGAGAGTA
1772010 CCTTGGGGCCTTAGAGCCTACCAAAGTAAATG
1 CCTTGGGGCCTTAGAGCCTACCAAAGTAAATG
1772042 CCTTGGGGCCTTAGAGCCTACCAAAGTAAATG
1 CCTTGGGGCCTTAGAGCCTACCAAAGTAAATG
1772074 CCTTGGGGCCTTAGAGCCTACC
1 CCTTGGGGCCTTAGAGCCTACC
1772096 CAAGGTCACC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (32 bp):
CCTTGGGGCCTTAGAGCCTACCAAAGTAAATG
Found at i:1775642 original size:24 final size:24
Alignment explanation
Indices: 1775615--1775686 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
1775605 GGGATCTAGC
*
1775615 GATTTGAATGTTTGGGATTTTAGG
1 GATTTAAATGTTTGGGATTTTAGG
* * *
1775639 GATTTTAATGTTTGGGACTTTAAG
1 GATTTAAATGTTTGGGATTTTAGG
* *
1775663 GATTTAAAT-TTAGGAATTTTAGG
1 GATTTAAATGTTTGGGATTTTAGG
1775686 G
1 G
1775687 CTTGGGAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 11 0.28
24 29 0.73
ACGTcount: A:0.26, C:0.01, G:0.28, T:0.44
Consensus pattern (24 bp):
GATTTAAATGTTTGGGATTTTAGG
Found at i:1779074 original size:31 final size:31
Alignment explanation
Indices: 1779010--1779085 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
1779000 ATTATAATCA
*
1779010 TTTTATGTAATGTTTTTAATATTTCTTTATG
1 TTTTATGTAATGTTTTTAATATTTCTCTATG
*
1779041 TTTTATGTAATGTTTTTAATATTTGTCCT-TG
1 TTTTATGTAATGTTTTTAATATTTCT-CTATG
*
1779072 TTTAATGTAATGTT
1 TTTTATGTAATGTT
1779086 AACTATTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (31 bp):
TTTTATGTAATGTTTTTAATATTTCTCTATG
Found at i:1779117 original size:13 final size:12
Alignment explanation
Indices: 1779091--1779124 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
1779081 ATGTTAACTA
*
1779091 TTTTTAATTTTG
1 TTTTTAATTATG
1779103 TTTTTATATTATG
1 TTTTTA-ATTATG
1779116 TTTTTAATT
1 TTTTTAATT
1779125 CCTGAAGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTTTAATTATG
Found at i:1779371 original size:9 final size:9
Alignment explanation
Indices: 1779347--1779391 Score: 58
Period size: 9 Copynumber: 5.0 Consensus size: 9
1779337 TTAAGTTTGC
1779347 AAGCATTACA
1 AAGCATTA-A
1779357 AA-CATTAA
1 AAGCATTAA
1779365 AAGCATTAA
1 AAGCATTAA
1779374 AAGCATTACA
1 AAGCATTA-A
1779384 AA-CATTAA
1 AAGCATTAA
1779392 CTCCAACACT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 4 0.12
9 24 0.73
10 5 0.15
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.22
Consensus pattern (9 bp):
AAGCATTAA
Found at i:1779998 original size:6 final size:6
Alignment explanation
Indices: 1779987--1780023 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
1779977 ATAGTTGAGC
* *
1779987 TAAAAT TAAAAT TAAAAT TAAAAT TGACAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT T
1780024 CGAACTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:1781107 original size:159 final size:160
Alignment explanation
Indices: 1780812--1781114 Score: 378
Period size: 159 Copynumber: 1.9 Consensus size: 160
1780802 AAAAACTGAC
* * * * **
1780812 AAAAGGGAAGATGCATCCCATAAGAAGCATTTTCACCTTTGTTTCGAGAATCTCTGTTATGTCAT
1 AAAAGGGAAAATGCATCCCACAAGAAGCACTTTCACCTTTGTTTCGAGAATCTATGCCATGTCAT
* * * * *
1780877 AATATCTCATCCCATTAGACAGATGAAGGGTTGATGTAAATAGTTCCTCAATTGGTAACGTCATT
66 AATATCTCATCCCATTAAACAGATGAAGGGTTGATGTAAATAGTTCCCCAACTGGTAACATCATA
*
1780942 TTTGCATATAATTGCCATAAAAATCTGAAA
131 TCTGCATATAATTGCCATAAAAATCTGAAA
* * * *
1780972 AAAAGGGAAAATGCGTCCTACAAGAAGCGCTTTCACC-TT-TTTCATAGAATCTATGCCATGTCA
1 AAAAGGGAAAATGCATCCCACAAGAAGCACTTTCACCTTTGTTTC-GAGAATCTATGCCATGTCA
* * * * *
1781035 TACTGTCTCATCCCATTAAACAGATG-AGGATTTGATGTGAATAGTTCCCCGACTGGTAACATCA
65 TAATATCTCATCCCATTAAACAGATGAAGG-GTTGATGTAAATAGTTCCCCAACTGGTAACATCA
1781099 TATCTGCATATAATTG
