Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008259.1 Hibiscus syriacus cultivar Beakdansim tig00110912_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: 2373650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:247397 original size:21 final size:22
Alignment explanation
Indices: 247367--247407 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
247357 ACAAGATTCG
*
247367 TAATTGTCAA-ATAAATAAACC
1 TAATTCTCAATATAAATAAACC
*
247388 TAATTCTCAATTTAAATAAA
1 TAATTCTCAATATAAATAAA
247408 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATTCTCAATATAAATAAACC
Found at i:250710 original size:19 final size:20
Alignment explanation
Indices: 250686--250727 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
250676 TTACCAAAAT
* *
250686 ATGTAT-TTTTATCCCATGA
1 ATGTATATTTTACCCCAAGA
250705 ATGTATATTTTACCCCAAGA
1 ATGTATATTTTACCCCAAGA
250725 ATG
1 ATG
250728 AAGTTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATATTTTACCCCAAGA
Found at i:253576 original size:45 final size:45
Alignment explanation
Indices: 253526--253895 Score: 560
Period size: 45 Copynumber: 8.2 Consensus size: 45
253516 TATTCATTAT
*
253526 TTTCATTTATGGAATCCTTTCATGCCTAGAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
* * *
253571 TTTCATTTATGGCATCATTTCATGCCTATAATGCACCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
* * *
253616 TTTCATTTATGGCATCCATTCATGCCTAGAATGCACCGTCATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
* * *
253661 TTTCATTTATGACATCCTTTCATGCCAATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
* *
253706 TTTCATTTATGGCATCCTTTCATGACTAGAATGTACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
* *
253751 TTTAATTTATAGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
*
253796 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
* * * * *
253841 TTTCATTTATGGCATCATTTCATGCATATAATGTACCGTTATGTA
1 TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
253886 TTTCATTTAT
1 TTTCATTTAT
253896 TCATTCATTT
Statistics
Matches: 293, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 293 1.00
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTAGAATGCACCGTTATGCA
Found at i:254402 original size:20 final size:20
Alignment explanation
Indices: 254377--254417 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
254367 TTCTGTAATC
254377 CATGGTATTGATACCTTTCT
1 CATGGTATTGATACCTTTCT
254397 CATGGTATTGATACCTTTCT
1 CATGGTATTGATACCTTTCT
254417 C
1 C
254418 TTAGTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (20 bp):
CATGGTATTGATACCTTTCT
Found at i:254424 original size:20 final size:20
Alignment explanation
Indices: 254381--254430 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
254371 GTAATCCATG
*
254381 GTATTGATACCTTTCTCATG
1 GTATTGATACCTTTCTCATA
*
254401 GTATTGATACCTTTCTCTTA
1 GTATTGATACCTTTCTCATA
*
254421 GTATCGATAC
1 GTATTGATAC
254431 TTCTATACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.44
Consensus pattern (20 bp):
GTATTGATACCTTTCTCATA
Found at i:254508 original size:115 final size:115
Alignment explanation
Indices: 254306--254527 Score: 365
Period size: 115 Copynumber: 1.9 Consensus size: 115
254296 ACCCCCCATG
* * *
254306 GTATCGATACTTCTATACTATGGTACCGATACTCCCTTTCAGTATCGATATCATTTCTACATTCT
1 GTATCGATACTTCTATACTATGGTACAGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
* * *
254371 GTAATCCATGGTATTGATACCTTTCTCAT-GGTATTGATACCTTTCTCTTA
66 GGAATCCATGGTATCGATACCTTTCTC-TCGGTATCGATACCTTTCTCTTA
254421 GTATCGATACTTCTATACTATGGTACAGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
1 GTATCGATACTTCTATACTATGGTACAGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
*
254486 GGAATCCCTGGTATCGATACCTTTCTCTCGGTATCGATACCT
66 GGAATCCATGGTATCGATACCTTTCTCTCGGTATCGATACCT
254528 ACAGCAATAT
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 1 0.01
115 98 0.99
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (115 bp):
GTATCGATACTTCTATACTATGGTACAGATACTCCATTTCAGTATCGATACCATTTCTACATTCT
GGAATCCATGGTATCGATACCTTTCTCTCGGTATCGATACCTTTCTCTTA
Found at i:260287 original size:43 final size:43
Alignment explanation
Indices: 260178--260406 Score: 257
Period size: 43 Copynumber: 5.2 Consensus size: 43
260168 TATTCCTTAC
* * * * *
260178 TTTCATTTATGGCATACTTTCATTCCTAGAATGTATTGTTATGCA
1 TTTCATTTATGGCATCCTTTCA-TGCTATAATGCA-CGTTATGCA
260223 TTTCATTTATGGCATCC-TTCATGCTATAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCTATAATGCA-CGTTATGCA
* *
260266 -TTCATTTATGGCATCCTTTCATGCCTATAATGTACGTTATGAA
1 TTTCATTTATGGCATCCTTTCATG-CTATAATGCACGTTATGCA
* * * * *
260309 TTTCATTTATGACATCCTTTTATACCTATAATGCA-TTTATGAA
1 TTTCATTTATGGCATCCTTTCAT-GCTATAATGCACGTTATGCA
*
260352 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTACGCA
1 TTTCATTTATGGCATCCTTTCATG-CTATAATGCA-CGTTATGCA
260397 TTTCATTTAT
1 TTTCATTTAT
260407 TCATTTATTT
Statistics
Matches: 158, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
42 16 0.10
43 69 0.44
44 42 0.27
45 31 0.20
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (43 bp):
TTTCATTTATGGCATCCTTTCATGCTATAATGCACGTTATGCA
Found at i:260357 original size:87 final size:87
Alignment explanation
Indices: 260178--260406 Score: 293
Period size: 87 Copynumber: 2.6 Consensus size: 87
260168 TATTCCTTAC
* * * ** *
260178 TTTCATTTATGGCATACTTTCATTCCTAGAATGTATTGTTATGCATTTCATTTATGGCATCCTTC
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGTACCGTTATGCATTTCATTTATGACATCCTTC
* *
260243 ATGCTATAATGCACCGTTATGCA
66 ATCCTATAATGCA-CGTTATGAA
*
260266 -TTCATTTATGGCATCCTTTCATGCCTATAATGTA-CGTTATGAATTTCATTTATGACATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGTACCGTTATGCATTTCATTTATGACATCC-TT
* *
260329 TATACCTATAATGCA-TTTATGAA
65 CAT-CCTATAATGCACGTTATGAA
* *
260352 TTTCATTTATGGCATCCTTTCATGCCTATAATGCACCGTTACGCATTTCATTTAT
1 TTTCATTTATGGCATCCTTTCATGCCTATAATGTACCGTTATGCATTTCATTTAT
260407 TCATTTATTT
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
86 29 0.23
87 68 0.55
88 27 0.22
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.44
Consensus pattern (87 bp):
TTTCATTTATGGCATCCTTTCATGCCTATAATGTACCGTTATGCATTTCATTTATGACATCCTTC
ATCCTATAATGCACGTTATGAA
Found at i:261005 original size:90 final size:91
Alignment explanation
Indices: 260831--261006 Score: 203
Period size: 90 Copynumber: 1.9 Consensus size: 91
260821 TCGACTTATA
* * * * *
260831 TATGGTACTGATACTCCCTTTCAGTATCGATACCATTTCTATATTCTGTAATCCATGGGATCAAT
1 TATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAATCCACGAGATCAAT
* ** *
260896 ACCTTTCTTAGTATCGATACTTCTAC
66 ACCTTACACAATATCGATACTTCTAC
* * * *
260922 TATGGTACCGATTCTCCC-TTCAGTATCGATACCATTTCTACATTCTGGAATCCCCGATATCGAT
1 TATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAATCCACGAGATCAAT
*
260986 ACC-TACAACAATATTGATACT
66 ACCTTAC-ACAATATCGATACT
261007 AATTGCATCA
Statistics
Matches: 70, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
89 2 0.03
90 52 0.74
91 16 0.23
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (91 bp):
TATGGTACCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTGGAATCCACGAGATCAAT
ACCTTACACAATATCGATACTTCTAC
Found at i:270111 original size:20 final size:20
Alignment explanation
Indices: 270068--270110 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
270058 ACACCTTGCA
**
270068 TTTTGCATATGCATTTTTAT
1 TTTTGCATATGCATTTAAAT
270088 TTTTGCA-ATGCATTTAAAT
1 TTTTGCATATGCATTTAAAT
270107 TTTT
1 TTTT
270111 TTGCACCGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (20 bp):
TTTTGCATATGCATTTAAAT
Found at i:277941 original size:37 final size:36
Alignment explanation
Indices: 277854--277941 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 36
277844 GTTTGACCTT
* *
277854 TGAAGCAAAGCAATATTAATCATTCACGAAAGAGTAG
1 TGAAGC-AATCAATATTAATCATTCACGAAAGAATAG
*
277891 TGAATCAAGTCAATATTAAGTC-TTCACGAAAGAATAG
1 TGAAGCAA-TCAATATTAA-TCATTCACGAAAGAATAG
277928 TGAAGCAGATCAAT
1 TGAAGCA-ATCAAT
277942 TGTTCAAGTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
36 2 0.05
37 39 0.89
38 3 0.07
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.24
Consensus pattern (36 bp):
TGAAGCAATCAATATTAATCATTCACGAAAGAATAG
Found at i:278054 original size:55 final size:55
Alignment explanation
Indices: 277940--278995 Score: 875
Period size: 55 Copynumber: 19.2 Consensus size: 55
277930 AAGCAGATCA
* * ** ** * * * ** *
277940 ATTGTTCAAGTCTTATACTCCTTGAAAGAAGAATGAATGGACTCGTTTGCCAAAA
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * ** * *
277995 ATTGTTCAATTCCTATACTCCCTGAAAAAATAGGGAACAAACCCATTTACTAAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * *
278050 ATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGAGGACAC-TTTTGCTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTT-CTGAAG
* * * * * *
278105 ATTGTTCGAGTCCTATACTCCTTGAAAGAAGACGGAGTGGACCTATTTTTTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * * *
278160 ATTGTTCGAGTCTTATACTCCCTAAAAGAAGAGGGAGCGGACACGTTTACTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * *
278215 AGTGTTCGAGTCCTATACTCCCTGAAAGAAGAGGGAGCAGACCCATTTCCCGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * *
278270 ATTGTTCAAGTCCTATACTCCTTAAAAGAA-ATAGGAGCGGA-CAAGTTTTTTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGA-GGGAGCGGACCCA-TTTTCTGAAG
* * * * * * *
278325 ATTGTTTAAGTCCTATACTCCTTGAAAGAAGATGGATCGGACCCGTTTACCGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * *
278380 ATTGTTCGAGTCCTATACT-CTTCGAAAGAAGAGGGAGCAGACCCGTTTCCTGAAG
1 ATTGTTCAAGTCCTATACTCCCT-GAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* ** ** *
278435 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAAGAGCATACACATTTTCTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * ** ** ** *
278490 ATTGTTTAAGTCCTATAGTCCTTGAATGAAGATAGAGCATACCTGTTTGCTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * ***
278545 ATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGTACATGTTTTCTGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * * * *
278600 ATTGTTCGAGTCCTATACTCCTTGAAAGAAGAGGGAGAGGACACGTTTGCTGAAA
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
** * * ** * *
278655 ATTGTTCAAGTATTATACTCCTTGAAAGAAGATGGAGCGGACCTGTTTGCCGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * * * **
278710 ATTATTCAAGTCCTATACTCTCTGAAAGAAGAGGGAGCGGGCCCATTTCCCAAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* ** * * * * ** * *
278765 ATCGTTCAAGTTTTATACTCCTTGAAATAAAAAGGAGCATACACATTTTCTTAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
* * *
278820 ATTGTTCGAGTCCTATACTCCCTGAAAGAATAGGGAGCGGACACATTTT-TCGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCT-GAAG
* * * *
278875 ATTGTTCAAGTTCTATACTCCCTGAAAAAAGAGGGAGCAGACCCATTTTCCGAAG
1 ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
** * *
278930 ATTGTTTGAGTCCTATACTCCC-GAAAATAAGAGGGAGCGGACCCGTTTTCCT-AAG
1 ATTGTTCAAGTCCTATACTCCCTG-AAAGAAGAGGGAGCGGACCCATTTT-CTGAAG
*
278985 ATTTTTCAAGT
1 ATTGTTCAAGT
278996 ATCACTTATT
Statistics
Matches: 816, Mismatches: 173, Indels: 24
0.81 0.17 0.02
Matches are distributed among these distances:
54 11 0.01
55 795 0.97
56 10 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (55 bp):
ATTGTTCAAGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACCCATTTTCTGAAG
Found at i:278987 original size:165 final size:165
Alignment explanation
Indices: 277940--278995 Score: 995
Period size: 165 Copynumber: 6.4 Consensus size: 165
277930 AAGCAGATCA
* * ** * * * ** * *
277940 ATTGTTCAAGTCTTATACTCCTTGAAAGAAGAATGAATGGACTCGTTTGCCAAAAATTGTTCAAT
1 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTCTGAAGATTGTTCAAG
* * * ** * * *
278005 TCCTATACTCCCTGAAAAAATAGGGAACAAACCCATTTACTAAAGATTGTTCGAGTCCTATACTC
66 TCCTATACTCCCTGAAAGAAGAGGGAGCGGACACTTTTACTGAAGATTGTTCGAGTCCTATACTC
* * *
278070 CCTGAAAGAATAGGGAG-AGGACAC-TTTTGCTGAAG
