Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008492.1 Hibiscus syriacus cultivar Beakdansim tig00111334_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: 1113585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:215361 original size:81 final size:81
Alignment explanation
Indices: 215226--215832 Score: 768
Period size: 81 Copynumber: 7.5 Consensus size: 81
215216 TAACATTTTT
* * * * *
215226 CATTTGGCATATAGGTGTAAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAATGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
215291 AAATGGCCTAGTTGTG
66 AAATGGCCTAGTTGTG
** ** *
215307 CATTTGGCAGAAAGGTGTCAATTATGTTAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
* * *
215372 AAATGGCCTAGCTATA
66 AAATGGCCTAGTTGTG
* * * * *
215388 CATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAAAGGTTAAAGACCATTAAGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
215453 AAATGACCTAGTTGTG
66 AAATGGCCTAGTTGTG
* * * ** * *
215469 CATTTGGCAGAAAGGTGTTAATTATTCCAGTTAGATAAACAATTAAAGACCATTGAGTAAAAAAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
215534 AAATGGCATAGTTGTG
66 AAATGGCCTAGTTGTG
* * *
215550 CATTTGGAAGAAAGGTAT-ATATTATGCCAGTTAGATGAATGGTTAAAGACCGTTGAGTAAAAGA
1 CATTTGGCAGAAAGGTGTCA-ATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGA
*
215614 TAAATGGCCTAGCTGTG
65 TAAATGGCCTAGTTGTG
* * *
215631 CATTTGGCAG-AAGTCTGTCAATTATGCTAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAAG
1 CATTTGGCAGAAAG-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGT-AAAAG
* *
215695 ATAAATGGCCTAGATATG
64 ATAAATGGCCTAGTTGTG
* * * *
215713 CATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAAGACCATTGAGCAAAAGAG
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
215778 AAATGGCCTAGTTTTG
66 AAATGGCCTAGTTGTG
* * * *
215794 CATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGATGAA
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
215833 ATGTTAAATG
Statistics
Matches: 449, Mismatches: 72, Indels: 10
0.85 0.14 0.02
Matches are distributed among these distances:
80 4 0.01
81 372 0.83
82 70 0.16
83 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (81 bp):
CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
AAATGGCCTAGTTGTG
Found at i:217394 original size:36 final size:36
Alignment explanation
Indices: 217340--217411 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
217330 ATCTGGCAAT
*
217340 TCTTCATGGAAGAATTCAAGAACAAGTATATGGGTG
1 TCTTCATGAAAGAATTCAAGAACAAGTATATGGGTG
* * *
217376 TCTTCATGAAATAGTTCAAGAACAAGTATGTGGGTG
1 TCTTCATGAAAGAATTCAAGAACAAGTATATGGGTG
217412 AACAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (36 bp):
TCTTCATGAAAGAATTCAAGAACAAGTATATGGGTG
Found at i:222397 original size:20 final size:20
Alignment explanation
Indices: 222326--222377 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
222316 TATTCAAGTG
222326 GTATCGATACCAAGAGGGGA
1 GTATCGATACCAAGAGGGGA
222346 GTATCGATACCAAGAGGGGA
1 GTATCGATACCAAGAGGGGA
222366 GTATCGATACCA
1 GTATCGATACCA
222378 TAAGGATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (20 bp):
GTATCGATACCAAGAGGGGA
Found at i:223332 original size:20 final size:20
Alignment explanation
Indices: 223286--223341 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
223276 ACCTATTCAA
223286 GTGGTATCGATACCA-AGAG
1 GTGGTATCGATACCATAGAG
*
223305 GGGAGTATCGATACCATA-AG
1 GTG-GTATCGATACCATAGAG
223325 GATGGTATCGATACCAT
1 G-TGGTATCGATACCAT
223342 TGATCACAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (20 bp):
GTGGTATCGATACCATAGAG
Found at i:223409 original size:22 final size:19
Alignment explanation
Indices: 223363--223417 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 19
223353 TGAAAAAATG
*
223363 GTATCGGTACCGTAATAGA
1 GTATCGATACCGTAATAGA
223382 GTATCGATACCGTAATAGAGTA
1 GTATCGATACCGTAAT--AG-A
223404 GTATCGATACCGTA
1 GTATCGATACCGTA
223418 GTGGGGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 15 0.47
21 2 0.06
22 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (19 bp):
GTATCGATACCGTAATAGA
Found at i:223837 original size:55 final size:55
Alignment explanation
Indices: 223766--223925 Score: 202
Period size: 55 Copynumber: 2.9 Consensus size: 55
223756 AATGGAATTA
* * * *
223766 TATGTGTGCAACACTAAGGAATTCATACTAAGTGTATGAATTTTTGTATGGGTAC
1 TATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCAC
* *
223821 TATGTGTGTAAAACTAAGAAATTCATACTCAGTGTATGAATTTCCT-TATGGGCAC
1 TATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTT-TTGTATGGGCAC
*
223876 TCA-GTGTGT-GAACTAAGAAATTCATACTAAGTGTATG-ATTTTTCGTATGG
1 T-ATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTTTT-GTATGG
223926 AAATAGATGT
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
52 1 0.01
53 4 0.04
54 31 0.34
55 54 0.59
56 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (55 bp):
TATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCAC
Found at i:225373 original size:81 final size:81
Alignment explanation
Indices: 224107--225358 Score: 1567
Period size: 81 Copynumber: 15.5 Consensus size: 81
224097 TTACTAAAGT
* * **
224107 GAAAGGTGTCAATTATGCCAGTTAGATGAACGAG-TAAAGACCGTTAAGTGAAAGATAAATGGTA
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACG-GTTAAAGACCGTTGAGTAAAAGATAAATGGCC
* *
224171 TGGCTGTGTATTTGGCA
65 TAGCTGTGCATTTGGCA
* * *
224188 GAAAGGTGTCAATTATGCCAGTTAGATGAACGAG-TAAAGACCGTTAAGTGAAAGATAAATGGCA
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACG-GTTAAAGACCGTTGAGTAAAAGATAAATGGCC
*
224252 TAGCTGTGCATTTGGTA
65 TAGCTGTGCATTTGGCA
* * * * * * * * **
224269 GAAGGGTTTCAATTATGTCAGTTAGATGAATGATCAAAGATCATTGAGTAAAAGATAAATGTACT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
*
224334 AGTTGTGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * * * ***
224350 GAAATGTGTTAATTATGCCAATTAGATGAACGGTTAAAGACCATTGAGTAAAAGATAAATGAAAT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* *
224415 AGATGTGCCTTTGGCA
66 AGCTGTGCATTTGGCA
* *
224431 TAAAGTTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* *
224496 AGCTATGCATTGGGCA
66 AGCTGTGCATTTGGCA
* * * *
224512 TAAAGGTGTCAATTAAGCCAGTTTGATGAACGGTTAAAGACTGTTGAGTAAAAGATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* ***
224577 AGTTGTGCATTCCTCA
66 AGCTGTGCATTTGGCA
*
224593 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAACATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* * **
224658 AGTTGTGCATTCGATA
66 AGCTGTGCATTTGGCA
* * * * *
224674 GAAATGTGTCAATTTTTCCAGTTAGATGAATGGTTAAAAACCGTTGAGTAAAAGATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
*
224739 AGCTATGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * * *
224755 GAAATGTGTCAATTATGCCAGTTAAATGAATGGTTAAAGACCATTGAGTAAAAGATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
224820 AGCTGTGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * *
224836 GAAAGGTGTCAATTATGCGAGTTAGATGAACGGTTAAA-ACCATTGAGTAAAAGATAAATGGGCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* *
224900 AGCTGTGTATTTGGAA
66 AGCTGTGCATTTGGCA
* * * **
224916 AAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACTGTTGAGTAAAAGATAAATGGTAT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* *
224981 AGTTGTGCCTTTGGCA
66 AGCTGTGCATTTGGCA
* * ** * * *
224997 GAAAGGTGTCAATTATGTCAGTTAAATGAACATTTAAAGATCGTTGAGTAATAGATAAATGGCCC
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
225062 AGCTGTGCATTTGGCA
66 AGCTGTGCATTTGGCA
* * * * * *
225078 TAAAGGTATCAATTATACCAGTTAGATGAACTGTTAAAGACCGTTGAGTAAAAGATGAATGGCAT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
*
225143 AGCTGTGCATTTGGAA
66 AGCTGTGCATTTGGCA
* * * * *
225159 AAAAGGTATCAATTATACCAGTTAGATGAACGGTTAAAAACCGTTGAGTAAAATATAAATGGCCT
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
* *
225224 AGCTGTGTATTTGGTA
66 AGCTGTGCATTTGGCA
*
225240 GAAAGGT-TCCAATTATGCCAGTTAGATGAACGGATAAAGACCGTTGAGTAAAAGATAAATGGCC
1 GAAAGGTGT-CAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCC
* *
225304 TACCTGTGCATTTGGTA
65 TAGCTGTGCATTTGGCA
* * * * *
225321 GAGATGTGTCAATAATGCAAGTTAGATGAAAGGTTAAA
1 GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAA
225359 TGCCTTTGGG
Statistics
Matches: 1021, Mismatches: 146, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
80 75 0.07
81 945 0.93
82 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (81 bp):
GAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCT
AGCTGTGCATTTGGCA
Found at i:227271 original size:25 final size:25
Alignment explanation
Indices: 227242--227325 Score: 159
Period size: 25 Copynumber: 3.4 Consensus size: 25
227232 CCATGAAAAC
227242 AAATGATTTCTAATTTTAAAAATGA
1 AAATGATTTCTAATTTTAAAAATGA
*
227267 AAATGATTTCTAATTTTAGAAATGA
1 AAATGATTTCTAATTTTAAAAATGA
227292 AAATGATTTCTAATTTTAAAAATGA
1 AAATGATTTCTAATTTTAAAAATGA
227317 AAATGATTT
1 AAATGATTT
227326 TCTTTTAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 57 1.00
ACGTcount: A:0.46, C:0.04, G:0.10, T:0.40
Consensus pattern (25 bp):
AAATGATTTCTAATTTTAAAAATGA
Found at i:228296 original size:24 final size:23
Alignment explanation
Indices: 228269--228326 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
228259 TATCCTACAG
228269 GGTACCGATACCCCTATACAAAGA
1 GGTACCGATACCCCTATACAAA-A
* * *
228293 GGTACTGATA--CCTATCCCAAA
1 GGTACCGATACCCCTATACAAAA
228314 GGTACCGATACCC
1 GGTACCGATACCC
228327 TTAGTGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 10 0.36
22 8 0.29
23 1 0.04
24 9 0.32
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (23 bp):
GGTACCGATACCCCTATACAAAA
Found at i:229631 original size:15 final size:15
Alignment explanation
Indices: 229611--229640 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
229601 TCATTTGATT
229611 TTAACTGTTTGAATC
1 TTAACTGTTTGAATC
229626 TTAACTGTTTGAATC
1 TTAACTGTTTGAATC
229641 CAAATACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TTAACTGTTTGAATC
Found at i:233590 original size:81 final size:81
Alignment explanation
Indices: 233455--234060 Score: 784
Period size: 81 Copynumber: 7.5 Consensus size: 81
233445 TAACCTTTTT
* * * * *
233455 CATTTGGCATATAGGTGTAAATTATACCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAATGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
233520 AAATGGCCTAGTTGTG
66 AAATGGCCTAGTTGTG
** ** *
233536 CATTTGGCAGAAAGGTGTCAATTATGTTAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
* * *
233601 AAATGGCCTAGCTATA
66 AAATGGCCTAGTTGTG
* * * *
233617 CATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAACGGTTAAAGACCATTAAGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
233682 AAATGACCTAGTTGTG
66 AAATGGCCTAGTTGTG
* * * * ** * *
233698 CATTTGGTAGAAAGGTGTTAATTATTCCAGTTAGATAAACAATTAAAGACCATTGAGTAAAAAAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
233763 AAATGGCATAGTTGTG
66 AAATGGCCTAGTTGTG
* * *
233779 CATTTGGAAGAAAGGTAT-ATATTATGCCAGTTAGATGAATGGTTAAAGACCGTTGAGTAAAAGA
1 CATTTGGCAGAAAGGTGTCA-ATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGA
*
233843 TAAATGGCCTAGCTGTG