129 TATCTGCATATAATTG
1781115 ACAGAAATAT
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
158 7 0.06
159 82 0.68
160 31 0.26
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (160 bp):
AAAAGGGAAAATGCATCCCACAAGAAGCACTTTCACCTTTGTTTCGAGAATCTATGCCATGTCAT
AATATCTCATCCCATTAAACAGATGAAGGGTTGATGTAAATAGTTCCCCAACTGGTAACATCATA
TCTGCATATAATTGCCATAAAAATCTGAAA
Found at i:1781458 original size:24 final size:24
Alignment explanation
Indices: 1781425--1781653 Score: 273
Period size: 24 Copynumber: 9.5 Consensus size: 24
1781415 TGGTATTTAA
* * **
1781425 AAAACCCTAAATCACTTTAACCAAA
1 AAAATCCTAAACCACTTTAACC-TT
1781450 AAAAT-CTAAACCACTTTAACCTT
1 AAAATCCTAAACCACTTTAACCTT
1781473 AAAATCCTAAACCACTTTAACCTT
1 AAAATCCTAAACCACTTTAACCTT
*
1781497 AAAATCCTAGACCACTTTAACCTT
1 AAAATCCTAAACCACTTTAACCTT
1781521 AAAATCCTAAACCACTTTAACCTT
1 AAAATCCTAAACCACTTTAACCTT
*
1781545 AAAATCCTAGACCACTTTAACCTT
1 AAAATCCTAAACCACTTTAACCTT
*
1781569 AAAATCCTAAACCACTTTAACCTA
1 AAAATCCTAAACCACTTTAACCTT
* ** * *
1781593 AAAACCCTAAATTATTTTAACCTA
1 AAAATCCTAAACCACTTTAACCTT
* * * *
1781617 AAAAACCTAAAACA-TTATAACATA
1 AAAATCCTAAACCACTT-TAACCTT
*
1781641 AAAACCCTAAACC
1 AAAATCCTAAACC
1781654 CTAAACCTAT
Statistics
Matches: 183, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
23 7 0.04
24 172 0.94
25 4 0.02
ACGTcount: A:0.46, C:0.27, G:0.01, T:0.26
Consensus pattern (24 bp):
AAAATCCTAAACCACTTTAACCTT
Found at i:1781876 original size:25 final size:25
Alignment explanation
Indices: 1781841--1781903 Score: 99
Period size: 25 Copynumber: 2.5 Consensus size: 25
1781831 ATTTTAATAA
1781841 AAAAAAACCTAAACCACTTCAACCT
1 AAAAAAACCTAAACCACTTCAACCT
* *
1781866 AAAAAATCCTAAACTACTTCAACCT
1 AAAAAAACCTAAACCACTTCAACCT
*
1781891 AAAAAAACATAAA
1 AAAAAAACCTAAA
1781904 AACCCTAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.57, C:0.25, G:0.00, T:0.17
Consensus pattern (25 bp):
AAAAAAACCTAAACCACTTCAACCT
Found at i:1781945 original size:24 final size:24
Alignment explanation
Indices: 1781900--1781954 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
1781890 TAAAAAAACA
* *
1781900 TAAAAACCCTAAACTACTTTAATT
1 TAAAAACCCTAAACCACATTAATT
* **
1781924 TAAAACCCCTAAACCACATTAACC
1 TAAAAACCCTAAACCACATTAATT
1781948 TAAAAAC
1 TAAAAAC
1781955 ATAAAACCCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAAAACCCTAAACCACATTAATT
Found at i:1782808 original size:129 final size:132
Alignment explanation
Indices: 1782668--1782934 Score: 504
Period size: 129 Copynumber: 2.0 Consensus size: 132
1782658 TAAGATATTA
1782668 ATTTCTCTGATAAGTAAAAGTTTTAAAGGTAATAAAAACAATGATAATATATACTTAGTATATAC
1 ATTT-TCTGATAAGTAAAAGTTTTAAAGGTAATAAAAACAATGATAATATATACTTAGTATATAC
1782733 ACACACACAAAAAAATTCTTGGTTTTATTTTAATATTATCTTTAATTTTT-AATCAT-GA-TTTT
65 ACACACACAAAAAAATTCTTGGTTTTATTTTAATATTATCTTTAATTTTTAAATCATGGATTTTT
1782795 TTT
130 TTT
1782798 ATTTTCTGATAAGTAAAAGTTTTAAAGGTAATAAAAACAATGATAATATATACTTAGTATATACA
1 ATTTTCTGATAAGTAAAAGTTTTAAAGGTAATAAAAACAATGATAATATATACTTAGTATATACA
1782863 CACACACAAAAAAATTCTTGGTTTTATTTTAATATTATCTTTAATTTTTAAATCATGGATTTTTT
66 CACACACAAAAAAATTCTTGGTTTTATTTTAATATTATCTTTAATTTTTAAATCATGGATTTTTT
1782928 TT
131 TT
1782930 ATTTT
1 ATTTT
1782935 TTATATAATA
Statistics
Matches: 134, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
129 110 0.82
130 10 0.07
131 2 0.01
132 12 0.09
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.44
Consensus pattern (132 bp):
ATTTTCTGATAAGTAAAAGTTTTAAAGGTAATAAAAACAATGATAATATATACTTAGTATATACA
CACACACAAAAAAATTCTTGGTTTTATTTTAATATTATCTTTAATTTTTAAATCATGGATTTTTT
TT
Done.