Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006530.1 Hibiscus syriacus cultivar Beakdansim tig00015919_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 612433
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 4
Found at i:224604 original size:63 final size:62
Alignment explanation
Indices: 224485--224608 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
224475 AACCTCGGCA
* * *
224485 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGATCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
* *
224547 ACTGTCCATATATCCCGAA-AGACATAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATAGATCCCGAAGA-ACATAGGTAA-ACTGTCCATATGTTCCGTAGAACATAGGTA
224609 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 26 0.47
63 28 0.51
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (62 bp):
ACTGTCCATAGATCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:230248 original size:2 final size:2
Alignment explanation
Indices: 230241--230280 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
230231 TTGTGTTGTC
230241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
230281 TATTTTAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:234439 original size:21 final size:20
Alignment explanation
Indices: 234411--234449 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
234401 CATTGCAGGA
*
234411 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
234431 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
234450 GACCCTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:250478 original size:20 final size:20
Alignment explanation
Indices: 250453--250500 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
250443 TTTTCCACGA
250453 ACTAGCTCAATTCACCCTTG
1 ACTAGCTCAATTCACCCTTG
250473 ACTAGCTCAATTCACCCTTG
1 ACTAGCTCAATTCACCCTTG
250493 ACTAGCTC
1 ACTAGCTC
250501 GAGCGCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.35, G:0.10, T:0.29
Consensus pattern (20 bp):
ACTAGCTCAATTCACCCTTG
Found at i:257911 original size:120 final size:120
Alignment explanation
Indices: 257688--257944 Score: 426
Period size: 120 Copynumber: 2.1 Consensus size: 120
257678 ATCATAAAAA
* * *
257688 TTCAATA-TAGATTCGAGAGAAAACCATAATATCTAATTATTTCCAATCGATAATAAATGACTTC
1 TTCAATATTA-ATTCGAGAGAAAACAATAATATCTAATTATTTCCAATCGACAATAAATGACCTC
* * *
257752 TCATGCCTTTAAGCAGTCATTTATTACTCCAACCGAAATGAAAAGATATTACTATT
65 TCATACCTTTAAGCAATCATTGATTACTCCAACCGAAATGAAAAGATATTACTATT
* *
257808 TTCATTATTAATTCGAGAGAAAACAATAATATCTAATTATTTCTAATCGACAATAAATGACCTCT
1 TTCAATATTAATTCGAGAGAAAACAATAATATCTAATTATTTCCAATCGACAATAAATGACCTCT
257873 CATACCTTTAAGCAATCATTGATTACTCCAACCGAAATGAAAAGATATTACTATT
66 CATACCTTTAAGCAATCATTGATTACTCCAACCGAAATGAAAAGATATTACTATT
257928 TTCAATATTAATTCGAG
1 TTCAATATTAATTCGAG
257945 TGTTATTTAT
Statistics
Matches: 127, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
120 125 0.98
121 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (120 bp):
TTCAATATTAATTCGAGAGAAAACAATAATATCTAATTATTTCCAATCGACAATAAATGACCTCT
CATACCTTTAAGCAATCATTGATTACTCCAACCGAAATGAAAAGATATTACTATT
Found at i:258922 original size:108 final size:109
Alignment explanation
Indices: 258774--259009 Score: 314
Period size: 108 Copynumber: 2.2 Consensus size: 109
258764 TCACCACACA
* * **
258774 TGACCAAAATGTAAAAACACGCCTAAATAAGGGGGACTAAACAGAAAATAACCCAAAAATACGTA
1 TGACCAACATGCAAAAACACGCCTAAATAAGGGGGACTAAACAGAAAATAACCCAAAAATACACA
* *
258839 GCATGCATAA-AAATGGGTAAATAGCAGAATCAGTTCTTACAGG
66 ACATGCATAAGAAATGGGTAAATAGCAGAATCAGTCCTTACAGG
* ** * * *
258882 TGACCAACATGCAAAAACACG-CTAAACTATGGGGGACTAAACATCAATTATCCCAAAAATATAC
1 TGACCAACATGCAAAAACACGCCTAAA-TAAGGGGGACTAAACAGAAAATAACCCAAAAATACAC
*
258946 AACATGCATAAGAAATGGGTAAATAGCAGAATCAGTCCTTACATG
65 AACATGCATAAGAAATGGGTAAATAGCAGAATCAGTCCTTACAGG
* *
258991 TGACTAACATTCAAAAACA
1 TGACCAACATGCAAAAACA
259010 TGCGAGAGTT
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
107 5 0.05
108 58 0.52
109 48 0.43
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (109 bp):
TGACCAACATGCAAAAACACGCCTAAATAAGGGGGACTAAACAGAAAATAACCCAAAAATACACA
ACATGCATAAGAAATGGGTAAATAGCAGAATCAGTCCTTACAGG
Found at i:259926 original size:3 final size:3
Alignment explanation
Indices: 259918--259946 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
259908 GGCCTGCACA
259918 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
259947 CGTCGGACGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:260702 original size:20 final size:19
Alignment explanation
Indices: 260673--260711 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
260663 TAATTAAATA
*
260673 AATATTTAAATTATATATTT
1 AATATCTAAATTAT-TATTT
260693 AATATCTAAATTATTATTT
1 AATATCTAAATTATTATTT
260712 TTATCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATCTAAATTATTATTT
Found at i:262299 original size:118 final size:114
Alignment explanation
Indices: 261780--262382 Score: 486
Period size: 115 Copynumber: 5.2 Consensus size: 114
261770 CTTATTATGA
* * * * * * * *
261780 ACGAGCTCATCTCATTATGAACTCTCTTCTGGAAACGTCGATCCACATTCTTCTGTGATGGATTT
1 ACGAGTTCTTCTCATTATGAACTCTTTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTT
* * *
261845 GAGTAAAGGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCAG
66 GA-AAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-GG
* * * * * * * *
261895 ACGGGTTCTTCTCATTTTGAACTCCCTTT-TGGAAATGTTGACCCACCT-CTTTTTTTATGGATT
1 ACGAGTTCTTCTCATTATGAACT-CTTTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATT
* * * * ** * *
261958 TGAGTAAAAAGATCAAACAAGTTCTT-TAAATAATGAACCCCTTCTTCTTTTG
65 TGA--AAAAAGGTCGAACAAGTTCTTCT-CATTATGAACTTCTTCTTCCTTGG
* * * * *
262010 AGGAGTTCTTCTAATTATGAGCTCTCATT-TGAAAGTGTTGATCCACCTCCTTCTGTGATGGATT
1 ACGAGTTCTTCTCATTATGAACTCT-TTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATT
* * * *
262074 TGAACGAAAGGTCGAACAGGTTTTTCTTATTATGAACTTCTTC-T--TTGG
65 TGAA-AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGG
* * * ** * * *
262122 ACAAGTTATTCTTATTATGAACT-TTCACTGAAAATGTTGATACACTTCCTTTTGTGATGGATTT
1 ACGAGTTCTTCTCATTATGAACTCTTTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTT
* * *
262186 GAAAAAATGGTCGAACATGTTCATCTCATTATGAAATTCTTCTCAATCCTTGG
66 GAAAAAA-GGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT---TCCTTGG
**
262239 TTGAGTTCTTCTCATTATGAACTCTTTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTT
1 ACGAGTTCTTCTCATTATGAACTCTTTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTT
* * * * *
262304 GAACAAAACGTCGAACAAGCTCTTTTCATTATGAACTTCTTCTCCCTCCTCGT
66 GAA-AAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT---TCCTTGG
** *
262357 ATAAGTTCTTCTCATTATAAACTCTT
1 ACGAGTTCTTCTCATTATGAACTCTT
262383 CGTTAAAAAT
Statistics
Matches: 382, Mismatches: 88, Indels: 33
0.76 0.17 0.07
Matches are distributed among these distances:
110 3 0.01
111 65 0.17
112 21 0.05
114 19 0.05
115 130 0.34
116 21 0.05
117 22 0.06
118 97 0.25
119 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (114 bp):
ACGAGTTCTTCTCATTATGAACTCTTTTCTGAAAATGTTGATCCACCTCCTTCTGTGATGGATTT
GAAAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGG
Found at i:262763 original size:36 final size:35
Alignment explanation
Indices: 262719--262787 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
262709 AGATGAAAAA
*
262719 AAATTGTTTCGAG-GAATAATATCTCAAGTGAGACG
1 AAATTGTTTCAAGAGAA-AATATCTCAAGTGAGACG
* *
262754 AAATCTGTTTCAAGAGAAACTATCTCGAGTGAGA
1 AAAT-TGTTTCAAGAGAAAATATCTCAAGTGAGA
262788 TGAAGTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 4 0.14
36 22 0.76
37 3 0.10
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (35 bp):
AAATTGTTTCAAGAGAAAATATCTCAAGTGAGACG
Found at i:265719 original size:43 final size:43
Alignment explanation
Indices: 265671--265754 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
265661 CAAGAATATT
*
265671 TTTTAATATGTTAGATTGATGTATTTGTGGATTATTACTTTAG
1 TTTTAATATGTTAGATTGATGTATTTATGGATTATTACTTTAG
* * * *
265714 TTTTAATATGTTGGTTTGGTGTATTTATGGATTTTTACTTT
1 TTTTAATATGTTAGATTGATGTATTTATGGATTATTACTTT
265755 GAAGTTTAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.57
Consensus pattern (43 bp):
TTTTAATATGTTAGATTGATGTATTTATGGATTATTACTTTAG
Found at i:274452 original size:21 final size:21
Alignment explanation
Indices: 274426--274480 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
274416 TAAATGCACC
274426 GAATTCGGTGCCCAATCCACA
1 GAATTCGGTGCCCAATCCACA
*
274447 GAATTCGGTGCCCAATCCACC
1 GAATTCGGTGCCCAATCCACA
*
274468 GAATTCGATGCCC
1 GAATTCGGTGCCC
274481 CCCTTAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.35, G:0.20, T:0.20
Consensus pattern (21 bp):
GAATTCGGTGCCCAATCCACA
Found at i:278867 original size:17 final size:17
Alignment explanation
Indices: 278841--278918 Score: 76
Period size: 17 Copynumber: 4.7 Consensus size: 17
278831 TTGTCCGAGA
*
278841 AATAAATATTATATTAT
1 AATAATTATTATATTAT
278858 AATAATTATTATATTAT
1 AATAATTATTATATTAT
278875 AAT--TT-TTATTATTAT
1 AATAATTATTA-TATTAT
*
278890 AA-AATTATAATTATTATT
1 AATAATTATTA-TATTA-T
278908 AAT-ATTATTAT
1 AATAATTATTAT
278919 TTTACAACGT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.06
15 10 0.19
16 2 0.04
17 28 0.54
18 9 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATAATTATTATATTAT
Found at i:278868 original size:3 final size:3
Alignment explanation
Indices: 278847--278919 Score: 53
Period size: 3 Copynumber: 25.3 Consensus size: 3
278837 GAGAAATAAA
* * * * *
278847 TAT TA- TAT TAT AAT AAT TAT TA- TAT TAT AAT TTT TAT TAT TA- TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
278892 AAT TAT AAT TAT TAT TAA TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
278920 TTACAACGTT
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
2 6 0.11
3 48 0.89
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:288502 original size:125 final size:125
Alignment explanation
Indices: 288280--288537 Score: 403
Period size: 125 Copynumber: 2.1 Consensus size: 125
288270 AATACCCACA
*
288280 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAGACCAATGAGGCATTGAGAA
1 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAAACCAATGAGGCATTGAGAA
** * * *
288345 TGAGCCTTACAATTTAAGGTTTTGGGGTATTTTGAAGGCCCGTA-CAAGTATAAGATAATG
66 TGAGCCTTACAATTTAAGGCGTTGGGGCATTTTGAAGACCCGTACCAA-TATAAGATAACG
*
288405 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAAACTAA-GAAGGCATTGAGA
1 TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAAACCAATG-AGGCATTGAGA
* *
288469 ATGAGCCTTACAATTTGAGGCGTTGGGGCATTTTGAAGACTCGTACCAATATAAGATAACG
65 ATGAGCCTTACAATTTAAGGCGTTGGGGCATTTTGAAGACCCGTACCAATATAAGATAACG
288530 TTGGGGCA
1 TTGGGGCA
288538 CAAGTGAAGG
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
124 1 0.01
125 118 0.97
126 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (125 bp):
TTGGGGCATGACTGAACCCACATCATGTTGAGATGACAAGATTCAAACCAATGAGGCATTGAGAA
TGAGCCTTACAATTTAAGGCGTTGGGGCATTTTGAAGACCCGTACCAATATAAGATAACG
Found at i:289742 original size:36 final size:36
Alignment explanation
Indices: 289701--290229 Score: 349
Period size: 36 Copynumber: 14.1 Consensus size: 36
289691 CCTCAGGGCA
*
289701 ATCTTAAGCCTTCACCGAAGACG-ATTGAAGCAATCC
1 ATCTTAAGCCTTCACCGAAGA-GTAGTGAAGCAATCC
* *
289737 ATCTTAAGCCTTCACAGAAGAGTAGTAAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AATCC
* * * *
289774 ATCAGTAAGCCTT--CCGAGCATGATTA-TTAAGTC-CTCCGGGCC
1 ATC-TTAAGCCTTCACCGA--A-GAGTAGTGAAG-CAAT-----CC
* *
289816 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* * *
289852 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGTAAACA
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
*
289888 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
*
289924 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* *
289960 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGTAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG-CAATCC
* * *
289997 ATCAGTAAGCC-TC-CCG-AGCA-TGATGATTAAGTC-CTCCGGGC
1 ATC-TTAAGCCTTCACCGAAG-AGT-A-G-TGAAG-CAAT-C---C
*
290038 AATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAATCC
1 -ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* *
290075 ATTTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AATCC
* * * * **** *** *
290112 ATCAGTAAGCCTCTCGAGCATGATGATTAAGTCCTCCGGGCA
1 ATC-TTAAGCCT-TC-A-C-CGAAGAGT-AGTGAAGCAATCC
*
290154 ATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* * * *
290190 ATCTTAAGCCTTTACAGAATAGTAGTGAAGAAAATCC
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG-CAATCC
290227 ATC
1 ATC
290230 AATAAACCTT
Statistics
Matches: 387, Mismatches: 66, Indels: 79
0.73 0.12 0.15
Matches are distributed among these distances:
35 4 0.01
36 223 0.58
37 41 0.11
38 33 0.09
39 8 0.02
40 10 0.03
41 33 0.09
42 20 0.05
43 13 0.03
44 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
Found at i:289824 original size:115 final size:115
Alignment explanation
Indices: 289622--290341 Score: 957
Period size: 115 Copynumber: 6.3 Consensus size: 115
289612 GGGCAAGTCA
*
289622 ATCTTAAGCCTTCACTGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATT
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATT
* *
289687 AAGTCCTCAGGGCAATCTTAAGCCTTCACCGAAGACG-ATTGAAGCAATCC
66 AAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGA-GTAGTGAAGCAATCC
* *
289737 ATCTTAAGCCTTCACAGAAGAGTAGTAAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATTATT
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATT
* * *
289802 AAGTCCTCCGGGCCATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAAACC
66 AAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* * * *