65 TAAATGGCCTAGTTGTG
* *
233860 CATTTGGCAG-AAGTCTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGA
1 CATTTGGCAGAAAG-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGA
* *
233924 TAAATGGCCTAGATATG
65 TAAATGGCCTAGTTGTG
* * * *
233941 CATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAAGACCATTGAGCAAAAGAG
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
234006 AAATGGCCTAGTTTTG
66 AAATGGCCTAGTTGTG
* * * *
234022 CATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGATGAA
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
234061 ATGTTAAATG
Statistics
Matches: 452, Mismatches: 69, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
80 4 0.01
81 444 0.98
82 4 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (81 bp):
CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
AAATGGCCTAGTTGTG
Found at i:238826 original size:81 final size:81
Alignment explanation
Indices: 238686--239288 Score: 764
Period size: 81 Copynumber: 7.5 Consensus size: 81
238676 TAACCTTTTT
* * * * * *
238686 CATTTGGCATATAGGTGTAAATTATACCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAATGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
238751 AAATGGCCTAGTTGTG
66 AAATGGCCTAGTTGTG
** ** *
238767 CATTTGGCAGAAAGGTGTCAATTATGTTAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
* * *
238832 AAATGGCCTAGCTATA
66 AAATGGCCTAGTTGTG
* * * *
238848 CATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAACGGTTAAAGACCATTAAGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
238913 AAATGACCTAGTTGTG
66 AAATGGCCTAGTTGTG
* * * * ** * *
238929 CATTTGGTAGAAAGGTGTTAATTATTCCAGTTAGATAAACAATTAAAGACCATTGAGTAAAAAAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
238994 AAATGGCATAGTTGTG
66 AAATGGCCTAGTTGTG
* * *
239010 CATTTGGAAGAAAGGTAT--A-TATGCCAGTTAGATGAATGGTTAAAGACCGTTGAGTAAAAGAT
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
239072 AAATGGCCTAGCTGTG
66 AAATGGCCTAGTTGTG
* *
239088 CATTTGGCAG-AAGTCTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGA
1 CATTTGGCAGAAAG-GTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGA
* *
239152 TAAATGGCCTAGATATG
65 TAAATGGCCTAGTTGTG
* * * *
239169 CATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAAGACCATTGAGCAAAAGAG
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
*
239234 AAATGGCCTAGTTTTG
66 AAATGGCCTAGTTGTG
* * * *
239250 CATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGATGAA
1 CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
239289 ATGTTAAATG
Statistics
Matches: 447, Mismatches: 70, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
77 3 0.01
78 61 0.14
79 1 0.00
80 1 0.00
81 378 0.85
82 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (81 bp):
CATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAAGACCGTTGAGTAAAAGAT
AAATGGCCTAGTTGTG
Found at i:239312 original size:321 final size:322
Alignment explanation
Indices: 238712--239320 Score: 911
Period size: 321 Copynumber: 1.9 Consensus size: 322
238702 GTAAATTATA
* *
238712 CCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAATGATAAATGGCCTAGTTGTGCATTTGGCAG
1 CCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAG
* **
238777 AAAGGTGTCAATTATGTTAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAATAAATGGCCTA
66 AAAGCTGTCAATTATGCCAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAATAAATGGCCTA
* *
238842 GCTATACATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAACGGTTAAAGACCATTAAGTA
131 GATATACATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAACGGTTAAAGACCATTAAGCA
* * * * * *
238907 AAAGATAAATGACCTAGTTGTGCATTTGGTAGAAAGGTGTTAATTATTCCAGTTAGATAAACAAT
196 AAAGAGAAATGACCTAGTTGTGCATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGATAAACAAT
238972 TAAAGACCATTGAGTAAAAAA-TAAATGGCATAGTTGTGCATTTGGAAGAAAGGTATATATG
261 TAAAGACCATTGAGTAAAAAACTAAATGGCATAGTTGTGCATTTGGAAGAAAGGTATATATG
* *
239033 CCAGTTAGATGAATGGTTAAAGACCGTTGAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAG
1 CCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAG
* *
239098 -AAGTCTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATAAATGGCCT
66 AAAG-CTGTCAATTATGCCAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAATAAATGGCCT
* * * * *
239162 AGATATGCATTTGGCAGAAAGGTGTCAATTATGTCAGTTAGATGAACGGTTAAAGACCATTGAGC
130 AGATATACATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAACGGTTAAAGACCATTAAGC
* * *
239227 AAAAGAGAAATGGCCTAGTTTTGCATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGATGAAA-T
195 AAAAGAGAAATGACCTAGTTGTGCATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGAT-AAACA
* * *
239291 GTTAAATG-CCTTTGGGTAAAAAACTAAATG
259 ATTAAA-GACCATTGAGTAAAAAACTAAATG
239321 AATTATAATG
Statistics
Matches: 256, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
320 3 0.01
321 243 0.95
322 10 0.04
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (322 bp):
CCAGTTAGATGAACGGTTAAAGACCGTTAAGTAAAAGATAAATGGCCTAGCTGTGCATTTGGCAG
AAAGCTGTCAATTATGCCAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAAATAAATGGCCTA
GATATACATTTGGCAAAAAGGTGTCAATTATGCCAGTTAAATGAACGGTTAAAGACCATTAAGCA
AAAGAGAAATGACCTAGTTGTGCATTAGGTAGAAAGGTGTCAATCATGCAAGTTAGATAAACAAT
TAAAGACCATTGAGTAAAAAACTAAATGGCATAGTTGTGCATTTGGAAGAAAGGTATATATG
Found at i:240849 original size:36 final size:36
Alignment explanation
Indices: 240795--240866 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
240785 ATCTGGCAAT
*
240795 TCTTCATGGAAGAATTCAAGAACAAGTATATGGGTG
1 TCTTCATGAAAGAATTCAAGAACAAGTATATGGGTG
* * *
240831 TCTTCATGAAATAGTTCAAGAACAAGTATGTGGGTG
1 TCTTCATGAAAGAATTCAAGAACAAGTATATGGGTG
240867 AACAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.29
Consensus pattern (36 bp):
TCTTCATGAAAGAATTCAAGAACAAGTATATGGGTG
Found at i:245792 original size:20 final size:20
Alignment explanation
Indices: 245767--245818 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
245757 TATTCAAGTG
245767 GTATCGATACCAAGAGGGGA
1 GTATCGATACCAAGAGGGGA
245787 GTATCGATACCAAGAGGGGA
1 GTATCGATACCAAGAGGGGA
245807 GTATCGATACCA
1 GTATCGATACCA
245819 TAAAGATGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (20 bp):
GTATCGATACCAAGAGGGGA
Found at i:246758 original size:962 final size:957
Alignment explanation
Indices: 244899--246781 Score: 3590
Period size: 962 Copynumber: 2.0 Consensus size: 957
244889 GTACCATTAT
244899 AAATCGTTATGCAAATTGTATATATTTTGTTGCTTCCGCACAAATATTTTTTTTAAAGGCCAATT
1 AAATCGTTATGCAAATTGTATATATTTTGTTGCTTCCGCACAAATATTTTTTTTAAAGGCCAATT
244964 CTTTAATACCCCAAATATCGAATCAGGGACTGTATTGAAAGAATTTAAGATTTGATGATTTATTT
66 CTTTAATACCCCAAATATCGAATCAGGGACTGTATTGAAAGAATTTAAGATTTGATGATTTATTT
245029 AATAAATTGATAAAAGATGAGAATGATTGGAAATAGTGGTTTAGACTAAATTGTAGCAATGGATG
131 AATAAATTGATAAAAGATGAGAATGATTGGAAATAGTGGTTTAGACTAAATTGTAGCAATGGATG
245094 ATTATGAGGGCATTTTGGTCCTTTAAGGGGAAAATGAACTTAAAATTTATTTTAATAAGATATTA
196 ATTATGAGGGCATTTTGGTCCTTTAAGGGGAAAATGAACTTAAAATTTATTTTAATAAGATATTA
*
245159 AATAAAGAGGGAAAAGGGAAATAGGTTACCAAAGTCATCCTCTTTTTCTTCTTTCTCTTCCTGTG
261 AATAAAGAGGGAAAAGGGAAATAGGTTACCAAAGTCATCCTCTTTTTCTTCTTTCTCTTCCTGCG
*
245224 GAAAGGCTCTCCTCTTTAGCTAAAGGTGAGTTTTCAATTTACTAGTTTATTCCGTCATTTTTGGT
326 GAAAGGCTCTCCTCCTTAGCTAAAGGTGAGTTTTCAATTTACTAGTTTATTCCGTCATTTTTGGT
245289 TGGCTTTTGAAGCATTGAGTATAATAGAAGTTTAAGGAAGGATTAAATGAGATCAAAACTAAGTT
391 TGGCTTTTGAAGCATTGAGTATAATAGAAGTTTAAGGAAGGATTAAATGAGATCAAAACTAAGTT
245354 ATGGATGAGATAATAGAGATTGAAGAAAATGGTTTTTGAGTGTTATGTTACAATATGAGTTTTAA
456 ATGGATGAGATAATAGAGATTGAAGAAAATGGTTTTTGAGTGTTATGTTACAATATGAGTTTTAA
245419 TGATGTTTGTTAGTATATTTGACTTGTCAAATATGTAAATAAGAGATTAGAGCATTGGATGGGTT
521 TGATGTTTGTTAGTATATTTGACTTGTCAAATATGTAAATAAGAGATTAGAGCATTGGATGGGTT
*
245484 TAAAAACATATTAGAAAAGTGGTGTGATTATAATAATTGAATGTTCTTAGAAGATTTTAAATGTT
586 TAAAAACATATTAGAAAAGTGGTGTGATTATAAGAATTGAATGTTCTTAGAAGATTTTAAATGTT
*
245549 TTAAGAAACTAAATGAAGGAAAGTTAGTATGAATAGGTAAAGAAGAGTTTAATAGTATTGTATGG
651 TTAAGAAACTAAATGAAGGAAAGTTAGTATAAATAGGTAAAGAAGAGTTTAATAGTATTGTATGG
*
245614 TGTAATCATAACGAAATTTGACCCCATTTGGGTGATAATCGGGTTAAAAACTGGAAATTATAGGC
716 TGTAATCATAACGAAATTTGACCCCATTTGGGTGATAATCGGGTTAAAAACTAGAAATTATAGGC
245679 ACGAGTATCGGTACTGATAGAACAATATCGATACTATAGGCTTAAAATCAATATCATCTAGTAAC
781 ACGAGTATCGGTACTGATAGAACAATATCGATACTATAGGCTTAAAATCAATATCATCTAGTAAC
*
245744 TAGTATTGATACCTATTCAAGTGGTATCGATACCAAGAGGGGAGTATCGATACCA-AGAGG-GGA
846 TAGTATTAATACCTATTCAAGTGGTATCGATACCAAGAGGGGAGTATCGATACCATA-AGGAGG-
245807 GTATCGATACCATAAAGATGGTATCGATACCATTGATCACAGAATGAAA
909 GTATCGATACCATAAAGATGGTATCGATACCATTGATCACAGAATGAAA
*
245856 AAATCGTTATGCAAATTGTATATATTTTGTTGCTTCCGTACAAATATTTTTTTTAAAGGCCAATT
1 AAATCGTTATGCAAATTGTATATATTTTGTTGCTTCCGCACAAATATTTTTTTTAAAGGCCAATT
**
245921 CTTTAATACCCCAAATATCGAATCAGGGACTGTATTGAAATTATTTAAGATTTGATGATTTATTT
66 CTTTAATACCCCAAATATCGAATCAGGGACTGTATTGAAAGAATTTAAGATTTGATGATTTATTT
245986 AATAAATTGATAAAAGATGAGAATGATTGGAAATAGTGGTTTAGACTAAATTGTAGCAATGGATG
131 AATAAATTGATAAAAGATGAGAATGATTGGAAATAGTGGTTTAGACTAAATTGTAGCAATGGATG
246051 ATTATGAGGGCATTTTGGTCCTTTAAGGGGAAAATGAACTTAAAATTTATTTTAATAAGATATTA
196 ATTATGAGGGCATTTTGGTCCTTTAAGGGGAAAATGAACTTAAAATTTATTTTAATAAGATATTA
246116 AATAAAGAGGGAAAAGGGAAAATAGGTTACCAAAAGTCATCCTCTTTTTCTTCTTTCTCTTCCTG
261 AATAAAGAGGGAAAAGGG-AAATAGGTTACC-AAAGTCATCCTCTTTTTCTTCTTTCTCTTCCTG
246181 CGGAAAGGCTCTCCTCCTTAGCTAAAGGTGAGTTTTCAATTTACTAGTTTATTCCGTCATTTTTG
324 CGGAAAGGCTCTCCTCCTTAGCTAAAGGTGAGTTTTCAATTTACTAGTTTATTCCGTCATTTTTG
246246 GTTGGCTTTTGAAGCATTGAGTATAATAGAAGTTTAAGGAAGGATTAAATGAGATCAAAACTAAG
389 GTTGGCTTTTGAAGCATTGAGTATAATAGAAGTTTAAGGAAGGATTAAATGAGATCAAAACTAAG
246311 TTATGGATGAGATAATAGAGATTGAAGAAAATGGGTTTTTGAGTGTTATGTTACAATATGAGTTT
454 TTATGGATGAGATAATAGAGATTGAAGAAAAT-GGTTTTTGAGTGTTATGTTACAATATGAGTTT
246376 TAATGATGTTTGTTAGTATATTTGACTTGTCAAATATGTAAATAAGAGATTAGAGGCATTGGATG
518 TAATGATGTTTGTTAGTATATTTGACTTGTCAAATATGTAAATAAGAGATTAGA-GCATTGGATG
*
246441 GGTTTAAAAACATATTAGAAAAAGTGGTGTGATTCTAAGAATTGAATGTTCTTAGAAGATTTTAA
582 GGTTTAAAAACATATTAG-AAAAGTGGTGTGATTATAAGAATTGAATGTTCTTAGAAGATTTTAA
246506 ATGTTTTAAGAAACTAAATGAAGGAAAGTTAGTATAAATAGGTAAAGAAGAGTTTAATAGTATTG
646 ATGTTTTAAGAAACTAAATGAAGGAAAGTTAGTATAAATAGGTAAAGAAGAGTTTAATAGTATTG
246571 TATGGTGTAATCATAACGAAATTTGACCCCATTTGGGTGATAATCGGGTTAAAAACTAGAAATTA
711 TATGGTGTAATCATAACGAAATTTGACCCCATTTGGGTGATAATCGGGTTAAAAACTAGAAATTA
246636 TAGGCACGAGTATCGGTACTGATAGAACAATATCGATACTATAGGCTTAAAATCAATATCATCTA
776 TAGGCACGAGTATCGGTACTGATAGAACAATATCGATACTATAGGCTTAAAATCAATATCATCTA
246701 GTAACTAGTATTAATACCTATTCAAGTGGTATCGATACCAAGAGGGGAGTATCGATACCATAAGG
841 GTAACTAGTATTAATACCTATTCAAGTGGTATCGATACCAAGAGGGGAGTATCGATACCATAAGG
*
246766 ATGGTATCGATACCAT
906 AGGGTATCGATACCAT
246782 TGATCACAGA
Statistics
Matches: 908, Mismatches: 11, Indels: 9
0.98 0.01 0.01
Matches are distributed among these distances:
957 275 0.30
958 12 0.01
959 193 0.21
960 86 0.09
961 28 0.03
962 312 0.34
963 2 0.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (957 bp):