131 CCTGAAAGAAGAGGGAGCA-GACCCATTTT-CCGAAG
* * * * *
278105 ATTGTTCGAGTCCTATACTCCTTGAAAGAAGACGGAGTGGAC-CTATTTTTTGAAGATTGTTCGA
1 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACAC-ATTTTCTGAAGATTGTTCAA
* * * *
278169 GTCTTATACTCCCTAAAAGAAGAGGGAGCGGACACGTTTACTGAAGAGTGTTCGAGTCCTATACT
65 GTCCTATACTCCCTGAAAGAAGAGGGAGCGGACACTTTTACTGAAGATTGTTCGAGTCCTATACT
*
278234 CCCTGAAAGAAGAGGGAGCAGACCCATTTCCCGAAG
130 CCCTGAAAGAAGAGGGAGCAGACCCATTTTCCGAAG
* * *
278270 ATTGTTCAAGTCCTATACTCCTTAAAAGAA-ATAGGAGCGGACA-AGTTTTTTGAAGATTGTTTA
1 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGA-AGGAGCGGACACA-TTTTCTGAAGATTGTTCA
* * * * * *
278333 AGTCCTATACTCCTTGAAAGAAGATGGATCGGACCCGTTTACCGAAGATTGTTCGAGTCCTATAC
64 AGTCCTATACTCCCTGAAAGAAGAGGGAGCGGACACTTTTACTGAAGATTGTTCGAGTCCTATAC
* *
278398 T-CTTCGAAAGAAGAGGGAGCAGACCC-GTTTCCTGAAG
129 TCCCT-GAAAGAAGAGGGAGCAGACCCATTTTCC-GAAG
* ** *
278435 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAAGAGCATACACATTTTCTGAAGATTGTTTAAG
1 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTCTGAAGATTGTTCAAG
* * * ** ** *
278500 TCCTATAGTCCTTGAATGAAGATAGAGCATAC-CTGTTTGCTGAAGATTGTTCGAGTCCTATACT
66 TCCTATACTCCCTGAAAGAAGAGGGAGCGGACACT-TTTACTGAAGATTGTTCGAGTCCTATACT
* *** *
278564 CCCTGAAAGAATAGGGAGC-GTACATGTTTTCTGAAG
130 CCCTGAAAGAAGAGGGAGCAG-ACCCATTTTCCGAAG
* * * * * *
278600 ATTGTTCGAGTCCTATACTCCTTGAAAGAAGAGGGAGAGGACACGTTTGCTGAAAATTGTTCAAG
1 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTCTGAAGATTGTTCAAG
** * * * * * *
278665 TATTATACTCCTTGAAAGAAGATGGAGCGGAC-CTGTTTGCCGAAGATTATTCAAGTCCTATACT
66 TCCTATACTCCCTGAAAGAAGAGGGAGCGGACACT-TTTACTGAAGATTGTTCGAGTCCTATACT
* * * * *
278729 CTCTGAAAGAAGAGGGAGCGGGCCCATTTCCCAAAG
130 CCCTGAAAGAAGAGGGAGCAGACCCATTTTCCGAAG
* ** * * ** * *
278765 ATCGTTCAAGTTTTATACTCCTTGAAATAAAAAGGAGCATACACATTTTCTTAAGATTGTTCGAG
1 ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTCTGAAGATTGTTCAAG
* * * *
278830 TCCTATACTCCCTGAAAGAATAGGGAGCGGACACATTTTTC-GAAGATTGTTCAAGTTCTATACT
66 TCCTATACTCCCTGAAAGAAGAGGGAGCGGACAC-TTTTACTGAAGATTGTTCGAGTCCTATACT
*
278894 CCCTGAAAAAAGAGGGAGCAGACCCATTTTCCGAAG
130 CCCTGAAAGAAGAGGGAGCAGACCCATTTTCCGAAG
** * * * * * *
278930 ATTGTTTGAGTCCTATACTCC-CGAAAATAAGAGGGAGCGGACCCGTTTTCCT-AAGATTTTTCA
1 ATTGTTCAAGTCCTATACTCCTTG-AAAGAAGAAGGAGCGGACACATTTT-CTGAAGATTGTTCA
278993 AGT
64 AGT
278996 ATCACTTATT
Statistics
Matches: 735, Mismatches: 137, Indels: 38
0.81 0.15 0.04
Matches are distributed among these distances:
164 12 0.02
165 702 0.96
166 20 0.03
167 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (165 bp):
ATTGTTCAAGTCCTATACTCCTTGAAAGAAGAAGGAGCGGACACATTTTCTGAAGATTGTTCAAG
TCCTATACTCCCTGAAAGAAGAGGGAGCGGACACTTTTACTGAAGATTGTTCGAGTCCTATACTC
CCTGAAAGAAGAGGGAGCAGACCCATTTTCCGAAG
Found at i:285538 original size:43 final size:42
Alignment explanation
Indices: 285485--285615 Score: 113
Period size: 32 Copynumber: 3.3 Consensus size: 42
285475 AGGATATTAT
*
285485 TTTTATATTTTATCTTTGTTATAGGTATTTTAGTTTAAATAG
1 TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
**
285527 TTTTAGTATTTTAAT-TAAGTTTTAGG-A---TA--TT--AT--
1 TTTTA-TATTTT-ATCTTTGTTTTAGGTATTTTAGTTTAAATAG
*
285560 TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTATAAATAG
1 TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
285602 TTTTAAGTATTTTA
1 TTTT-A-TATTTTA
285616 ATTAGGATTC
Statistics
Matches: 68, Mismatches: 6, Indels: 28
0.67 0.06 0.27
Matches are distributed among these distances:
31 2 0.03
32 15 0.22
33 6 0.09
35 2 0.03
36 2 0.03
37 2 0.03
38 1 0.01
39 2 0.03
40 2 0.03
42 10 0.15
43 15 0.22
44 9 0.13
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (42 bp):
TTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAG
Found at i:285561 original size:75 final size:75
Alignment explanation
Indices: 285414--285619 Score: 376
Period size: 75 Copynumber: 2.7 Consensus size: 75
285404 TTAAATATTT
285414 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAAGTTTTAGGA
285479 TATTATTTTTA
65 TATTATTTTTA
*
285490 TATTTTATCTTTGTTATAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGAT
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGAT
285555 ATTATTTTTA
66 ATTATTTTTA
*
285565 TATTTTATCTTTGTTTTAGGTATTTTAGTATAAATAGTTTTAAGTATTTTAATTA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTA
285620 GGATTCAAGA
Statistics
Matches: 126, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
75 78 0.62
76 48 0.38
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.59
Consensus pattern (75 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAAGTTTTAGGAT
ATTATTTTTA
Found at i:286241 original size:4 final size:4
Alignment explanation
Indices: 286232--286274 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
286222 TCGCTTTCAA
* * *
286232 TTAT TTAT TTAA TTCT TTCTT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TT
286275 TAAAATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
4 30 0.91
5 3 0.09
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:286275 original size:21 final size:21
Alignment explanation
Indices: 286232--286276 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
286222 TCGCTTTCAA
* *
286232 TTATTTATTTAATTCTTTCTT
1 TTATTTATTTAATTATTTATT
*
286253 TTATTTATTTATTTATTTATT
1 TTATTTATTTAATTATTTATT
286274 TTA
1 TTA
286277 AAATAATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATTTATTTAATTATTTATT
Found at i:291755 original size:6 final size:6
Alignment explanation
Indices: 291744--291782 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
291734 TTCGTTCTAT
*
291744 TTTTTA TTTTTA TTTTTA -TTTCA -TTTTA TTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
291783 TATTCGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTA
Found at i:291759 original size:5 final size:5
Alignment explanation
Indices: 291745--291817 Score: 58
Period size: 5 Copynumber: 13.8 Consensus size: 5
291735 TCGTTCTATT
* *
291745 TTTTA TTTTTA TTTTTA TTTCA TTTTA TTTTTA TTTT- TTATTCG TTTTA
1 TTTTA -TTTTA -TTTTA TTTTA TTTTA -TTTTA TTTTA TT-TT-A TTTTA
**
291794 TTTCG TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTT
291818 TTAGCAAACT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
4 2 0.04
5 34 0.61
6 18 0.32
7 2 0.04
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:291772 original size:16 final size:16
Alignment explanation
Indices: 291751--291817 Score: 66
Period size: 16 Copynumber: 4.2 Consensus size: 16
291741 TATTTTTTAT
291751 TTTTATTTTTATTTCA
1 TTTTATTTTTATTTCA
*
291767 TTTTATTTTTATTT-T
1 TTTTATTTTTATTTCA
** *
291782 TTATTCGTTTTATTTCG
1 TT-TTATTTTTATTTCA
*
291799 TTTTA-TTTTATTTTA
1 TTTTATTTTTATTTCA
291814 TTTT
1 TTTT
291818 TTAGCAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
15 14 0.33
16 26 0.62
17 2 0.05
ACGTcount: A:0.15, C:0.04, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTATTTTTATTTCA
Found at i:293894 original size:76 final size:76
Alignment explanation
Indices: 293721--293951 Score: 317
Period size: 76 Copynumber: 3.0 Consensus size: 76
293711 AATTAAACTC
* * *
293721 AAGTTTTAGGATAATATTTTAAATATTATATTTATCTTTTTTTTAGGTATTTTAGTTT-AATAGG
1 AAGTTTTAGGATATTATTTT---TA-TAT-TTTATCTTTGTTTTAGGTATTTTAGTTTAAATTGG
293785 --TTAGTATTTTAATT
61 TTTTAGTATTTTAATT
* *
293799 CAGTGTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATTGGTTTTA
1 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATTGGTTTTA
293864 GTATTTTAATT
66 GTATTTTAATT
*
293875 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAA-TAGTTTTA
1 AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATTGGTTTT-
*
293939 AGTGTTTTAATT
65 AGTATTTTAATT
293951 A
1 A
293952 GGATTTAAGA
Statistics
Matches: 140, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
73 27 0.19
74 8 0.06
75 8 0.06
76 80 0.57
78 17 0.12
ACGTcount: A:0.27, C:0.02, G:0.13, T:0.58
Consensus pattern (76 bp):
AAGTTTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATTGGTTTTA
GTATTTTAATT
Found at i:294597 original size:17 final size:18
Alignment explanation
Indices: 294575--294616 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
294565 CTTTCAATTA
294575 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATCT
*
294592 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
294610 TTTATTT
1 TTTATTT
294617 TAAAAACAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:294688 original size:19 final size:20
Alignment explanation
Indices: 294642--294709 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 20
294632 AAAACCCCCT
*
294642 TTTTATTACTAT-TATTTATTA
1 TTTTATTATTATCTA-TT-TTA
*
294663 TTTTATTATTTTCCT-TTTTA
1 TTTTATTATTAT-CTATTTTA
294683 -TTTATTATTATCTATTTTA
1 TTTTATTATTATCTATTTTA
294702 TTTTATTA
1 TTTTATTA
294710 AATCTTTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.05
19 15 0.38
20 10 0.25
21 12 0.30
23 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTATTATCTATTTTA
Found at i:295692 original size:10 final size:10
Alignment explanation
Indices: 295677--295701 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
295667 ACAGGAATGA
295677 AAAAAAAAAC
1 AAAAAAAAAC
295687 AAAAAAAAAC
1 AAAAAAAAAC
295697 AAAAA
1 AAAAA
295702 CAATATGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:299704 original size:22 final size:20
Alignment explanation
Indices: 299670--299709 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
299660 CAAGCATTGA
299670 ATTTTTTAAATAAATAAAGT
1 ATTTTTTAAATAAATAAAGT
299690 ATTTTTCTCAAATAAATAAA
1 ATTTTT-T-AAATAAATAAA
299710 CTAAGAACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTTTTTAAATAAATAAAGT
Found at i:307383 original size:12 final size:12
Alignment explanation
Indices: 307362--307395 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
307352 ATTCATATCA
307362 TATCATTATTCT
1 TATCATTATTCT
*
307374 TATTATTATTCT
1 TATCATTATTCT
307386 TATCATTATT
1 TATCATTATT
307396 AACATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
TATCATTATTCT
Found at i:308091 original size:28 final size:29
Alignment explanation
Indices: 308059--308113 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
308049 ATGTATTCTT
*
308059 TTTCATATAATCACGT-AGTCATATAATA
1 TTTCATATAATCACGTAAGTCACATAATA
* *
308087 TTTCATATGATCTCGTAAGTCACATAA
1 TTTCATATAATCACGTAAGTCACATAA
308114 CACAGATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTCATATAATCACGTAAGTCACATAATA
Found at i:312324 original size:128 final size:128
Alignment explanation
Indices: 312096--312327 Score: 285
Period size: 128 Copynumber: 1.8 Consensus size: 128
312086 TTTCAAATTT
* **
312096 GATCTTCTTGAAGAGTAGTGAAAAAAATCAACCTCTATTCAACTTCCCATGAAGAGTAGTAGAGT
1 GATCTTCTTGAAGAATAGTGAAAAAAATCAACCTCTATAAAACTTCCCATGAAGAGTAGTAGAGT
* * * *
312161 AAATCAAAATTTCTAGATTTGGTCTTTCAAAAGAGTAGTTAAGTAGTTCATTTTCCCATATTC
66 AAATCAAAATTTCTAAATATGATCTTCCAAAAGAGTAGTTAAGTAGTTCATTTTCCCATATTC
* *
312224 GATCTTCTTGAAGAATAGT-AAAGCAAAA-CAACCTC-ACTAAAACTTTCCATGAAGAGTAGTTG
1 GATCTTCTTGAAGAATAGTGAAA--AAAATCAACCTCTA-TAAAACTTCCCATGAAGAGTAGTAG
* *
312286 AGTGAAT-AAGAATTT-TCAAATATGATCTTCCTAAAGAGTAGT
63 AGTAAATCAA-AATTTCT-AAATATGATCTTCCAAAAGAGTAGT
312328 GAAGCAAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
127 7 0.08
128 77 0.88
129 4 0.05
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (128 bp):
GATCTTCTTGAAGAATAGTGAAAAAAATCAACCTCTATAAAACTTCCCATGAAGAGTAGTAGAGT
AAATCAAAATTTCTAAATATGATCTTCCAAAAGAGTAGTTAAGTAGTTCATTTTCCCATATTC
Found at i:312574 original size:14 final size:16
Alignment explanation
Indices: 312536--312576 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
312526 CATTGCATAT
312536 TATATAGGTTGTATATAA
1 TATATA-GTT-TATATAA
312554 TATATAGTTTATA-AA
1 TATATAGTTTATATAA
312569 TA-ATAGTT
1 TATATAGTT
312577 GCATGTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 4 0.17
16 4 0.17
17 3 0.13
