Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold553
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: 449280
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 3 of 4
Found at i:265781 original size:13 final size:13
Alignment explanation
Indices: 265763--265788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
265753 CAATTTTTTG
265763 TGTATCGATACAT
1 TGTATCGATACAT
265776 TGTATCGATACAT
1 TGTATCGATACAT
265789 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:266272 original size:51 final size:52
Alignment explanation
Indices: 266171--266279 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 52
266161 GATCCTAACA
***
266171 GATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATC
1 GATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATAATGTATC
*
266223 GATACATCTGGGCAAA-TTGCCTGCATGTATCGATACA-AAGATCAGTGTATC
1 GATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-AATGTATC
266274 GATACA
1 GATACA
266280 ATGTATCGAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
50 2 0.04
51 34 0.65
52 16 0.31
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (52 bp):
GATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATAATGTATC
Found at i:266286 original size:13 final size:13
Alignment explanation
Indices: 266268--266292 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
266258 CAAAGATCAG
266268 TGTATCGATACAA
1 TGTATCGATACAA
266281 TGTATCGATACA
1 TGTATCGATACA
266293 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:266372 original size:13 final size:13
Alignment explanation
Indices: 266354--266378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
266344 ACAAAAAAAA
266354 TGTATCGATACAT
1 TGTATCGATACAT
266367 TGTATCGATACA
1 TGTATCGATACA
266379 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:269026 original size:52 final size:53
Alignment explanation
Indices: 268960--269344 Score: 171
Period size: 52 Copynumber: 7.4 Consensus size: 53
268950 CAATTGTTCA
* *
268960 TAATTGGGGATACTCCAA-TCCCAGTTTTATTTTC-AAAACACTAATTTTCCTT
1 TAATCGGGGATACTCCAACTCCCA-TTTTATTTTCAAAAACACCAATTTTCCTT
* * *
269012 TAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTTTC-A
1 TAATCGGGGATACTCCAACTCCCATTTTATTTTCAAAAACACCAATTTTCCTT
* * * * * * * *
269064 CAATCGAGGATACTCCAAC-CTCA--TTATTTCATCAGGGATACTCCAA--TCCCGT
1 TAATCGGGGATACTCCAACTCCCATTTTATTT--TCA--AAAACACCAATTTTCCTT
* * * * *** *
269116 TACCTTCGAGGGGATACTCTC-AC-CCCAGCTTTA-TTTCCAAAATATTGA-TTT-CTCA
1 TA--ATC--GGGGATACTC-CAACTCCCA-TTTTATTTTCAAAAACACCAATTTTCCT-T
* * * * *
269171 TAATCGGAGATACTTCAAC-CCCGATTTTA-TTTCTAAAACACTAATTTT-CTA
1 TAATCGGGGATACTCCAACTCCC-ATTTTATTTTCAAAAACACCAATTTTCCTT
* *
269222 CAATCGGGGATACTCCAAC-CCCGATTTTATCTTC-AAAACACCAATTTTCCTT
1 TAATCGGGGATACTCCAACTCCC-ATTTTATTTTCAAAAACACCAATTTTCCTT
* * ** * *
269274 TAATCGGGGATATTCTAACTCTGATTTTA-TTTCAAAAAACACCAATTTTTC-A
1 TAATCGGGGATACTCCAACTCCCATTTTATTTTC-AAAAACACCAATTTTCCTT
* *
269326 CAATCGAGGATACTCCAAC
1 TAATCGGGGATACTCCAAC
269345 CTCGTTATTT
Statistics
Matches: 252, Mismatches: 56, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
49 6 0.02
50 1 0.00
51 78 0.31
52 93 0.37
53 43 0.17
54 6 0.02
55 3 0.01
56 16 0.06
57 1 0.00
58 2 0.01
59 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.34
Consensus pattern (53 bp):
TAATCGGGGATACTCCAACTCCCATTTTATTTTCAAAAACACCAATTTTCCTT
Found at i:269200 original size:51 final size:51
Alignment explanation
Indices: 269145--269345 Score: 167
Period size: 51 Copynumber: 3.9 Consensus size: 51
269135 TCACCCCAGC
* * * * *
269145 TTTATTTCCAAAATATTGA-TTTCTCATAATCGGAGATACTTCAACCCCGAT
1 TTTATTTCCAAAACACTAATTTTCT-ACAATCGGAGATACTCCAACCCCGAT
* *
269196 TTTATTTCTAAAACACTAATTTTCTACAATCGGGGATACTCCAACCCCGAT
1 TTTATTTCCAAAACACTAATTTTCTACAATCGGAGATACTCCAACCCCGAT
* ** * * * * *
269247 TTTATCTT-CAAAACACCAATTTTCCTTTAATCGGGGATATTCTAACTCTGAT
1 TTTAT-TTCCAAAACACTAATTTT-CTACAATCGGAGATACTCCAACCCCGAT
* *
269299 TTTATTTCAAAAAACACCAATTTT-TCACAATC-GAGGATACTCCAACC
1 TTTATTTC-CAAAACACTAATTTTCT-ACAATCGGA-GATACTCCAACC
269346 TCGTTATTTC
Statistics
Matches: 121, Mismatches: 22, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
51 60 0.50
52 47 0.39
53 14 0.12
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.35
Consensus pattern (51 bp):
TTTATTTCCAAAACACTAATTTTCTACAATCGGAGATACTCCAACCCCGAT
Found at i:269506 original size:79 final size:77
Alignment explanation
Indices: 269356--269614 Score: 297
Period size: 79 Copynumber: 3.3 Consensus size: 77
269346 TCGTTATTTC
**
269356 ATCGGGGATACTCC-ACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGGCTTTATT-CCAAAAT
*
269420 ATTGATTTCTCATA
64 ATTGATTTCTCACA
* ** *
269434 ATTGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTAGTTCC-TAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAA-CCCGGCTTTA-TTCCAAAAT
* *
269498 CATCGATTTTTCACA
64 -ATTGATTTCTCACA
* * * * *
269513 ACCGGGGATACTCCAACTCCGTTATTTTCAAGGGGATACTCTAACCCTGGCTTTATTTCCAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCC-GGCTTTA-TTCCAAAAT
269578 ATTGATTTCTCACA
64 ATTGATTTCTCACA
* *
269592 ATCGAGGATACTCCAGCCCCGTT
1 ATCGGGGATACTCCAACCCCGTT
269615 GTTATCTCAA
Statistics
Matches: 150, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
78 19 0.13
79 126 0.84
80 5 0.03
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.30
Consensus pattern (77 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCGGCTTTATTCCAAAATAT
TGATTTCTCACA
Found at i:273663 original size:62 final size:62
Alignment explanation
Indices: 273596--273736 Score: 246
Period size: 62 Copynumber: 2.3 Consensus size: 62
273586 TATGCAAATA
* *
273596 CGGAGGGTTACTCATGAGAGACATAGGTAATTTACATCCCGGAAGGTATTTCCATGCCTATG
1 CGGAGGGTTACTCACGAGAGACATAGGTAATTTACATCCCGGAAGGTATTGCCATGCCTATG
*
273658 CGGAGGGTTACTCACGAGAGACATAGGTAATTTACATCTCGGAAGGTATTGCCATGCCTATG
1 CGGAGGGTTACTCACGAGAGACATAGGTAATTTACATCCCGGAAGGTATTGCCATGCCTATG
*
273720 CGGAAGGTTACTCACGA
1 CGGAGGGTTACTCACGA
273737 AGGCAGATAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 75 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.26
Consensus pattern (62 bp):
CGGAGGGTTACTCACGAGAGACATAGGTAATTTACATCCCGGAAGGTATTGCCATGCCTATG
Found at i:275194 original size:51 final size:51
Alignment explanation
Indices: 275133--275233 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 51
275123 AAATAACAGG
*
275133 GTTGGAGTATCCCTGATTATAGAAAATCAGTATTTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAATCAGTATTTTAG-AAATAAAATCGGA
* * **
275184 GTTGGAGTATCCCCGATTGTGGAAAATTGGTATTTTAGAAATAAAATCGG
1 GTTGGAGTATCCCCGATTATAGAAAATCAGTATTTTAGAAATAAAATCGG
275234 GGTTTAAGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.32
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATAGAAAATCAGTATTTTAGAAATAAAATCGGA
Found at i:275244 original size:51 final size:51
Alignment explanation
Indices: 275133--275245 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
275123 AAATAACAGG
* *
275133 GTTGGAGTATCCCTGATTATAGAAAATCAGTATTTTGAAAATAAAATCGGA
1 GTTGAAGTATCCCCGATTATAGAAAATCAGTATTTTGAAAATAAAATCGGA
* * * ** *
275184 GTTGGAGTATCCCCGATTGTGGAAAATTGGTATTTT-AGAAATAAAATCGGG
1 GTTGAAGTATCCCCGATTATAGAAAATCAGTATTTTGA-AAATAAAATCGGA
*
275235 GTTTAAGTATC
1 GTTGAAGTATC
275246 TCCTTGGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.35, C:0.10, G:0.23, T:0.33
Consensus pattern (51 bp):
GTTGAAGTATCCCCGATTATAGAAAATCAGTATTTTGAAAATAAAATCGGA
Found at i:275353 original size:109 final size:109
Alignment explanation
Indices: 275216--275425 Score: 278
Period size: 109 Copynumber: 1.9 Consensus size: 109
275206 AAAATTGGTA
* * * *
275216 TTTTAGAAATAAAATCGGGGTTTAAGTATCTCCTTGGAAATAACAGAATTGGAGTATCCCCGATG
1 TTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAACAGAATTGGAGTATCCCCGATG
*
275281 AAATAACGAGGTT-AGAGTACCCCCGATTATGAAAAAAATAATAT
66 AAATAACGAGGTTGA-AGTACCCCCAATTATGAAAAAAATAATAT
* * * * ** *
275325 TTTTAGATATAAAGCCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCTGATG
1 TTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAACAGAATTGGAGTATCCCCGATG
* *
275390 AAATAACGGGGTTGAAGTATCCCCAATTATGAAAAA
66 AAATAACGAGGTTGAAGTACCCCCAATTATGAAAAA
275426 TTGGTGTTTT
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
109 85 0.99
110 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (109 bp):
TTTTAGAAATAAAACCGGGGTTGAAGTATCCCCTCGGAAATAACAGAATTGGAGTATCCCCGATG
AAATAACGAGGTTGAAGTACCCCCAATTATGAAAAAAATAATAT
Found at i:275380 original size:28 final size:28
Alignment explanation
Indices: 275340--275413 Score: 107
Period size: 28 Copynumber: 2.6 Consensus size: 28
275330 GATATAAAGC
275340 CGGGGTTGGAGTATCCCCTCG-GAAATAA
1 CGGGGTTGGAGTATCCCCT-GAGAAATAA
275368 CGGGGTTGGAGTAT-CCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCCTGA-GAAATAA
*
275396 CGGGGTTGAAGTATCCCC
1 CGGGGTTGGAGTATCCCC
275414 AATTATGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 1 0.02
27 4 0.10
28 34 0.81
29 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTGAGAAATAA
Found at i:275464 original size:51 final size:51
Alignment explanation
Indices: 275400--275565 Score: 158
Period size: 51 Copynumber: 3.3 Consensus size: 51
275390 AAATAACGGG
* * * *
275400 GTTGAAGTATCCCCAATTATGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
** ** * * *
275451 GTTGGAGTATCCCCGATTGCGGTAAATCGATGCTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
* * *
275502 GTTGGAGTA-CCCCTGATTAAGAAAAAGTGACGTTTTGGAAA-AGGAATCGG-
1 GTTGGAGTATCCCC-GATTAAGAAAAATTGATGTTTTGGAAATA-AAATCGGA
275552 GATTGGAGTATCCC
1 G-TTGGAGTATCCC
275566 TGAGATGAAA
Statistics
Matches: 91, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
50 6 0.07
51 82 0.90
52 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:277878 original size:19 final size:19
Alignment explanation
Indices: 277853--277907 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
277843 AAAAATGCCT
*
277853 GAATGTATCGATACATTGTA
1 GAATGTATCGATACAATG-A
277873 -AATGTATCGATACAATGA
1 GAATGTATCGATACAATGA
277891 GTAATGTATCGATACAA
1 G-AATGTATCGATACAA
277908 ATTGCAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
20 15 0.47
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (19 bp):
GAATGTATCGATACAATGA
Found at i:277898 original size:20 final size:20
Alignment explanation
Indices: 277854--277907 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
277844 AAAATGCCTG
*
277854 AATGTATCGATAC-ATTGTA
1 AATGTATCGATACAATAGTA
277873 AATGTATCGATACAATGAGT-
1 AATGTATCGATACAAT-AGTA
277893 AATGTATCGATACAA
1 AATGTATCGATACAA
277908 ATTGCAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 13 0.41
20 17 0.53
21 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACAATAGTA
Found at i:279211 original size:49 final size:49
Alignment explanation
Indices: 279088--279576 Score: 165
Period size: 49 Copynumber: 10.6 Consensus size: 49
279078 ATGTTAAAGA
* *
279088 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTTAAAATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAAATGAAGG
* * *
279137 TGCCAATTTGCTGATTCAAGGCCAGCGACAAT-GG-TTTTAAAGATGATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGA-AATCGGACTTTAAA-ATGAAGG
* * * * *
279186 TGCCAATATGCTGATTCACGACCAGCGATATTGGGC--T----T--A--
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAAATGAAGG
* * * * * * * *
279225 TGCCAATGTGTTAATTCACA-ACCGGC-AACATTGGACTTGAAGATGGTTAAGG
1 TGCCAATATGCTGATTCA-AGGCCAGCGAA-ATCGGACTTTAAAAT-G--AAGG
* * * * * *
279277 TGCCAATCTGCTGAGTCAAGGCCAGCGACATTGGTC-TTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAA-ATGAAGG
* ** *
279326 TGCCAATATGCTAATTCAAGGCCAGCGGTATTGGAC-TT---A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAAATGAAGG
* * * * * *
279369 TGCCAATACGCTGATTCAAGGCCAACGATATTGGGC-TTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAA-ATGAAGG
* * * * * *
279418 TGCCAATGTGTTGATTCAGGGCCAGCGACATTGGGC--T----T----G
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAAATGAAGG
* * * *
279457 TGCCAATGTGTTGATTCAAGGCCAGCGATATTGGAC-TT---A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAAATGAAGG
* * * * *
279500 TGCCAATGTGTTGATTCAAGGCTAGCGACATC-GACCTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAA-ATGAAGG
*
279549 TGCCAATATGCTGATTTAAGGCCAGCGA
1 TGCCAATATGCTGATTCAAGGCCAGCGA
279577 CATTGGGCTT
Statistics
Matches: 343, Mismatches: 57, Indels: 80
0.71 0.12 0.17
Matches are distributed among these distances:
38 1 0.00
39 60 0.17
40 1 0.00
42 3 0.01
43 71 0.21
45 2 0.01
47 2 0.01
48 10 0.03
49 159 0.46
50 3 0.01
51 4 0.01
52 26 0.08
53 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGAAATCGGACTTTAAAATGAAGG
Found at i:279386 original size:43 final size:43
Alignment explanation
Indices: 279273--279683 Score: 291
Period size: 49 Copynumber: 9.2 Consensus size: 43
279263 GAAGATGGTT