AAATCGTTATGCAAATTGTATATATTTTGTTGCTTCCGCACAAATATTTTTTTTAAAGGCCAATT
CTTTAATACCCCAAATATCGAATCAGGGACTGTATTGAAAGAATTTAAGATTTGATGATTTATTT
AATAAATTGATAAAAGATGAGAATGATTGGAAATAGTGGTTTAGACTAAATTGTAGCAATGGATG
ATTATGAGGGCATTTTGGTCCTTTAAGGGGAAAATGAACTTAAAATTTATTTTAATAAGATATTA
AATAAAGAGGGAAAAGGGAAATAGGTTACCAAAGTCATCCTCTTTTTCTTCTTTCTCTTCCTGCG
GAAAGGCTCTCCTCCTTAGCTAAAGGTGAGTTTTCAATTTACTAGTTTATTCCGTCATTTTTGGT
TGGCTTTTGAAGCATTGAGTATAATAGAAGTTTAAGGAAGGATTAAATGAGATCAAAACTAAGTT
ATGGATGAGATAATAGAGATTGAAGAAAATGGTTTTTGAGTGTTATGTTACAATATGAGTTTTAA
TGATGTTTGTTAGTATATTTGACTTGTCAAATATGTAAATAAGAGATTAGAGCATTGGATGGGTT
TAAAAACATATTAGAAAAGTGGTGTGATTATAAGAATTGAATGTTCTTAGAAGATTTTAAATGTT
TTAAGAAACTAAATGAAGGAAAGTTAGTATAAATAGGTAAAGAAGAGTTTAATAGTATTGTATGG
TGTAATCATAACGAAATTTGACCCCATTTGGGTGATAATCGGGTTAAAAACTAGAAATTATAGGC
ACGAGTATCGGTACTGATAGAACAATATCGATACTATAGGCTTAAAATCAATATCATCTAGTAAC
TAGTATTAATACCTATTCAAGTGGTATCGATACCAAGAGGGGAGTATCGATACCATAAGGAGGGT
ATCGATACCATAAAGATGGTATCGATACCATTGATCACAGAATGAAA
Found at i:246772 original size:20 final size:20
Alignment explanation
Indices: 246726--246781 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
246716 ACCTATTCAA
246726 GTGGTATCGATACCA-AGAG
1 GTGGTATCGATACCATAGAG
*
246745 GGGAGTATCGATACCATA-AG
1 GTG-GTATCGATACCATAGAG
246765 GATGGTATCGATACCAT
1 G-TGGTATCGATACCAT
246782 TGATCACAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (20 bp):
GTGGTATCGATACCATAGAG
Found at i:246849 original size:22 final size:19
Alignment explanation
Indices: 246803--246857 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 19
246793 TGAAAAAATG
*
246803 GTATCGGTACCGTAATAGA
1 GTATCGATACCGTAATAGA
246822 GTATCGATACCGTAATAGAGTA
1 GTATCGATACCGTAAT--AG-A
246844 GTATCGATACCGTA
1 GTATCGATACCGTA
246858 GTGGGGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 15 0.47
21 2 0.06
22 15 0.47
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (19 bp):
GTATCGATACCGTAATAGA
Found at i:247276 original size:55 final size:55
Alignment explanation
Indices: 247205--247364 Score: 202
Period size: 55 Copynumber: 2.9 Consensus size: 55
247195 AATGGCATTA
* * * *
247205 TATGTGTGCAACACTAAGGAATTCATACTAAGTGTATGAATTTTTGTATGGGTAC
1 TATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCAC
* *
247260 TATGTGTGTAAAACTAAGAAATTCATACTCAGTGTATGAATTTCCT-TATGGGCAC
1 TATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTT-TTGTATGGGCAC
*
247315 TCA-GTGTGT-GAACTAAGAAATTCATACTAAGTGTATG-ATTTTTCGTATGG
1 T-ATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTTTT-GTATGG
247365 AAATAGATGT
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
52 1 0.01
53 4 0.04
54 31 0.34
55 54 0.59
56 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (55 bp):
TATGTGTGTAAAACTAAGAAATTCATACTAAGTGTATGAATTTTTGTATGGGCAC
Found at i:248781 original size:81 final size:81
Alignment explanation
Indices: 247563--248766 Score: 1514
Period size: 81 Copynumber: 14.9 Consensus size: 81
247553 ATTCTAAGAT
** * *
247563 TAAAAGATAAATGGTATGGCTGTGTATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
247628 AG-TAAAGACCGTTAAG
66 -GTTAAAGACCGTTGAG
* * * * * * *
247644 TGAAAGATAAATGGCATAGCTGTGCATTTGGTAGAAGGGTTTCAATTATGTCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
* * * *
247709 ATCAAAGATCATTGAG
66 GTTAAAGACCGTTGAG
** * * * *
247725 TAAAAGATAAATGTACTAGTTGTGCATTTGGCAGAAATGTGTTAATTATGCCAATTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
247790 GTTAAAGACCATTGAG
66 GTTAAAGACCGTTGAG
*** * * * *
247806 TAAAAGATAAATGAAATAGATGTGCCTTTGGCATAAAGTTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
247871 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * *
247887 TAAAAGATAAATGGCCTAGCTATGCATTGGGCAGAAAGGTGTCAATTAAGCCAGTTTGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
247952 GTTAAAGACTGTTGAG
66 GTTAAAGACCGTTGAG
* ***
247968 TAAAAGATAAATGGCCTAGTTGTGCATTCCTCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
248033 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * ** * * * *
248049 TAAAACATAAATGGCCTAGTTGTGCATTCGATAGAAATGTGTCAATTTTTCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
248114 GTTAAAAACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * *
248130 TAAAAGATAAATGGCCTAGCTATGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAAATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
248195 GTTAAAGACCATTGAG
66 GTTAAAGACCGTTGAG
*
248211 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCGAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
248276 GTTAAA-ACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * **
248291 TAAAAGATAAATGGGCTAGCTGTGTATTTGGCAAAAATCTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
248356 GTTAAAGACTGTTGAG
66 GTTAAAGACCGTTGAG
** * * * * *
248372 TAAAAGATAAATGGTATAGTTGTGCCTTTGGCAGAAAGGTGTCAATTATGTCAGTTAAATGAACA
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
* *
248437 TTTAAAGATCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * *
248453 TAATAGATAAATGGCCCAGCTGTGCATTTGGCATAAAGGTATCAATTATACCAGTTAGATGAACT
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
248518 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * * *
248534 TAAAAGATGAATGGCATAGCTGTGCATTTGGAAAAAAGGTATCAATTATACCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
248599 GTTAAAAACCGTTGAG
66 GTTAAAGACCGTTGAG
* * *
248615 TAAAATATAAATGGCCTAGCTGTGTATTTGGTAGAAAGGT-TCCAATTATGCCAGTTAGATGAAC
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGT-CAATTATGCCAGTTAGATGAAC
*
248679 GGATAAAGACCGTTGAG
65 GGTTAAAGACCGTTGAG
* * * * * * *
248696 TAAAAGATAAATGGCCTACCTGTGCATTTGGTAGAGATGTGTCAATAATGCAAGTTAGATGAAAG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
248761 GTTAAA
66 GTTAAA
248767 TGCCTTTGGG
Statistics
Matches: 970, Mismatches: 149, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
80 74 0.08
81 895 0.92
82 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (81 bp):
TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
GTTAAAGACCGTTGAG
Found at i:250814 original size:25 final size:25
Alignment explanation
Indices: 250785--250868 Score: 150
Period size: 25 Copynumber: 3.4 Consensus size: 25
250775 CCATGAAAAC
*
250785 AAATGATTTCTACTTTTAAAAATGA
1 AAATGATTTCTAATTTTAAAAATGA
*
250810 AAATGATTTCTAATTTTAGAAATGA
1 AAATGATTTCTAATTTTAAAAATGA
250835 AAATGATTTCTAATTTTAAAAATGA
1 AAATGATTTCTAATTTTAAAAATGA
250860 AAATGATTT
1 AAATGATTT
250869 TCTTTTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (25 bp):
AAATGATTTCTAATTTTAAAAATGA
Found at i:251837 original size:24 final size:23
Alignment explanation
Indices: 251810--251867 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
251800 TATCCTACAG
251810 GGTACCGATACCCCTATACAAAGA
1 GGTACCGATACCCCTATACAAA-A
* * *
251834 GGTACTGATA--CCTATCCCAAA
1 GGTACCGATACCCCTATACAAAA
251855 GGTACCGATACCC
1 GGTACCGATACCC
251868 TTAGTGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
21 10 0.36
22 8 0.29
23 1 0.04
24 9 0.32
ACGTcount: A:0.33, C:0.31, G:0.17, T:0.19
Consensus pattern (23 bp):
GGTACCGATACCCCTATACAAAA
Found at i:253177 original size:15 final size:15
Alignment explanation
Indices: 253157--253186 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
253147 TCATTTGATT
253157 TTAACTGTTTGAATC
1 TTAACTGTTTGAATC
253172 TTAACTGTTTGAATC
1 TTAACTGTTTGAATC
253187 CAAATACTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TTAACTGTTTGAATC
Found at i:259171 original size:27 final size:27
Alignment explanation
Indices: 259111--259176 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
259101 GGACAAAAGG
* *
259111 TTTTATAAATTATAATGAAGTGCAAATT
1 TTTTATAAATTATAAT-AAGTGAAAACT
259139 TGTTTATAAATTATAAT-AGTGTAAAACT
1 T-TTTATAAATTATAATAAGTG-AAAACT
259167 TTTTATAAAT
1 TTTTATAAAT
259177 AATTTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 13 0.38
28 6 0.18
29 15 0.44
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (27 bp):
TTTTATAAATTATAATAAGTGAAAACT
Found at i:259545 original size:22 final size:22
Alignment explanation
Indices: 259513--259594 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
259503 GTACGGATGG
*
259513 TGGAAGAAGGCTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
259535 TGGAAGTAGGCTGCACGAATGC
1 TGGAAGTAGGCTGCACGAATGC
* *
259557 TGGAAGTTGGCTGCACGAATGA
1 TGGAAGTAGGCTGCACGAATGC
**
259579 TGGAAGCGGGCTGCAC
1 TGGAAGTAGGCTGCAC
259595 AGGTGTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.27, C:0.18, G:0.38, T:0.17
Consensus pattern (22 bp):
TGGAAGTAGGCTGCACGAATGC
Found at i:263380 original size:66 final size:66
Alignment explanation
Indices: 263263--263390 Score: 168
Period size: 66 Copynumber: 1.9 Consensus size: 66
263253 TAGGTTTGTA
* * * *
263263 AGGAATTACCAGTCGGTGCTAAATCTATAAAAGGAATTACAACCAGCGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCAGTGCAAAACCTATAAAAGGAATTACAACCAGCGACTGAACCTACCAGAGA
263328 T
66 T
* ** *
263329 AGGAATTACCAGTCAGTGCAAAACCTATACAAGGAATTA-AATGTAGTGACTGAACCTACCAG
1 AGGAATTACCAGTCAGTGCAAAACCTATAAAAGGAATTACAA-CCAGCGACTGAACCTACCAG
263391 TATTCGTACC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 2 0.04
66 51 0.96
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (66 bp):
AGGAATTACCAGTCAGTGCAAAACCTATAAAAGGAATTACAACCAGCGACTGAACCTACCAGAGA
T
Found at i:267462 original size:31 final size:31
Alignment explanation
Indices: 267424--267530 Score: 83
Period size: 31 Copynumber: 3.3 Consensus size: 31
267414 TTAGGTCCGT
267424 AAGGAATTACAAGTCGGTGCTGAACCTATAA
1 AAGGAATTACAAGTCGGTGCTGAACCTATAA
* * *
267455 AAGGAATTACCAA-TAGCG-ACTGAACCTGCCAGAGA
1 AAGGAATTA-CAAGTCG-GTGCTGAACCT---ATA-A
* * * *
267490 TAGTAATTACCAGTCGGTGCAGAACCTATAA
1 AAGGAATTACAAGTCGGTGCTGAACCTATAA
267521 AAGGAATTAC
1 AAGGAATTAC
267531 TCGCAGTGGC
Statistics
Matches: 56, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
31 28 0.50
32 6 0.11
34 5 0.09
35 17 0.30
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (31 bp):
AAGGAATTACAAGTCGGTGCTGAACCTATAA
Found at i:267544 original size:66 final size:66
Alignment explanation
Indices: 267428--267554 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
267418 GTCCGTAAGG
* * *
267428 AATTACAAGTCGGTGCTGAACCTATAAAAGGAATTACCAATAGCGACTGAACCTGCCAGAGATAG
1 AATTACAAGTCGGTGCAGAACCTATAAAAGGAATTACCAACAGCGACTGAACCTACCAGAGATAG
267493 T
66 T
* * * *
267494 AATTACCAGTCGGTGCAGAACCTATAAAAGGAATTACTC-GCAGTGGCTGAACCTACCAGAG
1 AATTACAAGTCGGTGCAGAACCTATAAAAGGAATTAC-CAACAGCGACTGAACCTACCAGAG
267555 TCTTCGTACC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.20
Consensus pattern (66 bp):
AATTACAAGTCGGTGCAGAACCTATAAAAGGAATTACCAACAGCGACTGAACCTACCAGAGATAG
T
Found at i:270937 original size:19 final size:20
Alignment explanation
Indices: 270915--270956 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
270905 AAATTTATAT
270915 AAAAATATTTAAA-ATTGAA
1 AAAAATATTTAAATATTGAA
* *
270934 AAAAGTATTTAAATATTTAA
1 AAAAATATTTAAATATTGAA
270954 AAA
1 AAA
270957 TAATTACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAAATATTTAAATATTGAA
Found at i:271252 original size:19 final size:20
Alignment explanation
Indices: 271228--271268 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
271218 ATTTCTATAA
271228 TTTTTT-AAATATTTTAATT
1 TTTTTTAAAATATTTTAATT
271247 TTTTTTAAAATATTTTAATT
1 TTTTTTAAAATATTTTAATT
271267 TT
1 TT
271269 AAATATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTAAAATATTTTAATT
Found at i:271276 original size:17 final size:17
Alignment explanation
Indices: 271249--271284 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
271239 TTTTAATTTT
271249 TTTTAAAATA-TTTTAA
1 TTTTAAAATATTTTTAA
271265 TTTTAAATATATTTTTAA
1 TTTTAAA-ATATTTTTAA
271283 TT
1 TT
271285 CTAACTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:274073 original size:18 final size:17
Alignment explanation
Indices: 274050--274106 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 17
274040 TAAGAGTTAG
274050 AATTTAAAATATATTTAA
1 AATTTAAAATAT-TTTAA
274068 AATTTAAAATATTTAATAA
1 AATTTAAAATATTT--TAA
*
274087 AA-TTAAAATATTTAAA
1 AATTTAAAATATTTTAA
274103 AATT
1 AATT
274107 ATAGAAATCG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
16 4 0.11
17 3 0.09
18 23 0.66
19 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTAAAATATTTTAA
Found at i:274083 original size:9 final size:9
Alignment explanation
Indices: 274051--274103 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
274041 AAGAGTTAGA
274051 ATTTAAAAT
1 ATTTAAAAT
*
274060 ATATTTAAA-
1 AT-TTAAAAT
274069 ATTTAAAAT
1 ATTTAAAAT
274078 ATTTAATAA-
1 ATTTAA-AAT
*
274087 AATTAAAAT
1 ATTTAAAAT
274096 ATTTAAAA
1 ATTTAAAA
274104 ATTATAGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 7 0.19
9 22 0.61
10 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
ATTTAAAAT
Found at i:277589 original size:27 final size:27
Alignment explanation
Indices: 277535--277591 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
277525 ACTTGCTCCT
* *
277535 AAAATTTAAAAAATATTTAAATATTTA
1 AAAATTTAAAAAATAATTAAATAATTA
*
277562 AAAATTT-AAAAATAATTACATAAATTA
1 AAAATTTAAAAAATAATTAAAT-AATTA
277589 AAA
1 AAA
277592 TATAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAATTTAAAAAATAATTAAATAATTA
Found at i:277591 original size:26 final size:26
Alignment explanation
Indices: 277534--277592 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
277524 TACTTGCTCC
* *
277534 TAAAATTTAAAAAATATTTAAATATT
1 TAAAATTTAAAAAATAATTAAATAAT
*
277560 TAAAAATTT-AAAAATAATTACATAAAT
1 T-AAAATTTAAAAAATAATTAAAT-AAT
277587 TAAAAT
1 TAAAAT
277593 ATAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAAATTTAAAAAATAATTAAATAAT
Found at i:277661 original size:8 final size:8
Alignment explanation
Indices: 277650--277688 Score: 51
Period size: 8 Copynumber: 4.5 Consensus size: 8
277640 CAAAATTTAT
277650 AAAAAATA
1 AAAAAATA
277658 AAAAATATTA
1 AAAAA-A-TA
277668 AAAGAAATA
1 AAA-AAATA
277677 AAAAAATA
1 AAAAAATA
277685 AAAA
1 AAAA
277689 TAAGAGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 14 0.50
9 6 0.21
10 6 0.21
11 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (8 bp):
AAAAAATA
Found at i:277677 original size:19 final size:18
Alignment explanation
Indices: 277641--277681 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
277631 AACTTATTTC
277641 AAAATTTATAAAAAATAA
1 AAAATTTATAAAAAATAA
277659 AAAATATTA-AAAGAAATAA
1 AAAAT-TTATAAA-AAATAA
277678 AAAA
1 AAAA
277682 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAATTTATAAAAAATAA
Found at i:277735 original size:18 final size:17
Alignment explanation
Indices: 277699--277761 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 17
277689 TAAGAGTTAT
277699 AATTAAAAATATATT-TAA
1 AATT-AAAATAT-TTATAA
277717 AATTAAAATATTTGATAAA
1 AATTAAAATATTT-AT-AA
*
277736 AATTAAAATATTTAAAA
1 AATTAAAATATTTATAA
277753 AATATAAAA
1 AAT-TAAAA
277762 ATCAAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 2 0.05
17 12 0.30
18 11 0.28
19 15 0.38
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTAAAATATTTATAA
Found at i:277763 original size:19 final size:19
Alignment explanation
Indices: 277715--277761 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
277705 AAATATATTT
277715 AAAATTAAAATATTTGATA
1 AAAATTAAAATATTTGATA
277734 AAAATTAAAATATTT-A-A
1 AAAATTAAAATATTTGATA
277751 AAAATATAAAA
1 AAAAT-TAAAA
277762 ATCAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.22
18 6 0.22
19 15 0.56
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAATTAAAATATTTGATA
Found at i:281285 original size:17 final size:17
Alignment explanation
Indices: 281265--281307 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
281255 AATAAAAAAT
281265 AAAAAAATTCAAAATTC
1 AAAAAAATTCAAAATTC
* *
281282 AAAAAAATTCTAAATTT
1 AAAAAAATTCAAAATTC
*
281299 AAAATAATT
1 AAAAAAATT
281308 ACATGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAAAATTCAAAATTC
Found at i:281335 original size:9 final size:9
Alignment explanation
Indices: 281323--281356 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
281313 AATTAAAATC
281323 TAAAAATAT
1 TAAAAATAT
281332 TAAAATATTAT
1 TAAAA-A-TAT
281343 TAAAAATAT
1 TAAAAATAT
281352 TAAAA
1 TAAAA
281357 TTCAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 13 0.57
10 2 0.09
11 8 0.35
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATAT
Found at i:284246 original size:25 final size:25
Alignment explanation
Indices: 284218--284300 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
284208 AAAATAAAAA
284218 AAATTCAAAATTCAAAAAAATATTT
1 AAATTCAAAATTCAAAAAAATATTT
* * **
284243 AAATATTCTAAAATTTAAAATAATTACAT
1 -AA-ATTC-AAAATTCAAAA-AAATATTT
* *
284272 AAATT-AAAATATCATAAAAATATTA
1 AAATTCAAAAT-TCAAAAAAATATTT
284297 AAAT
1 AAAT
284301 ATTATTAAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
25 13 0.30
26 6 0.14
27 7 0.16
28 12 0.28
29 5 0.12
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (25 bp):
AAATTCAAAATTCAAAAAAATATTT
Found at i:284250 original size:20 final size:20
Alignment explanation
Indices: 284213--284348 Score: 96
Period size: 19 Copynumber: 7.2 Consensus size: 20
284203 AATAAAAAAT
*
284213 AAAAAAA-ATTCAAA-ATTC
1 AAAAAAATATTAAAATATTC
*
284231 AAAAAAATATTTAAATATTC
1 AAAAAAATATTAAAATATTC
*
284251 --TAAAAT-TTAAAATAATT-
1 AAAAAAATATTAAAAT-ATTC
* *
284268 -ACATAA-ATTAAAATA-TC
1 AAAAAAATATTAAAATATTC
*
284285 ATAAAAATATTAAAATATT-
1 AAAAAAATATTAAAATATTC
*
284304 ATTAAAAATATTAAAA-ATTC
1 A-AAAAAATATTAAAATATTC
*
284324 AAAAAAATATTTAAATATTC
1 AAAAAAATATTAAAATATTC
284344 TAAAA
1 -AAAA
284349 TCATTTACAC
Statistics
Matches: 95, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
16 1 0.01
17 7 0.07
18 28 0.29
19 31 0.33
20 24 0.25
21 4 0.04
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATATTAAAATATTC
Found at i:284255 original size:19 final size:19
Alignment explanation
Indices: 284233--284348 Score: 100
Period size: 19 Copynumber: 6.2 Consensus size: 19
284223 CAAAATTCAA
*
284233 AAAAATATTTAAATATTCT
1 AAAAATATTAAAATATTCT
*
284252 -AAAAT-TTAAAATAAT-T
1 AAAAATATTAAAATATTCT
*
284268 ACATAA-ATTAAAATA-TCAT
1 A-AAAATATTAAAATATTC-T
*
284287 AAAAATATTAAAATATTATT
1 AAAAATATTAAAATATT-CT
*
284307 AAAAATATTAAAA-ATTCAA
1 AAAAATATTAAAATATTC-T
*
284326 AAAAATATTTAAATATTCT
1 AAAAATATTAAAATATTCT
284345 AAAA
1 AAAA
284349 TCATTTACAC
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
16 1 0.01
17 9 0.12
18 19 0.24
19 30 0.38
20 19 0.24
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATATTAAAATATTCT
Found at i:284315 original size:9 final size:9
Alignment explanation
Indices: 284286--284321 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
284276 TAAAATATCA
284286 TAAAAATAT
1 TAAAAATAT
284295 TAAAATATTAT
1 TAAAA-A-TAT
284306 TAAAAATAT
1 TAAAAATAT
284315 TAAAAAT
1 TAAAAAT
284322 TCAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.60
10 2 0.08
11 8 0.32
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAAATAT
Found at i:285863 original size:26 final size:27
Alignment explanation
Indices: 285807--285864 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
285797 TTGAGTCAAA
*
285807 TGGGT-AGGCCTGGCGGGTAGGACAAG
1 TGGGTCAGGCCTGGCGGATAGGACAAG
* *
285833 CGGGTCAGG-CTGGCGGATAGGACAGG
1 TGGGTCAGGCCTGGCGGATAGGACAAG
285859 TGGGTC
1 TGGGTC
285865 GGGTCCACGC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 24 0.89
27 3 0.11
ACGTcount: A:0.17, C:0.17, G:0.50, T:0.16
Consensus pattern (27 bp):
TGGGTCAGGCCTGGCGGATAGGACAAG
Found at i:287156 original size:9 final size:9
Alignment explanation
Indices: 287090--287172 Score: 57
Period size: 9 Copynumber: 9.1 Consensus size: 9
287080 TCAAAATTCA
287090 AAAAATATT
1 AAAAATATT
*
287099 -TAAATATTT
1 AAAAATA-TT
287108 AAAAAT-TT
1 AAAAATATT
287116 AAAAATAATT
1 AAAAAT-ATT
287126 ACATAAAT-TT
1 A-A-AAATATT
*
287136 AAATATCA-T
1 AAAAAT-ATT
*
287145 AAAAGTATT
1 AAAAATATT
*
287154 AAAAACATT
1 AAAAATATT
287163 AAAAATATT
1 AAAAATATT
287172 A
1 A
287173 TTAAAACTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
8 17 0.30
9 25 0.44
10 10 0.18
11 1 0.02
12 4 0.07
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATATT
Found at i:287679 original size:23 final size:23
Alignment explanation
Indices: 287653--287700 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
287643 CTATTTTTCT
287653 TATTTCTTATTTTCTTTTTTAAC
1 TATTTCTTATTTTCTTTTTTAAC
287676 TATTTCTTATTTTCTTTTTTAAC
1 TATTTCTTATTTTCTTTTTTAAC
287699 TA
1 TA
287701 ACTTTATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTCTTATTTTCTTTTTTAAC
Found at i:290967 original size:18 final size:18
Alignment explanation
Indices: 290946--291003 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
290936 TAAGAGTTAG
*
290946 AATTAAAAATATATTTAA
1 AATTAAAAATATATTAAA
* *
290964 AATTAAAATATTTAATAAA
1 AATTAAAA-ATATATTAAA
290983 AATT-AAAATAT-TTAAA
1 AATTAAAAATATATTAAA
290999 AATTA
1 AATTA
291004 TAGAAATCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.24
17 3 0.09
18 11 0.33
19 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAAATATATTAAA
Found at i:290976 original size:15 final size:15
Alignment explanation
Indices: 290956--290999 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 15
290946 AATTAAAAAT
290956 ATATTTAAAATTAAA
1 ATATTTAAAATTAAA
290971 ATATTTAATAAAAATTAAA
1 ATA-TT--T-AAAATTAAA
290990 ATATTTAAAA
1 ATATTTAAAA
291000 ATTATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
18 3 0.12
19 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATTTAAAATTAAA
Found at i:294477 original size:2 final size:2
Alignment explanation
Indices: 294470--294518 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
294460 TGCTCCTAAA
294470 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
294512 AT AT AT A
1 AT AT AT A
294519 AACATTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:296903 original size:23 final size:24
Alignment explanation
Indices: 296857--296903 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
