Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008208.1 Hibiscus syriacus cultivar Beakdansim tig00110830_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: 2533913
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:1286005 original size:45 final size:45
Alignment explanation
Indices: 1285956--1286573 Score: 903
Period size: 45 Copynumber: 13.7 Consensus size: 45
1285946 GGGAGCTTTT
*
1285956 TGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* ** *
1286001 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGGTCTTCACTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1286046 GGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1286091 TGATGTTTTCATAGCCTTCGGGTCATCTGTAAGTCCTTCAGTACA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1286136 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1286181 TGATGTTTTTAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* ** *
1286226 TAATGTTTTCAAATTCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
** * *
1286271 TGATGTTTTCAAATTCTTCGGGTCATCTGTATGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1286316 TGATGTTTTCAAAACCTTCGGGTCATATGTAAGCCGTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
1286361 TGATGTTTTAAAAGCCTTTGGGTAATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1286406 TGATGTTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTCCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1286451 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* ** *
1286496 TGATATTTTCAAAATCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1286541 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAG
1286574 ACCGATAGTG
Statistics
Matches: 510, Mismatches: 63, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 510 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1286821 original size:3 final size:3
Alignment explanation
Indices: 1286760--1286809 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
1286750 CTTTTCCTTT
* * *
1286760 TTA TT- TTA GTA TTA TTA ATA ATA TGTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
1286805 TTA TT
1 TTA TT
1286810 TATAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1302814 original size:20 final size:20
Alignment explanation
Indices: 1302774--1302812 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1302764 CATTGCAGGA
1302774 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCGACAAAAG
*
1302794 ATTTCATGGCCTTGACAAA
1 ATTT-ATGGCCTCGACAAA
1302813 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCGACAAAAG
Found at i:1303319 original size:30 final size:30
Alignment explanation
Indices: 1303284--1303357 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
1303274 AATTGGATTC
*
1303284 ATTTAGTGACCAAATTATAAA-TTTGGTAAA
1 ATTTAGTGACCAAAGTATAAACTTTGG-AAA
* *
1303314 GTTTAGTGACTAAAGTATAAACTTTGGAAA
1 ATTTAGTGACCAAAGTATAAACTTTGGAAA
*
1303344 ATTTAGGGACCAAA
1 ATTTAGTGACCAAA
1303358 ATGTAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 32 0.86
31 5 0.14
ACGTcount: A:0.42, C:0.08, G:0.18, T:0.32
Consensus pattern (30 bp):
ATTTAGTGACCAAAGTATAAACTTTGGAAA
Found at i:1315217 original size:81 final size:81
Alignment explanation
Indices: 1315126--1315693 Score: 567
Period size: 81 Copynumber: 7.0 Consensus size: 81
1315116 CACAGCTAAT
* ** * * *
1315126 CCATTATTCTTTTACTCAACAGTGTTTAACCATTTGTTTAACTGGAATAATTGACAAATTTCTGT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGC
*
1315191 AAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* * * * ** * *
1315207 ACATTATTCTTTTACTCAACGGTATTTAACCGTTCATATAACTGCCATAAATGA-AACCTTTTTG
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGAATAAATGACAA-ATTTCTG
*
1315271 CCAATTGCATAGTTAGG
65 CCAATTGCACAGTTAGG
* ** * ** **
1315288 CCATTATTCTTTTGCTCAATTGTATTCAACCATTCATCTAACTGGAATAAATGACACTTTTCTTT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGC
1315353 CAATTGCACAGTTAGG
66 CAATTGCACAGTTAGG
* * * * *
1315369 CCATTATTCTTTTACCCAACAGTATTTAATCATTCATCTAACTGGCATAAATGACACATTTCTAC
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGC
* *
1315434 CGATTGCATAGTTAGG
66 CAATTGCACAGTTAGG
* * * * * * * *
1315450 CCATTATTCTTTTACTCAACAATAATTAATCGTTCATCTAAATGGCATAAAAGACATATTTCTGC
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGC
*
1315515 CAA-TGACACAATTAGG
66 CAATTG-CACAGTTAGG
* **
1315531 CCATTATTCTTTTACTCAA-TGATATTTAA-CAGTTCATCTAACTGGCAA-AAATGACACCTTTC
1 CCATTATTCTTTTACTCAACAG-TATTTAACCA-TTCATCTAACTGG-AATAAATGACAAATTTC
1315593 TGCCAATTG-ACAGTTAGG
63 TGCCAATTGCACAGTTAGG
* * * ** *
1315611 CCATTATTCTTTTACTCAACATTATTTTACCGTTCATCTAACT-GACATAAATGACACCTTTCTA
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGA-ATAAATGACAAATTTCTG
*
1315675 TC-ATTGGCACAGTTAGG
65 CCAATT-GCACAGTTAGG
1315692 CC
1 CC
1315694 TAAAAGGCAC
Statistics
Matches: 405, Mismatches: 69, Indels: 26
0.81 0.14 0.05
Matches are distributed among these distances:
78 1 0.00
79 5 0.01
80 66 0.16
81 329 0.81
82 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGC
CAATTGCACAGTTAGG
Found at i:1315332 original size:162 final size:161
Alignment explanation
Indices: 1315126--1315693 Score: 649
Period size: 162 Copynumber: 3.5 Consensus size: 161
1315116 CACAGCTAAT
* ** * *
1315126 CCATTATTCTTTTACTCAACAGTGTTTAACCATTTGTTTAACTGGAATAATTGACAAATTTCTGT
1 CCATTATTCTTTTACTCAACAGT-ATTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGT
* * * *
1315191 AAATTGCACAGTTAGGACATTATTCTTTTACTCAACGGTATTTAACCGTTCATATAACTGCCATA
65 CAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATA
* *
1315256 AATGAAACCTTTTTGCCAATTGCATAGTTAGG
130 AATGACACCTTTCTGCCAATTGCATAGTTAGG
* ** ** *
1315288 CCATTATTCTTTTGCTCAATTGTATTCAACCATTCATCTAACTGGAATAAATGACACTTTTCTTT
1 CCATTATTCTTTTACTCAACAGTATT-AACCATTCATCTAACTGGAATAAATGACAAATTTCTGT
* * * *
1315353 CAATTGCACAGTTAGGCCATTATTCTTTTACCCAACAGTATTTAATCATTCATCTAACTGGCATA
65 CAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATA
* * *
1315418 AATGACACATTTCTACCGATTGCATAGTTAGG
130 AATGACACCTTTCTGCCAATTGCATAGTTAGG
* * * * * * * *
1315450 CCATTATTCTTTTACTCAACAATAATTAATCGTTCATCTAAATGGCATAAAAGACATATTTCTGC
1 CCATTATTCTTTTACTCAACAGT-ATTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGT
* * * * *
1315515 CAA-TGACACAATTAGGCCATTATTCTTTTACTCAATGATATTTAACAGTTCATCTAACTGGCAA
65 CAATTG-CACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCAT
*
1315579 AAATGACACCTTTCTGCCAATTG-ACAGTTAGG
129 AAATGACACCTTTCTGCCAATTGCATAGTTAGG
* * * ** *
1315611 CCATTATTCTTTTACTCAACATTATTTTACCGTTCATCTAACT-GACATAAATGACACCTTTCTA
1 CCATTATTCTTTTACTCAACAGTA-TTAACCATTCATCTAACTGGA-ATAAATGACAAATTTCTG
1315675 TC-ATTGGCACAGTTAGGCC
64 TCAATT-GCACAGTTAGGCC
1315694 TAAAAGGCAC
Statistics
Matches: 338, Mismatches: 61, Indels: 15
0.82 0.15 0.04
Matches are distributed among these distances:
160 3 0.01
161 76 0.22
162 256 0.76
163 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (161 bp):
CCATTATTCTTTTACTCAACAGTATTAACCATTCATCTAACTGGAATAAATGACAAATTTCTGTC
AATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAA
ATGACACCTTTCTGCCAATTGCATAGTTAGG
Found at i:1315542 original size:243 final size:241
Alignment explanation
Indices: 1315126--1315693 Score: 694
Period size: 243 Copynumber: 2.3 Consensus size: 241
1315116 CACAGCTAAT
* ** * * * * *
1315126 CCATTATTCTTTTACTCAACAGTGTTTAACCATTTGTTTAACTGGAATAATTGACAAATTTCTGT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAAATGACACATTTCTAT
* * ** * *
1315191 AAATTGCACAGTTAGGACATTATTCTTTTACTCAACGGTATTTAACCGTTCATATAACTGCCATA
66 -CATTGCACAGTTAGGCCATTATTCTTTTACTCAACAATAATTAACCGTTCATATAAATGCCATA
* * * * * *
1315256 AATGAAACCTTTTTGCCAATTGCATAGTTAGGCCATTATTCTTTTGCTCAATTG-TATTCAACCA
130 AAAGAAACATTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTCAA-TGATATTCAA-CA
* **
1315320 -TTCATCTAACTGG-AATAAATGACACTTTTCTTTCAATTGCACAGTTAGG
193 GTTCATCTAACTGGCAA-AAATGACACCTTTCTGCCAATTG-ACAGTTAGG
* * *
1315369 CCATTATTCTTTTACCCAACAGTATTTAATCATTCATCTAACTGGCATAAATGACACATTTCTAC
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAAATGACACATTTCTAT
* * * *
1315434 CGATTGCATAGTTAGGCCATTATTCTTTTACTCAACAATAATTAATCGTTCATCTAAATGGCATA
66 C-ATTGCACAGTTAGGCCATTATTCTTTTACTCAACAATAATTAACCGTTCATATAAATGCCATA
* * *
1315499 AAAGACATATTTCTGCCAA-TGACACAATTAGGCCATTATTCTTTTACTCAATGATATTTAACAG
130 AAAGAAACATTTCTGCCAATTG-CACAATTAGGCCATTATTCTTTTACTCAATGATATTCAACAG
1315563 TTCATCTAACTGGCAAAAATGACACCTTTCTGCCAATTGACAGTTAGG
194 TTCATCTAACTGGCAAAAATGACACCTTTCTGCCAATTGACAGTTAGG
* * * * *
1315611 CCATTATTCTTTTACTCAACATTATTTTACCGTTCATCTAACTGACATAAATGACACCTTTCTAT
1 CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAAATGACACATTTCTAT
1315676 CATTGGCACAGTTAGGCC
66 CATT-GCACAGTTAGGCC
1315694 TAAAAGGCAC
Statistics
Matches: 277, Mismatches: 42, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
241 3 0.01
242 85 0.31
243 187 0.68
244 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (241 bp):
CCATTATTCTTTTACTCAACAGTATTTAACCATTCATCTAACTGGCATAAATGACACATTTCTAT
CATTGCACAGTTAGGCCATTATTCTTTTACTCAACAATAATTAACCGTTCATATAAATGCCATAA
AAGAAACATTTCTGCCAATTGCACAATTAGGCCATTATTCTTTTACTCAATGATATTCAACAGTT
CATCTAACTGGCAAAAATGACACCTTTCTGCCAATTGACAGTTAGG
Found at i:1315755 original size:68 final size:68
Alignment explanation
Indices: 1315643--1316509 Score: 996
Period size: 68 Copynumber: 12.8 Consensus size: 68
1315633 TATTTTACCG
* * * *
1315643 TTCATCTAACTGACATAAATGACACCTTTCTATCATTGGCACAGTTAGGCCTAAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
1315708 CCT
66 CCT
* * * * *** *
1315711 TTCATCTAACTGACATAAATGAAACCTTTATGTCATTTGAACAGTTAGACCTCTCAGGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
1315776 CCT
66 CCT
* * *
1315779 TTCATCTAACTGGCATAAATGACACCTTTCTGTCACTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
1315844 CCT
66 CCT
** * * * * *
1315847 TTCATCTAGGTGGCTTAAATGACACCTCTATGTCATTTGCACAGTTTGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
1315912 CCT
66 CCT
* * * * *
1315915 TTCATCTAACTAGCATAAATGACAACTTTATGTCATTTGCACAGCTAGGCCTCAAAGGCACTGAG
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
*
1315980 GCT
66 CCT
* * * * * *
1315983 TTCATCTAACTGACATAAATGACACCTTTATGTCATTTTCATAGTTCGACCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
*
1316048 TCT
66 CCT
* * *
1316051 TTCATCTAACTGGCATAAATGACACCTTTTTGTCATTTGCACAATTAGGCCTCAAAA-TCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCT-AAAAGGCACTTA
1316115 GCCT
65 GCCT
* *** * * * * *
1316119 TTCATGTAACTATAATAAATGACATCTTTTTGTCATTTGTACAGTTAGGCCTCAAAGGCACTTAT
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
1316184 CCT
66 CCT
* * *
1316187 TTCATCTAACTGGTATAAATGACACCTTTATTTCATTTGCACAGTTAGG-CAACAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTA-AAAGGCACTTA
1316251 GCCT
65 GCCT
*
1316255 TTCATCTAACTGGCATAAATGACACCATTCTAT-T-ATTTGCACAGTTAGGCCTCAAAGGCACTT
1 TTCATCTAACTGGCATAAATGACACC-TT-TATGTCATTTGCACAGTTAGGCCTAAAAGGCACTT
*
1316318 AGTCT
64 AGCCT
* * * * ** *
1316323 TTTATCTAACT-ACATAAATGACACCTTTCA--TCATTTGCATAGTTA-GCCCACATGGGCAATT
1 TTCATCTAACTGGCATAAATGACACCTTT-ATGTCATTTGCACAGTTAGGCCTA-AAAGGCACTT
1316384 AGCCT
64 AGCCT
* * * *
1316389 TTCATCTAATTGGCATAAATGACACCTTTTTGTCATTTGTACAGTTATGCC-ATAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTA-AAAGGCACTTA
1316453 GCCT
65 GCCT
* * * * *
1316457 TTCATCTAATTGGCATAAATGACACATTTTTGTAATTTGCACTGTTAGGCCTA
1 TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTA
1316510 TAACCTTTTA
Statistics
Matches: 677, Mismatches: 108, Indels: 27
0.83 0.13 0.03
Matches are distributed among these distances:
65 5 0.01
66 35 0.05
67 33 0.05
68 590 0.87
69 11 0.02
70 3 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTATGTCATTTGCACAGTTAGGCCTAAAAGGCACTTAG
