Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004464.1 Hibiscus syriacus cultivar Beakdansim tig00009840_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: 466920
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 2 of 2
Found at i:206031 original size:95 final size:94
Alignment explanation
Indices: 205878--206119 Score: 260
Period size: 95 Copynumber: 2.7 Consensus size: 94
205868 TATAATATTA
* * *
205878 TATATATACAATAAAGCTTGAGTTGTCACTCTAGAGCAATTGGTTAAATGCCCCGACTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCACTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
*
205943 TAATATTCAGCTAGCCAGATAAAGGTGAT
66 TAAGATTCAGCTAGCCAGATAAAGGTGAT
* * *
205972 TATACTATACAATAAAGTTTGAGCTATCCCTCTA-AGGCAATTGGTTAAACGCCCTGACTTTATG
1 TATA-TATACAATAAAGCTTGAGCTATCACTCTAGA-GCAATTGGTTAAACGCCCCGACTTTATG
*
206036 GATAAGATTCAGCTA-ACA-ATAAA-G-G--
64 GATAAGATTCAGCTAGCCAGATAAAGGTGAT
* * * *
206061 TAT-T-TAC-AT--A--TTGAGCTATCCCTTTAGAGCAATTGGTAAAACGCCCCGGCTTTATGGA
1 TATATATACAATAAAGCTTGAGCTATCACTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
206119 T
66 T
206120 TTAGCTAGCC
Statistics
Matches: 133, Mismatches: 12, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
81 43 0.32
82 1 0.01
83 1 0.01
85 2 0.02
86 3 0.02
87 1 0.01
89 3 0.02
91 1 0.01
92 1 0.01
93 5 0.04
94 7 0.05
95 65 0.49
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTATCACTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGGA
TAAGATTCAGCTAGCCAGATAAAGGTGAT
Found at i:207468 original size:162 final size:162
Alignment explanation
Indices: 207279--208191 Score: 866
Period size: 162 Copynumber: 5.5 Consensus size: 162
207269 CAAGGGTTGT
* * *
207279 CTATCAGCC-AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGTCACATCATTTGCAGCATAGC
1 CTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGC
* * *
207343 TCAAGGCCAGAAGGGCTATCTGCCACCATGACCTTCGAGTTTGACTACGCTCAGCTCCAAGACAT
66 TCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
* *
207408 ATCATTTGTAGCATAACTTAAGTTGAGAAGGG
131 ATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* ** * *
207440 CTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGATACATCATTTGCAGTATAGA
1 CTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGC
* ** *
207505 TCAAGGCCAGATGGGCTATCTATCACCAAGAACTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
66 TCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
* *
207570 ATCATTTGCAGTATAACTTAAGTCGAGATGGG
131 ATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * *
207602 TTATCTGCCAACCAAAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCA
1 CTATCTG----CCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCA
* *** * * * *
207667 TAGCTTAAGTTGATAA-GGCTATCTGCCA--AAGA-CTCTCGAGTTCGATTACACTCAGCTTCGA
62 TAGCTCAAGGCCAGAAGGGCTATCTGCCACCAAGACCT-TCGAGTTCGACTACGCTCAGC-TCCA
* * * * * * * *
207728 GGGCACATCATTTACAACATAACTCAAGGCTATAAGGG
125 AGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * **
207766 TTATCTGTAACCAAACGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACGTATCATTTGCAGCA
1 CTATCTG---CCAAA-GACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCA
* * * * * * * * * *
207831 AAACTTAAGTCGAGAAGGGTTATCTTCCAACCAA-ATGTCTTCGAATTCGACTACGCTTAGCTCC
62 TAGCTCAAGGCCAGAAGGGCTATCTGCC-ACCAAGA--CCTTCGAGTTCGACTACGCTCAGCTCC
*
207895 AAGGCGTATCATTTGCAGCATAACTTAAGTCGAGAAGGG
124 AAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
** * * * ** *
207934 CTATCTGTTAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTTAAGCATAA
1 CTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAG
* * * * * * *
207999 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCAACTACACTCACCTCCAAGA
65 CTCAAGGCCAGAAGGGCTATCTGCCACC--AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
* *
208064 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGG
128 CATATCATTTGCAGCATAACTTAAGTCGAGAAGGG
* * * * * *
208099 CTATCTGCCAACCGAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCAAACCAAATTTACAG
1 CTATCTGCC-A---AAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATC--ATTTGCAG
* * *
208164 AATAGCCCAAGGCAAGAAGGGCTATCTG
60 CATAGCTCAAGGCCAGAAGGGCTATCTG
208192 TCAATAAATT
Statistics
Matches: 613, Mismatches: 114, Indels: 41
0.80 0.15 0.05
Matches are distributed among these distances:
161 8 0.01
162 145 0.24
163 30 0.05
164 119 0.19
165 124 0.20
166 61 0.10
167 2 0.00
168 50 0.08
169 43 0.07
170 31 0.05
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.25
Consensus pattern (162 bp):
CTATCTGCCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGC
TCAAGGCCAGAAGGGCTATCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCAT
ATCATTTGCAGCATAACTTAAGTCGAGAAGGG
Found at i:207658 original size:84 final size:82
Alignment explanation
Indices: 207288--208149 Score: 812
Period size: 84 Copynumber: 10.5 Consensus size: 82
207278 TCTATCAGCC
* * * * *
207288 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGTCACATCATTTGCAGCATAGCTCAAGGCCAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
207353 AAGGGCTATCTGCCACC-
66 AAGGGCTATCTG-CACCA
* * * * * *
207370 ATGACCTTCGAGTTTGACTACGCTCAGCTCCAAGACATATCATTTGTAGCATAACTTAAGTTGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
207435 AAGGGCTATCTG--CCA
66 AAGGGCTATCTGCACCA
** * * * *
207450 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGATACATCATTTGCAGTATAGA-TCAAGGCCA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATA-ACTTAAGTCGA
* *
207514 GATGGGCTATCTATCACC-
65 GAAGGGCTATCT-GCACCA
* * *
207532 AAGAACTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* *
207597 ATGGGTTATCTGCCAACCA
66 AAGGGCTATCTG-C-ACCA
* * * * * *
207616 AAGACCTTCAAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTTGAT
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
207681 AA-GGCTATCTG--CCA
66 AAGGGCTATCTGCACCA
* * * * * * * * *
207695 AAGA-CTCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCT
1 AAGACCT-TCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
207759 ATAAGGGTTATCTGTAACCA
64 AGAAGGGCTATCTG-CACCA
* ** *
207779 AACGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACGTATCATTTGCAGCAAAACTTAAGTCGA
1 AA-GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
* *
207844 GAAGGGTTATCTTCCAACCA
65 GAAGGGCTATC-TGC-ACCA
* * * **
207864 AATG-TCTTCGAATTCGACTACGCTTAGCTCCAAGGCGTATCATTTGCAGCATAACTTAAGTCGA
1 AA-GACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
**
207928 GAAGGGCTATCTG--TTA
65 GAAGGGCTATCTGCACCA
* * * * ** * * *
207944 AAGACCCTCGAGTTCGATTACACTCAGCTTCGAAGGCACATCATTTTAAGCATAACTCAAGGCTA
1 AAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGA
*
208009 GAAGGGTTATCTGTCACCAA
65 GAAGGGCTATCTG-CACC-A
* * * * *
208029 AAGACCTTCGAGTTCAACTACACTCACCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
*
208094 AAGGGCTATCTGCCAACCG
66 AAGGGCTATCTG-C-ACCA
* * * *
208113 AAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
208150 AACCAAATTT
Statistics
Matches: 638, Mismatches: 116, Indels: 50
0.79 0.14 0.06
Matches are distributed among these distances:
78 2 0.00
79 29 0.05
80 115 0.18
81 50 0.08
82 134 0.21
83 14 0.02
84 235 0.37
85 57 0.09
86 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (82 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
AAGGGCTATCTGCACCA
Found at i:208062 original size:249 final size:250
Alignment explanation
Indices: 207288--208149 Score: 1066
Period size: 249 Copynumber: 3.5 Consensus size: 250
207278 TCTATCAGCC
* * * * *
207288 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGTCACATCATTTGCAGCATAGCTCAAGGCCAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGAG
* * *
207353 AAGGGCTATCTGCC-ACC--ATGACCTTCGAGTTTGACTACGCTCAGCTCCAAGACATATCATTT
66 AAGGGCTATCTGCCAACCAAATGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATATCATTT
* * * *
207415 GTAGCATAACTTAAGTTGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGC-T
131 GCAGCATAACTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
* ** ** * * * * *
207479 CCAAGATACATCATTTGCAGTATAGA-TCAAGGCCAGATGGGCTATCTATCACC--
196 CGAAGGCACATCATTTTAAGCATA-ACTCAAGGCTAGAAGGGTTATCTGTCACCAA
* * * *
207532 AAGAACTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGAG
* * * *
207597 ATGGGTTATCTGCCAACCAAA-GACCTTC-AAGTTCGACTACACTCAGCTCCAAGGCACATCATT
66 AAGGGCTATCTGCCAACCAAATGACCTTCGAA-TTCGACTACGCTCAGCTCCAAGGCATATCATT
* * * *
207660 TACAGCATAGCTTAAGTTGATAA-GGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCT
130 TGCAGCATAACTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCT
* * * *
207724 TCGAGGGCACATCA-TTTACAACATAACTCAAGGCTATAAGGGTTATCTGTAACCAA
195 TCGAAGGCACATCATTTTA-AGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAA
* ** *
207780 ACGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACGTATCATTTGCAGCAAAACTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGAG
* * * * *
207845 AAGGGTTATCTTCCAACCAAATG-TCTTCGAATTCGACTACGCTTAGCTCCAAGGCGTATCATTT
66 AAGGGCTATCTGCCAACCAAATGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATATCATTT
* **
207909 GCAGCATAACTTAAGTCGAGAAGGGCTATCTGTTAAAGACCCTCGAGTTCGATTACACTCAGCTT
131 GCAGCATAACTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
207974 CGAAGGCACATCATTTTAAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAA
196 CGAAGGCACATCATTTTAAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAA
* * * *
208029 AAGACCTTCGAGTTCAACTACACTCACCTCCAAGACACATCATTTGCAGCATAGCTTAAGTCGAG
1 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGAG
* * * * * *
208094 AAGGGCTATCTGCCAACCGAA-GACCTTCGAGTTCGATTACACTCAACTCAAAGGCA
