Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012419.1 Corchorus capsularis cultivar CVL-1 contig12440, 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: 36506
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Found at i:363 original size:175 final size:175
Alignment explanation
Indices: 1--486 Score: 864
Period size: 175 Copynumber: 2.8 Consensus size: 175
*
1 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATAATAGTTAAGTAAGGACATTTA
1 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATAATAGTTAAGCAAGGACATTTA
66 AGATAATATATTTGAATAATAAGGGTACAATTGG-----C--AA--TTCTCAAAACTCGTACTTT
66 AGATAATATATTTGAATAATAAGGGTACAATTGGCAATTCAAAAGTTTCTCAAAACTCGTACTTT
122 TATATATAGTATAGAAATAAAGTAATTATAAAAATATTAGATTTA
131 TATATATAGTATAGAAATAAAGTAATTATAAAAATATTAGATTTA
*
167 ATTTAATTGAATAAAAATAGAGTTTCTAGTAAAATAAAACTATAATAGTTAAGCAAGGACATTTA
1 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATAATAGTTAAGCAAGGACATTTA
232 AGATAATATATTTGAATAATAAGGGTACAATTGGCAATTCAAAAGTTTCTCAAAACTCGTACTTT
66 AGATAATATATTTGAATAATAAGGGTACAATTGGCAATTCAAAAGTTTCTCAAAACTCGTACTTT
*
297 TATATATAGTATAGAAATAAAGTAATTATAAAGATATTAGATTTA
131 TATATATAGTATAGAAATAAAGTAATTATAAAAATATTAGATTTA
342 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATAATAGTTAAGCAAGGACATTTA
1 ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATAATAGTTAAGCAAGGACATTTA
* *
407 AGATAATATATTTAAATAATAAGGGTACAATTGACAATTCAAAAGTTTCTCAAAACTCGTACTTT
66 AGATAATATATTTGAATAATAAGGGTACAATTGGCAATTCAAAAGTTTCTCAAAACTCGTACTTT
472 TATATATAGTATAGA
131 TATATATAGTATAGA
487 TAGTAGTAGT
Statistics
Matches: 305, Mismatches: 6, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
166 97 0.32
171 1 0.00
173 2 0.01
175 205 0.67
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.34
Consensus pattern (175 bp):
ATTTAATTGAATAAAAATAGAGTTTCTAGTAGAATAAAACTATAATAGTTAAGCAAGGACATTTA
AGATAATATATTTGAATAATAAGGGTACAATTGGCAATTCAAAAGTTTCTCAAAACTCGTACTTT
TATATATAGTATAGAAATAAAGTAATTATAAAAATATTAGATTTA
Found at i:11627 original size:3 final size:3
Alignment explanation
Indices: 11619--11673 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
11609 TCCAATATAT
11619 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11667 AT- ATA AT
1 ATA ATA AT
11674 CAATGAATCT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18926 original size:14 final size:16
Alignment explanation
Indices: 18892--18929 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18882 GTTATATATG
18892 ATATATATAGGTACAT
1 ATATATATAGGTACAT
18908 ATATATATAGGT-CACT
1 ATATATATAGGTACA-T
18924 ATATAT
1 ATATAT
18930 GAGTGGCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 2 0.10
16 19 0.90
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (16 bp):
ATATATATAGGTACAT
Found at i:25241 original size:17 final size:16
Alignment explanation
Indices: 25219--25273 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 16
25209 ATCACCTCGC
25219 AGATCACTAGTGATCAA
1 AGATCACT-GTGATCAA
25236 AGATCACCTGTGATGC-A
1 AGATCA-CTGTGAT-CAA
*
25253 AGATCATCGGTGATCAA
1 AGATCA-CTGTGATCAA
25270 AGAT
1 AGAT
25274 TACAATGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 1 0.03
17 29 0.88
18 3 0.09
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (16 bp):
AGATCACTGTGATCAA
Found at i:28718 original size:25 final size:25
Alignment explanation
Indices: 28690--28737 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
28680 ACTATTTTAT
*
28690 TTTTACCATTTTACTATTTTAATAA
1 TTTTACCATCTTACTATTTTAATAA
28715 TTTTACCATCTTACTATTTTAAT
1 TTTTACCATCTTACTATTTTAAT
28738 TAAAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTACCATCTTACTATTTTAATAA
Found at i:31426 original size:23 final size:23
Alignment explanation
Indices: 31396--31447 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
31386 AAACCGAACC
*
31396 AGATCCAACTCGATTCGACTAAA
1 AGATCCAACTCGATTCGACCAAA
31419 AGATCCAACTCGATTCGACCAAA
1 AGATCCAACTCGATTCGACCAAA
*
31442 AAATCC
1 AGATCC
31448 GCTCAATTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.40, C:0.29, G:0.12, T:0.19
Consensus pattern (23 bp):
AGATCCAACTCGATTCGACCAAA
Found at i:32260 original size:108 final size:109
Alignment explanation
Indices: 32029--32318 Score: 435
Period size: 108 Copynumber: 2.7 Consensus size: 109
32019 TAAATTAAAA
* * *
32029 TGGTAAAAA-AAAATTA-TATAAA-ATATTGGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
32091 ATAAAATTGTATATTATAAAAAATTTTAATATATCCAAATTTTC
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
*
32135 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTACTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
* *
32200 ATAAAATTGTATATTAGAAAAAA-TTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
*
32243 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTTTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
32308 GTAGAATAAAA
61 GTAGAATAAAA
32319 CTAAGAAAGG
Statistics
Matches: 167, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
106 9 0.05