18 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (16 bp):
TATATAGTTTATATAA
Found at i:313274 original size:34 final size:36
Alignment explanation
Indices: 313207--313287 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 36
313197 TTGGGTCAGT
313207 TATATATATA-TTTAAATTAAATATATAAATATT-A
1 TATATATATATTTTAAATTAAATATATAAATATTAA
* *
313241 TATATATATATTTTAATTTAAAT-TA-AATTTATTAA
1 TATATATATATTTTAAATTAAATATATAA-ATATTAA
313276 TATTATATATAT
1 TA-TATATATAT
313288 AATAATTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 2 0.05
34 16 0.39
35 14 0.34
36 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
TATATATATATTTTAAATTAAATATATAAATATTAA
Found at i:313592 original size:3 final size:3
Alignment explanation
Indices: 313584--313608 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
313574 GAATTGGGTT
313584 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
313609 ATCGGGTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:313622 original size:12 final size:12
Alignment explanation
Indices: 313607--313652 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
313597 TGTTGTTGTT
*
313607 GTATCGGGTTGG
1 GTATCGGGTCGG
313619 GTATCGGGTCGG
1 GTATCGGGTCGG
*
313631 GTATCGGGCCGG
1 GTATCGGGTCGG
313643 GTAATCGGGT
1 GT-ATCGGGT
313653 AATCGGGGCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.11, C:0.15, G:0.48, T:0.26
Consensus pattern (12 bp):
GTATCGGGTCGG
Found at i:316956 original size:14 final size:14
Alignment explanation
Indices: 316933--316970 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
316923 ATTATTTCTT
316933 TATTTA-TTTATGTA
1 TATTTATTTTAT-TA
316947 TA-TTATTTTATTA
1 TATTTATTTTATTA
316960 TATTTATTTTA
1 TATTTATTTTA
316971 ATATGGGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (14 bp):
TATTTATTTTATTA
Found at i:322620 original size:21 final size:21
Alignment explanation
Indices: 322596--322638 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
322586 ATGGTGGATT
*
322596 TGGAAGGCGAGTCACAATCTA
1 TGGAAGACGAGTCACAATCTA
* *
322617 TGGAAGACGATTCGCAATCTA
1 TGGAAGACGAGTCACAATCTA
322638 T
1 T
322639 ATCTATTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
TGGAAGACGAGTCACAATCTA
Found at i:324414 original size:128 final size:126
Alignment explanation
Indices: 324186--324543 Score: 326
Period size: 128 Copynumber: 2.8 Consensus size: 126
324176 TTTCAAATTT
* *
324186 GATCTTCTTGAAGAGTAGTGAAA-AAAATCAACCTCTATTCAACTTCCCCTGAAGAGTAGTAGAG
1 GATCTTCTTGAAGAGTAGT-AAAGAAAATCAACCAC-ATTCAACTTTCCCTGAAGAGTAGTAGAG
* * * * * * * * *
324250 TAAATCAAAA-TTTCTAGATTTGGTCTTTCAAAAGAGTAGTTAAGTAGATCA-TTTTCCCATATT
64 TGAAT-AAAATTTTC-AAATATGGTCTTCCTAAAGAGTAGTGAAGCAAAT-AGTTTTACCATATT
324313 C
126 C
* * * * * *
324314 GATCTTCTTGAAGAATAGTAAAGCAAATCAACCGCACTACAACTTTCCATGAAGAGTAGTTGAGT
1 GATCTTCTTGAAGAGTAGTAAAGAAAATCAACCACA-TTCAACTTTCCCTGAAGAGTAGTAGAGT
* * * *
324379 GAATAAGAATTTTCAAATATGATCTTCCTAAAGAGTAGTGAAGCAAATAGTTTTATCATGTTT
65 GAATAA-AATTTTCAAATATGGTCTTCCTAAAGAGTAGTGAAGCAAATAGTTTTACCATATTC
* * * * * * *
324442 GATATTCTTAAAGAGTAGTGAGGAAAATCAACCACAATTCAACTTTCCCTGAAGAGAAGTGGATT
1 GATCTTCTTGAAGAGTAGTAAAGAAAATCAACCAC-ATTCAACTTTCCCTGAAGAGTAGTAGAGT
* * * *
324507 GAATAAAAATTTCCAAATCTGGTCATCTTAAAGAGTA
65 GAAT-AAAATTTTCAAATATGGTCTTCCTAAAGAGTA
324544 ACGAAGCATA
Statistics
Matches: 186, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
127 7 0.04
128 172 0.92
129 7 0.04
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (126 bp):
GATCTTCTTGAAGAGTAGTAAAGAAAATCAACCACATTCAACTTTCCCTGAAGAGTAGTAGAGTG
AATAAAATTTTCAAATATGGTCTTCCTAAAGAGTAGTGAAGCAAATAGTTTTACCATATTC
Found at i:325615 original size:23 final size:23
Alignment explanation
Indices: 325589--325649 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
325579 ATCAAGCATA
325589 ATAAC-AAATTAGGTAGCGCTTAT
1 ATAACGAAA-TAGGTAGCGCTTAT
*
325612 ATAACGTAATAGGTAGCGCTTAT
1 ATAACGAAATAGGTAGCGCTTAT
* *
325635 ATAATGTAATAGGTA
1 ATAACGAAATAGGTA
325650 ACGCCTTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 33 0.94
24 2 0.06
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (23 bp):
ATAACGAAATAGGTAGCGCTTAT
Found at i:328260 original size:21 final size:21
Alignment explanation
Indices: 328235--328289 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
328225 TCTTACCAAA
328235 GTATCGATACTTTTGTGTACG
1 GTATCGATACTTTTGTGTACG
328256 GTATCGATACTTTTGTGTACG
1 GTATCGATACTTTTGTGTACG
328277 GTATCGATACTTT
1 GTATCGATACTTT
328290 GGAGATGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.44
Consensus pattern (21 bp):
GTATCGATACTTTTGTGTACG
Found at i:328935 original size:21 final size:21
Alignment explanation
Indices: 328911--328962 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
328901 TATATAAACG
328911 TATTTTACCA-TTAAATTGGTA
1 TATTTTACCACTTAAATT-GTA
* *
328932 TATTTTTACAACTTACATTGTA
1 TA-TTTTACCACTTAAATTGTA
328954 TA-TTTACCA
1 TATTTTACCA
328963 ACTAATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.23
21 2 0.08
22 12 0.46
23 6 0.23
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (21 bp):
TATTTTACCACTTAAATTGTA
Found at i:328940 original size:22 final size:22
Alignment explanation
Indices: 328913--328958 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
328903 TATAAACGTA
*
328913 TTTTACCA-TTAAATTGGTATAT
1 TTTTACAACTTAAATT-GTATAT
*
328935 TTTTACAACTTACATTGTATAT
1 TTTTACAACTTAAATTGTATAT
328957 TT
1 TT
328959 ACCAACTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (22 bp):
TTTTACAACTTAAATTGTATAT
Found at i:330416 original size:66 final size:66
Alignment explanation
Indices: 330334--330467 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 66
330324 CAACCACTCT
*
330334 CATCACCCCCTTAAGTTCACCCCTCAATTCCAAAACTTCCTTT-ACCACTCCATCAATTTTTCCA
1 CATCACCACCTTAAGTTCACCCCTCAATTCCAAAACTT-CTTTCACCACTCCATCAATTTTTCCA
330398 CC
65 CC
* * * *
330400 CATCACCATCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCGCTCCATCTATTTTTCCAC
1 CATCACCACCTTAAGTTCACCCCTCAATTCCAAAACTTCTTTCACCACTCCATCAATTTTTCCAC
330465 C
66 C
330466 CA
1 CA
330468 CTTCCCCCCT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 4 0.06
66 58 0.94
ACGTcount: A:0.25, C:0.42, G:0.02, T:0.31
Consensus pattern (66 bp):
CATCACCACCTTAAGTTCACCCCTCAATTCCAAAACTTCTTTCACCACTCCATCAATTTTTCCAC
C
Found at i:330633 original size:12 final size:12
Alignment explanation
Indices: 330616--330649 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
330606 TATTACAATA
330616 TCTTCTTCCTTC
1 TCTTCTTCCTTC
*
330628 TCTTCTTCTTTC
1 TCTTCTTCCTTC
*
330640 TCCTCTTCCT
1 TCTTCTTCCT
330650 CTTTTGCCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTCTTCCTTC
Found at i:333063 original size:50 final size:50
Alignment explanation
Indices: 333004--333118 Score: 221
Period size: 50 Copynumber: 2.3 Consensus size: 50
332994 ACATGTTTAT
333004 AAAGTATCGATACTTTATAGACACTATTATTGCTTTTATTTTAAATTCCA
1 AAAGTATCGATACTTTATAGACACTATTATTGCTTTTATTTTAAATTCCA
*
333054 AAAGTATCGATACTTTATAGACGCTATTATTGCTTTTATTTTAAATTCCA
1 AAAGTATCGATACTTTATAGACACTATTATTGCTTTTATTTTAAATTCCA
333104 AAAGTATCGATACTT
1 AAAGTATCGATACTT
333119 ATTTGAATGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (50 bp):
AAAGTATCGATACTTTATAGACACTATTATTGCTTTTATTTTAAATTCCA
Found at i:333373 original size:183 final size:183
Alignment explanation
Indices: 333053--333601 Score: 794
Period size: 184 Copynumber: 3.0 Consensus size: 183
333043 TTTAAATTCC
* * *
333053 AAAAGTATCGATACTTTATAGACGCTATTATTGCTTTTATTTTAAATTCCAAAAGTATCGATACT
1 AAAA-TATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACT
* *
333118 TATTTGAATGGTATCAATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAACGAAA
65 TATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAA
* *
333183 TCGGTTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTAT
130 CCGGTTTTATCATATTTTTACCTGTTATATTGTTATGTATCAATACATATTTAT
*
333237 AAAATATCGATACTTTATAGGCACTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
1 AAAATATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
* *
333302 ATTTGAATGGTATCGATAACTTCAACATATTCGGCATCTCTATACCGGTTTTGTCATAATGAAAC
66 ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
* * * *
333367 CGGTTTTGTCATATTTTTTACATGTTATATTATTATGTATCAATACATGTTTAT
131 CGGTTTTATCATA-TTTTTACCTGTTATATTGTTATGTATCAATACATATTTAT
* * * **
333421 AAAGTATCGATACTTTATAGGCGTTATTATTGCTTTTCTTTTAAATTGAAAAAGTATTAATACTT
1 AAAATATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
* * * * * * * *
333486 ATTTGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTATCGGTTTTGTTATATTGAATC
66 ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
* * *
333551 TGGTTTTATCATATTTTTACCT-TATATGTTGTTATGTATCAATACGTATTT
131 CGGTTTTATCATATTTTTACCTGT-TATATTGTTATGTATCAATACATATTT
333602 TAATGGTATT
Statistics
Matches: 326, Mismatches: 37, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
182 1 0.00
183 160 0.49
184 165 0.51
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.44
Consensus pattern (183 bp):
AAAATATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
CGGTTTTATCATATTTTTACCTGTTATATTGTTATGTATCAATACATATTTAT
Found at i:333486 original size:184 final size:183
Alignment explanation
Indices: 333054--333601 Score: 801
Period size: 183 Copynumber: 3.0 Consensus size: 183
333044 TTAAATTCCA
* * *
333054 AAAGTATCGATACTTTATAGACGCTATTATTGCTTTTATTTTAAATTCCAAAAGTATCGATACTT
1 AAAGTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
* * *
333119 ATTTGAATGGTATCAATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAACGAAAT
66 ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
*
333184 CGGTTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTAT
131 CGGTTTTATCATATTTTTACCTGTTATATTGTTATGTATCAATACATATTTAT
* *
333237 AAAATATCGATACTTTATAGGCACTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
1 AAAGTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
* *
333302 ATTTGAATGGTATCGATAACTTCAACATATTCGGCATCTCTATACCGGTTTTGTCATAATGAAAC
66 ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
* * * *
333367 CGGTTTTGTCATATTTTTTACATGTTATATTATTATGTATCAATACATGTTTAT
131 CGGTTTTATCATA-TTTTTACCTGTTATATTGTTATGTATCAATACATATTTAT
* * **
333421 AAAGTATCGATACTTTATAGGCGTTATTATTGCTTTTCTTTTAAATTGAAAAAGTATTAATACTT
1 AAAGTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
* * * * * * * *
333486 ATTTGAATGGTATCGATACCTTCAACATATCCGGTAGCGCTTTATCGGTTTTGTTATATTGAATC
66 ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
* * *
333551 TGGTTTTATCATATTTTTACCT-TATATGTTGTTATGTATCAATACGTATTT
131 CGGTTTTATCATATTTTTACCTGT-TATATTGTTATGTATCAATACATATTT
333602 TAATGGTATT
Statistics
Matches: 325, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
182 1 0.00
183 163 0.50
184 161 0.50
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.44
Consensus pattern (183 bp):
AAAGTATCGATACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTGCAAAAGTATCGATACTT
ATTTGAATGGTATCGATACCTTCAACATATTCGGTATCTCTATACCGGTTTTGTCATAATGAAAC
CGGTTTTATCATATTTTTACCTGTTATATTGTTATGTATCAATACATATTTAT
Found at i:333835 original size:31 final size:31
Alignment explanation
Indices: 333800--333858 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
333790 TGTCCACATT
*
333800 ATCTAGTATTGGTTTGGGACCACTAGTTATA
1 ATCTAGGATTGGTTTGGGACCACTAGTTATA
333831 ATCTAGGATTGGTTTGGGACCACTAGTT
1 ATCTAGGATTGGTTTGGGACCACTAGTT
333859 TCTAACGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (31 bp):
ATCTAGGATTGGTTTGGGACCACTAGTTATA
Found at i:335345 original size:2 final size:2
Alignment explanation
Indices: 335338--335398 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
335328 ACTGCTACCT
335338 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
335380 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
335399 TAAATATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:337202 original size:30 final size:30