66 AAGGGCTATCTGCCAACCAAATGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCA
208150 AACCAAATTT
Statistics
Matches: 524, Mismatches: 80, Indels: 23
0.84 0.13 0.04
Matches are distributed among these distances:
244 69 0.13
245 43 0.08
246 89 0.17
247 1 0.00
248 130 0.25
249 188 0.36
250 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (250 bp):
AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACACATCATTTGCAGCATAACTTAAGTCGAG
AAGGGCTATCTGCCAACCAAATGACCTTCGAATTCGACTACGCTCAGCTCCAAGGCATATCATTT
GCAGCATAACTTAAGTTGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTT
CGAAGGCACATCATTTTAAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAA
Found at i:208767 original size:37 final size:36
Alignment explanation
Indices: 208726--208836 Score: 161
Period size: 37 Copynumber: 3.0 Consensus size: 36
208716 AACATAACGT
* *
208726 TAGAGTTCTACTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTT-TACTATGATTCAAACTCCTAAAAATAGGA
*
208763 TAGAGTGTTACCATGATTCAAACTCCTAAAAATAGGA
1 TAGAGT-TTACTATGATTCAAACTCCTAAAAATAGGA
208800 TAGAGTTTTACTATGATTCAAACTCCT-AAAATAGGA
1 TAGAG-TTTACTATGATTCAAACTCCTAAAAATAGGA
208836 T
1 T
208837 CATAAGCATT
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
36 10 0.15
37 56 0.82
38 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (36 bp):
TAGAGTTTACTATGATTCAAACTCCTAAAAATAGGA
Found at i:209353 original size:24 final size:23
Alignment explanation
Indices: 209309--209353 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
209299 TTATATTTTT
*
209309 TATCTTATTTTATTTTATTTCCC
1 TATCTTATTATATTTTATTTCCC
209332 TATCATTATTATATATTT-TTTC
1 TATC-TTATTATAT-TTTATTTC
209354 TCTCTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 12 0.63
25 3 0.16
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.64
Consensus pattern (23 bp):
TATCTTATTATATTTTATTTCCC
Found at i:209383 original size:16 final size:17
Alignment explanation
Indices: 209358--209391 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
209348 TTTTTCTCTC
*
209358 TATTATTTATCTATATG
1 TATTATTTATATATATG
209375 TATTATTATATATATAT
1 TATTATT-TATATATAT
209392 ATACATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTATTTATATATATG
Found at i:209527 original size:3 final size:3
Alignment explanation
Indices: 209519--209550 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
209509 TTACTTACTT
*
209519 TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
209551 CTATTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:209565 original size:9 final size:10
Alignment explanation
Indices: 209518--209564 Score: 53
Period size: 9 Copynumber: 4.6 Consensus size: 10
209508 TTTACTTACT
209518 TTTATTATTA
1 TTTATTATTA
209528 -TTATTATTA
1 TTTATTATTA
209537 GTATTATTATTA
1 -T-TTATTATTA
209549 TTCTATT-TTA
1 TT-TATTATTA
209559 TTTATT
1 TTTATT
209565 TATATTTACC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 13 0.39
10 6 0.18
11 5 0.15
12 9 0.27
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATTATTA
Found at i:210495 original size:29 final size:29
Alignment explanation
Indices: 210458--210546 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
210448 AAGTTATGAT
210458 TTATGATTTATGGTTTATAGGTTATTAGG
1 TTATGATTTATGGTTTATAGGTTATTAGG
* *
210487 TTATGATTTA-GAGTTCA-A-G---CT---
1 TTATGATTTATG-GTTTATAGGTTATTAGG
210508 TTATGATTTATGGTTTATAGGTTATTAGG
1 TTATGATTTATGGTTTATAGGTTATTAGG
210537 TTATGATTTA
1 TTATGATTTA
210547 GAGTTCAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 20
0.66 0.06 0.29
Matches are distributed among these distances:
21 14 0.30
22 2 0.04
23 1 0.02
24 1 0.02
26 1 0.02
27 1 0.02
28 2 0.04
29 24 0.52
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (29 bp):
TTATGATTTATGGTTTATAGGTTATTAGG
Found at i:210532 original size:50 final size:50
Alignment explanation
Indices: 210457--210567 Score: 213
Period size: 50 Copynumber: 2.2 Consensus size: 50
210447 TAAGTTATGA
210457 TTTATGATTTATGGTTTATAGGTTATTAGGTTATGATTTAGAGTTCAAGC
1 TTTATGATTTATGGTTTATAGGTTATTAGGTTATGATTTAGAGTTCAAGC
210507 TTTATGATTTATGGTTTATAGGTTATTAGGTTATGATTTAGAGTTCAAGC
1 TTTATGATTTATGGTTTATAGGTTATTAGGTTATGATTTAGAGTTCAAGC
*
210557 TTTATAATTTA
1 TTTATGATTTA
210568 AGTTTTTAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.50
Consensus pattern (50 bp):
TTTATGATTTATGGTTTATAGGTTATTAGGTTATGATTTAGAGTTCAAGC
Found at i:213686 original size:48 final size:48
Alignment explanation
Indices: 213615--213712 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
213605 ATAATGGCAG
*
213615 GGGAAAAAAGGTGGTATAGGGTTCCATACGACACGATGATATTTTAAA
1 GGGAAAAAAGGTGGTACAGGGTTCCATACGACACGATGATATTTTAAA
*
213663 GGGAAAAAAGGTGGTACAGGGTTCCATACGACACGATGATCTTTTAAA
1 GGGAAAAAAGGTGGTACAGGGTTCCATACGACACGATGATATTTTAAA
213711 GG
1 GG
213713 ATACATGCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (48 bp):
GGGAAAAAAGGTGGTACAGGGTTCCATACGACACGATGATATTTTAAA
Found at i:214951 original size:35 final size:36
Alignment explanation
Indices: 214912--214992 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 36
214902 GATCTGTAAA
* ** *
214912 GAATTACCAGCTCGATCGTTCTGAACCTA-TATAAG
1 GAATTACCAGCTCGACCGAGCTGAACCTACCATAAG
* * *
214947 GAATTACTAGTTTGACCGAGCTGAACCTACCATAAG
1 GAATTACCAGCTCGACCGAGCTGAACCTACCATAAG
214983 GAATTACCAG
1 GAATTACCAG
214993 TTTAATCATA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
35 23 0.62
36 14 0.38
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (36 bp):
GAATTACCAGCTCGACCGAGCTGAACCTACCATAAG
Found at i:224025 original size:91 final size:91
Alignment explanation
Indices: 223868--224051 Score: 269
Period size: 91 Copynumber: 2.0 Consensus size: 91
223858 ACTAGTATCA
* * * ** *
223868 ATAACTAATCATCAAAACTTAATTAATAGTCAGATGAGCTTTAATACTTCAGGTACACTTATTAG
1 ATAACTAATCATCAAAACTTAATTAAAAGTCAGACGAGCTTTAATACTTAAAATACACTTAATAG
* *
223933 TTTCTATGGATTATCCCATATATGTT
66 TTTCTATGAATTATCCCATAGATGTT
* * *
223959 ATAACTAATCATCAAAATTTAATTAAAAGTCATACGATCTTTAATACTTAAAATACACTTAATAG
1 ATAACTAATCATCAAAACTTAATTAAAAGTCAGACGAGCTTTAATACTTAAAATACACTTAATAG
224024 TTTCTATGAATTATCCCATAGATGTT
66 TTTCTATGAATTATCCCATAGATGTT
224050 AT
1 AT
224052 CATCTCAAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.38
Consensus pattern (91 bp):
ATAACTAATCATCAAAACTTAATTAAAAGTCAGACGAGCTTTAATACTTAAAATACACTTAATAG
TTTCTATGAATTATCCCATAGATGTT
Found at i:224462 original size:65 final size:65
Alignment explanation
Indices: 224358--224482 Score: 207
Period size: 65 Copynumber: 1.9 Consensus size: 65
224348 TAATGAACTG
224358 TTTTTGCTTGTAGTCTTGTCCCCTTTTTTCTAATTTAGCACAGAAATGAAAGCATACACACATAC
1 TTTTTGCTTGTAGTCTTGTCCCCTTTTTTCTAATTTAGCACAGAAATGAAAGCATACACACATAC
* * *
224423 TTTTTGCTTGTAGTCCTT-TTCCCTTTTTTCTAATTTAGCACAGAATTGCAAGCATACACA
1 TTTTTGCTTGTAGT-CTTGTCCCCTTTTTTCTAATTTAGCACAGAAATGAAAGCATACACA
224483 TATAGTCACA
Statistics
Matches: 56, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
65 53 0.95
66 3 0.05
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.41
Consensus pattern (65 bp):
TTTTTGCTTGTAGTCTTGTCCCCTTTTTTCTAATTTAGCACAGAAATGAAAGCATACACACATAC
Found at i:227600 original size:12 final size:13
Alignment explanation
Indices: 227583--227611 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
227573 TTTAATTGCG
227583 AAAATTAAAA-TT
1 AAAATTAAAATTT
227595 AAAATTAAAATTT
1 AAAATTAAAATTT
227608 AAAA
1 AAAA
227612 AATTCAATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:227717 original size:20 final size:21
Alignment explanation
Indices: 227683--227721 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
227673 GTTAAATAAT
227683 AGAATAAAATAAAATAAAATG
1 AGAATAAAATAAAATAAAATG
*
227704 AGAA-AAAATTAAATAAAA
1 AGAATAAAATAAAATAAAA
227722 AAAATTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (21 bp):
AGAATAAAATAAAATAAAATG
Found at i:229290 original size:36 final size:36
Alignment explanation
Indices: 229176--229295 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
229166 TGGCAACAAA
229176 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
229213 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* * *
229248 CTTTGAAAAATAGTTTTTCAAAGTTTAGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
229285 -GTTGAAAAATG
1 CTTTGAAAAATG
229296 ATAATGGGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 36 0.47
36 14 0.18
37 27 0.35
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:233825 original size:21 final size:21
Alignment explanation
Indices: 233801--233861 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
233791 AACTTTGAAA
233801 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
233822 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
233836 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
233857 AAATG
1 AAATG
233862 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:233837 original size:37 final size:36
Alignment explanation
Indices: 233793--233912 Score: 181
Period size: 35 Copynumber: 3.3 Consensus size: 36
233783 TGGCAACCAA
233793 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
233830 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
233865 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
233902 -GTTGAAAAATG
1 CTTTGAAAAATG
233913 ATAATGGGAT
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:234862 original size:72 final size:72
Alignment explanation
Indices: 234745--234880 Score: 227
Period size: 72 Copynumber: 1.9 Consensus size: 72
234735 ACCAATTCTG
* *
234745 TGTGCCTCTAGCATAGGCGCGTCTTCTAAAACCAAGATGCTGGCATGCCAGCAAATATCAAGAAG
1 TGTGCCTCGAGCATAGGCGCGCCTTCTAAAACCAAGATGCTGGCATGCCAGCAAATATCAAGAAG