CCT
Found at i:1316784 original size:55 final size:56
Alignment explanation
Indices: 1316716--1316821 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
1316706 ACATCTATTT
1316716 CCCATACGAAAATTCATACACTTAGTATGAATTTCTT-ATTTTTGCACACAAAGTG
1 CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTTGCACACAAAGTG
*
1316771 CCCATAC-ATAAATTCATACACTTAGTATGAGTTTCTTAAATTTTTGCACAC
1 CCCATACGA-AAATTCATACACTTAGTATGAATTTCTT-AATTTTTGCACAC
1316822 CTAGTGCCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
54 1 0.02
55 34 0.72
57 12 0.26
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (56 bp):
CCCATACGAAAATTCATACACTTAGTATGAATTTCTTAATTTTTGCACACAAAGTG
Found at i:1329927 original size:56 final size:57
Alignment explanation
Indices: 1329820--1329935 Score: 164
Period size: 56 Copynumber: 2.1 Consensus size: 57
1329810 CTATATGTGG
* *
1329820 AAAGCTAAGAAATTCATAAAACGTTTTATGAATTTTTGTATGGGCACTTTGTGTGCA
1 AAAGCTAAGAAATTCATAAAACGTTTTATGAATTTCTGTAAGGGCACTTTGTGTGCA
* * *
1329877 AAAGCTAATAAATTCATAATAA-G-TTTGTGAATTTCTGTAAGGGCACTTTGTGTGGA
1 AAAGCTAAGAAATTCATAA-AACGTTTTATGAATTTCTGTAAGGGCACTTTGTGTGCA
1329933 AAA
1 AAA
1329936 ATATTCATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
56 32 0.60
57 19 0.36
58 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.35
Consensus pattern (57 bp):
AAAGCTAAGAAATTCATAAAACGTTTTATGAATTTCTGTAAGGGCACTTTGTGTGCA
Found at i:1330240 original size:68 final size:68
Alignment explanation
Indices: 1330129--1330389 Score: 382
Period size: 68 Copynumber: 3.8 Consensus size: 68
1330119 AAGATTAATA
* * * * *
1330129 GCCTAGCTTTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAATGCTAAGTGCCTTT
1 GCCTACCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGCTAAGTGCCTTT
*
1330194 GAC
66 GAG
* *
1330197 GCCTATCTGTACATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTACCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGCTAAGTGCCTTT
1330262 GAG
66 GAG
* * *
1330265 GCCTACCTGTGCATTTGATAGAAAGGTGTCAATTATGTC-AGTTAGATGAAATGATAAGTGCCTT
1 GCCTACCTGTGCATTTGACAGAAAGGTGTCAATTATG-CAAGTTAGATGAAAGGCTAAGTGCCTT
1330329 TGAG
65 TGAG
*
1330333 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATG-ATAGTTAGATGAAAGGCTAA
1 GCCTACCTGTGCATTTGACAGAAAGGTGTCAATTATGCA-AGTTAGATGAAAGGCTAA
1330390 ATGTCTTTTA
Statistics
Matches: 174, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
68 173 0.99
69 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (68 bp):
GCCTACCTGTGCATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:1330544 original size:68 final size:68
Alignment explanation
Indices: 1330414--1330821 Score: 485
Period size: 68 Copynumber: 6.0 Consensus size: 68
1330404 AATATTAATA
* * * *
1330414 GCCTAGTTGTGGATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1330479 GAG
66 GAG
* * * * * * *
1330482 GCTTAACTATGCATTTGACAAAAAGGTGTCAATTATTCCAGTTAGATGAATGGCCAATTGCCTTT
1 GCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
1330547 GAC
66 GAG
* * * * * * *
1330550 GCCTAGCTGTACATTTGATAGAAATGAGTCAATTGTGCCAGTTAGATGAAAGGCTAAGTACCTTT
1 GCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
*
1330615 GAA
66 GAG
* ** * * *
1330618 GCCTAGTTGTGCATTTGACAAAAAATTGTCAATTATGTCAGTTAGAGGAAAGGCTAAGTACCTTT
1 GCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1330683 GAG
66 GAG
* * ** *
1330686 GCCTAACTGTGCATTTGACATAAAGGTGTCAATTATTACAGTTAGATGAAAGGATAAGTGCCTTT
1 GCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1330751 GAG
66 GAG
* * * *
1330754 GCCTAGCTGTGCATTTGA-AAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAATTGTCTT
1 GCCTAGCTGTGCATTTGACAA-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1330818 TGAG
65 TGAG
1330822 TTAAAGATTA
Statistics
Matches: 283, Mismatches: 56, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
67 1 0.00
68 282 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (68 bp):
GCCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
GAG
Found at i:1330595 original size:217 final size:216
Alignment explanation
Indices: 1330208--1331260 Score: 1226
Period size: 217 Copynumber: 4.9 Consensus size: 216
1330198 CCTATCTGTA
* * *
1330208 CATTTGACAGAAAGGTGTCAATTATGCAAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTACCT
1 CATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACT
* * *
1330273 GTGCATTTGATAGAAAGGTGTCAATTATGT-CAGTTAGATGAAATGATAAGTGCCTTTGAGGCCT
66 GTGCATTTGACAAAAAGGTGTCAATTAT-TCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCT
* ** *
1330337 AGCTGTGCATTTGACAGAAAGGTGTCAATTATGATAGTTAGATGAAAGGCTAAATGTCTTTTAGT
130 AGCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGTCTTTGAGT
1330402 TAAATATTAATAGCCTAGTTGTG
195 TAAA-ATTAATAGCCTAGTTGTG
* *
1330425 GATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCTTAACT
1 CATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACT
* * ** * *
1330490 ATGCATTTGACAAAAAGGTGTCAATTATTCCAGTTAGATGAATGGCCAATTGCCTTTGACGCCTA
66 GTGCATTTGACAAAAAGGTGTCAATTATTCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTA
* * * * * **
1330555 GCTGTACATTTGATAGAAATGAGTCAATTGTGCCAGTTAGATGAAAGGCT-AA-G----T-ACCT
131 GCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGTCTTTGAGTT
*
1330613 ----TTGA-AGCCTAGTTGTG
196 AAAATTAATAGCCTAGTTGTG
* * ** * * *
1330629 CATTTGACAAAAAATTGTCAATTATGTCAGTTAGAGGAAAGGCTAAGTACCTTTGAGGCCTAACT
1 CATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACT
* *
1330694 GTGCATTTGACATAAAGGTGTCAATTATTACAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTA
66 GTGCATTTGACAAAAAGGTGTCAATTATTCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTA
* * *
1330759 GCTGTGCATTTGAAAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAATTGTCTTTGAGTT
131 GCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGTCTTTGAGTT
*
1330824 AAAGATTAATTA-CCTGGTTGTG
196 AAA-ATTAA-TAGCCTAGTTGTG
* * * * * *
1330846 CATTTGATTGAAATGTGTCAATTATTG-TAGTTAGATGAAAGGCTAAGTGCCCTTGAGGCATAGC
1 CATTTGATAGAAAGGTGTCAATTA-TGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAAC
* * * * * * *
1330910 TATACATTTGACAGAAAA-GTGTCAATTATGCTAGTTAGATGAAAGGCTACGTGGCTTTGAGGCC
65 TGTGCATTTGACA-AAAAGGTGTCAATTATTCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCC
* * * * *
1330974 TAGTTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGCCTTTGAG
129 TAGCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGTCTTTGAG
1331039 TTAAAAATTAATAGCCTAG-TGTTG
194 TT-AAAATTAATAGCCTAGTTG-TG
* * * * * *
1331063 CATTTGATAGAAAGGTTTCGATTATGCCAGATAGATAAAAGGGTAAGTGCCTTTGAGGCCTAGCT
1 CATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACT
* * * * * *
1331128 GTGCATTTGACAGAAAGGTGTCAGTTGTGCCAGTTAGATGAAAGGTTAAGTGACTTTGAGGCCTA
66 GTGCATTTGACAAAAAGGTGTCAATTATTCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTA
* * * *
1331193 GCTGCTG-ATTTGAAAGAAAGATGTCAATTAAGCCAGTTAGATG-AAGGTCCAAATGCCTTTGAG
131 GCTG-TGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG-CTAAATGTCTTTGAG
1331256 TTAAA
194 TTAAA
1331261 GAACTAAATG
Statistics
Matches: 708, Mismatches: 104, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
204 170 0.24
205 4 0.01
206 1 0.00
210 3 0.00
211 3 0.00
215 1 0.00
216 22 0.03
217 493 0.70
218 11 0.02
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (216 bp):
CATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACT
GTGCATTTGACAAAAAGGTGTCAATTATTCCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTA
GCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGTCTTTGAGTT
AAAATTAATAGCCTAGTTGTG
Found at i:1330955 original size:68 final size:67
Alignment explanation
Indices: 1330846--1331038 Score: 235
Period size: 68 Copynumber: 2.8 Consensus size: 67
1330836 CCTGGTTGTG
* * *
1330846 CATTTGATTGAAATGTGTCAATTATTG-TAGTTAGATGAAAGGCTAAGTGCCCTTGAGGCATAGC
1 CATTTGA-AGAAAAGTGTCAATTA-TGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCATAGC
1330910 TATA
64 TATA
* * * *
1330914 CATTTGACAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGCTACGTGGCTTTGAGGCCTAGTT
1 CATTTGA-AGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCATAGCT
* *
1330979 GTG
65 ATA
* * *
1330982 CATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGCCTTTGAG
1 CATTTGAAGAAAA-GTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1331039 TTAAAAATTA
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 7 0.06
68 101 0.94
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (67 bp):
CATTTGAAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCATAGCTA
TA
Found at i:1330968 original size:149 final size:149
Alignment explanation
Indices: 1330693--1330970 Score: 396
Period size: 149 Copynumber: 1.9 Consensus size: 149
1330683 GAGGCCTAAC
* *
1330693 TGTGCATTTGACATAAAGGTGTCAATTATTACAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCT
1 TGTGCATTTGACATAAAGGTGTCAATTATTACAGTTAGATGAAAGGATAAGTGCCCTTGAGGCAT
* * * * * *
1330758 AGCTGTGCATTTGAAAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGTTAATTGTCTTTGAGT
66 AGCTATACATTTGAAAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGGCTTTGAGT
1330823 TAAAGATTAATTACCTGGT
131 TAAAGATTAATTACCTGGT
* * ** *
1330842 TGTGCATTTGA-TTGAAATGTGTCAATTATTGTAGTTAGATGAAAGGCTAAGTGCCCTTGAGGCA
1 TGTGCATTTGACAT-AAAGGTGTCAATTATTACAGTTAGATGAAAGGATAAGTGCCCTTGAGGCA
* * *
1330906 TAGCTATACATTTGACAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGCTACGTGGCTTTGAG
65 TAGCTATACATTTGAAAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGGCTTTGAG
1330971 GCCTAGTTGT
Statistics
Matches: 112, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
148 1 0.01
149 111 0.99
ACGTcount: A:0.31, C:0.11, G:0.24, T:0.33
Consensus pattern (149 bp):
TGTGCATTTGACATAAAGGTGTCAATTATTACAGTTAGATGAAAGGATAAGTGCCCTTGAGGCAT
AGCTATACATTTGAAAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGGCTTTGAGT
TAAAGATTAATTACCTGGT
Found at i:1331110 original size:81 final size:81
Alignment explanation
Indices: 1330971--1331119 Score: 219
Period size: 81 Copynumber: 1.8 Consensus size: 81
1330961 TGGCTTTGAG
* *
1330971 GCCTAGTTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGCCTTT
1 GCCTAGTTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGATAGATAAAAGGATAAGTGCCTTT
1331036 GAGTTAAAAATTAATA
66 GAGTTAAAAATTAATA
* * * * *
1331052 GCCTAG-TGTTGCATTTGATAGAAAGGTTTCGATTATGCCAGATAGATAAAAGGGTAAGTGCCTT
1 GCCTAGTTG-TGCATTTGAAAAAAAGGTGTCAATTATGCCAGATAGATAAAAGGATAAGTGCCTT
1331116 TGAG
65 TGAG
1331120 GCCTAGCTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
80 2 0.03
81 58 0.97
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.31
Consensus pattern (81 bp):
GCCTAGTTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGATAGATAAAAGGATAAGTGCCTTT
GAGTTAAAAATTAATA
Found at i:1331185 original size:149 final size:149
Alignment explanation
Indices: 1330914--1331187 Score: 395
Period size: 149 Copynumber: 1.8 Consensus size: 149
1330904 CATAGCTATA
* * * * * *
1330914 CATTTGACAGAAAAGTGTCAATTATGCTAGTTAGATGAAAGGCTACGTGGCTTTGAGGCCTAGTT
1 CATTTGACAGAAAAGTGTCAATTATGCCAGATAGATAAAAGGCTAAGTGCCTTTGAGGCCTAGCT
*
1330979 GTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGCCTTTGAGTTAAA
66 GTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGACTTTGAGTTAAA
1331044 AATTAATAGCCTAGTGTTG
131 AATTAATAGCCTAGTGTTG
* * * * *
1331063 CATTTGATAGAAAGGTTTCGATTATGCCAGATAGATAAAAGGGTAAGTGCCTTTGAGGCCTAGCT
1 CATTTGACAGAAAAGTGTCAATTATGCCAGATAGATAAAAGGCTAAGTGCCTTTGAGGCCTAGCT
* * * * *
1331128 GTGCATTTGACAGAAAGGTGTCAGTTGTGCCAGTTAGATGAAAGGTTAAGTGACTTTGAG
66 GTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGACTTTGAG
1331188 GCCTAGCTGC
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