296847 TTTTGGTCAA
*
296857 AGTCAATGGTCAACGGGTTGACTC
1 AGTCAATGGTCAACGGGTTAACTC
296881 AGTCAAT-GTCAACGAGG-TAACTC
1 AGTCAATGGTCAACG-GGTTAACTC
296904 GATGAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (24 bp):
AGTCAATGGTCAACGGGTTAACTC
Found at i:298483 original size:18 final size:18
Alignment explanation
Indices: 298449--298487 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
298439 AAATATATTT
298449 AAAACTAAAATATTTAATA
1 AAAACTAAAATATTTAA-A
*
298468 AAAATTAAAATA-TTAAA
1 AAAACTAAAATATTTAAA
298485 AAA
1 AAA
298488 TTATAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAACTAAAATATTTAAA
Found at i:305772 original size:23 final size:24
Alignment explanation
Indices: 305726--305772 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
305716 TTTTGGTCAA
*
305726 AGTCAATGGTCAACGGGTTGACTC
1 AGTCAATGGTCAACGGGTTAACTC
305750 AGTCAAT-GTCAACGAGG-TAACTC
1 AGTCAATGGTCAACG-GGTTAACTC
305773 GATGAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.30, C:0.21, G:0.26, T:0.23
Consensus pattern (24 bp):
AGTCAATGGTCAACGGGTTAACTC
Found at i:307116 original size:2 final size:2
Alignment explanation
Indices: 307109--307149 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
307099 TTTGCTCCGA
307109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
307150 CATTAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:307367 original size:18 final size:18
Alignment explanation
Indices: 307333--307371 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
307323 AAATATATTT
307333 AAAACTAAAATATTTAATA
1 AAAACTAAAATATTTAA-A
*
307352 AAAATTAAAATA-TTAAA
1 AAAACTAAAATATTTAAA
307369 AAA
1 AAA
307372 TTATAGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 4 0.21
19 11 0.58
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAACTAAAATATTTAAA
Found at i:310864 original size:2 final size:2
Alignment explanation
Indices: 310851--310881 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
310841 TCCTAAAATA
*
310851 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
310882 AACATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:310905 original size:26 final size:27
Alignment explanation
Indices: 310876--310927 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
310866 TATATATATA
310876 TATATAAACA-TTAAAAATTCAAAAAG
1 TATATAAACATTTAAAAATTCAAAAAG
* * *
310902 TATATAAATATTTTAAAATTTAAAAA
1 TATATAAACATTTAAAAATTCAAAAA
310928 TAATTACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
TATATAAACATTTAAAAATTCAAAAAG
Found at i:321507 original size:134 final size:131
Alignment explanation
Indices: 321283--322065 Score: 787
Period size: 134 Copynumber: 5.9 Consensus size: 131
321273 ACCGGGACAA
* * *
321283 GTCCCTCTTTTCCAAGATTTAATATTCCCTAAGTGACAGC-GATACAAGTCTTCCTTGATTCAAT
1 GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGA-ACAAGTCTGCC-CGATTCAAT
* * *
321347 CTTCCCTAAGTGACTGTA--GAATGGATCAACTACCACATATCTGATATTCCCTTCAGAAGAAGT
64 CTTCCCT-AGTGA-T-AACGGAATGGATCAACTACCCCAGATCTGATATTCCCTTCAGAAGAAG-
321410 AGAACAT
125 AGAACAT
* *
321417 GTCCCTCTTTTCCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCTGCTCCGATTCAGTC
1 GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTGC-CCGATTCAATC
* * * * *
321482 TTCCCTGAGTGATAACGGAATGGATCAACT-CTTCCAAATTTGATATTCCCTTGAGAATAATTG-
65 TTCCCT-AGTGATAACGGAATGGATCAACTAC-CCCAGATCTGATATTCCCTTCAGAAGAA--GA
321545 GAACAT
126 GAACAT
* * *
321551 GTCCCTCTTTTCCAAGATTTAATATTCCCCGAGTGACAACAGAACAAGTCTGCCCTGATTCAATC
1 GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTGCCC-GATTCAATC
* * * * * * *
321616 TTCCCTGAGTGACAATGAAATGGATCAACTCCCCCAGATCTGATATTACTTTCAGAAGAAGCGAA
65 TTCCCT-AGTGATAACGGAATGGATCAACTACCCCAGATCTGATATTCCCTTCAGAAGAAGAG-A
321681 ACAT
128 ACAT
* * * * * *
321685 GTCCCTCTTTTACAAGATTTGATATTCCCTAAGTGACAGCAGAACAAGTCTACCCCAATTCAATC
1 GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGAACAAGTCT-GCCCGATTCAATC
* * * * * *
321750 TTCCCTAAGTGACAGC-AAATGGATCAACTTCCCCAGATCTGATATTCCCTTTAG-AGAAAGCGT
65 TTCCCT-AGTGATAACGGAATGGATCAACTACCCCAGATCTGATATTCCCTTCAGAAG-AAGAG-
321813 AACAT
127 AACAT
* * *
321818 GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTAAGAGCGGAACCAGTCTGCCCGAATTCAATC
1 GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCG-ATTCAATC
* * * * * *
321883 TTCTCTATGTGATAGCGGAATTGATCAACTCCCCCAGATTTGATATTCCCTTTAGAAGAAGAGGA
65 TTCCCTA-GTGATAACGGAATGGATCAACTACCCCAGATCTGATATTCCCTTCAGAAGAAGA-GA
321948 ACA-
128 ACAT
* * * *
321951 GATCTCTC-TTT-CAAGATTTGATATTCCCTGAGTGACAGTGGAACAAATCTGCCTCGATTCAAT
1 G-TCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTGCC-CGATTCAAT
* * * * *
322014 CTTCCCTATGTGATAGCGGAATGAACCAAC-ATCCCCATATATGATATTCCCT
64 CTTCCCTA-GTGATAACGGAATGGATCAACTA-CCCCAGATCTGATATTCCCT
322066 GAGTGACAGT
Statistics
Matches: 555, Mismatches: 73, Indels: 44
0.83 0.11 0.07
Matches are distributed among these distances:
132 95 0.17
133 119 0.21
134 330 0.59
135 10 0.02
136 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (131 bp):
GTCCCTCTTTTCCAAGATTTAATATTCCCTGAGTGACAGCGGAACAAGTCTGCCCGATTCAATCT
TCCCTAGTGATAACGGAATGGATCAACTACCCCAGATCTGATATTCCCTTCAGAAGAAGAGAACA
T
Found at i:322248 original size:15 final size:15
Alignment explanation
Indices: 322212--322240 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
322202 TTAATTCCGC
322212 TATAATTATTATTAT
1 TATAATTATTATTAT
322227 TATAATTATTATTA
1 TATAATTATTATTA
322241 ATTAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATAATTATTATTAT
Found at i:331309 original size:134 final size:133
Alignment explanation
Indices: 330926--331606 Score: 788
Period size: 134 Copynumber: 5.1 Consensus size: 133
330916 GTTTAATTTG
* * *
330926 CAGATCTGATATTACCTTTAGAAGAAGCGGACCAAGTCCCTC-TTTCCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTTAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCT
* * *
330990 GAGTGACAGCGGAACAAGTCTGCCCTGATTCAATCTTCCCTGAGTGATAGCGGAATGGATCAACT
66 GAGTGACAGTGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
331055 CCC
131 CCC
* *
331058 CAAGATCTGATATTCCCTTCAGAAGAAGCAG-ACATGTCCCTCTTTTCCAAGA-TTGATATTCCC
1 C-AGATCTGATATTCCCTTTAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCC
* * * * * * * *
331121 TGAGT-ACAGTGGAACAAGTTTTCCCTGATTTAATATTCCCTGTGTGACAACGGAATGAATCAAC
65 TGAGTGACAGTGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAAC
*
331185 TCCTT
130 TCC-C
* *
331190 CAGATCTGATATTGCCTTTAGAAGAAACGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCT
1 CAGATCTGATATTCCCTTTAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCT
* * * * *
331255 GAGTGATAGTGGGACAAGTATTCCCCGATTCAATCTTCCCTAAGTGACAGCGGAATGGATCAACT
66 GAGTGACAGTGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
331320 CCCCC
131 --CCC
* * *
331325 CAGATCTGATATTCCCTTTAG-AGAAAGCGGAACATATCCC-CTTTACCAAGATTTGATATTCTC
1 CAGATCTGATATTCCCTTTAGAAG-AAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCC
* * * ** * * *
331388 TGAGTGCCAGCGGAACAAGTCTGCCTCGATTC-ATCTTCTATGAATGACATGCTGAATGGGTCAA
65 TGAGTGACAGTGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACA-GCGGAATGGATCAA
331452 CTCCCCC
129 CT--CCC
* * * ** *
331459 CAGATTTGATATTCCCTTCAGAAGAAGTGGAACAAATCTCTC-TTT-CAAGATTTGATATT-CCT
1 CAGATCTGATATTCCCTTTAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCT
* * * * **
331521 GAGTGATAGTGGAACAAGTCTGCCTCGATTCAATCTTCCCTGAGTAACAGTGGAATAAATCAACA
66 GAGTGACAGTGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAAC-
331586 TCCC
130 TCCC
331590 CAGATCTGATATTCCCT
1 CAGATCTGATATTCCCT
331607 AAGTGACAGC
Statistics
Matches: 467, Mismatches: 68, Indels: 29
0.83 0.12 0.05
Matches are distributed among these distances:
131 97 0.21
132 88 0.19
133 92 0.20
134 151 0.32
135 37 0.08
136 2 0.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (133 bp):
CAGATCTGATATTCCCTTTAGAAGAAGCGGAACATGTCCCTCTTTTCCAAGATTTGATATTCCCT
GAGTGACAGTGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAGTGACAGCGGAATGGATCAACT
CCC
Found at i:339436 original size:33 final size:33
Alignment explanation
Indices: 339399--339613 Score: 188
Period size: 33 Copynumber: 6.6 Consensus size: 33
339389 AAAATTCATG
* * * *
339399 ACTTTTGGAGGTAACATTTGGTGAAGTGACATA
1 ACTTTTAGAGGCACCATTTGGTGAAGAGACATA
* *
339432 ACTTTTAGAGGCACCCTTTGGTGAAGTGACATA
1 ACTTTTAGAGGCACCATTTGGTGAAGAGACATA
*
339465 ACTTTTAGAGGCACCCTTTGGTGAAGAGACATA
1 ACTTTTAGAGGCACCATTTGGTGAAGAGACATA
* * * *
339498 ACTTTTAGAGGTACCATTTCGTGAAGAGATACA
1 ACTTTTAGAGGCACCATTTGGTGAAGAGACATA
* *
339531 ACTTTTGGAGGCACC-TCTAGGTG-A-AGACATGA
1 ACTTTTAGAGGCACCAT-TTGGTGAAGAGACAT-A
* ** **
339563 A-TTTTGGAGTTACC-TCTTGGTGAAGAGACACG
1 ACTTTTAGAGGCACCAT-TTGGTGAAGAGACATA
* *
339595 ACTATTGGAGGCACCATTT
1 ACTTTTAGAGGCACCATTT
339614 TGGCGAAACA
Statistics
Matches: 152, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
31 22 0.14
32 6 0.04
33 123 0.81
34 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (33 bp):
ACTTTTAGAGGCACCATTTGGTGAAGAGACATA
Found at i:339926 original size:2 final size:2
Alignment explanation
Indices: 339919--339997 Score: 131
Period size: 2 Copynumber: 39.5 Consensus size: 2
339909 ATGCAACAAC
* *
339919 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
339961 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
339998 GTCCTCTGAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:343911 original size:20 final size:20
Alignment explanation
Indices: 343886--343938 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
343876 CTTCACACTT
343886 GCAAGATAAATCTTACCTTG
1 GCAAGATAAATCTTACCTTG
* *
343906 GCAAGATGAATCTTTCCTTG
1 GCAAGATAAATCTTACCTTG
*
343926 GAAAGATAAATCT
1 GCAAGATAAATCT
343939 ATTCCTCACT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (20 bp):
GCAAGATAAATCTTACCTTG
Found at i:345226 original size:32 final size:33
Alignment explanation
Indices: 345185--345309 Score: 111
Period size: 32 Copynumber: 3.9 Consensus size: 33
345175 AAAAGTCATG
345185 ACTTTTGGAGGCA-ACTTTGGTAAAGAGACATA
1 ACTTTTGGAGGCACACTTTGGTAAAGAGACATA
* *
345217 ACTTTTGGAGGCACCCTTTGGTGAAGAGAC--A
1 ACTTTTGGAGGCACACTTTGGTAAAGAGACATA
* * *
345248 ACTTTTAGAGACACCAC-TTGGAAAAGAG-CA-A
1 ACTTTTGGAGGCA-CACTTTGGTAAAGAGACATA
* *
345279 TGCTTTTGGAGGCAC-CTCTTGGTGAAGAGAC
1 -ACTTTTGGAGGCACACT-TTGGTAAAGAGAC
345310 GCGACTCTTG
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
30 2 0.03
31 23 0.31
32 34 0.46
33 15 0.20
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (33 bp):
ACTTTTGGAGGCACACTTTGGTAAAGAGACATA
Found at i:351024 original size:40 final size:40
Alignment explanation
Indices: 350961--351042 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 40
350951 ATAGGAGTCA
* *
350961 AATATTGCACAATAGTGCAGAGGTCGAGCCTTGCTCACCT
1 AATAATGCACAATAGTGCAGAGGTCGAGCCTTGCCCACCT
* * * *
351001 AATAATGCACCATAGTGCTGAGGTCGGGCTTTGCCCACCT
1 AATAATGCACAATAGTGCAGAGGTCGAGCCTTGCCCACCT
351041 AA
1 AA
351043 CTTGTATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.24
Consensus pattern (40 bp):