234810 CACTGGT
66 CACTGGT
* * *
234817 TGTGCCTCGCGCATAGGCGCGCCTTTTAAAACCAAGATGGTGGCATGCCAGCAAATATCAAGAA
1 TGTGCCTCGAGCATAGGCGCGCCTTCTAAAACCAAGATGCTGGCATGCCAGCAAATATCAAGAA
234881 ATGAACTGAG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 59 1.00
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.21
Consensus pattern (72 bp):
TGTGCCTCGAGCATAGGCGCGCCTTCTAAAACCAAGATGCTGGCATGCCAGCAAATATCAAGAAG
CACTGGT
Found at i:236814 original size:35 final size:35
Alignment explanation
Indices: 236763--236842 Score: 142
Period size: 35 Copynumber: 2.3 Consensus size: 35
236753 AACACAATCA
*
236763 TCAATTACATTCTAAACCTCAAATTCCAAAATATT
1 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
*
236798 TCAATTACATTTTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
236833 TCAATTACAT
1 TCAATTACAT
236843 GCCCAACCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAATTCCAAAATACT
Found at i:237688 original size:36 final size:35
Alignment explanation
Indices: 237632--237725 Score: 109
Period size: 36 Copynumber: 2.7 Consensus size: 35
237622 AATGAATTAT
* * * * *
237632 GAATTTGAGGTTGAGCATGTAATTAAAGTTTTTTTG
1 GAATTTGAGGTTTAGAATGTAATTAAA-CTATTTTA
* *
237668 GAGTTTGAGGTTTAGAATGTAATTGAACTATTTTA
1 GAATTTGAGGTTTAGAATGTAATTAAACTATTTTA
237703 GAATTT-AGGTTTAGAATGTAATT
1 GAATTTGAGGTTTAGAATGTAATT
237726 GATTATTGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
34 17 0.34
35 10 0.20
36 23 0.46
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.44
Consensus pattern (35 bp):
GAATTTGAGGTTTAGAATGTAATTAAACTATTTTA
Found at i:245334 original size:18 final size:17
Alignment explanation
Indices: 245290--245334 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
245280 TTGGTCTCCA
245290 TTCTTTTTCACGTTTTT
1 TTCTTTTTCACGTTTTT
* *
245307 TTTTTCTTTCTCGCTTTTT
1 TTCTT-TTTCACG-TTTTT
245326 TTCTTTTTC
1 TTCTTTTTC
245335 GAACAACATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.17
18 10 0.43
19 9 0.39
ACGTcount: A:0.02, C:0.20, G:0.04, T:0.73
Consensus pattern (17 bp):
TTCTTTTTCACGTTTTT
Found at i:245350 original size:26 final size:26
Alignment explanation
Indices: 245321--245387 Score: 64
Period size: 29 Copynumber: 2.5 Consensus size: 26
245311 TCTTTCTCGC
*
245321 TTTTTTTCTTTTTCGAACAACATTTTTT
1 TTTTTTTCTTTTTCGAACAAC--TTATT
* *
245349 TTTCTTTTTTTTTTCGAACTAC-TATT
1 TTT-TTTTCTTTTTCGAACAACTTATT
*
245375 TTTCTTTCTTTTT
1 TTTTTTTCTTTTT
245388 TTCTTTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 8 0.24
26 6 0.18
28 3 0.09
29 16 0.48
ACGTcount: A:0.13, C:0.15, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTTTTTCTTTTTCGAACAACTTATT
Found at i:245363 original size:29 final size:30
Alignment explanation
Indices: 245323--245389 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
245313 TTTCTCGCTT
*
245323 TTTTTCTTTTTCGAACAAC-ATTTTTTTTTC
1 TTTTT-TTTTTCGAACAACTATTTTTCTTTC
*
245353 TTTTTTTTTTCGAACTACTATTTTTCTTTC
1 TTTTTTTTTTCGAACAACTATTTTTCTTTC
245383 TTTTTTT
1 TTTTTTT
245390 CTTTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.13, C:0.15, G:0.03, T:0.69
Consensus pattern (30 bp):
TTTTTTTTTTCGAACAACTATTTTTCTTTC
Found at i:250225 original size:19 final size:19
Alignment explanation
Indices: 250188--250224 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
250178 TGACCAAAGT
250188 CTATATTTGATTTTGAAAA
1 CTATATTTGATTTTGAAAA
250207 CTAT-TTTGATTTTGAAAA
1 CTATATTTGATTTTGAAAA
250225 ATAAGCGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (19 bp):
CTATATTTGATTTTGAAAA
Found at i:255222 original size:21 final size:23
Alignment explanation
Indices: 255178--255225 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
255168 TTTATTGAAA
* *
255178 TATTTTTATATAAATATAGTTTT
1 TATTTTTATAAAAAAATAGTTTT
255201 TATTTTT-TAAAAAAAT-GTTTT
1 TATTTTTATAAAAAAATAGTTTT
255222 TATT
1 TATT
255226 CACCCACGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 7 0.30
23 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTTTTATAAAAAAATAGTTTT
Found at i:260401 original size:7 final size:7
Alignment explanation
Indices: 260384--260418 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
260374 ATAACCATAA
260384 TTTTATAT
1 TTTTAT-T
260392 TTTTATT
1 TTTTATT
260399 TTTTATT
1 TTTTATT
260406 TTTTATT
1 TTTTATT
260413 TTTTAT
1 TTTTAT
260419 AATATAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTATT
Found at i:275552 original size:212 final size:212
Alignment explanation
Indices: 275141--275553 Score: 776
Period size: 212 Copynumber: 1.9 Consensus size: 212
275131 AGTAAAATAG
275141 GAATAATAATTTAAAATTAAAATTTCCTGCCCCAAATAATATTTACCCTAAATTCTTTTTTATTC
1 GAATAATAATTTAAAATTAAAATTTCCTGCCCCAAATAATATTTACCCTAAATTCTTTTTTATTC
275206 CTACTCGGACATAATCTCTATCCCATATTTCTTGAATAAATCTTAATGGCATATATTTTAATTCA
66 CTACTCGGACATAATCTCTATCCCA-ATTTCTTGAATAAATCTTAATGGCATATATTTTAATTCA
275271 CATACTTTGAACAGAAATAAAGCAGGAAATAAATCAAGCATCGAGGTTTTAAAATGAAGTTTTGG
130 CATACTTTGAACAGAAATAAAGCAGGAAATAAATCAAGCATCGAGGTTTTAAAATGAAGTTTTGG
275336 GTGGGAATTCCTTGCAGT
195 GTGGGAATTCCTTGCAGT
275354 GAATAATAA-TTAAAATTAAAATTTCCTGCCCCAAATAATATTTACCCTAAATTCTTTTTTATTC
1 GAATAATAATTTAAAATTAAAATTTCCTGCCCCAAATAATATTTACCCTAAATTCTTTTTTATTC
275418 CTACTCGGACATAATCTCTATCCC-ATTTCTTGAATAAATCTTAATGGCATATATTTCTAATTCA
66 CTACTCGGACATAATCTCTATCCCAATTTCTTGAATAAATCTTAATGGCATATATTT-TAATTCA
*
275482 CATACTTTGAACAGAAATAAAGCAGGAAATAAATCAAGCATCTAGGTTTTAAAATGAAGTTTTGG
130 CATACTTTGAACAGAAATAAAGCAGGAAATAAATCAAGCATCGAGGTTTTAAAATGAAGTTTT-G
275547 GGTGGGA
194 GGTGGGA
275554 TCTAATTCCT
Statistics
Matches: 197, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
210 32 0.16
211 69 0.35
212 87 0.44
213 9 0.05
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (212 bp):
GAATAATAATTTAAAATTAAAATTTCCTGCCCCAAATAATATTTACCCTAAATTCTTTTTTATTC
CTACTCGGACATAATCTCTATCCCAATTTCTTGAATAAATCTTAATGGCATATATTTTAATTCAC
ATACTTTGAACAGAAATAAAGCAGGAAATAAATCAAGCATCGAGGTTTTAAAATGAAGTTTTGGG
TGGGAATTCCTTGCAGT
Found at i:277463 original size:12 final size:11
Alignment explanation
Indices: 277448--277679 Score: 56
Period size: 11 Copynumber: 21.6 Consensus size: 11
277438 AATTAAACAA
277448 ATAAATAA-AT
1 ATAAATAATAT
277458 AT--ATAATAT
1 ATAAATAATAT
277467 ATAAAATAATAT
1 AT-AAATAATAT
277479 AGT--A-AATA-
1 A-TAAATAATAT
277487 AT-AATAATAT
1 ATAAATAATAT
*
277497 ATAAATGATAT
1 ATAAATAATAT
*
277508 -TATATACTATAT
1 ATAAATA--ATAT
**
277520 ATATCGTAATAT
1 ATA-AATAATAT
277532 ATATAATAATACT
1 ATA-AATAATA-T
277545 AT-AAT-ATA-
1 ATAAATAATAT
*
277553 AT-ACTAATAT
1 ATAAATAATAT
277563 ATAAA-AATAT
1 ATAAATAATAT
** *
277573 ATGTATACTAT
1 ATAAATAATAT
*
277584 AT-ACT-ATAT
1 ATAAATAATAT
*
277593 AATATATAATAT
1 -ATAAATAATAT
* *
277605 ATACCAT-ATAG
1 ATA-AATAATAT
*
277616 ATATATAATAT
1 ATAAATAATAT
277627 ATATAA-AATAT
1 ATA-AATAATAT
277638 CATACCATATAATAT
1 -ATA--A-ATAATAT
*
277653 AT-ACT-ATAT
1 ATAAATAATAT
277662 A-AAATAATAT
1 ATAAATAATAT
277672 ATATAATA
1 ATA-AATA
277680 TGATATAATA
Statistics
Matches: 165, Mismatches: 25, Indels: 62
0.65 0.10 0.25
Matches are distributed among these distances:
7 1 0.01
8 10 0.06
9 25 0.15
10 33 0.20
11 40 0.24
12 39 0.24
13 7 0.04
14 5 0.03
15 5 0.03
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAAATAATAT
Found at i:277467 original size:7 final size:7
Alignment explanation
Indices: 277455--277680 Score: 129
Period size: 7 Copynumber: 32.7 Consensus size: 7
277445 CAAATAAATA
277455 AATATAT
1 AATATAT
277462 AATATAT
1 AATATAT
277469 AA-A-AT
1 AATATAT
277474 AATATAGT
1 AATATA-T
277482 AAATAATAAT
1 -AAT-AT-AT
277492 AATATAT
1 AATATAT
277499 AA-ATGAT
1 AATAT-AT
*
277506 ATTATAT
1 AATATAT
*
277513 ACTATAT
1 AATATAT
*
277520 -ATATCGT
1 AATAT-AT
277527 AATATAT
1 AATATAT
277534 -ATA-AT
1 AATATAT
277539 AATACTAT
1 AATA-TAT
277547 -A-ATAT
1 AATATAT
*
277552 AATA-CT
1 AATATAT
277558 AATATAT
1 AATATAT
*
277565 AA-AAAT
1 AATATAT
*
277571 ATATGTAT
1 A-ATATAT
*
277579 ACTATAT
1 AATATAT
*
277586 ACTATAT
1 AATATAT
277593 AATATAT
1 AATATAT
277600 AATATAT
1 AATATAT
**
277607 ACCATAT
1 AATATAT
277614 AGATATAT
1 A-ATATAT
277622 AATATAT
1 AATATAT
277629 -ATA-A-
1 AATATAT
277633 AATATCAT
1 AATAT-AT
**
277641 ACCATAT
1 AATATAT
277648 AATATAT
1 AATATAT
*
277655 ACTATAT
1 AATATAT
*
277662 AAAATA-
1 AATATAT
277668 ATATATAT
1 A-ATATAT
277676 AATAT
1 AATAT
277681 GATATAATAA
Statistics
Matches: 169, Mismatches: 25, Indels: 50
0.69 0.10 0.20
Matches are distributed among these distances:
5 13 0.08
6 28 0.17
7 95 0.56
8 23 0.14
9 6 0.04
10 3 0.02
11 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.38
Consensus pattern (7 bp):
AATATAT
Found at i:277468 original size:2 final size:2
Alignment explanation
Indices: 277456--277686 Score: 90
Period size: 2 Copynumber: 119.5 Consensus size: 2
277446 AAATAAATAA
* *
277456 AT AT AT A- AT AT AT A- AA AT A- AT AT AGT AA AT A- AT A- AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
277493 AT AT AT AA AT GAT AT -T AT AT ACT AT AT AT AT CGT A- AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT A-T AT AT AT AT -AT AT AT AT AT
* *
277534 AT A- AT A- AT ACT AT A- AT AT A- AT ACT A- AT AT AT AA AA AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* *
277573 AT GT AT ACT AT AT ACT AT AT A- AT AT AT A- AT AT AT ACC AT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
277614 AG AT AT AT A- AT AT AT AT A- AA AT AT CAT ACC AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT
*
277655 ACT AT AT A- AA AT A- AT AT AT AT A- AT AT GAT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
277687 ATAAAAAGGA
Statistics