149 108 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (149 bp):
CATTTGACAGAAAAGTGTCAATTATGCCAGATAGATAAAAGGCTAAGTGCCTTTGAGGCCTAGCT
GTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGATAAGTGACTTTGAGTTAAA
AATTAATAGCCTAGTGTTG
Found at i:1331235 original size:68 final size:68
Alignment explanation
Indices: 1331052--1331237 Score: 232
Period size: 68 Copynumber: 2.7 Consensus size: 68
1331042 AAAATTAATA
* * * * * *
1331052 GCCTAG-TGTTGCATTTGATAGAAAGGTTTCGATTATGCCAGATAGATAAAAGGGTAAGTGCCTT
1 GCCTAGCTG-TGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGGTAAGTGACTT
1331116 TGAG
65 TGAG
* * * *
1331120 GCCTAGCTGTGCATTTGACAGAAAGGTGTCAGTTGTGCCAGTTAGATGAAAGGTTAAGTGACTTT
1 GCCTAGCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGGTAAGTGACTTT
1331185 GAG
66 GAG
* *
1331188 GCCTAGCTGCTG-ATTTGAAAGAAAGATGTCAATTAAGCCAGTTAGATGAA
1 GCCTAGCTG-TGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1331238 GGTCCAAATG
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
68 98 0.96
69 4 0.04
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (68 bp):
GCCTAGCTGTGCATTTGAAAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGGTAAGTGACTTT
GAG
Found at i:1340457 original size:46 final size:46
Alignment explanation
Indices: 1340383--1341169 Score: 981
Period size: 46 Copynumber: 17.2 Consensus size: 46
1340373 CGGTTAATAT
* * * * * *
1340383 ACCGTTATGTATTTTCATTTGTAGCATCCTTTTATGCCAATTATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * *
1340429 ACTGTTATGCATTTTCATTTATGACATCCATTCATGCCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* *
1340475 ACCGTTATGCATTTTTATTTATGGCATCCATTCATGCCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* ** *
1340521 TCCGTTATGCATTTTCATTTATTACATCCTTTCATGCTGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * * *
1340567 ACTC-TTTTGCATTTTTATTTATGGCATCCTTTCATTCCGAAAATGC
1 AC-CGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
*
1340613 ACCGTTATGTATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
*
1340659 ACCGTTATGCATTTTCATTTATGGTATCCTTTCATGCCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* *
1340705 ACCATTATGCATTTTCATTTATGGCATCATTTCATGCCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
** * * **
1340751 ACCGTTATGCATTTTCATTTATGGTTTTCTTTCATGCCAATAACAC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * *
1340797 ACCGTTATGTATTTTCATTTATGGCATCATTTCATGCCAATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* *
1340843 ACCGTTATGTATTTTCATTTATGGCATCCTTTCATGCCAATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * *
1340889 ACCGTTATGCTTTTTGATTTATGGCATCCTTTCATGTCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * ** * * * *
1340935 TCCGTTATGCATTATCATTTATATCATCCTTTTATGCCAATAGTAC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * * * *
1340981 ACCATTATGCATTTTAATTTATGGCATCCTTTCATGGCAATAATAC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * *
1341027 ATCGTTATGCATTTTCATTTATGTCATACTTTCA-GTCCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATG-CCGATAATGC
* * *
1341073 ACCGTTATGCATTTGCATTTATGGAATCCTTTCATACCGATAATGC
1 ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
* * *
1341119 ACCGTTATGCATTTTCATTGCA--ACATCCTTTCATGTCG-TAATGC
1 ACCGTTATGCATTTTCATT-TATGGCATCCTTTCATGCCGATAATGC
1341163 ACCGTTA
1 ACCGTTA
1341170 CAAATTTCTA
Statistics
Matches: 639, Mismatches: 97, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
44 13 0.02
45 14 0.02
46 610 0.95
47 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (46 bp):
ACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGC
Found at i:1344826 original size:54 final size:53
Alignment explanation
Indices: 1344527--1344834 Score: 300
Period size: 54 Copynumber: 5.7 Consensus size: 53
1344517 GTGTACTATA
* *
1344527 GGCACTAAATGTGCAACT-CAGTGAATTCATCATATATTGATGAACAACTATTTC
1 GGCACTAAGTGTGCAACTACA--GAATTCATCATATGTTGATGAACAACTATTTC
* *
1344581 AGCACTAAGTGTGCAACT-CATTGAATTCATCATATGTTGATGAGA-AAATATTTC
1 GGCACTAAGTGTGCAACTACA--GAATTCATCATATGTTGATGA-ACAACTATTTC
* * * * **
1344635 GACACTAAGTCTGCTACTCACAGAATTCATCATATGTTGATGAACATCCGTTTC
1 GGCACTAAGTGTGCAACT-ACAGAATTCATCATATGTTGATGAACAACTATTTC
* * * * * * *
1344689 GGAAATAAGTGTGCAACTCACGGAATTCATCACATGTTGATGACCAATTTTTTC
1 GGCACTAAGTGTGCAACT-ACAGAATTCATCATATGTTGATGAACAACTATTTC
*
1344743 GGCACTAAGTGTGCAACT-CACGAAATTCATCATATGTTGATGAACAACTATTTA
1 GGCACTAAGTGTGCAACTACA-G-AATTCATCATATGTTGATGAACAACTATTTC
* * * *
1344797 GGCACTATGTGTCCAACCTACAGAGTTCATAATATGTT
1 GGCACTAAGTGTGCAA-CTACAGAATTCATCATATGTT
1344835 TATTAATGAT
Statistics
Matches: 209, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
52 1 0.00
53 2 0.01
54 198 0.95
55 4 0.02
56 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (53 bp):
GGCACTAAGTGTGCAACTACAGAATTCATCATATGTTGATGAACAACTATTTC
Found at i:1344834 original size:162 final size:162
Alignment explanation
Indices: 1344536--1344834 Score: 390
Period size: 162 Copynumber: 1.8 Consensus size: 162
1344526 AGGCACTAAA
*
1344536 TGTGCAACTCAGTGAATTCATCATATATTGATGAACAACTATTTCAGCACTAAGTGTGCAACTCA
1 TGTGCAACTCAGTGAATTCATCACATATTGATGAACAACTATTTCAGCACTAAGTGTGCAACTCA
* * * * *
1344601 TTGAATTCATCATATGTTGATGAGAAAATATTTCGACACTAAGTCTGCTACTCACAGAATTCATC
66 TCGAATTCATCATATGTTGATGAGAAAATATTTAGACACTAAGTCTCCAACTCACAGAATTCATA
1344666 ATATGTTGATGAACATCCGTTTCGGAAATAAG
131 ATATGTTGATGAACATCCGTTTCGGAAATAAG
* * * * *
1344698 TGTGCAACTCACG-GAATTCATCACATGTTGATGACCAATTTTTTCGGCACTAAGTGTGCAACTC
1 TGTGCAACTCA-GTGAATTCATCACATATTGATGAACAACTATTTCAGCACTAAGTGTGCAACTC
* * * * *
1344762 A-CGAAATTCATCATATGTTGATGA-ACAACTATTTAGGCACTATGTGTCCAAC-CTACAGAGTT
65 ATCG-AATTCATCATATGTTGATGAGA-AAATATTTAGACACTAAGTCTCCAACTC-ACAGAATT
1344824 CATAATATGTT
127 CATAATATGTT
1344835 TATTAATGAT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
161 3 0.03
162 113 0.97
163 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (162 bp):
TGTGCAACTCAGTGAATTCATCACATATTGATGAACAACTATTTCAGCACTAAGTGTGCAACTCA
TCGAATTCATCATATGTTGATGAGAAAATATTTAGACACTAAGTCTCCAACTCACAGAATTCATA
ATATGTTGATGAACATCCGTTTCGGAAATAAG
Found at i:1344917 original size:22 final size:22
Alignment explanation
Indices: 1344887--1344934 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1344877 TGATAATAAC
*
1344887 TTGA-AAATAATGAATTGCTAT
1 TTGATAAATAATGAATTACTAT
1344908 TTGATAAATAATGAATTACTAT
1 TTGATAAATAATGAATTACTAT
1344930 TTGAT
1 TTGAT
1344935 CGATATGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (22 bp):
TTGATAAATAATGAATTACTAT
Found at i:1348219 original size:21 final size:21
Alignment explanation
Indices: 1348193--1348233 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348183 TATAATTATA
*
1348193 CATCGATACTCTACTACAGTG
1 CATCGATACACTACTACAGTG
*
1348214 CATCGATTCACTACTACAGT
1 CATCGATACACTACTACAGT
1348234 AATTTCAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (21 bp):
CATCGATACACTACTACAGTG
Found at i:1353491 original size:20 final size:22
Alignment explanation
Indices: 1353443--1353495 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1353433 ATGCAAAAAT
*
1353443 GGTATCGATACCATAGTATAGT
1 GGTATCGATACCATAGTATAGG
* *
1353465 AGTATCGATACCAT-G-GTAGG
1 GGTATCGATACCATAGTATAGG
1353485 GGTATCGATAC
1 GGTATCGATAC
1353496 TATTCAGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 13 0.48
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
GGTATCGATACCATAGTATAGG
Found at i:1353890 original size:54 final size:54
Alignment explanation
Indices: 1353825--1354104 Score: 398
Period size: 54 Copynumber: 5.2 Consensus size: 54
1353815 TACTATAGGA
*
1353825 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTAATGAACAACCGTTTCGGC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGC
* * * * *
1353879 ACTAAGGGTGCAACTCATGGAATTTATCATATGTTGATGAACAACTGTTTCGGC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGC
* * * * * *
1353933 ACTAAGAGTGTAATTCACGGAATTCATCATATGTTGATGAACAACCATTTCGGA
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGC
* *
1353987 ACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAACAACCGTTTCGGC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGC
* * *
1354041 ACTAAGTGTGCAACTCACAAAATTCATCATATGTTGATGAATAACCGTTTAGGC
1 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGC
*
1354095 ACTATGTGTG
1 ACTAAGTGTG
1354105 TAATCCACAG
Statistics
Matches: 202, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 202 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAACAACCGTTTCGGC
Found at i:1354098 original size:162 final size:162
Alignment explanation
Indices: 1353822--1354135 Score: 466
Period size: 162 Copynumber: 1.9 Consensus size: 162
1353812 GTCTACTATA
*
1353822 GGAACTAAGTGTGCAACTCACGAAATTCATCATATGTTAATGAACAACCGTTTCGGCACTAAGGG
1 GGAACTAAGTGTGCAACTCACAAAATTCATCATATGTTAATGAACAACCGTTTCGGCACTAAGGG
*** * * * * *
1353887 TGCAACTCATGGAATTTATCATATGTTGATGAACAACTGTTTCGGCACTAAGAGTGTAATTCACG
66 TGCAACTCACAAAATTCATCATATGTTGATGAACAACCGTTTAGGCACTAAGAGTGTAATCCACA
*
1353952 GAATTCATCATATGTTGATGAACAACCATTTC
131 GAATTCATAATATGTTGATGAACAACCATTTC
* * *
1353984 GGAACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAACAACCGTTTCGGCACTAAGTG
1 GGAACTAAGTGTGCAACTCACAAAATTCATCATATGTTAATGAACAACCGTTTCGGCACTAAGGG
* * *
1354049 TGCAACTCACAAAATTCATCATATGTTGATGAATAACCGTTTAGGCACTATGTGTGTAATCCACA
66 TGCAACTCACAAAATTCATCATATGTTGATGAACAACCGTTTAGGCACTAAGAGTGTAATCCACA
* *
1354114 GAGTTCATAATATGTTTATGAA
131 GAATTCATAATATGTTGATGAA
1354136 TGACCGTATA
Statistics
Matches: 134, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
162 134 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (162 bp):
GGAACTAAGTGTGCAACTCACAAAATTCATCATATGTTAATGAACAACCGTTTCGGCACTAAGGG
TGCAACTCACAAAATTCATCATATGTTGATGAACAACCGTTTAGGCACTAAGAGTGTAATCCACA
GAATTCATAATATGTTGATGAACAACCATTTC
Found at i:1360047 original size:55 final size:55
Alignment explanation
Indices: 1359964--1360367 Score: 456
Period size: 55 Copynumber: 7.3 Consensus size: 55
1359954 TTTATTAGAA
* * *
1359964 TGCACA-AGTAGTGCCTATACGG-TAATTCATCAACTCTTGATGAATTCTGTGGTTT
1 TGCACACA-TAGTGCCTGTACGGCT-ATTCATCAACTCATGATGAATTCTGTGGATT
* * *
1360019 TGTACATATAGTGCATGTACGGCTATTCATCAACTCATGATGAATT-TCGTGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCT-GTGGATT
* * *
1360074 TGCGCACATAGTTCCTGTACGGCTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCTGTGGATT
* *
1360129 TGCACACATAGTGCATGTACGGCTATTCATAAACTCATGATGAATT-TCGTGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCT-GTGGATT
* * * * * ** *
1360184 TTCACACATAGTTCCTATACGACTATTCATTAACTCATGATGAATTCCATTGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCTGTGGATT
* * ** * * *
1360239 TGCACACAAAGTGCGTGTAAAGCTATGCATCAACACATGATGAATTTTGTGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCTGTGGATT
* * * * * *
1360294 TGTACACATAATGCCTGCACGGCTATTCATCAACACATAATAAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCTGTGGATT
1360349 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCCTGTA
1360368 GTACACTTAG
Statistics
Matches: 289, Mismatches: 54, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
54 1 0.00
55 286 0.99
56 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGCTATTCATCAACTCATGATGAATTCTGTGGATT
Found at i:1360814 original size:20 final size:21
Alignment explanation
Indices: 1360786--1360835 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1360776 TTTTGAAATG
1360786 GTATCGATACCTT-CCCTTCA
1 GTATCGATACCTTCCCCTTCA
* *
1360806 GTGTCGATA-CTTCCCCTTCT
1 GTATCGATACCTTCCCCTTCA
1360826 GTATCGATAC
1 GTATCGATAC
1360836 TGATTGAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.18, C:0.32, G:0.14, T:0.36
Consensus pattern (21 bp):
GTATCGATACCTTCCCCTTCA
Found at i:1363286 original size:29 final size:29