Alignment explanation
Indices: 337127--337204 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 30
337117 TATTAACGGT
* *
337127 ATAAA-ATATCATGTATGAAATTGAGAATTT
1 ATAAACAT-TCATGTATGAAACTGAGAATTA
*
337157 TTAAACATT-ATGTATGAAACTGAGAATTGA
1 ATAAACATTCATGTATGAAACTGAGAATT-A
*
337187 ATATAC-TTCATGTATGAA
1 ATAAACATTCATGTATGAA
337205 TAGGATAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 20 0.50
30 18 0.45
31 2 0.05
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (30 bp):
ATAAACATTCATGTATGAAACTGAGAATTA
Found at i:343173 original size:21 final size:21
Alignment explanation
Indices: 343143--343183 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
343133 ATAATTTTGA
*
343143 AAAATTTTAT-TTATTTAAAAT
1 AAAATATTATATT-TTTAAAAT
343164 AAAATATTATATTTTTAAAA
1 AAAATATTATATTTTTAAAA
343184 ATATTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATATTATATTTTTAAAAT
Found at i:343184 original size:22 final size:22
Alignment explanation
Indices: 343142--343186 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
343132 TATAATTTTG
* *
343142 AAAAATTTTATTTATTTAAAAT
1 AAAAATTATATTTATTAAAAAT
343164 AAAATATTATATTT-TTAAAAAT
1 AAAA-ATTATATTTATTAAAAAT
343186 A
1 A
343187 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAATTATATTTATTAAAAAT
Found at i:343484 original size:6 final size:6
Alignment explanation
Indices: 343473--343509 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
343463 TTTTTAATCA
343473 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC A
1 AAATTC AAATTC AAATTC AAATTC AAATTC AAATTC A
343510 TAAAGTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATTC
Found at i:344869 original size:2 final size:2
Alignment explanation
Indices: 344862--344924 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
344852 CGGTTTTTCC
344862 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
344904 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
344925 GTTTACCTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:347481 original size:21 final size:21
Alignment explanation
Indices: 347455--347568 Score: 110
Period size: 21 Copynumber: 5.4 Consensus size: 21
347445 TTGAAGTTCG
*
347455 CGTTGCGATTTATTACAAGTT
1 CGTTGCGATTTATTCCAAGTT
* *
347476 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
347495 CGCGTTGCAATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAGTT
*
347518 CGTTGCGA--TAGTCCAAGTTT
1 CGTTGCGATTTATTCCAAG-TT
*
347538 GCGTTGCGATTTATTCCAAATT
1 -CGTTGCGATTTATTCCAAGTT
347560 CGTTGCGAT
1 CGTTGCGAT
347569 AGTCCAAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
19 16 0.21
20 2 0.03
21 39 0.52
22 2 0.03
23 16 0.21
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:347573 original size:42 final size:42
Alignment explanation
Indices: 347448--347575 Score: 211
Period size: 42 Copynumber: 3.0 Consensus size: 42
347438 AAAGGGGTTG
* *
347448 AAGTTCGCGTTGCGATTTATTACAAGTTCGTTGCGATAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCC
*
347490 AAGTTCGCGTTGCAATTTATTCCAAGTTCGTTGCGATAGTCC
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCC
* *
347532 AAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCC
1 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCC
347574 AA
1 AA
347576 AATCGCAACG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 80 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCC
Found at i:347576 original size:19 final size:19
Alignment explanation
Indices: 347510--347576 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
347500 TGCAATTTAT
*
347510 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
347529 TCCAAGTTTGCGTTGCGATTTAT
1 TCCAA-ATT-CGTTGCGA--TAG
347552 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
347571 TCCAAA
1 TCCAAA
347577 ATCGCAACGA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 16 0.40
22 2 0.05
23 7 0.17
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:348330 original size:6 final size:6
Alignment explanation
Indices: 348319--348345 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
348309 TCTCGTCTCG
348319 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
348346 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:348491 original size:21 final size:21
Alignment explanation
Indices: 348466--348637 Score: 194
Period size: 21 Copynumber: 8.3 Consensus size: 21
348456 GGAATAAATT
*
348466 GCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTGGACTATC
* * *
348487 ACAA--CGAACTTGGAATAAATT
1 GCAACGCGAACTTGGACT--ATC
* *
348508 GCAACACGAACTTCGACTATC
1 GCAACGCGAACTTGGACTATC
*
348529 GCAA--CGAACTTGGAATAAATC
1 GCAACGCGAACTTGGACT--ATC
*
348550 ACAACGCGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
348571 GCAA--CGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
348590 GCAACGCGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
348611 GCAACGCGAACTTGGACTATC
1 GCAACGCGAACTTGGACTATC
348632 GCAACG
1 GCAACG
348638 AATTTGGAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
19 39 0.30
21 68 0.53
23 21 0.16
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (21 bp):
GCAACGCGAACTTGGACTATC
Found at i:348500 original size:42 final size:42
Alignment explanation
Indices: 348438--348626 Score: 256
Period size: 42 Copynumber: 4.5 Consensus size: 42
348428 TGCGATTTTG
* * *
348438 GACTATCGGAACGAATTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* * *
348480 GACTATCACAACGAACTTGGAATAAATTGCAACACGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
348522 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
348564 GACTATCGCAACGAACTTGGACT--ATCGCAACGCGAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
348604 GACTATCGCAACGCGAACTTGGA
1 GACTATCGCAA--CGAACTTGGA
348627 CTATCGCAAC
Statistics
Matches: 134, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 27 0.20
42 107 0.80
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:348516 original size:23 final size:23
Alignment explanation
Indices: 348448--348565 Score: 74
Period size: 23 Copynumber: 5.5 Consensus size: 23
348438 GACTATCGGA
*
348448 ACGAATTTGGAATAAATTGCAAC
1 ACGAACTTGGAATAAATTGCAAC
* * *
348471 GCGAACTTCGACT--A-T-C-AC
1 ACGAACTTGGAATAAATTGCAAC
348489 AACGAACTTGGAATAAATTGCAAC
1 -ACGAACTTGGAATAAATTGCAAC
* * *
348513 ACGAACTTCGACT--ATCGC-A-
1 ACGAACTTGGAATAAATTGCAAC
**
348532 ACGAACTTGGAATAAATCACAAC
1 ACGAACTTGGAATAAATTGCAAC
*
348555 GCGAACTTGGA
1 ACGAACTTGGA
348566 CTATCGCAAC
Statistics
Matches: 71, Mismatches: 14, Indels: 20
0.68 0.13 0.19
Matches are distributed among these distances:
18 2 0.03
19 22 0.31
20 2 0.03
21 10 0.14
22 2 0.03
23 31 0.44
24 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (23 bp):
ACGAACTTGGAATAAATTGCAAC
Found at i:348645 original size:61 final size:61
Alignment explanation
Indices: 348435--348645 Score: 223
Period size: 61 Copynumber: 3.4 Consensus size: 61
348425 CGTTGCGATT
* * * * *
348435 TTGGACTATCGGAACGAATTTGGAATAAATTGCAACGCGAACTTCGACTATCACAA--CGAAC
1 TTGGACTATCGCAACGAACTTGGACT--ATCGCAACGCGAACTTGGACTATCACAACGCGAAC
* * * *
348496 TTGGAATAAATTGCAACACGAACTTCGACTATCGCAA--CGAACTTGGAATAAATCACAACGCGA
1 TTGGACT--ATCGC-A-ACGAACTTGGACTATCGCAACGCGAACTTGGACT--ATCACAACGCGA
348559 AC
60 AC
*
348561 TTGGACTATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCACAACGCGAAC
*
348622 TTGGACTATCGCAACGAATTTGGA
1 TTGGACTATCGCAACGAACTTGGA
348646 AAATCGCATT
Statistics
Matches: 125, Mismatches: 15, Indels: 20
0.78 0.09 0.12
Matches are distributed among these distances:
61 71 0.57
62 1 0.01
63 31 0.25
64 1 0.01
65 21 0.17
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (61 bp):
TTGGACTATCGCAACGAACTTGGACTATCGCAACGCGAACTTGGACTATCACAACGCGAAC
Found at i:348678 original size:21 final size:21
Alignment explanation
Indices: 348649--348697 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
348639 ATTTGGAAAA
* *
348649 TCGCATTGCGATAGTCGATGT
1 TCGCGTTGCGATAATCGATGT
348670 TCGCGTTGCGATAATCGATGT
1 TCGCGTTGCGATAATCGATGT
348691 TCGCGTT
1 TCGCGTT
348698 ACGAATCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAATCGATGT
Found at i:354634 original size:109 final size:109
Alignment explanation
Indices: 354514--354717 Score: 277
Period size: 109 Copynumber: 1.9 Consensus size: 109
354504 GTAAAAGCAC
* * * *
354514 GCTAAACTTAGAGGGAC-CAAATAGTGAATAACCCAAAAATTATGAAGCATGCAAAGAAAAGAGA
1 GCTAAACTTAGAGGGACTAAAATA-TGAATAACCAAAAAATTATAAAGCACGCAAAGAAAAGAGA
354578 AAATAACA-ATTTTAAACCCTATAGGTGACCAGAATAAAAAAACAA
65 AAATAACAGA-TTTAAACCCTATAGGTGACCAGAATAAAAAAACAA
* * *
354623 GCTAAAGTTAGAGGGACTAAAATATGAATAACCAAAAAATTATAAAGCACGCAACGAAAAGGGAA
1 GCTAAACTTAGAGGGACTAAAATATGAATAACCAAAAAATTATAAAGCACGCAAAGAAAAGAGAA
* ***
354688 AGTAACAGATTTGGTCCCTATAGGTGACCA
66 AATAACAGATTTAAACCCTATAGGTGACCA
354718 AAATTTAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 76 0.93
110 6 0.07
ACGTcount: A:0.49, C:0.15, G:0.18, T:0.18
Consensus pattern (109 bp):
GCTAAACTTAGAGGGACTAAAATATGAATAACCAAAAAATTATAAAGCACGCAAAGAAAAGAGAA
AATAACAGATTTAAACCCTATAGGTGACCAGAATAAAAAAACAA
Found at i:355598 original size:11 final size:11
Alignment explanation
Indices: 355584--355644 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
355574 TTGGATTTTG
355584 GTTGGGCCTTA
1 GTTGGGCCTTA
** *
355595 GTTGGGTTTTG
1 GTTGGGCCTTA
355606 GTTGGGCCTTA
1 GTTGGGCCTTA
* **
355617 GTTAGGTTTTA
1 GTTGGGCCTTA
355628 GTTGGGCCTTA
1 GTTGGGCCTTA
355639 GTTGGG
1 GTTGGG
355645 TTTTTGCTGG
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 38 1.00
ACGTcount: A:0.08, C:0.10, G:0.39, T:0.43
Consensus pattern (11 bp):
GTTGGGCCTTA
Found at i:355604 original size:22 final size:22
Alignment explanation
Indices: 355573--355648 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
355563 GGGTATTTAG
*
355573 GTTGGATTTTGGTTGGGCCTTA
1 GTTGGGTTTTGGTTGGGCCTTA
355595 GTTGGGTTTTGGTTGGGCCTTA
1 GTTGGGTTTTGGTTGGGCCTTA
* *
355617 GTTAGGTTTTAGTTGGGCCTTA
1 GTTGGGTTTTGGTTGGGCCTTA
355639 GTTGGGTTTT
1 GTTGGGTTTT
355649 TGCTGGGTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.08, C:0.08, G:0.37, T:0.47
Consensus pattern (22 bp):
GTTGGGTTTTGGTTGGGCCTTA
Found at i:357556 original size:83 final size:83
Alignment explanation
Indices: 357468--357630 Score: 211
Period size: 83 Copynumber: 2.0 Consensus size: 83
357458 TGCAAATGAG
* * *
357468 TAGTACTTTAGTGGCATTTTTATAAAAATGGCGCAATATG-GTTCACCTATAGTGGCATTTTTTC
1 TAGTACTTTAGCGGCATTTTTATAAAAACGGCGCAATA-GAGTTCACCTATAGTGGCATTTTTCC
* * *
357532 AATAAGCGCCTCAAAAAAT
65 AAAAAACACCTCAAAAAAT
* * * * *
357551 TAGTACTTTAGCGGCGTTTTTATATAAACGTCGTAATAGAGTTCATCTATAGTGGCATTTTTCCA
1 TAGTACTTTAGCGGCATTTTTATAAAAACGGCGCAATAGAGTTCACCTATAGTGGCATTTTTCCA
357616 AAAAACACCTCAAAA
66 AAAAACACCTCAAAA
357631 GAGTTGTATA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
82 1 0.01
83 67 0.99
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (83 bp):
TAGTACTTTAGCGGCATTTTTATAAAAACGGCGCAATAGAGTTCACCTATAGTGGCATTTTTCCA
AAAAACACCTCAAAAAAT
Found at i:361264 original size:24 final size:25
Alignment explanation
Indices: 361228--361274 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
361218 TTATTTTATG
361228 AATATAATATTAA-TAAAATATTTT
1 AATATAATATTAATTAAAATATTTT
* *
361252 AATATCATTTTAATTAAAATATT
1 AATATAATATTAATTAAAATATT
361275 AATTATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
AATATAATATTAATTAAAATATTTT
Found at i:361329 original size:26 final size:24
Alignment explanation
Indices: 361265--361330 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
361255 ATCATTTTAA
361265 TTAAAATAT-TAATTATTAAAATAT
1 TTAAAATATAT-ATTATTAAAATAT
*
361289 TTAAAATATAT-TTATTAATAT-T
1 TTAAAATATATATTATTAAAATAT
361311 TCTAATAATATAATATTATT
1 T-TAA-AATAT-ATATTATT
361331 TTTTTAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.33