* * *
279273 AAGGTGCCAATCTGCTGAGTCAAGGCCAGCGACATTGGTCTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----TA
* **
279322 AAGGTGCCAATATGCTAATTCAAGGCCAGCGGTATTGGACTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * * *
279365 AAGGTGCCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T-----TA
* * * *
279414 AAGGTGCCAATGTGTTGATTCAGGGCCAGCGACATTGGGCTT-
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * *
279456 ---GTGCCAATGTGTTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* * * *
279496 AAGGTGCCAATGTGTTGATTCAAGGCTAGCGACA-TCGACCTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGA-CTT----A
* *
279543 TGAAGGTGCCAATATGCTGATTTAAGGCCAGCGACATTGGGCTT-
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
* *
279587 ---GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A
* * *
279631 CAAGGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTA
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
279675 AAGGTGCCA
1 AAGGTGCCA
279684 CAGAGTTGTG
Statistics
Matches: 298, Mismatches: 37, Indels: 60
0.75 0.09 0.15
Matches are distributed among these distances:
39 72 0.24
42 3 0.01
43 79 0.27
44 2 0.01
47 1 0.00
48 36 0.12
49 103 0.35
50 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (43 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
Found at i:279390 original size:92 final size:90
Alignment explanation
Indices: 279271--279498 Score: 273
Period size: 92 Copynumber: 2.5 Consensus size: 90
279261 TTGAAGATGG
* * *
279271 TTAAGGTGCCAATCTGCTGAGTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATG
1 TTAAGGTGCCAATC-GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATATG
**
279336 CTAATTCAAGGCCAGCGGTATTGGAC
65 CTAATTCAAGGCCAGCGACATTGGAC
* * *
279362 TTAAAGGTGCCAATACGCTGATTCAAGGCCAACGATATTGGGCTTAAAGATAAAGGTGCCAATGT
1 TT-AAGGTGCCAAT-CGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATAT
* * * *
279427 GTTGATTCAGGGCCAGCGACATTGGGC
64 GCTAATTCAAGGCCAGCGACATTGGAC
* *
279454 TT---GTGCCAATGTGTTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 TTAAGGTGCCAAT-CGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
279499 GTGCCAATGT
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
88 38 0.32
91 2 0.02
92 78 0.66
93 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (90 bp):
TTAAGGTGCCAATCGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATAAAGGTGCCAATATGC
TAATTCAAGGCCAGCGACATTGGAC
Found at i:279411 original size:232 final size:223
Alignment explanation
Indices: 279036--279653 Score: 645
Period size: 232 Copynumber: 2.7 Consensus size: 223
279026 TGAAGAAGAA
* * * * *
279036 TGCCAATGTGCTGAGACAAGGCCAACGACATTGGGCTTAGGAATGTTAAAGATGCCAATATGCTG
1 TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGCCTTA--AA-GATAAAGGTGCCAATATGCTG
* * *
279101 ATTCAAGGCCAACGATATCGGACTTTAAAATGAAGGTGCCAATTTGCTGATTCAAGGCCAGCGAC
63 ATTCAAGGCCAGCGATATTGGAC-TT---A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGAC
* * * * *
279166 AATGGTTTTAAAGATGATGGTGCCAATATGCTGATTCACGACCAGCGATATTGGGCTTATGCCAA
122 ATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCACGACCAGCGACATTGGGCTTATGCCAA
*
279231 TGTGTTAATTCACA-ACCGGCAACATTGGACTTGAAGATGGTTAAGG
187 TGTGTTAATTCA-AGACCAGCAACATTGGACTT----A-----AAGG
* * *
279277 TGCCAATCTGCTGAGTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTAATT
1 TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGCCTTAAAGATAAAGGTGCCAATATGCTGATT
* * * * *
279342 CAAGGCCAGCGGTATTGGACTTAAAGGTGCCAATACGCTGATTCAAGGCCAACGATATTGGGCTT
66 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
* * * * * *
279407 AAAGATAAAGGTGCCAATGTGTTGATTCAGGGCCAGCGACATTGGGCTTGTGCCAATGTGTTGAT
131 AAAGATAAAGGTGCCAATATGCTGATTCACGACCAGCGACATTGGGCTTATGCCAATGTGTTAAT
* * *
279472 TCAAGGCCAGCGATATTGGACTTAAAGG
196 TCAAGACCAGCAACATTGGACTTAAAGG
* * * * * *
279500 TGCCAATGTGTTGATTCAAGGCTAGCGACATCGACCTTAAAGATGAAGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGCCTTAAAGATAAAGGTGCCAATATGCTGATT
* * * *
279565 TAAGGCCAGCGACATTGGGCTT----GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
66 CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
*
279626 AAAGA-CAAGGTGCCAATATGCTGATTCA
131 AAAGATAAAGGTGCCAATATGCTGATTCA
279654 AGGCTAGCAA
Statistics
Matches: 325, Mismatches: 51, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
218 20 0.06
219 39 0.12
223 78 0.24
228 1 0.00
231 1 0.00
232 108 0.33
234 1 0.00
237 2 0.01
238 38 0.12
239 2 0.01
241 35 0.11
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.26
Consensus pattern (223 bp):
TGCCAATGTGCTGAGTCAAGGCCAGCGACATTGGCCTTAAAGATAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
AAAGATAAAGGTGCCAATATGCTGATTCACGACCAGCGACATTGGGCTTATGCCAATGTGTTAAT
TCAAGACCAGCAACATTGGACTTAAAGG
Found at i:279471 original size:39 final size:40
Alignment explanation
Indices: 279417--279626 Score: 190
Period size: 39 Copynumber: 5.0 Consensus size: 40
279407 AAAGATAAAG
*
279417 GTGCCAATGTGTTGATTCAGGGCCAGCGACATTGGGCTT-
1 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGGCTTA
* *
279456 GTGCCAATGTGTTGATTCAAGGCCAGCGATATTGGACTTAAA
1 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGGCTT--A
* * **
279498 GGTGCCAATGTGTTGATTCAAGGCTAGCGACATCGACCTTAAAGATGAA
1 -GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGGC-T-----T--A
* * *
279547 GGTGCCAATATGCTGATTTAAGGCCAGCGACATTGGGCTT-
1 -GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGGCTTA
* *
279587 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA
1 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGGCTTA
279627 AAGACAAGGT
Statistics
Matches: 141, Mismatches: 19, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
39 72 0.51
43 33 0.23
44 1 0.01
48 1 0.01
49 34 0.24
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGGCTTA
Found at i:279520 original size:21 final size:21
Alignment explanation
Indices: 279456--279520 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
279446 CATTGGGCTT
279456 GTGCCAATGTGTTGATTCAA-
1 GTGCCAATGTGTTGATTCAAG
** * *
279476 G-GCCAGCGATATTGGACTTAAAG
1 GTGCCAATG-TGTT-GA-TTCAAG
279499 GTGCCAATGTGTTGATTCAAG
1 GTGCCAATGTGTTGATTCAAG
279520 G
1 G
279521 CTAGCGACAT
Statistics
Matches: 32, Mismatches: 8, Indels: 9
0.65 0.16 0.18
Matches are distributed among these distances:
19 5 0.16
20 4 0.12
21 8 0.25
22 6 0.19
23 4 0.12
24 5 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (21 bp):
GTGCCAATGTGTTGATTCAAG
Found at i:279564 original size:131 final size:131
Alignment explanation
Indices: 279325--279661 Score: 449
Period size: 131 Copynumber: 2.5 Consensus size: 131
279315 AAAGATAAAG
* * * *
279325 GTGCCAATATGCTAATTCAAGGCCAGCGGTATTGGACTTAAAGGTGCCAATACGCTGATTCAAGG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
* * * * ** * * *
279390 CCAACGATATTGGGCTTAAAGATAAAGGTGCCAATGTGTTGATTCAGGGCCAGCGACATTGGGCT
66 CTAGCGACATCGACCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCT
279455 T
131 T
* * *
279456 GTGCCAATGTGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
* *
279521 CTAGCGACATCGACCTTAAAGATGAAGGTGCCAATATGCTGATTTAAGGCCAGCGACATTGGGCT
66 CTAGCGACATCGACCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCT
279586 T
131 T
* *
279587 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATATGCTGATT
279652 CAAGGCTAGC
61 CAAGGCTAGC
279662 AATATTGGAC
Statistics
Matches: 178, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
131 149 0.84
135 1 0.01
136 28 0.16
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (131 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
CTAGCGACATCGACCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGGCT
T
Found at i:279617 original size:88 final size:88
Alignment explanation
Indices: 279456--279674 Score: 269
Period size: 88 Copynumber: 2.5 Consensus size: 88
279446 CATTGGGCTT
* * * *
279456 GTGCCAATGTGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTTGATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--A-GTGCCAATGTGCTGATTCAAGG
* *
279521 CTAGCGACATCGACCTTAAAGATGAAG
63 CCAGCGACATCGACCTTAAAGA-CAAG
* *
279548 GTGCCAATATGCTGATTTAAGGCCAGCGACATTGGGCTT-GTGCCAATGTGCTGATTCAAGGCCA
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCA
* **
279612 GCGACATTGGTCTTAAAGACAAG
66 GCGACATCGACCTTAAAGACAAG
* * *
279635 GTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTTA
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
279675 AAGGTGCCAC
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
87 37 0.34
88 39 0.35
92 34 0.31
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (88 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGTGCCAATGTGCTGATTCAAGGCCA
GCGACATCGACCTTAAAGACAAG
Found at i:279989 original size:134 final size:131
Alignment explanation
Indices: 279674--280328 Score: 703
Period size: 134 Copynumber: 4.9 Consensus size: 131
279664 TATTGGACTT
* * * * * *
279674 AAAGGTGCCACAGAGTTGTGGACAT-ACAGGAAAAAGCGATGCCACGGAGGTGGGGGCTTAAAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAG-G-TGCCACGGAGTTGTGGACTT-AAAA
** * * * * *
279738 GGAAAAGGGTGCCATAGAGTTGTGGACTTAA-AAAGAAAAAGATGCCACGGAGTTGTGGACTTAA
62 GGAAAAAAGTGCCACAGAGTTGTGGACTTAAGGAA-AAAAGGATGCCATGGAGTTGTGGGCTTAA
279802 AAAGAA
126 AAAGAA
* * *
279808 AAAGATGCCACGGAGTTATGGACTTAAATGGAACAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* ** * * *
279873 AAAAAATGCCATGGAGTTGTGGACTTATAGGAAAAAAGGATGCCATAGAGGTGTGGGCTTAAAAG
65 AAAAAGTGCCACAGAGTTGTGGACTTA-AGGAAAAAAGGATGCCATGGAGTTGTGGGCTTAAAAA
279938 GAA
129 GAA
* *
279941 AAAGGGTGCCACGGAGTTGTGGACTTAAATGGAACAAAGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGGTGCCACGGAGTTGTGGACTTAAAAGG
* * * * *
280006 AAAAAAATGCCACAGAGTTGTGGACTTTTAGGAAAAAGGGATGCCACGGAGGTGTGGGCTTAAAA
64 AAAAAAGTGCCACAGAGTTGTGGAC-TTAAGGAAAAAAGGATGCCATGGAGTTGTGGGCTTAAAA
*
280071 GGAAA
128 AG-AA
* * * * * * *
280076 AAAAGTGCCACGAAGTCGTGGACTTAAAAAGAAAAGGTGCCACGGAGTTATGGGCTTTAAAAAGA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
280141 AAAATGTGCCAC-GAGTTGTGGACTTAA-AAAAAAAGG-TGCCATGGAGTTGTGGGCTTTAAAAA
65 AAAAAGTGCCACAGAGTTGTGGACTTAAGGAAAAAAGGATGCCATGGAGTTGTGGGC-TTAAAAA
280203 GAA
129 GAA
* * * *
280206 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAGGTGCCACAGAATTGTGGACTTAATAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * * *
280271 CAAAGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAAGG-TGCCATTGACTTGTGGGCTT
66 AAAAGTGCCACAGAGTTGTGGACTT--AAGGAAAAAAGGATGCCATGGAGTTGTGGGCTT
280329 TGAAGGTTGC
Statistics
Matches: 448, Mismatches: 60, Indels: 29
0.83 0.11 0.05
Matches are distributed among these distances:
129 17 0.04
130 79 0.18
131 16 0.04
132 58 0.13
133 80 0.18
134 185 0.41
135 13 0.03
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.20
Consensus pattern (131 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
AAAAGTGCCACAGAGTTGTGGACTTAAGGAAAAAAGGATGCCATGGAGTTGTGGGCTTAAAAAGA
A
Found at i:280324 original size:33 final size:33
Alignment explanation
Indices: 279674--280313 Score: 670
Period size: 33 Copynumber: 19.3 Consensus size: 33
279664 TATTGGACTT
* * *
279674 AAAGGTGCCACAGAGTTGTGGACAT-ACAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
279706 AAAGCGATGCCACGGAGGTGGGGGCTTAAAAAGGAA
1 AAAG-G-TGCCACGGAGTTGTGGACTT-AAAAGGAA
* ** *
279742 AAGGGTGCCATAGAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
279775 AAAGATGCCACGGAGTTGTGGACTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
279808 AAAGATGCCACGGAGTTATGGACTTAAATGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
279841 CAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
** * *
279874 AAAAATGCCATGGAGTTGTGGACTT-ATAGGAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGG-AA
** * *
279907 AAAGGATGCCATAGAGGTGTGGGCTTAAAAGGAA
1 AAAGG-TGCCACGGAGTTGTGGACTTAAAAGGAA
*
279941 AAAGGGTGCCACGGAGTTGTGGACTTAAATGGAA
1 AAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAA
279975 CAAA-GTGCCACGGAGTTGTGGACTTAAAAGGAA
1 -AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
** * **
280008 AAAAATGCCACAGAGTTGTGGACTT-TTAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
280040 AAAGGGATGCCACGGAGGTGTGGGCTTAAAAGGAAA
1 AAA-GG-TGCCACGGAGTTGTGGACTTAAAAGG-AA
* * * *
280076 AAAAGTGCCACGAAGTCGTGGACTTAAAAAG-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
280108 AAAGGTGCCACGGAGTTATGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
280142 AAATGTGCCAC-GAGTTGTGGACTTAAAA--AA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
280172 AAAGGTGCCATGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
280206 AAAGGTGCCACGGAGTTGTGGACTTAAAAAG-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
280238 AAAGGTGCCACAGAATTGTGGACTTAATAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
280271 CAAA-GTGCCACGGAGTTGTGGACTTAAAAGGAA