Alignment explanation
Indices: 1363254--1363364 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
1363244 GCACCCATTT
* *
1363254 CGAATTAATTACCATAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
1363283 CGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1363312 CGAATTATTTACCAGAAAAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
1363341 CGAATTATTTACCAGAATAGCACC
1 CGAATTATTTACCAGAATAGCACC
1363365 GGTCAATTGT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1370720 original size:29 final size:29
Alignment explanation
Indices: 1370688--1370770 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
1370678 GCAACCATTT
*
1370688 CGAATTAATTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1370717 CGAAATATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1370746 TGAATTATTTACCAGAATAGCACCA
1 CGAATTATTTACCAGAATAGCACCA
1370771 GTCAACGGTC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.11, T:0.20
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1370736 original size:58 final size:58
Alignment explanation
Indices: 1370661--1370770 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
1370651 GCCCTTTTTA
***
1370661 AAATATTTACCAAAATAGCAACCATTTC-GAATTAATTACCAGAATAGCACCAAAACCG
1 AAATATTTACCAAAATAGC-ACCAAAACTGAATTAATTACCAGAATAGCACCAAAACCG
* *
1370719 AAATATTTACCAGAATAGCACCAAAACTGAATTATTTACCAGAATAGCACCA
1 AAATATTTACCAAAATAGCACCAAAACTGAATTAATTACCAGAATAGCACCA
1370771 GTCAACGGTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 5 0.11
58 41 0.89
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (58 bp):
AAATATTTACCAAAATAGCACCAAAACTGAATTAATTACCAGAATAGCACCAAAACCG
Found at i:1379641 original size:20 final size:21
Alignment explanation
Indices: 1379612--1379663 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1379602 AAAGAAGTTG
*
1379612 AAGTATATGAATT-CATTGGT
1 AAGTAGATGAATTACATTGGT
*
1379632 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAATTACATTGGT
* *
1379653 AAATAGGTGAA
1 AAGTAGATGAA
1379664 GTGCTTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (21 bp):
AAGTAGATGAATTACATTGGT
Found at i:1379653 original size:21 final size:20
Alignment explanation
Indices: 1379612--1379654 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1379602 AAAGAAGTTG
*
1379612 AAGTATATGAATTCATTGGT
1 AAGTAGATGAATTCATTGGT
*
1379632 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAATT-CATTGGT
1379653 AA
1 AA
1379655 ATAGGTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (20 bp):
AAGTAGATGAATTCATTGGT
Found at i:1381782 original size:78 final size:78
Alignment explanation
Indices: 1381667--1381812 Score: 186
Period size: 77 Copynumber: 1.9 Consensus size: 78
1381657 ATATAGTAAG
*** * * *
1381667 TAAACATTAAAAGAATATAATTTTGATTACAACTCTTTTATTTGATATTTAATTCGGAATAATTA
1 TAAACATTAAAAGAATATAATACAGATTACAACTCTTTAATGT-ATATTTAATTCGAAATAATTA
1381732 AATAAGATTTTAAA
65 AATAAGATTTTAAA
* * * *
1381746 TAAACATTAAAA-ATTATAATACAGATTATAAGTCTTTAATGTATATTTAATTTGAAATAATTAA
1 TAAACATTAAAAGAATATAATACAGATTACAACTCTTTAATGTATATTTAATTCGAAATAATTAA
1381810 ATA
66 ATA
1381813 TTTTTTTCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
77 23 0.40
78 22 0.39
79 12 0.21
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (78 bp):
TAAACATTAAAAGAATATAATACAGATTACAACTCTTTAATGTATATTTAATTCGAAATAATTAA
ATAAGATTTTAAA
Found at i:1390686 original size:21 final size:22
Alignment explanation
Indices: 1390662--1390711 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1390652 ATAAATTACC
1390662 TTGGTAAGTAGATGAAGTA-TT
1 TTGGTAAGTAGATGAAGTACTT
* * *
1390683 TTGGTAAATAGGTTAAGTACTT
1 TTGGTAAGTAGATGAAGTACTT
1390705 TT-GTAAG
1 TTGGTAAG
1390712 CGTCTCTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.40
Consensus pattern (22 bp):
TTGGTAAGTAGATGAAGTACTT
Found at i:1393161 original size:19 final size:19
Alignment explanation
Indices: 1393137--1393183 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1393127 GAAATCCCTT
*
1393137 TGAAAATACATAATTTTAA
1 TGAAAATACATAACTTTAA
* *
1393156 TGAAAATATATGACTTTAA
1 TGAAAATACATAACTTTAA
1393175 TGAAAATAC
1 TGAAAATAC
1393184 GTGGTCTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (19 bp):
TGAAAATACATAACTTTAA
Found at i:1396912 original size:81 final size:81
Alignment explanation
Indices: 1396772--1397223 Score: 546
Period size: 81 Copynumber: 5.6 Consensus size: 81
1396762 ATTAATTGCC
* * * *
1396772 TCAATCATGCCATTTAGATGAAAGGATAAATGCCTTTGAGTTAAAGATTAATTGTCTAGCTATGT
1 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTGT
1396837 ATTTGATAGAAAGGTG
66 ATTTGATAGAAAGGTG
* * * *
1396853 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAAATTGATTGACTAGCTGTGC
1 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTGT
**
1396918 ATTTGGCAGAAAGGTG
66 ATTTGATAGAAAGGTG
* * * * * * * * *
1396934 TCACTCATGCCAATTAGAGGAAAGGTTAAATGCCTTTGTGATAAATATTAAATGCCAAGCTGTGT
1 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTGT
1396999 ATTTGATAGAAAGGTG
66 ATTTGATAGAAAGGTG
* *
1397015 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGTTGTGC
1 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTGT
* * * *
1397080 ATTCGAAACAAAAGTG
66 ATTTGATAGAAAGGTG
** * * *
1397096 TCAATCATG-TTGTTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAAATGCCTAGATGTC
1 TCAATCATGCCAG-TTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTG
* * *
1397160 CACTTGGTAGAAAGGTG
65 TATTTGATAGAAAGGTG
* * * * *
1397177 TCAATCATGCAAGTTAGATGAATGGCTAAATGTCTTTGTGTAAAAGA
1 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGA
1397224 GTAAATGCAT
Statistics
Matches: 314, Mismatches: 55, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
80 1 0.00
81 312 0.99
82 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTGTGT
ATTTGATAGAAAGGTG
Found at i:1397216 original size:243 final size:242
Alignment explanation
Indices: 1396772--1397220 Score: 632
Period size: 243 Copynumber: 1.9 Consensus size: 242
1396762 ATTAATTGCC
* * *
1396772 TCAATCATGCCATTTAGATGAAAGGATAAATGCCTTTGAGTTAAAGATTAATTGTCTAGCTATGT
1 TCAATCATGCCAGTTAGATGAAAGGATAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTATGC
* * * *
1396837 ATTTGATAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAAATT
66 ATTCGAAACAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAAATT
* * * * * * *
1396902 GATTGACTAGCTGTGCATTTGGCAGAAAGGTGTCACTCATGCCAATTAGAGGAAAGGTTAAATGC
131 AAATGACTAGATGTCCACTTGGCAGAAAGGTGTCAATCATGCCAATTAGAGGAAAGGCTAAATGC
1396967 CTTTGTGATAAATATTAAATGCCAAGCTGTGTATTTGATAGAAAGGTG
196 CTTTGTG-TAAATATTAAATGCCAAGCTGTGTATTTGATAGAAAGGTG
* * *
1397015 TCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGATTAATTGCCTAGTTGTGC
1 TCAATCATGCCAGTTAGATGAAAGGATAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTATGC
** *
1397080 ATTCGAAACAAAAGTGTCAATCATG-TTGTTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAGAT
66 ATTCGAAACAAAAGTGTCAATCATGCCAG-TTAGATGAAAGGCTAAATGCCTTTGAGTTAAAAAT
* * * *
1397144 TAAATGCCTAGATGTCCACTTGGTAGAAAGGTGTCAATCATG-CAAGTTAGATGAATGGCTAAAT
130 TAAATGACTAGATGTCCACTTGGCAGAAAGGTGTCAATCATGCCAA-TTAGAGGAAAGGCTAAAT
*
1397208 GTCTTTGTGTAAA
194 GCCTTTGTGTAAA
1397221 AGAGTAAATG
Statistics
Matches: 179, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
242 8 0.04
243 171 0.96
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (242 bp):
TCAATCATGCCAGTTAGATGAAAGGATAAATGCCTTTGAGTTAAAGATTAATTGCCTAGCTATGC
ATTCGAAACAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAAAAATT
AAATGACTAGATGTCCACTTGGCAGAAAGGTGTCAATCATGCCAATTAGAGGAAAGGCTAAATGC
CTTTGTGTAAATATTAAATGCCAAGCTGTGTATTTGATAGAAAGGTG
Found at i:1402754 original size:81 final size:81
Alignment explanation
Indices: 1402587--1403729 Score: 1443
Period size: 81 Copynumber: 14.1 Consensus size: 81
1402577 ATTGTATAGT
** * * * *
1402587 TGTGCATTTGGTAGAAATGTGTTAATCATGCCAGTTAGATGGAAGGCTAAATGCCTCTTGAGTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCT-TTGAGTTA
* *
1402652 AAGATTAATTGCCTAGA
65 AAGATTAAATGCCTAGC
* * * * * * *
1402669 TGTGCATTTGATAGAAAAGTGTCAATTATGCTAGTTAGATAAAAGGTTAAATACCTTTGAGTAAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
*
1402734 AGATTAATTGCCTAGC
66 AGATTAAATGCCTAGC
* *
1402750 TGTGCATTTGACAGAAATA-TGTCAATCATGCCAGTTAGATGAAAGGATAAATGCATTTGAGTTA
1 TGTGCATTTGACAGAAA-AGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTA
*
1402814 AAGATTAATTGCCTAGC
65 AAGATTAAATGCCTAGC
* *
1402831 TGTGTATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
* *
1402896 AGATTAATTGCCTAGT
66 AGATTAAATGCCTAGC
* * **
1402912 TGTGCATTTGGCAGAAAGGTGTCAATCATGCCAGTTAGATGAAACACTAAATGCCTTTGAGTTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
1402977 AGATTAAATGCCTAGC
66 AGATTAAATGCCTAGC
* * * *
1402993 TGTGCATTTGACAGAAATGTGTAAATCATGCCAGTTAGATGAAAGGCGAAATACCTTTGAGTTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
1403058 AGATTAAATGCCTAGC
66 AGATTAAATGCCTAGC
* * * *
1403074 TATGCATTTGATAGAAATA-TGTCAATCATGCCAGTTAGATGAAAGGATAAAGGCCTTTGAGTTA
1 TGTGCATTTGACAGAAA-AGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTA
** *
1403138 AAGATTAGTTGCCTAGT
65 AAGATTAAATGCCTAGC
** * * *
1403155 TGTGCATTTGGTAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTATATGCCTTTGAGGTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
1403220 AGATTAAATGCCTAGC
66 AGATTAAATGCCTAGC
* * *
1403236 TGTACATTTGGA-AGAAAAGTGTCAATCATGCCAATTAGATGAAACGCTAAATGCCTTTGAGTTA
1 TGTGCATTT-GACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTA
1403300 AAGATTAAATGCCTAGC
65 AAGATTAAATGCCTAGC
* * *
1403317 TGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGG-TGAAATACCTATGAGTTA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCT-AAATGCCTTTGAGTTA
1403381 AAGATTAAATGCCTAGC
65 AAGATTAAATGCCTAGC
** * * * * *
1403398 TACGCATTTGACACAAATGTGTCAATTATGCCAGTTAGATGAAAGGATAAAGGCCTTTGAGTTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
* ** * *
1403463 ATATTAGTTGCCTTGT
66 AGATTAAATGCCTAGC
** * *
1403479 TGTGCATTTGGTAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGGTAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
1403544 AGATTAAATGCCTAGC
66 AGATTAAATGCCTAGC
* * * *
1403560 TGTGCATTTGGA-AGAAAAGTGTCTATCATGCCAGTTAGATGAAAGGGTAGATGCCTTTGAGGTA
1 TGTGCATTT-GACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTA
*
1403624 AAGATTAAATGCCTAGT
65 AAGATTAAATGCCTAGC
* ** * * * * * * *
1403641 TGTGCATTTGGCAGAATGGTGTCAATCATACAAGTTATATGAAATGCTAAATTCCTTTGGGTAAA
1 TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
* *
1403706 AGACTAAAT-CCATAAC
66 AGATTAAATGCC-TAGC
1403722 TGTGCATT
1 TGTGCATT
1403730 ATTCACATAA
Statistics
Matches: 929, Mismatches: 121, Indels: 23
0.87 0.11 0.02
Matches are distributed among these distances:
80 6 0.01
81 872 0.94
82 51 0.05
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (81 bp):
TGTGCATTTGACAGAAAAGTGTCAATCATGCCAGTTAGATGAAAGGCTAAATGCCTTTGAGTTAA
AGATTAAATGCCTAGC
Found at i:1422023 original size:65 final size:64
Alignment explanation
Indices: 1421861--1422070 Score: 189
Period size: 65 Copynumber: 3.2 Consensus size: 64
1421851 TTTTTCAAAG
* * * * * *
1421861 TGATGCACCGATGCACCAATCCATGCATCGATGCGC-CATGA-ATTAAATTG-AACATCAAATAC
1 TGATGCATCGATGCACC-ATACATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
1421923 ATT
62 ATT
* *
1421926 TCATGCATCGATGCA-CATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCATA-CATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
1421989 TT
63 TT
* * * * *
1421991 TGATGCATCGATGCACCAGT-CATGTATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCA-TACATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
1422055 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1422071 TCTTAGTGCA