107 5 0.03
108 62 0.37
109 62 0.37
110 1 0.01
113 28 0.17
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTC
Found at i:33978 original size:6 final size:6
Alignment explanation
Indices: 33967--34000 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
33957 ACTCAAATCC
33967 TAGAGA TAGAGA TAGAGA TAGAGA -AGGAGA TAGA
1 TAGAGA TAGAGA TAGAGA TAGAGA TA-GAGA TAGA
34001 CCTATCTCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.04
6 24 0.92
7 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
TAGAGA
Found at i:34178 original size:18 final size:18
Alignment explanation
Indices: 34157--34192 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
34147 ACCGCGACCA
34157 CCACCACCACCAAGAAAC
1 CCACCACCACCAAGAAAC
* *
34175 CCACCACCTCCAATAAAC
1 CCACCACCACCAAGAAAC
34193 TTAATGCCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.50, G:0.03, T:0.06
Consensus pattern (18 bp):
CCACCACCACCAAGAAAC
Found at i:34221 original size:33 final size:33
Alignment explanation
Indices: 34178--34246 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
34168 AAGAAACCCA
* *
34178 CCACCTCCAATAAACTTAATGCCACCACCACTT
1 CCACCACCAATAAACTTAATGCCACCACCACCT
* *
34211 CCACCACCAATAAACTTGATGCCACCTCCACCT
1 CCACCACCAATAAACTTAATGCCACCACCACCT
34244 CCA
1 CCA
34247 ATAGACTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.32, C:0.45, G:0.04, T:0.19
Consensus pattern (33 bp):
CCACCACCAATAAACTTAATGCCACCACCACCT
Found at i:34275 original size:30 final size:29
Alignment explanation
Indices: 34232--34416 Score: 122
Period size: 30 Copynumber: 6.5 Consensus size: 29
34222 AAACTTGATG
*
34232 CCACCTCCACCTCCAATAG-ACTCAGCACCA
1 CCACCACCACCTCCAA-AGAACTCA-CACCA
* *
34262 CCACCACCTCCTCCAAGGAAC-C-CACCA
1 CCACCACCACCTCCAAAGAACTCACACCA
**
34289 CCACCACCACCTCCACCAAGGAAC-C-CACTG
1 CCACCACCACCTCCA--AA-GAACTCACACCA
*
34319 CCACCACCACCGCCAACAG-ACTCCACACCA
1 CCACCACCACCTCCAA-AGAACT-CACACCA
* *
34349 CCACCACCACCTCCAAGGAAC-C-CACCG
1 CCACCACCACCTCCAAAGAACTCACACCA
* * *
34376 CCGCCACCACCTCCACTAG-ACTCA-A-TA
1 CCACCACCACCTCCA-AAGAACTCACACCA
34403 CCACCACCACCTCC
1 CCACCACCACCTCC
34417 GCCTTCAAAT
Statistics
Matches: 124, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
27 54 0.44
28 6 0.05
29 6 0.05
30 58 0.47
ACGTcount: A:0.30, C:0.55, G:0.08, T:0.08
Consensus pattern (29 bp):
CCACCACCACCTCCAAAGAACTCACACCA
Found at i:34287 original size:27 final size:27
Alignment explanation
Indices: 34257--36361 Score: 225
Period size: 27 Copynumber: 73.8 Consensus size: 27
34247 ATAGACTCAG
*
34257 CACCACCACCACCTCCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
34284 CACCACCACCACCACCTCCACCAAGGAACC
1 CACCACCACCACCACCT---CCAAGGAACC
** * * *
34314 CACTGCCACCACCACCGCCAACAGACTCC
1 CACCACCACCACCACCTCCAA-GGA-ACC
34343 ACACCACCACCACCACCTCCAAGGAACC
1 -CACCACCACCACCACCTCCAAGGAACC
* * * *
34371 CACCGCCGCCACCACCTCCACTAGACTCAATAC
1 CACCACCACCACCACCTCCA--AG---GAA-CC
* * * **
34404 CACCACCACCTCCGCCTTCAAATAACTC
1 CACCACCACCACCACCTCCAAGGAAC-C
* * **
34432 GA-CTCCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * * ** *
34458 CAACACCTCCAACA-GACC---TAA--
1 CACCACCACCACCACCTCCAAGGAACC
34479 CACCACCACC---ACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * * *
34503 CACCATCGCCACCACCTCCAACAGATTCAACAT
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* ** **
34536 CACCACCACCTCCA-CTATTAAATAACTC
1 CACCACCACCACCACCT-CCAAGGAAC-C
* ** *
34564 GA-CACCACGTCCACCTCCAAGGAACT
1 CACCACCACCACCACCTCCAAGGAACC
* *
34590 CACCGCCACCACCACCTCCAA-CAGACTC
1 CACCACCACCACCACCTCCAAGGA-AC-C
**
34618 AACACCACCACCACCACCTTCGCCTTCAAATAACTC
1 --CACCACCACCACCACC-T---C--CAAGGAAC-C
* ** *
34654 GACC-CCACGTCCACCTCCAAGGAATC
1 CACCACCACCACCACCTCCAAGGAACC
* * *
34680 CACCACCACCATCTCCTCCAACAGAATTAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* *
34713 CACCACCACCACCACCTCCAA-CAGACT
1 CACCACCACCACCACCTCCAAGGA-ACC
* *
34740 CAACACCACCACCACCTCCAACTGATTCAACAC
1 CACCACCACCACCACCTCCAA--G---GAAC-C
** * * ** *
34773 CACCACCACCTTCTCCTTCAAATAACT
1 CACCACCACCACCACCTCCAAGGAACC
* ** *
34800 CAACACCACGTCCACCTCCAAGGAATC
1 CACCACCACCACCACCTCCAAGGAACC
* * * *
34827 CACCACCACCATCTCCCCCAACAGAATTAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* * *
34860 CACCACCACCACCACTTCCAA-CAGACT
1 CACCACCACCACCACCTCCAAGGA-ACC
* *
34887 CAACACCACCACCACCTCCAACAGATTCAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* ** * * **
34920 CACAACCACCTTCGCCTTCAAATAACTC
1 CACCACCACCACCACCTCCAAGGAAC-C
* **
34948 GA-CACCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * * * *
34974 CACCGCCACCACCTCCTACAATAGAA-T
1 CACCACCACCACCACCTCCAA-GGAACC
* * *
35001 TAACACCACCACCACCTTCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * *
35028 CACCACCGCCACCAACTCCAACAGATTCAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* * * *
35061 CACCACCACCTCCATCTTCGAA-TAACTC
1 CACCACCACCACCA-CCTCCAAGGAAC-C
* **
35089 GA-CACCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* *