289852 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGTAAA-CAATC-CTAAGCCTTCACCGA--A-GA-GT
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTT--CCGAGCATGATG-
* * *
289911 AGTGAAG-CAAT-C---C-ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
63 A-TTAAGTC-CTCCGGGCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* *
289960 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGTAAATCCATCAGTAAGCCTCCCGAGCATGATGATT
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATT
*
290025 AAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAATCC
66 AAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
*
290075 ATTTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCC-TCTCGAGCATGATGAT
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTC-CGAGCATGATGAT
*
290139 TAAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGGAGTGAAGCAATCC
65 TAAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
* * * * * * *
290190 ATCTTAAGCCTTTACAGAATAGTAGTGAAGAAAATCCATCAATAAACCTTCCAAGCATGATGATG
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATT
* * * *
290255 AAGTCCTCCGGGCCATTTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCA
66 AAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGC-AATCC
* *
290306 ATCCTAAGCCTTCACCA-AAGAGTAGTGAAACAAATC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGCAAATC
290342 GATTTCGAGT
Statistics
Matches: 537, Mismatches: 46, Indels: 43
0.86 0.07 0.07
Matches are distributed among these distances:
108 72 0.13
109 5 0.01
110 13 0.02
111 5 0.01
112 6 0.01
113 14 0.03
114 7 0.01
115 379 0.71
116 34 0.06
117 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (115 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCCGAGCATGATGATT
AAGTCCTCCGGGCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAATCC
Found at i:290537 original size:17 final size:17
Alignment explanation
Indices: 290515--290551 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
290505 TTGTCCGAGA
290515 AATAAATATTATATTAT
1 AATAAATATTATATTAT
*
290532 AATAAATATTGTATTAT
1 AATAAATATTATATTAT
290549 AAT
1 AAT
290552 TATTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AATAAATATTATATTAT
Found at i:290558 original size:17 final size:16
Alignment explanation
Indices: 290521--290590 Score: 56
Period size: 16 Copynumber: 4.3 Consensus size: 16
290511 GAGAAATAAA
* *
290521 TATTATATTATAATAAA
1 TATT-TATTATAATTAT
290538 TATTGTATTATAATTAT
1 TATT-TATTATAATTAT
290555 TA-TTATTATAAATTA-
1 TATTTATTAT-AATTAT
*
290570 TAATTATTATTAA-TAT
1 TATTTATTA-TAATTAT
290586 TATTT
1 TATTT
290591 TTTTACAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
15 10 0.22
16 18 0.40
17 17 0.38
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (16 bp):
TATTTATTATAATTAT
Found at i:295008 original size:120 final size:117
Alignment explanation
Indices: 294795--295034 Score: 347
Period size: 120 Copynumber: 2.0 Consensus size: 117
294785 AGTTATTAAT
* * *
294795 TGAGGGTCTTGAGCAAAAGAAAAAAATGTTGAGGTCGAGGGAGAAATAGATAGGATTATTGGGTC
1 TGAGGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTC
** *
294860 GACAATGATGAATTGAATTGTTTTTTTTTTTTGTTAC-AAAAGTTTAAGTCAGGAG
66 GACAATGATGAATTGAA--GAGTGTTTTTTTTGTTACAAAAAG-TT-AGTCAGGAG
* **
294915 TGAGGGTCCTGAGCAGAAGATCAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTC
1 TGAGGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTC
*
294980 GACATTGATGAATTGAAGAGTGTTTTTTTTGTTACAAAAAGTTAGTCAGGAG
66 GACAATGATGAATTGAAGAGTGTTTTTTTTGTTACAAAAAGTTAGTCAGGAG
295032 TGA
1 TGA
295035 TTCTCCCAGA
Statistics
Matches: 109, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
117 12 0.11
118 17 0.16
119 5 0.05
120 75 0.69
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (117 bp):
TGAGGGTCCTGAGCAAAAGAAAAAAATGTTGAGGTCGAGAGAGAAATAGATAAGATTATTGGGTC
GACAATGATGAATTGAAGAGTGTTTTTTTTGTTACAAAAAGTTAGTCAGGAG
Found at i:297426 original size:11 final size:11
Alignment explanation
Indices: 297410--297472 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
297400 AAAATTACAT
297410 TATTAAAAATA
1 TATTAAAAATA
297421 TATTAAAAATA
1 TATTAAAAATA
* ***
297432 CATTATTGATA
1 TATTAAAAATA
297443 -ATTATAAAAT-
1 TATTA-AAAATA
297453 T-TTAAAAATA
1 TATTAAAAATA
297463 TATTAAAAAT
1 TATTAAAAAT
297473 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:297982 original size:7 final size:7
Alignment explanation
Indices: 297970--298050 Score: 83
Period size: 7 Copynumber: 11.6 Consensus size: 7
297960 ATTTGTAATG
297970 AACCCTA
1 AACCCTA
297977 AACCCTA
1 AACCCTA
*
297984 AAACCTA
1 AACCCTA
**
297991 AACTATA
1 AACCCTA
*
297998 AACTCTA
1 AACCCTA
* *
298005 AACCATG
1 AACCCTA
298012 AACCCTA
1 AACCCTA
298019 AACCCTA
1 AACCCTA
*
298026 AA-CTTA
1 AACCCTA
298032 AATCCCTA
1 AA-CCCTA
298040 AACCCTA
1 AACCCTA
298047 AACC
1 AACC
298051 AAATCCAATT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
6 5 0.08
7 50 0.83
8 5 0.08
ACGTcount: A:0.46, C:0.35, G:0.01, T:0.19
Consensus pattern (7 bp):
AACCCTA
Found at i:305103 original size:36 final size:36
Alignment explanation
Indices: 305056--305385 Score: 171
Period size: 36 Copynumber: 9.4 Consensus size: 36
305046 TTAGAAAATT
* * *
305056 TATATATTATATAATTTTTGAAAATATTTTTAAATA-
1 TATATAATATAT-ATTTTTAAAAACATTTTTAAATAC
*
305092 TATATAATATATAAGTTTTTGAAAACA--TTT--ATA-
1 TATATAATATAT-A-TTTTTAAAAACATTTTTAAATAC
* *
305125 TAT-T-ATATA-GTTTTT-AAAACA-TTTTAAAAAC
1 TATATAATATATATTTTTAAAAACATTTTTAAATAC
* * * *
305156 TTATATAATGTATAGTTTTAAAAACATTTTTTGAAAAAT
1 -TATATAATATATATTTTTAAAAACA-TTTTT-AAATAC
* * * *
305195 TATATGATATATAGTTTTAAAAAAACATTTTTGAAAAAT
1 TATATAATATATA-TTTT-TAAAAACATTTTT-AAATAC
* *
305234 TATATAATATATAGTTTTAAAAATATTTTTTTGAAA-AC
1 TATATAATATATATTTTTAAAAACA--TTTTT-AAATAC
*
305272 T-TAT-ATA-ATATTTTT-AAAACATTTTGAAA-AC
1 TATATAATATATATTTTTAAAAACATTTTTAAATAC
* * *
305303 TATATAATATATAGTTTTGAAAACTCTTTTTAAA-A-
1 TATATAATATATATTTTTAAAAAC-ATTTTTAAATAC
* * *
305338 -ATATAATATATAGTTTAAAAAATATTTTTGAAATA-
1 TATATAATATATATTTTTAAAAACATTTTT-AAATAC
*
305373 TATATATTATATA
1 TATATAATATATA
305386 GTATTATTAT
Statistics
Matches: 241, Mismatches: 28, Indels: 50
0.76 0.09 0.16
Matches are distributed among these distances:
27 6 0.02
28 8 0.03
30 2 0.01
31 11 0.05
32 11 0.05
33 15 0.06
34 39 0.16
35 20 0.08
36 41 0.17
37 20 0.08
38 20 0.08
39 41 0.17
40 7 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
TATATAATATATATTTTTAAAAACATTTTTAAATAC
Found at i:305122 original size:65 final size:62
Alignment explanation
Indices: 305045--305326 Score: 181
Period size: 65 Copynumber: 4.1 Consensus size: 62
305035 AGAAAACGAC
* * *
305045 TTTAGAAA-ATTTATATATTATATAATTTTTGAAAATATTTTTAAATA-TATATAATATATAAGT
1 TTTAAAAACATTTATATATTATATAATTTTT-AAAACA-TTTTAAAAACTATATAATATAT-AG-
305108 T
62 T
* * *
305109 TTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTAAAAACTTATATAATGTATAGT
1 TTTAAAAACATTTATATATTATATAATTTTTAAAACATTTTAAAAAC-TATATAATATATAGT
* * *
305172 TTTAAAAACATTTTTTGAAAAATTATATGATATATAGTTTTAAAAAAACATTTTTGAAAAATTAT
1 TTTAAAAACA---TTT-----A-TATAT--TATATAATTTT--TAAAACA-TTTT-AAAAACTAT
305237 ATAATATATAGT
51 ATAATATATAGT
* * * *
305249 TTTAAAAATATTTTTTTGAAAACTTATATAATATTTTTAAAACATTTTGAAAACTATATAATATA
1 TTTAAAAACA--TTTAT--ATA-TTATAT-A-ATTTTTAAAACATTTTAAAAACTATATAATATA
305314 TAGT
59 TAGT
*
305318 TTTGAAAAC
1 TTTAAAAAC
305327 TCTTTTTAAA
Statistics
Matches: 176, Mismatches: 19, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
63 18 0.10
64 13 0.07
65 32 0.18
66 3 0.02
69 26 0.15
70 5 0.03
71 12 0.07
72 8 0.05
73 5 0.03
74 11 0.06
76 11 0.06
77 27 0.15
78 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (62 bp):
TTTAAAAACATTTATATATTATATAATTTTTAAAACATTTTAAAAACTATATAATATATAGT
Found at i:305138 original size:27 final size:29
Alignment explanation
Indices: 305092--305148 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
305082 TTTTTAAATA
305092 TATATAATATATAAGTTTTTGAAAACATT
1 TATATAATATATAAGTTTTTGAAAACATT
*
305121 TATATATTATAT-AGTTTTT-AAAACATT
1 TATATAATATATAAGTTTTTGAAAACATT
305148 T
1 T
305149 TAAAAACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.33
28 7 0.26
29 11 0.41
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (29 bp):
TATATAATATATAAGTTTTTGAAAACATT
Found at i:305155 original size:38 final size:37
Alignment explanation
Indices: 305107--305387 Score: 266
Period size: 39 Copynumber: 7.7 Consensus size: 37
305097 AATATATAAG
* *
305107 TTTTTGAAAACATTTATATATTATATAGTTTTTAAAACA
1 TTTTTGAAAA-A-TTATATAATATATAGTTTTAAAAACA
*
305146 -TTTT-AAAAACTTATATAATGTATAGTTTTAAAAACA
1 TTTTTGAAAAA-TTATATAATATATAGTTTTAAAAACA
*
305182 TTTTTTGAAAAATTATATGATATATAGTTTTAAAAAAACA
1 -TTTTTGAAAAATTATATAATATATAGTTTT--AAAAACA
*
305222 TTTTTGAAAAATTATATAATATATAGTTTTAAAAATA
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
*
305259 TTTTTTTGAAAACTTATAT-A-ATAT--TTTT-AAAACA
1 --TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* *
305293 -TTTTG-AAAACTATATAATATATAGTTTTGAAAAC-
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* * *
305327 TCTTTT-TAAAA--ATATAATATATAGTTTAAAAAATA
1 T-TTTTGAAAAATTATATAATATATAGTTTTAAAAACA
* *
305362 TTTTTGAAATA-TATATATTATATAGT
1 TTTTTGAAAAATTATATAATATATAGT
305388 ATTATTATTA
Statistics
Matches: 206, Mismatches: 18, Indels: 39
0.78 0.07 0.15
Matches are distributed among these distances:
30 8 0.04
31 6 0.03
32 4 0.02
34 33 0.16
35 13 0.06
36 45 0.22
37 14 0.07
38 26 0.13
39 50 0.24
40 7 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAAATTATATAATATATAGTTTTAAAAACA
Found at i:305159 original size:29 final size:28
Alignment explanation
Indices: 305099--305162 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
305089 ATATATATAA
* *
305099 TATATAAGTTTTTGAAAACATTTATATAT
1 TATAT-AGTTTTTGAAAACATTTAAAAAT
305128 TATATAGTTTTT-AAAACATTTTAAAAACT
1 TATATAGTTTTTGAAAACA-TTTAAAAA-T
305157 TATATA
1 TATATA
305163 ATGTATAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.19
28 13 0.42
29 12 0.39
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (28 bp):
TATATAGTTTTTGAAAACATTTAAAAAT
Found at i:305414 original size:14 final size:14
Alignment explanation
Indices: 305389--305442 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
305379 TTATATAGTA
305389 TTATTATTATTTATT
1 TTATT-TTATTTATT
305404 TTATTTTATTTCATT
1 TTATTTTATTT-ATT
* *
305419 TTA-TTAATTTAAT
1 TTATTTTATTTATT
*
305432 TTAATTTATTT
1 TTATTTTATTT
305443 TGTTTTGTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 5 0.15
14 18 0.53
15 11 0.32
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTTTATTTATT
Found at i:305419 original size:15 final size:15
Alignment explanation
Indices: 305389--305424 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
305379 TTATATAGTA
305389 TTATTATTATTTATT
1 TTATTATTATTTATT
305404 TTATT-TTATTTCATT
1 TTATTATTATTT-ATT
305419 TTATTA
1 TTATTA
305425 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTATTATTTATT
Found at i:306443 original size:9 final size:9
Alignment explanation
Indices: 306429--306467 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
306419 AATTAACTTA
306429 TTTTTAATT
1 TTTTTAATT
306438 TTTTTAA-T
1 TTTTTAATT
306446 TTTTTAATT
1 TTTTTAATT
306455 TTTTTATATT
1 TTTTTA-ATT
306465 TTT
1 TTT
306468 CTTTATCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.29
9 14 0.50
10 6 0.21
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTAATT
Found at i:306448 original size:8 final size:8
Alignment explanation
Indices: 306429--306458 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
306419 AATTAACTTA
306429 TTTTTAATT
1 TTTTTAA-T
306438 TTTTTAAT
1 TTTTTAAT
306446 TTTTTAAT
1 TTTTTAAT
306454 TTTTT
1 TTTTT
306459 TATATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTAAT
Found at i:306451 original size:17 final size:18
Alignment explanation
Indices: 306429--306467 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
306419 AATTAACTTA
306429 TTTTTAATTTTTTTA-AT
1 TTTTTAATTTTTTTATAT
306446 TTTTTAATTTTTTTATAT
1 TTTTTAATTTTTTTATAT
306464 TTTT
1 TTTT
306468 CTTTATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTAATTTTTTTATAT
Found at i:306531 original size:9 final size:9
Alignment explanation
Indices: 306508--306566 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
306498 TTCAATTTCG
*
306508 TTTTTTATA
1 TTTTTTATT
*
306517 TCTTTTATT
1 TTTTTTATT
306526 TTTTTTATT
1 TTTTTTATT
306535 TATTCTCTTATT
1 T-TT-T-TTATT
306547 TTTTTTATT
1 TTTTTTATT
306556 ATTTTTTATT
1 -TTTTTTATT
306566 T
1 T
306567 AGTTGCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 22 0.51
10 12 0.28
11 3 0.07
12 6 0.14
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTATT
Found at i:306545 original size:21 final size:22
Alignment explanation
Indices: 306511--306555 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
306501 AATTTCGTTT
*
306511 TTTATATCTTTTATTTTTTTTA
1 TTTATATCTCTTATTTTTTTTA
306533 TTTAT-TCTCTTATTTTTTTTA
1 TTTATATCTCTTATTTTTTTTA
306554 TT
1 TT
306556 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTATATCTCTTATTTTTTTTA
Found at i:311123 original size:165 final size:165
Alignment explanation
Indices: 310794--311764 Score: 1008
Period size: 165 Copynumber: 5.8 Consensus size: 165
310784 AAACTTACAA
* * *
310794 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTG---CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
310859 CAAGGCATATCATTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACC-AAAGACCTTC
63 CAAGGCACATCA-TTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAAGACCTTC
*
310923 GAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAG
126 GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
* * * * * *
310963 CATAGCTTAAGTCGAGAAGGGCTATCTGCC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGA
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCA
* ** * * * *
311027 GGGCACATCATTTACAGCATAACTCCAGGCTAGCAGGGTTATCTGTCACCAAAAGACCTTCGAGT
65 AGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGT
* * * * *
311092 TTGACTACGCTCATCTCCGAGGCATATCATTTGCAA
130 TCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
* * **
311128 CATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAACGACCTTCGAGTTCCACTACGCTCTTCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAA--AA-GACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
311193 CAAGGCACATCATTTACATCATAGCTTAAGTCAAGAAGGGATATCTG---CCAAAA-ACCTTCGA
63 CAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAAGACCTTCGA
* ** * * *
311254 GTTCGATTACATTCAGCTTCGAGGGCACATCATTTACAG
128 GTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAG
* * * * * *
311293 CATAACTCAAGGCTAGAAGGGTTGTTTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTG---CCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
311358 CAAGGCACATCATTTACAACATAACTTAAGTCGATAAGGGTTATCTGCCAACC-AAAGACCTTCG
63 CAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAAGACCTTCG
* *
311422 AGTTCGACTACGTTCAACTCCAAGGCACCATCATTTGCAG
127 AGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAG
* * * ** * * * *
311462 CATAGCTTAAAGTCGAGAAGGGCTATCTGTC-AAAGACCCGCGAGTTGGATTACACTCAGCTTCG
1 CATAACTT-AAGTCGAGAAGGGTTATCTGCCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCC
* * * * * *
311526 AGGGTACATCATTTACAGCATAACTGAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAG
64 AAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAAGACCTTCGAG
* *
311591 TTCAACTACGCTCAGCTCTAAGGCACATCATTTGCAG
129 TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
* * *
311628 TATAACTTAAGTCGAGAAGGGTTATCTGTCAACCGAAGACCTTCAAGTTCGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGCCAA---AAGACCTTCGAGTTCGACTACGCTCAGCTC
* * * *
311693 CAAGGCACATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AACGAAGACCTGT
63 CAAGGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAA--AAGACCT-T
311756 CGAGTTCGA
125 CGAGTTCGA
311765 TTTCATTCTG
Statistics
Matches: 653, Mismatches: 123, Indels: 52
0.79 0.15 0.06
Matches are distributed among these distances:
164 23 0.04
165 256 0.39
166 64 0.10
167 77 0.12
168 103 0.16
169 115 0.18
170 15 0.02
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (165 bp):
CATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA
GGCACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAAGACCTTCGAGTT
CGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
Found at i:311134 original size:84 final size:83
Alignment explanation
Indices: 310794--311764 Score: 1017
Period size: 84 Copynumber: 11.6 Consensus size: 83
310784 AAACTTACAA
* * *
310794 CATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
310859 CAAGGCATATCATTTTGCAG
65 CAAGGCACATCA-TTTGCAG
** *
310879 CATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
310944 CAAGGCACATCATTTGCAG
65 CAAGGCACATCATTTGCAG
* * * * *
310963 CATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TC
* * *
311025 GAGGGCACATCATTTACAG
65 CAAGGCACATCATTTGCAG
** * * * * *
311044 CATAACTCCAGGCTAGCAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCATCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
* * *
311109 CGAGGCATATCATTTGCAA
65 CAAGGCACATCATTTGCAG
* * **
311128 CATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAACGACCTTCGAGTTCCACTACGCTCTTCT
1 CATAACTTAAGTCGAGAAGGGTTATCTGT-C-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
* *
311192 CCAAGGCACATCATTTACAT
64 CCAAGGCACATCATTTGCAG
* * * * * **
311212 CATAGCTTAAGTCAAGAAGGGATATCTG---CCAAAAACCTTCGAGTTCGATTACATTCAGCTTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TC
* * *
311274 GAGGGCACATCATTTACAG
65 CAAGGCACATCATTTGCAG
* * * * * *
311293 CATAACTCAAGGCTAGAAGGGTTGTTTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
* *
311358 CAAGGCACATCATTTACAA
65 CAAGGCACATCATTTGCAG
* * * *
311377 CATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGTTCAACTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
311442 CAAGGCACCATCATTTGCAG
65 CAAGGCA-CATCATTTGCAG
* * ** * * *
311462 CATAGCTTAAAGTCGAGAAGGGCTATCTGT---CAAAGACCCGCGAGTTGGATTACACTCAGCTT
1 CATAACTT-AAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC-T
* * * *
311524 CGAGGGTACATCATTTACAG
64 CCAAGGCACATCATTTGCAG
* * * *
311544 CATAACTGAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
311609 TAAGGCACATCATTTGCAG
65 CAAGGCACATCATTTGCAG
* * *
311628 TATAACTTAAGTCGAGAAGGGTTATCTGTCAACCGAAGACCTTCAAGTTCGACTACGCTCAGCTC
1 CATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTC
*
311693 CAAGGCACATCATTTGCAT
65 CAAGGCACATCATTTGCAG
* * * * *
311712 CATAGCTTAAGTCGAGAAGGGCTATCTGCCAAACGAAGACCTGTCGAGTTCGA
1 CATAACTTAAGTCGAGAAGGGTTATCTGTC-ACCAAAGACCT-TCGAGTTCGA
311765 TTTCATTCTG
Statistics
Matches: 728, Mismatches: 134, Indels: 48
0.80 0.15 0.05
Matches are distributed among these distances:
80 50 0.07
81 96 0.13
82 40 0.05
83 7 0.01
84 342 0.47
85 172 0.24
86 21 0.03
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
CATAACTTAAGTCGAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCC
AAGGCACATCATTTGCAG
Found at i:311240 original size:249 final size:249
Alignment explanation
Indices: 310788--311744 Score: 1493
Period size: 249 Copynumber: 3.8 Consensus size: 249
310778 TTAATAAAAC
*
310788 TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
1 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* * *
310853 CAGCTCCAAGGCATATCATTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGA
66 CAGCTCCAAGGCACATCA-TTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGA
*
310918 CCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
130 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
310983 GCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
195 GCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * *
311038 TTACAGCATAACTCCAGGCTAGCAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCT
1 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* * * *
311103 CATCTCCGAGGCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAACGAC
66 CAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGAC
* ** * * *
311168 CTTCGAGTTCCACTACGCTCTTCTCCAAGGCACATCATTTACATCATAGCTTAAGTCAAGAAGGG
131 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
* * * *
311233 ATATCTGCCAAAAACCTTCGAGTTCGATTACATTCAGCTTCGAGGGCACATCAT
196 CTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * *
311287 TTACAGCATAACTCAAGGCTAGAAGGGTTGTTTGTCACCAAAAGACCTTCGAGTTTGACTACGCT
1 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* * *
311352 CAGCTCCAAGGCACATCATTTACAACATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAAGAC
66 CAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGAC
* *
311417 CTTCGAGTTCGACTACGTTCAACTCCAAGGCACCATCATTTGCAGCATAGCTTAAAGTCGAGAAG
131 CTTCGAGTTCGACTACGCTCAGCTCCAAGGCA-CATCATTTGCAGCATAGCTT-AAGTCGAGAAG
* * * *
311482 GGCTATCTGTCAAAGACCCGCGAGTTGGATTACACTCAGCTTCGAGGGTACATCAT
194 GGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* *
311538 TTACAGCATAACTGAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCT
1 TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* ** *
311603 CAGCTCTAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGT-CAACCGAAGA
66 CAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCT-TCCAACCAAAGA
* *
311667 CCTTCAAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCATCATAGCTTAAGTCGAGAAGG
130 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
311732 GCTATCTGCCAAA
195 GCTATCTGCCAAA
311745 CGAAGACCTG
Statistics
Matches: 641, Mismatches: 63, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
249 323 0.50
250 114 0.18
251 204 0.32
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (249 bp):
TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGAC
CTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
CTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
Found at i:311740 original size:500 final size:502
Alignment explanation
Indices: 310788--311780 Score: 1559
Period size: 500 Copynumber: 2.0 Consensus size: 502
310778 TTAATAAAAC
310788 TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
1 TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* * *
310853 CAGCTCCAAGGCATATCATTTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGA
66 CAGCTCCAAGGCACATCATTTTACAACATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGA
* *
310918 CCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
131 CCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
*
310983 GCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATA
196 GCTATCTGCCAAAGACCCGCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATA
* * ** * *
311048 ACTCCAGGCTAGCAGGGTTATCTGTCACCAAAAGACCTTCGAGTTTGACTACGCTCATCTCCGAG
261 ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAG
* *
311113 GCATATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAACGACCTTCGAGTTC
326 GCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAACGACCTTCAAGTTC
**
311178 CACTACGCTCTTCTCCAAGGCACATCATTTACATCATAGCTTAAGTCAAGAAGGGATATCTGCC-
391 CACTACGCTCAGCTCCAAGGCACATCATTTACATCATAGCTTAAGTCAAGAAGGGATATCTGCCA
311242 AA-AA-ACCT-TCGAGTTCGATTACATTCAGCTTCGAGGGCACATCAT
456 AACAAGACCTGTCGAGTTCGATTACATTCAGC-TCGAGGGCACATCAT
* * * *
311287 TTACAGCATAACTCAAGGCTAGAAGGGTTGTTTGTCACCAAAAGACCTTCGAGTTTGACTACGCT
1 TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
* *
311352 CAGCTCCAAGGCACATCA-TTTACAACATAACTTAAGTCGATAAGGGTTATCTGCCAACCAAAGA
66 CAGCTCCAAGGCACATCATTTTACAACATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGA
*
311416 CCTTCGAGTTCGACTACGTTCAACTCCAAGGCACCATCATTTGCAGCATAGCTTAAAGTCGAGAA
131 CCTTCGAGTTCGACTACGCTCAACTCCAAGGCA-CATCATTTGCAGCATAGCTT-AAGTCGAGAA
* * *
311481 GGGCTATCTGTCAAAGACCCGCGAGTTGGATTACACTCAGCTTCGAGGGTACATCATTTACAGCA
194 GGGCTATCTGCCAAAGACCCGCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCA
* *
311546 TAACTGAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCTA
259 TAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCA
**
311611 AGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTGT-CAACCGAA-GACCTTCAA
324 AGGCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCT-TCCAACC-AACGACCTTCAA
* * * *
311674 GTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCATCATAGCTTAAGTCGAGAAGGGCTATCT
387 GTTCCACTACGCTCAGCTCCAAGGCACATCATTTACATCATAGCTTAAGTCAAGAAGGGATATCT
* *
311739 GCCAAACGAAGACCTGTCGAGTTCGATTTCATTCTGCTCGAG
452 GCCAAAC-AAGACCTGTCGAGTTCGATTACATTCAGCTCGAG
311781 ATGGACTCGA
Statistics
Matches: 449, Mismatches: 36, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
498 72 0.16
499 98 0.22
500 244 0.54
501 5 0.01
503 2 0.00
504 9 0.02
505 19 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (502 bp):
TTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCT
CAGCTCCAAGGCACATCATTTTACAACATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGA
CCTTCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGG
GCTATCTGCCAAAGACCCGCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATA
ACTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAG
GCACATCATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAACGACCTTCAAGTTC
CACTACGCTCAGCTCCAAGGCACATCATTTACATCATAGCTTAAGTCAAGAAGGGATATCTGCCA
AACAAGACCTGTCGAGTTCGATTACATTCAGCTCGAGGGCACATCAT
Found at i:312177 original size:66 final size:64
Alignment explanation
Indices: 312102--312224 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 64
312092 ACTTTCGAAA
* *
312102 ATTTATATATTATATAGTTTTTGAAAATATTTTTAAAA-TATATATAATATATAAGTTTTTGAAA
1 ATTTATATATTATATAGTTTTT-AAAACATTTTAAAAACT-TATATAATATAT-AGTTTTTGAAA
312166 AC
63 AC
*
312168 ATTTATATATTATATAGTTTTTAAAACATTTTAAAAACTTATATAATGTATAGTTTT
1 ATTTATATATTATATAGTTTTTAAAACATTTTAAAAACTTATATAATATATAGTTTT
312225 AAAAATATTT
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
64 6 0.11
65 24 0.45
66 23 0.43
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (64 bp):
ATTTATATATTATATAGTTTTTAAAACATTTTAAAAACTTATATAATATATAGTTTTTGAAAAC
Found at i:312182 original size:38 final size:37
Alignment explanation
Indices: 312066--312310 Score: 110
Period size: 38 Copynumber: 6.8 Consensus size: 37
312056 TTTTAACAAA
* * ** *
312066 ATATAATATATAATTTTCAGAAAACGACTTTCGAAAATTT
1 ATATAATATATAGTTTT-TGAAAAC-A-TTTATAAAATAT
* * *
312106 ATATATTATATAGTTTTTGAAAATATTTTTAAAATAT
1 ATATAATATATAGTTTTTGAAAACATTTATAAAATAT
312143 ATATAATATATAAGTTTTTGAAAACA--T-T----TAT
1 ATATAATATAT-AGTTTTTGAAAACATTTATAAAATAT
312174 ATAT--TATATAGTTTTT-AAAACATTT-TAAAA-ACTT
1 ATATAATATATAGTTTTTGAAAACATTTATAAAATA--T
* * * *
312208 ATATAATGTATAG-TTTTAAAAATATTTTTTGAAAA-ATT
1 ATATAATATATAGTTTTTGAAAACA-TTTAT-AAAATA-T
* ***
312246 ATATGATATATAGTTTAAAAAAAACATTT-TGAAAA-ATT
1 ATATAATATATAGTTT-TTGAAAACATTTAT-AAAATA-T
*
312284 ATATAATATATAG-TTTTAAAAACATTT
1 ATATAATATATAGTTTTTGAAAACATTT
312311 TTTGAAAACT
Statistics
Matches: 169, Mismatches: 19, Indels: 38
0.75 0.08 0.17
Matches are distributed among these distances:
27 6 0.04
28 7 0.04
29 7 0.04
31 7 0.04
32 1 0.01
34 5 0.03
35 5 0.03
36 22 0.13
37 24 0.14
38 49 0.29
39 15 0.09
40 21 0.12
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (37 bp):
ATATAATATATAGTTTTTGAAAACATTTATAAAATAT
Found at i:312189 original size:29 final size:28