Matches: 176, Mismatches: 19, Indels: 68
0.67 0.07 0.26
Matches are distributed among these distances:
1 21 0.12
2 132 0.75
3 23 0.13
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (2 bp):
AT
Found at i:277494 original size:18 final size:16
Alignment explanation
Indices: 277448--277502 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 16
277438 AATTAAACAA
277448 ATAAAT-AAAT-ATAT
1 ATAAATAAAATAATAT
*
277462 AATATATAAAATAATAT
1 -ATAAATAAAATAATAT
277479 AGTAAATAATAATAATAT
1 A-TAAATAA-AATAATAT
277497 ATAAAT
1 ATAAAT
277503 GATATTATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 15 0.44
18 9 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
ATAAATAAAATAATAT
Found at i:277554 original size:5 final size:5
Alignment explanation
Indices: 277458--277689 Score: 70
Period size: 5 Copynumber: 47.6 Consensus size: 5
277448 ATAAATAAAT
* *
277458 ATATA ATAT- ATA-A A-ATA ATATA GTA-A ATAATA ATA-A TATATA A-ATG
1 ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA -ATATA ATATA
* * * *
277504 ATATT ATATA CTAT- ATAT- ATCGTA ATAT- ATATA ATAATA CTATA ATATA
1 ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA
* * *
277553 ATACTA ATAT- ATAAAA ATATA TGTATA CTAT- ATACT- ATATA ATAT-
1 ATA-TA ATATA AT-ATA ATATA -ATATA ATATA ATA-TA ATATA ATATA
* * * **
277598 ATA-A TATATA CCATAT- AGAT- ATATA ATATA TATAAA ATATC ATACC
1 ATATA -ATATA --ATATA ATATA ATATA ATATA -ATATA ATATA ATATA
* *
277644 ATATA ATAT- ATACT- ATATA AAATA ATAT- ATATA ATATG ATATA ATA
1 ATATA ATATA ATA-TA ATATA ATATA ATATA ATATA ATATA ATATA ATA
277690 AAAAGGAACC
Statistics
Matches: 171, Mismatches: 29, Indels: 54
0.67 0.11 0.21
Matches are distributed among these distances:
3 1 0.01
4 43 0.25
5 97 0.57
6 26 0.15
7 4 0.02
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:277566 original size:66 final size:65
Alignment explanation
Indices: 277457--277672 Score: 205
Period size: 66 Copynumber: 3.4 Consensus size: 65
277447 AATAAATAAA
*
277457 TATATAATATATAAAATAATATAGTAAATAATAATAATATATAAATGATAT-TATATACTATATA
1 TATATAATATATAAAATAATATAGTAAATAATAATAATATATAAA-AATATATATATACTATATA
277521 -
65 C
* * * *
277521 TATCGTAATATATATAATAATACTA-TAATATAATACTAATATATAAAAATATATGTATACTATA
1 TAT-ATAATATATAAAATAATA-TAGTAA-ATAATAATAATATATAAAAATATATATATACTATA
277585 TAC
63 TAC
** * * * *
277588 TATATAATATAT--AAT-ATATACCATATAGATATATAATATATATAAA-ATAT-CATACCATAT
1 TATATAATATATAAAATAATATAGTAAATA-ATA-ATAATATATAAAAATATATATATACTATAT
*
277648 AA
64 AC
*
277650 TATATACTATATAAAATAATATA
1 TATATAATATATAAAATAATATA
277673 TATAATATGA
Statistics
Matches: 127, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
62 25 0.20
63 11 0.09
64 21 0.17
65 28 0.22
66 39 0.31
67 3 0.02
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (65 bp):
TATATAATATATAAAATAATATAGTAAATAATAATAATATATAAAAATATATATATACTATATAC
Found at i:277573 original size:53 final size:49
Alignment explanation
Indices: 277458--277685 Score: 155
Period size: 55 Copynumber: 4.4 Consensus size: 49
277448 ATAAATAAAT
*
277458 ATATAATATATAAAATA-ATATAGTAA-ATA-ATAATAATATATAA-ATG
1 ATATAATATATAAAATATATAT-GTAATATATATAATAATATATAATATA
**
277504 ATAT--TATATACTATATATATCGTAATATATATAATAATACTATAATATA
1 ATATAATATATAAAATATATAT-GTAATATATATAATAATA-TATAATATA
277553 ATACTAATATATAAAA-ATATATGTATACTATATACTATATAATATATAATATA
1 ATA-TAATATATAAAATATATATGTA-A-TATATA-TA-ATAATATATAATATA
* * * ** *
277606 TACCATATAGATATATAATATATATAAAATATCATACCATATAATATATACTATATA
1 -A-TATA-ATATATAAAATATATATGTAATAT-ATA-TA-ATAATATATA--ATATA
* *
277663 AAATAATATATATAATATGATAT
1 ATATAATATATAAAATAT-ATAT
277686 AATAAAAAGG
Statistics
Matches: 148, Mismatches: 14, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
44 9 0.06
45 8 0.05
46 7 0.05
47 9 0.06
48 5 0.03
49 5 0.03
50 4 0.03
51 7 0.05
52 13 0.09
53 11 0.07
54 24 0.16
55 33 0.22
56 8 0.05
57 5 0.03
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (49 bp):
ATATAATATATAAAATATATATGTAATATATATAATAATATATAATATA
Found at i:277653 original size:31 final size:30
Alignment explanation
Indices: 277455--277692 Score: 127
Period size: 31 Copynumber: 7.6 Consensus size: 30
277445 CAAATAAATA
** *
277455 AATAT-ATAATATATAAAATAATATAGTAAAT
1 AATATAAT-ATATATAAAAT-ATATACCATAT
*
277486 AATAATAATATATA-AATGATATTATATACTATAT
1 AAT-ATAATATATATAA--A-A-TATATACCATAT
*
277520 ATATCGTAATATATATAATAATACTATA--ATAT
1 A-AT-ATAATATATATAA-AATA-TATACCATAT
* *
277552 AATACTAATATATAAAAATATATGTATACTATAT
1 AATA-TAATATATATAAA-ATA--TATACCATAT
* *
277586 ACTAT-ATA-ATATATAATATATACCATAT
1 AATATAATATATATAAAATATATACCATAT
277614 AGATATATAATATATATAAAATATCATACCATAT
1 --A-ATATAATATATATAAAATAT-ATACCATAT
*
277648 AATAT-ATACTATATAAAATA-ATA-TATAT
1 AATATAATA-TATATAAAATATATACCATAT
*
277676 AATATGATATA-ATAAAA
1 AATATAATATATATAAAA
277693 AGGAACCCTA
Statistics
Matches: 170, Mismatches: 15, Indels: 48
0.73 0.06 0.21
Matches are distributed among these distances:
27 6 0.04
28 20 0.12
29 6 0.04
30 8 0.05
31 44 0.26
32 23 0.14
33 16 0.09
34 32 0.19
35 13 0.08
36 2 0.01
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (30 bp):
AATATAATATATATAAAATATATACCATAT
Found at i:282886 original size:16 final size:17
Alignment explanation
Indices: 282865--282896 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
282855 TAAATAACAT
282865 AAATAAAATG-CAATAA
1 AAATAAAATGCCAATAA
282881 AAATAAAATGCCAATA
1 AAATAAAATGCCAATA
282897 TCGAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (17 bp):
AAATAAAATGCCAATAA
Found at i:285888 original size:168 final size:168
Alignment explanation
Indices: 285595--285910 Score: 470
Period size: 168 Copynumber: 1.9 Consensus size: 168
285585 ATTGTCTGTC
* *
285595 ACCTTGGAGATTATTTCTCTCGAAACAAAATTTAGTCTCGCTTGAGACATTTTCCTTTGAAGCCC
1 ACCTTGGAGATTATTTCTCTCGAAACAAAATTTAGTCTCGCTTGAGACAGTTTCCCTTGAAGCCC
* * * * * **
285660 AAATTTTGGAGTTGTTTCACTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAATGA
66 AAATTTCGAAGTTGTTTCACTAGAAACAAAATTGAGCTCACTTGAGATTATTTACCTAAAAACAA
*
285725 ATTTTGTCTCGCTTGAGACAATTTCTCTTGAAGCATAA
131 ATTTCGTCTCGCTTGAGACAATTTCTCTTGAAGCATAA
* * * * * *
285763 ACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTTGCTTGAGACAGTTTCCCTTGAATCCC
1 ACCTTGGAGATTATTTCTCTCGAAACAAAATTTAGTCTCGCTTGAGACAGTTTCCCTTGAAGCCC
* *
285828 AAATTTCGAAGTTGTTTCACTAGAAACAAAATTGAGCTGACTTGAGATTGTTTACCTAAAAACAA
66 AAATTTCGAAGTTGTTTCACTAGAAACAAAATTGAGCTCACTTGAGATTATTTACCTAAAAACAA
285893 ATTTCGTCTCGCTTGAGA
131 ATTTCGTCTCGCTTGAGA
285911 TAGTTTTCCC
Statistics
Matches: 130, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
168 130 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (168 bp):
ACCTTGGAGATTATTTCTCTCGAAACAAAATTTAGTCTCGCTTGAGACAGTTTCCCTTGAAGCCC
AAATTTCGAAGTTGTTTCACTAGAAACAAAATTGAGCTCACTTGAGATTATTTACCTAAAAACAA
ATTTCGTCTCGCTTGAGACAATTTCTCTTGAAGCATAA
Found at i:287335 original size:74 final size:77
Alignment explanation
Indices: 287249--287447 Score: 264
Period size: 74 Copynumber: 2.6 Consensus size: 77
287239 CCGTTGTACA
* * *
287249 AGGGGGGAATCGGTACCCCCT-TGGGGGAGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGAGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
**
287313 -CAAAACTGTTT
66 CCAAAACCATTT
* *
287324 A-GGGGGAATCGGTTCCTCCTATGGGGGA-ATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGAGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
287387 CCAAAACCATTT
66 CCAAAACCATTT
* *
287399 AGGGGGGAATCAGTTCCTCCTATGAGGGG-GAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTATG-GGGGAG-ATCGGTTCCCTCCGAGCA
287448 ATCTGAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
74 49 0.45
75 18 0.17
76 21 0.19
77 4 0.04
78 17 0.16
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGAGATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:287813 original size:38 final size:38
Alignment explanation
Indices: 287762--287837 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
287752 ATTACTCCCC
287762 CTTACTTTAACACTTCTTCAATTTATCATGTAAAACAT
1 CTTACTTTAACACTTCTTCAATTTATCATGTAAAACAT
287800 CTTACTTTAACACTTCTTCAATTTATCATGTAAAACAT
1 CTTACTTTAACACTTCTTCAATTTATCATGTAAAACAT
287838 TTAACACCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (38 bp):
CTTACTTTAACACTTCTTCAATTTATCATGTAAAACAT
Found at i:288118 original size:15 final size:15
Alignment explanation
Indices: 288098--288139 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
288088 ACCATTCATA
*
288098 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
288113 AATCCACAAAATCAAAC
1 AAT-C-CAAAATCAAAC
288130 AATCCAAAAT
1 AATCCAAAAT
288140 ATTCAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.57, C:0.29, G:0.00, T:0.14
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:288124 original size:17 final size:17
Alignment explanation
Indices: 288102--288135 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
288092 TTCATAAATC
*
288102 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
288119 CAAAATCAAACAATCCA
1 CAAAATCAAACAATCCA
288136 AAATATTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:289773 original size:16 final size:15
Alignment explanation
Indices: 289742--289781 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
289732 ACCATTCATA
*
289742 AATCCAAAATCCAAC
1 AATCCAAAATCAAAC
289757 AATCCACAAATCAAAC
1 AATCCA-AAATCAAAC
289773 AAT-CAAAAT
1 AATCCAAAAT
289782 GTTGAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 8 0.35
16 11 0.48
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (15 bp):
AATCCAAAATCAAAC
Found at i:291757 original size:20 final size:20
Alignment explanation