1 -AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
280304 AAAGGTGCCA
1 AAAGGTGCCA
280314 TTGACTTGTG
Statistics
Matches: 507, Mismatches: 78, Indels: 45
0.80 0.12 0.07
Matches are distributed among these distances:
30 11 0.02
31 10 0.02
32 81 0.16
33 227 0.45
34 150 0.30
35 14 0.03
36 14 0.03
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:280371 original size:28 final size:28
Alignment explanation
Indices: 280304--280414 Score: 136
Period size: 28 Copynumber: 4.0 Consensus size: 28
280294 TTAAAAGGAA
*
280304 AAAGG-TGCCATTGACTTGTGGGC-TTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTT
*
280330 GAAGGTTGCCACTGACTTGTGGGCTTTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTT
*
280358 AAAGGTTGCCACTGACTTGTGGGCTTTGA
1 AAAGGTTGCCACTGACTTGTGGGCTTT-T
* * * *
280387 AAAAGATGCCACTAACTTGTGGACTTTT
1 AAAGGTTGCCACTGACTTGTGGGCTTTT
280415 GAAAAAGATG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 4 0.05
27 17 0.23
28 29 0.40
29 23 0.32
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (28 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTT
Found at i:280376 original size:55 final size:55
Alignment explanation
Indices: 280304--280475 Score: 157
Period size: 57 Copynumber: 3.0 Consensus size: 55
280294 TTAAAAGGAA
* * * * *
280304 AAAGGTGCCATTGACTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTT
1 AAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGACTTTT
280358 AAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGACTTTT
1 AAAGG-TGCCACTGACTTGTGGGCTTTG-AAAAGATGCCACTAACTTGTGGACTTTT
* * * * * *
280415 GAAAAAGATGACACTAACTAGTGGGCTTTGGAGAAAAGATTGCCACTGAGTTGTGGACTTT
1 ---AAAGGTGCCACTGACTTGTGGGCTTT---GAAAAGA-TGCCACTAACTTGTGGACTTT
280476 GAAGAAAAAA
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
54 5 0.05
55 21 0.22
57 23 0.24
59 18 0.19
60 4 0.04
61 6 0.06
62 20 0.21
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.31
Consensus pattern (55 bp):
AAAGGTGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGACTTTT
Found at i:280418 original size:30 final size:30
Alignment explanation
Indices: 280301--280538 Score: 175
Period size: 30 Copynumber: 8.0 Consensus size: 30
280291 GACTTAAAAG
* * *
280301 GAAAAAGGTGCCATTGACTTGTGGGC-TTT
1 GAAAAAGATGCCACTGACTTGTGGACTTTT
* * *
280330 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGACTTTT
* * *
280358 --AAAGGTTGCCACTGACTTGTGGGC-TTT
1 GAAAAAGATGCCACTGACTTGTGGACTTTT
*
280385 GAAAAAGATGCCACTAACTTGTGGACTTTT
1 GAAAAAGATGCCACTGACTTGTGGACTTTT
* * * * *
280415 GAAAAAGATGACACTAACTAGTGGGCTTTG
1 GAAAAAGATGCCACTGACTTGTGGACTTTT
* *
280445 GAGAAAAGATTGCCACTGAGTTGTGGACTTTGAA
1 GA-AAAAGA-TGCCACTGACTTGTGGACTTT--T
* * *
280479 GAAAAAAAATGCCACTGAGTCGTGGAC-TTT
1 G-AAAAAGATGCCACTGACTTGTGGACTTTT
* *
280509 GAGAAAAGATGCCACTGAGTCGTGGACTTT
1 GA-AAAAGATGCCACTGACTTGTGGACTTT
280539 AAGAAGAGAG
Statistics
Matches: 176, Mismatches: 21, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
27 23 0.13
28 26 0.15
29 22 0.12
30 55 0.31
31 8 0.05
32 18 0.10
33 17 0.10
34 6 0.03
35 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (30 bp):
GAAAAAGATGCCACTGACTTGTGGACTTTT
Found at i:282173 original size:76 final size:78
Alignment explanation
Indices: 282079--282228 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 78
282069 TGATTATGAG
* * * * *
282079 AATAACGGGGTTGGAGTATCCCCGATGA-AG-AATTGATGTTTTGGAAATAAAACCGGGGTTGGA
1 AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
282142 GTATCCCCCCGAA
66 GTATCCCCCCGAA
*
282155 AATAACGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1 AATAACGGGGATGGAGTATCCCCGATGA-GAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
282220 AGTATCCCC
65 AGTATCCCC
282229 GATGATGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 26 0.40
78 2 0.03
79 37 0.57
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (78 bp):
AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
GTATCCCCCCGAA
Found at i:282445 original size:51 final size:50
Alignment explanation
Indices: 282160--282446 Score: 299
Period size: 51 Copynumber: 5.6 Consensus size: 50
282150 CCGAAAATAA
* * * *
282160 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAA
1 CGGGGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTAGAAATAAAAC
* * * * *
282211 CGGGGTTGGAGTATCCCCGATGATGAAAAGTTAGTATTTTGGAAATACAAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAA-TTAGTGTTTTAGAAATAAAAC
* *
282262 CGGAGTTGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAG-AAATAAAAC
* * * * *
282313 CGAGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTCT-GAGAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGA-AATAAAAC
* * * * *
282364 CGGAGTTGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGAAATAAAAC
282415 CGGGGTTGGAGTATCCCCGATTATGCAAAATT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATT
282447 GAGAAAACTT
Statistics
Matches: 201, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
50 6 0.03
51 188 0.94
52 7 0.03
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:282447 original size:102 final size:100
Alignment explanation
Indices: 282166--282447 Score: 352
Period size: 102 Copynumber: 2.8 Consensus size: 100
282156 ATAACGGGGA
* *
282166 TGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTATGA-AAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
* * * *
282231 TGATGAAAAGTTAGTATTTTGGAAATACAATCGGAGT
65 TTATGAAAA-TTGGTATTCTGGAAATAAAATCGGAGT
** *
282268 TGGAGTATCCCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCGAGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCG
* *
282332 ATTGTGGAAAATTGGTGTTCT-GAGAATAAAATCGGAGT
64 ATTAT-GAAAATTGGTATTCTGGA-AATAAAATCGGAGT
* * *
282370 TGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
282435 TTATGCAAAATTG
65 TTATG-AAAATTG
282448 AGAAAACTTG
Statistics
Matches: 155, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
101 4 0.03
102 143 0.92
103 8 0.05
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (100 bp):
TGGAGTATCCCCGATTATGAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGAT
TATGAAAATTGGTATTCTGGAAATAAAATCGGAGT
Found at i:284812 original size:13 final size:13
Alignment explanation
Indices: 284794--284819 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
284784 ACAAAGATCC
284794 ATGTATCGATACA
1 ATGTATCGATACA
284807 ATGTATCGATACA
1 ATGTATCGATACA
284820 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:284815 original size:33 final size:33
Alignment explanation
Indices: 284773--284839 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
284763 AAAATTTCCA
***
284773 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
284806 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
284839 A
1 A
284840 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:284883 original size:19 final size:18
Alignment explanation
Indices: 284859--284926 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
284849 CAGTAGCTAA
284859 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
284878 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
284893 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
284910 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
284927 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:284899 original size:13 final size:13
Alignment explanation
Indices: 284881--284905 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284871 ACAATACTTA
284881 TGTATCGATACAT
1 TGTATCGATACAT
284894 TGTATCGATACA
1 TGTATCGATACA
284906 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:284903 original size:32 final size:32
Alignment explanation
Indices: 284862--284924 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
284852 TAGCTAATTA
*
284862 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
284894 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
284925 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:285006 original size:21 final size:21
Alignment explanation
Indices: 284982--285038 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
284972 CATTTGTAGG
284982 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
285003 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
285024 ATGTATCGATACATT
1 ATGTATCGATACATT
285039 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:285049 original size:1 final size:1
Alignment explanation
Indices: 285043--285086 Score: 61
Period size: 1 Copynumber: 44.0 Consensus size: 1
285033 TACATTTAAA
***
285043 TTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
285087 CAAACACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.05, C:0.02, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:285087 original size:19 final size:19
Alignment explanation
Indices: 285052--285089 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
285042 ATTTTTTTTT
285052 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
285071 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
285090 ACACTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTCAA
Found at i:285766 original size:55 final size:55
Alignment explanation
Indices: 285682--286860 Score: 1786
Period size: 55 Copynumber: 21.4 Consensus size: 55
285672 ATAAGTTGTA
* * ** * *
285682 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAA-AGGCG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
285737 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCCACTTGTGTGGGCTTTGAA-AAGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
285792 TCCTGCTCTTTGGGGAAT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
285847 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
285902 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
285957 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
286012 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
286067 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGA-AAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
286122 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
286177 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
286232 TCCTGCTCTTTGAGGACTGGAAAATGCCTCCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
*
286287 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
286342 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
286397 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
286452 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
286507 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
286562 TCCTGCTCTTTGAGGACTGGACAA-TGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGA-AAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
286617 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
*
286672 TCCTGCTCTTTGGGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGGAAA-GTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
* *
286727 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
* *
286782 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
286837 TCCTGCTCTTTGAGGACTGGAAAG
1 TCCTGCTCTTTGAGGACTGGAAAG
286861 CGGAAGGAGA
Statistics
Matches: 1060, Mismatches: 37, Indels: 54
0.92 0.03 0.05
Matches are distributed among these distances:
53 4 0.00
54 31 0.03
55 991 0.93
56 30 0.03
57 4 0.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
Found at i:286066 original size:29 final size:29
Alignment explanation
Indices: 285978--286066 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
285968 GAGGACTGAA
285978 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
286007 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
286033 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
286062 AGGTG
1 AGGTG
286067 TCCTGCTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:286696 original size:26 final size:26
Alignment explanation
Indices: 286608--286697 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
286598 GTGTGGGCTT
*
286608 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGGGGAC
** *
286634 TGAAAGGTG-CCACCAACTTGTGTGGG-C
1 TGAAAGGTGTCCTGC-TCTT-TG-GGGAC
*
286661 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGGGGAC
286689 TGAAAGGTG
1 TGAAAGGTG
286698 CCACCAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 14
0.68 0.13 0.20
Matches are distributed among these distances:
25 3 0.06
26 17 0.35
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:287865 original size:27 final size:27
Alignment explanation
Indices: 287832--287902 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 27
287822 TTCCTTTTCT
*
287832 CTCTTTTTCTTTGTTTTGTTTTTTTTG
1 CTCTTTTTTTTTGTTTTGTTTTTTTTG
* *
287859 -TGTTTTTTTTTTGCTTT-TTTTTTTTG
1 CT-CTTTTTTTTTGTTTTGTTTTTTTTG
*
287885 CTCTTTTTTTTTTTTTTG
1 CTCTTTTTTTTTGTTTTG