Alignment explanation
Indices: 312142--312198 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
312132 TTTTAAAATA
312142 TATATAATATATAAGTTTTTGAAAACATT
1 TATATAATATATAAGTTTTT-AAAACATT
*
312171 TATATATTATAT-AGTTTTTAAAACATT
1 TATATAATATATAAGTTTTTAAAACATT
312198 T
1 T
312199 TAAAAACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 9 0.33
28 7 0.26
29 11 0.41
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (28 bp):
TATATAATATATAAGTTTTTAAAACATT
Found at i:312209 original size:29 final size:28
Alignment explanation
Indices: 312149--312212 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
312139 ATATATATAA
* *
312149 TATATAAGTTTTTGAAAACATTTATATAT
1 TATAT-AGTTTTTGAAAACATTTAAAAAT
312178 TATATAGTTTTT-AAAACATTTTAAAAACT
1 TATATAGTTTTTGAAAACA-TTTAAAAA-T
312207 TATATA
1 TATATA
312213 ATGTATAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 6 0.19
28 13 0.42
29 12 0.39
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (28 bp):
TATATAGTTTTTGAAAACATTTAAAAAT
Found at i:312239 original size:76 final size:74
Alignment explanation
Indices: 312157--312401 Score: 273
Period size: 76 Copynumber: 3.4 Consensus size: 74
312147 AATATATAAG
*
312157 TTTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTAAAAACTTATATAATGTATAGT
1 TTTTTGAAAACA-TTATATA-TATATAGTTTTTAAAACATTTTAAAAACTTATATAATATATAGT
*
312222 TTTAAAAATAT
64 TTTAAAAACAT
**
312233 TTTTTGAAAA-ATTATATGATATATAGTTTAAAAAAAACATTTTGAAAAA-TTATATAATATATA
1 TTTTTGAAAACATTATAT-ATATATAGTTT--TTAAAACATTTT-AAAAACTTATATAATATATA
312296 GTTTTAAAAACAT
62 GTTTTAAAAACAT
* *
312309 TTTTTGAAAAC--T-TATATA-ATA-TTTTTAAAACATTTTGAAAAC-TATATAATATATAATTT
1 TTTTTGAAAACATTATATATATATAGTTTTTAAAACATTTTAAAAACTTATATAATATATAGTTT
312368 TAAAAAC-T
66 TAAAAACAT
*
312376 CTTTTT-AAAA-A-TATA-CTATATAGTTT
1 -TTTTTGAAAACATTATATATATATAGTTT
312402 AAAAAATATT
Statistics
Matches: 149, Mismatches: 9, Indels: 29
0.80 0.05 0.16
Matches are distributed among these distances:
67 8 0.05
68 37 0.25
69 13 0.09
71 3 0.02
72 3 0.02
73 3 0.02
74 19 0.13
75 3 0.02
76 55 0.37
77 5 0.03
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (74 bp):
TTTTTGAAAACATTATATATATATAGTTTTTAAAACATTTTAAAAACTTATATAATATATAGTTT
TAAAAACAT
Found at i:312314 original size:38 final size:38
Alignment explanation
Indices: 312157--312435 Score: 245
Period size: 38 Copynumber: 7.7 Consensus size: 38
312147 AATATATAAG
* *
312157 TTTTTGAAAACATTTATATATTATATAGTTTTTAAAACA-
1 TTTTTGAAAA-A-TTATATAATATATAGTTTTAAAAACAT
* *
312196 -TTTT-AAAAACTTATATAATGTATAGTTTTAAAAATAT
1 TTTTTGAAAAA-TTATATAATATATAGTTTTAAAAACAT
* * * *
312233 TTTTTGAAAAATTATATGATATATAGTTTAAAAAAAAC
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
*
312271 ATTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
*
312309 TTTTTGAAAACTTATAT-A-ATAT--TTTT-AAAACA-
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
* *
312341 -TTTTG-AAAACTATATAATATATAATTTTAAAAAC-T
1 TTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
*
312376 CTTTTT--AAAA--ATATACTATATAG-TTTAAAAA-AT
1 -TTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
* *
312409 ATTTTTGAAATA-TATATATTATATAGT
1 -TTTTTGAAAAATTATATAATATATAGT
312436 ATTATTATTA
Statistics
Matches: 200, Mismatches: 24, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
30 8 0.04
31 6 0.03
32 4 0.02
33 20 0.10
34 19 0.09
35 8 0.04
36 43 0.22
37 9 0.05
38 78 0.39
39 5 0.03
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
TTTTTGAAAAATTATATAATATATAGTTTTAAAAACAT
Found at i:312390 original size:34 final size:34
Alignment explanation
Indices: 312172--312427 Score: 111
Period size: 36 Copynumber: 7.3 Consensus size: 34
312162 GAAAACATTT
* * * *
312172 ATATATTATATAGTTTTTAAAAC-ATTTTAAAAA
1 ATATAATATATAATTTTAAAAACTATTTTTAAAA
* *
312205 CTTATATAATGTATAGTTTTAAAAA-TATTTTTTGAAAA
1 ---ATATAATATATAATTTTAAAAACTA-TTTTT-AAAA
* * *
312243 ATTATATGATATATAGTTTAAAAAAAAC-ATTTTGAAAAA
1 A-TATA--ATATATAATTT--TAAAAACTATTTT-TAAAA
*
312282 TTATATAATATATAGTTTTAAAAAC-ATTTTTTGAAAA
1 --ATATAATATATAATTTTAAAAACTA-TTTTT-AAAA
* * *
312319 CT-T-ATATA-ATATTTTTAAAAC-ATTTTGAAAA
1 ATATAATATATA-ATTTTAAAAACTATTTTTAAAA
*
312350 CTATATAATATATAATTTTAAAAACTCTTTTTAAAA
1 --ATATAATATATAATTTTAAAAACTATTTTTAAAA
* * * *
312386 ATATACTATAT-AGTTTAAAAAATATTTTT-GAA
1 ATATAATATATAATTTTAAAAACTATTTTTAAAA
312418 ATAT-ATATAT
1 ATATAATATAT
312428 TATATAGTAT
Statistics
Matches: 176, Mismatches: 23, Indels: 47
0.72 0.09 0.19
Matches are distributed among these distances:
31 9 0.05
32 11 0.06
33 31 0.18
34 12 0.07
35 17 0.10
36 40 0.23
37 12 0.07
38 25 0.14
39 8 0.05
40 10 0.06
41 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (34 bp):
ATATAATATATAATTTTAAAAACTATTTTTAAAA
Found at i:312467 original size:15 final size:15
Alignment explanation
Indices: 312437--312469 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
312427 TTATATAGTA
312437 TTATTATTATTTATT
1 TTATTATTATTTATT
312452 TTATT-TTATTTCATT
1 TTATTATTATTT-ATT
312467 TTA
1 TTA
312470 CTAATTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATTATTTATT
Found at i:313541 original size:10 final size:10
Alignment explanation
Indices: 313526--313559 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
313516 AATTAACTTC
313526 TTTTTTT-TA
1 TTTTTTTATA
313535 TTTTTTTATA
1 TTTTTTTATA
*
313545 TGTTTTTATA
1 TTTTTTTATA
313555 TTTTT
1 TTTTT
313560 CTTTATCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:313618 original size:21 final size:21
Alignment explanation
Indices: 313594--313639 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
313584 TTATTATTCA
313594 ATTTCGTTT-TTTATATCTCTT
1 ATTTCGTTTATTTAT-TCTCTT
**
313615 ATTTTTTTTATTTATTCTCTT
1 ATTTCGTTTATTTATTCTCTT
313636 ATTT
1 ATTT
313640 TTTTATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (21 bp):
ATTTCGTTTATTTATTCTCTT
Found at i:313640 original size:21 final size:21
Alignment explanation
Indices: 313603--313669 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
313593 AATTTCGTTT
313603 TTTATATCTCTTATTTTTTTTA
1 TTTAT-TCTCTTATTTTTTTTA
313625 TTTATTCTCTTA-TTTTTTTA
1 TTTATTCTCTTATTTTTTTTA
* * *
313645 -TTATTTTTTTATTAATTTTTA
1 TTTATTCTCTTATT-TTTTTTA
313666 TTTA
1 TTTA
313670 GTTGCTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 9 0.23
20 9 0.23
21 13 0.33
22 8 0.21
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTATTCTCTTATTTTTTTTA
Found at i:313649 original size:19 final size:20
Alignment explanation
Indices: 313600--313649 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
313590 TTCAATTTCG
313600 TTTTTTA-TA-TCTCTTATT
1 TTTTTTATTATTCTCTTATT
313618 TTTTTTATTTATTCTCTTA-T
1 TTTTTTA-TTATTCTCTTATT
313638 TTTTTTATTATT
1 TTTTTTATTATT
313650 TTTTTATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.24
19 5 0.17
20 10 0.34
21 7 0.24
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTATTATTCTCTTATT
Found at i:313650 original size:11 final size:11
Alignment explanation
Indices: 313616--313664 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
313606 ATATCTCTTA
313616 TTTTTT-TTAT
1 TTTTTTATTAT
* *
313626 TTATTCTCTTAT
1 TT-TTTTATTAT
313638 TTTTTTATTAT
1 TTTTTTATTAT
313649 TTTTTTATTAAT
1 TTTTTTATT-AT
313661 TTTT
1 TTTT
313665 ATTTAGTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 2 0.06
11 19 0.58
12 12 0.36
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:314573 original size:16 final size:16
Alignment explanation
Indices: 314552--314584 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
314542 GCTCCTGAAA
*
314552 TTTTTTGGAGTTCGAG
1 TTTTTTCGAGTTCGAG
314568 TTTTTTCGAGTTCGAG
1 TTTTTTCGAGTTCGAG
314584 T
1 T
314585 CGAGTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.27, T:0.52
Consensus pattern (16 bp):
TTTTTTCGAGTTCGAG
Found at i:314606 original size:31 final size:30
Alignment explanation
Indices: 314571--314630 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
314561 GTTCGAGTTT
*
314571 TTTCGAGTTCGAGTCGAGTTTCAATAATATA
1 TTTCGAGTTCGAGTCGAGCTTC-ATAATATA
*
314602 TTTCGAGTTCGAGTTGAGCTTCATAATAT
1 TTTCGAGTTCGAGTCGAGCTTCATAATAT
314631 TTATCTCGCG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (30 bp):
TTTCGAGTTCGAGTCGAGCTTCATAATATA
Found at i:316467 original size:41 final size:40
Alignment explanation
Indices: 316380--316473 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 40
316370 CCTACAAAAG
*
316380 CGCAACGCGA-TCTTAAATTCGCAACGCGAACTCCAAATT
1 CGCAACGCGATTTTTAAATTCGCAACGCGAACTCCAAATT
* * *
316419 TGTAACGCGATTTTTCAAATTCGCAACGCG-ATTCCCAGAA-T
1 CGCAACGCGATTTTT-AAATTCGCAACGCGAACT-CCA-AATT
316460 CGCAACGCGATTTT
1 CGCAACGCGATTTT
316474 AAAAGCGCGT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
39 8 0.18
40 5 0.11
41 30 0.67
42 2 0.04
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (40 bp):
CGCAACGCGATTTTTAAATTCGCAACGCGAACTCCAAATT
Found at i:316650 original size:22 final size:22
Alignment explanation
Indices: 316625--316675 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
316615 TCACTCTCTA
*
316625 CGGCGACATCCGTCCCCATCTC
1 CGGCGACATCCGTCCCCATATC
316647 CGGCGACATCCGTCCCCATATC
1 CGGCGACATCCGTCCCCATATC
316669 CGGCGAC
1 CGGCGAC
316676 CCCCCTCTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.47, G:0.22, T:0.16
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATATC
Found at i:317033 original size:14 final size:14
Alignment explanation
Indices: 317014--317040 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
317004 AACGCGAAAT
317014 GAAAATCGCAACGA
1 GAAAATCGCAACGA
317028 GAAAATCGCAACG
1 GAAAATCGCAACG
317041 CAATTTTAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.22, T:0.07
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:317062 original size:19 final size:20
Alignment explanation
Indices: 317040--317080 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
317030 AAATCGCAAC
317040 GCAATTTT-AGTTTCGCGTT
1 GCAATTTTCAGTTTCGCGTT
*
317059 GCAATTTTCATTTTCGCGTT
1 GCAATTTTCAGTTTCGCGTT
317079 GC
1 GC
317081 GATTCTCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.46
Consensus pattern (20 bp):
GCAATTTTCAGTTTCGCGTT
Found at i:317746 original size:29 final size:29
Alignment explanation
Indices: 317725--318019 Score: 473
Period size: 29 Copynumber: 10.1 Consensus size: 29
317715 TGCCTAATAG
*
317725 GTAATTATTTTTAAAAGGGTGCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
317754 GTAATTAATTTTAAAAGGGTGCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
* * *
317783 ATAATTATTTTTAAAATGGTGCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
*
317812 GTAATTAATTTTAAAATGGTGCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
317841 GTAATTAATTTTAAAAGGGTGCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
* *
317870 GTAATTATTTTTAAAAGGGTGCTATTTTT
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
317899 GTAATTAATTTTAAAAGGGTGCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
* *
317928 TTAATTAATTTTAAAAGGGTTCTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
*
317957 GTAATTAATTTTAAAAGGGTGTTATTTTC
1 GTAATTAATTTTAAAAGGGTGCTATTTTC
* *
317986 GTAATTAATTTTAGAAAGGGTGATAGTTTC
1 GTAATTAATTTTA-AAAGGGTGCTATTTTC
318016 GTAA
1 GTAA
318020 AAGTTGATTG
Statistics
Matches: 247, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
29 229 0.93
30 18 0.07
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (29 bp):
GTAATTAATTTTAAAAGGGTGCTATTTTC
Found at i:318394 original size:11 final size:11
Alignment explanation
Indices: 318378--318405 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
318368 TTTATAAACA
318378 ATGACTGATAT
1 ATGACTGATAT
318389 ATGACTGATAT
1 ATGACTGATAT
318400 ATGACT
1 ATGACT
318406 ATTGATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (11 bp):
ATGACTGATAT
Found at i:322520 original size:12 final size:12
Alignment explanation
Indices: 322503--322527 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
322493 TTACATTTTC
322503 ACTGATCATAAG
1 ACTGATCATAAG
322515 ACTGATCATAAG
1 ACTGATCATAAG
322527 A
1 A
322528 GCTTAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGATCATAAG
Found at i:324621 original size:37 final size:37
Alignment explanation
Indices: 324565--324690 Score: 116
Period size: 37 Copynumber: 3.3 Consensus size: 37
324555 AAAAGTTGAT
*
324565 TTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGC
1 TTGTTTAATTGATGTGGAAATAAGAATTATTTTTTGC
* *
324602 TTGTTTAATTGATTTGG-AA-AAG--TTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATGTGGAAATAAGAATT-ATTT-T-----TTG-C
*
324643 TTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGC
1 TTGTTTAATTGATGTGGAAATAAGAATTATTTTTTGC
324680 TTGTTTAATTG
1 TTGTTTAATTG
324691 CTTGATTTGT
Statistics
Matches: 71, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
33 2 0.03
34 4 0.06
35 4 0.06
36 2 0.03
37 26 0.37
38 3 0.04
40 3 0.04
41 15 0.21
42 2 0.03
43 4 0.06
44 4 0.06
45 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.19, T:0.49
Consensus pattern (37 bp):
TTGTTTAATTGATGTGGAAATAAGAATTATTTTTTGC
Found at i:324638 original size:78 final size:79
Alignment explanation
Indices: 324546--324714 Score: 277
Period size: 78 Copynumber: 2.1 Consensus size: 79
324536 GCTTGTTTAA
324546 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA-
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAAT
324610 TTGATTTGGAAAAG
66 TTGATTTGGAAAAG
* *
324624 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAGAATTATTTTTTGCTTGTTTAAT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAA-
*
324689 TGCTTGATTTGTAAAAG
65 T--TTGATTTGGAAAAG
324706 TTGATTTGT
1 TTGATTTGT
324715 TGTTTAATCT
Statistics