35115 CACCGCCACCACCACCTCCAATAGATTCAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* * * **
35148 CACCACCACCTCCGCCTTCAAATAACTC
1 CACCACCACCACCACCTCCAAGGAAC-C
* * **
35176 GA--ATTCACTTCCACCTCCAAGGAACC
1 CACCA-CCACCACCACCTCCAAGGAACC
* * *
35202 CACCACCACCACCTCCTCCAACAGAA-T
1 CACCACCACCACCACCTCCAA-GGAACC
* *
35229 TAACACCACCACCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * *
35256 CACCACCGCCACCACCTCCAACAGATTCAACAT
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* * **
35289 CACCACCACCTCCA-CTATCAAATAACTC
1 CACCACCACCACCACCT-CCAAGGAAC-C
* ***
35317 GA-CACCACGTTCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* *
35343 CACCTCCACCACCACCTCCAA-CAGACTC
1 CACCACCACCACCACCTCCAAGGA-AC-C
**
35371 AACACCACCACCACCACCTTCGTCTTCAAATAACTC
1 --CACCACCACCACCA-C--C-TC--CAAGGAAC-C
* ** *
35407 AACC-CCACGTCCACCTCCAAGGAATC
1 CACCACCACCACCACCTCCAAGGAACC
* *
35433 CACCACCACCACCTCCTCCAACAGAATTAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
*
35466 CACCACCACCACCACCTCCAACAGATTCAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
** * * ** *
35499 CACCACCACCTTCGCCTTCAAATAACT
1 CACCACCACCACCACCTCCAAGGAACC
* ** *
35526 CAACACCACGTCCACCTCCAAGGAATC
1 CACCACCACCACCACCTCCAAGGAACC
* * * **
35553 CACCACCACCATCTCCTCCAACAGAATTAA
1 CACCACCACCACCACCTCCAA-GGAA--CC
* *
35583 CACCACCACCACCACCGTCTTCAA-CAGACT
1 CACCACCACCACCACC-TC--CAAGGA-ACC
* *
35613 CAACACCACCACCACCTCCAACAGATTCAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
** * * **
35646 CACCACCACCTTCGCCTTCAAATAACTC
1 CACCACCACCACCACCTCCAAGGAAC-C
* ** *
35674 GA-CACCACGTCCACCACCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * ** * *
35700 CACCGCCACCACCTCCTATAACAGAA-T
1 CACCACCACCACCACCTCCAA-GGAACC
* *
35727 TAACACCACCACCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * * * *
35754 CACCGCCACCACCTCCTACAACAGAA-T
1 CACCACCACCACCACCTCCAA-GGAACC
* *
35781 TAACACCACCACCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
*
35808 CACCACCGCCACCACCTCCAACAGAGTCAACAC
1 CACCACCACCACCACCTCC-A-AG-G--AAC-C
* * * *
35841 CACTACCACCTCCACCTTCGAA-TAACTC
1 CACCACCACCACCACC-TCCAAGGAAC-C
* **
35869 GA-CACCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * * *
35895 CA-CGCCACCACCACCTCCAATAGATTCAA
1 CACCACCACCACCACCTCCAA-GGA-AC-C
* **
35924 CACCACCACCACCTACGCCTTCAAATAACTC
1 CACCACCACCACC-A--CCTCCAAGGAAC-C
* * **
35955 GA-CTCCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* *
35981 CACCACCGCCACCACCTCCTCCAACAGAA-C
1 CACCA---CCACCACCACCTCCAA-GGAACC
* *
36011 TAACACCACCACCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* ** *
36038 CACCACCGCCACCACCTCAAACAGATTCAACAT
1 CACCACCACCACCACCTC---CA-A-GGAAC-C
* **
36071 CACCACCACCTCCACCAT-CAAATAACTC
1 CACCACCACCACCACC-TCCAAGGAAC-C
* **
36099 TA-CACCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * * *
36125 CACCGCCACCACCATCTCCAA-CAGACT
1 CACCACCACCACCACCTCCAAGGA-ACC
*
36152 CAACACCACCACCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* * ** *
36179 CACCACCTCCAACAGATTC----AA--
1 CACCACCACCACCACCTCCAAGGAACC
* * * **
36200 CACCACCACCACCTCCTCAAACCGAATT
1 CACCACCACCACCACCTCCAA-GGAACC
* * *
36228 AACC-CCACCACCTCCACCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
* *
36254 CACCGCCACCACCACCTCCAACAGACTTAACAC
1 CACCACCACCACCACCTCC-A-AG---GAAC-C
* * * ** *
36287 CACCACCACCTCCGCCTTCAAATAACT
1 CACCACCACCACCACCTCCAAGGAACC
* * **
36314 CAACTCCACGTCCACCTCCAAGGAACC
1 CACCACCACCACCACCTCCAAGGAACC
*
36341 CACCACCACCACCATCTCCAA
1 CACCACCACCACCACCTCCAA
36362 CAGATTTAAC
Statistics
Matches: 1451, Mismatches: 440, Indels: 374
0.64 0.19 0.17
Matches are distributed among these distances:
18 1 0.00
19 2 0.00
21 20 0.01
22 2 0.00
23 4 0.00
24 8 0.01
26 81 0.06
27 687 0.47
28 96 0.07
29 35 0.02
30 138 0.10
31 22 0.02
32 55 0.04
33 270 0.19
34 14 0.01
36 14 0.01
37 2 0.00
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (27 bp):
CACCACCACCACCACCTCCAAGGAACC
Found at i:34321 original size:87 final size:87
Alignment explanation
Indices: 34230--34391 Score: 254
Period size: 87 Copynumber: 1.9 Consensus size: 87
34220 ATAAACTTGA
* * * *
34230 TGCCACCTCCACCTCCAATAGACT-CAGCACCACCACCACCTCCTCCAAGGAACCCACCACCACC
1 TGCCACCACCACCGCCAACAGACTCCA-CACCACCACCACCACCTCCAAGGAACCCACCACCACC
34294 ACCACCTCCACCAAGGAACCCAC
65 ACCACCTCCACCAAGGAACCCAC
* *
34317 TGCCACCACCACCGCCAACAGACTCCACACCACCACCACCACCTCCAAGGAACCCACCGCCGCCA
1 TGCCACCACCACCGCCAACAGACTCCACACCACCACCACCACCTCCAAGGAACCCACCACCACCA
34382 CCACCTCCAC
66 CCACCTCCAC
34392 TAGACTCAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
87 66 0.97
88 2 0.03
ACGTcount: A:0.29, C:0.55, G:0.09, T:0.07
Consensus pattern (87 bp):
TGCCACCACCACCGCCAACAGACTCCACACCACCACCACCACCTCCAAGGAACCCACCACCACCA
CCACCTCCACCAAGGAACCCAC
Found at i:34323 original size:57 final size:57
Alignment explanation
Indices: 34257--34413 Score: 176
Period size: 57 Copynumber: 2.8 Consensus size: 57
34247 ATAGACTCAG
* * * *
34257 CACCACCACCACCTCCTCCAA-GGAAC-CCACCACCACCACCACCTCCACCAAGGAACC