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 64 0.53
66 5 0.04
67 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
TGATGCATCGATGCACCATACATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:1427909 original size:42 final size:44
Alignment explanation
Indices: 1427862--1427953 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 44
1427852 TGCTTCATGT
1427862 ATCGATACACC-T-AACAGTGCA-TCGATGCAT-CCTTGAATGTGC
1 ATCGATACACCATGAA-AGTGCACT-GATGCATGCCTTGAATGTGC
*
1427904 ATCGATACACCATGAAGGTGCACTGATGCATGCCTTGAATGTGC
1 ATCGATACACCATGAAAGTGCACTGATGCATGCCTTGAATGTGC
1427948 ATCGAT
1 ATCGAT
1427954 GCACAGGGTC
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
42 11 0.24
43 13 0.29
44 21 0.47
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (44 bp):
ATCGATACACCATGAAAGTGCACTGATGCATGCCTTGAATGTGC
Found at i:1427924 original size:21 final size:20
Alignment explanation
Indices: 1427862--1427925 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
1427852 TGCTTCATGT
1427862 ATCGATACACCT-AACAGTGC
1 ATCGATACACCTGAA-AGTGC
* *
1427882 ATCGATGCATCCTTGAATGTGC
1 ATCGATACA-CC-TGAAAGTGC
*
1427904 ATCGATACACCATGAAGGTGC
1 ATCGATACACC-TGAAAGTGC
1427925 A
1 A
1427926 CTGATGCATG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.22
21 13 0.36
22 13 0.36
23 2 0.06
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGATACACCTGAAAGTGC
Found at i:1427947 original size:23 final size:22
Alignment explanation
Indices: 1427878--1427956 Score: 99
Period size: 23 Copynumber: 3.6 Consensus size: 22
1427868 ACACCTAACA
1427878 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
* * *
1427900 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCATCCTTGAAT
1427921 GTGCA-CTGATGCATGCCTTGAAT
1 GTGCATC-GATGCAT-CCTTGAAT
1427944 GTGCATCGATGCA
1 GTGCATCGATGCA
1427957 CAGGGTCATG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.02
21 16 0.34
22 12 0.26
23 17 0.36
24 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:1427975 original size:43 final size:43
Alignment explanation
Indices: 1427862--1427979 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
1427852 TGCTTCATGT
*
1427862 ATCGATACACC--TAACAGTGCATCGATGCATCCTTGAATGTGC
1 ATCGATACACCAGGAACA-TGCATCGATGCATCCTTGAATGTGC
* **
1427904 ATCGATACACCATGAAGGTGCA-CTGATGCATGCCTTGAATGTGC
1 ATCGATACACCAGGAACATGCATC-GATGCAT-CCTTGAATGTGC
* **
1427948 ATCGATGCA-CAGGGTCATGCATCGATGCATCC
1 ATCGATACACCAGGAACATGCATCGATGCATCC
1427980 GTCGGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
42 14 0.23
43 25 0.40
44 23 0.37
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (43 bp):
ATCGATACACCAGGAACATGCATCGATGCATCCTTGAATGTGC
Found at i:1429510 original size:21 final size:21
Alignment explanation
Indices: 1429469--1429511 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1429459 CCCCGGGAGA
*
1429469 TAGCTCTTCACGAGCTGCTCC
1 TAGCTCTTCACGAGCTCCTCC
* *
1429490 TAGCTCTTCTCGTGCTCCTCC
1 TAGCTCTTCACGAGCTCCTCC
1429511 T
1 T
1429512 CCTCCTCCGG
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:0.09, C:0.40, G:0.16, T:0.35
Consensus pattern (21 bp):
TAGCTCTTCACGAGCTCCTCC
Found at i:1430188 original size:31 final size:31
Alignment explanation
Indices: 1430153--1430215 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1430143 AAAAGGGGGG
1430153 AAGTGTTAAAATCTTAAAAGGGAGAAGTGTT
1 AAGTGTTAAAATCTTAAAAGGGAGAAGTGTT
* *
1430184 AAGTGTTCAAATGTTAAAAGGGAGAAGTGTT
1 AAGTGTTAAAATCTTAAAAGGGAGAAGTGTT
1430215 A
1 A
1430216 TAGTAAGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.29
Consensus pattern (31 bp):
AAGTGTTAAAATCTTAAAAGGGAGAAGTGTT
Found at i:1434958 original size:18 final size:17
Alignment explanation
Indices: 1434935--1434988 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
1434925 GGAATGTTTA
1434935 TGAGGGAATTGAAATCTG
1 TGAGGGAATTG-AATCTG
*
1434953 TGAGGGAATTTGAATCTT
1 TGAGGGAA-TTGAATCTG
*
1434971 TCA-GGAATTGGAATCTG
1 TGAGGGAATT-GAATCTG
1434988 T
1 T
1434989 CAAAAATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 2 0.06
17 11 0.35
18 15 0.48
19 3 0.10
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (17 bp):
TGAGGGAATTGAATCTG
Found at i:1439188 original size:3 final size:3
Alignment explanation
Indices: 1439180--1439216 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1439170 TGTATAATTT
1439180 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1439217 ACCTATATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1442514 original size:44 final size:44
Alignment explanation
Indices: 1442354--1442616 Score: 368
Period size: 44 Copynumber: 6.0 Consensus size: 44
1442344 ATACCATGAG
* ** * *
1442354 TGGCACGTTTCTGCCAATAATGTTCCGTTATGCA-TTCCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* *
1442397 TGGCACCTTTCTACCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* * *
1442441 TGACACC-TTCTGCCAAAAATGCACAATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* *
1442484 TGGTAGCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* * * *
1442528 TGGCACCTTTCTGCCAATAATGCACCGTTCTACATTTCCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1442572 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1442616 T
1 T
1442617 TTTAGAGTAG
Statistics
Matches: 193, Mismatches: 25, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
43 66 0.34
44 127 0.66
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.38
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
Found at i:1445618 original size:17 final size:17
Alignment explanation
Indices: 1445596--1445648 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1445586 AATTAAGAGT
1445596 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
1445613 TAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAAC
*
1445630 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
1445647 TA
1 TA
1445649 ACTTTATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1448462 original size:44 final size:43
Alignment explanation
Indices: 1448302--1448564 Score: 321
Period size: 44 Copynumber: 6.0 Consensus size: 43
1448292 ATACCATGAG
*** * *
1448302 TGGCACGTTTCTGCCAATAATGTTTCGTTATGCA-TTCCATTTA
1 TGGCAC-TTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
*
1448345 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCA-CTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* * * **
1448389 TGACACCTTCTGCCAAAAATGCAAAATTATGCATTTTCATTTA
1 TGGCACTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
*
1448432 TGGTAGCTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCA-CTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
* * * * *
1448476 TGGCACCGTTCTGCCAATAATGCACCGTTCTACATTTCCATTTA
1 TGGCA-CTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1448520 TGGCACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1 TGGCAC-TTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
1448564 T
1 T
1448565 TTTAGAGTAG
Statistics
Matches: 188, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
43 66 0.35
44 122 0.65
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.38
Consensus pattern (43 bp):
TGGCACTTTCTGCCAATAATGCACCATTATGCATTTTCATTTA
Found at i:1451565 original size:17 final size:17
Alignment explanation
Indices: 1451543--1451595 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1451533 AATTAAGAGT
1451543 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
1451560 TAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAAC
*
1451577 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
1451594 TA
1 TA
1451596 ACTTTATTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1454534 original size:17 final size:17
Alignment explanation
Indices: 1454512--1454564 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1454502 AATTAAGAGT
1454512 TAGTTTAATAAATAAAC
1 TAGTTTAATAAATAAAC
* *
1454529 TAGTTTGATGAATTAAA-
1 TAGTTTAAT-AAATAAAC
* *
1454546 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATAAAC
1454563 TA
1 TA
1454565 ACTTTATTCA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
16 4 0.14
17 18 0.64
18 6 0.21
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATAAAC
Found at i:1458408 original size:17 final size:17
Alignment explanation
Indices: 1458386--1458438 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
1458376 AATTAAGAGT
1458386 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
1458403 TAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAAC
*
1458420 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
1458437 TA
1 TA
1458439 ACTTTATTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1458451 original size:18 final size:17
Alignment explanation
Indices: 1458389--1458444 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1458379 TAAGAGTTAG
* *
1458389 TTTAATAAATGAACTAG
1 TTTAATTAATGAACTAC
* * *
1458406 TTTGATGAATGAACTAG
1 TTTAATTAATGAACTAC
1458423 TTTAATTAATGAACTAAC
1 TTTAATTAATGAACT-AC
1458441 TTTA
1 TTTA
1458445 TTCAATGTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
17 28 0.85
18 5 0.15
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (17 bp):
TTTAATTAATGAACTAC
Found at i:1459986 original size:46 final size:46
Alignment explanation
Indices: 1459873--1460507 Score: 858
Period size: 46 Copynumber: 13.8 Consensus size: 46
1459863 GTATATTTTA
* * * *
1459873 ATGCATTAATACATCCATTCATGCATTTTAGTTATGGCATCCTTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC-TTTC
* ** * *
1459920 AAGCCTTAATTAATCCTTTCATGCATTTTAGTTATGACATCCTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* * **
1459966 ATGCCTTAATGTATCATTTCATGCATTTTTAATTATGTAATCCTTTC
1 ATGCCTTAATGCATCCTTTCATGCA-TTTTAATTATGGCATCCTTTC
* * *
1460013 ATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCCTTTA
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
*
1460059 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCGTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* * * * *
1460105 ATGCCTTAATGAATTCTTTCATGTATTTTAATCATGGCATCCGTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* * *
1460151 ATGCC-TAATGCATCATTTCATGCATTTTAATTATGACATCTTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* * *
1460196 ATGCCTTAATGCATCCTTTCATACATTTTAATTATGACATCCGTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* * *
1460242 AAGCCTTAATGAATCCTTTCATGCATTTTAATTATGGTATCCTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
** * *
1460288 ACACCTTAATACATCCTTTCATGCATTTTAATTATGGCATCCGTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* *
1460334 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGAATCCGTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* * *
1460380 ATGCCTAAATGCATCCTTTCATGCATTTTAGTTATGGCATCCGTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
*
1460426 ATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTC
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
* *
1460472 ATGCCTTAATGCAACTTTTCATGCATTTTAATTATG
1 ATGCCTTAATGCATCCTTTCATGCATTTTAATTATG
1460508 AATTCGATTT
Statistics
Matches: 523, Mismatches: 63, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
45 37 0.07
46 408 0.78
47 78 0.15
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (46 bp):
ATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTC
Found at i:1459987 original size:20 final size:20
Alignment explanation
Indices: 1459962--1460036 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 20
1459952 TATGACATCC
1459962 TTTCATGCCTTAATGTATCA
1 TTTCATGCCTTAATGTATCA
* *
1459982 TTTCATGCATTTTTAATTATGTAATCC
1 TTTCATGC---CTT-A--ATGT-ATCA
*
1460009 TTTCATGCCTTAATGCATCA
1 TTTCATGCCTTAATGTATCA
1460029 TTTCATGC
1 TTTCATGC