Matches: 84, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
78 62 0.74
82 22 0.26
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.49
Consensus pattern (79 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAAT
TTGATTTGGAAAAG
Found at i:324646 original size:14 final size:14
Alignment explanation
Indices: 324610--324646 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
324600 GCTTGTTTAA
*
324610 TTGATTTGGAAAAG
1 TTGATTTGTAAAAG
324624 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
324638 TTGATTTGT
1 TTGATTTGT
324647 TTAATTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:324789 original size:20 final size:20
Alignment explanation
Indices: 324760--324969 Score: 200
Period size: 20 Copynumber: 10.8 Consensus size: 20
324750 TTGCGATTTT
324760 CGCG-TAGTCAAATTCGCAA
1 CGCGATAGTCAAATTCGCAA
324779 CGCGATAGTCAAATTCGCAA
1 CGCGATAGTCAAATTCGCAA
**
324799 CGCGATAGTCAAATTCGCGT
1 CGCGATAGTCAAATTCGCAA
* *
324819 TGCGATAGTCAAATTCACAA
1 CGCGATAGTCAAATTCGCAA
* **
324839 CGCGAAAGTCAAATTCGCCT
1 CGCGATAGTCAAATTCGCAA
* * **
324859 TGCGAT--T----TTTGCGT
1 CGCGATAGTCAAATTCGCAA
*
324873 TGCGATAGTCAAATTCGCAA
1 CGCGATAGTCAAATTCGCAA
* *
324893 CACGATAGTCAAATTCGTAA
1 CGCGATAGTCAAATTCGCAA
*
324913 CGCGATAGTCAAATTTGCAA
1 CGCGATAGTCAAATTCGCAA
*
324933 CGCGATAGTCAAATTTGCAA
1 CGCGATAGTCAAATTCGCAA
** *
324953 CGTAAAAGTCAAATTCG
1 CGCGATAGTCAAATTCG
324970 TTGCGAATTC
Statistics
Matches: 156, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.07
16 1 0.01
18 1 0.01
19 4 0.03
20 139 0.89
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (20 bp):
CGCGATAGTCAAATTCGCAA
Found at i:324903 original size:54 final size:56
Alignment explanation
Indices: 324764--324919 Score: 190
Period size: 54 Copynumber: 2.8 Consensus size: 56
324754 GATTTTCGCG
324764 TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCGTTGCGA
1 TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATA-T---ATTCGCGTTGCGA
* * *** *
324824 TAGTCAAATTCACAACGCGAAAGTCAAATTCGCCTTGCGAT-T-TTTGCGTTGCGA
1 TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATATATTCGCGTTGCGA
* *
324878 TAGTCAAATTCGCAACACGATAGTCAAATTCGTAACGCGATA
1 TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATA
324920 GTCAAATTTG
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
54 45 0.55
58 1 0.01
60 36 0.44
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (56 bp):
TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATATATTCGCGTTGCGA
Found at i:324938 original size:74 final size:74
Alignment explanation
Indices: 324800--324938 Score: 179
Period size: 74 Copynumber: 1.9 Consensus size: 74
324790 AATTCGCAAC
**** ***
324800 GCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCACAACGCGAAAGTCAAATTCGCCTTGCGAT
1 GCGATAGTCAAATTCGCAACACGATAGTCAAATTCACAACGCGAAAGTCAAATTCGCAACGCGAT
324865 TTTTGCGTT
66 TTTTGCGTT
** * *
324874 GCGATAGTCAAATTCGCAACACGATAGTCAAATTCGTAACGCGATAGTCAAATTTGCAACGCGAT
1 GCGATAGTCAAATTCGCAACACGATAGTCAAATTCACAACGCGAAAGTCAAATTCGCAACGCGAT
324939 AGTCAAATTT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
74 54 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.27
Consensus pattern (74 bp):
GCGATAGTCAAATTCGCAACACGATAGTCAAATTCACAACGCGAAAGTCAAATTCGCAACGCGAT
TTTTGCGTT
Found at i:324938 original size:114 final size:114
Alignment explanation
Indices: 324764--324969 Score: 322
Period size: 114 Copynumber: 1.8 Consensus size: 114
324754 GATTTTCGCG
* ***
324764 TAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCGTTGCGATAGTC
1 TAGTCAAATTCGCAACACGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTC
*
324829 AAATTCACAACGCGAAAGTCAAATTCGCCTTGCGATTTTTGCGTTGCGA
66 AAATTCACAACGCAAAAGTCAAATTCGCCTTGCGATTTTTGCGTTGCGA
* *
324878 TAGTCAAATTCGCAACACGATAGTCAAATTCGTAACGCGATAGTCAAATTTGCAACGCGATAGTC
1 TAGTCAAATTCGCAACACGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTC
** *
324943 AAATTTGCAACGTAAAAGTCAAATTCG
66 AAATTCACAACGCAAAAGTCAAATTCG
324970 TTGCGAATTC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 82 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (114 bp):
TAGTCAAATTCGCAACACGATAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACGCGATAGTC
AAATTCACAACGCAAAAGTCAAATTCGCCTTGCGATTTTTGCGTTGCGA
Found at i:328306 original size:14 final size:16
Alignment explanation
Indices: 328271--328307 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
328261 GAAATCATTG
328271 AAAATTATATAGAAAT
1 AAAATTATATAGAAAT
*
328287 AAAATTATGTA-AAA-
1 AAAATTATATAGAAAT
328301 AAAATTA
1 AAAATTA
328308 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 3 0.15
16 10 0.50
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTATATAGAAAT
Found at i:328499 original size:20 final size:20
Alignment explanation
Indices: 328440--328500 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
328430 TACCCAAAAC
*
328440 ATTCGTGTTGCGAATTCGAAA
1 ATTCGTGTTGCAAATTC-AAA
* * *
328461 A-TCGAGTTGTGAAA-ACAAA
1 ATTCGTGTTG-CAAATTCAAA
328480 ATTCGTGTTGCAAATTCAAA
1 ATTCGTGTTGCAAATTCAAA
328500 A
1 A
328501 ATCGAATTGC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 7 0.23
20 20 0.67
21 3 0.10
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.30
Consensus pattern (20 bp):
ATTCGTGTTGCAAATTCAAA
Found at i:328522 original size:40 final size:40
Alignment explanation
Indices: 328440--328536 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
328430 TACCCAAAAC
* * *
328440 ATTCGTGTTGCGAATTCGAAAATCGAGTTGTGAAAACAAA
1 ATTCGTGTTGCGAATTCAAAAATCGAATTGCGAAAACAAA
* ****
328480 ATTCGTGTTGCAAATTCAAAAATCGAATTGCGAATTTGAA
1 ATTCGTGTTGCGAATTCAAAAATCGAATTGCGAAAACAAA
328520 ATTCAGTGTTGCGAATT
1 ATTC-GTGTTGCGAATT
328537 TGGTAATCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 36 0.77
41 11 0.23
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (40 bp):
ATTCGTGTTGCGAATTCAAAAATCGAATTGCGAAAACAAA
Found at i:328566 original size:20 final size:20
Alignment explanation
Indices: 328550--328666 Score: 144
Period size: 20 Copynumber: 5.8 Consensus size: 20
328540 TAATCGCGTT
*
328550 GCGATTTACACATTCGCAAC
1 GCGATTTACAAATTCGCAAC
328570 GCGATTTACAAATTCGCAAC
1 GCGATTTACAAATTCGCAAC
*
328590 GCGATTTACACATTCGCAAC
1 GCGATTTACAAATTCGCAAC
***
328610 GCGATTTACAAATTCGCGTT
1 GCGATTTACAAATTCGCAAC
** *
328630 GCGTATTTGGAAAATCGCAAC
1 GCG-ATTTACAAATTCGCAAC
*
328651 GCGATTTACATATTCG
1 GCGATTTACAAATTCG
328667 TGTTACGATT
Statistics
Matches: 80, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 66 0.82
21 14 0.17
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (20 bp):
GCGATTTACAAATTCGCAAC
Found at i:328660 original size:41 final size:41
Alignment explanation
Indices: 328563--328684 Score: 129
Period size: 41 Copynumber: 3.0 Consensus size: 41
328553 ATTTACACAT
*** ** * *
328563 TCGCAACGCGATTTACAAATTCGCAACGCG-ATTTACACAT
1 TCGCAACGCGATTTACAAATTCGCGTTGCGTATTTGGAAAA
328603 TCGCAACGCGATTTACAAATTCGCGTTGCGTATTTGGAAAA
1 TCGCAACGCGATTTACAAATTCGCGTTGCGTATTTGGAAAA
* * * *
328644 TCGCAACGCGATTTACATATTCGTGTTACGATTTTTGGAAA
1 TCGCAACGCGATTTACAAATTCGCGTTGCG-TATTTGGAAA
328685 CTGTGTTGCG
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
40 27 0.39
41 33 0.48
42 9 0.13
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (41 bp):
TCGCAACGCGATTTACAAATTCGCGTTGCGTATTTGGAAAA
Found at i:331353 original size:76 final size:76
Alignment explanation
Indices: 331180--331938 Score: 852
Period size: 76 Copynumber: 10.0 Consensus size: 76
331170 ACATTAACAT
* * * *
331180 GTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAACAGTGAAACTTAACATTGACTCACAC
1 GTAATTCCAGCACTAAACTT-ATCACAT---AATTCCAGCAGTGAAACTTAACATTGACTTACAC
331244 -AGTGAAATGAATAC
62 TAGTGAAATGAATAC
* * * * * ** * *
331258 GTAAATCTAACACTAAACTTATGACATGATTTTAGCAGTGAAATTTAACATTTACTTACACTAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAGT
*
331323 GAAATGAATAT
66 GAAATGAATAC
* * * * * * * * *
331334 GTGATTCTAGCACTGAACTTAAT-ATATGATTTCAGAAGTGAAACTTAACATTGACTTACCCAAG
1 GTAATTCCAGCACTAAACTT-ATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAG
331398 TGAAATGAATAC
65 TGAAATGAATAC
* * * * * *
331410 GTAATTCTAGCACTAAACTTATCACATAATTTCAACAGTGAAACTTAACATTGAATTATACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAGT
331475 GAAATGAATAC
66 GAAATGAATAC
* * * * * * **
331486 GTAGTTCCAGCGCTAAACTTATCACATAGTTCCAGTAGTGAAACTTAACATTAACTTACACCAAC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAGT
331551 GAAATGAATAC
66 GAAATGAATAC
* * *
331562 GAAATTCCAGCACT-AACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTTACACTAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAGT
331626 GAAATGAATAC
66 GAAATGAATAC
* * * * *
331637 GTAATTCC-GACACTAAACTTATCACCTAATTCTAACAATGAAATTTAACATTGACTTACACCT-
1 GTAATTCCAG-CACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACA-CTA
*
331700 GTAAAATGAATAC
64 GTGAAATGAATAC
* * **
331713 GTAATTCCAACACTAAACTTATCACATAATTCCAACAACGAAACTTAACATTGACTTACA-TAAG
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACT-AG
331777 TGAAATGAATAC
65 TGAAATGAATAC
* * * *
331789 TTAATTTCAGCACTAAACTTATCACATAATTCCCGCAGTGAAATTTAACATTGACTTACACTAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAGT
331854 GAAATGAATA-
66 GAAATGAATAC
* * * *
331864 -TAAATTCCAGCACTAAACTTATCACATAATTCCTGCAGTGAAACTTAATATTGATTTACACAAG
1 GT-AATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAG
331928 TGAAATGAATA
65 TGAAATGAATA
331939 TGCAACAGTG
Statistics
Matches: 587, Mismatches: 82, Indels: 27
0.84 0.12 0.04
Matches are distributed among these distances:
74 3 0.01
75 161 0.27
76 397 0.68
77 5 0.01
78 19 0.03
79 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (76 bp):
GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACTAGT
GAAATGAATAC
Found at i:331653 original size:227 final size:228
Alignment explanation
Indices: 331180--331938 Score: 883
Period size: 227 Copynumber: 3.3 Consensus size: 228
331170 ACATTAACAT
* * *
331180 GTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAACAGTGAAACTTAACATTGACTCACA-
1 GTAATTCCAGCACTAAACTT-ATCACAT-A-ATTTC-AACAGTGAAACTTAACATTGACTTACAC
* * * ** *
331243 CAGTGAAATGAATACGTAAATCTAACACTAAACTTATGACAT-GATTTTAGCAGTGAAATTTAAC
62 CAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACATAG-TTCCAGCAGTGAAACTTAAC
* * * * * * * * *
331307 ATTTACTTACACTAGTGAAATGAATATGTGATTCTAGCACTGAACTTAAT-ATATGATTTCAG-A
126 ATTAACTTACACTAATGAAATGAATACGTAATTCCAGCACTAAACTT-ATCACATAATTCCAGCA
* * *
331370 AGTGAAACTTAACATTGACTTACCCAAGTGAAATGAATAC
190 A-TGAAATTTAACATTGACTTACACTAGTGAAATGAATAC
* * *
331410 GTAATTCTAGCACTAAACTTATCACATAATTTCAACAGTGAAACTTAACATTGAATTATACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTTCAACAGTGAAACTTAACATTGACTTACACCAGT
* * * *
331475 GAAATGAATACGTAGTTCCAGCGCTAAACTTATCACATAGTTCCAGTAGTGAAACTTAACATTAA
66 GAAATGAATACGTAATTCCAACACTAAACTTATCACATAGTTCCAGCAGTGAAACTTAACATTAA
* * *
331540 CTTACACCAACGAAATGAATACGAAATTCCAGCACT-AACTTATCACATAATTCCAGCAATGAAA
131 CTTACACTAATGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAATGAAA
331604 TTTAACATTGACTTACACTAGTGAAATGAATAC
196 TTTAACATTGACTTACACTAGTGAAATGAATAC
* * * *
331637 GTAATTCC-GACACTAAACTTATCACCTAA-TTCTAACAATGAAATTTAACATTGACTTACACCT
1 GTAATTCCAG-CACTAAACTTATCACATAATTTC-AACAGTGAAACTTAACATTGACTTACACCA
* * * **
331700 GTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCCAACAACGAAACTTAACATT
64 GTGAAATGAATACGTAATTCCAACACTAAACTTATCACATAGTTCCAGCAGTGAAACTTAACATT
* * * * *
331765 GACTTACA-TAAGTGAAATGAATACTTAATTTCAGCACTAAACTTATCACATAATTCCCGCAGTG
129 AACTTACACTAA-TGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAATG
331829 AAATTTAACATTGACTTACACTAGTGAAATGAATA-
193 AAATTTAACATTGACTTACACTAGTGAAATGAATAC
* ** * * *
331864 -TAAATTCCAGCACTAAACTTATCACATAATTCCTGCAGTGAAACTTAATATTGATTTACACAAG
1 GT-AATTCCAGCACTAAACTTATCACATAATTTCAACAGTGAAACTTAACATTGACTTACACCAG
331928 TGAAATGAATA
65 TGAAATGAATA
331939 TGCAACAGTG
Statistics
Matches: 452, Mismatches: 65, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
226 9 0.02
227 265 0.59
228 152 0.34
229 2 0.00
230 22 0.05
231 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (228 bp):
GTAATTCCAGCACTAAACTTATCACATAATTTCAACAGTGAAACTTAACATTGACTTACACCAGT
GAAATGAATACGTAATTCCAACACTAAACTTATCACATAGTTCCAGCAGTGAAACTTAACATTAA
CTTACACTAATGAAATGAATACGTAATTCCAGCACTAAACTTATCACATAATTCCAGCAATGAAA
TTTAACATTGACTTACACTAGTGAAATGAATAC
Found at i:331766 original size:303 final size:304
Alignment explanation
Indices: 331180--331938 Score: 915
Period size: 303 Copynumber: 2.5 Consensus size: 304
331170 ACATTAACAT
* * * *
331180 GTAATTCCAGCACTAAA-TTAAACACATCACAATTCTAACAGTGAAACTTAACATTGACTCACA-
1 GTAATTCCAGCACTAAACTT-ATCACAT---AATTCCAGCAGTGAAACTTAACATTGACTTACAC
* * * * **
331243 CAGTGAAATGAATACGTAAA-TCTAACACTAAACTTATGACATGATTTTAGCAGTGAAATTTAAC
62 CAGTGAAATGAATACG-AAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAAC
* * * * * * * * *
331307 ATTTACTTACACTAGTGAAATGAATATGTGATTCTAGCACTGAACTTAATATATGATTTCAGAAG
126 ATTGACTTACACTAGTGAAATGAATACGTAATTCGAGCACTAAACTTAATACATAATTTAACAAG
* * *
331372 TGAAACTTAACATTGACTTACCCAAGTGAAATGAATACGTAATTCTAGCACTAAACTTATCACAT
191 TGAAACTTAACATTGACTTACCCAAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACAT
* ** * *
331437 AATTTCAACAGTGAAACTTAACATTGAATTATACCAGTGAAATGAATAC
256 AATTCCAACAACGAAACTTAACATTGAATTACACAAGTGAAATGAATAC
* * * * * **
331486 GTAGTTCCAGCGCTAAACTTATCACATAGTTCCAGTAGTGAAACTTAACATTAACTTACACCAAC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
331551 GAAATGAATACGAAATTCCAGCACT-AACTTATCACATAATTCCAGCAATGAAATTTAACATTGA
66 GAAATGAATACGAAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGA
*
331615 CTTACACTAGTGAAATGAATACGTAATTCCGA-CACTAAACTT-ATCACCTAATTCTAACAA-TG
131 CTTACACTAGTGAAATGAATACGTAATT-CGAGCACTAAACTTAAT-ACATAATT-TAACAAGTG
* *
331677 AAATTTAACATTGACTTACACC-TGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATA
193 AAACTTAACATTGACTTAC-CCAAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATA
* *
331741 ATTCCAACAACGAAACTTAACATTGACTTACATAAGTGAAATGAATAC
257 ATTCCAACAACGAAACTTAACATTGAATTACACAAGTGAAATGAATAC
* * * * *
331789 TTAATTTCAGCACTAAACTTATCACATAATTCCCGCAGTGAAATTTAACATTGACTTACACTAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
* * * *
331854 GAAATGAATA-TAAATTCCAGCACTAAACTTATCACATAATTCCTGCAGTGAAACTTAATATTGA
66 GAAATGAATACGAAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGA
* *
331918 TTTACACAAGTGAAATGAATA
131 CTTACACTAGTGAAATGAATA
331939 TGCAACAGTG
Statistics
Matches: 386, Mismatches: 59, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
302 15 0.04
303 319 0.83
304 29 0.08
306 21 0.05
307 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (304 bp):
GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
GAAATGAATACGAAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAATTTAACATTGA
CTTACACTAGTGAAATGAATACGTAATTCGAGCACTAAACTTAATACATAATTTAACAAGTGAAA
CTTAACATTGACTTACCCAAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTC
CAACAACGAAACTTAACATTGAATTACACAAGTGAAATGAATAC
Found at i:341726 original size:3 final size:3
Alignment explanation
Indices: 341713--341788 Score: 143
Period size: 3 Copynumber: 25.0 Consensus size: 3
341703 GTCCTGATTG
341713 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
341759 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
341789 CGTTTGAAAA
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 69 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:343405 original size:14 final size:14
Alignment explanation
Indices: 343378--343418 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
343368 GAATAATTTT
343378 TAAATCCTTAAACTC
1 TAAATCC-TAAACTC
343393 TAAATCCTAAACTC
1 TAAATCCTAAACTC
* *
343407 GAAACCCTAAAC
1 TAAATCCTAAAC
343419 ATTAAACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 17 0.71
15 7 0.29
ACGTcount: A:0.44, C:0.29, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAATCCTAAACTC
Found at i:349988 original size:69 final size:69
Alignment explanation
Indices: 349725--349967 Score: 290
Period size: 69 Copynumber: 3.5 Consensus size: 69
349715 TACAATAATA
* * * *
349725 TGCTCCCTTGTGAGTCACTCTAATCCTTC-AGAGCTCCCGTACGAGTCAACCGAAATAATTACGA
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGAG-GCTCCCGTACGAGTCACCCAAAATAATTACGA
349789 TTAGG
65 TTAGG
* * * *
349794 TGCTCCCGTGCAAGTCACTCTAATCTTTCGAGACTCCCGTACAAGTCACCCAAAATAATTACGAT
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGAGGCTCCCGTACGAGTCACCCAAAATAATTACGAT
*
349859 TTGG
66 TAGG
* * * * ** * * *
349863 TGCTCCCGTGTGAGTCACTCTAATCTTTTGGGGCTTTCGTGCGAGTCACCCAGAATAATCACGAT
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGAGGCTCCCGTACGAGTCACCCAAAATAATTACGAT
349928 TAGG
66 TAGG
* *
349932 TTCTCCCTTGCGAGTCACTCTAATCCTTCGAGGCTC
1 TGCTCCCGTGCGAGTCACTCTAATCCTTCGAGGCTC
349968 ATGTGTGAGT
Statistics
Matches: 145, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
69 143 0.99
70 2 0.01
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.29
Consensus pattern (69 bp):
TGCTCCCGTGCGAGTCACTCTAATCCTTCGAGGCTCCCGTACGAGTCACCCAAAATAATTACGAT
TAGG
Found at i:350260 original size:76 final size:76
Alignment explanation
Indices: 350169--350368 Score: 319
Period size: 76 Copynumber: 2.6 Consensus size: 76
350159 ACAATTCTAG
* **
350169 CAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTATGA
1 CAGTGAAAATTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTACCA
*
350234 CATGATTTCAA
66 CATCATTTCAA
*
350245 CAGTGAAAATTAACATTAACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTACCA
1 CAGTGAAAATTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTACCA
*
350310 CATCATTTCAG
66 CATCATTTCAA
* * *
350321 TAGTGAAATTTAACATTGACTTACACTAGTGAAATGAATACGTAATTC
1 CAGTGAAAATTAACATTGACTTACACCAGTGAAATGAATACGTAATTC
350369 CAGTAGTGAA
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 114 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (76 bp):
CAGTGAAAATTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTACCA
CATCATTTCAA
Found at i:350376 original size:51 final size:51
Alignment explanation
Indices: 350318--350421 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
350308 CACATCATTT
* * * **
350318 CAGTAGTGAAATTTAACATTGACTTACACTAGTGAAATGAATACGTAATTC
1 CAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTC
*
350369 CAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACTTAATTC
1 CAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTC
350420 CA
1 CA
350422 ACACTAAGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.29
Consensus pattern (51 bp):
CAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTC
Found at i:350387 original size:127 final size:127
Alignment explanation
Indices: 350246--350497 Score: 360
Period size: 127 Copynumber: 2.0 Consensus size: 127
350236 TGATTTCAAC
** * *
350246 AGTGAAAATTAACATTAACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAAACTTACCAC
1 AGTGAAAATTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAAACTTACCAC
* * * * * * * *
350311 ATCATTTCAGTAGTGAAATTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGT
66 ATAATTCCAGCAGTAAAACTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCAGT
* * * *
350373 AGTGAAACTTAACATTAACTTACACCAACGAAATGAATACTTAATTCCAACACTAAGCTTATCAC
1 AGTGAAAATTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAAACTTACCAC
350438 ATAATTCCAGCAGTAAAACTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCA
66 ATAATTCCAGCAGTAAAACTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCA
350498 TCACTAAACT
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
127 109 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.28
Consensus pattern (127 bp):
AGTGAAAATTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAAACTTACCAC
ATAATTCCAGCAGTAAAACTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCAGT
Found at i:350443 original size:76 final size:76
Alignment explanation
Indices: 350363--350660 Score: 398
Period size: 76 Copynumber: 3.9 Consensus size: 76
350353 AATGAATACG
* * * *
350363 TAATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACTTAATTCCAACACTA
1 TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACATAATTCCAACACTA
*
350428 AGCTTATCACA
66 AACTTATCACA
* * * *
350439 TAATTCCAGCAGTAAAACTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCATCACTA
1 TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACATAATTCCAACACTA
*
350504 AACTTATCACC
66 AACTTATCACA
* * * *
350515 TAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACATAATTCCAACACTA
1 TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACATAATTCCAACACTA
350580 AACTTATCACA
66 AACTTATCACA
* * * * * * * *
350591 TAATTCTACCTGTTAAACTTAACATTGACTTACATCAATGAAATGAATACGTAACTCCAGCACTA
1 TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACATAATTCCAACACTA
350656 AACTT
66 AACTT
350661 TGAAGCTTAA
Statistics
Matches: 193, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
76 193 1.00
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (76 bp):
TAATTCCAGCAGTGAAACTTAACATTGACTTACACCAATGAAATGAATACATAATTCCAACACTA
AACTTATCACA
Found at i:350533 original size:203 final size:203
Alignment explanation
Indices: 350161--350573 Score: 567
Period size: 203 Copynumber: 2.0 Consensus size: 203
350151 AACACATCAC
* * ** * *
350161 AATTCTAGCAGTGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCTAGCACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAA
* * * * *
350226 ACTTATGACATGATTTCAACAGTGAAAATTAACATTAACTTACACCAGTGAAATGAATACGTAAT
66 ACTTATCACATAATTCCAACAGTGAAAATTAACATTAACTTACACCAGTGAAATAAATACATAAT
* * * * * * *
350291 TCTAGCACTAAACTTACCACATCATTTCAGTAGTGAAATTTAACATTGACTTACACTAGTGAAAT
131 TCCAGCACTAAACTTACCACATAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAAT
*
350356 GAATACGT
196 GAATACAT
* *
350364 AATTCCAGTAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACTTAATTCCAACACTAA
1 AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAA
* * *
350429 GCTTATCACATAATTCCAGCAGT-AAAACTTAACATTGACTTACACCAGTGAAATAAATACATAA
66 ACTTATCACATAATTCCAACAGTGAAAA-TTAACATTAACTTACACCAGTGAAATAAATACATAA
* * *
350493 TTCCATCACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAA
130 TTCCAGCACTAAACTTACCACATAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAA
350558 TGAATACAT
195 TGAATACAT
350567 AATTCCA
1 AATTCCA
350574 ACACTAAACT
Statistics
Matches: 182, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
202 4 0.02
203 178 0.98
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (203 bp):
AATTCCAGCAGTGAAACTTAACATTAACTTACACCAACGAAATGAATACGTAATTCCAACACTAA
ACTTATCACATAATTCCAACAGTGAAAATTAACATTAACTTACACCAGTGAAATAAATACATAAT
TCCAGCACTAAACTTACCACATAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAAT
GAATACAT
Found at i:350752 original size:213 final size:210
Alignment explanation
Indices: 350456--351026 Score: 574
Period size: 213 Copynumber: 2.6 Consensus size: 210
350446 AGCAGTAAAA
* *
350456 CTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCATCACTAAACTTATCACCTAATTC
1 CTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCAGCACTAAACTTATCACATAATTC
*
350521 CAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACATAATTCCAACACTAAACTTA
66 CAGCAATGAAATTTAACATTGACTTACACCAGTAAAACGAATACATAATTCCAACACTAAACTTA
* * *
350586 TCACATAATTCTACCT-GTTAAACTTAACATTGACTTACATCAATGAAATGAATACGTAACTCCA
131 TCACATAATTC-ACCTAGTGAAACTTAACATTGACTTACACCAACGAAATGAATACGTAACTCCA
350650 GCACTAAACTTTGAAG
195 GCACTAAACTTTGAAG
* * *
350666 CTTAACATTGACTTACATCAGTGAAATGAATATGTA-ATATTTCTAGCACTAAACTTATCACATA
1 CTTAACATTGACTTACACCAGTGAAAT-AA-A--TACATAATTCCAGCACTAAACTTATCACATA
* * * * *
350730 ATTTTC-GCAGTGAAATTTAACATTGACTTACACTAGTGAAACGAATACGTAATTCCAACACTAA
62 A-TTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAACGAATACATAATTCCAACACTAA
** * * *
350794 ACTTATCACATAATTCATGTAGTGAAACTTAACATTGACTTACACCAGCGAAATGAATA-ATAAT
126 ACTTATCACATAATTCACCTAGTGAAACTTAACATTGACTTACACCAACGAAATGAATACGTAAC
* * *
350858 TCTAGCATTAAATTTATCACTTAATTCCAGTAGTGAAA
191 TCCAGCACT--A---A--AC-----T----T--TGAAG
* * * * *
350896 CTTAACATTGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTTTCACATAAGTC
1 CTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCAGCACTAAACTTATCACATAATTC
* * * * * * * * *
350961 AAGGAGTGAAACTGAACATTGACTTACACTAGTGAAATGAATACATAATTCCAGCACTAAACTTA
66 CAGCAATGAAATTTAACATTGACTTACACCAGTAAAACGAATACATAATTCCAACACTAAACTTA
351026 T
131 T
351027 GATTTCACAT
Statistics
Matches: 297, Mismatches: 38, Indels: 35
0.80 0.10 0.09
Matches are distributed among these distances:
210 26 0.09
211 2 0.01
212 13 0.04
213 128 0.43
214 6 0.02
217 1 0.00
219 2 0.01
224 1 0.00
226 3 0.01
227 83 0.28
228 2 0.01
229 1 0.00
230 29 0.10
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.30
Consensus pattern (210 bp):
CTTAACATTGACTTACACCAGTGAAATAAATACATAATTCCAGCACTAAACTTATCACATAATTC
CAGCAATGAAATTTAACATTGACTTACACCAGTAAAACGAATACATAATTCCAACACTAAACTTA
TCACATAATTCACCTAGTGAAACTTAACATTGACTTACACCAACGAAATGAATACGTAACTCCAG
CACTAAACTTTGAAG
Found at i:350776 original size:137 final size:134
Alignment explanation
Indices: 350533--350797 Score: 345
Period size: 137 Copynumber: 2.0 Consensus size: 134
350523 GCAATGAAAT
*
350533 TTAACATTGACTTACACCAGTAAAATGAATACATAATTCCAACACTAAACTTATCACATAATTCT
1 TTAACATTGACTTACACCAGTAAAATGAATAAATAATTCCAACACTAAACTTATCACATAATTCT
* * * *
350598 ACCTGTTAAACTTAACATTGACTTACATCAATGAAATGAATACGTAACTCCAGCACTAAACTTTG
66 ACCAGTGAAACTTAACATTGACTTACATCAATGAAACGAATACGTAACTCCAACACTAAACTTTG
350663 AAGC
131 AAGC
* * * * *
350667 TTAACATTGACTTACATCAGTGAAATGAATATGTAATATTTCTAGCACTAAACTTATCACATAAT
1 TTAACATTGACTTACACCAGTAAAATGAATA---AATAATTCCAACACTAAACTTATCACATAAT
* * * *
350732 T-TTCGCAGTGAAATTTAACATTGACTTACA-CTAGTGAAACGAATACGTAATTCCAACACTAAA
63 TCTAC-CAGTGAAACTTAACATTGACTTACATC-AATGAAACGAATACGTAACTCCAACACTAAA
350795 CTT
126 CTT
350798 ATCACATAAT
Statistics
Matches: 112, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
134 29 0.26
136 3 0.03
137 80 0.71
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (134 bp):
TTAACATTGACTTACACCAGTAAAATGAATAAATAATTCCAACACTAAACTTATCACATAATTCT
ACCAGTGAAACTTAACATTGACTTACATCAATGAAACGAATACGTAACTCCAACACTAAACTTTG
AAGC
Found at i:350826 original size:76 final size:76
Alignment explanation
Indices: 350661--351026 Score: 443
Period size: 76 Copynumber: 4.8 Consensus size: 76
350651 CACTAAACTT
* * *
350661 TGAAGCTTAACATTGACTTACA-TCAGTGAAATGAATATGTAATATTTCTAGCACTAAACTTATC
1 TGAAACTTAACATTGACTTACACT-AGTGAAATGAATACGT-A-A-TTCCAGCACTAAACTTATC
* *
350725 ACATAATT-TTCGCAG
62 ACATAATTCAT-GTAG
* * *
350740 TGAAATTTAACATTGACTTACACTAGTGAAACGAATACGTAATTCCAACACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
350805 AATTCATGTAG
66 AATTCATGTAG
* * * * * * *
350816 TGAAACTTAACATTGACTTACACCAGCGAAATGAATA-ATAATTCTAGCATTAAATTTATCACTT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
350880 AATTCCA-GTAG
66 AATT-CATGTAG
* * *
350891 TGAAACTTAACATTGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTTTCACAT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
* * *
350956 AAGTCAAGGAG
66 AATTCATGTAG
* *
350967 TGAAACTGAACATTGACTTACACTAGTGAAATGAATACATAATTCCAGCACTAAACTTAT
1 TGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