1 CACCGCCACCACCACCTCCAACAG-ACTCCA-CACCACCACCACCACCACCAAGGAACC
* * *
34314 CACTGCCACCACCACCGCCAACAGACTCCACACCACCACCACCACCTCCAAGGAACC
1 CACCGCCACCACCACCTCCAACAGACTCCACACCACCACCACCACCACCAAGGAACC
* * *
34371 CACCGCCGCCACCACCTCC-ACTAGACTCAATACCACCACCACC
1 CACCGCCACCACCACCTCCAAC-AGACTCCACACCACCACCACC
34414 TCCGCCTTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
56 2 0.02
57 79 0.93
58 4 0.05
ACGTcount: A:0.31, C:0.55, G:0.08, T:0.06
Consensus pattern (57 bp):
CACCGCCACCACCACCTCCAACAGACTCCACACCACCACCACCACCACCAAGGAACC
Found at i:34502 original size:132 final size:132
Alignment explanation
Indices: 34347--34588 Score: 380
Period size: 132 Copynumber: 1.8 Consensus size: 132
34337 GACTCCACAC
* *
34347 CACCACCACCACCTCCAAGGAACCCACCGCCGCCACCACCTCC-ACTAGACTCAATACCACCACC
1 CACCACCACCACCTCCAAGGAACCCACCACCGCCACCACCTCCAAC-AGACTCAACACCACCACC
* *
34411 ACCTCCGCCT-TCAAATAACTCGACTCCACGTCCACCTCCAAGGAACCCAACACCTCCAACAGAC
65 ACCTCC-ACTATCAAATAACTCGACACCACGTCCACCTCCAAGGAACCCAACACCTCCAACAGAC
34475 CTAA
129 CTAA
* * *
34479 CACCACCACCACCTCCAAGGAACCCACCATCGCCACCACCTCCAACAGATTCAACATCACCACCA
1 CACCACCACCACCTCCAAGGAACCCACCACCGCCACCACCTCCAACAGACTCAACACCACCACCA
*
34544 CCTCCACTATTAAATAACTCGACACCACGTCCACCTCCAAGGAAC
66 CCTCCACTATCAAATAACTCGACACCACGTCCACCTCCAAGGAAC
34589 TCACCGCCAC
Statistics
Matches: 100, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
131 2 0.02
132 96 0.96
133 2 0.02
ACGTcount: A:0.32, C:0.48, G:0.08, T:0.12
Consensus pattern (132 bp):
CACCACCACCACCTCCAAGGAACCCACCACCGCCACCACCTCCAACAGACTCAACACCACCACCA
CCTCCACTATCAAATAACTCGACACCACGTCCACCTCCAAGGAACCCAACACCTCCAACAGACCT
AA
Found at i:34580 original size:87 final size:86
Alignment explanation
Indices: 34478--36030 Score: 660
Period size: 87 Copynumber: 17.8 Consensus size: 86
34468 AACAGACCTA
* * * *
34478 ACACCACCACCACCTCCAAGGAACCCACCATCGCCACCACCTCCAACAGATTCAACATCACCACC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTCAACACCACCACC
*
34543 ACCTCCACTATTAAATAACTCG
66 ACCTCCACT-TCAAATAACTCG
* * * *
34565 ACACCACGTCCACCTCCAAGGAACTCACCGCCACCACCACCTCCAACAGACTCAACACCACCACC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTC-A-A-CACCACC
34630 ACCACCTTCGC-CTTCAAATAACTCG
63 ACCACC-TC-CACTTCAAATAACTCG
* * * * *
34655 ACCCCACGTCCACCTCCAAGGAATCCACCACCACCATCTCCTCCAACAGAATT-AACACCACCAC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAG-ATTCAACACCACCAC
* * * * *
34719 CACCACCACCTCCAACAGACTCA
65 CACCTCCACTTCAAATA-ACTCG
* * * * ** ** * * *
34742 ACACCACCACCACCTCCAACTGATTCAACACCACCACCACCTTCTCCTTCA-AAT-AAC-TCAAC
1 ACACCACCTCCACCTCCAA-GGA-AC-CCACCACCACCACCACCTCCAACAGATTCAACACCACC
* * ** *
34804 ACCACGTCCACCTCCAAGGAA-TCC
63 ACCACCTCCA-CTTCAAATAACTCG
* * *
34828 ACCACCACCATCTC-CC-CCAACAGAATTAACACCACCACCACCACCACTTCCAACAGACTCAAC
1 A-CACCACC-TC-CACCTCC-A-AG---GAAC-CCACCACCACCACCACCTCCAACAGATTCAAC
* * * *
34891 ACCACCACCACCTCCA--ACAGATTCAACACC
57 ACCACCACCACCTCCACTTCA-AAT-AACTCG
* * * ** * ** * * * *
34921 ACAACCACCTTCGCCTTCAAATAACTCGA-CACCACGTCCACCTCCAA-GGA-AC-CCACCGCCA
1 AC-ACCACCTCCACCTCCAAGGAAC-CCACCACCACCACCACCTCCAACAGATTCAACACCACCA
* * **
34982 CCACCT-C-CTAC-AATAGAATTA
64 CCACCTCCACTTCAAATA-ACTCG
* * * *
35003 ACACCACCACCACCTTCAAGGAACCCACCACCGCCACCAACTCCAACAGATTCAACACCACCACC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTCAACACCACCACC
*
35068 ACCTCCATCTTCGAATAACTCG
66 ACCTCCA-CTTCAAATAACTCG
* * *
35090 ACACCACGTCCACCTCCAAGGAACCCACCGCCACCACCACCTCCAATAGATTCAACACCACCACC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTCAACACCACCACC
*
35155 ACCTCCGCCTTCAAATAACTCG
66 ACCTCC-ACTTCAAATAACTCG
* * *
35177 A-ATTCACTTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGAATT-AACACCACCA
1 ACA-CCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAG-ATTCAACACCACCA
** *
35240 CCACCT---C--CAAGGAAC-CC
64 CCACCTCCACTTCAAATAACTCG
* * * ** * * * * *
35257 ACCACCGCCACCACCTCCAA-CAGATTCAACATCACCACCACCTCCACTATCA-AAT-AACTCGA
1 A-CACCACCTCCACCTCCAAGGA-ACCCACCACCACCACCACCTCCA--A-CAGATTCAACACCA
* * * ** *
35319 -CACCACGTTCACCTCCAAGGAAC-CC
61 CCACCACCTCCA-CTTCAAATAACTCG
* * * ** * *
35344 ACCTCCACCACCACCTCCAA-CAGACTCAACACCACCACCACCACCTTCGTCTTCA-AAT-AACT
1 A-CACCACCTCCACCTCCAAGGA-AC-C--CACCACCACCACCACC-TC--CAACAGATTCAACA
* * * ** *
35406 CAACC-CCACGTCCACCTCCAAGGAA-TCC
58 CCACCACCACCTCCA-CTTCAAATAACTCG
* * *
35434 ACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCACCTCCAACAGATTCAACAC
1 A-CACCACCTCCACCTCC-A-AG---GAAC-CCACCACCACCACCACCTCCAACAGATTCAACAC
*
35499 CACCACCACCTTCGC-CTTCAAATAACTCA
59 CACCACCACC-TC-CACTTCAAATAACTCG
* * * *
35528 ACACCACGTCCACCTCCAAGGAATCCACCACCACCATCTCCTCCAACAGAATT-AACACCACCAC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAG-ATTCAACACCACCAC
* * * *
35592 CACCACCGTCTTCAACA-GACTCA
65 CACCTCC-ACTTCAA-ATAACTCG
* * ** * ** * * *
35615 ACACCACCACCACCTCCAA-CAGATTCAACACCACCACCACCTTCGCCTTCA-AAT-AACTCGA-
1 ACACCACCTCCACCTCCAAGGA-ACCCACCACCACCACCACC-T--CCAACAGATTCAACACCAC
* ** **