287903 AAGAGAAGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (27 bp):
CTCTTTTTTTTTGTTTTGTTTTTTTTG
Found at i:287868 original size:13 final size:13
Alignment explanation
Indices: 287835--287897 Score: 74
Period size: 13 Copynumber: 4.7 Consensus size: 13
287825 CTTTTCTCTC
* *
287835 TTTTTCTTTGTTT
1 TTTTTTTTTGCTT
287848 TGTTTTTTTTG-TGT
1 T-TTTTTTTTGCT-T
287862 TTTTTTTTTGCTT
1 TTTTTTTTTGCTT
287875 TTTTTTTTTGCTCT
1 TTTTTTTTTGCT-T
287889 TTTTTTTTT
1 TTTTTTTTT
287898 TTTTGAAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
13 24 0.53
14 21 0.47
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTGCTT
Found at i:287881 original size:11 final size:11
Alignment explanation
Indices: 287845--287895 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 11
287835 TTTTTCTTTG
287845 TTTTG-TTTTT
1 TTTTGCTTTTT
*
287855 TTTGTGTTTTTT
1 TTT-TGCTTTTT
287867 TTTTGCTTTTTTT
1 TTTTGC--TTTTT
287880 TTTTGCTCTTTT
1 TTTTGCT-TTTT
287892 TTTT
1 TTTT
287896 TTTTTTGAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 3 0.09
11 5 0.14
12 16 0.46
13 11 0.31
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (11 bp):
TTTTGCTTTTT
Found at i:300492 original size:76 final size:78
Alignment explanation
Indices: 300398--300547 Score: 223
Period size: 79 Copynumber: 1.9 Consensus size: 78
300388 TGATTATGAG
* * * * *
300398 AATAACGGGGTTGGAGTATCCCCGATGA-AG-AATTGATGTTTTGGAAATAAAACCGGGGTTGGA
1 AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
300461 GTATCCCCTCGAA
66 GTATCCCCTCGAA
*
300474 AATAACGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
1 AATAACGGGGATGGAGTATCCCCGATGA-GAGAAATTAATATTTTAGAAATAAAAACGGGGTTGG
300539 AGTATCCCC
65 AGTATCCCC
300548 GATGATGAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 26 0.40
78 2 0.03
79 37 0.57
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (78 bp):
AATAACGGGGATGGAGTATCCCCGATGAGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGA
GTATCCCCTCGAA
Found at i:300757 original size:153 final size:153
Alignment explanation
Indices: 300479--300766 Score: 350
Period size: 153 Copynumber: 1.9 Consensus size: 153
300469 TCGAAAATAA
* *
300479 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTAT
1 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
* * * * *
300544 CCCCGATGATGAAAAATTAGTATTTTGGAAATACAATCGGAGTTGGAGTATCCCTGATTATAG-A
66 CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTAT-GCA
300608 AAATTGGTGTTTTGAAAATAAAAC
130 AAATTGGTGTTTTGAAAATAAAAC
* * ** * *
300632 CGGGGTTGGAGTATCCCCGATTGTG-GAAAATTGGTGTTCTGAG-AATAAAATCGGAGTTGGAGT
1 CGGGGATGGAGTATCCCCGATTATGAG-AAATTAATATT-TGAGAAATAAAAACGGAGTTGGAGT
* * * * *
300695 GTCCCCGATTG-TGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGATTATG
64 ATCCCCGA-TGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATG
300759 CAAAATTG
128 CAAAATTG
300767 AGAAAACTTG
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
152 2 0.02
153 106 0.94
154 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (153 bp):
CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTGAGAAATAAAAACGGAGTTGGAGTAT
CCCCGATGATGAAAAATTAATATTTTAGAAATAAAACCGGAGTTGGAGTATCCCCGATTATGCAA
AATTGGTGTTTTGAAAATAAAAC
Found at i:300764 original size:51 final size:50
Alignment explanation
Indices: 300479--300765 Score: 299
Period size: 51 Copynumber: 5.6 Consensus size: 50
300469 TCGAAAATAA
* * * *
300479 CGGGGATGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAA
1 CGGGGTTGGAGTATCCCCGATTATGA-AAATTAGTGTTTTAGAAATAAAAC
* * * * *
300530 CGGGGTTGGAGTATCCCCGATGATGAAAAATTAGTATTTTGGAAATACAAT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATTAGTGTTTTAGAAATAAAAC
* * *
300581 CGGAGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTT-GAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAG-AAATAAAAC
* * * *
300632 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTCT-GAGAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGA-AATAAAAC
* * * * *
300683 CGGAGTTGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAAC
1 CGGGGTTGGAGTATCCCCGATTAT-GAAAATTAGTGTTTTAGAAATAAAAC
300734 CGGGGTTGGAGTATCCCCGATTATGCAAAATT
1 CGGGGTTGGAGTATCCCCGATTATG-AAAATT
300766 GAGAAAACTT
Statistics
Matches: 201, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
50 3 0.01
51 194 0.97
52 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAATTAGTGTTTTAGAAATAAAAC
Found at i:300766 original size:102 final size:101
Alignment explanation
Indices: 300485--300766 Score: 361
Period size: 102 Copynumber: 2.8 Consensus size: 101
300475 ATAACGGGGA
* *
300485 TGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAAAACGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTATGA-AAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
* * * *
300550 TGATGAAAAATTAGTATTTTGGAAATACAATCGGAGT
65 TTATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
* **
300587 TGGAGTATCCCTGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCGGGGTTGGAGTATCCCCG
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCCG
* * *
300651 ATTGTGGAAAATTGGTGTTCT-GAGAATAAAATCGGAGT
64 ATTATGAAAAATTGGTATTCTGGA-AATAAAATCGGAGT
* * *
300689 TGGAGTGTCCCCGATTGTGGAAAATTAATGTTTTAGAAGTAAAACCGGGGTTGGAGTATCCCCGA
1 TGGAGTATCCCCGATTAT-GAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGA
*
300754 TTATGCAAAATTG
65 TTATGAAAAATTG
300767 AGAAAACTTG
Statistics
Matches: 155, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
101 3 0.02
102 149 0.96
103 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (101 bp):
TGGAGTATCCCCGATTATGAAAATTAATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCGAT
TATGAAAAATTGGTATTCTGGAAATAAAATCGGAGT
Found at i:303146 original size:13 final size:13
Alignment explanation
Indices: 303128--303153 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303118 ACAAAGATCC
303128 ATGTATCGATACA
1 ATGTATCGATACA
303141 ATGTATCGATACA
1 ATGTATCGATACA
303154 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:303149 original size:33 final size:33
Alignment explanation
Indices: 303107--303173 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
303097 AAAATTTCCA
***
303107 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
303140 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
303173 A
1 A
303174 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:303217 original size:19 final size:18
Alignment explanation
Indices: 303193--303260 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
303183 CAGTAGCTAA
303193 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
303212 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
303227 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
303244 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
303261 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:303233 original size:13 final size:13
Alignment explanation
Indices: 303215--303239 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303205 ACAATACTTA
303215 TGTATCGATACAT
1 TGTATCGATACAT
303228 TGTATCGATACA
1 TGTATCGATACA
303240 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:303237 original size:32 final size:32
Alignment explanation
Indices: 303196--303258 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
303186 TAGCTAATTA
*
303196 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
303228 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
303259 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:303340 original size:21 final size:21
Alignment explanation
Indices: 303316--303372 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
303306 CATTTGTAGG
303316 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
303337 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
303358 ATGTATCGATACATT
1 ATGTATCGATACATT
303373 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:303383 original size:1 final size:1
Alignment explanation
Indices: 303377--303427 Score: 75
Period size: 1 Copynumber: 51.0 Consensus size: 1
303367 TACATTTAAA
***
303377 TTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
303428 CAAACACTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:303415 original size:25 final size:25
Alignment explanation
Indices: 303381--303430 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
303371 TTTAAATTTT
303381 TTTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTTCAA
303406 TTTTTTTTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTTTTTTTCAA
303431 ACACTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (25 bp):
TTTTTTTTTTTTTTTTTTTTTTCAA
Found at i:308931 original size:13 final size:13
Alignment explanation
Indices: 308913--308937 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308903 CAAAGATCAG
308913 TGTATCGATACAA
1 TGTATCGATACAA
308926 TGTATCGATACA
1 TGTATCGATACA
308938 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:309018 original size:13 final size:13
Alignment explanation
Indices: 309000--309024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
308990 CAAAAAAATA
309000 TGTATCGATACAT
1 TGTATCGATACAT
309013 TGTATCGATACA
1 TGTATCGATACA
309025 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:309232 original size:13 final size:13
Alignment explanation
Indices: 309200--309238 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
309190 GATTCGGGCT
309200 TAACAAAAAGTTA
1 TAACAAAAAGTTA
309213 T---AAAAAGTTA
1 TAACAAAAAGTTA
309223 TAACAAAAAGTTA
1 TAACAAAAAGTTA
309236 TAA
1 TAA
309239 AAACCTGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 10 0.43
13 13 0.57
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (13 bp):
TAACAAAAAGTTA
Found at i:310041 original size:55 final size:52
Alignment explanation
Indices: 309937--310221 Score: 197
Period size: 48 Copynumber: 5.7 Consensus size: 52
309927 GAAAAGTGAT
* * * * * * **
309937 AAAGATGCCAATATGTTGATTCACGGCGAACGATATTGGGCTTAAAGATGAGAA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
309991 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAA-GATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
310044 AAAGTTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
310091 ---G-TGCCAATGTGTTGATTCAAGGTCAGCTACATTGGACTTAAAGAT-G-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * * * *
310137 -AAGGTGCCAATATGCTGATTTAAGGCCAACGATATTGGACTT-AA-A-GG-
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
310184 CAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTG
310222 GGCTTAAAAG
Statistics
Matches: 193, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
43 34 0.18
44 3 0.02
45 1 0.01
46 1 0.01
47 2 0.01
48 38 0.20
49 31 0.16
50 1 0.01
51 2 0.01
52 35 0.18
53 4 0.02
54 4 0.02
55 37 0.19
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (52 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:310110 original size:43 final size:44
Alignment explanation
Indices: 310043--310232 Score: 211
Period size: 48 Copynumber: 4.1 Consensus size: 44
310033 TTAAAGATGG
*
310043 AAAAGTTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
310087 -AAAGGTGCCAATGTGTTGATTCAAGGTCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
310130 AAAGATGAAGGTGCCAATATGCTGATTTAAGGCCAACGATATTGGACTT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
310179 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 -AA---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
310227 AAAAGG
1 AAAAGG
310233 AGACGCCACC
Statistics
Matches: 121, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
43 38 0.31
44 4 0.03
47 4 0.03
48 40 0.33
49 35 0.29
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:310119 original size:95 final size:93
Alignment explanation
Indices: 309991--310221 Score: 302
Period size: 92 Copynumber: 2.4 Consensus size: 93
309981 AAGATGAGAA
* *
309991 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTTGCCAAT
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT-G--AAGGTGCCAAT
* *
310056 ATGCTGATTCAAGGCCAGCTATATTGGACTT
63 ATGCTGATTCAAGGCCAACGATATTGGACTT
* * *
310087 AAAGG-TGCCAATGTGTTGATTCAAGGTCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
1 AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATG
*
310151 CTGATTTAAGGCCAACGATATTGGACTT
66 CTGATTCAAGGCCAACGATATTGGACTT
* *
310179 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTG
1 AAAGG--A--TGCCAATGTGCTGATTCAAGGCCAGCTACATTG
310222 GGCTTAAAAG
Statistics
Matches: 118, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
92 43 0.36
94 1 0.01
95 40 0.34
96 5 0.04
97 29 0.25
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (93 bp):
AAAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGGTGCCAATATG
CTGATTCAAGGCCAACGATATTGGACTT
Found at i:310183 original size:92 final size:95
Alignment explanation