AATAATGCACAATAGTGCAGAGGTCGAGCCTTGCCCACCT
Found at i:354326 original size:19 final size:20
Alignment explanation
Indices: 354287--354326 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
354277 TTCAGGTGGT
**
354287 ATCGATTCCCCCTAGGGGGA
1 ATCGATTCCCCCTAGAAGGA
354307 ATCGATTCCCCCTA-AAGGA
1 ATCGATTCCCCCTAGAAGGA
354326 A
1 A
354327 AAATGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (20 bp):
ATCGATTCCCCCTAGAAGGA
Found at i:354989 original size:38 final size:38
Alignment explanation
Indices: 354933--355028 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
354923 TATAAGACAT
* * *
354933 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACAACCTTCGGG
* *
354971 ATGACAGGTCCTTCGGGACACATATGACAACCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACAACCTTCGGG
355009 ATGATAGGTCCTTCGGGACA
1 ATGATAGGTCCTTCGGGACA
355029 TTTGTACGAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACAACCTTCGGG
Found at i:357039 original size:10 final size:10
Alignment explanation
Indices: 357024--357048 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
357014 TGGGAATTCA
357024 ATTAGAAGCC
1 ATTAGAAGCC
357034 ATTAGAAGCC
1 ATTAGAAGCC
357044 ATTAG
1 ATTAG
357049 TAATGATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (10 bp):
ATTAGAAGCC
Found at i:361148 original size:20 final size:20
Alignment explanation
Indices: 361119--361156 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
361109 AGTATGTTCA
*
361119 GGGGGTATCGATTCCCCCTG
1 GGGGGAATCGATTCCCCCTG
361139 GGGGGAATCGATTCCCCC
1 GGGGGAATCGATTCCCCC
361157 AAAAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.32, G:0.34, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCCTG
Found at i:361830 original size:38 final size:38
Alignment explanation
Indices: 361782--361871 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
361772 TATAAAACAT
* *
361782 ATGATAGGTCCTAT-GGGACACATATTACATCCTTCGGG
1 ATGATAGGTCCT-TCAGGACACATATGACATCCTTCGGG
*
361820 ATGACAGGTCCTTCAGGACACATATGACATCCTTCGGG
1 ATGATAGGTCCTTCAGGACACATATGACATCCTTCGGG
361858 ATGATAGGTCCTTC
1 ATGATAGGTCCTTC
361872 GAGACATTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
37 1 0.02
38 46 0.98
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (38 bp):
ATGATAGGTCCTTCAGGACACATATGACATCCTTCGGG
Found at i:374146 original size:33 final size:33
Alignment explanation
Indices: 374109--374173 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
374099 TCATCCTAAA
*
374109 ATTTTAATTTAATAATAAATAAAATATTAAAAT
1 ATTTTAATTCAATAATAAATAAAATATTAAAAT
* *
374142 ATTTTCATTCAATAATAAATAAAATCTTAAAA
1 ATTTTAATTCAATAATAAATAAAATATTAAAA
374174 GTTATTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (33 bp):
ATTTTAATTCAATAATAAATAAAATATTAAAAT
Found at i:374671 original size:21 final size:21
Alignment explanation
Indices: 374646--374693 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
374636 CCTAATATTG
374646 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
374667 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
374688 TAATGT
1 CAATGT
374694 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:379322 original size:21 final size:21
Alignment explanation
Indices: 379297--379344 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
379287 CCTAATATTG
379297 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
379318 CAATGTCAAAATTTGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
379339 TAATGT
1 CAATGT
379345 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:383140 original size:20 final size:19
Alignment explanation
Indices: 383117--383164 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
383107 GCCGGTCACC
383117 CCGGTTTTCCCGGTT-TTCA
1 CCGGTTTT-CCGGTTCTTCA
*
383136 GCCGGTTCTTCCGGTTCTTTA
1 -CCGGTT-TTCCGGTTCTTCA
383157 CCGGTTTT
1 CCGGTTTT
383165 GTGTTAATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 18 0.72
21 5 0.20
ACGTcount: A:0.04, C:0.29, G:0.23, T:0.44
Consensus pattern (19 bp):
CCGGTTTTCCGGTTCTTCA
Found at i:386051 original size:28 final size:29
Alignment explanation
Indices: 386005--386062 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
385995 AGTCTTTTGA
386005 AAAAAAACCCATTGAGACCCAACACTCGGG
1 AAAAAAACCCATT-AGACCCAACACTCGGG
386035 AAAAAAACCCATT-GACCCAACACTCGGG
1 AAAAAAACCCATTAGACCCAACACTCGGG
386063 TGAGGTAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 15 0.54
30 13 0.46
ACGTcount: A:0.43, C:0.31, G:0.16, T:0.10
Consensus pattern (29 bp):
AAAAAAACCCATTAGACCCAACACTCGGG
Found at i:387570 original size:19 final size:20
Alignment explanation
Indices: 387546--387583 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
387536 AATAATAAAT
*
387546 TTTAATA-AAAAACTTTATG
1 TTTAATATAAAAAATTTATG
387565 TTTAATATAAAAAATTTAT
1 TTTAATATAAAAAATTTAT
387584 CCAAACAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
TTTAATATAAAAAATTTATG
Found at i:387767 original size:21 final size:20
Alignment explanation
Indices: 387743--387793 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 20
387733 TGAAAATTTT
387743 ATTTTTTATTTTTAAAAATAA
1 ATTTTTTATTTTTAAAAAT-A
* *
387764 ATTTATTATTTTTTTAAAAATC
1 ATTT-TT-TATTTTTAAAAATA
387786 ATTTTTTA
1 ATTTTTTA
387794 AAATGTAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 6 0.24
22 6 0.24
23 12 0.48
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTTATTTTTAAAAATA
Found at i:387851 original size:24 final size:25
Alignment explanation
Indices: 387812--387862 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
387802 CCCTTCATCA
**
387812 ACCCACACGTGTCCCTT-TCCCCCT
1 ACCCACACGTCCCCCTTCTCCCCCT
*
387836 ACCCACACGTCCCCCTTCTCCGCCT
1 ACCCACACGTCCCCCTTCTCCCCCT
387861 AC
1 AC
387863 ATCCCCACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.14, C:0.57, G:0.08, T:0.22
Consensus pattern (25 bp):
ACCCACACGTCCCCCTTCTCCCCCT
Found at i:387933 original size:17 final size:17
Alignment explanation
Indices: 387911--387944 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
387901 GGAAAAACTC
387911 TCTCAAATGCTCACCGT
1 TCTCAAATGCTCACCGT
387928 TCTCAAATGCTCACCGT
1 TCTCAAATGCTCACCGT
387945 GAACTGCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.12, T:0.29
Consensus pattern (17 bp):
TCTCAAATGCTCACCGT
Found at i:388699 original size:53 final size:53
Alignment explanation
Indices: 388627--388742 Score: 162
Period size: 53 Copynumber: 2.2 Consensus size: 53
388617 GCTGCACCTA
* *
388627 AGTGCCGAAATGGTAATTCACAAACTCATTATGAAT-TCCATGGATGCACGCAT
1 AGTGACGAAATGGTAATTCACAAACTCATTATGAATAT-CATGGATGCACACAT
* * *
388680 AGTGACGAAATGGTCATTCATAAACTCATTATGAATATCATGGGTGCACACAT
1 AGTGACGAAATGGTAATTCACAAACTCATTATGAATATCATGGATGCACACAT
*
388733 AGTGTCGAAA
1 AGTGACGAAA
388743 GTACATATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
53 55 0.98
54 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (53 bp):
AGTGACGAAATGGTAATTCACAAACTCATTATGAATATCATGGATGCACACAT
Found at i:388834 original size:49 final size:49
Alignment explanation
Indices: 388762--388858 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
388752 GTACTGATAT
* *
388762 AAAAATGTAACATATGCATTAAACAAAATCGATCGATAAGCATCATACG
1 AAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATACG
* *
388811 AAAAATGCAACTTATGCATTAAACAAAATCGATCTATAACCATCATAC
1 AAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATAC
388859 ACAAAGTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.24
Consensus pattern (49 bp):
AAAAATGCAACATATGCATTAAACAAAATCGATCGATAACCATCATACG
Found at i:388904 original size:18 final size:18
Alignment explanation
Indices: 388881--388936 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
388871 GAAATGCACC
388881 TATGAATCTCAATACACA
1 TATGAATCTCAATACACA
388899 TATGAATCTCAATACACA
1 TATGAATCTCAATACACA
*
388917 TATGAATCTCAATGCACA
1 TATGAATCTCAATACACA
388935 TA
1 TA
388937 CAATGGGCCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (18 bp):
TATGAATCTCAATACACA
Found at i:391729 original size:2 final size:2
Alignment explanation
Indices: 391724--391752 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
391714 CATTTTTTAT
391724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
391753 CGTATAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:391903 original size:13 final size:13
Alignment explanation
Indices: 391885--391910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
391875 CACTAGAAAT
391885 GAAAGAGAAGATA
1 GAAAGAGAAGATA
391898 GAAAGAGAAGATA
1 GAAAGAGAAGATA
391911 TGAGCTACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.08
Consensus pattern (13 bp):
GAAAGAGAAGATA
Found at i:392919 original size:19 final size:19
Alignment explanation
Indices: 392883--392920 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
392873 TGGTGAGGAC
*
392883 ACCTAAATATCCAGAGATG
1 ACCTAAATATCCAAAGATG
392902 ACCTAAAT-TCCCAAAGATG
1 ACCTAAATAT-CCAAAGATG
392921 CCACATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.42, C:0.24, G:0.13, T:0.21
Consensus pattern (19 bp):
ACCTAAATATCCAAAGATG
Found at i:394788 original size:25 final size:26
Alignment explanation
Indices: 394730--394789 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
394720 AACCGACCAC
*
394730 AATATTTTTTGAATGAATGTAATGAA
1 AATATTATTTGAATGAATGTAATGAA
* *
394756 TATA-TATTTGAATGAATGT-TTGAA
1 AATATTATTTGAATGAATGTAATGAA
394780 AATATTATTT
1 AATATTATTT
394790 CTATTTGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.24
25 19 0.66
26 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (26 bp):
AATATTATTTGAATGAATGTAATGAA
Found at i:394796 original size:31 final size:31
Alignment explanation
Indices: 394760--395099 Score: 304
Period size: 31 Copynumber: 10.5 Consensus size: 31
394750 AATGAATATA
*
394760 TATTTGAATGAATGTTTGAAAATATTATTTC
1 TATTTGAATGAATGTTTGTAAATATTATTTC
* *
394791 TATTTGAATGAATTTTTAGCTGTAAATATTATTTA
1 TATTTGAATGAA-TGTT---TGTAAATATTATTTC
*
394826 TATTTGAATGAATGTTTAACTATAAATATTATTTC
1 TATTTGAATGAATG-TT---TGTAAATATTATTTC
** *
394861 TATTTGAATGGTTGTTTAATTGTAAATATTATTTA
1 TATTTGAATGAATG--T--TTGTAAATATTATTTC
* * *
394896 TATTTAAATGAATATTTGTAAACATTATTTC
1 TATTTGAATGAATGTTTGTAAATATTATTTC
* **
394927 TATTTGAATGGACATTTGTAAATATTATTTC
1 TATTTGAATGAATGTTTGTAAATATTATTTC
* * *
394958 TATTTGAATAAATATTTGTAAATATTGTTTC
1 TATTTGAATGAATGTTTGTAAATATTATTTC
* * *
394989 TATTTGAATAAATATTTGTAAATATTGTTTC
1 TATTTGAATGAATGTTTGTAAATATTATTTC
*
395020 TATTTGAATGAATGTTTAACTATAAATATTATTT-
1 TATTTGAATGAATG-TT---TGTAAATATTATTTC
** *
395054 TAATTTGAACAAATGTTTGTAAATATTATTTT
1 T-ATTTGAATGAATGTTTGTAAATATTATTTC
*
395086 TATTTGAATAAATG
1 TATTTGAATGAATG
395100 ATTATAAACC
Statistics
Matches: 262, Mismatches: 33, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
31 148 0.56
32 6 0.02
33 1 0.00
34 4 0.02
35 100 0.38
36 2 0.01
38 1 0.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.50
Consensus pattern (31 bp):
TATTTGAATGAATGTTTGTAAATATTATTTC
Found at i:395001 original size:97 final size:99
Alignment explanation