24 14 0.39
25 3 0.08
26 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTAAAATATATATTATTAAAATAT
Found at i:361484 original size:19 final size:18
Alignment explanation
Indices: 361460--361528 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
361450 AAATTATTAA
361460 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
361479 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
361497 ATTTATATAATAATCTAATAAT
1 A-TTAT-TAATAA--TAATAAT
361519 ATT-TTAATAA
1 ATTATTAATAA
361529 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 7 0.17
19 18 0.45
20 4 0.10
21 3 0.08
22 5 0.12
23 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:361542 original size:23 final size:23
Alignment explanation
Indices: 361523--361567 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
361513 AATAATATTT
361523 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
361546 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
361568 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:361660 original size:21 final size:21
Alignment explanation
Indices: 361641--361695 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
361631 ATACCAATAT
*
361641 TAATATTTTTATTAATAATAAA
1 TAATA-TTTTAATAATAATAAA
361663 TAATATTTTAATAATAAATAAA
1 TAATATTTTAATAAT-AATAAA
361685 T--TATTTTAATA
1 TAATATTTTAATA
361696 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 10 0.32
21 9 0.29
22 12 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATATTTTAATAATAATAAA
Found at i:361666 original size:22 final size:22
Alignment explanation
Indices: 361653--361695 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
361643 ATATTTTTAT
361653 TAAT-AATAAATAATATTTTAA
1 TAATAAATAAATAATATTTTAA
361674 TAATAAATAAAT--TATTTTAA
1 TAATAAATAAATAATATTTTAA
361694 TA
1 TA
361696 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATAAATAAATAATATTTTAA
Found at i:361673 original size:18 final size:20
Alignment explanation
Indices: 361652--361695 Score: 74
Period size: 18 Copynumber: 2.3 Consensus size: 20
361642 AATATTTTTA
361652 TTAATAATAAAT-AA-TATT
1 TTAATAATAAATAAATTATT
361670 TTAATAATAAATAAATTATT
1 TTAATAATAAATAAATTATT
361690 TTAATA
1 TTAATA
361696 TTTTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 12 0.50
19 2 0.08
20 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATAATAAATAAATTATT
Found at i:361700 original size:49 final size:51
Alignment explanation
Indices: 361640--361740 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 51
361630 TATACCAATA
**
361640 TTAATATTTTTATTAATAATAA-A-TAATATTTTAATAATAAATAA-ATTATT
1 TTAATATTTTTAAAAATAATAATATTAA-ATTTT-ATAATAAATAATATTATT
* *
361690 TTAATA-TTTTAAAAATAATAATATTAAGTTTTATGATAAATAATATTATT
1 TTAATATTTTTAAAAATAATAATATTAAATTTTATAATAAATAATATTATT
361740 T
1 T
361741 ATTGTATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
49 23 0.52
50 18 0.41
51 3 0.07
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (51 bp):
TTAATATTTTTAAAAATAATAATATTAAATTTTATAATAAATAATATTATT
Found at i:361805 original size:24 final size:24
Alignment explanation
Indices: 361778--361835 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 24
361768 TTTTTAAAAA
361778 TTTAATCAACTAGTGGAAAATG-GG
1 TTTAATCAACTAGTGGAAAA-GAGG
361802 TTTAAAT-AACTAGTGGAAAAGAGG
1 TTT-AATCAACTAGTGGAAAAGAGG
*
361826 TTTAAACAAC
1 TTTAATCAAC
361836 ATCTTCCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
24 24 0.80
25 3 0.10
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (24 bp):
TTTAATCAACTAGTGGAAAAGAGG
Found at i:362298 original size:5 final size:5
Alignment explanation
Indices: 362279--362315 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
362269 AACTCCTGCA
*
362279 TCCCT TCCCC TTCCCC TCCCC TCCCC TCCCC TCCCC T
1 TCCCC TCCCC -TCCCC TCCCC TCCCC TCCCC TCCCC T
362316 TGTACAACAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.73, G:0.00, T:0.27
Consensus pattern (5 bp):
TCCCC
Found at i:362836 original size:21 final size:21
Alignment explanation
Indices: 362811--362858 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
362801 CCTAATATTG
362811 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
362832 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
362853 TAATGT
1 CAATGT
362859 ATGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:367488 original size:21 final size:21
Alignment explanation
Indices: 367463--367510 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
367453 CCTAATATTG
367463 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
367484 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
367505 TAATGT
1 CAATGT
367511 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:369337 original size:60 final size:60
Alignment explanation
Indices: 369211--369346 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
369201 ATTACGACTC
* * * *
369211 TCATTTTAAATTAGTCTATAAACTATTAAATATTTTAATTTTATCCCTAAACTATAACTA
1 TCATTCTAAATTAGTCTATAAACTATTAAATATTTTAATCTCATCCCCAAACTATAACTA
* * * * **
369271 TTATTCTAGATTAGTCT-TCAAACTTTTGAATATTTTAATCTCATCCCCAAACTATGGTCT-
1 TCATTCTAAATTAGTCTAT-AAACTATTAAATATTTTAATCTCATCCCCAAACTAT-AACTA
369331 TCATTCTAAATTAGTC
1 TCATTCTAAATTAGTC
369347 CCCGAAATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
59 1 0.02
60 59 0.95
61 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.05, T:0.44
Consensus pattern (60 bp):
TCATTCTAAATTAGTCTATAAACTATTAAATATTTTAATCTCATCCCCAAACTATAACTA
Found at i:369662 original size:55 final size:55
Alignment explanation
Indices: 369577--369680 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
369567 ATAGTTTAGG
* * * *
369577 GATGAGATTAGAATGTTCAAAAGTTTAAGGA-CTAATTTAGAAA-GAGAGTCATTAT
1 GATGAAATTAAAATATTCAAAAGTCTAAGGATC-AATTTA-AAATGAGAGTCATTAT
*
369632 GATGAAATTAAAATATTTAAAAGTCTAAGGATCAATTTAAAATGAGAGT
1 GATGAAATTAAAATATTCAAAAGTCTAAGGATCAATTTAAAATGAGAGT
369681 TATAATTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
54 3 0.07
55 38 0.90
56 1 0.02
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (55 bp):
GATGAAATTAAAATATTCAAAAGTCTAAGGATCAATTTAAAATGAGAGTCATTAT
Found at i:371994 original size:7 final size:7
Alignment explanation
Indices: 371979--372374 Score: 219
Period size: 7 Copynumber: 53.1 Consensus size: 7
371969 TATGTTATAG
*
371979 TATAGTA
1 TATATTA
371986 TATATTA
1 TATATTA
371993 TAGTATATAA
1 TA-TAT-T-A
372003 TATATTA
1 TATATTA
*
372010 TATAATA
1 TATATTA
372017 TATACTGTA
1 TATA-T-TA
372026 T-TATTA
1 TATATTA
372032 TATATATA
1 TATAT-TA
372040 GTATATAATA
1 -TATAT--TA
372050 TATATTA
1 TATATTA
372057 TATATAGTA
1 TATAT--TA
372066 TATTATTA
1 TA-TATTA
372074 TATATTA
1 TATATTA
* *
372081 TAGCATAA
1 TA-TATTA
372089 TATATTA
1 TATATTA
*
372096 TTATAGTA
1 -TATATTA
372104 TATATTA
1 TATATTA
372111 TATTATATA
1 TA-TAT-TA
372120 GTATATTA
1 -TATATTA
*
372128 TTATAGTA
1 -TATATTA
372136 TAATATTA
1 T-ATATTA
372144 TATATTA
1 TATATTA
*
372151 TATACTA
1 TATATTA
372158 TAGTATATA
1 TA-TAT-TA
372167 TTATATTA
1 -TATATTA
372175 TATAGTGTA
1 TATA-T-TA
372184 T-TATTA
1 TATATTA
*
372190 TTATAGTA
1 -TATATTA
372198 TATATTTA
1 TATA-TTA
372206 TTATATTA
1 -TATATTA
372214 TATA-TA
1 TATATTA
*
372220 TTATAGTA
1 -TATATTA
372228 TTATATTA
1 -TATATTA
372236 TATATTA
1 TATATTA
372243 TAGTA-T-
1 TA-TATTA
372249 T-TATTA
1 TATATTA
372255 TATATTA
1 TATATTA
372262 TATA-TA
1 TATATTA
*
372268 TTTATTA
1 TATATTA
372275 TATTATTA
1 TA-TATTA
372283 TAATATTA
1 T-ATATTA
*
372291 TATTATACA
1 TA-TAT-TA
372300 TATATTA
1 TATATTA
*
372307 TATGTTA
1 TATATTA
372314 TAGTA-T-
1 TA-TATTA
*
372320 CA-ATTA
1 TATATTA
372326 TATATTA
1 TATATTA
372333 TATCA-TA
1 TAT-ATTA
372340 T-TATT-
1 TATATTA
372345 T-TATTA
1 TATATTA
372351 TATATAGTA
1 TATAT--TA
372360 TAGTATT-
1 TA-TATTA
372367 TATATTA
1 TATATTA
372374 T
1 T
372375 TAAAACATTT
Statistics
Matches: 314, Mismatches: 25, Indels: 100
0.72 0.06 0.23
Matches are distributed among these distances:
4 3 0.01
5 8 0.03
6 23 0.07
7 130 0.41
8 88 0.28
9 46 0.15
10 16 0.05
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (7 bp):
TATATTA
Found at i:371994 original size:12 final size:12
Alignment explanation
Indices: 371974--372355 Score: 263
Period size: 12 Copynumber: 31.4 Consensus size: 12
371964 CCGTTTATGT
* *
371974 TATAGTATAGTA
1 TATATTATATTA
*
371986 TATATTATAGTA
1 TATATTATATTA
*
371998 TATAATATATTA
1 TATATTATATTA
372010 TATAATATATACTGTA
1 TAT-AT-TATA-T-TA
372026 T-TATTATA-TA
1 TATATTATATTA
*
372036 TATAGTATA-TA
1 TATATTATATTA
372047 -ATA-TATATTA
1 TATATTATATTA
372057 TATATAGTATATTA
1 TATAT--TATATTA
372071 T-TA-TATATTA
1 TATATTATATTA
* *
372081 TAGCATAATA-TA
1 TA-TATTATATTA
*
372093 T-TATTATAGTA
1 TATATTATATTA
372104 TATATTATATTA
1 TATATTATATTA
*
372116 TATAGTATATTA
1 TATATTATATTA
* *
372128 TTATAGTATAATA
1 -TATATTATATTA
372141 T-TA-TATATTA
1 TATATTATATTA
* *
372151 TATACTATAGTA
1 TATATTATATTA
372163 TATATTATATTA
1 TATATTATATTA
* *
372175 TATAGTGTATTA
1 TATATTATATTA
*
372187 T-TATTATAGTA
1 TATATTATATTA
372198 TATATT-TATTA
1 TATATTATATTA
372209 TATTATATATATTA
1 TA-TAT-TATATTA
372223 TAGTATTATATTA
1 TA-TATTATATTA
*
372236 TATATTATAGTA
1 TATATTATATTA
*
372248 TTTATTATATATTA
1 TATA-T-TATATTA
*
372262 TATATATTTATTA
1 TATAT-TATATTA
*
372275 TATTATTATAATA
1 TA-TATTATATTA
*
372288 TTATATTATA-CA
1 -TATATTATATTA
372300 TATATTATATGT-
1 TATATTATAT-TA
*
372312 TATAGTATCAATTA
1 TATATTAT--ATTA
*
372326 TATATTATATCA
1 TATATTATATTA
*
372338 TATTATTTTATTA
1 TA-TATTATATTA
372351 TATAT
1 TATAT
372356 AGTATAGTAT
Statistics
Matches: 301, Mismatches: 37, Indels: 64
0.75 0.09 0.16
Matches are distributed among these distances:
9 4 0.01
10 28 0.09
11 41 0.14
12 111 0.37
13 65 0.22
14 47 0.16
15 2 0.01
16 3 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (12 bp):
TATATTATATTA
Found at i:372153 original size:5 final size:5
Alignment explanation
Indices: 371986--372374 Score: 176
Period size: 5 Copynumber: 76.6 Consensus size: 5
371976 TAGTATAGTA
* *
371986 TATAT TATAGT ATATAA TATAT TATAT AATA- TATACT GTATTAT TATAT
1 TATAT TATA-T -TATAT TATAT TATAT TATAT TATA-T -TA-TAT TATAT
* * * *
372035 ATATAG TATAT AATA- TATAT TATA- TATAG TATAT TAT-T ATATAT TATAG
1 -TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT TATAT
* *
372084 CATAA TATA- T-TAT TATAGT ATATAT TATAT TATAT AGTATAT TAT-T
1 TATAT TATAT TATAT TATA-T -TATAT TATAT TATAT --TATAT TATAT
* *
372130 ATAGTAT AATAT TATA- TAT-T ATATAC TATAGT ATATAT TATAT TATAT
1 -TA-TAT TATAT TATAT TATAT -TATAT TATA-T -TATAT TATAT TATAT
*
372178 AGTGTAT TATTAT TATAGT ATATAT T-TAT TATAT TATA- TATAT TATA-
1 --TATAT TA-TAT TATA-T -TATAT TATAT TATAT TATAT TATAT TATAT
* *
372225 -GTAT TATATT ATATAT TATAG TAT-T TAT-T ATATAT TATA- TATAT
1 TATAT TATA-T -TATAT TATAT TATAT TATAT -TATAT TATAT TATAT
* * *
372269 T-TAT TATAT TATTAT AATAT TATAT TATACA TATAT TATATGT TATAG
1 TATAT TATAT TA-TAT TATAT TATAT TATA-T TATAT TATA--T TATAT
* * * *
372317 TATCAA T-TA- TATAT TATAT CATAT TAT-T T-TAT TATA- TATAG TATAG
1 TAT-AT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
372363 TAT-T TATAT TAT
1 TATAT TATAT TAT
372375 TAAAACATTT
Statistics
Matches: 301, Mismatches: 32, Indels: 102
0.69 0.07 0.23
Matches are distributed among these distances:
3 6 0.02
4 51 0.17
5 171 0.57
6 33 0.11
7 38 0.13
8 2 0.01
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (5 bp):
TATAT
Found at i:372366 original size:25 final size:26
Alignment explanation
Indices: 372102--372376 Score: 113
Period size: 26 Copynumber: 10.1 Consensus size: 26
372092 ATTATTATAG
* *
372102 TATATATTATATTATATAGTATATTAT
1 TATATATTATATCATAT-TTATATTAT
* *
372129 TATAGTATAATATTATATATTATATACTAT
1 TATA-TATTATATCATAT-TTATAT--TAT
* * *
372159 AGTATATATTATATTATATAGTGTATTAT
1 --TATATATTATATCATAT-TTATATTAT
* *