Indices: 309990--310229 Score: 306
Period size: 95 Copynumber: 2.5 Consensus size: 95
309980 AAAGATGAGA
* * *
309990 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGTTGCCAA
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAA
* *
310055 TATGCTGATTCAAGGCCAGCTATATTGGACTT
64 TATGCTGATTCAAGGCCAACGATATTGGACTT
* *
310087 -AAAGGTGCCAATGTGTTGATTCAAGGTCAGCTACATTGGACTTAAAGAT-G-AAGGTGCCAATA
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
*
310149 TGCTGATTTAAGGCCAACGATATTGGACTT
66 TGCTGATTCAAGGCCAACGATATTGGACTT
* * *
310179 AAAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAA
1 -AA---AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
310230 AGGAGACGCC
Statistics
Matches: 125, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
92 38 0.30
94 2 0.02
95 40 0.32
96 5 0.04
97 40 0.32
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (95 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATA
TGCTGATTCAAGGCCAACGATATTGGACTT
Found at i:310306 original size:28 final size:28
Alignment explanation
Indices: 310249--310372 Score: 126
Period size: 28 Copynumber: 4.3 Consensus size: 28
310239 CACCAACTTG
*
310249 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTG-AAGG-TTGCCACT-GACT
* *
310278 TGTGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
310306 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * *
310334 TGTGGGCTTTTGAAAAGGGTGCCACTAACG
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
310364 TGTGGGCTT
1 TGTGGGCTT
310373 AAAAGGAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.04
28 44 0.54
29 12 0.15
30 22 0.27
ACGTcount: A:0.18, C:0.15, G:0.31, T:0.36
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:310407 original size:34 final size:35
Alignment explanation
Indices: 310364--310436 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
310354 GCCACTAACG
* * *
310364 TGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAGT
1 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
*
310398 TGTGAGCTTACAAAAGAAAAAGAGTGCCATGGAGT
1 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
310433 TGTG
1 TGTG
310437 GACTTTGGAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.36, C:0.10, G:0.33, T:0.22
Consensus pattern (35 bp):
TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
Found at i:310613 original size:29 final size:29
Alignment explanation
Indices: 310299--310615 Score: 210
Period size: 29 Copynumber: 10.6 Consensus size: 29
310289 GAAGGTTGCT
* * *
310299 ACTGACTTGTGGGCTTT-TAAAGGTTGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
* *
310327 ACTGACTTGTGGGCTTTTGAAAAGGGTGCC
1 ACTGACTTGTGGGC-TTTGAAAAAGATGCC
* * * *
310357 ACTAACGTGTGGGCTTAAAAGGAAAAAGAGTGCT
1 ACTGACTTGTGGGCTT----TGAAAAAGA-TGCC
* * * *
310391 ACGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCC
1 ACTGACTTGTGGGCTT-----TGAAAAAGA-TGCC
* * * *
310426 A-TGGAGTTGTGGACTTTGGACAAGATGCC
1 ACT-GACTTGTGGGCTTTGAAAAAGATGCC
* * * * *
310455 ACCGACTTGTGGGATTCGGAAAAGGGTGCC
1 ACTGACTTGTGGGCTT-TGAAAAAGATGCC
* * * *
310485 ACCGATTTGTGGGCTTTG--AAGGTTGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
*
310512 ACTGACTTGTGGACTTTGAAAAAGATGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
*
310541 ACTAACTTGTGGGCTTTGAAAAAGATGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
*
310570 ACTAACTTGTGGGCTTTGAAAAAGATGCC
1 ACTGACTTGTGGGCTTTGAAAAAGATGCC
*
310599 ACTGACTTGTAGGCTTT
1 ACTGACTTGTGGGCTTT
310616 TGAAGGGTAA
Statistics
Matches: 232, Mismatches: 44, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
27 23 0.10
28 14 0.06
29 99 0.43
30 49 0.21
33 6 0.03
34 14 0.06
35 27 0.12
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (29 bp):
ACTGACTTGTGGGCTTTGAAAAAGATGCC
Found at i:314051 original size:52 final size:52
Alignment explanation
Indices: 313980--314129 Score: 192
Period size: 52 Copynumber: 2.9 Consensus size: 52
313970 CCGAAATATG
*
313980 AAAATTTGCCTGCATGTATCGATACATTTAATCGTGTATCGATACATATGAGC
1 AAAA-TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATATGAGC
* * * *
314033 AAAATTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAAATTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATATGAGC
* * *** *
314085 AAATTTGCCTACATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAAATTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACA
314130 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
52 80 0.95
53 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (52 bp):
AAAATTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATATGAGC
Found at i:314136 original size:13 final size:13
Alignment explanation
Indices: 314118--314155 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
314108 CAAAGATTAG
314118 TGTATCGATACAA
1 TGTATCGATACAA
314131 TGTATCGATACAA
1 TGTATCGATACAA
314144 TGTATCGATACA
1 TGTATCGATACA
314156 TTTTTTTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:314202 original size:19 final size:19
Alignment explanation
Indices: 314178--314262 Score: 92
Period size: 19 Copynumber: 4.7 Consensus size: 19
314168 TAGCTTAAAT
314178 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
314197 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
314210 TGTATCGATACAATACTTA
1 TGTATCGATACAAAACTTA
* *
314229 TGTATCGATACAACACTTTT
1 TGTATCGATACAAAAC-TTA
314249 TGTATCGATACAAA
1 TGTATCGATACAAA
314263 TCATTGAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 26 0.46
20 15 0.27
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:314215 original size:13 final size:13
Alignment explanation
Indices: 314197--314221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314187 ACAAAACTTA
314197 TGTATCGATACAT
1 TGTATCGATACAT
314210 TGTATCGATACA
1 TGTATCGATACA
314222 ATACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:314217 original size:32 final size:32
Alignment explanation
Indices: 314176--314240 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
314166 AGTAGCTTAA
314176 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
314208 ATTGTATCGATACAATACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
314240 A
1 A
314241 ACACTTTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:316768 original size:19 final size:20
Alignment explanation
Indices: 316724--316776 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
316714 CTGCCAGTTT
* **
316724 CATGTATCGATACAGTTGTC
1 CATGTATCGATACAGATGAA
316744 CATGTATCGATACA-ATGAA
1 CATGTATCGATACAGATGAA
316763 CATGTATCGATACA
1 CATGTATCGATACA
316777 TTCAAGGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAGATGAA
Found at i:317304 original size:19 final size:19
Alignment explanation
Indices: 317282--317357 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
317272 AAAAAAAGAG
317282 ATTTCTCCCCCTAAAAAAA
1 ATTTCTCCCCCTAAAAAAA
*
317301 A-TT-T-CCCTTAAAAAAA
1 ATTTCTCCCCCTAAAAAAA
* * **
317317 ACTTCTCCCCCTTAAACGA
1 ATTTCTCCCCCTAAAAAAA
*
317336 ATATCTCCCCCTTTAAAAAAA
1 ATTTCTCCCCC--TAAAAAAA
317357 A
1 A
317358 AATTTCTCTC
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 12 0.29
17 3 0.07
18 3 0.07
19 18 0.43
21 6 0.14
ACGTcount: A:0.41, C:0.30, G:0.01, T:0.28
Consensus pattern (19 bp):
ATTTCTCCCCCTAAAAAAA
Found at i:325427 original size:33 final size:32
Alignment explanation
Indices: 325371--325437 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
325361 GTTACAAGCT
325371 ATGTATCGATACATTTCTTCATGTATCAATACA
1 ATGTATCGATACATTTC-TCATGTATCAATACA
*
325404 ATGTATCGATACATTGTAC-CATGTATCGATACA
1 ATGTATCGATACATT-T-CTCATGTATCAATACA
325437 A
1 A
325438 ATAGTGATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
ATGTATCGATACATTTCTCATGTATCAATACA
Found at i:327613 original size:156 final size:155
Alignment explanation
Indices: 327289--327705 Score: 527
Period size: 156 Copynumber: 2.7 Consensus size: 155
327279 CCTCGACGTG
* * *
327289 AAAGTGGACCCAGCGATTA-CCTAGGACTCAGTTTTATAGGAAAATTACGAAAATA-CTCTCAAG
1 AAAGTGGACCTAGTGA-TAGCCTAGGACTCAGTTTTA-A--AAAATTACGAAAATACCACT-AAG
* *
327352 GGATACCTTTGACGTAAAAGTACCCAATACCCCTAAAGGACTTAAAAAGGATAATAGATGAGATG
61 GGATACCTTTGATGTAAAAGTACCCAATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATG
* *
327417 AACCTATCTTAAATATCTACCTTCGGCATA
126 AACCTATCCTAAATATCTACCTTCGACATA
** * *
327447 AAAACGGACCTAGTGATAGCCTATGACTCAGTTTTGAAAAAATTACGAAAATACCACTAAAGGAT
1 AAAGTGGACCTAGTGATAGCCTAGGACTCAGTTTT-AAAAAATTACGAAAATACCACTAAGGGAT
** *
327512 ACCTTCAATGTAAAAGTACCCAATACCCTTAAAAGACTTAAAAAGGATAATAGATGAGATGAACC
65 ACCTTTGATGTAAAAGTACCCAATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACC
327577 TATCCTAAATATCTACCTTCGACATA
130 TATCCTAAATATCTACCTTCGACATA
* * ** * * *
327603 AAAGTGGACCTGGTGATAGCTTAGGACTC-GATCATAAAAAATTATGAAAATGCCCCT-AGGAGA
1 AAAGTGGACCTAGTGATAGCCTAGGACTCAG-TTTTAAAAAATTACGAAAATACCACTAAGG-GA
**
327666 TACCTTTGATGTAAAAGTACCCGGTACCCTTAAAGGACTT
64 TACCTTTGATGTAAAAGTACCCAATACCCTTAAAGGACTT
327706 GGGATAATGC
Statistics
Matches: 224, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
154 2 0.01
155 57 0.25
156 131 0.58
157 5 0.02
158 28 0.12
159 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (155 bp):
AAAGTGGACCTAGTGATAGCCTAGGACTCAGTTTTAAAAAATTACGAAAATACCACTAAGGGATA
CCTTTGATGTAAAAGTACCCAATACCCTTAAAGGACTTAAAAAGGATAATAGATGAGATGAACCT
ATCCTAAATATCTACCTTCGACATA
Found at i:329911 original size:164 final size:166
Alignment explanation
Indices: 329609--330052 Score: 483
Period size: 164 Copynumber: 2.7 Consensus size: 166
329599 ATGAGAGTTT
* * * ** **
329609 AATAACAATATTAGATGAATTTTAAAAATTTTAAATCAA-AAAAATCCCCCCAAAAATATTTACG
1 AATAATAATATTTGATAAATTTTAAAAATTAAAAAGAAAGAAAAATCCCCCCAAAAA-ATTTACG
* * * * *
329673 AAGTGGAGAACTCGGTATTTTAGAAAAAAAGAGAATTTCAAGAAAAAAATTCAAAATTCATGGAA
65 AAGTAGAAAACTCCGTATTTTAGAAAAAAAGAGAAATTCAAGAAAAAAATGCAAAATTCATGGAA
329738 ATAAATGAATTTTTGAAAACTGAATTAATA-GAAAATA
130 ATAAATGAATTTTTGAAAACTGAATTAATATG-AAATA
*
329775 AATAATAATATTTGATAAATTTTAAAAA-TAAAAAGAAAGAAAAATCCCCCCAAAAAATTTTCGG
1 AATAATAATATTTGATAAATTTTAAAAATTAAAAAGAAAGAAAAATCCCCCCAAAAAATTTAC-G
* * *
329839 AA-TAGAAAACTCCGTATTTT-GAAAAATAGGGAAATTCAA-AGAAAAAATGCAAAATTTATGGA
65 AAGTAGAAAACTCCGTATTTTAGAAAAAAAGAGAAATTCAAGA-AAAAAATGCAAAATTCATGGA
* *
329901 AATGAATGAATTTTTGAAAATTGAATTAATATGAAATA
129 AATAAATGAATTTTTGAAAACTGAATTAATATGAAATA
* * *** * * *
329939 TATAATAATATTTGATGAATTTTAAAAATTAAAAATCGAGAAAAATCCTCTCGAAAAAATTTACA
1 AATAATAATATTTGATAAATTTTAAAAATTAAAAAGAAAGAAAAATCC-CCCCAAAAAATTTACG
** * * *
330004 AAAAAGAAAA-TCCCGTAATTTA-AAAATAAGAGGAATTCAA-AAAGAAAAT
65 AAGTAGAAAACT-CCGTATTTTAGAAAAAAAGAGAAATTCAAGAAA-AAAAT
330053 CAATAACTCT
Statistics
Matches: 235, Mismatches: 33, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
163 1 0.00
164 95 0.40
165 48 0.20
166 91 0.39
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.27
Consensus pattern (166 bp):
AATAATAATATTTGATAAATTTTAAAAATTAAAAAGAAAGAAAAATCCCCCCAAAAAATTTACGA
AGTAGAAAACTCCGTATTTTAGAAAAAAAGAGAAATTCAAGAAAAAAATGCAAAATTCATGGAAA
TAAATGAATTTTTGAAAACTGAATTAATATGAAATA
Found at i:331194 original size:60 final size:61
Alignment explanation
Indices: 331130--331621 Score: 403
Period size: 60 Copynumber: 8.2 Consensus size: 61
331120 ATCAAGTATC
* * * *
331130 GTCAAATGAA-GAAAAACTTGACTGAATATAGTCAA-ACAGGGTAATATTTGATCGAGTACA
1 GTCAAATGAAGGATAAACTTGACTGAATACAGTCAAGA-AGGGTAAGATTTGACCGAGTACA
* ** * * * * *
331190 GTCAAAT-AACGATAGTCTT-AATCGAATATAGTTAA-AAGAGATAAGATTTGATCGAGTACA
1 GTCAAATGAAGGATAAACTTGACT-GAATACAGTCAAGAAG-GGTAAGATTTGACCGAGTACA
* * ** * **
331250 GTCAAAT-AAGGA-AAGACTTGATTGAATACAGTCAAGAAGAGTAAGATTTGATCTAAATATG
1 GTCAAATGAAGGATAA-ACTTGACTGAATACAGTCAAGAAGGGTAAGATTTGA-CCGAGTACA
* * * *
331311 GTCAAATG-AGGATAAACTTGAAC-GAATACAATCAAGAGGGGTAAAATTTGACTGAGTACA
1 GTCAAATGAAGGATAAACTTG-ACTGAATACAGTCAAGAAGGGTAAGATTTGACCGAGTACA
* * * *
331371 ATAAAATG-AGGATAGA-TTCGACTGAATACAGTCAAGAGGGGTAAGATTTGACCGAGTACA
1 GTCAAATGAAGGATAAACTT-GACTGAATACAGTCAAGAAGGGTAAGATTTGACCGAGTACA
* * *
331431 GTCAAAT-AAGGATAAACTTGGCCGAATACAATCAAG-A--GTAAGATTTGACCGAGTACA
1 GTCAAATGAAGGATAAACTTGACTGAATACAGTCAAGAAGGGTAAGATTTGACCGAGTACA
* * * *
331488 GCCAAAT-AAGGATAAACTTGA-TCGAATACAGTCAAGATGGGTAAGATTTGACCAAGTATA
1 GTCAAATGAAGGATAAACTTGACT-GAATACAGTCAAGAAGGGTAAGATTTGACCGAGTACA
* * * * *
331548 GTCAAATG-AGGATAGACTTAACCGAATACAGTTAA-AAGGGGTAAGATTTGACCAAGTACA
1 GTCAAATGAAGGATAAACTTGACTGAATACAGTCAAGAA-GGGTAAGATTTGACCGAGTACA
*
331608 ATCAAATG-AGGATA
1 GTCAAATGAAGGATA
331622 CGTCAAAAGG
Statistics
Matches: 353, Mismatches: 58, Indels: 42
0.78 0.13 0.09
Matches are distributed among these distances:
57 51 0.14
59 12 0.03
60 237 0.67
61 50 0.14
62 3 0.01
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.24
Consensus pattern (61 bp):
GTCAAATGAAGGATAAACTTGACTGAATACAGTCAAGAAGGGTAAGATTTGACCGAGTACA