35676 CACCACGTCCACCACCAAGGAAC-C-
62 CACCACCTCCA-CTTCAAATAACTCG
* * * ** * * * * *
35700 -CACCGCCACCACCTCCTATAACAGAA-TTAACACCACCACCACCTCCAA-GGA-AC-CCACCGC
1 ACACCACCTCCACCTCC---AA-GGAACCCACCACCACCACCACCTCCAACAGATTCAACACCAC
* * **
35760 CACCACCT-C-CTACAACAGAA-TTA
62 CACCACCTCCACTTCAA-ATAACTCG
* * * *
35783 ACACCACCACCACCTCCAAGGAACCCACCACCGCCACCACCTCCAACAGAGTCAACACCACTACC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTCAACACCACCACC
*
35848 ACCTCCACCTTCGAATAACTCG
66 ACCTCCA-CTTCAAATAACTCG
* * *
35870 ACACCACGTCCACCTCCAAGGAACCCA-CGCCACCACCACCTCCAATAGATTCAACACCACCACC
1 ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTCAACACCACCACC
35934 ACCTACGC-CTTCAAATAACTCG
66 ACCT-C-CACTTCAAATAACTCG
* * * *
35956 ACTCCACGTCCACCTCCAAGGAACCCACCACCGCCACCACCTCCTCCAACAGA-ACTAACACCAC
1 ACACCACCTCCACCTCCAAGGAACCCACCA---CCACCACCACCTCCAACAGATTC-AACACCAC
36020 CACCACCTCCA
62 CACCACCTCCA
36031 AGGAACCCAC
Statistics
Matches: 1129, Mismatches: 224, Indels: 224
0.72 0.14 0.14
Matches are distributed among these distances:
80 8 0.01
81 99 0.09
82 20 0.02
83 8 0.01
84 82 0.07
85 6 0.01
86 95 0.08
87 432 0.38
88 47 0.04
89 7 0.01
90 210 0.19
91 20 0.02
92 22 0.02
93 63 0.06
94 5 0.00
95 4 0.00
96 1 0.00
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.13
Consensus pattern (86 bp):
ACACCACCTCCACCTCCAAGGAACCCACCACCACCACCACCTCCAACAGATTCAACACCACCACC
ACCTCCACTTCAAATAACTCG
Found at i:34630 original size:60 final size:60
Alignment explanation
Indices: 34566--36471 Score: 346
Period size: 60 Copynumber: 33.1 Consensus size: 60
34556 AATAACTCGA
* * * *
34566 CACCACGTCCACCTCCAAGGAACTCACCGCCACCACCACCTCCAACAGACTCAACACCACCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATC-A-A-CACCAC
* * * ** ** *
34629 CACCACCTTCGCCTTCAAATAACTCGACC-CCACGTCCACCTCCAA-GGAATC--CACCAC
1 CACCACCTCCACCTCCAAGCAACTC-ACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * ** * *
34686 CACCATCTCCTCCAACAGAATTAACACCACCACCACCACCACCTCCAACAGACTCAACACCAC
1 CACCACCTCCACC-TC-CAAGCAAC-TCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * ** ** ** * *
34749 CACCACCTCCAACT-GATTCAA--CACCACCACCACCTTCTCCTTCA-AAT-AAC-TCAA
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * * *
34803 CACCACGTCCACCTCCAAGGAA-TCCACCACCACCATCTCCCCCAACAGAATTAACACCAC
1 CACCACCTCCACCTCCAAGCAACT-CACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * *
34863 CACCACCACCACTTCCAA-CAGACTCAACACCACCACCACCTCCAACAGATTCAACACCAC
1 CACCACCTCCACCTCCAAGCA-ACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * ** ** * * *
34923 AACCACCTTCGCCTTCAAATAACTCGA-CACCACGTCCACCTCCAA-GGAA-C-CCACCGC
1 CACCACCTCCACCTCCAAGCAACTC-ACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * *
34980 CACCACCT---CCTACAATAG-AA-TTAACACCACCACCACCTTC-A-AG---GAAC-CCAC
1 CACCACCTCCACCT-CCA-AGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * * * * * *
35031 CACCGCCACCAACTCCAA-CAGATTCAACACCACCACCACCTCCATCTTCGAAT-AACTCGA-
1 CACCACCTCCACCTCCAAGCA-ACTCACCACCACCACCACCTCCAAC--AGAATCAACACCAC
* * * * * *
35091 CACCACGTCCACCTCCAAGGAACCCACCGCCACCACCACCTCCAATAGATTCAACACCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * ** * ** * *
35151 CACCACCTCCGCCTTCAAATAACTCGA--ATTCACTTCCACCTCCAA-GGAA-C-CCACCAC
1 CACCACCTCCACCTCCAAGCAACTC-ACCA-CCACCACCACCTCCAACAGAATCAACACCAC
* * * *
35208 CACCACCT---CCTCCAA-CAGAATTAACACCACCACCACCTCC-A-AG---GAAC-CCAC
1 CACCACCTCCACCTCCAAGCA-ACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * * * *
35259 CACCGCCACCACCTCCAA-CAGATTCAACATCACCACCACCTCCACTATCA-AAT-AACTCGA-
1 CACCACCTCCACCTCCAAGCA-ACTCACCACCACCACCACCTCCA--A-CAGAATCAACACCAC
* * * * * *
35319 CACCACGTTCACCTCCAAGGAACCCACCTCCACCACCACCTCCAACAGACTCAACACCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * ** ** *
35379 CACCACCACCTTCGTCTTCAAATAACTCAACC-CCACGTCCACCTCCAA-GGAATC--CACCAC
1 CACCACCTCC-AC--CTCCAAGCAACTC-ACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * ** * *
35439 CACCACCTCCTCCAACAGAATTAACACCACCACCACCACCACCTCCAACAGATTCAACACCAC
1 CACCACCTCCACC-TC-CAAGCAAC-TCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * ** * ** *
35502 CACCACCTTCGCCTTCAAATAACTCAACACCACGTCCACCTCCAA-GGAATC--CACCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * ** * *
35559 CACCATCTCCTCCAAC-AG-AATTAACACCACCACCACCACCGTCTTCAACAGACTCAACACCAC
1 CACCACCTCCACCTCCAAGCAACT--CACCACCACCACCACC-TC--CAACAGAATCAACACCAC
* ** ** ** * ** * *
35622 CACCACCTCCAAC-AGATTCAA--CACCACCACCACCTTCGCCTTCA-AAT-AACTCGA-
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * * * ** *
35676 CACCACGTCCACCACCAAGGAACCCACCGCCACCACCTCCTATAACAGAAT-TA-A-CAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * * *
35733 CACCA---CCACCTCCAAGGAACCCACCGCCACCACCTCCTACAACAGAAT-TA-A-CAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * *
35787 CACCA---CCACCTCCAAGGAACCCACCACCGCCACCACCTCCAACAGAGTCAACACCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * ** * * * *
35844 TACCACCTCCACCTTCGAA-TAACTCGA-CACCACGTCCACCTCCAA-GGAACCCACGCCAC