Indices: 291728--291765 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
291718 CAGAACCCCA
*
291728 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCCTGT
*
291748 GGGGGAATCGGTTCCCCT
1 GGGGGAATCGATTCCCCT
291766 TCAAAGGGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCCTGT
Found at i:291794 original size:19 final size:20
Alignment explanation
Indices: 291748--291807 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 20
291738 ATTCCCCTGT
291748 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TC-AA
291771 GGGGGAATCGGTTCCCTC-A
1 GGGGGAATCGGTTCCCTCAA
* *
291790 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
291808 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.17, C:0.27, G:0.35, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Found at i:295647 original size:22 final size:21
Alignment explanation
Indices: 295605--295644 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
295595 GAGTTTGTTT
*
295605 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
295626 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
295645 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:299750 original size:18 final size:19
Alignment explanation
Indices: 299681--299763 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 19
299671 AACAGAACCC
299681 CAGGGGGGTATCGATTCCCCT
1 CAGGGGGG-ATCGATT-CCCT
** *
299702 GTGGGGGGAATCGGTTCCCCTT
1 CAGGGGGG-ATCGATT-CCC-T
* *
299724 CAAAGGGGGATCGGTTCCCT
1 C-AGGGGGGATCGATTCCCT
299744 CAGGGGGGATCGATTCCCT
1 CAGGGGGGATCGATTCCCT
299763 C
1 C
299764 TGCACAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 17 0.33
20 2 0.04
21 19 0.37
22 8 0.16
23 5 0.10
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (19 bp):
CAGGGGGGATCGATTCCCT
Found at i:305701 original size:76 final size:76
Alignment explanation
Indices: 305534--305742 Score: 280
Period size: 75 Copynumber: 2.8 Consensus size: 76
305524 CCGTTGTACA
* * * * *
305534 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
**
305598 CAAAACTGTTT
66 CAAAACCATTT
*
305609 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
305673 CCAAAACCATTT
66 -CAAAACCATTT
* * *
305685 AGGGGGGAATCAGTTCCTCCTATGAGGGGGAATCGGTTCCCTCTGAGCAATCT-GAAAT
1 AGGGGGGAATCGGTTCCTCCTATG-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAAT
305743 TTTTGGCTTT
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
75 56 0.47
76 32 0.27
77 5 0.04
78 26 0.22
ACGTcount: A:0.22, C:0.23, G:0.32, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
CAAAACCATTT
Found at i:306150 original size:104 final size:104
Alignment explanation
Indices: 305970--306260 Score: 393
Period size: 104 Copynumber: 2.8 Consensus size: 104
305960 ATGTTTCAAC
* * * *
305970 ACTCTTCAACATAGATAAGCAGTGTCGTCTTCAACACCAGATTATCTCCAGATTCAATCGACTTT
1 ACTCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAGATTATCTCCAGATTGACTCGACTTT
* *
306035 CTCAACAAGAAGGAACAACATAATCTGAAAGCAGCCAGA
66 CTCAACAAGAAGGAACAACATAACCTGAAAGCAGCCAAA
* * * * *
306074 ACTCTTCGACGTGGATGAGCAGTGGCGTCTTCAACACCAGATTATCTCCAGATTGACTCGGCTTC
1 ACTCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAGATTATCTCCAGATTGACTCGACTTT
* * *
306139 CTCAATAAGAAGGAATAACATCACCTGAAAGCAGCCAAA
66 CTCAACAAGAAGGAACAACATAACCTGAAAGCAGCCAAA
* * ** * *
306178 ACTCTTCAACATGGATGAACAATGTCGTCTTCAATGCCAAATTATCTCCAGATTGACCCGACTTT
1 ACTCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAGATTATCTCCAGATTGACTCGACTTT
*
306243 CTCAACGAGAAGGAACAA
66 CTCAACAAGAAGGAACAA
306261 AGTCGTCTTC
Statistics
Matches: 159, Mismatches: 28, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
104 159 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (104 bp):
ACTCTTCAACATGGATGAGCAGTGTCGTCTTCAACACCAGATTATCTCCAGATTGACTCGACTTT
CTCAACAAGAAGGAACAACATAACCTGAAAGCAGCCAAA
Found at i:308719 original size:17 final size:18
Alignment explanation
Indices: 308679--308719 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
308669 GTGCAAATAA
308679 GTTTTTTGTCTTAAAAAT
1 GTTTTTTGTCTTAAAAAT
*
308697 GATTTTTT-TCTTAAAATT
1 G-TTTTTTGTCTTAAAAAT
308715 GTTTT
1 GTTTT
308720 AAATGACGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 11 0.52
19 6 0.29
ACGTcount: A:0.24, C:0.05, G:0.10, T:0.61
Consensus pattern (18 bp):
GTTTTTTGTCTTAAAAAT
Found at i:315849 original size:6 final size:6
Alignment explanation
Indices: 315838--315871 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
315828 CAATCGGCAT
315838 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGA
1 TGGAGA TGGAGA TGGAGA TGGAGA TGGAGA TGGA
315872 AGGGAAGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
TGGAGA
Found at i:321922 original size:33 final size:33
Alignment explanation
Indices: 321885--321952 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
321875 TTACCAGATG
** *
321885 CCGCCACCGCCGCCATCACCTAGTTTTATGACC
1 CCGCCACCGCCGCCATCACAGAGTTATATGACC
* *
321918 CCGCCGCCGCCGCCGTCACAGAGTTATATGACC
1 CCGCCACCGCCGCCATCACAGAGTTATATGACC
321951 CC
1 CC
321953 TCCTGGAGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.46, G:0.19, T:0.18
Consensus pattern (33 bp):
CCGCCACCGCCGCCATCACAGAGTTATATGACC
Found at i:322387 original size:24 final size:25
Alignment explanation
Indices: 322360--322416 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 25
322350 TTTATACTTG
*
322360 TATTTA-GTACTTTTTTATTGTAGT
1 TATTTATGGACTTTTTTATTGTAGT
*
322384 TATTTATTGGACTTTTTTATTGTAAT
1 TATTTA-TGGACTTTTTTATTGTAGT
*
322410 TTTTTAT
1 TATTTAT
322417 TATTTATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 6 0.21
25 1 0.04
26 21 0.75
ACGTcount: A:0.21, C:0.04, G:0.11, T:0.65
Consensus pattern (25 bp):
TATTTATGGACTTTTTTATTGTAGT
Found at i:322389 original size:13 final size:13
Alignment explanation
Indices: 322370--322417 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
322360 TATTTAGTAC
*
322370 TTTTTTATTGTAG
1 TTTTTTATTGTAA
* * *
322383 TTATTTATTGGAC
1 TTTTTTATTGTAA
322396 TTTTTTATTGTAA
1 TTTTTTATTGTAA
322409 TTTTTTATT
1 TTTTTTATT
322418 ATTTATCATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (13 bp):
TTTTTTATTGTAA
Found at i:322397 original size:26 final size:26
Alignment explanation
Indices: 322368--322417 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
322358 TGTATTTAGT
*
322368 ACTTTTTTATTGTAGTTATTTATTGG
1 ACTTTTTTATTGTAATTATTTATTGG
*
322394 ACTTTTTTATTGTAATTTTTTATT
1 ACTTTTTTATTGTAATTATTTATT
322418 ATTTATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.10, T:0.66
Consensus pattern (26 bp):
ACTTTTTTATTGTAATTATTTATTGG
Found at i:338152 original size:23 final size:23
Alignment explanation
Indices: 338125--338173 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
338115 TGGTGGTTGG
338125 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
338148 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
338171 TTT
1 TTT
338174 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:345012 original size:20 final size:20
Alignment explanation
Indices: 344989--345033 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
344979 TTAACTTTTT
*
344989 CTTTTCTCTTTC-TTCCTTAA
1 CTTTTCTATTTCATT-CTTAA
*
345009 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATTCTTAA
345029 CTTTT
1 CTTTT
345034 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTATTTCATTCTTAA
Found at i:348294 original size:23 final size:23
Alignment explanation
Indices: 348264--348312 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
348254 TGGTGGTTGG
*
348264 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
348287 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
348310 TTT
1 TTT
348313 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:358488 original size:15 final size:17
Alignment explanation
Indices: 358463--358505 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
358453 ATTTAGAATG
*
358463 TTCAAGTACCCGGAAG-
1 TTCATGTACCCGGAAGA
358479 TT-ATGTACCCGGAAGA
1 TTCATGTACCCGGAAGA
358495 TTCATGTACCC
1 TTCATGTACCC
358506 ACATTTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 12 0.50
16 4 0.17
17 8 0.33
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (17 bp):
TTCATGTACCCGGAAGA
Found at i:358609 original size:2 final size:2
Alignment explanation
Indices: 358534--358591 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
358524 TACCCGATTC
358534 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
358576 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
358592 TTTTTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:358789 original size:22 final size:24
Alignment explanation
Indices: 358764--358815 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 24
358754 AATTAATAAA
358764 AAAAATTAAAAAAATA-AAA-CTT
1 AAAAATTAAAAAAATACAAACCTT
* *
358786 -AAAATT-ACATAATACAAACCTT
1 AAAAATTAAAAAAATACAAACCTT
358808 AAAAATTA
1 AAAAATTA
358816 GAAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
22 3 0.12
23 6 0.25
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATTAAAAAAATACAAACCTT
Found at i:358882 original size:23 final size:23
Alignment explanation
Indices: 358838--358902 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 23
358828 TAATATTTAG
**
358838 ATAAAAATAT-TAATAAACCTAAA
1 ATAAAAATATATTTTAAA-CTAAA
358861 ATAAAAATATATTTTAAAC----
1 ATAAAAATATATTTTAAACTAAA
358880 -TAAAAATATATTTTAAACTAAA
1 ATAAAAATATATTTTAAACTAAA
358902 A
1 A
358903 ATATATATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
18 18 0.53
23 11 0.32
24 5 0.15
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (23 bp):
ATAAAAATATATTTTAAACTAAA
Found at i:358908 original size:20 final size:18