Indices: 394880--395100 Score: 239
Period size: 97 Copynumber: 2.3 Consensus size: 99
394870 GGTTGTTTAA
* *
394880 TTGTAAATATTATTTATA-TT---TAAATGAATATTTGTAAACATTATTTCTATTTGAATGGA-C
1 TTGTAAATATTATTTCTATTTGAATAAATGAATATTTGTAAACATTATTTCTATTTGAATGAATC
* *
394940 ATT-TGTAAATATTATTTCT-ATTTGAATAAATAT
66 ATTATATAAATATTATTT-TAATTTGAACAAATAT
* * * *
394973 TTGTAAATATTGTTTCTATTTGAAT--A--AATATTTGTAAATATTGTTTCTATTTGAATGAATG
1 TTGTAAATATTATTTCTATTTGAATAAATGAATATTTGTAAACATTATTTCTATTTGAATGAATC
* *
395034 TTTAACTATAAATATTATTTTAATTTGAACAAATGT
66 ATT-A-TATAAATATTATTTTAATTTGAACAAATAT
*
395070 TTGTAAATATTATTTTTATTTGAATAAATGA
1 TTGTAAATATTATTTCTATTTGAATAAATGA
395101 TTATAAACCT
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
93 46 0.45
94 4 0.04
95 1 0.01
96 1 0.01
97 49 0.48
99 1 0.01
101 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (99 bp):
TTGTAAATATTATTTCTATTTGAATAAATGAATATTTGTAAACATTATTTCTATTTGAATGAATC
ATTATATAAATATTATTTTAATTTGAACAAATAT
Found at i:395114 original size:31 final size:31
Alignment explanation
Indices: 395040--395114 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
395030 AATGTTTAAC
* *
395040 TATAAATATTATTTTAATTTGAACAAATGTT
1 TATAAACATTATTTTAATTTGAACAAATGAT
* * * *
395071 TGTAAATATTATTTTTATTTGAATAAATGAT
1 TATAAACATTATTTTAATTTGAACAAATGAT
*
395102 TATAAACCTTATT
1 TATAAACATTATT
395115 ACAATTGTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (31 bp):
TATAAACATTATTTTAATTTGAACAAATGAT
Found at i:396219 original size:18 final size:18
Alignment explanation
Indices: 396196--396243 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
396186 ATGCAAAAAT
396196 GGTACCGATACTCAAAGG
1 GGTACCGATACTCAAAGG
396214 GGTACCGATACTCAAAGG
1 GGTACCGATACTCAAAGG
396232 GGTACCGATACT
1 GGTACCGATACT
396244 ACTATGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (18 bp):
GGTACCGATACTCAAAGG
Found at i:405383 original size:16 final size:15
Alignment explanation
Indices: 405336--405390 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 15
405326 ACAATCTAAC
*
405336 TTAATTTTAAAAAAA
1 TTAATTTAAAAAAAA
* *
405351 -TAATTTAATATAAA
1 TTAATTTAAAAAAAA
405365 TTAATTTAAAAACAAA
1 TTAATTTAAAAA-AAA
405381 TTAATTTAAA
1 TTAATTTAAA
405391 TCAAATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 11 0.33
15 9 0.27
16 13 0.39
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAATTTAAAAAAAA
Found at i:405764 original size:19 final size:19
Alignment explanation
Indices: 405737--405776 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
405727 CGGGAAGATA
*
405737 CACGAAATCGTAGAGTCTT
1 CACGAAATCGTAGAGACTT
* *
405756 CACGTAATCGTGGAGACTT
1 CACGAAATCGTAGAGACTT
405775 CA
1 CA
405777 AAGCTTGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (19 bp):
CACGAAATCGTAGAGACTT
Found at i:406468 original size:31 final size:31
Alignment explanation
Indices: 406433--406491 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
406423 TTTGACGTAA
* *
406433 AAACTTTAAATAAAATATTAATTTAACCCTT
1 AAACTTGAAATAAAATATCAATTTAACCCTT
*
406464 AAACTTGAGATAAAATATCAATTTAACC
1 AAACTTGAAATAAAATATCAATTTAACC
406492 TCTAAATCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (31 bp):
AAACTTGAAATAAAATATCAATTTAACCCTT
Found at i:424466 original size:20 final size:20
Alignment explanation
Indices: 424438--424476 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
424428 GAAATCTTGT
*
424438 TCTTCTCTTCTTTGTCTATC
1 TCTTCTCTTCTTCGTCTATC
*
424458 TCTTTTCTTCTTCGTCTAT
1 TCTTCTCTTCTTCGTCTAT
424477 TTTTCTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (20 bp):
TCTTCTCTTCTTCGTCTATC
Found at i:441587 original size:30 final size:28
Alignment explanation
Indices: 441553--441614 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 28
441543 ATTGATAAAA
441553 TAAGCTTACGAGCTTATGGAATTTAAATGG
1 TAAGCTTACGAGCTTATGGAA--TAAATGG
* *
441583 TAAGCTTACGAGTTTATGGGATAAATGG
1 TAAGCTTACGAGCTTATGGAATAAATGG
441611 TAAG
1 TAAG
441615 AGATTTTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 11 0.37
30 19 0.63
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (28 bp):
TAAGCTTACGAGCTTATGGAATAAATGG
Found at i:442011 original size:20 final size:20
Alignment explanation
Indices: 441986--442034 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
441976 AAGGGGTACT
441986 GATTCCCCCTACAGGGAACC
1 GATTCCCCCTACAGGGAACC
*
442006 GATTCCCTCTACAGGGAACC
1 GATTCCCCCTACAGGGAACC
442026 GATTCCCCC
1 GATTCCCCC
442035 ACTGTCTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.41, G:0.18, T:0.18
Consensus pattern (20 bp):
GATTCCCCCTACAGGGAACC
Found at i:443783 original size:21 final size:22
Alignment explanation
Indices: 443758--443803 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
443748 AATAGCCTGG
443758 TTTCATG-AAATTTATCCTTA-A
1 TTTCATGTAAATTTA-CCTTATA
*
443779 TTTCATGTTAATTTACCTTATA
1 TTTCATGTAAATTTACCTTATA
443801 TTT
1 TTT
443804 AAGCTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCATGTAAATTTACCTTATA
Found at i:449274 original size:57 final size:58
Alignment explanation
Indices: 449151--449458 Score: 282
Period size: 57 Copynumber: 5.4 Consensus size: 58
449141 GCTAACCATG
* * * *
449151 ATTTTTAGGGGTTTCTTGATG--T-TTTCAAATGAA-TTTTTGAAAGAATCTAAGCCT-
1 ATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAACATTTT-AAAAAAGCTAAGCCTA
* * *
449205 ATTTTTAGGGGTTTCTTGATGATTATTTCCAATGAACATTTTAAAAAAGGTAAGCCTA
1 ATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAACATTTTAAAAAAGCTAAGCCTA
* *
449263 ATTTTCA-GGGTTTCTTGATGATTATTTCTAATGAAC-TTTTAAAAGAAGCTAAGCCTC
1 ATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAACATTTTAAAA-AAGCTAAGCCTA
* * * *
449320 ATTTTCAGGGGTTTCTTGATAATTATTTCAAATG-A-ATTTTTAAGAAGCTAAGCCAA
1 ATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAACATTTTAAAAAAGCTAAGCCTA
* * * * * *
449376 ATTTTTAGGGGTTTCTTAATGA-TATCTGT-AAACGAA-AGTTTTTAAGAAA-CTAAGCTTG
1 ATTTTCAGGGGTTTCTTGATGATTAT-T-TCAAATGAACA--TTTTAAAAAAGCTAAGCCTA
* *
449434 GTTTTCAAGGGTTTCTTGATGATTA
1 ATTTTCAGGGGTTTCTTGATGATTA
449459 AGTCCTTCGG
Statistics
Matches: 211, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
54 21 0.10
55 3 0.01
56 43 0.20
57 77 0.36
58 58 0.27
59 9 0.04
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (58 bp):
ATTTTCAGGGGTTTCTTGATGATTATTTCAAATGAACATTTTAAAAAAGCTAAGCCTA
Found at i:449318 original size:114 final size:113
Alignment explanation
Indices: 449105--449398 Score: 319
Period size: 114 Copynumber: 2.6 Consensus size: 113
449095 TTTTAAAGGC
* * * * * * *
449105 TTCTTGATATATTGCTTTCAAAAGAATTTGATAGAAGCTAA-CCATGATTTTTAGGGGTTTCTTG
1 TTCTTGATA-ATT-ATTTCAAATGAATTTTAAAAAAGCTAAGCCA-AATTTTCAGGGGTTTCTTG
* * * *
449169 ATG--TTTTCAAATGAATTTTTGAAAGAATCTAAGCCT-ATTTTTAGGGGT
63 ATGATTTTTCAAATGAACTTTTAAAAGAAGCTAAGCCTCATTTTCAGGGGT
* * * *
449217 TTCTTGATGATTATTTCCAATGAACATTTTAAAAAAGGTAAGCCTAATTTTCA-GGGTTTCTTGA
1 TTCTTGATAATTATTTCAAATG-A-ATTTTAAAAAAGCTAAGCCAAATTTTCAGGGGTTTCTTGA
*
449281 TGATTATTTCTAATGAACTTTTAAAAGAAGCTAAGCCTCATTTTCAGGGGT
64 TGATT-TTTCAAATGAACTTTTAAAAGAAGCTAAGCCTCATTTTCAGGGGT
* * * *
449332 TTCTTGATAATTATTTCAAATGAATTTTTAAGAAGCTAAGCCAAATTTTTAGGGGTTTCTTAATG
1 TTCTTGATAATTATTTCAAATGAATTTTAAAAAAGCTAAGCCAAATTTTCAGGGGTTTCTTGATG
449397 AT
66 AT
449399 ATCTGTAAAC
Statistics
Matches: 150, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
110 7 0.05
111 17 0.11
112 26 0.17
113 26 0.17
114 43 0.29
115 31 0.21
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (113 bp):
TTCTTGATAATTATTTCAAATGAATTTTAAAAAAGCTAAGCCAAATTTTCAGGGGTTTCTTGATG
ATTTTTCAAATGAACTTTTAAAAGAAGCTAAGCCTCATTTTCAGGGGT
Found at i:449354 original size:58 final size:58
Alignment explanation
Indices: 449137--449398 Score: 317
Period size: 57 Copynumber: 4.6 Consensus size: 58
449127 AGAATTTGAT
* * *
449137 AGAAGCTAA-CCATGATTTTTAGGGGTTTCTTGATG--T-TTTCAAATGAATTTTTGAA
1 AGAAGCTAAGCC-TAATTTTTAGGGGTTTCTTGATGATTATTTCAAATGAACTTTTAAA
* *
449192 AGAATCTAAGCCT-ATTTTTAGGGGTTTCTTGATGATTATTTCCAATGAACATTTTAAA
1 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTCAAATGAAC-TTTTAAA
* * *
449250 A-AAGGTAAGCCTAATTTTCA-GGGTTTCTTGATGATTATTTCTAATGAACTTTTAAA
1 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTCAAATGAACTTTTAAA
* * * *
449306 AGAAGCTAAGCCTCATTTTCAGGGGTTTCTTGATAATTATTTCAAATGAA-TTTT-TA
1 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTCAAATGAACTTTTAAA
* *
449362 AGAAGCTAAGCCAAATTTTTAGGGGTTTCTTAATGAT
1 AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGAT
449399 ATCTGTAAAC
Statistics
Matches: 181, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
54 21 0.12
55 9 0.05
56 44 0.24
57 68 0.38
58 39 0.22
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (58 bp):
AGAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTCAAATGAACTTTTAAA
Found at i:451389 original size:20 final size:20
Alignment explanation
Indices: 451366--451412 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
451356 AAGTAAATCC
* *
451366 TTCGGGCCATTAGTAAGTCT
1 TTCGAGCCATTAGCAAGTCT
451386 TTCGAGCCATTAGCAAGTCT
1 TTCGAGCCATTAGCAAGTCT
451406 TTCGAGC
1 TTCGAGC
451413 ATGAAGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.32
Consensus pattern (20 bp):
TTCGAGCCATTAGCAAGTCT
Found at i:453238 original size:108 final size:108
Alignment explanation
Indices: 453120--453330 Score: 254
Period size: 108 Copynumber: 2.0 Consensus size: 108
453110 TCCCTAAACA
* *
453120 TTTAGCGTGTTTTTACAGTT-TGGTCACCTGCAGGGAC-TAAAATTGCT-CTTTT-CATTTTCTG
1 TTTAGCGTGTTTTTACA-TTCTGGTCAACTGCAGGG-CTTAAAATTG-TAATTTTCCATTTTCT-
*
453181 TGCGTGCCTTTTA-TTTTTTGGGTTATTCATGT-TTTAGTCCCTATTAT
62 TGCATG-CTTTTATTTTTTTGGGTTATTC-TGTATTTAGTCCCTATTAT
* * * *
453228 TTTAGCGTGTTTTTGCATTCTGGTCAACTGTAGGGCTTAGAATTGTAATTTTCCCTTTTCTTGCA
1 TTTAGCGTGTTTTTACATTCTGGTCAACTGCAGGGCTTAAAATTGTAATTTTCCATTTTCTTGCA
*
453293 TGCTTTTATTTTTTTGGGTTATTCTGTATTTGGTCCCT
66 TGCTTTTATTTTTTTGGGTTATTCTGTATTTAGTCCCT
453331 GTAATTTAGG
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
107 13 0.15
108 69 0.78
109 7 0.08
ACGTcount: A:0.15, C:0.16, G:0.19, T:0.50
Consensus pattern (108 bp):
TTTAGCGTGTTTTTACATTCTGGTCAACTGCAGGGCTTAAAATTGTAATTTTCCATTTTCTTGCA
TGCTTTTATTTTTTTGGGTTATTCTGTATTTAGTCCCTATTAT
Found at i:455250 original size:21 final size:24
Alignment explanation
Indices: 455204--455252 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
455194 CGAGCAACTC
455204 AAAAATATATATATTATCTTTCAA
1 AAAAATATATATATTATCTTTCAA
455228 AAAAATA-ATATATTAT-TTT-AA
1 AAAAATATATATATTATCTTTCAA
455249 AAAA
1 AAAA
455253 TAAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 6 0.24
22 3 0.12
23 9 0.36
24 7 0.28
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAAATATATATATTATCTTTCAA
Found at i:455261 original size:20 final size:23
Alignment explanation
Indices: 455204--455262 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
455194 CGAGCAACTC
*
455204 AAAAATATATATATTATCTTTCA
1 AAAAATAAATATATTATCTTTCA
455227 AAAAA-ATAATATATTAT-TTT-A
1 AAAAATA-AATATATTATCTTTCA