Found at i:331301 original size:30 final size:31
Alignment explanation
Indices: 331153--331538 Score: 102
Period size: 30 Copynumber: 12.9 Consensus size: 31
331143 AAACTTGACT
* * * *
331153 GAATATAGTCAAA-CAGGGTAATATTTGATC
1 GAATACAGTCAAAGAAGAGTAAGATTTGATC
* * *
331183 GAGTACAGTCAAATAACGA-T-AG-TCTTAATC
1 GAATACAGTCAAAGAA-GAGTAAGAT-TTGATC
* *
331213 GAATATAGT-TAA-AAGAGATAAGATTTGATC
1 GAATACAGTCAAAGAAGAG-TAAGATTTGATC
* * * * *
331243 GAGTACAGTCAAATAAG-GAAAGACTTGATT
1 GAATACAGTCAAAGAAGAGTAAGATTTGATC
331273 GAATACAGTC-AAGAAGAGTAAGATTTGATC
1 GAATACAGTCAAAGAAGAGTAAGATTTGATC
* ** * * *
331303 TAAATATGGTCAAATGAGGA-TAA-ACTTGAAC
1 -GAATACAGTCAAA-GAAGAGTAAGATTTGATC
* * * *
331334 GAATACAATC-AAGAGGGGTAAAATTTGA-C
1 GAATACAGTCAAAGAAGAGTAAGATTTGATC
* * * * *
331363 TGAGTACAAT-AAA-ATGAGGATAGATTCGA-C
1 -GAATACAGTCAAAGAAGAGTA-AGATTTGATC
* * *
331393 TGAATACAGTC-AAGAGGGGTAAGATTTGACC
1 -GAATACAGTCAAAGAAGAGTAAGATTTGATC
* * * **
331424 GAGTACAGTCAAATAAG-GATAA-ACTTGGCC
1 GAATACAGTCAAAGAAGAG-TAAGATTTGATC
* *
331454 GAATACAATC----AAGAGTAAGATTTGACC
1 GAATACAGTCAAAGAAGAGTAAGATTTGATC
* * * *
331481 GAGTACAGCCAAATAAG-GATAA-ACTTGATC
1 GAATACAGTCAAAGAAGAG-TAAGATTTGATC
* *
331511 GAATACAGTC-AAGATGGGTAAGATTTGA
1 GAATACAGTCAAAGAAGAGTAAGATTTGA
331539 CCAAGTATAG
Statistics
Matches: 260, Mismatches: 64, Indels: 64
0.67 0.16 0.16
Matches are distributed among these distances:
26 6 0.02
27 16 0.06
28 6 0.02
29 26 0.10
30 156 0.60
31 37 0.14
32 9 0.03
33 4 0.02
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.24
Consensus pattern (31 bp):
GAATACAGTCAAAGAAGAGTAAGATTTGATC
Found at i:331700 original size:105 final size:105
Alignment explanation
Indices: 331526--331719 Score: 298
Period size: 105 Copynumber: 1.8 Consensus size: 105
331516 CAGTCAAGAT
* * * * *
331526 GGGTAAGATTTGACCAAGTATAGTCAAATGAGGATAGACTTAACCGAATACAGTTAAAAGGGGTA
1 GGGTAAGATTTGACCAAGTACAGTCAAATGAGGACAAACTTAACCGAATACAATCAAAAGGGGTA
331591 AGATTTGACCAAGTACAATCAAATGAGGATACGTCAAAAG
66 AGATTTGACCAAGTACAATCAAATGAGGATACGTCAAAAG
* * * *
331631 GGGTAAGATTTGACCGAGTACAGTCAAATGAGGACAAACTTGATCGAATACAATCAAGAGGGGTA
1 GGGTAAGATTTGACCAAGTACAGTCAAATGAGGACAAACTTAACCGAATACAATCAAAAGGGGTA
*
331696 AGATTTGACCGAGTACAATCAAAT
66 AGATTTGACCAAGTACAATCAAAT
331720 AAAAAAAACT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 79 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (105 bp):
GGGTAAGATTTGACCAAGTACAGTCAAATGAGGACAAACTTAACCGAATACAATCAAAAGGGGTA
AGATTTGACCAAGTACAATCAAATGAGGATACGTCAAAAG
Found at i:331713 original size:30 final size:29
Alignment explanation
Indices: 331627--331718 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
331617 GGATACGTCA
*
331627 AAAGGGGTAAGATTTGACCGAGTACAGTC
1 AAAGGGGTAAGATTTGACCGAGTACAATC
* * * * *
331656 AAATGAGG-ACAAACTTGATCGAATACAATC
1 AAA-GGGGTA-AGATTTGACCGAGTACAATC
331686 AAGAGGGGTAAGATTTGACCGAGTACAATC
1 AA-AGGGGTAAGATTTGACCGAGTACAATC
331716 AAA
1 AAA
331719 TAAAAAAAAC
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
29 5 0.10
30 41 0.85
31 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (29 bp):
AAAGGGGTAAGATTTGACCGAGTACAATC
Found at i:331772 original size:30 final size:29
Alignment explanation
Indices: 331695--331780 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
331685 CAAGAGGGGT
*
331695 AAGATTTGACCGAGTACAATCAAATAAAA
1 AAGATTTGACCGAGTACAGTCAAATAAAA
* * *
331724 AAAACTTGACCGAATACAGTCAAGA-AAAGA
1 AAGATTTGACCGAGTACAGTCAA-ATAAA-A
*
331754 AAGATTTGATCGAGTACAGTCAAATAA
1 AAGATTTGACCGAGTACAGTCAAATAA
331781 GGATAAACTT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 23 0.50
30 23 0.50
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (29 bp):
AAGATTTGACCGAGTACAGTCAAATAAAA
Found at i:331793 original size:30 final size:30
Alignment explanation
Indices: 331640--331993 Score: 195
Period size: 30 Copynumber: 11.8 Consensus size: 30
331630 GGGGTAAGAT
* * * *
331640 TTGACCGAGTACAGTCAAATGAGGACAAAC
1 TTGATCGAATACAGTCAAATAAGGATAAAC
* * * * *
331670 TTGATCGAATACAATC-AAGAGGGGTAAGAT
1 TTGATCGAATACAGTCAAATAAGGATAA-AC
* * * * *
331700 TTGACCGAGTACAATCAAATAA-AAAAAAC
1 TTGATCGAATACAGTCAAATAAGGATAAAC
* * *
331729 TTGACCGAATACAGTCAAGA-AAAGA-AAGAT
1 TTGATCGAATACAGTCAA-ATAAGGATAA-AC
*
331759 TTGATCGAGTACAGTCAAATAAGGATAAAC
1 TTGATCGAATACAGTCAAATAAGGATAAAC
* * * * *
331789 TTGATCAAATACAGTC-AAGAGGGGTAAGAT
1 TTGATCGAATACAGTCAAATAAGGATAA-AC
* * *
331819 TTGATCGAATATAGTAAAATGAGGATAAAC
1 TTGATCGAATACAGTCAAATAAGGATAAAC
* * * * * *
331849 TTGA-CTGAATACGGT-TAAGAGGGGTAAAAT
1 TTGATC-GAATACAGTCAAATAAGGAT-AAAC
* * *
331879 TTGATCGAGTATAGTCAAATGAGGATAAAC
1 TTGATCGAATACAGTCAAATAAGGATAAAC
* * *
331909 TTGATCAAATACAGTCAAGAT--GGGTAAGAT
1 TTGATCGAATACAGTCAA-ATAAGGATAA-AC
* * *
331939 TTGATCGAGTATAGTAAAATAAGGATAAAC
1 TTGATCGAATACAGTCAAATAAGGATAAAC
*
331969 TTGATCGAATACAGTCAAATGAGGA
1 TTGATCGAATACAGTCAAATAAGGA
331994 AAGTCTTAAC
Statistics
Matches: 236, Mismatches: 71, Indels: 34
0.69 0.21 0.10
Matches are distributed among these distances:
29 49 0.21
30 162 0.69
31 25 0.11
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (30 bp):
TTGATCGAATACAGTCAAATAAGGATAAAC
Found at i:331818 original size:60 final size:60
Alignment explanation
Indices: 331619--331986 Score: 454
Period size: 60 Copynumber: 6.2 Consensus size: 60
331609 TCAAATGAGG
* * * *
331619 ATAC-GTCAAAAGGGGTAAGATTTGACCGAGTACAGTCAAATGAGGACAAACTTGATCGA
1 ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCGA
* * * * * *
331678 ATACAATCAAGAGGGGTAAGATTTGACCGAGTACAATCAAATAA-AAAAAACTTGACCGA
1 ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCGA
*** * *
331737 ATACAGTCAAGAAAAGAAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCAA
1 ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCGA
* * * *
331797 ATACAGTCAAGAGGGGTAAGATTTGATCGAATATAGTAAAATGAGGATAAACTTGA-CTGA
1 ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATC-GA
* * * * * *
331857 ATACGGTTAAGAGGGGTAAAATTTGATCGAGTATAGTCAAATGAGGATAAACTTGATCAA
1 ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCGA
* * *
331917 ATACAGTCAAGATGGGTAAGATTTGATCGAGTATAGTAAAATAAGGATAAACTTGATCGA
1 ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCGA
331977 ATACAGTCAA
1 ATACAGTCAA
331987 ATGAGGAAAG
Statistics
Matches: 265, Mismatches: 40, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
59 54 0.20
60 210 0.79
61 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.23
Consensus pattern (60 bp):
ATACAGTCAAGAGGGGTAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCGA
Found at i:331874 original size:284 final size:282
Alignment explanation
Indices: 331342--331905 Score: 776
Period size: 284 Copynumber: 2.0 Consensus size: 282
331332 ACGAATACAA
* * * * *
331342 TCAAGAGGGGTAAAATTTGACTGAGTACAATAAAATGAGGATAGATTCGACTGAATACAGTCAAG
1 TCAAAAGGGGTAAAATTTGACCGAGTACAATAAAATGAGGACAAATTCGACTGAATACAATCAAG
* * * * *
331407 AGGGGTAAGATTTGACCGAGTACAGTCAAATAAGGATAAACTTGGCCGAATACAATCAAGAGTAA
66 AGGGGTAAGATTTGACCGAGTACAATCAAATAAGAAAAAACTTGACCGAATACAATCAAGAGAAA
* *
331472 GATTTGACCGAGTACAGCCAAATAAGGATAAACTTGATCGAATACAGTCAAGATGGGTAAGATTT
131 GATTTGACCGAGTACAGCCAAATAAGGATAAACTTGATCAAATACAGTCAAGAGGGGTAAGATTT
* * *
331537 GACCAAGTATAGTCAAATGAGGATAGACTTAACCGAATACAGTTAAAAGGGGTAAGATTTGACCA
196 GACCAAGTATAGTAAAATGAGGATAAACTTAACCGAATACAGTTAAAAGGGGTAAAATTTGACCA
331602 AGTACAATCAAATGAGGATACG
261 AGTACAATCAAATGAGGATACG
* * *
331624 TCAAAAGGGGTAAGATTTGACCGAGTACAGTCAAATGAGGACAAACTT-GA-TCGAATACAATCA
1 TCAAAAGGGGTAAAATTTGACCGAGTACAATAAAATGAGGACAAA-TTCGACT-GAATACAATCA
*
331687 AGAGGGGTAAGATTTGACCGAGTACAATCAAATAA-AAAAAACTTGACCGAATACAGTCAAGAAA
64 AGAGGGGTAAGATTTGACCGAGTACAATCAAATAAGAAAAAACTTGACCGAATACAATCAAG---
* *
331751 AGAAAGATTTGATCGAGTACAGTCAAATAAGGATAAACTTGATCAAATACAGTCAAGAGGGGTAA
126 AGAAAGATTTGACCGAGTACAGCCAAATAAGGATAAACTTGATCAAATACAGTCAAGAGGGGTAA
* * * * *
331816 GATTTGATCGAA-TATAGTAAAATGAGGATAAACTTGACTGAATACGGTTAAGAGGGGTAAAATT
191 GATTTGA-CCAAGTATAGTAAAATGAGGATAAACTTAACCGAATACAGTTAAAAGGGGTAAAATT
* * * *
331880 TGATCGAGTATAGTCAAATGAGGATA
255 TGACCAAGTACAATCAAATGAGGATA
331906 AACTTGATCA
Statistics
Matches: 246, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
281 23 0.09
282 84 0.34
283 2 0.01
284 134 0.54
285 3 0.01
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.22
Consensus pattern (282 bp):
TCAAAAGGGGTAAAATTTGACCGAGTACAATAAAATGAGGACAAATTCGACTGAATACAATCAAG
AGGGGTAAGATTTGACCGAGTACAATCAAATAAGAAAAAACTTGACCGAATACAATCAAGAGAAA
GATTTGACCGAGTACAGCCAAATAAGGATAAACTTGATCAAATACAGTCAAGAGGGGTAAGATTT
GACCAAGTATAGTAAAATGAGGATAAACTTAACCGAATACAGTTAAAAGGGGTAAAATTTGACCA
AGTACAATCAAATGAGGATACG
Found at i:333158 original size:20 final size:20
Alignment explanation
Indices: 333025--333161 Score: 193
Period size: 20 Copynumber: 6.8 Consensus size: 20
333015 TTTTCACAAT
* * *
333025 TTGTATTGATGCATTATTCA
1 TTGTATCGATACATTGTTCA
*
333045 TTGTATCGATACACTGTTCA
1 TTGTATCGATACATTGTTCA
*
333065 TTGTATCGATACACTGTTCA
1 TTGTATCGATACATTGTTCA
*
333085 TTGTATCGATACACTGTTCA
1 TTGTATCGATACATTGTTCA
* *
333105 TTATATCGATACATTATTCA
1 TTGTATCGATACATTGTTCA
*
333125 TTATATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
333145 TTGTATCGATACATTGT
1 TTGTATCGATACATTGT
333162 ATCGATACAT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 108 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:333161 original size:13 final size:13
Alignment explanation
Indices: 333143--333171 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
333133 ATACATTGTT
333143 CATTGTATCGATA
1 CATTGTATCGATA
333156 CATTGTATCGATA
1 CATTGTATCGATA
333169 CAT
1 CAT
333172 ACTGGGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:335612 original size:49 final size:50
Alignment explanation
Indices: 335509--335637 Score: 129
Period size: 49 Copynumber: 2.6 Consensus size: 50
335499 AAATTTCTAG
* * * * **
335509 ATTTTTCATCTCGGGGATACTCCAACCCTGGCATTATTTCTAAAATATTG
1 ATTTTTCATATCGGGGATACTCCAACCCCGACATTATTTCTAAAACATCA
* **
335559 ATTTTTCAT-TCGGGGATACTCTAACCCCGATTTTATTT-TCAAAACATCA
1 ATTTTTCATATCGGGGATACTCCAACCCCGACATTATTTCT-AAAACATCA
*
335608 ATTTTTCATAATC-GGGATACTCCAATCCCG
1 ATTTTTCAT-ATCGGGGATACTCCAACCCCG
335638 TTATTTTCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
48 1 0.02
49 39 0.59
50 24 0.36
51 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (50 bp):
ATTTTTCATATCGGGGATACTCCAACCCCGACATTATTTCTAAAACATCA
Found at i:335731 original size:79 final size:79
Alignment explanation
Indices: 335570--335954 Score: 386
Period size: 79 Copynumber: 4.9 Consensus size: 79
335560 TTTTTCATTC
* *
335570 GGGGATACTCTAACCCCGATTTTATTT-TCAAAACATCAATTTTTCATAATC-GGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACATCGATTTTTCATAATCGGGGATACTCCAA
* *
335633 TCCCGTTATTTTCAA
65 CCCCGTTATTTTCGA
** * * * * *
335648 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCAAAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAAC
* *
335713 CCCGTTATTTTGGC
66 CCCGTTATTTTCGA
** * * * * *
335727 GGGGATACTCCAACCCC-AGCCTTATTTCTAAAGCTTCGATTTTTCACAATCGAGGACACTCCAA
1 GGGGATACTCCAACCCCGA-TTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAA
* * **
335791 CCTCATTATTTTTTA
65 CCCCGTTATTTTCGA
* * * * *
335806 GGGGATACTCCAACCCCGATTTTATTTTTAAAACACCGA-TTTTCTATAATCAGAGATACTCCAT
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTC-ATAATCGGGGATACTCCAA
*
335870 CCCTGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * * *
335885 GGGGATACTCTAACCCCGATTTTATTT-TCAAAACATC-ATTTTCCATAATCGGGGATACTCTAG
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAAACATCGATTTTTCATAATCGGGGATACTCCAA
335948 CCCCGTT
65 CCCCGTT
335955 GTTATCCCCA
Statistics
Matches: 246, Mismatches: 54, Indels: 14
0.78 0.17 0.04
Matches are distributed among these distances:
78 68 0.28
79 177 0.72
80 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAACATCGATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:337323 original size:20 final size:20
Alignment explanation
Indices: 337298--337337 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
337288 TCCCGTTGCT
*
337298 ATGTATTGATACAATTCATA
1 ATGTATTGATACAATACATA
337318 ATGTATTGATACAATACATA
1 ATGTATTGATACAATACATA
337338 TGGATGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (20 bp):
ATGTATTGATACAATACATA
Found at i:343107 original size:51 final size:51
Alignment explanation
Indices: 343052--343164 Score: 163
Period size: 51 Copynumber: 2.2 Consensus size: 51
343042 TAACTAGAAG
* *
343052 TATCGATACATTGAAAAATGTATCAATACATCTGGGTAAAAAGATAGAATA
1 TATCGATACATTAAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATA
* * * *
343103 TATCGATATATTAAAAAATGTATCGATACATTTGGGTAAAAAGACAGAATG
1 TATCGATACATTAAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATA
*
343154 TATTGATACAT
1 TATCGATACAT