Alignment explanation
Indices: 358857--358914 Score: 98
Period size: 18 Copynumber: 3.2 Consensus size: 18
358847 TTAATAAACC
*
358857 TAAAATAAAAATATATTT
1 TAAACTAAAAATATATTT
358875 TAAACTAAAAATATATTT
1 TAAACTAAAAATATATTT
*
358893 TAAACTAAAAATATATAT
1 TAAACTAAAAATATATTT
358911 TAAA
1 TAAA
358915 ACATAAGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAACTAAAAATATATTT
Found at i:362217 original size:23 final size:23
Alignment explanation
Indices: 362191--362235 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
362181 ATATATAATA
362191 TTATAGATACTTTCTATTAACCT
1 TTATAGATACTTTCTATTAACCT
**
362214 TTATAGATTTTTTCTATTAACC
1 TTATAGATACTTTCTATTAACC
362236 GAAAATCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (23 bp):
TTATAGATACTTTCTATTAACCT
Found at i:362808 original size:8 final size:8
Alignment explanation
Indices: 362789--362857 Score: 59
Period size: 8 Copynumber: 8.2 Consensus size: 8
362779 TCAACGCCGA
362789 TCAAC-GG
1 TCAACGGG
*
362796 TCAACGAG
1 TCAACGGG
362804 TCAACGGG
1 TCAACGGG
362812 TCAACGGG
1 TCAACGGG
*
362820 TCAGGTCGGG
1 TCA--ACGGG
362830 TCAACGGG
1 TCAACGGG
* *
362838 TGAGGTCGGG
1 TCA--ACGGG
362848 TCAACGGG
1 TCAACGGG
362856 TC
1 TC
362858 GGGTCGGGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
7 5 0.10
8 31 0.63
10 13 0.27
ACGTcount: A:0.22, C:0.23, G:0.39, T:0.16
Consensus pattern (8 bp):
TCAACGGG
Found at i:362894 original size:18 final size:18
Alignment explanation
Indices: 362808--362897 Score: 146
Period size: 18 Copynumber: 5.0 Consensus size: 18
362798 AACGAGTCAA
*
362808 CGGGTCAACGGGTCAGGT
1 CGGGTCAACGGGTCGGGT
362826 CGGGTCAACGGGT-GAGGT
1 CGGGTCAACGGGTCG-GGT
362844 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
*
362862 CGGGTTAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
362880 CGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGT
362898 TGTGACCGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
18 66 0.99
19 1 0.01
ACGTcount: A:0.13, C:0.20, G:0.49, T:0.18
Consensus pattern (18 bp):
CGGGTCAACGGGTCGGGT
Found at i:364953 original size:63 final size:63
Alignment explanation
Indices: 364839--364962 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
364829 ACCTAAGGGA
* **
364839 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGACCGTGGAGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCGGGACCGCAGAGCCTACCTAAGAAC
* *
364902 ACATCTTAGGGCCAT-AGGGCCTACCCGAGA-ATGATCTCAGGG-CCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCC-TGAGAGCCTACCCAAGATA-GATCTC-GGGACCGCAGAGCCTACCTAAGA
364963 GTCACATTAG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCGGGACCGCAGAGCCTACCTAAGAAC
Found at i:367599 original size:18 final size:18
Alignment explanation
Indices: 367576--367610 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
367566 TCAACGTGTC
367576 AACGGGTCGGGTCGGGTT
1 AACGGGTCGGGTCGGGTT
367594 AACGGGTCGGGTCGGGT
1 AACGGGTCGGGTCGGGT
367611 CAAAGCCGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.51, T:0.20
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTT
Found at i:367674 original size:93 final size:93
Alignment explanation
Indices: 367515--367706 Score: 384
Period size: 93 Copynumber: 2.1 Consensus size: 93
367505 TTTAATGCCC
367515 GGTCAAAGCCGGTCAAAGTTTTGGTCAACAGTGGTCAACGCCGATCAACGGTCAACGTGTCAACG
1 GGTCAAAGCCGGTCAAAGTTTTGGTCAACAGTGGTCAACGCCGATCAACGGTCAACGTGTCAACG
367580 GGTCGGGTCGGGTTAACGGGTCGGGTCG
66 GGTCGGGTCGGGTTAACGGGTCGGGTCG
367608 GGTCAAAGCCGGTCAAAGTTTTGGTCAACAGTGGTCAACGCCGATCAACGGTCAACGTGTCAACG
1 GGTCAAAGCCGGTCAAAGTTTTGGTCAACAGTGGTCAACGCCGATCAACGGTCAACGTGTCAACG
367673 GGTCGGGTCGGGTTAACGGGTCGGGTCG
66 GGTCGGGTCGGGTTAACGGGTCGGGTCG
367701 GGTCAA
1 GGTCAA
367707 CGGGTCGGGT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 99 1.00
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.20
Consensus pattern (93 bp):
GGTCAAAGCCGGTCAAAGTTTTGGTCAACAGTGGTCAACGCCGATCAACGGTCAACGTGTCAACG
GGTCGGGTCGGGTTAACGGGTCGGGTCG
Found at i:367692 original size:18 final size:18
Alignment explanation
Indices: 367666--367716 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
367656 CGGTCAACGT
367666 GTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
*
367684 GTTAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCGG
367702 GTCAACGGGTCGGGT
1 GTCAACGGGTCGGGT
367717 TGTGACCGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.12, C:0.20, G:0.49, T:0.20
Consensus pattern (18 bp):
GTCAACGGGTCGGGTCGG
Found at i:372674 original size:17 final size:18
Alignment explanation
Indices: 372649--372688 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
372639 CAACGGTCAA
372649 GGGTCAACGGGTC-GGTC
1 GGGTCAACGGGTCGGGTC
*
372666 GGGTTAACGGGTCGGGTC
1 GGGTCAACGGGTCGGGTC
372684 GGGTC
1 GGGTC
372689 GGTTCAACGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.10, C:0.20, G:0.50, T:0.20
Consensus pattern (18 bp):
GGGTCAACGGGTCGGGTC
Found at i:372697 original size:23 final size:22
Alignment explanation
Indices: 372656--372705 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
372646 CAAGGGTCAA
372656 CGGGTCGGTCGGGTTAACGGGT
1 CGGGTCGGTCGGGTTAACGGGT
372678 CGGGTCGGGTC-GGTTCAACGGGT
1 CGGGTC-GGTCGGGTT-AACGGGT
372701 CGGGT
1 CGGGT
372706 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.08, C:0.20, G:0.50, T:0.22
Consensus pattern (22 bp):
CGGGTCGGTCGGGTTAACGGGT
Found at i:373127 original size:31 final size:31
Alignment explanation
Indices: 373092--373155 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
373082 AAAACATAAA
* * *
373092 ATATGGTCACTTTCGTTTTTATTTAATTAAG
1 ATATGATCACTTCCATTTTTATTTAATTAAG
373123 ATATGATCACTTCCATTTTTATTTAATTAAG
1 ATATGATCACTTCCATTTTTATTTAATTAAG
373154 AT
1 AT
373156 GTAGTCATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (31 bp):
ATATGATCACTTCCATTTTTATTTAATTAAG
Found at i:378316 original size:32 final size:32
Alignment explanation
Indices: 378216--378326 Score: 170
Period size: 33 Copynumber: 3.4 Consensus size: 32
378206 ACAAAGCTTA
*
378216 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACTTCCAAGTT
*
378248 CGATAAATTAAAATACTTAAAAACTTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
*
378281 CGATAAATTCAAATACTTAAAAACTT-CAAGTT
1 CGAT-AATTGAAATACTTAAAAACTTCCAAGTT
378313 CGATAATTGAAATA
1 CGATAATTGAAATA
378327 AAGTTTACGA
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 9 0.12
32 14 0.19
33 51 0.69
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACTTCCAAGTT
Found at i:378338 original size:21 final size:21
Alignment explanation
Indices: 378313--378354 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
378303 ACTTCAAGTT
378313 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAATAAAGTTTA
378334 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAATAAAGTTTA
378355 AAAATAAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (21 bp):
CGATAATTGAAATAAAGTTTA
Found at i:382089 original size:63 final size:65
Alignment explanation
Indices: 381936--382099 Score: 199
Period size: 63 Copynumber: 2.5 Consensus size: 65
381926 TCTGGGCAAG
*
381936 ATGCATCGATGCATAGGTTGTGCACCGATGCATACCTAAAAATAATAATAAACATCGAAGGTAGT
1 ATGCATCGATGCATAGGTTGTGCACCGATGCAT-CCTAAAAATAATAATAAACATCGAAGGTAAT
382001 T
65 T
* * * ** * * *
382002 AGTGCATCGATGCACAGGTAGTGCATCGATGCATCCT-TCAA-GATGA-AAACATCGAATGTAAT
1 A-TGCATCGATGCATAGGTTGTGCACCGATGCATCCTAAAAATAATAATAAACATCGAAGGTAAT
382064 AT
65 -T
382066 ATGCATCGATGCATAGGTTGTGCACCGATGCATC
1 ATGCATCGATGCATAGGTTGTGCACCGATGCATC
382100 TGTGAGAGAA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
63 44 0.52
64 5 0.06
65 2 0.02
66 4 0.05
67 29 0.35
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.26
Consensus pattern (65 bp):
ATGCATCGATGCATAGGTTGTGCACCGATGCATCCTAAAAATAATAATAAACATCGAAGGTAATT
Found at i:382503 original size:59 final size:59
Alignment explanation
Indices: 382431--383334 Score: 1073
Period size: 59 Copynumber: 15.3 Consensus size: 59
382421 TTTACCAAAT
* * * *
382431 GGCACTATA-TGTGCAAAAATGTTAAGGAAAGCATACT-AAGTGTATGGATTTCCATATAG
1 GGCACTA-AGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
* *
382490 AGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
** * * * * *
382549 GGCACTTTGTGTGCTAAAATGGTAAGGGAATCATACT-AAGTGTATGGATTTCTATAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
* *
382607 AAGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAG
1 -GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
** * * * *
382667 GGCACTTTGTGTGCTAAAATGGTAAGGGAATCATACT-AAGTGTATGGATTTCCATAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
** *
382725 GAGCACTTTGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATAT-G
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
* ** *
382784 GAGCATTTTGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
** * * * * *
382844 GGCACTTTGTGTGCTAAAATGGTAAGGGAATCATACT-AAGTGTATGGATTTCTATA-AG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
* * *
382902 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
* * *
382962 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCTATAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
* * *
383020 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
* * *
383080 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCTATAT-G
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
* * *
383138 GAGCACTAAGTGTGCTAAAATGTGAAGGAAAACATATTGAATATATGTATTTCCATATAG
1 G-GCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
* * * *