351027 GATTTCACAT
Statistics
Matches: 249, Mismatches: 33, Indels: 13
0.84 0.11 0.04
Matches are distributed among these distances:
75 66 0.27
76 145 0.58
77 2 0.01
78 1 0.00
79 34 0.14
80 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
AATTCATGTAG
Found at i:350944 original size:151 final size:151
Alignment explanation
Indices: 350661--351026 Score: 482
Period size: 151 Copynumber: 2.4 Consensus size: 151
350651 CACTAAACTT
* * *
350661 TGAAGCTTAACATTGACTTACATCAGTGAAATGAATATGTAATATTTCTAGCACTAAACTTATCA
1 TGAAACTTAACATTGACTTACACCAGTGAAATG-A-A--TAATAATTCTAGCACTAAACTTATCA
* * * *
350726 CATAATTTTCGCAGTGAAATTTAACATTGACTTACACTAGTGAAACGAATACGTAATTCCAACAC
62 CATAATTTCCGCAGTGAAACTTAACATTGACTTAAACCAGTGAAACGAATACGTAATTCCAACAC
* * *
350791 TAAACTTATCACATAATTCATGTAG
127 TAAACTTATCACATAAGTCAAGGAG
* * * *
350816 TGAAACTTAACATTGACTTACACCAGCGAAATGAATAATAATTCTAGCATTAAATTTATCACTTA
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATAATAATTCTAGCACTAAACTTATCACATA
* * *
350881 A-TTCCAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAATGAATACGTAATTCCAGCACTAA
66 ATTTCC-GCAGTGAAACTTAACATTGACTTAAACCAGTGAAACGAATACGTAATTCCAACACTAA
*
350945 ACTTTTCACATAAGTCAAGGAG
130 ACTTATCACATAAGTCAAGGAG
* * *
350967 TGAAACTGAACATTGACTTACACTAGTGAAATGAATACATAATTCCAGCACTAAACTTAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATA-ATAATTCTAGCACTAAACTTAT
351027 GATTTCACAT
Statistics
Matches: 185, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
150 3 0.02
151 131 0.71
152 19 0.10
153 1 0.01
154 1 0.01
155 30 0.16
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (151 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATAATAATTCTAGCACTAAACTTATCACATA
ATTTCCGCAGTGAAACTTAACATTGACTTAAACCAGTGAAACGAATACGTAATTCCAACACTAAA
CTTATCACATAAGTCAAGGAG
Found at i:359764 original size:2 final size:2
Alignment explanation
Indices: 359757--359786 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
359747 TCTTTTTAAA
359757 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
359787 TATTCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360074 original size:156 final size:157
Alignment explanation
Indices: 359818--360101 Score: 466
Period size: 156 Copynumber: 1.8 Consensus size: 157
359808 ACTCCATTCA
* *
359818 AACATATCAAAATGTGTAGGTTCCCTAGAACCATACACCCACCTGCACATTAAGTAAGGCCATGA
1 AACACATCAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACATTAAGTAAGGCCATGA
359883 GCACAAAGCCGAGGAGCCTGCGAAAATACTTCCTCCAACAATAC-CCCCAAATAAAACATTTTAT
66 GCACAAAGCCGAGGAGCCTGCGAAAATACTTCCTCCAACAATACTCCCCAAATAAAACATTTTAT
359947 CAAAAACCAAAGTAATCCATCCAGCCC
131 CAAAAACCAAAGTAATCCATCCAGCCC
* * *
359974 AACACATCATAATGTGTAGGTTCCCCAGAACCATACACCCACC-GTCACATTAGGTAAGGCCCTG
1 AACACATCAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTG-CACATTAAGTAAGGCCATG
* *
360038 AGCACAAAGCCGAGGAGCCTG-TAAGTATACTTCCTCCAACAATACTCCCCAAATAAAACATTTT
65 AGCACAAAGCCGAGGAGCCTGCGAA-AATACTTCCTCCAACAATACTCCCCAAATAAAACATTTT
360102 CCGTCCGTAA
Statistics
Matches: 118, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
155 3 0.03
156 97 0.82
157 18 0.15
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.20
Consensus pattern (157 bp):
AACACATCAAAATGTGTAGGTTCCCCAGAACCATACACCCACCTGCACATTAAGTAAGGCCATGA
GCACAAAGCCGAGGAGCCTGCGAAAATACTTCCTCCAACAATACTCCCCAAATAAAACATTTTAT
CAAAAACCAAAGTAATCCATCCAGCCC
Found at i:360159 original size:24 final size:24
Alignment explanation
Indices: 360127--360190 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
360117 TATATAAAAA
*
360127 ATCAGAACATAATTCAGATCAGAT
1 ATCAGAACATAATCCAGATCAGAT
* * * *
360151 ATCATAACAAAATCCAGGTCAGGT
1 ATCAGAACATAATCCAGATCAGAT
360175 ATCAGAACATAATCCA
1 ATCAGAACATAATCCA
360191 AATCGAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAACATAATCCAGATCAGAT
Found at i:362271 original size:17 final size:17
Alignment explanation
Indices: 362249--362282 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
362239 TTTTGGTCAA
*
362249 AGTCAACGGTCAACAGC
1 AGTCAACAGTCAACAGC
*
362266 AGTCAATAGTCAACAGC
1 AGTCAACAGTCAACAGC
362283 TCGATACAGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (17 bp):
AGTCAACAGTCAACAGC
Found at i:367769 original size:3 final size:3
Alignment explanation
Indices: 367763--367819 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
367753 TTGGGCTTGC
* *
367763 AAT AAT AAT AAT ATT AAT AA- AAT AAT AAT AGT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
*
367808 AGT AAT AAT AAT
1 AAT AAT AAT AAT
367820 CTCTGCAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:368423 original size:41 final size:41
Alignment explanation
Indices: 368378--368468 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 41
368368 GATGAATCAG
* * * * *
368378 AGGATTTATCATCTTGCCCGGAAGACTGACAGATGACCCTA
1 AGGATTTAACATCATGCCCGAAAGACTGACAAATGACCCGA
*
368419 AGGATTTAAACATCATGCTCGAAAGACTGACAAATGACCCGA
1 AGGATTT-AACATCATGCCCGAAAGACTGACAAATGACCCGA
368461 AGGATTTA
1 AGGATTTA
368469 CATATTTGTG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 8 0.19
42 35 0.81
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (41 bp):
AGGATTTAACATCATGCCCGAAAGACTGACAAATGACCCGA
Found at i:369946 original size:42 final size:41
Alignment explanation
Indices: 369899--369993 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
369889 GATGTGAGAC
*
369899 TTCAAAATGCCACACATA-AAT-TATTTTTGACTGAAATGGGCT
1 TTCAAAATGCC-C-CA-ACAATCTATTTATGACTGAAATGGGCT
* *
369941 TTCAAAATGCCCCAACATTCTATTTATGTCTGAAATGGGCT
1 TTCAAAATGCCCCAACAATCTATTTATGACTGAAATGGGCT
*
369982 TTCAACATGCCC
1 TTCAAAATGCCC
369994 TAGCATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 1 0.02
40 4 0.09
41 31 0.66
42 11 0.23
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (41 bp):
TTCAAAATGCCCCAACAATCTATTTATGACTGAAATGGGCT
Found at i:377510 original size:3 final size:3
Alignment explanation
Indices: 377502--377561 Score: 68
Period size: 3 Copynumber: 19.7 Consensus size: 3
377492 ATTAAGCATG
* *
377502 TAA TAA TAA TAAA TAT TAA T-A TAA TAA TAA TAG TAA TAA TAAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
377548 TAG TAA TAA TAA TA
1 TAA TAA TAA TAA TA
377562 TATACAAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.83
4 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:377548 original size:16 final size:16
Alignment explanation
Indices: 377505--377559 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
377495 AAGCATGTAA
* *
377505 TAATAATAAATATTAA
1 TAATAATAAATAATAG
377521 T-ATAAT-AATAATAG
1 TAATAATAAATAATAG
377535 TAATAATAAATAATAG
1 TAATAATAAATAATAG
377551 TAATAATAA
1 TAATAATAA
377560 TATATACAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 7 0.20
15 10 0.29
16 18 0.51
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (16 bp):
TAATAATAAATAATAG
Found at i:379468 original size:3 final size:3
Alignment explanation
Indices: 379460--379505 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
379450 ATTTGGGTTT
379460 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
379506 AGGGATCTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:379962 original size:44 final size:42
Alignment explanation
Indices: 379914--379995 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 42
379904 AAGGTGATGT
*
379914 TGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGTTGGCAC
1 TGATCCAACTCCTTATATGAT-GAATCGAGCAAAG-GTTGGCAC
* *
379958 TGATCCAACTCCTTATGTGATGAATCGAGCTAAGGTTG
1 TGATCCAACTCCTTATATGATGAATCGAGCAAAGGTTG
379996 AACAAGTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 4 0.11
43 12 0.34
44 19 0.54
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (42 bp):
TGATCCAACTCCTTATATGATGAATCGAGCAAAGGTTGGCAC
Found at i:380001 original size:166 final size:166
Alignment explanation
Indices: 379670--380148 Score: 671
Period size: 166 Copynumber: 2.9 Consensus size: 166
379660 TCCTCGAATG
* *
379670 AGTTCTTCTCATTATTAAC-TC-TCTACTGGAAAAA--TTGATCCACCTCCTTCTATGATGAAAT
1 AGTTCTTCTCATTATAAACTTCTTC-ACT--AAAAATGTTGATCCACCTCCTTCTGTGATGAAAT
** * * * *
379731 CAAGCGAAAAGGCGATGCTGATCCAATTTCTTATATGATGG-ATCGAGCAAAGTGCTGATGTTGA
63 CAAGAAAAAAGGTGATGATGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGCTGGTGTTGA
* ** *
379795 TCTAACTCCTTATGTGATGGGTGGAGCTAAGGTTGAACA
128 TCCAACTCCTTATGTGATGAATCGAGCTAAGGTTGAACA
*
379834 AGTTCTTCTCATTATAAACTTCTTCACTAAAAATGTTGATCCACCTTCTTCTGTGATGAAATCAA
1 AGTTCTTCTCATTATAAACTTCTTCACTAAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAA
* * * ***
379899 GTAAAAAGGTGATGTTGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGTTGGCACTGATCC
66 GAAAAAAGGTGATGATGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGCTGGTGTTGATCC
379964 AACTCCTTATGTGATGAATCGAGCTAAGGTTGAACA
131 AACTCCTTATGTGATGAATCGAGCTAAGGTTGAACA
* * **
380000 AGTTCTTCTCATTATGAACTTCTTCATTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCAA
1 AGTTCTTCTCATTATAAACTTCTTCACTAAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAA
380065 GAAAAAAGGTGATGATGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGCTGGTGTTGATCC
66 GAAAAAAGGTGATGATGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGCTGGTGTTGATCC
* *
380130 AACTTCTTATGCGATGAAT
131 AACTCCTTATGTGATGAAT
380149 GTCTATACCT
Statistics
Matches: 280, Mismatches: 30, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
163 5 0.02
164 18 0.06
165 66 0.24
166 191 0.68
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (166 bp):
AGTTCTTCTCATTATAAACTTCTTCACTAAAAATGTTGATCCACCTCCTTCTGTGATGAAATCAA
GAAAAAAGGTGATGATGATCCAACTTCTTATATGATGGAATCGAGCAAAGTGCTGGTGTTGATCC
AACTCCTTATGTGATGAATCGAGCTAAGGTTGAACA
Found at i:380101 original size:44 final size:44
Alignment explanation
Indices: 380053--380139 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
380043 CCTCCTTCTG
*
380053 TGATGAAATCAAGAAAAAAGGTGATGATGATCCAACTTCTTATA
1 TGATGAAATCAAGAAAAAAGCTGATGATGATCCAACTTCTTATA
* * * ** * *
380097 TGATGGAATCGAGCAAAGTGCTGGTGTTGATCCAACTTCTTAT
1 TGATGAAATCAAGAAAAAAGCTGATGATGATCCAACTTCTTAT
380140 GCGATGAATG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (44 bp):
TGATGAAATCAAGAAAAAAGCTGATGATGATCCAACTTCTTATA
Found at i:380441 original size:2 final size:2
Alignment explanation
Indices: 380436--380507 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
380426 CACATATAAC
380436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
380478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
380508 GGATACATAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:381838 original size:3 final size:3
Alignment explanation
Indices: 381806--381856 Score: 50
Period size: 3 Copynumber: 16.7 Consensus size: 3
381796 TAACCTACAA
* * *
381806 AAT AA- AAT AAAT AAAT AAA AAT ATT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
381852 AAT AA
1 AAT AA
381857 ACGAATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 31 0.77
4 7 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:383076 original size:18 final size:18
Alignment explanation
Indices: 383049--383087 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
383039 ATATGATTAT
*
383049 TTTAGGTTTTCATCTCCG
1 TTTAGCTTTTCATCTCCG
*
383067 TTTAGCTTTTCATCTCTG
1 TTTAGCTTTTCATCTCCG
383085 TTT
1 TTT
383088 GTTGTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.13, T:0.56
Consensus pattern (18 bp):
TTTAGCTTTTCATCTCCG
Found at i:385132 original size:42 final size:41
Alignment explanation
Indices: 385084--385222 Score: 161
Period size: 42 Copynumber: 3.3 Consensus size: 41
385074 AATTACGGTA
*
385084 TTTGTATTAGAAACGCCGCTATAGAACATGACTGTTGCGGCG
1 TTTGTA-TAAAAACGCCGCTATAGAACATGACTGTTGCGGCG
* *
385126 TTTGTATAAAAAACGCCACTATAGAACATGACTGTTGCGACG
1 TTTGTAT-AAAAACGCCGCTATAGAACATGACTGTTGCGGCG
* * * * * *
385168 TTTGTACAAAATGCGCCGCTATAGAACCTTACCTGTTGTGGTG
1 TTTGTATAAAA-ACGCCGCTATAGAACATGA-CTGTTGCGGCG
385211 TTTGTATAAAAA
1 TTTGTATAAAAA
385223 ACACCACTAT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
41 5 0.06
42 58 0.72
43 18 0.22
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (41 bp):
TTTGTATAAAAACGCCGCTATAGAACATGACTGTTGCGGCG
Found at i:392508 original size:115 final size:114
Alignment explanation
Indices: 392355--392833 Score: 482
Period size: 115 Copynumber: 4.1 Consensus size: 114
392345 GGGTCGAACA
* * * * * * *
392355 CATTATGTACTTCTTCTT-TTTCAGATGAGTTCTTCTCATTTTGAACTCCCTTTTGGAAATATTG
1 CATTATGAACTTCTTCTTCTTT-GGACGAGTTCTTCTCATTATGAACTCTCTTTTGAAAATGTTG
* * * * **
392419 ACCCACCTCTTTTTTTTATGGATTTGAGTAAAAACATCGAACAAGTTCTTCT
65 ATCCACCTCATTTTGTGATGGATTTGA--AAAAAGGTCGAACAAGTTCTTCT
* * *
392471 CATTATGAAC-CCTTCTTCTTTGGACGAGTTTTTCTCATTATGAAATCTCTTTTGAAAATGTTGA
1 CATTATGAACTTCTTCTTCTTTGGACGAGTTCTTCTCATTATGAACTCTCTTTTGAAAATGTTGA
* * *
392535 TTCACCTCCTTCTGTGATGGATTTGAAAGAAAGGTCGAACAAGTTCTTCT
66 TCCACCTCATTTTGTGATGGATTTGAAA-AAAGGTCGAACAAGTTCTTCT
* * * * **
392585 CGTTATGAACTTCTTCTTCTTTGGACAAGTTATTCTCATTATGAACTTTC-ACTGAAAATGTTGA
1 CATTATGAACTTCTTCTTCTTTGGACGAGTTCTTCTCATTATGAACTCTCTTTTGAAAATGTTGA
* *
392649 TCCACCTCATTTTGTGATGGATTTGAAAAAAAGGTCAAACATGTTCTTCT
66 TCCACCTCATTTTGTGATGGATTTG-AAAAAAGGTCGAACAAGTTCTTCT
* * *
392699 CATTATGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATG-A-TCGTTTTTCTTAAAAT
1 CATTATGAACTTCTTCT---TCTTTGGACGAGTTCTTCTCATTATGAACTC-TCTTT-TGAAAAT
* * * * * * * *
392762 GTTGATCAACCTCCTTCTGTGATGGATATGACCAAAAGGTTGAATAAGCTCTTCT
61 GTTGATCCACCTCATTTTGTGATGGATTTGA-AAAAAGGTCGAACAAGTTCTTCT
392817 CATTATGAACTTCTTCT
1 CATTATGAACTTCTTCT
392834 CCCTCTTTGT
Statistics
Matches: 302, Mismatches: 50, Indels: 20
0.81 0.13 0.05
Matches are distributed among these distances:
113 2 0.01
114 97 0.32
115 99 0.33
116 14 0.05
117 24 0.08
118 66 0.22
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.41
Consensus pattern (114 bp):
CATTATGAACTTCTTCTTCTTTGGACGAGTTCTTCTCATTATGAACTCTCTTTTGAAAATGTTGA
TCCACCTCATTTTGTGATGGATTTGAAAAAAGGTCGAACAAGTTCTTCT
Found at i:392743 original size:232 final size:229
Alignment explanation
Indices: 392411--392833 Score: 550
Period size: 232 Copynumber: 1.8 Consensus size: 229
392401 TCCCTTTTGG
* * * * *
392411 AAATATTGACCCACCTCTTTTTTTTATGGATTTGAGTAAAAACATCGAACAAGTTCTTCTCATTA
1 AAATATTGACCCACCTCATTTTGTGATGGATTTGAGAAAAAACATCAAACAAGTTCTTCTCATTA
* *
392476 TGAACCCTTCTTCTTTGGACGAGTTTTTCTCATTATGAAATC-TCTTT-TGAAAATGTTGATTC-
66 TGAACCCTTCTTCATTGGACGAGTTCTTCTCATTATG--ATCGTCTTTCTGAAAATGTTGA-TCA
* * *
392538 ACCTCCTTCTGTGATGGATTTGA-AAGAAAGGTCGAACAAGTTCTTCTCGTTATGAACTTCTTCT
128 ACCTCCTTCTGTGATGGATATGACAA-AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT
392602 TCTTTGGACAAGTTATTCTCATTATGAACTTTCACTGA
192 TCTTTGGACAAGTTATTCTCATTATGAACTTTCACTGA
* * ** *
392640 AAATGTTGATCCACCTCATTTTGTGATGGATTTGA-AAAAAAGGTCAAACATGTTCTTCTCATTA
1 AAATATTGACCCACCTCATTTTGTGATGGATTTGAGAAAAAACATCAAACAAGTTCTTCTCATTA
* * *
392704 TGAACTTCTTCTCCCTCATTGGACGAGTTCTTCTCATTATGATCGTTTTTCTTAAAATGTTGATC
66 TGAAC-CCTTCT---TCATTGGACGAGTTCTTCTCATTATGATCGTCTTTCTGAAAATGTTGATC
* * *
392769 AACCTCCTTCTGTGATGGATATGACCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCT
127 AACCTCCTTCTGTGATGGATATGACAAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCT
392834 CCCTCTTTGT
Statistics
Matches: 165, Mismatches: 21, Indels: 13
0.83 0.11 0.07
Matches are distributed among these distances:
228 29 0.18
229 35 0.21
230 3 0.02
231 6 0.04
232 91 0.55
233 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (229 bp):
AAATATTGACCCACCTCATTTTGTGATGGATTTGAGAAAAAACATCAAACAAGTTCTTCTCATTA
TGAACCCTTCTTCATTGGACGAGTTCTTCTCATTATGATCGTCTTTCTGAAAATGTTGATCAACC
TCCTTCTGTGATGGATATGACAAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTT
TGGACAAGTTATTCTCATTATGAACTTTCACTGA
Found at i:392799 original size:118 final size:112
Alignment explanation
Indices: 392436--392861 Score: 460
Period size: 114 Copynumber: 3.7 Consensus size: 112
392426 TCTTTTTTTT
** *
392436 ATGGATTTGAGTAAAAACATCGAACAAGTTCTTCTCATTATGAAC-CCTTCTTCTTTGGACGAGT
1 ATGGATTTGA--AAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGGACGAGT
*
392500 TTTTCTCATTATGAAATCTCTTT-TGAAAATGTTGATTCACCTCCTTCTGTG
64 TTTTCTCATTATG--ATCTTTTTCTGAAAATGTTGA-TCACCTCCTTCTGTG
* *
392551 ATGGATTTGAAAGAAAGGTCGAACAAGTTCTTCTCGTTATGAACTTCTTCTTCTTTGGACAAGTT
1 ATGGATTTGAAA-AAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGGACGAGTT
* * ** * *
392616 ATTCTCATTATGAACTTTCACTGAAAATGTTGATCCACCTCATTTTGTG
65 TTTCTCATTATGATCTTTTTCTGAAAATGTTGAT-CACCTCCTTCTGTG
* * *
392665 ATGGATTTGAAAAAAAGGTCAAACATGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGA
1 ATGGATTTG-AAAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT---TCTTTGGACGA
* *
392730 GTTCTTCTCATTATGATCGTTTTTCTTAAAATGTTGATCAACCTCCTTCTGTG
62 GTTTTTCTCATTATGATC-TTTTTCTGAAAATGTTGATC-ACCTCCTTCTGTG
* * * * * * *
392783 ATGGATATGACCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGTATGA
1 ATGGATTTGA-AAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT---TCTTTGGACGA
*
392848 GTTTTTCTTATTAT
62 GTTTTTCTCATTAT
392862 AAACTCTTCA
Statistics
Matches: 264, Mismatches: 36, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
113 7 0.03
114 96 0.36
115 42 0.16
117 27 0.10
118 92 0.35
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (112 bp):
ATGGATTTGAAAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGGACGAGTTT
TTCTCATTATGATCTTTTTCTGAAAATGTTGATCACCTCCTTCTGTG
Found at i:392879 original size:118 final size:112
Alignment explanation
Indices: 392436--392885 Score: 449
Period size: 118 Copynumber: 3.9 Consensus size: 112
392426 TCTTTTTTTT
** *
392436 ATGGATTTGAGTAAAAACATCGAACAAGTTCTTCTCATTATGAAC-CCTTCTTCTTTGGACGAGT
1 ATGGATTTGA--AAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGGACGAGT
392500 TTTTCTCATTATGAAATCTCTT-TTGAAAATGTTGATTCACCTCCTTCTGTG
64 TTTTCTCATTAT-AAA-CTCTTCTTGAAAATGTTGA-TCACCTCCTTCTGTG
* *
392551 ATGGATTTGAAAGAAAGGTCGAACAAGTTCTTCTCGTTATGAACTTCTTCTTCTTTGGACAAGTT
1 ATGGATTTGAAA-AAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGGACGAGTT
* * * * *
392616 ATTCTCATTATGAACT-TTCACTGAAAATGTTGATCCACCTCATTTTGTG
65 TTTCTCATTATAAACTCTTC-TTGAAAATGTTGAT-CACCTCCTTCTGTG
* * *
392665 ATGGATTTGAAAAAAAGGTCAAACATGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGACGA
1 ATGGATTTG-AAAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT---TCTTTGGACGA
* * * *
392730 GTTCTTCTCATTATGATCGTTTTTCTT-AAAATGTTGATCAACCTCCTTCTGTG
62 GTTTTTCTCATTATAAAC--TCTTCTTGAAAATGTTGATC-ACCTCCTTCTGTG
* * * * * * *
392783 ATGGATATGACCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGTATGA
1 ATGGATTTGA-AAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT---TCTTTGGACGA
* * *
392848 GTTTTTCTTATTATAAACTCTTCATTAAAAATATTGAT
62 GTTTTTCTCATTATAAACTCTTC-TTGAAAATGTTGAT
392886 GGGTCTGCTT
Statistics
Matches: 283, Mismatches: 36, Indels: 29
0.81 0.10 0.08
Matches are distributed among these distances:
112 2 0.01
113 5 0.02
114 98 0.35
115 41 0.14
116 4 0.01
117 29 0.10
118 99 0.35
119 2 0.01
120 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.40
Consensus pattern (112 bp):
ATGGATTTGAAAAAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTGGACGAGTTT
TTCTCATTATAAACTCTTCTTGAAAATGTTGATCACCTCCTTCTGTG
Found at i:396722 original size:16 final size:16
Alignment explanation
Indices: 396696--396735 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
396686 GTTATGAAAT
396696 TAATG-AAAGAATAGAA
1 TAATGTAAAGAATA-AA
396712 -AATGTAAAGAATAAA
1 TAATGTAAAGAATAAA
396727 TAATGTAAA
1 TAATGTAAA
396736 AAATGACAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (16 bp):
TAATGTAAAGAATAAA
Found at i:398524 original size:12 final size:12
Alignment explanation
Indices: 398496--398535 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
398486 AATAAATAGA
398496 AAATGTAGAATGC
1 AAATGTA-AATGC
*
398509 AAATGTAAATGT
1 AAATGTAAATGC
*
398521 AAATGAAAATGC
1 AAATGTAAATGC
398533 AAA
1 AAA
398536 AGCAAAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.23
Consensus pattern (12 bp):
AAATGTAAATGC
Found at i:398530 original size:18 final size:19
Alignment explanation
Indices: 398496--398531 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
398486 AATAAATAGA
*
398496 AAATGTAGAATGCAAATGT
1 AAATGTAGAATGAAAATGT
398515 AAATGTA-AATGAAAATG
1 AAATGTAGAATGAAAATG
398532 CAAAAGCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (19 bp):
AAATGTAGAATGAAAATGT
Found at i:400365 original size:41 final size:41
Alignment explanation
Indices: 400316--400470 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
400306 TAGTTGAAAA
400316 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
400357 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
*
400398 TTGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
400439 TCGCGTTGCGATAGTCTA-ATGTGTCGTTGCGA
1 TCGCGTTGCGATAGTCTACA-GTGTCGTTGCGA
400471 GTCTACAGTG
Statistics
Matches: 111, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
40 1 0.01
41 110 0.99
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
Found at i:400486 original size:60 final size:60
Alignment explanation
Indices: 400401--400530 Score: 208
Period size: 60 Copynumber: 2.1 Consensus size: 60
400391 TTCCATTTTG
*
400401 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTA-ATGTGT
1 CGTTGCG--AGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTCTACA-GTGT
*
400463 CGTTGCGAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTGTACAGTGT
1 CGTTGCGAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTCTACAGTGT
400523 CGTTGCGA
1 CGTTGCGA
400531 TTTTCCATTT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
60 57 0.88
61 1 0.02
62 7 0.11
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.36
Consensus pattern (60 bp):
CGTTGCGAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTCTACAGTGT
Found at i:400505 original size:101 final size:101
Alignment explanation
Indices: 400360--400571 Score: 363
Period size: 101 Copynumber: 2.1 Consensus size: 101
400350 TTCCATTTCG
* *
400360 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTTGCGTTGCGATAGTCTACAGTGTCGT
1 CGTTGCG--AGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTCTACAGTGTCGT
400425 TGCGATTTTCCATTTCGCGTTGCGATAGTCTA-ATGTGT
64 TGCGATTTTCCATTTCGCGTTGCGATAGTCTACA-GTGT
*
400463 CGTTGCGAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTGTACAGTGTCGTTG
1 CGTTGCGAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTCTACAGTGTCGTTG
400528 CGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
66 CGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
400564 CGTTGCGA
1 CGTTGCGA
400572 TTTTCCAAAT
Statistics
Matches: 105, Mismatches: 3, Indels: 4
0.94 0.03 0.04
Matches are distributed among these distances:
101 97 0.92
102 1 0.01
103 7 0.07
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (101 bp):
CGTTGCGAGTCTACAGTGTCGTTGCGATTTTCCATCTCGCGTTGCGATAGTCTACAGTGTCGTTG
CGATTTTCCATTTCGCGTTGCGATAGTCTACAGTGT
Found at i:400523 original size:41 final size:41
Alignment explanation
Indices: 400463--400601 Score: 212
Period size: 41 Copynumber: 3.5 Consensus size: 41
400453 TCTAATGTGT
*
400463 CGTTGCG--AGTCTACAGTGTCGTTGCGATTTTCCATCTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATATCG
* *
400502 CGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATATCG
* *
400543 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATATCG
400583 CGTTGCGATAGTCTACAGT
1 CGTTGCGATAGTCTACAGT
400602 AAATTAAAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
39 7 0.08
40 19 0.21
41 66 0.72
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATATCG
Found at i:400552 original size:142 final size:144
Alignment explanation
Indices: 400290--400597 Score: 493
Period size: 142 Copynumber: 2.2 Consensus size: 144
400280 TTCAGTATCG
400290 CAAATTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCC
1 CAAATTCGCGTTGCGATAGTCT-AAAATCGCGTTGCGA-AGTCTACAGTGTCGTTGCGATTTTCC
* *
400354 ATTTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTTGCGTTGCGATAGTCTACAG
64 ATCTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAG
400419 TGTCGTTGCGATTTTC
129 TGTCGTTGCGATTTTC
* **
400435 C-ATTTCGCGTTGCGATAGTCTAATGT-GTCGTTGCG-AGTCTACAGTGTCGTTGCGATTTTCCA
1 CAAATTCGCGTTGCGATAGTCTAAAATCG-CGTTGCGAAGTCTACAGTGTCGTTGCGATTTTCCA
*
400497 TCTCGCGTTGCGATAGTGTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
65 TCTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGT
400562 GTCGTTGCGATTTTC
130 GTCGTTGCGATTTTC
400577 CAAATT--CGTTGCGATAGTCTA
1 CAAATTCGCGTTGCGATAGTCTA
400598 CAGTAAATTA
Statistics
Matches: 153, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
141 15 0.10
142 105 0.69
143 4 0.03
144 27 0.18
145 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.37
Consensus pattern (144 bp):
CAAATTCGCGTTGCGATAGTCTAAAATCGCGTTGCGAAGTCTACAGTGTCGTTGCGATTTTCCAT
CTCGCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTG
TCGTTGCGATTTTC
Found at i:400692 original size:6 final size:6
Alignment explanation
Indices: 400681--400754 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
400671 GACACGTATT
400681 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
400729 ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
400755 CGAGACGAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:401267 original size:6 final size:6
Alignment explanation
Indices: 401256--401390 Score: 270
Period size: 6 Copynumber: 22.5 Consensus size: 6
401246 TCTCGTCTCG
401256 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
401304 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
401352 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
401391 AATACGTGTC
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 129 1.00
ACGTcount: A:0.00, C:0.16, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:401488 original size:19 final size:18
Alignment explanation
Indices: 401464--401553 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 18
401454 ACTGTAGACT
*
401464 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAA-ATGGAAA
401483 ATCGCAACGCGAAATGGAAA
1 ATCGCAA--CGAAATGGAAA
* **
401503 ATCGCAACGACACTGTAGACT
1 ATCGCAACGA-AATG--GAAA
401524 ATCGCAACGCGAAATGGAAA
1 ATCGCAA--CGAAATGGAAA
401544 ATCGCAACGA
1 ATCGCAACGA
401554 CACTGTAGAC
Statistics
Matches: 57, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
18 6 0.11
19 10 0.18
20 22 0.39
21 13 0.23
22 3 0.05
23 3 0.05
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAACGAAATGGAAA
Found at i:401502 original size:20 final size:20
Alignment explanation
Indices: 401477--401596 Score: 95
Period size: 20 Copynumber: 5.9 Consensus size: 20
401467 GCAACGAATT
401477 TGGAAAATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAAA
*
401497 TGGAAAATCGCAA--CGACAC
1 TGGAAAATCGCAACGCGA-AA
**
401516 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
*
401538 TGGAAAATCGCAA--CGACAC
1 TGGAAAATCGCAACGCGA-AA
**
401557 TGTAGACTATCGCAACGCGAAA
1 TG--GAAAATCGCAACGCGAAA
*
401579 AGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
401597 TTTTCAACTA
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
18 6 0.08
19 6 0.08
20 36 0.47
21 18 0.23
22 5 0.06
23 6 0.08
ACGTcount: A:0.41, C:0.23, G:0.23, T:0.12
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAA
Done.