1460037 ATTTTAGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
20 19 0.44
21 3 0.07
23 3 0.07
24 3 0.07
26 4 0.09
27 11 0.26
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTCATGCCTTAATGTATCA
Found at i:1467224 original size:46 final size:47
Alignment explanation
Indices: 1467174--1467346 Score: 153
Period size: 46 Copynumber: 3.7 Consensus size: 47
1467164 TTTAGTCTTT
* * *
1467174 ATTCAT-TAATTTCAGTTATGGTCTTTTTTCATGCATTAATACATCC
1 ATTCATGTAATTTTAGTTATGGTCTCTTTTCATGCCTTAATACATCC
* *
1467220 ATTCATG-CATTTTAGTTATGGTATCCTTTTCATGCCTTAATGA-ATCC
1 ATTCATGTAATTTTAGTTATGGTCT-CTTTTCATGCCTTAAT-ACATCC
* * * * *
1467267 TTTCATG-CACTTTAGTTATGG-CATCCTTTCATGCCTTAATGCATCC
1 ATTCATGTAATTTTAGTTATGGTC-TCTTTTCATGCCTTAATACATCC
* *
1467313 TTTCATGT-ATTTTAGTTATGG-CATCCTTTCATGC
1 ATTCATGTAATTTTAGTTATGGTC-TCTTTTCATGC
1467347 ATTTTAATTA
Statistics
Matches: 110, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
46 71 0.65
47 38 0.35
48 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (47 bp):
ATTCATGTAATTTTAGTTATGGTCTCTTTTCATGCCTTAATACATCC
Found at i:1467272 original size:20 final size:20
Alignment explanation
Indices: 1467242--1467319 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1467232 TAGTTATGGT
*
1467242 ATCCTTTTCATGCCTTAATGA
1 ATCC-TTTCATGCCTTAATGC
1467263 ATCCTTTCATGCACTTTAGTTATGGC
1 ATCCTTTCATGC-C-TTA---AT-GC
1467289 ATCCTTTCATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
1467309 ATCCTTTCATG
1 ATCCTTTCATG
1467320 TATTTTAGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
20 21 0.42
21 7 0.14
22 3 0.06
24 3 0.06
25 3 0.06
26 13 0.26
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.42
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:1467272 original size:47 final size:46
Alignment explanation
Indices: 1467200--1467346 Score: 215
Period size: 46 Copynumber: 3.2 Consensus size: 46
1467190 TATGGTCTTT
* * *
1467200 TTTCATGCATTAAT-ACATCCATTCATGCATTTTAGTTATGGTATCC
1 TTTCATGCCTTAATGA-ATCCTTTCATGCATTTTAGTTATGGCATCC
*
1467246 TTTTCATGCCTTAATGAATCCTTTCATGCACTTTAGTTATGGCATCC
1 -TTTCATGCCTTAATGAATCCTTTCATGCATTTTAGTTATGGCATCC
* *
1467293 TTTCATGCCTTAATGCATCCTTTCATGTATTTTAGTTATGGCATCC
1 TTTCATGCCTTAATGAATCCTTTCATGCATTTTAGTTATGGCATCC
1467339 TTTCATGC
1 TTTCATGC
1467347 ATTTTAATTA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
46 51 0.55
47 40 0.43
48 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (46 bp):
TTTCATGCCTTAATGAATCCTTTCATGCATTTTAGTTATGGCATCC
Found at i:1467346 original size:72 final size:72
Alignment explanation
Indices: 1467263--1467707 Score: 460
Period size: 72 Copynumber: 6.3 Consensus size: 72
1467253 GCCTTAATGA
* * * *
1467263 ATCCTTTCATGCACTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGTATTTTAG
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1467328 TTATGGC
66 TTATGGC
* *
1467335 ATCCTTTCATGCATTTTAATTATGGCAT-CTGTTCATGCCTTAATACATCCTTTCATGTATTTTA
1 ATCCTTTCATGCATTTTAATTATGGCATCCT-TTCATGCCTTAATGCATCCTTTCATGCATTTTA
1467399 ATTATGGC
65 ATTATGGC
* * *
1467407 ATTCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGAATCCATTCATGC
1 A-TCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATGC
*
1467472 --CTT-A--AT-GC
59 ATTTTAATTATGGC
* * *
1467480 GTCCTTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAATGAATCCTTTCATGCATTTTAA
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
*
1467545 TTATGAC
66 TTATGGC
* * * *
1467552 ATCCATTCATGCATTTTAATTATGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTTAG
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
*
1467617 TTATGGA
66 TTATGGC
* * * *
1467624 ATACGTTCATGC--TTT-A--AT-GCATCCTTTCATGCCTTATTGCATCCTTTTATGC--TTT-A
1 ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1467680 --AT-GC
66 TTATGGC
* *
1467684 ACCCTTTCATGTATTTTAATTATG
1 ATCCTTTCATGCATTTTAATTATG
1467708 AATTCGATTA
Statistics
Matches: 315, Mismatches: 37, Indels: 48
0.79 0.09 0.12
Matches are distributed among these distances:
60 9 0.03
61 2 0.01
62 3 0.01
63 1 0.00
64 3 0.01
65 2 0.01
66 43 0.14
67 4 0.01
68 2 0.01
69 3 0.01
70 5 0.02
71 4 0.01
72 176 0.56
73 36 0.11
74 4 0.01
75 2 0.01
76 2 0.01
77 2 0.01
78 2 0.01
79 10 0.03
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.44
Consensus pattern (72 bp):
ATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
TTATGGC
Found at i:1467384 original size:46 final size:45
Alignment explanation
Indices: 1467334--1467563 Score: 255
Period size: 46 Copynumber: 4.8 Consensus size: 45
1467324 TTAGTTATGG
1467334 CATCCTTTCATGCATTTTAATTATGGCATCTGTTCATGCCTTAATA
1 CATCCTTTCATGCATTTTAATTATGGCATCT-TTCATGCCTTAATA
* *
1467380 CATCCTTTCATGTATTTTAATTATGGCATTCCTTTCATGCATTTTAATTA
1 CATCCTTTCATGCATTTTAATTATGGCA-T-CTTTCATGC--CTTAA-TA
* * *
1467430 TGGCATCCTTTCATGCATTTTAATTATGGAATCCATTCATGCCTTAATG
1 ---CATCCTTTCATGCATTTTAATTATGGCAT-CTTTCATGCCTTAATA
* *
1467479 CGTCCTTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAATGA
1 CATCCTTTCATGCATTTTAATTATGGCAT-CTTTCATGCCTTAAT-A
* *
1467526 -ATCCTTTCATGCATTTTAATTATGACATCCATTCATGC
1 CATCCTTTCATGCATTTTAATTATGGCAT-CTTTCATGC
1467564 ATTTTAATTA
Statistics
Matches: 159, Mismatches: 16, Indels: 18
0.82 0.08 0.09
Matches are distributed among these distances:
46 102 0.64
47 8 0.05
48 2 0.01
49 5 0.03
50 6 0.04
52 10 0.06
53 26 0.16
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (45 bp):
CATCCTTTCATGCATTTTAATTATGGCATCTTTCATGCCTTAATA
Found at i:1467431 original size:99 final size:97
Alignment explanation
Indices: 1467307--1467563 Score: 353
Period size: 99 Copynumber: 2.7 Consensus size: 97
1467297 ATGCCTTAAT
* **
1467307 GCATCCTTTCATGTATTTTAGTTATGGCATCCTTTCATGCATTTTAATTATGGCATCTGTTCATG
1 GCATCCTTTCATG-ATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCATTCATG
*
1467372 CCTTAATACATCCTTTCATGTATTTTAATTATG
65 CCTTAATACATCCTTTCATGCATTTTAATTATG
*
1467405 GCATTCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGAATCCATTCAT
1 GCA-TCCTTTCATG-ATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCATTCAT
* *
1467470 GCCTTAATGCGTCCTTTCATGCATTTTAATTATG
64 GCCTTAATACATCCTTTCATGCATTTTAATTATG
** * *
1467504 GCATCCTTTCAT-ACCTT-A--AT-GAATCCTTTCATGCATTTTAATTATGACATCCATTCATGC
1 GCATCCTTTCATGATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCATTCATGC
1467564 ATTTTAATTA
Statistics
Matches: 145, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
92 37 0.26
93 2 0.01
95 1 0.01
96 3 0.02
98 12 0.08
99 90 0.62
ACGTcount: A:0.24, C:0.21, G:0.11, T:0.44
Consensus pattern (97 bp):
GCATCCTTTCATGATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGCATCCATTCATGC
CTTAATACATCCTTTCATGCATTTTAATTATG
Found at i:1467569 original size:118 final size:118
Alignment explanation
Indices: 1467409--1467655 Score: 377
Period size: 118 Copynumber: 2.1 Consensus size: 118
1467399 ATTATGGCAT
* *
1467409 TCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCATTTTAATTATGGAATCCATTCATGCCT
1 TCCTTTCATGCATTTTAATTATGACATCCATTCATGCATTTTAATTATGGAATCCATTCATGCCT
* * * * *
1467474 TAATGCGTCCTTTCATGCATTTTAATTATGGCATCCTTTCATACCTTAATGAA
66 TAATGCATCATTTCATGCATTTTAATTATGGAATACGTTCATACCTTAATGAA
* *
1467527 TCCTTTCATGCATTTTAATTATGACATCCATTCATGCATTTTAATTATGGCATCCGTTCATGCCT
1 TCCTTTCATGCATTTTAATTATGACATCCATTCATGCATTTTAATTATGGAATCCATTCATGCCT
* * * *
1467592 TAATGCATCATTTCATGCATTTTAGTTATGGAATACGTTCATGCTTTAATGCA
66 TAATGCATCATTTCATGCATTTTAATTATGGAATACGTTCATACCTTAATGAA
1467645 TCCTTTCATGC
1 TCCTTTCATGC
1467656 CTTATTGCAT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (118 bp):
TCCTTTCATGCATTTTAATTATGACATCCATTCATGCATTTTAATTATGGAATCCATTCATGCCT
TAATGCATCATTTCATGCATTTTAATTATGGAATACGTTCATACCTTAATGAA
Found at i:1467607 original size:46 final size:46
Alignment explanation
Indices: 1467557--1467655 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
1467547 ATGACATCCA
* *
1467557 TTCATGCATTTTAATTATGGCATCCGTTCATGCCTTAATGCATCAT
1 TTCATGCATTTTAATTATGGAATACGTTCATGCCTTAATGCATCAT
* * *
1467603 TTCATGCATTTTAGTTATGGAATACGTTCATGCTTTAATGCATCCT
1 TTCATGCATTTTAATTATGGAATACGTTCATGCCTTAATGCATCAT
1467649 TTCATGC
1 TTCATGC
1467656 CTTATTGCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.42
Consensus pattern (46 bp):
TTCATGCATTTTAATTATGGAATACGTTCATGCCTTAATGCATCAT
Found at i:1467654 original size:20 final size:20
Alignment explanation
Indices: 1467460--1467694 Score: 101
Period size: 20 Copynumber: 10.6 Consensus size: 20
1467450 TAATTATGGA
* *
1467460 ATCCATTCATGCCTTAATGC
1 ATCCTTTCATGCTTTAATGC
*
1467480 GTCCTTTCATGCATTTTAATTATGGC
1 ATCCTTTCATGC--TTT-A--AT-GC
* * *
1467506 ATCCTTTCATACCTTAATGA
1 ATCCTTTCATGCTTTAATGC
1467526 ATCCTTTCATGCATTTTAATTATGAC
1 ATCCTTTCATGC--TTT-A--ATG-C
*
1467552 ATCCATTCATGCATTTTAATTATGGC
1 ATCCTTTCATGC--TTT-A--AT-GC
* *
1467578 ATCCGTTCATGCCTTAATGC
1 ATCCTTTCATGCTTTAATGC
* *
1467598 ATCATTTCATGCATTTTAGTTATGGA
1 ATCCTTTCATGC--TTTA---AT-GC
* *
1467624 ATACGTTCATGCTTTAATGC
1 ATCCTTTCATGCTTTAATGC
* *
1467644 ATCCTTTCATGCCTTATTGC
1 ATCCTTTCATGCTTTAATGC
*
1467664 ATCCTTTTATGCTTTAATGC
1 ATCCTTTCATGCTTTAATGC
*
1467684 ACCCTTTCATG
1 ATCCTTTCATG
1467695 TATTTTAATT
Statistics
Matches: 166, Mismatches: 30, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
20 77 0.46
21 6 0.04
22 7 0.04
23 4 0.02
24 8 0.05
25 7 0.04
26 56 0.34
27 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (20 bp):
ATCCTTTCATGCTTTAATGC
Found at i:1475751 original size:17 final size:17
Alignment explanation
Indices: 1475698--1475774 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
1475688 TGAAACAACT
* * *
1475698 ATGAGCTATTTTAATAA
1 ATGAACTATTTTAGTTA
* *
1475715 ATGAACTAGTTT-GATGA
1 ATGAACTATTTTAG-TTA
1475732 ATGAACTATTTTAGTTA
1 ATGAACTATTTTAGTTA
*
1475749 ATGAACTAACTTTA-TTCA
1 ATGAACT-ATTTTAGTT-A
1475767 ATGAACTA
1 ATGAACTA
1475775 ATACTATTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 35 0.71
18 14 0.29
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (17 bp):
ATGAACTATTTTAGTTA
Found at i:1475769 original size:18 final size:18
Alignment explanation
Indices: 1475731--1475775 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1475721 TAGTTTGATG
*
1475731 AATGAACT-ATTTTAGTT
1 AATGAACTAACTTTAGTT
1475748 AATGAACTAACTTTA-TT
1 AATGAACTAACTTTAGTT
1475765 CAATGAACTAA
1 -AATGAACTAA
1475776 TACTATTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (18 bp):
AATGAACTAACTTTAGTT
Found at i:1481729 original size:13 final size:13
Alignment explanation
Indices: 1481711--1481735 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1481701 AATTCTATCC
1481711 CTTTCATTTCTTT
1 CTTTCATTTCTTT
1481724 CTTTCATTTCTT
1 CTTTCATTTCTT
1481736 ATTTCCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTCATTTCTTT
Found at i:1481899 original size:17 final size:17
Alignment explanation
Indices: 1481877--1481921 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1481867 ACATCACTAT
**
1481877 TGAATGAACTAGTTTGA
1 TGAATGAACTAGTTCAA
1481894 TGAATGAACTAGTTCAA
1 TGAATGAACTAGTTCAA
*
1481911 TCAATGAACTA
1 TGAATGAACTA
1481922 CTTAGTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (17 bp):
TGAATGAACTAGTTCAA
Found at i:1481933 original size:17 final size:17
Alignment explanation
Indices: 1481913--1481967 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1481903 TAGTTCAATC
* *
1481913 AATGAACTACTTAGTTA
1 AATGAACTACATAGCTA
* *
1481930 AATGAATTGCATAGCTA
1 AATGAACTACATAGCTA
1481947 AATGAACTACAT-GCTTA
1 AATGAACTACATAGC-TA
1481964 AATG
1 AATG
1481968 CAATCAATGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 2 0.06
17 29 0.94
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (17 bp):
AATGAACTACATAGCTA
Found at i:1488882 original size:19 final size:20