1 CACCACCTCCACC-TCCAAGCAACTC-ACCACCACCACCACCTCCAACAGAATCAACACCAC
* ** ** * ** * *
35903 CACCACCTCCA-ATAGATTCAA--CACCACCACCACCTA-CGCCTTCA-AAT-AACTCGA-
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACC-ACCTCCAACAGAATCAACACCAC
* * * * * *
35957 CTCCACGTCCACCTCCAAGGAACCCACCACCGCCACCACCTCCTCCAACAGAA-CTA-A-CAC
1 CACCACCTCCACCTCCAAGCAACTCACCA---CCACCACCACCTCCAACAGAATCAACACCAC
* * * * * *
36017 CACCA---CCACCTCCAAGGAACCCACCACCGCCACCACCTCAAACAGATTCAACATCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
** ** *
36074 CACCACCTCCACCAT-CAAATAACTCTA-CACCACGTCCACCTCC-A-AG---GAAC-CCAC
1 CACCACCTCCACC-TCCAAGCAACTC-ACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * *
36128 CGCCACCACCATCTCCAA-CAGACTCAACACCACCACCACCTCC-A-AG----GA-A-C-C
1 CACCACCTCCACCTCCAAGCA-ACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* ** ** * * * *
36179 CACCACCTCCAAC-AGATTCAA--CACCACCACCACCTCCTCAAACCGAAT-TA-ACC-C
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * *
36233 CACCACCTCCA---CCAAGGAACCCACCGCCACCACCACCTCCAACAGACTTAACACCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * ** * * ** *
36290 CACCACCTCCGCCTTCAAATAACTCAACTCCACGTCCACCTCC-A-AG---GAAC-CCAC
1 CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
* * * * ** * *
36344 CACCACCACCATCTCCAA-CAGATTTAACACCACCACCACCTCCTCCTTCA-AAT-AACTCGA-
1 CACCACCTCCACCTCCAAGCA-A-CT--CACCACCACCACCACCTCCAACAGAATCAACACCAC
* * ** * *
36404 CACCACGTCCACCTCCAAGGAA-TCCACCGTCGCCACCACCTCCAACAGAATCTACACCAC
1 CACCACCTCCACCTCCAAGCAACT-CACCACCACCACCACCTCCAACAGAATCAACACCAC
36464 CACCACCT
1 CACCACCT
36472 ACGCCTTCAA
Statistics
Matches: 1335, Mismatches: 358, Indels: 303
0.67 0.18 0.15
Matches are distributed among these distances:
48 16 0.01
49 1 0.00
50 3 0.00
51 32 0.02
52 8 0.01
53 17 0.01
54 317 0.24
55 41 0.03
56 26 0.02
57 224 0.17
58 28 0.02
59 71 0.05
60 387 0.29
61 42 0.03
62 9 0.01
63 105 0.08
64 8 0.01
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.13
Consensus pattern (60 bp):
CACCACCTCCACCTCCAAGCAACTCACCACCACCACCACCTCCAACAGAATCAACACCAC
Found at i:34773 original size:24 final size:27
Alignment explanation
Indices: 34716--36299 Score: 324
Period size: 27 Copynumber: 55.6 Consensus size: 27
34706 TTAACACCAC
34716 CACCACCACCACCTCCAACAGACTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* *
34743 CACCACCACCACCTCCAACTGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
*
34770 CACCACCACCACCTTCTCCTTCAA-ATAACTCAA
1 CACCACCACCA-C--CT-C--CAACA-GACTCAA
** * * *
34803 CACCACGTCCACCTCCAA-GGAATCCAC
1 CACCACCACCACCTCCAACAGACT-CAA
* * * *
34830 CACCACCATCTCCCCCAACAGAATTAACACCA
1 CACCACCACCACCTCCAACAG-ACT--CA--A
*
34862 CCACCACCACCACTTCCAACAGACTCAA
1 -CACCACCACCACCTCCAACAGACTCAA
*
34890 CACCACCACCACCTCCAACAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
34917 CACCACAACCACCTTCGCCTTCAA-ATAACTCGA
1 CACCACCACCACC-T---C--CAACA-GACTCAA
** * * *
34950 CACCACGTCCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * * * * *
34977 CGCCACCACCTCCTACAATAGAATTAA
1 CACCACCACCACCTCCAACAGACTCAA
* * * *
35004 CACCACCACCACCTTCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * *
35031 CACCGCCACCAACTCCAACAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
35058 CACCACCACCACCTCCATCTTCGAATAACTCGA
1 CACCACCACCACCTCCA---AC--A-GACTCAA
** * * *
35091 CACCACGTCCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * *
35118 CGCCACCACCACCTCCAATAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
*
35145 CACCACCACCACCTCCGCCTTCAA-ATAACTCGAA
1 CACCACCACCACCT----C--CAACA-GACTC-AA
** ** * * *
35179 -TTCACTTCCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * *
35205 CACCACCACCTCCTCCAACAGAATTAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
35232 CACCACCACCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* *
35259 CACCGCCACCACCTCCAACAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
35286 CATCACCACCACCTCCACTATCAAATAACTCGA
1 CACCACCACCACCTCCA--A-C--A-GACTCAA
*** * * *
35319 CACCACGTTCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
*
35346 CTCCACCACCACCTCCAACAGACTCAACA
1 CACCACCACCACCTCCAACAGACTC-A-A
*
35375 CCACCACCACCACCTTCGTCTTCAA-ATAACTCAA
1 -CACCACCACCA-C--C-TC--CAACA-GACTCAA
* ** * * *
35409 CCCCACGTCCACCTCCAA-GGAATCCAC
1 CACCACCACCACCTCCAACAGACT-CAA
* *
35436 CACCACCACCTCCTCCAACAGAATTAACACCA
1 CACCACCACCACCTCCAACAG-ACT--CA--A
*
35468 CCACCACCACCACCTCCAACAGATTCAA
1 -CACCACCACCACCTCCAACAGACTCAA
*
35496 CACCACCACCACCTTCGCCTTCAA-ATAACTCAA
1 CACCACCACCACC-T---C--CAACA-GACTCAA
** * * *
35529 CACCACGTCCACCTCCAA-GGAATCCAC
1 CACCACCACCACCTCCAACAGACT-CAA
* * * *
35556 CACCACCATCTCCTCCAACAGAATTAACAC
1 CACCACCACCACCTCCAACAG-ACT--CAA
35586 CACCACCACCACCGTCTTCAACAGACTCAA
1 CACCACCACCACC-TC--CAACAGACTCAA
*
35616 CACCACCACCACCTCCAACAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* *
35643 CACCACCACCACCTTCGCCTTCAA-ATAACTCGA
1 CACCACCACCACC-T---C--CAACA-GACTCAA
** * * * *
35676 CACCACGTCCACCACCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * ** * *