372188 TATTATAGTATAT-ATTTATTATATTA-
1 TA-TATATTATATCATAT-TTATATTAT
372214 TATATATTATAGT-ATTATATTATA-TAT
1 TATATATTATA-TCA-TAT-TTATATTAT
*
372241 TATAGTATT-TATTATATATTATATATATT
1 TATA-TATTATATCATAT-TTATAT-TA-T
*
372270 TATTATATTATTATAATA-TTATATTAT
1 TA-TATATTA-TATCATATTTATATTAT
* * * *
372297 ACATATATTATAT-GT-TATAGTATCAAT
1 -TATATATTATATCATATTTA-TAT-TAT
*
372324 TATATATTATATCATA-TTATTTTAT
1 TATATATTATATCATATTTATATTAT
372349 TATATA-TAGTAT-AGTATTTATATTAT
1 TATATATTA-TATCA-TATTTATATTAT
372375 TA
1 TA
372377 AAACATTTTT
Statistics
Matches: 200, Mismatches: 22, Indels: 53
0.73 0.08 0.19
Matches are distributed among these distances:
24 3 0.01
25 24 0.12
26 45 0.22
27 44 0.22
28 36 0.18
29 16 0.08
30 5 0.03
31 23 0.12
32 4 0.02
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (26 bp):
TATATATTATATCATATTTATATTAT
Found at i:372389 original size:137 final size:134
Alignment explanation
Indices: 371979--372399 Score: 358
Period size: 137 Copynumber: 3.1 Consensus size: 134
371969 TATGTTATAG
* * * *
371979 TATAGTATA-TATTATAGTAT-ATA--ATATATTATATAATATATACTGTATTATTATATATATA
1 TATATTATATTATTATAGTATAATATTATATATTATAT-ATATA-GC-ATA-TATTATATTTATA
* * * * *
372040 GTATATAATATATATTATATATAGTATATTATTATATAT-TATAGCATAATATATTATTATAGTA
62 GTATA-ATTATATATTATATATATTATTTTATTATATATATATAGTAT-TTATATTATTA-A-TA
* *
372104 TATATTATATTA
123 TATTTTTTATTA
* *
372116 TATAGTATATTATTATAGTATAATATTATATATTATATACTATAGTATATATTATATTATATAGT
1 TATATTATATTATTATAGTATAATATTATATATTATATA-TATAGCATATATTATATT-TATA--
* * * *
372181 GTATTATTATTATAGTATATAT-TTATTATATTATATATATTATAGTA-TTATATTATATATTAT
62 GTATAATTA-TATATTATATATATTATTTTATTATATATA-TATAGTATTTATATTAT-TAATAT
* *
372244 AGTATTTATTA
124 ATTTTTTATTA
* *
372255 TATATTATATATATT-TATTATATTATTATAATATTATAT-TATA-CATATATTATATGTTATAG
1 TATATTATAT-TATTATAGTATAATATTAT-ATATTATATATATAGCATATATTATAT-TTATAG
* *
372317 TATCAATTATATATTATATCATATTATTTTATTATATATAGTATAGTATTTATATTATTAAAACA
63 TAT-AATTATATATTATAT-ATATTATTTTATTATATATA-TATAGTATTTATATTATTAATATA
*
372382 TTTTTTATTT
125 TTTTTTATTA
*
372392 TATTTTAT
1 TATATTAT
372400 TTTCAGGTCC
Statistics
Matches: 233, Mismatches: 32, Indels: 38
0.77 0.11 0.13
Matches are distributed among these distances:
135 13 0.06
136 6 0.03
137 65 0.28
138 33 0.14
139 40 0.17
140 38 0.16
141 32 0.14
142 6 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (134 bp):
TATATTATATTATTATAGTATAATATTATATATTATATATATAGCATATATTATATTTATAGTAT
AATTATATATTATATATATTATTTTATTATATATATATAGTATTTATATTATTAATATATTTTTT
ATTA
Found at i:384627 original size:24 final size:24
Alignment explanation
Indices: 384582--384631 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
384572 TGGTGGTTGG
*
384582 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
384606 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
384630 TT
1 TT
384632 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:390233 original size:24 final size:24
Alignment explanation
Indices: 390188--390237 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
390178 TGGTGGTTGG
*
390188 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
390212 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
390236 TT
1 TT
390238 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:392525 original size:5 final size:4
Alignment explanation
Indices: 392517--392780 Score: 80
Period size: 3 Copynumber: 73.2 Consensus size: 4
392507 CCATTTATGT
*
392517 TATA GTATA -ATA TATA T-TA TAGTA TATGG TATA T-TA TATA -ATA TATA
1 TATA -TATA TATA TATA TATA TA-TA TAT-A TATA TATA TATA TATA TATA
* *
392564 GTGTA T-TA T-TA T-TA T-TA T-TA TAGTA TAT- TATC TAT- TATA -ATA
1 -TATA TATA TATA TATA TATA TATA TA-TA TATA TATA TATA TATA TATA
* *
392606 TATA TATT TAT- TACA T-TA TAT- TATA TATA T-TA TAT- TAT- TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
392648 T-TA TATA T-TA TATA T-TA TA-A TATT TAT- TAT- TTTA T-TA TAGTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA-TA
** * *
392690 T-TA TAT- TATA CGTA TAT- TATA TAT- TATA TGT- TATA GTATC TAT-
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA -TATA TATA
* *
392733 TATA TAT- TATA TCATA T-TA T-TT TAT- TATA TATA T-TA TA-A TATT
1 TATA TATA TATA T-ATA TATA TATA TATA TATA TATA TATA TATA TATA
392776 TATA T
1 TATA T
392781 GATTATATTT
Statistics
Matches: 204, Mismatches: 18, Indels: 75
0.69 0.06 0.25
Matches are distributed among these distances:
3 106 0.52
4 70 0.34
5 28 0.14
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (4 bp):
TATA
Found at i:392537 original size:7 final size:7
Alignment explanation
Indices: 392522--392792 Score: 137
Period size: 7 Copynumber: 38.1 Consensus size: 7
392512 TATGTTATAG
*
392522 TATAATA
1 TATATTA
392529 TATATTA
1 TATATTA
*
392536 TAGTATATGG
1 TA-TAT-T-A
392546 TATATTA
1 TATATTA
*
392553 TATAATA
1 TATATTA
392560 TATAGTGTA
1 TATA-T-TA
392569 T-TATTA
1 TATATTA
392575 T-TATTA
1 TATATTA
392581 T-TA-TA
1 TATATTA
392586 GTATATTA
1 -TATATTA
*
392594 TCTATTA
1 TATATTA
392601 TA-ATATA
1 TATAT-TA
392608 TATATT-
1 TATATTA
*
392614 TAT-TACA
1 TATAT-TA
392621 TTATATTA
1 -TATATTA
392629 TATA-TA
1 TATATTA
392635 TTATATTA
1 -TATATTA
392643 TTATATTA
1 -TATATTA
392651 TATATTA
1 TATATTA
392658 TATATTA
1 TATATTA
392665 TAATATT-
1 T-ATATTA
392672 TATTATT-
1 TA-TATTA
392679 T-TATTA
1 TATATTA
392685 TAGTATTA
1 TA-TATTA
392693 TAT-TATA
1 TATAT-TA
392700 CGTATATTA
1 --TATATTA
392709 TATATTA
1 TATATTA
*
392716 TAT-GT-
1 TATATTA
*
392721 TATAGTA
1 TATATTA
*
392728 TCTATTA
1 TATATTA
392735 TATATTA
1 TATATTA
392742 TATCA-TA
1 TAT-ATTA
*
392749 T-TATTT
1 TATATTA
392755 TAT-TATA
1 TATAT-TA
392762 TATATTA
1 TATATTA
392769 TAATATTTA
1 T-ATA-TTA
392778 TATGATTA
1 TAT-ATTA
392786 TAT-TTA
1 TATATTA
392792 T
1 T
392793 TAAAATTATT
Statistics
Matches: 214, Mismatches: 15, Indels: 71
0.71 0.05 0.24
Matches are distributed among these distances:
5 11 0.05
6 33 0.15
7 100 0.47
8 49 0.23
9 18 0.08
10 3 0.01
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (7 bp):
TATATTA
Found at i:392537 original size:12 final size:12
Alignment explanation
Indices: 392517--392774 Score: 95
Period size: 12 Copynumber: 21.1 Consensus size: 12
392507 CCATTTATGT
*
392517 TATAGTATAATA
1 TATATTATAATA
*
392529 TATATTATAGTA
1 TATATTATAATA
** *
392541 TATGGTATATTA
1 TATATTATAATA
* *
392553 TATAATATATAGTG
1 TAT-AT-TATAATA
*
392567 TATTATTATTATTA
1 TA-TATTA-TAATA
* *
392581 TTATAGTATATTA
1 -TATATTATAATA
*
392594 TCTATTATAATA
1 TATATTATAATA
*
392606 TATA-TAT-TTA
1 TATATTATAATA
*
392616 TTACATTATATTATA
1 -TATATTATA--ATA
*
392631 TATATTATATTA
1 TATATTATAATA
392643 TTATATTATATATTA
1 -TATATTATA-A-TA
392658 TATATTATAATA
1 TATATTATAATA
*
392670 TTTATTAT--T-
1 TATATTATAATA
*
392679 T-TATTATAGTA
1 TATATTATAATA
*
392690 TTATATTATACGTA
1 -TATATTATA-ATA
*
392704 TAT-TATATATTA
1 TATAT-TATAATA
* *
392716 TATGTTATAGTA
1 TATATTATAATA
*
392728 TCTATTAT-ATA
1 TATATTATAATA
*
392739 T-TA-TATCATA
1 TATATTATAATA
* *
392749 TTATTTTATTATA
1 -TATATTATAATA
392762 TATATTATAATA
1 TATATTATAATA
392774 T
1 T
392775 TTATATGATT
Statistics
Matches: 189, Mismatches: 32, Indels: 50
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.03
9 4 0.02
10 9 0.05
11 10 0.05
12 79 0.42
13 38 0.20
14 36 0.19
15 7 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (12 bp):
TATATTATAATA
Found at i:392542 original size:22 final size:21
Alignment explanation
Indices: 392517--392788 Score: 150
Period size: 22 Copynumber: 13.0 Consensus size: 21
392507 CCATTTATGT
*
392517 TATAGTATAATATATATTATA
1 TATAGTATATTATATATTATA
392538 GTATATGGTATATTATATA--ATA
1 -TATA--GTATATTATATATTATA
*
392560 TATAGTGTATTAT-TATTATTA
1 TATAGTATATTATATATTA-TA
*
392581 TTATAGTATATTATCTATTATAA
1 -TATAGTATATTATATATTAT-A
*
392604 TATA-TATATTTATTACATTATA
1 TATAGTATA-TTA-TATATTATA
392626 TTATA-TATATTATATTATTATA
1 -TATAGTATATTATA-TATTATA
392648 T-TA-TATATTATATATTATA
1 TATAGTATATTATATATTATA
*
392667 -ATA-TTTATTAT-T-TTAT-
1 TATAGTATATTATATATTATA
*
392683 TATAGTAT-TATATTATACGTATA
1 TATAGTATAT-TA-TATA-TTATA
*
392706 T-TA-TATATTATATGTTATA
1 TATAGTATATTATATATTATA
* *
392725 -GTA-TCTATTATATATTATA
1 TATAGTATATTATATATTATA
* *
392744 TCATATTATTTTAT-TATATATA
1 T-ATAGTATATTATATAT-TATA
*
392766 TTATAATAT-TTATATGATTATA
1 -TATAGTATATTATAT-ATTATA
392788 T
1 T
392789 TTATTAAAAT
Statistics
Matches: 203, Mismatches: 17, Indels: 61
0.72 0.06 0.22
Matches are distributed among these distances:
17 8 0.04
18 7 0.03
19 45 0.22
20 16 0.08
21 28 0.14
22 64 0.32
23 24 0.12
24 11 0.05
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (21 bp):
TATAGTATATTATATATTATA
Found at i:392556 original size:19 final size:19
Alignment explanation
Indices: 392534--392594 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
392524 TAATATATAT
*
392534 TATAGTATATGGTATATTA
1 TATAATATATGGTATATTA
392553 TATAATATATAGTGTATTATTA
1 TATAATATAT-G-GTA-TATTA
* *
392575 T-TATTATTATAGTATATTA
1 TATAATA-TATGGTATATTA
392594 T
1 T
392595 CTATTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 15 0.43
20 4 0.11
21 7 0.20
22 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (19 bp):
TATAATATATGGTATATTA
Found at i:392775 original size:17 final size:17
Alignment explanation
Indices: 392516--392787 Score: 130
Period size: 17 Copynumber: 16.3 Consensus size: 17
392506 CCCATTTATG
* *
392516 TTATAGTATAATATATA
1 TTATAATATTATATATA
* *
392533 TTATAGTA-TATGGTATA
1 TTATAATATTAT-ATATA
392550 TTAT-ATA--ATATATA
1 TTATAATATTATATATA
* * *
392564 GTGTATTATTAT-TATTA
1 TTATAATATTATATA-TA
* *
392581 TTATAGTA-TATTATCTA
1 TTATAATATTA-TATATA
392598 TTATAATA-TATATAT-
1 TTATAATATTATATATA
* *
392613 TTATTACATTATAT-TA
1 TTATAATATTATATATA
392629 -TAT-ATATTATAT-TA
1 TTATAATATTATATATA
*
392643 TTATATTATATATTATATA
1 TTATAATAT-TA-TATATA
*
392662 TTATAATATT-TATTATT
1 TTATAATATTATA-TATA
* *
392679 TTATTATAGTAT-TATA
1 TTATAATATTATATATA
*
392695 TTATACGTA-TATTATATA
1 TTATA-ATATTA-TATATA
*
392713 TTAT-ATGTTATAGTATCTA
1 TTATAATATTATA-TA--TA
392732 TTAT-ATATTATATCATA
1 TTATAATATTATAT-ATA
**
392749 TTATTTTATTATATATA
1 TTATAATATTATATATA
392766 TTATAATATT-TATATGA
1 TTATAATATTATATAT-A
392783 TTATA
1 TTATA
392788 TTTATTAAAA
Statistics
Matches: 199, Mismatches: 30, Indels: 52
0.71 0.11 0.19
Matches are distributed among these distances:
14 16 0.08
15 17 0.09
16 39 0.20
17 80 0.40
18 23 0.12
19 24 0.12
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TTATAATATTATATATA
Found at i:396814 original size:16 final size:16
Alignment explanation
Indices: 396793--396830 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
396783 GATATGTCAC
396793 GGTTGCAACTGTGTCT
1 GGTTGCAACTGTGTCT
396809 GGTTGCAACTGTGTCT
1 GGTTGCAACTGTGTCT
396825 GGTTGC
1 GGTTGC
396831 TAGCATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.34, T:0.37
Consensus pattern (16 bp):
GGTTGCAACTGTGTCT
Found at i:401065 original size:14 final size:14
Alignment explanation
Indices: 401046--401087 Score: 84
Period size: 14 Copynumber: 3.0 Consensus size: 14
401036 GCCAATACCT
401046 TTGGGTAAAATGTA
1 TTGGGTAAAATGTA
401060 TTGGGTAAAATGTA
1 TTGGGTAAAATGTA
401074 TTGGGTAAAATGTA
1 TTGGGTAAAATGTA
401088 CCATTAGAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
TTGGGTAAAATGTA
Found at i:402566 original size:644 final size:646
Alignment explanation
Indices: 401337--402627 Score: 2489
Period size: 644 Copynumber: 2.0 Consensus size: 646
401327 TTCGTTTTCG
401337 CTTGCTCACATGGATTTGTTTATTATTTTTAAATTGTCACCTAATAATTCCGTTAATGTATTAAC
1 CTTGCTCACATGGATTTGTTTATTATTTTTAAATTGTCACCTAATAATTCCGTTAATGTATTAAC
*
401402 AAAAATTAACGGCTGAAGGACTTAAACCAGAATGATCTATAATGTAAGGGATAAAGCGTGTTTAA
66 AAAAATTAACGGCTGAAGGACTTAAACCAGAAGGATCTATAATGTAAGGGATAAAGCGTGTTTAA
401467 TTTTTGAACCGGTGACTAAAACGATCAGACTAGAAACAAAGGGGACTATTTATATAGTTTACCAC