343165 CTAGGTAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.45, C:0.09, G:0.16, T:0.30
Consensus pattern (51 bp):
TATCGATACATTAAAAAATGTATCAATACATCTGGGTAAAAAGACAGAATA
Found at i:346494 original size:13 final size:13
Alignment explanation
Indices: 346476--346501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
346466 CAATTTTTTG
346476 TGTATCGATACAT
1 TGTATCGATACAT
346489 TGTATCGATACAT
1 TGTATCGATACAT
346502 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:346516 original size:32 final size:33
Alignment explanation
Indices: 346456--346519 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
346446 TACAAGCCAA
** *
346456 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
346489 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
346520 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:349107 original size:13 final size:13
Alignment explanation
Indices: 349071--349108 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
349061 ATAATCCCCC
*
349071 TGTATCGATAAAG
1 TGTATCGATACAG
*
349084 TGTATCGATACAT
1 TGTATCGATACAG
349097 TGTATCGATACA
1 TGTATCGATACA
349109 AAGAAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:351210 original size:15 final size:15
Alignment explanation
Indices: 351190--351220 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
351180 ATTTCGTTTG
*
351190 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
351205 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
351220 G
1 G
351221 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:355297 original size:13 final size:13
Alignment explanation
Indices: 355279--355304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
355269 TAATTTTTTG
355279 TGTATCGATACAT
1 TGTATCGATACAT
355292 TGTATCGATACAT
1 TGTATCGATACAT
355305 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:360313 original size:13 final size:13
Alignment explanation
Indices: 360295--360319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
360285 ATACAAAAAA
360295 TGTATCGATACAT
1 TGTATCGATACAT
360308 TGTATCGATACA
1 TGTATCGATACA
360320 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:366759 original size:15 final size:15
Alignment explanation
Indices: 366736--366773 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
366726 CGAGTCAACT
366736 TCATCATTATCATCA
1 TCATCATTATCATCA
* *
366751 TCATTATTATCTTCA
1 TCATCATTATCATCA
366766 TCATCATT
1 TCATCATT
366774 GATGGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (15 bp):
TCATCATTATCATCA
Found at i:368391 original size:13 final size:13
Alignment explanation
Indices: 368373--368397 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
368363 CAATTCTTCA
368373 TGTATCGATACAT
1 TGTATCGATACAT
368386 TGTATCGATACA
1 TGTATCGATACA
368398 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:368408 original size:33 final size:32
Alignment explanation
Indices: 368353--368417 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
368343 TTTGGGACAA
*
368353 TGTATCGATACAATTCTTCATGTATCGATACAT
1 TGTATCGATACAATTC-TCATGTAACGATACAT
368386 TGTATCGATACAATGTGC-CATGTAACGATACA
1 TGTATCGATACAAT-T-CTCATGTAACGATACA
368418 AATAGTGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (32 bp):
TGTATCGATACAATTCTCATGTAACGATACAT
Found at i:368510 original size:32 final size:33
Alignment explanation
Indices: 368469--368532 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
368459 CAATTGTGCT
* *
368469 TGTATTGATACAATG-ATCATGAATCGATACAA
1 TGTATTGATACAAAGCATAATGAATCGATACAA
*
368501 TGTATTGATACAAAGCATAATGTATCGATACA
1 TGTATTGATACAAAGCATAATGAATCGATACA
368533 TCTGGATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATTGATACAAAGCATAATGAATCGATACAA
Found at i:373153 original size:12 final size:11
Alignment explanation
Indices: 373136--373161 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
373126 TTAAATATAC
373136 AAAAAAAAAAG
1 AAAAAAAAAAG
373147 AAAAAAAAAAG
1 AAAAAAAAAAG
373158 AAAA
1 AAAA
373162 GGTAAGCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:376910 original size:18 final size:19
Alignment explanation
Indices: 376889--376931 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
376879 AAAAAATTCA
376889 AAATTTATGAAAA-TGAAT
1 AAATTTATGAAAACTGAAT
*
376907 AAATTTTTGAAAACTGAAT
1 AAATTTATGAAAACTGAAT
*
376926 TAATTT
1 AAATTT
376932 GAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (19 bp):
AAATTTATGAAAACTGAAT
Found at i:376953 original size:164 final size:162
Alignment explanation
Indices: 376452--377462 Score: 846
Period size: 164 Copynumber: 6.4 Consensus size: 162
376442 GTTTATTAAC
* * * * * * *
376452 AATATTAGATGAA-TTTAAAATTTTAAATCAAGAAAAAT-CTCCTCAAAAATATTTATGAAGTAG
1 AATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCTCC-CAAAAA-AATTACGGAGTAG
** * *
376515 AAAAC-TCGATATCTCGAAAATAAAAG--ATTTCAAA-AAAAAATCCAAAACTCATGCAAAA-GA
64 AAAACTTCG-TAT-TTTAAAA-AAAAGAAATTT-AAAGAAAAAATTCAAAATTCATG-AAAATGA
* * * * * *
376575 ATTAAATTTTCAAAATTGATTTAATGTGAAATAAATAAT
124 ATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* ** * *
376614 AATATTTGATGAATTTTAAAAATAAAAAACCAAGAAGAGTTCC-CTCGAAAAAAATTAC-TATGT
1 AATATTTGATGAATTTTAAAAATTAAAAA-CAAGAA-AAATCCTC-CCAAAAAAATTACGGA-GT
* * * * * *
376677 AGAAAAC-TCTGTATTTTGAAAAAAGGAGAATTTCAAGAAAAAAATTCAAAATTTATGGAAATAA
62 AGAAAACTTC-GTATTTTAAAAAAAAGA-AATTTAAAG-AAAAAATTCAAAATTCATGAAAATGA
* *
376741 ATGAATTTTTGAAAATTGAATTAATGTGAAATAAATAAT
124 ATGAATTTTTGAAAACTGAATTAATATGAAATAAATAAT
376780 AATATTTGATGAA-TTTAAAAATTAAAAACCAAGAAAAATCCTCCCAAAGAAAATTACGGAGTAG
1 AATATTTGATGAATTTTAAAAATTAAAAA-CAAGAAAAATCCTCCCAAA-AAAATTACGGAGTAG
* * * *
376844 AAAACTCCGTATTTTAAAAAAAGAGAAATTTTAAGAAAAAATTCAAAATTTATGAAAATGAATAA
64 AAAACTTCGTATTTTAAAAAAA-AGAAATTTAAAGAAAAAATTCAAAATTCATGAAAATGAATGA
*
376909 ATTTTTGAAAACTGAATTAATTTGAAATAAATAAT
128 ATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* * * *
376944 AATATTTGATAAATTTTAAAAA-T----A-AA-AAAAATCC-CCTAAAAAAATTATGGAGTGGAA
1 AATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCTCCCAAAAAAATTACGGAGTAGAA
* * ** ** * * * *
377001 AACTTTGTATTTTGTAAGTAGGGGAATTTCAAAAAAAAAATTCAAAATTCTTGGAAATGAATGAA
66 AACTTCGTATTTT-AAAAAAAAGAAATTT-AAAGAAAAAATTCAAAATTCATGAAAATGAATGAA
* *
377066 TTTTTGAAAACTAAATTAATATAAAAT-AA-AAT
129 TTTTTGAAAACTGAATTAATATGAAATAAATAAT
* * * * **
377098 AATATTTGATGAATTTTAAAAATCCAAAAACAAGAAAAAT-TTGCCC--AAAATTTTCAAAGTAG
1 AATATTTGATGAATTTTAAAAAT-TAAAAACAAGAAAAATCCT-CCCAAAAAAATTACGGAGTAG
** *
377160 AAAACTTCGTATTGCGAAAAAAAAGAAATTTAAAGAAAAAATTTAAAATTCAT-AGAAATGAATG
64 AAAACTTCGTATT-TTAAAAAAAAGAAATTTAAAGAAAAAATTCAAAATTCATGA-AAATGAATG
*
377224 AATTTTTGAAAACTGAATTAATATAAAATAAATAAT
127 AATTTTTGAAAACTGAATTAATATGAAATAAATAAT
* *
377260 AATATTTGATGAA---T----GTT----A-AA-AAAAAT-C-CCCAAAAAAATTACGGAATAGAA
1 AATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCTCCCAAAAAAATTACGGAGTAGAA
* ** * * * *
377310 AACTTAGTATTTCGAAAAAAAG-ATTTTTAAGGAAAAATTCAAAATTCATGGAAATGAATGAATT
66 AACTTCGTATTTTAAAAAAAAGAAATTTAAAGAAAAAATTCAAAATTCATGAAAATGAATGAATT
377374 TTTGAAAACTGAATTAATATGAAATAAATAAT
131 TTTGAAAACTGAATTAATATGAAATAAATAAT
* * * *
377406 AATATTTGATGAATTTTAAAAATTAAAAACTATG-AAAATCCTCTCGAAAAATTTACG
1 AATATTTGATGAATTTTAAAAATTAAAAAC-AAGAAAAATCCTCCCAAAAAAATTACG
377463 AAAAAGAAAA
Statistics
Matches: 688, Mismatches: 107, Indels: 109
0.76 0.12 0.12
Matches are distributed among these distances:
146 83 0.12
147 8 0.01
148 29 0.04
149 3 0.00
150 1 0.00
153 2 0.00
154 24 0.03
155 35 0.05
156 61 0.09
157 9 0.01
158 2 0.00
159 7 0.01
160 59 0.09
161 47 0.07
162 38 0.06
163 18 0.03
164 107 0.16
165 84 0.12
166 71 0.10
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (162 bp):
AATATTTGATGAATTTTAAAAATTAAAAACAAGAAAAATCCTCCCAAAAAAATTACGGAGTAGAA
AACTTCGTATTTTAAAAAAAAGAAATTTAAAGAAAAAATTCAAAATTCATGAAAATGAATGAATT
TTTGAAAACTGAATTAATATGAAATAAATAAT
Found at i:377293 original size:146 final size:145
Alignment explanation
Indices: 376860--377427 Score: 471
Period size: 146 Copynumber: 3.7 Consensus size: 145
376850 CCGTATTTTA
* * *
376860 AAAAAAGAGAAATTTTAAGAAAAAATTCAAAATTTAT-GAAAATGAATAAATTTTTGAAAACTGA
1 AAAAAA-AG-AATTTAAAGAAAAAATTCAAAATTCATAG-AAATGAATGAATTTTTGAAAACTGA
* * * *
376924 ATTAATTTGAAATAAATAATAATATTTGATAAATTTTAAAAATAAAAAAAATCCCCTAAAAAAAT
63 ATTAATATAAAATAAATAATAATATTTGATGAA-TGT-----TAAAAAAAATCCCC--AAAAAAT
* * * * * **
376989 TATGGAGTGGAAAACTTTGTATTTTG
120 TACGAAATAGAAAACTTAGTATTGCG
* *** * * * *
377015 TAAGTAGGGGAATTTCAAAAAAAAAATTCAAAATTCTTGGAAATGAATGAATTTTTGAAAACTAA
1 -AA-AAAAAGAATTT-AAAGAAAAAATTCAAAATTCATAGAAATGAATGAATTTTTGAAAACTGA
* *
377080 ATTAATATAAAAT-AA-AATAATATTTGATGAATTTTAAAAATCCAAAAACAAGAAAAATTTGCC
63 ATTAATATAAAATAAATAATAATATTTGATGAA-TGT-----T------A-AA-AAAAA--TCCC
* * *
377143 C-AAAATTTTC-AAAGTAGAAAACTTCGTATTGCG
112 CAAAAAATTACGAAA-TAGAAAACTTAGTATTGCG
*
377176 AAAAAAAAGAAATTTAAAGAAAAAATTTAAAATTCATAGAAATGAATGAATTTTTGAAAACTGAA
1 -AAAAAAAG-AATTTAAAGAAAAAATTCAAAATTCATAGAAATGAATGAATTTTTGAAAACTGAA
*
377241 TTAATATAAAATAAATAATAATATTTGATGAATGTTAAAAAAAATCCCCAAAAAAATTACGGAAT
64 TTAATATAAAATAAATAATAATATTTGATGAATGTTAAAAAAAATCCCC-AAAAAATTACGAAAT
*
377306 AGAAAACTTAGTATTTCG
128 AGAAAACTTAGTATTGCG
* * * *
377324 AAAAAAAGATTTTTAAGGAAAAATTCAAAATTCATGGAAATGAATGAATTTTTGAAAACTGAATT
1 AAAAAAAGAATTTAAAGAAAAAATTCAAAATTCATAGAAATGAATGAATTTTTGAAAACTGAATT
* *
377389 AATATGAAATAAATAATAATATTTGATGAATTTTAAAAA
66 AATATAAAATAAATAATAATATTTGATGAATGTTAAAAA
377428 TTAAAAACTA
Statistics
Matches: 345, Mismatches: 47, Indels: 50
0.78 0.11 0.11
Matches are distributed among these distances:
146 93 0.27
147 8 0.02
148 29 0.08
149 4 0.01
150 1 0.00
154 25 0.07
155 7 0.02
156 56 0.16
157 2 0.01
160 61 0.18
161 34 0.10
162 21 0.06
164 4 0.01
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.31
Consensus pattern (145 bp):
AAAAAAAGAATTTAAAGAAAAAATTCAAAATTCATAGAAATGAATGAATTTTTGAAAACTGAATT
AATATAAAATAAATAATAATATTTGATGAATGTTAAAAAAAATCCCCAAAAAATTACGAAATAGA
AAACTTAGTATTGCG
Found at i:379168 original size:13 final size:13
Alignment explanation
Indices: 379150--379175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
379140 TAGAGCAAGT
379150 ATGTATCGATACA
1 ATGTATCGATACA
379163 ATGTATCGATACA
1 ATGTATCGATACA
379176 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:381440 original size:21 final size:22
Alignment explanation
Indices: 381394--381438 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
381384 TTTCAAGATG
381394 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
381416 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
381436 AAA
1 AAA
381439 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:383234 original size:15 final size:15
Alignment explanation
Indices: 383214--383244 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
383204 TAAAAATGTC
*
383214 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
383229 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
383244 C
1 C
383245 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:385341 original size:13 final size:13
Alignment explanation
Indices: 385323--385348 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
385313 ACATTTTTCC
385323 TTGTATCGATACA
1 TTGTATCGATACA
385336 TTGTATCGATACA
1 TTGTATCGATACA
385349 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:385512 original size:20 final size:20
Alignment explanation
Indices: 385469--385514 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
385459 AAATCTTTTG
385469 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
385490 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
385510 CAAAA
1 CAAAA
385515 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:391511 original size:11 final size:12
Alignment explanation
Indices: 391480--391512 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
391470 TTCCCTAATT
391480 TCTCCAAAACCA
1 TCTCCAAAACCA
*
391492 TCACCAAAACC-
1 TCTCCAAAACCA
391503 TCTCCAAAAC
1 TCTCCAAAAC
391513 GCTTATTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (12 bp):
TCTCCAAAACCA
Found at i:399779 original size:13 final size:13
Alignment explanation
Indices: 399761--399785 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
399751 AAGAGGAAGT
399761 TGTATCGATACAA
1 TGTATCGATACAA
399774 TGTATCGATACA
1 TGTATCGATACA
399786 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:399866 original size:13 final size:13
Alignment explanation
Indices: 399848--399872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
399838 ATTACTCAAA
399848 TGTATCGATACAT
1 TGTATCGATACAT
399861 TGTATCGATACA
1 TGTATCGATACA
399873 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:399924 original size:52 final size:52
Alignment explanation
Indices: 399861--400005 Score: 220
Period size: 52 Copynumber: 2.8 Consensus size: 52