35703 CGCCACCACCTCCTATAACAGAATTAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
35730 CACCACCACCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * * * *
35757 CGCCACCACCTCCTACAACAGAATTAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
35784 CACCACCACCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* *
35811 CACCGCCACCACCTCCAACAGAGTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* * * *
35838 CACCACTACCACCTCCACCTTCGAATAACTCGA
1 CACCACCACCACCTCCA---AC--A-GACTCAA
** * *
35871 CACCACGTCCACCTCCAA-GGAAC-CCA
1 CACCACCACCACCTCCAACAG-ACTCAA
* * *
35897 CGCCACCACCACCTCCAATAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* *
35924 CACCACCACCACCTACGCCTTCAA-ATAACTCGA
1 CACCACCACCACCT----C--CAACA-GACTCAA
* ** * *
35957 CTCCACGTCCACCTCCAA-GGAACCCACCA
1 CACCACCACCACCTCCAACAG-ACTCA--A
* *
35986 CCGCCACCACCTCCTCCAACAGAACT-AA
1 -CACCACCACCACCTCCAACAG-ACTCAA
* * *
36014 CACCACCACCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* * *
36041 CACCGCCACCACCTCAAACAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
36068 CATCACCACCACCTCCACCATCAAATAACTCTA
1 CACCACCACCACCTCCA--A-C--A-GACTCAA
** * * *
36101 CACCACGTCCACCTCCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* *
36128 CGCCACCACCATCTCCAACAGACTCAA
1 CACCACCACCACCTCCAACAGACTCAA
*
36155 CACCACCACCACCTCC-A-AG----GA
1 CACCACCACCACCTCCAACAGACTCAA
*
36176 -A-C-CCACCACCTCCAACAGATTCAA
1 CACCACCACCACCTCCAACAGACTCAA
* * *
36200 CACCACCACCACCTCCTCAAACCGAATTAA
1 CACCACCACCACCT-C-C-AACAGACTCAA
* * * * * *
36230 CCCCACCACCTCCACCAA-GGAACCCAC
1 CACCACCACCACCTCCAACAG-ACTCAA
* *
36257 CGCCACCACCACCTCCAACAGACTTAA
1 CACCACCACCACCTCCAACAGACTCAA
36284 CACCACCACCACCTCC
1 CACCACCACCACCTCC
36300 GCCTTCAAAT
Statistics
Matches: 1096, Mismatches: 318, Indels: 286
0.64 0.19 0.17
Matches are distributed among these distances:
18 11 0.01
19 2 0.00
20 3 0.00
21 1 0.00
24 1 0.00
25 3 0.00
26 36 0.03
27 624 0.57
28 25 0.02
29 21 0.02
30 90 0.08
31 15 0.01
32 20 0.02
33 230 0.21
34 5 0.00
35 2 0.00
36 7 0.01
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.12
Consensus pattern (27 bp):
CACCACCACCACCTCCAACAGACTCAA
Found at i:34809 original size:147 final size:147
Alignment explanation
Indices: 34574--36334 Score: 1303
Period size: 147 Copynumber: 12.3 Consensus size: 147
34564 GACACCACGT
* * * *
34574 CCACCTCCAAGGAACTCACCGCCACCACCACCTCCAACAGACTCAACACCACCACCACCACCTTC
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAGATTC-A-A-CACCACCACCACCTTC
* * * *
34639 GCCTTCAAATAACTCGACCCCACGTCCACCTCCAAGGAATCCACCACCACCATCTCCTCCAACAG
63 GCCTTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAG
34704 AATTAACACCACCACCACCA
128 AATTAACACCACCACCACCA
* *
34724 CCACCTCCAACAG-ACTCAACACCACCACCACCTCCAACTGATTCAACACCACCACCACCTTCTC
1 CCACCTCCAA-AGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGC
* * *
34788 CTTCAAATAACTCAACACCACGTCCACCTCCAAGGAATCCACCACCACCATCTCCCCCAACAGAA
65 CTTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGAA
34853 TTAACACCACCACCACCA
130 TTAACACCACCACCACCA
* *
34871 CCACTTCCAACAG-ACTCAACACCACCACCACCTCCAACAGATTCAACACCACAACCACCTTCGC
1 CCACCTCCAA-AGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGC
* * * *
34935 CTTCAAATAACTCGACACCACGTCCACCTCCAAGGAACCCACCGCCACCACCTCCTACAATAGAA
65 CTTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGAA
35000 TT---A--A-CACCACCA
130 TTAACACCACCACCACCA
* * * * * * * **
35012 CCACCTTCAAGGAACCCACCACCGCCACCAACTCCAACAGATTCAACACCACCACCACCTCCATC
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGCC
* * * * *
35077 TTCGAATAACTCGACACCACGTCCACCTCCAAGGAACCCACCGCCACCACCACCTCCAATAG-AT
66 TTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGAAT
*
35141 TCAACACCACCACCACCT
131 T-AACACCACCACCACCA
* * * ** ** * * *
35159 CCGCCTTCAAATAACTCGAA-TTCACTTCCACCTCCAA-GGA-AC-CCACCACCACCACC-T--C
1 CCACCTCCAAAGAACTC-AACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGC
* * * ** * *
35217 CTCCAACAGAA-TTAACACCACCACCACCTCCAAGGAACCCACCACCGCCACCACCTCCAACAG-
65 CTTCAA-ATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGA
* *
35280 ATTCAACATCACCACCACCT
129 ATT-AACACCACCACCACCA
* * * *** * ** * *
35300 CCA-CTATCAAATAACTCGACACCACGTTCACCTCCAA-GGAACCCACCTCCACCACCACCTCCA
1 CCACCT-CCAAAGAACTCAACACCACCACCACCTCCAACAG-ATTCAACACCACCACCACCT---
* * ** * * * ** * ** * ** *
35363 ACAGAC-TCAACACCAC-CACCACCACCTTCGTCTTCAAATAACTCAACC-CCACGTCCACCTCC
61 TC-GCCTTCAA-ATAACTCAACACCACGTCCACCTCCAAGGAAC-CCACCACCACCACCTCCTCC
*
35425 AA-GGAA-T----CCACCACCACCA
123 AACAGAATTAACACCACCACCACCA
* *
35444 CCTCCTCCAACAGAATTAACACCACCACCACCACCACCTCCAACAGATTCAACACCACCACCACC
1 CCACCTCCAA-AGAACT--CA--A-CACCACCACCACCTCCAACAGATTCAACACCACCACCACC
* *
35509 TTCGCCTTCAAATAACTCAACACCACGTCCACCTCCAAGGAATCCACCACCACCATCTCCTCCAA
60 TTCGCCTTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAA
35574 CAGAATTAACACCACCACCACCA
125 CAGAATTAACACCACCACCACCA