Alignment explanation
Indices: 1488844--1488883 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1488834 ATCATTCACT
*
1488844 TGCATACTATATGATTTTCA
1 TGCATAATATATGATTTTCA
*
1488864 TGCATAATATA-GGTTTTCA
1 TGCATAATATATGATTTTCA
1488883 T
1 T
1488884 ATATTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (20 bp):
TGCATAATATATGATTTTCA
Found at i:1489208 original size:40 final size:41
Alignment explanation
Indices: 1489152--1489306 Score: 201
Period size: 40 Copynumber: 3.9 Consensus size: 41
1489142 TTGGGACAGT
* * *
1489152 TTAGTGGAGTATTTGGAAGACATATACATCTTACAAACAAC
1 TTAGTGGAGCATTTGGAAGACATATACAACTCACAAACAAC
*
1489193 TTAGTGG-GCATTTGGAAGACATATACAACACACAAACAAC
1 TTAGTGGAGCATTTGGAAGACATATACAACTCACAAACAAC
* * * *
1489233 TTAGTGAAGCA--T-GAATACATATACAACTCATAAACAGC
1 TTAGTGGAGCATTTGGAAGACATATACAACTCACAAACAAC
*
1489271 TTAGTGGAGCATTTGGAAGACATATACAGCTCACAA
1 TTAGTGGAGCATTTGGAAGACATATACAACTCACAA
1489307 CTGAACCAAC
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
38 32 0.33
39 1 0.01
40 36 0.37
41 28 0.29
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (41 bp):
TTAGTGGAGCATTTGGAAGACATATACAACTCACAAACAAC
Found at i:1490294 original size:16 final size:16
Alignment explanation
Indices: 1490260--1490296 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1490250 GTAAGTTATC
*
1490260 TTCATTTTCTTACTAT
1 TTCATTTTCTTAATAT
*
1490276 TTCATTTTCTTAATCT
1 TTCATTTTCTTAATAT
1490292 TTCAT
1 TTCAT
1490297 ATTTTCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (16 bp):
TTCATTTTCTTAATAT
Found at i:1490374 original size:17 final size:17
Alignment explanation
Indices: 1490349--1490381 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1490339 ATCCTACCTT
1490349 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
*
1490366 TACCCTAACCATTTCT
1 TACCATAACCATTTCT
1490382 TTTAAGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:1496861 original size:24 final size:24
Alignment explanation
Indices: 1496833--1496886 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1496823 TCTATGTCTT
*
1496833 CAATGGTCACATCCTTTAAGCTTC
1 CAATGGTCACATCCTTTAAACTTC
* *
1496857 CAATGGTTACGTCCTTTAAACTTC
1 CAATGGTCACATCCTTTAAACTTC
1496881 CAATGG
1 CAATGG
1496887 CCACGACCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (24 bp):
CAATGGTCACATCCTTTAAACTTC
Found at i:1508728 original size:15 final size:15
Alignment explanation
Indices: 1508693--1508735 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1508683 GAAATATGAA
*
1508693 ATAAGAAATGGAA-G
1 ATAAGAAATGAAATG
1508707 A-AAGAAATGAAATG
1 ATAAGAAATGAAATG
*
1508721 ATAAGAAAGGAAATG
1 ATAAGAAATGAAATG
1508736 GAAATGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.40
14 3 0.12
15 12 0.48
ACGTcount: A:0.60, C:0.00, G:0.26, T:0.14
Consensus pattern (15 bp):
ATAAGAAATGAAATG
Found at i:1508741 original size:21 final size:19
Alignment explanation
Indices: 1508704--1508742 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
1508694 TAAGAAATGG
1508704 AAGAAAGAAATGAAATGAT
1 AAGAAAGAAATGAAATGAT
1508723 AAGAAAGGAAATGGAAATGA
1 AAGAAA-GAAAT-GAAATGA
1508743 AAGTAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 5 0.28
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (19 bp):
AAGAAAGAAATGAAATGAT
Found at i:1509146 original size:20 final size:22
Alignment explanation
Indices: 1509121--1509164 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
1509111 CACCCGCGGC
1509121 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
*
1509141 ATCCATCCATCCATATATATAT
1 ATCCATCCACCCATATATATAT
1509163 AT
1 AT
1509165 ATTATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:1509158 original size:2 final size:2
Alignment explanation
Indices: 1509153--1509211 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
1509143 CCATCCATCC
1509153 AT AT AT AT AT AT AT -T AT AT -T AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1509192 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1509212 TTTAAAAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1509553 original size:17 final size:17
Alignment explanation
Indices: 1509504--1509553 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
1509494 ATTTTTCATA
1509504 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
1509521 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
1509535 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
1509552 TT
1 TT
1509554 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:1513109 original size:40 final size:40
Alignment explanation
Indices: 1513054--1513215 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
1513044 TGCAGGTTTA
1513054 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * * *
1513094 TAATACATTTCGGTGTAAATGTTGGGCACGACCTCATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1513134 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1513174 TAATACACTTCGGTGTATATAGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1513214 TA
1 TA
1513216 GCACTACAGT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1513409 original size:45 final size:45
Alignment explanation
Indices: 1513320--1513530 Score: 311
Period size: 45 Copynumber: 4.7 Consensus size: 45
1513310 GTAAGCATGC
*
1513320 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1513364 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1513409 AAATAAGCTTACGAGCTTAT-GATATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGA-ATAAATGGTAAGTATATTGGTA
* * * * *
1513454 AAATAAGATTGCGAGCTTATGTAATAAATGGTAACTATTTTGG-A
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
1513498 CAAATAAGCTTACAAGCTTATGGGATAAATGGT
1 -AAATAAGCTTACGAGCTTATGGAATAAATGGT
1513531 GAGAAATTTT
Statistics
Matches: 152, Mismatches: 11, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
44 28 0.18
45 123 0.81
46 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:1514693 original size:29 final size:26
Alignment explanation
Indices: 1514624--1514699 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 26
1514614 AAATTCAGTA
* *
1514624 AAGAAAAAGTACAAGCACTC-AAAAG
1 AAGAAAAAATTCAAGCACTCAAAAAG
1514649 AAGAAAAAATTCAAGCACTCAAAAAG
1 AAGAAAAAATTCAAGCACTCAAAAAG
*
1514675 AAGAAAGAAAAGTTGAAGCACTCAA
1 AAG-AA-AAAA-TTCAAGCACTCAA
1514700 CAACAAGTCT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 18 0.41
26 8 0.18
27 2 0.05
28 4 0.09
29 12 0.27
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.11
Consensus pattern (26 bp):
AAGAAAAAATTCAAGCACTCAAAAAG
Found at i:1518975 original size:24 final size:24
Alignment explanation
Indices: 1518926--1518977 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1518916 GGTACAACTT
* *
1518926 CCTTACATCAAGTGGCATCAGAAG
1 CCTTACATCAAGCGGAATCAGAAG
1518950 CCTTACATCAAGCGGTAATCAG-AG
1 CCTTACATCAAGCGG-AATCAGAAG
1518974 CCTT
1 CCTT
1518978 GGTGGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (24 bp):
CCTTACATCAAGCGGAATCAGAAG
Found at i:1522109 original size:47 final size:47
Alignment explanation
Indices: 1522015--1522142 Score: 190
Period size: 47 Copynumber: 2.8 Consensus size: 47
1522005 GTAACCATGC
*
1522015 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
* * * *
1522059 AAATAAGCTTACGATCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
1522106 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAG
1 AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAG
1522143 AGATTTTATA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
44 22 0.30
46 1 0.01
47 51 0.69
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (47 bp):
AAATAAGCTTATGAGCTTATGGAATTTAAATGGTAAGTATATTGGAA
Found at i:1529409 original size:47 final size:45
Alignment explanation
Indices: 1529315--1529487 Score: 240
Period size: 47 Copynumber: 3.8 Consensus size: 45
1529305 GTAACCATGC
* * * *
1529315 AAATAAGCTTATGAGCTTATGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
*
1529359 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGCTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGGTA
1529406 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATTTTGGTA
* *
1529453 AAATAAACTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1529488 AGATTTTATA
Statistics
Matches: 118, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.19
45 11 0.09
46 1 0.01
47 83 0.70
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATTTTGGTA
Found at i:1540966 original size:16 final size:16
Alignment explanation
Indices: 1540945--1540982 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1540935 CTTGGCTTGC
1540945 TTTCTTTTTGATTTT-T
1 TTTCTTTTT-ATTTTCT
*
1540961 TTTCTTTTTCTTTTCT
1 TTTCTTTTTATTTTCT
1540977 TTTCTT
1 TTTCTT
1540983 CTTTTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTATTTTCT
Found at i:1540979 original size:20 final size:21
Alignment explanation
Indices: 1540962--1541019 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 21
1540952 TTGATTTTTT
1540962 TTCTTTTTCTTTTC-TT-TTC
1 TTCTTTTTCTTTTCTTTATTC
1540981 TTC-TTTTCTGTTT-TTTATTC
1 TTCTTTTTCT-TTTCTTTATTC
1541001 TTCTTTTTGTCTTTTCTTT
1 TTC-TTTT-TCTTTTCTTT
1541020 CTTTTTGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 6 0.19
22 6 0.19
23 6 0.19
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (21 bp):
TTCTTTTTCTTTTCTTTATTC
Found at i:1540984 original size:13 final size:12
Alignment explanation
Indices: 1540956--1541019 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 12
1540946 TTCTTTTTGA
1540956 TTTT-TTTTC-T
1 TTTTCTTTTCTT
1540966 TTTTCTTTTCTT
1 TTTTCTTTTCTT
1540978 TTCTTCTTTTCTGTT
1 TT-TTCTTTTC--TT
*
1540993 TTTTATTCTTCTT
1 TTTTCTT-TTCTT
1541006 TTTGTCTTTTCTT
1 TTT-TCTTTTCTT
1541019 T
1 T
1541020 CTTTTTGTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
10 4 0.09
11 5 0.11
12 3 0.07
13 19 0.42
14 7 0.16
15 7 0.16
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.80
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:1541004 original size:28 final size:27
Alignment explanation
Indices: 1540965--1541017 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
1540955 ATTTTTTTTC
*
1540965 TTTTTCTTTTCTTTTCT-TCTTTTCTGT
1 TTTTTATTTTCTTTT-TGTCTTTTCTGT
1540992 TTTTTATTCTTCTTTTTGTCTTTTCT
1 TTTTTATT-TTCTTTTTGTCTTTTCT
1541018 TTCTTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (27 bp):
TTTTTATTTTCTTTTTGTCTTTTCTGT
Found at i:1541014 original size:36 final size:36
Alignment explanation
Indices: 1540944--1541026 Score: 109
Period size: 36 Copynumber: 2.3 Consensus size: 36
1540934 CCTTGGCTTG
*
1540944 CTTTCTTTTTGATTTTTTTTCTTTTTCTTTTCTTTT
1 CTTTCTTTTTGATTTTTTTTCTTTTTCTTGTCTTTT
1540980 C-TTCTTTTCTG-TTTTTTATTCTTCTTT-TTGTCTTTT
1 CTTTCTTTT-TGATTTTTT-TTCTT-TTTCTTGTCTTTT
1541016 CTTTCTTTTTG
1 CTTTCTTTTTG
1541027 TACTCCAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
35 13 0.31
36 19 0.45
37 10 0.24
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (36 bp):
CTTTCTTTTTGATTTTTTTTCTTTTTCTTGTCTTTT
Found at i:1541021 original size:20 final size:20
Alignment explanation
Indices: 1540965--1541022 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1540955 ATTTTTTTTC
1540965 TTTT-TCTTTTCTTTTCTTCT
1 TTTTGTCTTTTC-TTTCTTCT
1540985 TTTCTGT-TTTT-TATTCTTCT
1 TTT-TGTCTTTTCT-TTCTTCT
1541005 TTTTGTCTTTTCTTTCTT
1 TTTTGTCTTTTCTTTCTT
1541023 TTTGTACTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
19 4 0.12
20 22 0.67
21 6 0.18
22 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTGTCTTTTCTTTCTTCT
Found at i:1543786 original size:2 final size:2
Alignment explanation
Indices: 1543779--1543814 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1543769 TGGAAGCGGA
*