383198 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATACT-AAGTGTATGGATTTCAATATGG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAA-TATATGGATTTCCATATAG
383257 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
1 GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
*
383316 GGCATTATA-TGTGCTAAAA
1 GGCACTA-AGTGTGCTAAAA
383335 ATGGTAAAAG
Statistics
Matches: 729, Mismatches: 91, Indels: 50
0.84 0.10 0.06
Matches are distributed among these distances:
58 23 0.03
59 681 0.93
60 25 0.03
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (59 bp):
GGCACTAAGTGTGCTAAAATGTTAAGGAAATCATATTGAATATATGGATTTCCATATAG
Found at i:383583 original size:44 final size:44
Alignment explanation
Indices: 383528--383759 Score: 367
Period size: 44 Copynumber: 5.2 Consensus size: 44
383518 GTACGTATAT
* *
383528 ATAATGATAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGA
1 ATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
*
383572 ATAATGGTAAGTAGATT-GTAAAATAAGCTTACGAGCTTATGGA
1 ATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
* *
383615 AAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAA
1 ATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
383659 ATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
1 ATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
* * *
383703 AAAATGGTAAGTATATATTGGTAAAATAAGCTTACAAGCTTAAGGA
1 ATAATGGTAAG--TATATTGGTAAAATAAGCTTACGAGCTTATGGA
383749 ATAATGGTAAG
1 ATAATGGTAAG
383760 AAGATTGATA
Statistics
Matches: 173, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
43 40 0.23
44 92 0.53
46 41 0.24
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (44 bp):
ATAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGA
Found at i:383638 original size:87 final size:87
Alignment explanation
Indices: 383530--383766 Score: 393
Period size: 87 Copynumber: 2.7 Consensus size: 87
383520 ACGTATATAT
*
383530 AATGATAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTAGATTGTAAAA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTAGATTGTAAAA
383595 TAAGCTTACGAGCTTATGGAAA
66 TAAGCTTACGAGCTTATGGAAA
* * *
383617 AATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGAAATAATGGTAAGTATATTGGTAAA
1 AATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTAGATT-GTAAA
383682 ATAAGCTTACGAGCTTATGGAAA
65 ATAAGCTTACGAGCTTATGGAAA
* *
383705 AATGGTAAGTATATATTGGTAAAATAAGCTTACAAGCTTAAGGAATAATGGTAAGAAGATTG
1 AATGGTAAG--TATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTAGATTG
383767 ATAAGAAATG
Statistics
Matches: 138, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
87 55 0.40
88 37 0.27
89 1 0.01
90 45 0.33
ACGTcount: A:0.42, C:0.06, G:0.22, T:0.30
Consensus pattern (87 bp):
AATGGTAAGTATATTGGTAAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTAGATTGTAAAA
TAAGCTTACGAGCTTATGGAAA
Found at i:388735 original size:25 final size:26
Alignment explanation
Indices: 388653--388737 Score: 88
Period size: 25 Copynumber: 3.4 Consensus size: 26
388643 TCGTAGATCT
* *
388653 AGTATTACACTCGAAAGTGTCTCGT-
1 AGTATTGCACTCGAAAGTGCCTCGTA
*
388678 AGTATTACACTCGAAAGTGCCTC--A
1 AGTATTGCACTCGAAAGTGCCTCGTA
* *
388702 ATGTGTTGCACTCGTAAGTGCCTCGTA
1 A-GTATTGCACTCGAAAGTGCCTCGTA
388729 AG-ATTGCAC
1 AGTATTGCAC
388738 CATGGGTACC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 1 0.02
25 47 0.92
26 1 0.02
27 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (26 bp):
AGTATTGCACTCGAAAGTGCCTCGTA
Found at i:396600 original size:209 final size:209
Alignment explanation
Indices: 396240--396644 Score: 810
Period size: 209 Copynumber: 1.9 Consensus size: 209
396230 AGTTAAACTA
396240 AAAACACATGTATTTGAGCAAAAATCTTTTGAAAATAGAGTTAATTGCGCATAAGCACCCTTAAG
1 AAAACACATGTATTTGAGCAAAAATCTTTTGAAAATAGAGTTAATTGCGCATAAGCACCCTTAAG
396305 CTATGCCCAGATGCTATATTAGTCCCCCATTTTTGAAACCTTTTAAATTCTTCTCTAAACTATTA
66 CTATGCCCAGATGCTATATTAGTCCCCCATTTTTGAAACCTTTTAAATTCTTCTCTAAACTATTA
396370 ATATCATTTCAAATACTTCCTTTTGTTAGTTTAACAAATTATTTGATCATTCAATGTCAATTTGA
131 ATATCATTTCAAATACTTCCTTTTGTTAGTTTAACAAATTATTTGATCATTCAATGTCAATTTGA
396435 AATGATATTTGAGC
196 AATGATATTTGAGC
396449 AAAACACATGTATTTGAGCAAAAATCTTTTGAAAATAGAGTTAATTGCGCATAAGCACCCTTAAG
1 AAAACACATGTATTTGAGCAAAAATCTTTTGAAAATAGAGTTAATTGCGCATAAGCACCCTTAAG
396514 CTATGCCCAGATGCTATATTAGTCCCCCATTTTTGAAACCTTTTAAATTCTTCTCTAAACTATTA
66 CTATGCCCAGATGCTATATTAGTCCCCCATTTTTGAAACCTTTTAAATTCTTCTCTAAACTATTA
396579 ATATCATTTCAAATACTTCCTTTTGTTAGTTTAACAAATTATTTGATCATTCAATGTCAATTTGA
131 ATATCATTTCAAATACTTCCTTTTGTTAGTTTAACAAATTATTTGATCATTCAATGTCAATTTGA
396644 A
196 A
396645 TCCGACCTAA
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
209 196 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.38
Consensus pattern (209 bp):
AAAACACATGTATTTGAGCAAAAATCTTTTGAAAATAGAGTTAATTGCGCATAAGCACCCTTAAG
CTATGCCCAGATGCTATATTAGTCCCCCATTTTTGAAACCTTTTAAATTCTTCTCTAAACTATTA
ATATCATTTCAAATACTTCCTTTTGTTAGTTTAACAAATTATTTGATCATTCAATGTCAATTTGA
AATGATATTTGAGC
Found at i:397079 original size:15 final size:17
Alignment explanation
Indices: 397054--397096 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
397044 ATTTAGAATG
* *
397054 TTCAAGTACCCGGAAG-
1 TTCATGTACCCGCAAGA
397070 TT-ATGTACCCGCAAGA
1 TTCATGTACCCGCAAGA
397086 TTCATGTACCC
1 TTCATGTACCC
397097 ACATTTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 8 0.35
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (17 bp):
TTCATGTACCCGCAAGA
Found at i:397446 original size:18 final size:18
Alignment explanation
Indices: 397425--397465 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
397415 TTAAGAAACC
*
397425 TAAAATAAAAATATATTT
1 TAAAATAAAAATATATAT
*
397443 TAAACTAAAAATATATAT
1 TAAAATAAAAATATATAT
397461 TAAAA
1 TAAAA
397466 CATAAGAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAATAAAAATATATAT
Found at i:403790 original size:26 final size:26
Alignment explanation
Indices: 403761--403815 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
403751 CACAATTCAC
*
403761 ATCATAATCCGAATCAAACAATAATA
1 ATCATAATCCAAATCAAACAATAATA
* *
403787 ATCATTATCCAAATCAAACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
403813 ATC
1 ATC
403816 CGAGTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.51, C:0.20, G:0.02, T:0.27
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:403880 original size:26 final size:26
Alignment explanation
Indices: 403850--403900 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
403840 TTAAGAATAA
403850 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
403876 ATTATCTAAATCAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
403901 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.04, T:0.29
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:404002 original size:40 final size:39
Alignment explanation
Indices: 403932--404013 Score: 103
Period size: 40 Copynumber: 2.1 Consensus size: 39
403922 ATATATTAAC
* *
403932 ATAATTTAAATTAATATATTCTTATGATATTTTATAATTT
1 ATAATTTAAATTAATATATTATTATGATA-TTTATAAATT
* *
403972 ATAATTTAAA-TATTATTATTATTATTATATTTATAAATT
1 ATAATTTAAATTAATA-TATTATTATGATATTTATAAATT
404011 ATA
1 ATA
404014 TAAATAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 16 0.43
40 21 0.57
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
ATAATTTAAATTAATATATTATTATGATATTTATAAATT
Found at i:405967 original size:14 final size:14
Alignment explanation
Indices: 405948--405976 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
405938 CAAATATATA
405948 ATAATTTATAGTTT
1 ATAATTTATAGTTT
405962 ATAATTTATAGTTT
1 ATAATTTATAGTTT
405976 A
1 A
405977 AATATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
ATAATTTATAGTTT
Found at i:406174 original size:21 final size:23
Alignment explanation
Indices: 406150--406193 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
406140 AATAATCTAA
*
406150 ATTAATTTAA-TTTA-AGAATAT
1 ATTAATATAATTTTATAGAATAT
406171 ATTAATATAATTTTATAGAATAT
1 ATTAATATAATTTTATAGAATAT
406194 GATTGGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (23 bp):
ATTAATATAATTTTATAGAATAT
Found at i:412389 original size:8 final size:8
Alignment explanation
Indices: 412378--412404 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
412368 TTTCAAAGGC
412378 ATGCACCG
1 ATGCACCG
412386 ATGCACCG
1 ATGCACCG
412394 ATGCACCG
1 ATGCACCG
412402 ATG
1 ATG
412405 AATAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.26, T:0.15
Consensus pattern (8 bp):
ATGCACCG
Found at i:412481 original size:63 final size:63
Alignment explanation
Indices: 412414--412571 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 63
412404 GAATAAATTG
* **
412414 AACATCGAATGCATTTCATGCACCGATGCATATCCATGCATCGATGTACTTGGATT-TTATGAA
1 AACATCGAATGCATTTCATGCACCGATGCATATCCATGCATCGATGCAC-CAGATTATTATGAA
* * * * **
412477 AACATCGAATGCATTTGATGCTCTGATGCATATCCATGCATCGATGCACCAGATTATTTTTCA
1 AACATCGAATGCATTTCATGCACCGATGCATATCCATGCATCGATGCACCAGATTATTATGAA
* *
412540 AACATCGAATGCATTTTATGCATCGATGCATA
1 AACATCGAATGCATTTCATGCACCGATGCATA
412572 CTTAGTGCAC
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
62 4 0.05
63 77 0.95
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (63 bp):
AACATCGAATGCATTTCATGCACCGATGCATATCCATGCATCGATGCACCAGATTATTATGAA
Found at i:420899 original size:63 final size:62
Alignment explanation
Indices: 420821--421044 Score: 222
Period size: 63 Copynumber: 3.5 Consensus size: 62
420811 TTTTCAAAGG
* * **
420821 CATGCACCGATGCATATTCATGCACCGATGCACCGATGAATAAATTGAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCACCGATGCACC-ATGGATATTTTGAACATCGAATGCATTT
* * *