131 TTTTTGAACCGGTGACTAAAACGATCAGACTAGAAACAAAGGGGACTATTTATATAGTTTACCAC
*
401532 ATATGTATATATATACATATACGTCTTTACTACAGTAAATTTTTGAACCTATATGTACATAATTT
196 ATATATATATATATACATATACGTCTTTACTACAGTAAATTTTTGAACCTATATGTACATAATTT
401597 TTTTATTTACCCAAAATTACTTTCACTTATATATATAAACTTATATTATGTTCCATTTATCATAT
261 TTTTATTTACCCAAAATTACTTTCACTTATATATATAAACTTATATTATGTTCCATTTATCATAT
* *
401662 ATAACACTACTCTATTCTTTAATTTTTAAAATCGTTACCTTTGCTTAGTTGAAATTACTGAGAAC
326 ATAACACCACTCCATTCTTTAATTTTTAAAATCGTTACCTTTGCTTAGTTGAAATTACTGAGAAC
401727 TGAGATTTGATCAAAACATACATATGTTTTTGTTTTTCTTGCAGGATACTTTACCTAATTTCTTT
391 TGAGATTTGATCAAAACATACATATGTTTTTGTTTTTCTTGCAGGATACTTTACCTAATTTCTTT
401792 AAAAAGCACGAGTACTTCTAAGCGCCCTAGAATATCCTCTTCTAACTCTAGTGAAAAGAGTTTTA
456 AAAAAGCACGAGTACTTCTAAGCGCCCTAGAATATCCTCTTCTAACTCTAGTGAAAAGAGTTTTA
401857 GATCCTTGTGCATTAATGAATTGGGTAGGCAAAACATACTTTCTATATATGTAAATTTCTTTGAG
521 GATCCTTGTGCATTAATGAATTGGGTAGGCAAAACATACTTTCTATATATGTAAATTTCTTTGAG
401922 TCTTTTTCGATCCGAGGTTAGTGTTACGTGTTTTAGGTGTTTGCAATTTGGTGC-AGTATA
586 TCTTTTTCGATCCGAGGTTAGTGTTACGTGTTTTAGGTGTTTGCAATTTGGTGCAAGTATA
401982 CTTGCTCACATGGATTTGTTTATTATTTTTAAATTGTCACCTAATAATTCCGTTAATGTATTAAC
1 CTTGCTCACATGGATTTGTTTATTATTTTTAAATTGTCACCTAATAATTCCGTTAATGTATTAAC
*
402047 AAAAATTAACGGCTGAAGGACTTAAACCAGACGGATCTATAATGTAAGGGATAAAGCGTGTTTAA
66 AAAAATTAACGGCTGAAGGACTTAAACCAGAAGGATCTATAATGTAAGGGATAAAGCGTGTTTAA
*
402112 TTTTTGAACCGGTGACTAAAGTCGATCAGACTAGAAACAAAGGGGACTATTTATATAGTTTA-C-
131 TTTTTGAACCGGTGACTAAA-ACGATCAGACTAGAAACAAAGGGGACTATTTATATAGTTTACCA
402175 CATATATATATATATACATATACGTCTTTACTACAGTAAATTTTTGAACCTATATGTACATAATT
195 CATATATATATATATACATATACGTCTTTACTACAGTAAATTTTTGAACCTATATGTACATAATT
402240 TTTTTATTTACCCAAAATTACTTTCACTTATATATATAAACTTATATTATGTTCCATTTATCATA
260 TTTTTATTTACCCAAAATTACTTTCACTTATATATATAAACTTATATTATGTTCCATTTATCATA
402305 TATAACACCACTCCATTCTTTAATTTTTAAAATCGTTACCTTTGCTTAGTTGAAATTACTGAGAA
325 TATAACACCACTCCATTCTTTAATTTTTAAAATCGTTACCTTTGCTTAGTTGAAATTACTGAGAA
402370 CTGAGATTTGATCAAAACATACATATGTTTTTGTTTTTCTTGCAGGATACTTTACCTAATTTCTT
390 CTGAGATTTGATCAAAACATACATATGTTTTTGTTTTTCTTGCAGGATACTTTACCTAATTTCTT
*
402435 TAAAAAGCACGAGTACTTCTAAGCGCCCTAGAATATCCTCTTCTAGCTCTAGTGAAAAGAGTTTT
455 TAAAAAGCACGAGTACTTCTAAGCGCCCTAGAATATCCTCTTCTAACTCTAGTGAAAAGAGTTTT
402500 AGATCCTTGTGCATTAATGAATTGGGTAGGCAAAACATACTTTCTATATATGTAAATTTCTTTGA
520 AGATCCTTGTGCATTAATGAATTGGGTAGGCAAAACATACTTTCTATATATGTAAATTTCTTTGA
402565 GTCTTTTTCGATCCGAGGTTAGTGTTACGTGTTTTAGGTGTTTGCAATTTGGTGCAAGTATA
585 GTCTTTTTCGATCCGAGGTTAGTGTTACGTGTTTTAGGTGTTTGCAATTTGGTGCAAGTATA
402627 C
1 C
402628 ACGTCACAAG
Statistics
Matches: 637, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
644 441 0.69
645 156 0.24
646 40 0.06
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (646 bp):
CTTGCTCACATGGATTTGTTTATTATTTTTAAATTGTCACCTAATAATTCCGTTAATGTATTAAC
AAAAATTAACGGCTGAAGGACTTAAACCAGAAGGATCTATAATGTAAGGGATAAAGCGTGTTTAA
TTTTTGAACCGGTGACTAAAACGATCAGACTAGAAACAAAGGGGACTATTTATATAGTTTACCAC
ATATATATATATATACATATACGTCTTTACTACAGTAAATTTTTGAACCTATATGTACATAATTT
TTTTATTTACCCAAAATTACTTTCACTTATATATATAAACTTATATTATGTTCCATTTATCATAT
ATAACACCACTCCATTCTTTAATTTTTAAAATCGTTACCTTTGCTTAGTTGAAATTACTGAGAAC
TGAGATTTGATCAAAACATACATATGTTTTTGTTTTTCTTGCAGGATACTTTACCTAATTTCTTT
AAAAAGCACGAGTACTTCTAAGCGCCCTAGAATATCCTCTTCTAACTCTAGTGAAAAGAGTTTTA
GATCCTTGTGCATTAATGAATTGGGTAGGCAAAACATACTTTCTATATATGTAAATTTCTTTGAG
TCTTTTTCGATCCGAGGTTAGTGTTACGTGTTTTAGGTGTTTGCAATTTGGTGCAAGTATA
Found at i:407529 original size:29 final size:29
Alignment explanation
Indices: 407495--407553 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
407485 CCTAAATTAA
* *
407495 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGCCAGTGCTTACATCAATTTAGT
407524 TTTGATGCCAGTGCTTACATCAATTTAGT
1 TTTGATGCCAGTGCTTACATCAATTTAGT
407553 T
1 T
407554 AAGGTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (29 bp):
TTTGATGCCAGTGCTTACATCAATTTAGT
Found at i:408803 original size:34 final size:35
Alignment explanation
Indices: 408745--408814 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
408735 ACAAAAACAA
408745 ATGCAAAGCACATGAAAATGATTAATATGCAAACG
1 ATGCAAAGCACATGAAAATGATTAATATGCAAACG
408780 ATGCAAAGCACATG-AAATGATTAATATGCAAACG
1 ATGCAAAGCACATGAAAATGATTAATATGCAAACG
408814 A
1 A
408815 AAAGATGCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 21 0.60
35 14 0.40
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (35 bp):
ATGCAAAGCACATGAAAATGATTAATATGCAAACG
Found at i:416236 original size:20 final size:19
Alignment explanation
Indices: 416213--416257 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
416203 AAAAAAATTT
*
416213 AAAAAACTTAAAAAATAAA
1 AAAAAAATTAAAAAATAAA
416232 AAAAATAATTAAAAAATAAA
1 AAAAA-AATTAAAAAATAAA
*
416252 ACAAAA
1 AAAAAA
416258 TTTATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAATTAAAAAATAAA
Found at i:426372 original size:79 final size:79
Alignment explanation
Indices: 426241--426474 Score: 301
Period size: 79 Copynumber: 3.0 Consensus size: 79
426231 ATAAAATATA
* * * * * *
426241 CTTTTATGCTGATAATGCACCCATATGCATTTC-AGTGATCG-CATCATTTCATGCCAATAATAC
1 CTTTTATGATGACAATGTACCCATATACATTTCAACT-AT-GACATCATTTCATGCCAATAATGC
*
426304 ATCCATATGCATTATT
64 ACCCATATGCATTATT
* * * * * *
426320 CTTTTATTATGATATTGTACCCATATACATTTCAGCTATGACTTCCTTTCATGCCAATAATGCAC
1 CTTTTATGATGACAATGTACCCATATACATTTCAACTATGACATCATTTCATGCCAATAATGCAC
426385 CCATATGCATTATT
66 CCATATGCATTATT
* *
426399 CTTTTATGCTGACAATGTACCCATATACATTTCAACTATGACATCATTTCATGCTAATAATGCAC
1 CTTTTATGATGACAATGTACCCATATACATTTCAACTATGACATCATTTCATGCCAATAATGCAC
426464 CCATATGCATT
66 CCATATGCATT
426475 TTTATTTTCA
Statistics
Matches: 134, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
78 1 0.01
79 132 0.99
80 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (79 bp):
CTTTTATGATGACAATGTACCCATATACATTTCAACTATGACATCATTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:433327 original size:78 final size:79
Alignment explanation
Indices: 433172--433404 Score: 326
Period size: 78 Copynumber: 3.0 Consensus size: 79
433162 ATAAAATATA
* * * *
433172 CTTTTATGCTGATAATGCACCCATATGCATTTTAG-TGATGGCATCCTTTCATGCCAATAATGCA
1 CTTTTATGCTGATAATGTACCCATATACATTTCAGCT-ATGGCATCATTTCATGCCAATAATGCA
* *
433236 CTCATATGAATTATT
65 CCCATATGCATTATT
** *
433251 CTTTTATGCTGATAATGTACCCATATACATTTCAGCTATAACA-CTTTTCATGCCAATAATGCAC
1 CTTTTATGCTGATAATGTACCCATATACATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
433315 CCATATGCATTATT
66 CCATATGCATTATT
* * * *
433329 CTTTTATACTGACAATGTACCCATATACATTTCAGCCATGGTATCATTTCATGCCAATAATGCAC
1 CTTTTATGCTGATAATGTACCCATATACATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
433394 CCATATGCATT
66 CCATATGCATT
433405 TATATTTTCA
Statistics
Matches: 137, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
78 69 0.50
79 67 0.49
80 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (79 bp):
CTTTTATGCTGATAATGTACCCATATACATTTCAGCTATGGCATCATTTCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:457127 original size:247 final size:241
Alignment explanation
Indices: 456681--457169 Score: 883
Period size: 247 Copynumber: 2.0 Consensus size: 241
456671 TCATTTTGCC
456681 CAACATTCTCATATATACATACCATCACTAACTTACTTAGGTACATAGTAAAGTGATTTGATTTA
1 CAACATTCTCATATATACATACCATCACTAACTTACTTAGGTACATAGTAAAGTGATTTGATTTA
456746 ACTTATCAATTTCTCCAATCCCTGTGGATATGATACTCACATCACTGTATTACTTGTTGATTGTT
66 ACTTATCAATTTCTCCAATCCCTGTGGATATGATACTCACATCACTGTATTACTTGTTGATTGTT
456811 TAAACTTGCACATATTTCCGCAACCTATATAGTATCACAAATCGTGGACATTCACGTAGATCTTT
131 TAAACTTGCACATATTTCCGCAACCTATATAGTATCACAAATCGTGGACATTCACGTAGATCTTT
456876 CCTAAC-CTCTCGATATTTGACATATATTCC-AGAAGAATGACAAT
196 CCTAACTCTCTCGATATTTGACATATATTCCTAGAAGAATGACAAT
456920 CAACATTCTCATATATACATACCATCACTAACTTTACTTAGGTAACATAGTAAAGTGATTTGATT
1 CAACATTCTCATATATACATACCATCACTAAC-TTACTTAGGT-ACATAGTAAAGTGATTTGATT
*
456985 TAACTTATCAATTTCATCTAATCCCTGTGGATATGATACTCACTCATCACTGTATTACTTGTTTG
64 TAACTTATCAATTTC-TCCAATCCCTGTGGATATGATACTCA--CATCACTGTATTACTTG-TTG
457050 ATTGTTTAAACTTGCACATATTTCCGCAACCATATATAGTAGTCACAAATCGTGGACATTCACGT
125 ATTGTTTAAACTTGCACATATTTCCGCAACC-TATATAGTA-TCACAAATCGTGGACATTCACGT
457115 AGATCTTTCCTAACTCTCTCGATATTTGACATATATTCCTAGAAGAATGACAAT
188 AGATCTTTCCTAACTCTCTCGATATTTGACATATATTCCTAGAAGAATGACAAT
457169 C
1 C
457170 TCTCAAAAGC
Statistics
Matches: 239, Mismatches: 1, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
239 32 0.13
240 10 0.04
241 36 0.15
242 25 0.10
244 17 0.07
245 34 0.14
246 9 0.04
247 37 0.15
248 24 0.10
249 15 0.06
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (241 bp):
CAACATTCTCATATATACATACCATCACTAACTTACTTAGGTACATAGTAAAGTGATTTGATTTA
ACTTATCAATTTCTCCAATCCCTGTGGATATGATACTCACATCACTGTATTACTTGTTGATTGTT
TAAACTTGCACATATTTCCGCAACCTATATAGTATCACAAATCGTGGACATTCACGTAGATCTTT
CCTAACTCTCTCGATATTTGACATATATTCCTAGAAGAATGACAAT
Found at i:468372 original size:38 final size:38
Alignment explanation
Indices: 468321--468399 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
468311 ACTTTTTCAT
* *
468321 TATCGGGTTAAGTATCCTTTGTGGTTCCATATAATTGC
1 TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
468359 TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
1 TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
468397 TAT
1 TAT
468400 GGCTATCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (38 bp):
TATCGGGTTAAGTATCCTTTGTGGTTCCACATAATTAC
Found at i:470084 original size:21 final size:21
Alignment explanation
Indices: 470041--470084 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
470031 CGATGAGCCA
*
470041 TGGCTTTGTAATAGATATGCT
1 TGGCTTTGTAATAGATATCCT
* *
470062 TGGCTTTGTAATATATTTCCT
1 TGGCTTTGTAATAGATATCCT
470083 TG
1 TG
470085 ATTCTTGATT
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:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (21 bp):
TGGCTTTGTAATAGATATCCT
Found at i:482191 original size:9 final size:9
Alignment explanation
Indices: 482179--482209 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
482169 ACCCCTTTTA
482179 TTTTTTATT
1 TTTTTTATT
482188 TTTTTTA-T
1 TTTTTTATT
482196 TTTTTTATT
1 TTTTTTATT
482205 TTTTT
1 TTTTT
482210 CTTTTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTATT
Found at i:482215 original size:9 final size:8
Alignment explanation
Indices: 482174--482216 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
482164 CTTGAACCCC
482174 TTTTA-TT
1 TTTTATTT
482181 TTTTATTTT
1 TTTTA-TTT
482190 TTTTATTT
1 TTTTATTT
482198 TTTTATTT
1 TTTTATTT
*
482206 TTTTCTTT
1 TTTTATTT
482214 TTT
1 TTT
482217 CTCTATCTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
7 5 0.15
8 21 0.64
9 7 0.21
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:482216 original size:17 final size:17
Alignment explanation
Indices: 482174--482209 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
482164 CTTGAACCCC
482174 TTTTA-TTTTTTATTTT
1 TTTTATTTTTTTATTTT
482190 TTTTATTTTTTTATTTT
1 TTTTATTTTTTTATTTT
482207 TTT
1 TTT
482210 CTTTTTTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTATTTTTTTATTTT
Found at i:485722 original size:2 final size:2
Alignment explanation
Indices: 485675--485705 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
485665 GAACAAGATG
485675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
485706 CATACAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:492954 original size:27 final size:28
Alignment explanation
Indices: 492916--492977 Score: 90
Period size: 27 Copynumber: 2.2 Consensus size: 28
492906 GAACCTGACA
* *
492916 CCGACCCGAATATCACACTT-AAAAAAC
1 CCGACCCAAATATCAAACTTAAAAAAAC
492943 CCGACCCAAATATCAAACTTAAAAAAAC
1 CCGACCCAAATATCAAACTTAAAAAAAC
*
492971 ACGACCC
1 CCGACCC
492978 GACCTGATCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 18 0.58