1543779 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1543815 GTTGGTGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1547070 original size:13 final size:15
Alignment explanation
Indices: 1547047--1547078 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1547037 CTTCTTTCCA
1547047 TTTTGCTTTCTTT-G
1 TTTTGCTTTCTTTAG
1547061 TTTT-CTTTCTTTAG
1 TTTTGCTTTCTTTAG
1547075 TTTT
1 TTTT
1547079 TCTTCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.75
Consensus pattern (15 bp):
TTTTGCTTTCTTTAG
Found at i:1547378 original size:2 final size:2
Alignment explanation
Indices: 1547371--1547408 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1547361 TATGGAAACA
1547371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1547409 GTTGGTGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550659 original size:13 final size:15
Alignment explanation
Indices: 1550636--1550667 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1550626 CTTCTTTCCA
1550636 TTTTGCTTTCTTT-G
1 TTTTGCTTTCTTTAG
1550650 TTTT-CTTTCTTTAG
1 TTTTGCTTTCTTTAG
1550664 TTTT
1 TTTT
1550668 TCTTCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.03, C:0.12, G:0.09, T:0.75
Consensus pattern (15 bp):
TTTTGCTTTCTTTAG
Found at i:1550969 original size:2 final size:2
Alignment explanation
Indices: 1550962--1551029 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
1550952 TGGAAACAAA
1550962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1551004 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1551030 GTTGGTGATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1558556 original size:23 final size:25
Alignment explanation
Indices: 1558516--1558569 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
1558506 TTTTTTCTTT
1558516 TTTCTTCCTCTTTGAGTGCTTTCAA
1 TTTCTTCCTCTTTGAGTGCTTTCAA
* *
1558541 TTTCTT-CT-TTTGAGTGCTTTGAT
1 TTTCTTCCTCTTTGAGTGCTTTCAA
1558564 TTTCTT
1 TTTCTT
1558570 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 2 0.07
25 6 0.22
ACGTcount: A:0.09, C:0.19, G:0.13, T:0.59
Consensus pattern (25 bp):
TTTCTTCCTCTTTGAGTGCTTTCAA
Found at i:1560547 original size:48 final size:48
Alignment explanation
Indices: 1560491--1560583 Score: 186
Period size: 48 Copynumber: 1.9 Consensus size: 48
1560481 ACATCCATGG
1560491 TGTGATCAAGTCATGGAGAAAATTAGAGTTTGTTTGGATCGTATCGGA
1 TGTGATCAAGTCATGGAGAAAATTAGAGTTTGTTTGGATCGTATCGGA
1560539 TGTGATCAAGTCATGGAGAAAATTAGAGTTTGTTTGGATCGTATC
1 TGTGATCAAGTCATGGAGAAAATTAGAGTTTGTTTGGATCGTATC
1560584 AATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.29, C:0.09, G:0.28, T:0.34
Consensus pattern (48 bp):
TGTGATCAAGTCATGGAGAAAATTAGAGTTTGTTTGGATCGTATCGGA
Found at i:1578504 original size:12 final size:12
Alignment explanation
Indices: 1578487--1578511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1578477 TTTCAACACA
1578487 CTCATCTTCACT
1 CTCATCTTCACT
1578499 CTCATCTTCACT
1 CTCATCTTCACT
1578511 C
1 C
1578512 GAGACCTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.44, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCATCTTCACT
Found at i:1579036 original size:2 final size:2
Alignment explanation
Indices: 1579029--1579068 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1579019 TGGAAGCTGA
1579029 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1579069 GTTGGTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1582293 original size:19 final size:20
Alignment explanation
Indices: 1582269--1582311 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1582259 AGCATTTATC
**
1582269 TTCATT-AAAATTGTGTATT
1 TTCATTAAAAATCATGTATT
1582288 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
1582308 TTCA
1 TTCA
1582312 AAGGGGCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1582727 original size:35 final size:35
Alignment explanation
Indices: 1582653--1582757 Score: 156
Period size: 35 Copynumber: 3.0 Consensus size: 35
1582643 CTATTTGTTT
*
1582653 ATCACCATCTTCCATCACCATTTTCACGCCTATAAC
1 ATCACCATCTTCCATCACCA-TTTCACGCCTATATC
*
1582689 ATCACCATCTTCCATCACCATTGCACGCCTATATC
1 ATCACCATCTTCCATCACCATTTCACGCCTATATC
* * *
1582724 ATCACCAACTTCTATCACCATTTCACGCCGATAT
1 ATCACCATCTTCCATCACCATTTCACGCCTATAT
1582758 AACCACCAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 43 0.68
36 20 0.32
ACGTcount: A:0.28, C:0.38, G:0.05, T:0.30
Consensus pattern (35 bp):
ATCACCATCTTCCATCACCATTTCACGCCTATATC
Found at i:1584175 original size:20 final size:19
Alignment explanation
Indices: 1584138--1584177 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1584128 AAGATAATGC
*
1584138 ATGAAGCTTAAGAGCTAAT
1 ATGAAGCTTAAGAACTAAT
*
1584157 ATGAATGCTTATGAACTAAT
1 ATGAA-GCTTAAGAACTAAT
1584177 A
1 A
1584178 AAATGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (19 bp):
ATGAAGCTTAAGAACTAAT
Found at i:1585708 original size:24 final size:24
Alignment explanation
Indices: 1585614--1585700 Score: 95
Period size: 24 Copynumber: 3.6 Consensus size: 24
1585604 GGAGGATTGG
* *
1585614 AGGACGTGAGCATTGAGAA-ATTAA
1 AGGACGTGACCATTG-GAAGCTTAA
* **
1585638 AGGTCGTGACCATTGGAATTTTAA
1 AGGACGTGACCATTGGAAGCTTAA
*
1585662 AGGATGTGACCATTGGAAGCTTAA
1 AGGACGTGACCATTGGAAGCTTAA
*
1585686 AGTACGTGACCATTG
1 AGGACGTGACCATTG
1585701 ATGACTTAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.06
24 50 0.94
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (24 bp):
AGGACGTGACCATTGGAAGCTTAA
Found at i:1593646 original size:21 final size:19
Alignment explanation
Indices: 1593598--1593649 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
1593588 CGGCCAAGAG
*
1593598 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
1593617 CAGGTATTTTCATTTAAAAGT
1 CATGTATTTTCA-TTAAAA-T
1593638 CATGTATTTTCA
1 CATGTATTTTCA
1593650 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 12 0.43
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:1594366 original size:10 final size:9
Alignment explanation
Indices: 1594351--1594413 Score: 54
Period size: 10 Copynumber: 6.2 Consensus size: 9
1594341 ATTGGAGTGC
1594351 AAAAAGAAA
1 AAAAAGAAA
1594360 GAAAAAGACAA
1 -AAAAAGA-AA
1594371 AAGAAGAGAAA
1 AA-AA-AGAAA
*
1594382 AAAAATTAAA
1 AAAAA-GAAA
1594392 AAAGAAGAAA
1 AAA-AAGAAA
1594402 ATAAAAGAAA
1 A-AAAAGAAA
1594412 AA
1 AA
1594414 GAGAAGTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
9 2 0.04
10 28 0.62
11 12 0.27
12 3 0.07
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:1594384 original size:20 final size:19
Alignment explanation
Indices: 1594354--1594415 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 19
1594344 GGAGTGCAAA
*
1594354 AAGAAAGAAAAAGACAAAAG
1 AAGAAAAAAAAAGA-AAAAG
*
1594374 AAGAGAAAAAAAATTAAAAAAG
1 AAGA-AAAAAAAA--GAAAAAG
*
1594396 AAGAAAATAAAAGAAAAAG
1 AAGAAAAAAAAAGAAAAAG
1594415 A
1 A
1594416 GAAGTTCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 7 0.20
20 4 0.11
21 14 0.40
22 9 0.26
23 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (19 bp):
AAGAAAAAAAAAGAAAAAG
Found at i:1594412 original size:19 final size:20
Alignment explanation
Indices: 1594355--1594415 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
1594345 GAGTGCAAAA
1594355 AGAAAGAAAAAGACAAAAGAAG
1 AGAAA-AAAAAGA-AAAAGAAG
*
1594377 AGAAAAAAAATTAAAAAAGAAG
1 AGAAAAAAAA--GAAAAAGAAG
*
1594399 A-AAATAAAAGAAAAAGA
1 AGAAAAAAAAGAAAAAGA
1594416 GAAGTTCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 7 0.21
21 12 0.35
22 14 0.41
23 1 0.03
ACGTcount: A:0.77, C:0.02, G:0.16, T:0.05
Consensus pattern (20 bp):
AGAAAAAAAAGAAAAAGAAG
Found at i:1594651 original size:17 final size:18
Alignment explanation
Indices: 1594625--1594659 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1594615 ACCTTTGAAT
1594625 CATTTCTTCTAC-CTTTC
1 CATTTCTTCTACTCTTTC
*
1594642 CATTTTTTCTACTCTTTC
1 CATTTCTTCTACTCTTTC
1594660 TACCCTAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.57
Consensus pattern (18 bp):
CATTTCTTCTACTCTTTC
Found at i:1604775 original size:19 final size:21
Alignment explanation
Indices: 1604751--1604802 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
1604741 CGGCCAAGAG
*
1604751 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
1604770 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
1604791 CATGTATTTTCA
1 CATGTATTTTCA
1604803 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:1606657 original size:24 final size:24
Alignment explanation
Indices: 1606624--1606674 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1606614 TTCAGCAAAG
* *
1606624 AAATTGAAGCACTCCAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAGA
1606648 AAATTCAAGCACTCAAAAAGAAGA
1 AAATTCAAGCACTCAAAAAGAAGA
1606672 AAA
1 AAA
1606675 GAAAAGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.59, C:0.16, G:0.14, T:0.12
Consensus pattern (24 bp):
AAATTCAAGCACTCAAAAAGAAGA
Found at i:1608091 original size:21 final size:19
Alignment explanation
Indices: 1608067--1608105 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1608057 CCTCCCTGGT
1608067 TTATTAATTCTATTCATTTTG
1 TTATTAATT-T-TTCATTTTG
*
1608088 TTATTAGTTTTTCATTTT
1 TTATTAATTTTTCATTTT
1608106 ATAACTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.67
Consensus pattern (19 bp):
TTATTAATTTTTCATTTTG
Found at i:1613148 original size:19 final size:19
Alignment explanation
Indices: 1613126--1613178 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1613116 TGAACTTCTC
* *
1613126 TTTTTCTTTTCTTTTCTTA
1 TTTTTCTCTTCTTTTCTGA
1613145 TTTTTCTCTTCTTTTCTGA
1 TTTTTCTCTTCTTTTCTGA
1613164 TTTTTCTCTTCTTTT
1 TTTTTCTCTTCTTTT
1613179 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTCTCTTCTTTTCTGA
Found at i:1617662 original size:19 final size:19
Alignment explanation
Indices: 1617640--1617692 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1617630 TGAACTTCTC
* *
1617640 TTTTTCTTTTCTTTTCTTA
1 TTTTTCTCTTCTTTTCTGA
1617659 TTTTTCTCTTCTTTTCTGA
1 TTTTTCTCTTCTTTTCTGA
1617678 TTTTTCTCTTCTTTT
1 TTTTTCTCTTCTTTT
1617693 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTCTCTTCTTTTCTGA
Found at i:1622250 original size:19 final size:19
Alignment explanation
Indices: 1622228--1622280 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
1622218 TGAACTTCTC
* *
1622228 TTTTTCTTTTCTTTTCTTA
1 TTTTTCTCTTCTTTTCTGA
1622247 TTTTTCTCTTCTTTTCTGA
1 TTTTTCTCTTCTTTTCTGA
1622266 TTTTTCTCTTCTTTT
1 TTTTTCTCTTCTTTT
1622281 TGCACTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTCTCTTCTTTTCTGA
Found at i:1623041 original size:19 final size:20
Alignment explanation
Indices: 1623000--1623050 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1622990 GAAACCCCTT
*
1623000 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
1623020 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
1623039 TGAAGATACATG
1 TGAAAATACATG
1623051 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:1626440 original size:8 final size:8
Alignment explanation
Indices: 1626427--1626452 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1626417 GAATTTCTTT
1626427 TTCTTTTC
1 TTCTTTTC
1626435 TTCTTTTC
1 TTCTTTTC
1626443 TTCTTTTC
1 TTCTTTTC
1626451 TT
1 TT
1626453 TTTCTGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:1626766 original size:22 final size:19
Alignment explanation
Indices: 1626741--1626786 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 19
1626731 AATAAAGGGT
1626741 AATAATATAAGTAATGAAAATA
1 AATAA-ATAAG-AATG-AAATA
1626763 AAT-AATAAGAATGAAATA
1 AATAAATAAGAATGAAATA
1626781 AATAAA
1 AATAAA
1626787 GGATAGAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 5 0.22
21 1 0.04
22 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (19 bp):
AATAAATAAGAATGAAATA
Done.