455248 AAAAATAAAT-TATTA
1 AAAAATAAATATATTA
455263 ATAATATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 5 0.15
21 9 0.27
22 5 0.15
23 14 0.42
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAAATAAATATATTATCTTTCA
Found at i:455880 original size:40 final size:41
Alignment explanation
Indices: 455800--455896 Score: 101
Period size: 40 Copynumber: 2.3 Consensus size: 41
455790 TTCATTTCTA
* *
455800 ATTTCAAAATTATTTCACATTTAAATTGTAAATCTCTATTTT
1 ATTTC-AAATTATTTCACACTTAAATTGTAAATATCTATTTT
*
455842 -TTTCAAATTATTTCAC-CTTAACATT-TAAATTATTTATTTT
1 ATTTCAAATTATTTCACACTTAA-ATTGTAAA-TATCTATTTT
*
455882 AATCTCAAATTATTT
1 -ATTTCAAATTATTT
455897 TAAATTTAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
39 8 0.17
40 23 0.49
41 4 0.09
42 12 0.26
ACGTcount: A:0.35, C:0.12, G:0.01, T:0.52
Consensus pattern (41 bp):
ATTTCAAATTATTTCACACTTAAATTGTAAATATCTATTTT
Found at i:457401 original size:58 final size:59
Alignment explanation
Indices: 457319--457489 Score: 166
Period size: 59 Copynumber: 2.9 Consensus size: 59
457309 TGGCACTTTG
* * * * * *
457319 TGTGCCAAAATGTTAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCA-CTGA
1 TGTGCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTCCAGATAGAGCATCTGA
* * ** * * * *
457377 GTGTGCT-AAGTGGTAAGGGAATCATATTAAAAATATGGATTTCCAGATAGGGTATTTTA
1 -TGTGCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTCCAGATAGAGCATCTGA
* * *
457436 TGTTCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTCTAGATAAAGCA
1 TGTGCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTCCAGATAGAGCA
457490 CTAAGGGTCC
Statistics
Matches: 87, Mismatches: 23, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
58 41 0.47
59 46 0.53
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.32
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTCCAGATAGAGCATCTGA
Found at i:457551 original size:118 final size:117
Alignment explanation
Indices: 457319--457583 Score: 305
Period size: 118 Copynumber: 2.3 Consensus size: 117
457309 TGGCACTTTG
* * * * * * * * *
457319 TGTGCCAAAATGTTAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTATATGGATTTCCAGATAAAGCACTAAGGGTCCT
* * * * *
457384 AAGTGGTAAGGGAATCATATTAAAAATATGGATTTCCAGATAGGGTATTTTA
66 AAGAGATAAGGAAATCATATTAAAAATATGGATTTCCACATAGGGTATTTCA
* * *
457436 TGTTCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTCTAGATAAAGCACTAAGGGTCCT
1 TGTGCTAAAATGGTAAGGAAATCATACTAAGTATATGGATTTCCAGATAAAGCACTAAGGGTCCT
* *** *
457501 ATGAAGATAAGGAAATCATATTAATGGTATGGATTTTCACATAGGGTATTTCA
66 AAG-AGATAAGGAAATCATATTAAAAATATGGATTTCCACATAGGGTATTTCA
**
457554 TGTGCTAAAATGGTAACAAAATCATACTAA
1 TGTGCTAAAATGGTAAGGAAATCATACTAA
457584 ATGTATGAAT
Statistics
Matches: 121, Mismatches: 26, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
117 55 0.45
118 66 0.55
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.31
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAAGTATATGGATTTCCAGATAAAGCACTAAGGGTCCT
AAGAGATAAGGAAATCATATTAAAAATATGGATTTCCACATAGGGTATTTCA
Found at i:457576 original size:59 final size:59
Alignment explanation
Indices: 457513--457624 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
457503 GAAGATAAGG
* * * *
457513 AAATCATA-TTAATGGTATGGA-TTTTCACATAGGGTATTTCATGTGCTAAAATGGTAACA
1 AAATCATACTAAAT-GTATGAATTTTTCA-ATAGGGCACTTCATGTGCTAAAATGGTAACA
* *
457572 AAATCATACTAAATGTATGAATTTTTGAATAGGGCACTTCGTGTGCTAAAATG
1 AAATCATACTAAATGTATGAATTTTTCAATAGGGCACTTCATGTGCTAAAATG
457625 AAAGGGGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 36 0.80
60 9 0.20
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (59 bp):
AAATCATACTAAATGTATGAATTTTTCAATAGGGCACTTCATGTGCTAAAATGGTAACA
Found at i:457810 original size:17 final size:18
Alignment explanation
Indices: 457785--457818 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
457775 ATTGTAGTAT
457785 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
457802 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
457819 TATCAGAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:464193 original size:58 final size:59
Alignment explanation
Indices: 464111--464270 Score: 178
Period size: 58 Copynumber: 2.7 Consensus size: 59
464101 TGGCACTTTG
* * * * *
464111 TGTGCCAAAATGTTAAGGAAATCATACTGAGTGTATGGATTTCCATATAGAGCACTGGG
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTATATGGATTTCCATATAGAGCACTGGA
* * ** * * **
464170 TGTGCT-AAGTGGTAAGGGAATCATATTGAAAATATGGATTTCCATATAGGGCATTTTA
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTATATGGATTTCCATATAGAGCACTGGA
* *
464228 TGTTCTAAAATGGTAAGGGAATCATACTAAGTATATGGATTTC
1 TGTGCTAAAATGGTAAGGGAATCATACTGAGTATATGGATTTC
464271 TAGATAAAGC
Statistics
Matches: 81, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
58 45 0.56
59 36 0.44
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.33
Consensus pattern (59 bp):
TGTGCTAAAATGGTAAGGGAATCATACTGAGTATATGGATTTCCATATAGAGCACTGGA
Found at i:464603 original size:17 final size:18
Alignment explanation
Indices: 464578--464611 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
464568 ATTGTAGTAT
464578 ATTCATTGGA-ATTAAAG
1 ATTCATTGGAGATTAAAG
*
464595 ATTCCTTGGAGATTAAA
1 ATTCATTGGAGATTAAA
464612 TATCATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (18 bp):
ATTCATTGGAGATTAAAG
Found at i:469015 original size:3 final size:3
Alignment explanation
Indices: 469007--469031 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
468997 TTTATTTTAT
469007 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
469032 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:469050 original size:20 final size:20
Alignment explanation
Indices: 469025--469065 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
469015 ATAATAATAA
469025 TAATAATTATTATTATTATT
1 TAATAATTATTATTATTATT
*
469045 TAATAATTATTATTTTTATT
1 TAATAATTATTATTATTATT
469065 T
1 T
469066 TCATGCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TAATAATTATTATTATTATT
Found at i:469053 original size:17 final size:16
Alignment explanation
Indices: 469028--469062 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
469018 ATAATAATAA
*
469028 TAATTATTATTATTATT
1 TAATAATTATTATT-TT
469045 TAATAATTATTATTTT
1 TAATAATTATTATTTT
469061 TA
1 TA
469063 TTTTCATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATAATTATTATTTT
Found at i:485313 original size:3 final size:3
Alignment explanation
Indices: 485305--485367 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
485295 ATTAATTAAT
*
485305 TAA TAA TAA -GA TAA T-A TAA T-A TAA T-A TAA T-A TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
485347 TAA TAA TAA TAAA TAA -AA TAA
1 TAA TAA TAA T-AA TAA TAA TAA
485368 ATGAAATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 16
0.74 0.03 0.24
Matches are distributed among these distances:
2 13 0.26
3 34 0.68
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:485318 original size:8 final size:7
Alignment explanation
Indices: 485301--485362 Score: 56
Period size: 8 Copynumber: 8.4 Consensus size: 7
485291 ATTAATTAAT
*
485301 TAATTAA
1 TAATAAA
485308 TAATAAGA
1 TAATAA-A
485316 TAATATAA
1 TAATA-AA
485324 T-ATAATA
1 TAATAA-A
485331 TAATATAA
1 TAATA-AA
485339 TAATAAAA
1 TAAT-AAA
485347 TAAT-AA
1 TAATAAA
485353 TAATAAA
1 TAATAAA
485360 TAA
1 TAA
485363 AATAAATGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
6 7 0.15
7 15 0.32
8 22 0.47
9 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (7 bp):
TAATAAA
Found at i:485323 original size:5 final size:5
Alignment explanation
Indices: 485293--485366 Score: 66
Period size: 5 Copynumber: 15.0 Consensus size: 5
485283 GTATTAAAAT
*
485293 TAAT- TAAT- TAAT- TAATAA TAAGA TAATA TAATA TAATA TAATA TAATAA
1 TAATA TAATA TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAAT-A
* *
485342 TAAAA TAATAA TAATA -AATA AAATA
1 TAATA TAAT-A TAATA TAATA TAATA
485367 AATGAAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
4 16 0.26
5 33 0.54
6 12 0.20
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (5 bp):
TAATA
Found at i:485377 original size:18 final size:18
Alignment explanation
Indices: 485315--485367 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
485305 TAATAATAAG
*
485315 ATAAT-ATAATATAATATA
1 ATAATAATAA-ATAAAATA
485333 AT-ATAAT-AATAAAATA
1 ATAATAATAAATAAAATA
485349 ATAATAATAAATAAAATA
1 ATAATAATAAATAAAATA
485367 A
1 A
485368 ATGAAATAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
16 9 0.29
17 8 0.26
18 14 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATAATAAATAAAATA
Found at i:485837 original size:124 final size:123
Alignment explanation
Indices: 485615--486240 Score: 726
Period size: 124 Copynumber: 5.2 Consensus size: 123
485605 ATTCTTCTCT
** * ** * * *
485615 TTCAGATGAGTTCTTCTCATTATGAACACT-TATGGCAATGTTGATGCTGATCTATCTCATTTTG
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAATTGATGTTGATCTATCTCCTTCTG
* * *
485679 CGATAGAATCATGCAAAACGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
65 TGATAGAGTCATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
485738 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGTTGATCTATCTCCTTCTG
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAATTGATGTTGATCTATCTCCTTCTG
*
485803 TGATAGAGTCATGCAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
65 TGATAGAGTCATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
*
485862 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAATTGATGATGATCTATCTCCTTCTG
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAATTGATGTTGATCTATCTCCTTCTG
* *
485927 TGATAGAGTCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTC
65 TGATAGAGTCATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
* **
485986 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA---A--TTGATCCA--T-C--GAGT
1 TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATTGATGTTGATCTATCTCCTTCTGT
* ** * * * *
486041 GAT-GAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTC
66 GATAG-AGTCATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
* * * *
486099 TTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGG--CA---ATGTTGATCCA--T-C--GTG
1 TTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAATTGATGTTGATCTATCTCCTTCTG
* * *
486153 TGAT-GAATTCAAGCAAAATA-TTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTC
65 TGATAG-AGTCATGCAAAA-AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
486212 TTCAGATGAGTTCTTCTCATTATGAACTT
1 TTCAGATGAGTTCTTCTCATTATGAACTT
486241 ATTCTTCCTT
Statistics
Matches: 462, Mismatches: 35, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
111 2 0.00
112 2 0.00
113 175 0.38
114 2 0.00
115 1 0.00
116 1 0.00
118 6 0.01
120 1 0.00
123 32 0.07
124 240 0.52
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (123 bp):
TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAATTGATGTTGATCTATCTCCTTCTGT
GATAGAGTCATGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
Done.