420884 CATGCACCGATGCATATCCATGCATCGTTGCA-CTTGGAT-TTTATGAAAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCACCGATGCACCATGGATATTT-TG--AACATCGAATGCATTT
* * * *
420947 GATGCACCGATGCATATCCATGCATCGATGCACCA-GGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCATATCCATGCACCGATGCACCATGGATA-TTTT-GAACATCGAATGCATTT
* * *
421010 TATGCATCGATGCATA-CTTAGTGCACCGATGCACC
1 CATGCACCGATGCATATC-CA-TGCACCGATGCACC
421045 GAGTGTTCCA
Statistics
Matches: 136, Mismatches: 16, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
60 1 0.01
61 6 0.04
62 2 0.01
63 109 0.80
64 15 0.11
65 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (62 bp):
CATGCACCGATGCATATCCATGCACCGATGCACCATGGATATTTTGAACATCGAATGCATTT
Found at i:430067 original size:35 final size:34
Alignment explanation
Indices: 429982--430068 Score: 88
Period size: 35 Copynumber: 2.5 Consensus size: 34
429972 AATATAATTT
*
429982 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* * *
430016 TAAATTATAACCAAATTACAATAACTGATATTAAATTG
1 TAAA-TACAACAAAATTACAATAA--GA-ATTAAATGG
430054 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
430069 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
34 4 0.09
35 25 0.57
36 2 0.05
37 4 0.09
38 9 0.20
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:432338 original size:17 final size:18
Alignment explanation
Indices: 432318--432356 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
432308 ATTATATTAG
432318 TAAAAT-ATTAAATAAAA
1 TAAAATGATTAAATAAAA
* *
432335 TAAAATGCTTAAATAAAT
1 TAAAATGATTAAATAAAA
432353 TAAA
1 TAAA
432357 TACATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
TAAAATGATTAAATAAAA
Found at i:435031 original size:3 final size:3
Alignment explanation
Indices: 435023--435048 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
435013 GGGTTTTTTC
435023 GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GT
435049 GTCCGGTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:436406 original size:416 final size:402
Alignment explanation
Indices: 435610--436427 Score: 1201
Period size: 416 Copynumber: 2.0 Consensus size: 402
435600 TTTATTTTTT
* * * *
435610 ATTAAATTTAAAAATTTATAAAATAATCTTTAATTTTATTTACTTTTATAAAATAATTTTTGGAG
1 ATTAAATTTAAAAATTTATAAAATAATATTTAAATTTAATTACTGTTATAAAATAATTTTTGGAG
*
435675 TTCATTTATCATTATTTTTATAAAAATTCAATTATTACTTTATAATAGTTTAATAAATTTAAAAA
66 TTCATTTATCATTATTTTTATAAAAACTCAATTATTACTTTATAATAGTTTAATAAATTTAAAAA
* * * *
435740 TCAATTTGTAGTTTTTAAAATTTCAACAATTAAATTTTTTTTATTGCTGCATTAAAATAATTTTT
131 TCAAATTGTAGTTTTAAAAATTTCAACAATTAAATTTTTTATATTGCCGCATTAAAATAATTTTT
* *
435805 TAGAGTTGATTTATCACTATTTTTATAACATCCAATTATTACATTATAATAATAAATTAAATTGT
196 TAGAGTTGATTTATCACTATTTTTATAACATACAATTATTACATTATAATAATAAATTAAATGGT
* * *
435870 TTTTAAAATTACAATATTCAAATGTATTTTATCCACTTTTGAAGCATAATTCTAAATTTTAAGCT
261 TTTTAAAATTACAATATTCAAATGTATTTTATCCACCTTTGAAGCATAATTCTAAATATTAAGCG
435935 GGTAAGTGCAACATAGTCATACCTAAAATATTATTAATTATTCATAATTAATAAATAAAAGAAAA
326 GGTAAGTGCAACATAGTCATACCTAAAATATTATTAATTATTCATAATTAATAAATAAAAGAAAA
436000 TTAAATGGATAA
391 TTAAATGGATAA
*
436012 ATTAAATTTTAAAATTTATAAAATAATATTTAAATTTAATTACTGTTATAAAATAATTTTTGGAG
1 ATTAAATTTAAAAATTTATAAAATAATATTTAAATTTAATTACTGTTATAAAATAATTTTTGGAG
* *
436077 TTCATTTATCATTATATTTTTTATAAATACTCAATTATTACTTTATAATATTTTAATAAATTTAA
66 TTCATTTATCA-T-TA-TTTTTATAAAAACTCAATTATTACTTTATAATAGTTTAATAAATTTAA
*
436142 AAATCAAATTGTAGTTTTAAAAATTTCAACAATTAAAAAATTAAATTATTAAAAATATTGCCG-T
128 AAATCAAATTGTAGTTTTAAAAATTTCAACAATT---AAATT---TT-TT----ATATTGCCGCA
* * * * *
436206 TATAAAAT-ATTTTTTAGGGTTGATTTAT-ATTATTTTTATAACTTACAATTATTACTTTGTAAT
182 T-TAAAATAATTTTTTAGAGTTGATTTATCACTATTTTTATAACATACAATTATTACATTATAAT
* * *
436269 AATAAATTTAATGGTTTTTTAAAATTACAATATTCAAATGTATTTTATCCTGCCTTTGAAGTATA
246 AATAAATTAAATGG-TTTTTAAAATTACAATATTCAAATGTATTTTATCC-ACCTTTGAAGCATA
* * *
436334 ATTCTAAATATTAAGCGGGTAAGTGCAACATAGTCATATCTAAAATATTGTTAATTATTTATAAT
309 ATTCTAAATATTAAGCGGGTAAGTGCAACATAGTCATACCTAAAATATTATTAATTATTCATAAT
436399 TAATAAATAAAAGAAAATTAAATGGATAA
374 TAATAAATAAAAGAAAATTAAATGGATAA
436428 CATAAAACAT
Statistics
Matches: 370, Mismatches: 29, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
402 71 0.19
403 1 0.00
404 2 0.01
405 77 0.21
408 5 0.01
411 2 0.01
412 2 0.01
414 42 0.11
415 55 0.15
416 113 0.31
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (402 bp):
ATTAAATTTAAAAATTTATAAAATAATATTTAAATTTAATTACTGTTATAAAATAATTTTTGGAG
TTCATTTATCATTATTTTTATAAAAACTCAATTATTACTTTATAATAGTTTAATAAATTTAAAAA
TCAAATTGTAGTTTTAAAAATTTCAACAATTAAATTTTTTATATTGCCGCATTAAAATAATTTTT
TAGAGTTGATTTATCACTATTTTTATAACATACAATTATTACATTATAATAATAAATTAAATGGT
TTTTAAAATTACAATATTCAAATGTATTTTATCCACCTTTGAAGCATAATTCTAAATATTAAGCG
GGTAAGTGCAACATAGTCATACCTAAAATATTATTAATTATTCATAATTAATAAATAAAAGAAAA
TTAAATGGATAA
Found at i:443846 original size:21 final size:23
Alignment explanation
Indices: 443820--443861 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
443810 TTAAACACAA
443820 TGTG-AACTTTGA-AGCTTAAAC
1 TGTGAAACTTTGAGAGCTTAAAC
*
443841 TGTGAAACTTTTAGAGCTTAA
1 TGTGAAACTTTGAGAGCTTAA
443862 GGATTAGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (23 bp):
TGTGAAACTTTGAGAGCTTAAAC
Found at i:443959 original size:23 final size:23
Alignment explanation
Indices: 443914--443986 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
443904 GTTAAAAAAT
* * **
443914 GAATATGTTTACAAATGCCAAAC
1 GAATATGTTCACGAATGTTAAAC
443937 GAATATGTTCACGAATGTTAAAC
1 GAATATGTTCACGAATGTTAAAC
** *
443960 GCAA-ATGTTCGTGAATGTTAAAT
1 G-AATATGTTCACGAATGTTAAAC
443983 GAAT
1 GAAT
443987 TGAACATTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.05
23 37 0.90
24 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (23 bp):
GAATATGTTCACGAATGTTAAAC
Found at i:447467 original size:18 final size:18
Alignment explanation
Indices: 447444--447479 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
447434 ACTGGGATCA
447444 ATACGATGAAGCTTCAAC
1 ATACGATGAAGCTTCAAC
447462 ATACGATGAAGCTTCAAC
1 ATACGATGAAGCTTCAAC
447480 TTACAGCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
ATACGATGAAGCTTCAAC
Found at i:452616 original size:24 final size:24
Alignment explanation
Indices: 452564--452617 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
452554 TAGTATATTC
452564 TTAT-AATATTTTATAGTTTATAG
1 TTATAAATATTTTATAGTTTATAG
* *
452587 TT-TAAATATTATTATTG-TTATAT
1 TTATAAATATT-TTATAGTTTATAG
452610 TTATAAAT
1 TTATAAAT
452618 TATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 15 0.58
24 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (24 bp):
TTATAAATATTTTATAGTTTATAG
Found at i:454270 original size:21 final size:21
Alignment explanation
Indices: 454244--454284 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
454234 CTATATAAAC
454244 AATTTAA-TTTAAGAATAAATT
1 AATTTAATTTTAA-AATAAATT
454265 AATTTAATTTTAAAATAAAT
1 AATTTAATTTTAAAATAAAT
454285 ATATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATTTAATTTTAAAATAAATT
Found at i:454307 original size:11 final size:11
Alignment explanation
Indices: 454291--454315 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
454281 AAATATATAA
454291 AATATTGTAAT
1 AATATTGTAAT
454302 AATATTGTAAT
1 AATATTGTAAT
454313 AAT
1 AAT
454316 TTAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
AATATTGTAAT
Found at i:454658 original size:17 final size:18
Alignment explanation
Indices: 454638--454678 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
454628 AATTTAAGAA
454638 TAAAT-TATATAAAAATT
1 TAAATATATATAAAAATT
*
454655 TAAATAATATATAATAATT
1 TAAAT-ATATATAAAAATT
454674 TAAAT
1 TAAAT
454679 CAATTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
19 16 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATATATATAAAAATT
Found at i:454693 original size:57 final size:54
Alignment explanation
Indices: 454599--454707 Score: 148
Period size: 57 Copynumber: 2.0 Consensus size: 54
454589 TCCTTATTAT
*
454599 ATTTAAAAATTATATAAATTAATTAATTTAATTTAAGAATAAATT-ATATAAAA
1 ATTTAAAAATTATATAAATTAATCAATTTAATTTAAGAATAAATTAATATAAAA
* *
454652 ATTTAAATAATATATAATAATTTAAATCAATTTAATTTAAGAATATATTAATATAA
1 ATTTAAA-AAT-TAT-ATAAATT-AATCAATTTAATTTAAGAATAAATTAATATAA
454708 TTTAAAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
53 7 0.15
54 3 0.06
55 3 0.06
56 6 0.12
57 23 0.48
58 6 0.12
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (54 bp):
ATTTAAAAATTATATAAATTAATCAATTTAATTTAAGAATAAATTAATATAAAA
Found at i:459092 original size:15 final size:16
Alignment explanation
Indices: 459069--459102 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
459059 AATCTGATCC
*
459069 AAATGTAAAAAT-ATT
1 AAATATAAAAATAATT
459084 AAATATAAAAATAATT
1 AAATATAAAAATAATT
459100 AAA
1 AAA
459103 ATCCATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATATAAAAATAATT
Found at i:463162 original size:12 final size:12
Alignment explanation
Indices: 463145--463174 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
463135 TTATACAAAT
463145 CACATCATCTAA
1 CACATCATCTAA
463157 CACATCATCTAA
1 CACATCATCTAA
463169 CACATC
1 CACATC
463175 GTGTCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (12 bp):
CACATCATCTAA
Found at i:463317 original size:25 final size:26
Alignment explanation
Indices: 463289--463338 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
463279 TTAAGAATAA
463289 ATTATCCAAATC-AACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
463314 ATTATCCAAATCAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
463339 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.50, C:0.18, G:0.04, T:0.28
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Done.