28 13 0.42
ACGTcount: A:0.47, C:0.34, G:0.06, T:0.13
Consensus pattern (28 bp):
CCGACCCAAATATCAAACTTAAAAAAAC
Found at i:494944 original size:54 final size:54
Alignment explanation
Indices: 494870--495084 Score: 171
Period size: 54 Copynumber: 4.0 Consensus size: 54
494860 TTCCGTTAAA
* * * * * * * *
494870 AATGACTGATCACCTGTGTGCTTCAGTCTAGAATCTGGCACCTCTGTTCTTTGT
1 AATGATTGAGCACCTTTGTGCTTCAATCTAGAATCTGGAACCTATGTGCTTTGG
* * * *
494924 AATGATTGAGCACTTTTGTGCTTCAAACTAGGATTTGGAACCTATGTGCTTTGG
1 AATGATTGAGCACCTTTGTGCTTCAATCTAGAATCTGGAACCTATGTGCTTTGG
* * * * * * **
494978 GATTATTGAGCACCTTTGTGCTTCAATCTAAAAT-TTGTACCTATGAGCTTTAA
1 AATGATTGAGCACCTTTGTGCTTCAATCTAGAATCTGGAACCTATGTGCTTTGG
* * * * * * *
495031 AATTGATTGAACACCTCTGTGCATCAATCTAGAGTCTGGCACCTCTATGCTTTG
1 AA-TGATTGAGCACCTTTGTGCTTCAATCTAGAATCTGGAACCTATGTGCTTTG
495085 ACAAACGACT
Statistics
Matches: 123, Mismatches: 36, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
53 15 0.12
54 96 0.78
55 12 0.10
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (54 bp):
AATGATTGAGCACCTTTGTGCTTCAATCTAGAATCTGGAACCTATGTGCTTTGG
Found at i:497759 original size:23 final size:23
Alignment explanation
Indices: 497733--497776 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
497723 TATTAAGTAC
**
497733 CGCTTATATAATGTAATAGGTAG
1 CGCTTATATAATAAAATAGGTAG
497756 CGCTTATATAATAAAATAGGT
1 CGCTTATATAATAAAATAGGT
497777 TAATTACTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (23 bp):
CGCTTATATAATAAAATAGGTAG
Found at i:497849 original size:87 final size:87
Alignment explanation
Indices: 497698--498092 Score: 569
Period size: 87 Copynumber: 4.5 Consensus size: 87
497688 TCATTTAACC
* * *
497698 GGAAATATTA-CAAAGTACAATAACATATTAAGTACCGCTTATATAATGTAATAGGTAGCGCTTA
1 GGAAATATTATC-AAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTA
497762 TATAATAAAATAGGTTAATTACT
65 TATAATAAAATAGGTTAATTACT
* *
497785 GGAAATATTATCAAGCACAATAATATATTAGGTACCGCTTATATAATGTAAT-GTGTATCACTTA
1 GGAAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAG-GTAGCACTTA
*
497849 TATAATAAAATAGGTTAATTAAT
65 TATAATAAAATAGGTTAATTACT
* * *
497872 GGAAATATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTAT
1 GGAAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTAT
497937 ATAATAAAATAGGTTAATTACT
66 ATAATAAAATAGGTTAATTACT
* * * * *
497959 AGAAACATTATCAAGCACAATAACATATTAGGTATCACTTATATAATGTAATAGGTAACACTTAT
1 GGAAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTAT
*
498024 ATAATAAAATAAGTTAATTACT
66 ATAATAAAATAGGTTAATTACT
* * * * * *
498046 AGAAACATTATCAAGCACAATAACGTAATAAGTAACGCTTATATAAT
1 GGAAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAAT
498093 AAAATATGTT
Statistics
Matches: 280, Mismatches: 25, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
86 1 0.00
87 277 0.99
88 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (87 bp):
GGAAATATTATCAAGCACAATAACATATTAGGTACCGCTTATATAATGTAATAGGTAGCACTTAT
ATAATAAAATAGGTTAATTACT
Found at i:497926 original size:23 final size:23
Alignment explanation
Indices: 497900--497950 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
497890 AATAACATAT
**
497900 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
497923 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
497946 TAGGT
1 TAGGT
497951 TAATTACTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.22, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:498034 original size:23 final size:23
Alignment explanation
Indices: 497987--498034 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
497977 AATAACATAT
* **
497987 TAGGTATCACTTATATAATGTAA
1 TAGGTAACACTTATATAATAAAA
498010 TAGGTAACACTTATATAATAAAA
1 TAGGTAACACTTATATAATAAAA
498033 TA
1 TA
498035 AGTTAATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.35
Consensus pattern (23 bp):
TAGGTAACACTTATATAATAAAA
Found at i:498652 original size:24 final size:23
Alignment explanation
Indices: 498625--498680 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
498615 TTACCAAGGA
498625 TAACAATAAAATAATATTATTTCT
1 TAACAATAAAATAATATTATTT-T
*
498649 TAACAA-AATAATATTATTATTTT
1 TAACAATAA-AATAATATTATTTT
498672 TAA-AATAAA
1 TAACAATAAA
498681 TATTGCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 3 0.10
23 8 0.28
24 18 0.62
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
TAACAATAAAATAATATTATTTT
Found at i:499027 original size:199 final size:198
Alignment explanation
Indices: 498682--499122 Score: 645
Period size: 199 Copynumber: 2.2 Consensus size: 198
498672 TAAAATAAAT
* *
498682 ATTGCAAATTTACCTATTACATTATAATTATCTGTTTCGATGTTTTTGGGATCGATACAATTTTT
1 ATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATAC-ATTTTT
*
498747 AAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACA
65 AAATGTATCGACACTTTATGTATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACA
*
498812 AACTTAAAATGTGTCGATACATTATGTAGACATATTTTCTCATAAAACCGGTATATTTATACCGA
130 AACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACCG-
498877 G-TAC
194 GTTAC
* * *
498881 ATTGTAAATTTACCTATTACATTGTAATTATCAGTTTCAATGTTTTTGTGATCGATAC-TTTTAA
1 ATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATACATTTT--
* * *
498945 TAAATGTATCGACACTTTATGTATGCACCTCGTTTGGCATTCATTCTGGACAAATGTATCGACAC
64 TAAATGTATCGACACTTTATGTATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACAC
*** * * * * *
499010 -TTTTTAAATTTGTGTCGATACATTATGTTGACCTATTCTCTCATAAGATCGGTATATTTATACC
129 AAACTTAAA-ATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACC
499074 GGTTAC
193 GGTTAC
*
499080 ATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
1 ATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGT
499123 AACATATGTG
Statistics
Matches: 217, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
197 4 0.02
198 6 0.03
199 207 0.95
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (198 bp):
ATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTTTGGGATCGATACATTTTTA
AATGTATCGACACTTTATGTATGCACCTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAA
ACTTAAAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACCGGTATATTTATACCGGT
TAC
Found at i:499262 original size:31 final size:30
Alignment explanation
Indices: 499227--499308 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
499217 AATAAATATT
*
499227 AAATATAATTTATAATAATTTTATT-TTAATA
1 AAATATAA-TAATAATAATTTT-TTATTAATA
* *
499258 AAATATAATAATCATAATTTTTTATTTATA
1 AAATATAATAATAATAATTTTTTATTAATA
499288 AAATTATAGAT-ATAAT-ATTTT
1 AAA-TATA-ATAATAATAATTTT
499309 AATAGTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 2 0.05
30 24 0.55
31 16 0.36
32 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (30 bp):
AAATATAATAATAATAATTTTTTATTAATA
Found at i:500424 original size:2 final size:2
Alignment explanation
Indices: 500417--500471 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
500407 CATTTGCATT
500417 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
500459 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
500472 GCATTTCATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:502389 original size:15 final size:15
Alignment explanation
Indices: 502369--502398 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
502359 CATCGTTAAA
502369 AAAATCGACATACTT
1 AAAATCGACATACTT
*
502384 AAAATCGACGTACTT
1 AAAATCGACATACTT
502399 TTTTATTTTT
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:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (15 bp):
AAAATCGACATACTT
Found at i:507862 original size:18 final size:17
Alignment explanation
Indices: 507839--507874 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
507829 ATTAGAACAT
507839 AATTTTAATGGCTTCAAA
1 AATTTTAATGGCTT-AAA
507857 AATTTTAATGGCTTAAA
1 AATTTTAATGGCTTAAA
507874 A
1 A
507875 TACAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (17 bp):
AATTTTAATGGCTTAAA
Found at i:511074 original size:5 final size:5
Alignment explanation
Indices: 511060--511502 Score: 146
Period size: 5 Copynumber: 86.6 Consensus size: 5
511050 TTATAAAATA
* * *
511060 ATAAT AATAAT ATAAA ACTAAT ATTAAT A-ATAT ATACT CTAAT ATAA-
1 ATAAT -ATAAT ATAAT A-TAAT A-TAAT ATA-AT ATAAT ATAAT ATAAT
* *
511107 A-AAT ATAAT AT-AT A-AAT AT-AT ATTAT GATATAC ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATA-AT ATAAT ATAAT ATAAT
** ** ** *
511155 ACCAT ATAAT ACCAT ATAAT A-ATAT ATATAT ATACAT ATTGT ATACT
1 ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATA-AT ATAAT ATAAT
* *
511202 GTAA- AT-AT ACAAT ATAAT ACT-AT ATAAT AATAAT A-ATAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT -ATAAT ATA-AT ATAAT
*
511246 AT-AT ATAATAT ATAAT ATAA- AT-AT ATATT ATAAT ACTATAT AATAAT
1 ATAAT AT-A-AT ATAAT ATAAT ATAAT ATAAT ATAAT A-TA-AT -ATAAT
* **
511293 ATAAT AT-AT AAAAT -TTTT ACT-AT ATAAT ATAAT ATAAT A-ATAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATA-AT ATAAT
*
511341 ACATAAT AT-AT A-ATAT ATAAT AT-A- ACAAT ATAATTT ATAAT ATAAAGT
1 --ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAA--T ATAAT AT-AA-T
* * *
511389 ATATT ACTACTAT ATAAT ATAAGG CTAAT ATATAT ATACTAT ATAAT ATAATCT
1 ATAAT A-TA--AT ATAAT ATAA-T ATAAT ATA-AT ATA--AT ATAAT ATAA--T
* * * *
511443 TTAAT AT-AT A-ACAT GT-AT ATAAT ATAAT ATTAT ATAAT ATATT ATAAT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
511491 AT-AT ATAAT ATA
1 ATAAT ATAAT ATA
511503 TATTGTACAC
Statistics
Matches: 329, Mismatches: 51, Indels: 115
0.66 0.10 0.23
Matches are distributed among these distances:
3 5 0.02
4 47 0.14
5 181 0.55
6 59 0.18
7 34 0.10
8 3 0.01
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:511121 original size:7 final size:7
Alignment explanation
Indices: 511057--511504 Score: 188
Period size: 7 Copynumber: 61.4 Consensus size: 7
511047 TATTTATAAA
511057 ATAATA-
1 ATAATAT
511063 ATAATAAT
1 ATAAT-AT
511071 ATAA-A-
1 ATAATAT
511076 ACTAATAT
1 A-TAATAT
511084 -TAATA-
1 ATAATAT
511089 ATATATACT
1 ATA-ATA-T
*
511098 CTAATAT
1 ATAATAT
*
511105 A-AAAAT
1 ATAATAT
511111 ATAATAT
1 ATAATAT
511118 ATAAATAT
1 AT-AATAT
511126 ATATTATGAT
1 ATA--AT-AT
511136 ATACATAAT
1 ATA-AT-AT
511145 ATAATAT
1 ATAATAT
**
511152 AATACCAT
1 -ATAATAT
*
511160 ATAATACC
1 ATAATA-T
511168 AT-ATA-
1 ATAATAT
511173 ATAATAT
1 ATAATAT
511180 AT-ATAT
1 ATAATAT
511186 ATACATAT
1 ATA-ATAT
*
511194 -TGTATACT
1 AT-AATA-T
*
511202 GTAA-AT
1 ATAATAT
511208 ATACA-AT
1 ATA-ATAT
511215 ATAATACT
1 ATAATA-T
511223 AT-ATA-
1 ATAATAT
511228 ATAATA-
1 ATAATAT
511234 ATAATAT
1 ATAATAT
511241 ATAATATAT
1 AT-A-ATAT
511250 ATAATAT
1 ATAATAT
511257 ATAATAT
1 ATAATAT
511264 A-AATAT
1 ATAATAT
*
511270 ATATTAT
1 ATAATAT
*
511277 AATACTAT
1 -ATAATAT
511285 ATAATAAT
1 ATAAT-AT
511293 ATAATAT
1 ATAATAT
*
511300 ATAAAAT
1 ATAATAT
**
511307 -TTTTACT
1 ATAATA-T
511314 AT-ATAAT
1 ATAAT-AT
511321 ATAATAT
1 ATAATAT
511328 AATAATAT
1 -ATAATAT
*
511336 ATAATAC
1 ATAATAT
511343 ATAATAT
1 ATAATAT
511350 ATAATAT
1 ATAATAT
511357 ATAATAT
1 ATAATAT
511364 A-ACA-AT
1 ATA-ATAT
*
511370 ATAATTT
1 ATAATAT
511377 ATAATAT
1 ATAATAT
511384 A-AAGTAT
1 ATAA-TAT
511391 ATTACTACTAT
1 A-TA--A-TAT
511402 ATAATAT
1 ATAATAT
511409 AAGGCTAATAT
1 -A---TAATAT
511420 AT-ATAT
1 ATAATAT
511426 ACTATATAAT
1 A-TA-AT-AT
*
511436 ATAATCT
1 ATAATAT
*
511443 TTAATAT
1 ATAATAT
511450 ATAACATGTAT
1 AT-A-A--TAT
511461 ATAATAT
1 ATAATAT
*
511468 AATATTAT
1 -ATAATAT
511476 ATAATAT
1 ATAATAT
*
511483 ATTATA-
1 ATAATAT
511489 AT-ATAT
1 ATAATAT
511495 ATAATAT
1 ATAATAT
511502 ATA
1 ATA
511505 TTGTACACTA
Statistics
Matches: 347, Mismatches: 34, Indels: 121
0.69 0.07 0.24
Matches are distributed among these distances:
5 8 0.02
6 67 0.19
7 150 0.43
8 69 0.20
9 25 0.07
10 12 0.03
11 16 0.05
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (7 bp):
ATAATAT
Done.