399851 ATCGATACAT
***
399861 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
399913 TGTATCGATACA-TTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAAT-AAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
399965 TGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTAATAAATGTATCGATACATGCAGGCAA
400006 CTTTTCATAT
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
51 3 0.04
52 79 0.94
53 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTAATAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:408624 original size:31 final size:31
Alignment explanation
Indices: 408555--408633 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
408545 CCCTTTTACC
*
408555 TTTGTCCTTAAAAAGCAAGACATTTTCCTTA
1 TTTGTCCTCAAAAAGCAAGACATTTTCCTTA
* *
408586 TTTGTCCTCAAAGAGCAAGACATTTT-CTTT
1 TTTGTCCTCAAAAAGCAAGACATTTTCCTTA
*
408616 TTTAGTCCTCAAATAGCA
1 TTT-GTCCTCAAAAAGCA
408634 GGATGCCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
30 6 0.14
31 37 0.86
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.38
Consensus pattern (31 bp):
TTTGTCCTCAAAAAGCAAGACATTTTCCTTA
Found at i:408765 original size:73 final size:72
Alignment explanation
Indices: 408611--410052 Score: 1092
Period size: 73 Copynumber: 19.9 Consensus size: 72
408601 CAAGACATTT
* * *
408611 TCTTTTTTAGTCCTCAAATAGCAGGATGCC---TTTTTTTTCAAAGCCCACATAAGCTGGTGGCA
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGCA
408673 CCCTTTA
66 CCCTTTA
* * ** *
408680 TCTTCTTTTAGTCCTCAAAAAATAGGATGCCTTTTCTTTTTTTCAAAGCCCACACAAACTGGTGG
1 TCTT-TTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTTTTCAAAGCCCACACAAGCTGGTGG
* *
408745 AACCTTTTA
64 CACCCTTTA
* * * *
408754 TCTTTTTTAGTCCTTAAAGAGCAAGACT-CCTTTTCTTTTTATCAAAGCCCACACAAGCTGGTGG
1 TCTTTTTCAGTCCTCAAAGAGCAGGA-TGCCTTTT-TTTTTTTCAAAGCCCACACAAGCTGGTGG
*
408818 TACCC-TTA
64 CACCCTTTA
* * ** * ** * * * *
408826 TCTTTTTCAATCCTAAAAGAGCAGGACACCTATCCTTTTTCCTAAAGCTCACCCAAGCTGTTGGC
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTC-AAAGCCCACACAAGCTGGTGGC
*
408891 ACCTTTTA
65 ACCCTTTA
* * * * **
408899 TTTTTTTCAATCTTCAAAGAGCAAGACACCTTTTCTTTTTCTTCAAAGCCCACACAAGCTGGTGG
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTGG
*
408964 CACCTTTTA
64 CACCCTTTA
* * * * * * * *
408973 T-TTTTTCAATCTTTAAAGAGCATGATGCCTTTTCTTTTTCTTCAAAGCCTATATAAGCTGGCGG
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTGG
*
409037 CACCTTTTA
64 CACCCTTTA
* * * * ** * * * * *
409046 TCCTTTTCAATTCTCAAAAAGCATAATG-CTTTTTTTTTCTTCAAAGCCTACACGAGTTGATGGT
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTT-TTCAAAGCCCACACAAGCTGGTGGC
409110 A-CCTTTA
65 ACCCTTTA
* * * * **
409117 TCTTTTTCAATCCTCAAAGAGCATGA--CCTTTTTTTTTTTCAAAGCCCACATAAACAAGTGGCA
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGCA
*
409180 CCGTTTA
66 CCCTTTA
* * * * * * * * **
409187 TCTTTTTTTAGTCCTTAAAGAGTAGGA-GACCTTTTATTTCTTCAAAGTCCATATAAGCTAATGG
1 TC-TTTTTCAGTCCTCAAAGAGCAGGATG-CCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGG
409251 CACCCTTTA
64 CACCCTTTA
* * * *
409260 TCTTTTTTTAGTCTTCAAAGAGCAGGATGCTTTTTCTTTTTCTTCAAAGTCCACACAAGCTGGTG
1 TC-TTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTG
409325 GCACCCTTTA
63 GCACCCTTTA
* * * * * * *
409335 TCTTTGTT-AGTCCTCAAAGAGTAGGATG-GTTTTTTTTCTTCAAAGCCCAAACAAACTAGTAGC
1 TCTTT-TTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGC
409398 ACCCTTTA
65 ACCCTTTA
* * * * * *
409406 TCTATTTT-AGTACTCAAAGAGCAAGACGCTTTTTCTTTTTCTTCAAAGCCTACACAAGTTGGTG
1 TCT-TTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTG
*
409470 GCACCTTTTA
63 GCACCCTTTA
* * * * * * *
409480 TCTTTTTCAGTTCAT-AAAGAACATGA--CACTTTTTTTTTCTTCAAAGCTCAAATAAGCCGGTG
1 TCTTTTTCAG-TCCTCAAAGAGCAGGATGC-CTTTTTTTTT-TTCAAAGCCCACACAAGCTGGTG
409542 GCACCCTTTA
63 GCACCCTTTA
* * * ** * * * * *
409552 TCTTTTTCAATCCTCAAAAAACAAAATGCCTTTTTTTCTTTAAAAGCCCATACAAACTGGTGGTA
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGCA
409617 CCCTTTA
66 CCCTTTA
* ** **
409624 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTCTTTCAAAGCCCACATAAATTATTGGC
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTT-TTTCAAAGCCCACACAAGCTGGTGGC
409689 ACCCTTTA
65 ACCCTTTA
* * * * * * * * * *
409697 TATTTTTCAGT-TTGTAAAGAGCATGAAGCTTTTTCTTTTTCTTCAAATCCAACATAAGTTGGTG
1 TCTTTTTCAGTCCT-CAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTG
*
409761 GCACCTTTTA
63 GCACCCTTTA
* * * * ** *
409771 TCTTTTTCAGTCCTCAAAAAGCATGACGCTTTTTCTTTTTCTTCAAAGCCCACACAAATTAGTGG
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTGG
409836 CACCCTTTA
64 CACCCTTTA
* * * * * *
409845 TATTTTTCAATCCAT-AAATAGTAGGATG-C-TTTTTTTGTTCAAAGCCCACACAAGCTGGTTGC
1 TCTTTTTCAGTCC-TCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGC
*
409907 ACCTTTTA
65 ACCCTTTA
* * * * * * *
409915 TCTTTTTTAGTCTTCAAATAGTAGGATGCCTTTTTTTTTATAAAAGCCCACACAAGTTGGTGGCA
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGCA
409980 -CCTTTA
66 CCCTTTA
* * * ** * * *
409986 TCTTTTTTAATCCTCAAAGAGTAGGACACCTTTTCTTTTTCTTTAAAGCCCACATAAGTTGGTGG
1 TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTT-TTTTT-TTCAAAGCCCACACAAGCTGGTGG
410051 CA
64 CA
410053 TTTATCTAGG
Statistics
Matches: 1116, Mismatches: 215, Indels: 80
0.79 0.15 0.06
Matches are distributed among these distances:
69 22 0.02
70 90 0.08
71 142 0.13
72 231 0.21
73 323 0.29
74 269 0.24
75 39 0.03
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (72 bp):
TCTTTTTCAGTCCTCAAAGAGCAGGATGCCTTTTTTTTTTTCAAAGCCCACACAAGCTGGTGGCA
CCCTTTA
Found at i:408918 original size:145 final size:146
Alignment explanation
Indices: 408640--410052 Score: 876
Period size: 145 Copynumber: 9.7 Consensus size: 146
408630 AGCAGGATGC
* * * * **
408640 CTTTTTTTTCAAAGCCCACATAAGCTGGTGGCACCCTTTATCTTCTTTTAGTCCTCAAAA-AATA
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCC-TTATCTT-TTTCAATCCT-AAAAGAGCA
* * *
408704 GGATGCCTTTTCTTTTT-TTCAAAGCCCACACAAACTGGTGGAACCTTTTATCTTTTTT-AGTCC
63 GGATGCCTTTTCTTTTTCTTCAAAG-CCACACAAGCTGGTGGCACCTTTTAT-TTTTTTCAAT-C
408767 TT-AAAGAGCAAGACTCCTTTT
125 TTCAAAGAGCAAGACTCCTTTT
* *
408788 CTTTTT-ATCAAAGCCCACACAAGCTGGTGGTACCCTTATCTTTTTCAATCCTAAAAGAGCAGGA
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTATCTTTTTCAATCCTAAAAGAGCAGGA
** * * * * *
408852 CACCTATCCTTTTTCCT-AAAGCTCACCCAAGCTGTTGGCACCTTTTATTTTTTTCAATCTTCAA
66 TGCCTTTTCTTTTTCTTCAAAGC-CACACAAGCTGGTGGCACCTTTTATTTTTTTCAATCTTCAA
*
408916 AGAGCAAGACACCTTTT
130 AGAGCAAGACTCCTTTT
* * * *
408933 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAT-TTTTTCAATCTTTAAAGAGCATG
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACC-CTTATCTTTTTCAATCCTAAAAGAGCAGG
* * * **
408997 ATGCCTTTTCTTTTTCTTCAAAGCCTATATAAGCTGGCGGCACCTTTTATCCTTTTCAAT-TCTC
65 ATGCCTTTTCTTTTTCTTCAAAGCC-ACACAAGCTGGTGGCACCTTTTATTTTTTTCAATCT-TC
* *
409061 AAAAAGCATA-A-TGCTTTT
128 AAAGAGCA-AGACTCCTTTT
* * * * * * * *
409079 -TTTTTCTTCAAAGCCTACACGAGTTGATGGTACCTTTATCTTTTTCAATCCTCAAAGAGCATGA
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTATCTTTTTCAATCCTAAAAGAGCAGGA
* * ** * * *
409143 --CCTTTT-TTTTT-TTCAAAGCCCACATAAACAAGTGGCACCGTTTATCTTTTTTTAGTCCTT-
66 TGCCTTTTCTTTTTCTTCAAAG-CCACACAAGCTGGTGGCACCTTTTAT-TTTTTTCAAT-CTTC
* * **
409203 AAAGAGTAGGAGACC-TTT
128 AAAGAGCAAGACTCCTTTT
* * * * ** * * * *
409221 -TATTTCTTCAAAGTCCATATAAGCTAATGGCACCCTTTATCTTTTTTTAGTCTTCAAAGAGCAG
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCC-TTATC-TTTTTCAATCCTAAAAGAGCAG
* * * * *
409285 GATGCTTTTTCTTTTTCTTCAAAGTCCACACAAGCTGGTGGCACCCTTTATCTTTGTT-AGTCCT
64 GATGCCTTTTCTTTTTCTTCAAAG-CCACACAAGCTGGTGGCACCTTTTAT-TTTTTTCAATCTT
* * **
409349 CAAAGAGTAGGA-T-GGTTT
127 CAAAGAGCAAGACTCCTTTT
* * * * * * * *
409367 -TTTTTCTTCAAAGCCCAAACAAACTAGTAGCACCCTTTATCTATTTT-AGTACTCAAAGAGCAA
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCC-TTATCT-TTTTCAATCCTAAAAGAGCAG
* * * * * *
409430 GACGCTTTTTCTTTTTCTTCAAAGCCTACACAAGTTGGTGGCACCTTTTATCTTTTTCAGTTCAT
64 GATGCCTTTTCTTTTTCTTCAAAGCC-ACACAAGCTGGTGGCACCTTTTATTTTTTTCA-ATCTT
* * *
409495 -AAAGAACATGAC-ACTTTT
127 CAAAGAGCAAGACTCCTTTT
* * * * * *
409513 -TTTTTCTTCAAAGCTCAAATAAGCCGGTGGCACCCTTTATCTTTTTCAATCCTCAAAA-AACAA
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCC-TTATCTTTTTCAATCCT-AAAAGAGCAG
* * * * * * * * * *
409576 AATGCCTTTT-TTTCT-TTAAAAGCCCATACAAACTGGTGGTACCCTTTATCTTTTTCAGTCCTC
64 GATGCCTTTTCTTTTTCTTCAAAG-CCACACAAGCTGGTGGCACCTTTTATTTTTTTCAATCTTC
*
409639 AAAGAGCAGGA-TGCC-TTT
128 AAAGAGCAAGACT-CCTTTT
* ** ** * * * *
409657 -TTTTTCTTTCAAAGCCCACATAAATTATTGGCACCCTTTATATTTTTCAGT-TTGTAAAGAGCA
1 CTTTTTC-TTCAAAGCCCACACAAGCTGGTGGCACCC-TTATCTTTTTCAATCCT-AAAAGAGCA
* * * * * * * * *
409720 TGAAGCTTTTTCTTTTTCTTCAAATCCAACATAAGTTGGTGGCACCTTTTATCTTTTTCAGTCCT
63 GGATGCCTTTTCTTTTTCTTCAAAGCC-ACACAAGCTGGTGGCACCTTTTATTTTTTTCAATCTT
* * * *
409785 CAAAAAGCATGACGCTTTTT
127 CAAAGAGCAAGACTCCTTTT
** * * * *
409805 CTTTTTCTTCAAAGCCCACACAAATTAGTGGCACCCTTTATATTTTTCAATCC-ATAAATAGTAG
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCC-TTATCTTTTTCAATCCTA-AAAGAGCAG
* * *
409869 GATG-C--TT-TTTTTGTTCAAAGCCCACACAAGCTGGTTGCACCTTTTATCTTTTTT-AGTCTT
64 GATGCCTTTTCTTTTTCTTCAAAG-CCACACAAGCTGGTGGCACCTTTTAT-TTTTTTCAATCTT
* * *
409929 CAAATAGTAGGA-TGCCTTTT
127 CAAAGAGCAAGACT-CCTTTT
* * * * * * *
409949 -TTTTT-ATAAAAGCCCACACAAGTTGGTGGCACCTTTATCTTTTTTAATCCTCAAAGAGTAGGA
1 CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTATCTTTTTCAATCCTAAAAGAGCAGGA
** * * *
410012 CACCTTTTCTTTTTCTTTAAAGCCCACATAAGTTGGTGGCA
66 TGCCTTTTCTTTTTCTTCAAAG-CCACACAAGCTGGTGGCA
410053 TTTATCTAGG
Statistics
Matches: 1008, Mismatches: 201, Indels: 115
0.76 0.15 0.09
Matches are distributed among these distances:
141 49 0.05
142 73 0.07
143 21 0.02
144 154 0.15
145 285 0.28
146 185 0.18
147 141 0.14
148 94 0.09
149 6 0.01
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (146 bp):
CTTTTTCTTCAAAGCCCACACAAGCTGGTGGCACCCTTATCTTTTTCAATCCTAAAAGAGCAGGA
TGCCTTTTCTTTTTCTTCAAAGCCACACAAGCTGGTGGCACCTTTTATTTTTTTCAATCTTCAAA
GAGCAAGACTCCTTTT
Found at i:411969 original size:78 final size:79
Alignment explanation
Indices: 411864--412060 Score: 218
Period size: 78 Copynumber: 2.5 Consensus size: 79
411854 AATAACGGGG
* * * * ** * *
411864 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTAG
*
411928 A-AAAAAAATCGAGA
65 AGAAAAAAACCGAGA
*
411942 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGA
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
* * * *
412007 GAATAAAGCCGGGG
66 GAAAAAAACCGAGA
* * *
412021 TTGGAGCATCCCCTCGGAAGTAACGGGGTTGGAGTATCCC
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
412061 TGATGAAATA
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
77 1 0.01
78 54 0.54
79 45 0.45
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.24
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
GAAAAAAACCGAGA
Found at i:412059 original size:28 final size:28
Alignment explanation
Indices: 412016--412087 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
412006 AGAATAAAGC
* *
412016 CGGGGTTGGAGCATCCCCTCG-GAAGTAA
1 CGGGGTTGGAGTATCCCCT-GAGAAATAA
412044 CGGGGTTGGAGTAT-CCCTGATGAAATAA
1 CGGGGTTGGAGTATCCCCTGA-GAAATAA
*
412072 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
412088 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
26 1 0.03
27 4 0.11
28 32 0.84
29 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTGAGAAATAA
Found at i:412079 original size:107 final size:107
Alignment explanation
Indices: 411942--412249 Score: 320
Period size: 107 Copynumber: 2.9 Consensus size: 107
411932 AAAATCGAGA
* *
411942 TTGGAGTATCCCCTCGA--AAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-TTT
1 TTGGAGTAT-CCCT-GATGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTT
* * *
412004 T-GAGAATAAAGCCGGGGTTGGAGCATCCCCTCGGAAGTAACGGGG
64 TGGA-AATAAA-CCGGAGTTGGAGCATCCCCTCAGAAATAACGGGG
* * * * ***
412049 TTGGAGTATCCCTGATGAAATAACGAGGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTG
1 TTGGAGTATCCCTGATGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTTG
* *
412114 GAAATAAATCGGAGTTGGAGTATCCCCTCAGAAATAACGGGG
66 GAAATAAACCGGAGTTGGAGCATCCCCTCAGAAATAACGGGG
* * *** *
412156 TTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTT
1 TTGGAGTATCCCTGATGAAATAACGGGGTTGGAGTATCCCCGATTGTG-AGAAATCAAT-ATTTT
* *
412220 TGGAAATAAAATCGGAGTTGGAGTATCCCC
64 TGGAAAT-AAACCGGAGTTGGAGCATCCCC
412250 GATTATAGAA
Statistics
Matches: 173, Mismatches: 21, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
105 2 0.01
106 30 0.17
107 96 0.55
108 21 0.12
109 24 0.14
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.27
Consensus pattern (107 bp):
TTGGAGTATCCCTGATGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATATTTTTG
GAAATAAACCGGAGTTGGAGCATCCCCTCAGAAATAACGGGG
Done.