** *
35597 CCGTCTTCAACAG-ACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGC
1 CCACCTCCAA-AGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGC
* * * **
35661 CTTCAAATAACTCGACACCACGTCCACCACCAAGGAACCCACCGCCACCACCTCCTATAACAGAA
65 CTTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGAA
35726 TT---A--A-CACCACCA
130 TTAACACCACCACCACCA
* * * * * *
35738 CCACCTCCAAGGAACCCACCGCCACCACCTCCTACAACAGAATT-AACACCACCACCACC-T---
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAG-ATTCAACACCACCACCACCTTCGC
** * * * ** * * * * * **
35798 C--CAAGGAACCCACCACCGCCACCACCTCCAACAGAGTCAACACCACTACCACCTCCACCTTC-
65 CTTCAAATAACTCAACACCACGTCCACCTCCAA-GGA-AC-CCACCACCACCACCTCCTCCAACA
* * **
35860 GAA-TAACTCGA-CACCACGT
127 GAATTAACACCACCACCACCA
* * * * *
35879 CCACCTCCAAGGAAC-CCACGCCACCACCACCTCCAATAGATTCAACACCACCACCACCTACGCC
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGCC
* *
35943 TTCAAATAACTCGACTCCACGTCCACCTCCAAGGAACCCACCACCGCCACCACCTCCTCCAACAG
66 TTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCA---CCACCACCTCCTCCAACAG
*
36008 AACT---A--A-CACCACCA
128 AATTAACACCACCACCACCA
* * * * * * * *
36022 CCACCTCCAAGGAACCCACCACCGCCACCACCTCAAACAGATTCAACATCACCACCACCTCCACC
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGCC
* * *
36087 ATCAAATAACTCTACACCACGTCCACCTCCAAGGAACCCACCGCCACCACCAT-CTCCAACAG-A
66 TTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACC-TCCTCCAACAGAA
*
36150 CT--CA--A-CACCACCA
130 TTAACACCACCACCACCA
*
36163 CCACCTCC-AAG-----GA-A-C-CCACCACCTCCAACAGATTCAACACCACCACCACC-T--CC
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGCC
* * * ** * * * *
36216 -TCAAACCGAA-TTAACCCCACCACCTCCACCAAGGAACCCACCGCCACCACCACCTCCAACAGA
66 TTCAAA--TAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGA
* *
36279 CTTAACACCACCACCACCT
129 ATTAACACCACCACCACCA
* * * * **
36298 CCGCCTTCAAATAACTCAACTCCACGTCCACCTCCAA
1 CCACCTCCAAAGAACTCAACACCACCACCACCTCCAA
36335 GGAACCCACC
Statistics
Matches: 1297, Mismatches: 228, Indels: 178
0.76 0.13 0.10
Matches are distributed among these distances:
128 5 0.00
129 45 0.03
130 3 0.00
132 35 0.03
133 1 0.00
134 2 0.00
135 34 0.03
136 5 0.00
137 5 0.00
138 15 0.01
139 3 0.00
140 48 0.04
141 325 0.25
142 10 0.01
143 29 0.02
144 136 0.10
145 9 0.01
146 46 0.04
147 391 0.30
148 7 0.01
149 5 0.00
150 107 0.08
151 7 0.01
152 2 0.00
153 22 0.02
ACGTcount: A:0.33, C:0.48, G:0.06, T:0.12
Consensus pattern (147 bp):
CCACCTCCAAAGAACTCAACACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGCC
TTCAAATAACTCAACACCACGTCCACCTCCAAGGAACCCACCACCACCACCTCCTCCAACAGAAT
TAACACCACCACCACCA
Found at i:35474 original size:33 final size:33
Alignment explanation
Indices: 35432--35628 Score: 150
Period size: 33 Copynumber: 6.3 Consensus size: 33
35422 TCCAAGGAAT
35432 CCACCACCACCACCTCCTCCAACAGAATTAACA
1 CCACCACCACCACCTCCTCCAACAGAATTAACA
*
35465 CCACCACCACCACCACCTCCAACAG-ATT--CA
1 CCACCACCACCACCTCCTCCAACAGAATTAACA
* * * **
35495 ACACCACCACCACCTTCGCCTTCA-AA-TAAC-
1 CCACCACCACCACCTCCTCCAACAGAATTAACA
* * ** * *
35525 TCAACACCACGTCCACCTCCAA-GGAA-T--C-
1 CCACCACCACCACCTCCTCCAACAGAATTAACA
*
35553 -CACCACCACCATCTCCTCCAACAGAATTAACA
1 CCACCACCACCACCTCCTCCAACAGAATTAACA
* * *
35585 CCACCACCACCACCGT-CTTCAACAGACTCAACA
1 CCACCACCACCACC-TCCTCCAACAGAATTAACA
35618 CCACCACCACC
1 CCACCACCACC
35629 TCCAACAGAT
Statistics
Matches: 126, Mismatches: 27, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
27 16 0.13
28 4 0.03
29 2 0.02
30 37 0.29
31 2 0.02
32 3 0.02
33 61 0.48
34 1 0.01
ACGTcount: A:0.34, C:0.49, G:0.05, T:0.13
Consensus pattern (33 bp):
CCACCACCACCACCTCCTCCAACAGAATTAACA
Found at i:35653 original size:120 final size:117
Alignment explanation
Indices: 34859--36389 Score: 538
Period size: 114 Copynumber: 13.4 Consensus size: 117
34849 AGAATTAACA
* * * * *
34859 CCACCACCACCACCACTTCCAACAG-ACT--CAACACCACCACCACCTCCAACAGATTCAACACC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
* ** * * * *
34921 ACAACCACCTTCGCCTTCA-AAT-AACTCGA-CACCACGTCCACCTCCAAGGAAC
66 ACCACCACC-T--CCAACAGATTCAACACCACCACCACGTCCACCTCCAAGGAAT
* * * * * * *
34973 CCACCGCCACCACCTCCTACAATAGAATT-A-A-CACCACCACCACCTTCAA-GGAACCCACCAC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAG-ACTCAACAC
* * * * * *
35034 CGCCACCAACTCCAACAGATTCAACACCACCACCACCTCCATCTTCGAA-TAACT
65 CACCACCACCTCCAACAGATTCAACACCACCACCACGTCCA-CCTCCAAGGAA-T
* ** * * ** * * *
35088 CGA-CACCACGTCCACCTCCAA-GGAA--CCCACCGCCACCACCACCTCCAATAGATTCAACACC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
* * ** * * *
35149 ACCACCACCTCC-GC--CTTCAA-ATAACTCGAATTCACTTCCACCTCCAAGGAAC
66 ACCACCACCTCCAACAGATTCAACACCAC-C--A-CCACGTCCACCTCCAAGGAAT
* * *
35201 CCACCACCACCACCTCCTCCAACAGAATT-A-A-CACCACCACCACCTCCAA-GGAACCCACCAC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAG-ACTCAACAC
* * * * **
35262 CGCCACCACCTCCAACAGATTCAACATCACCACCACCTCCA-CTATCAAATAACT
65 CACCACCACCTCCAACAGATTCAACACCACCACCACGTCCACCT-CCAAGGAA-T
* *** * * ** *
35316 CGA-CACCACGTTCACCTCCAA-GGAA--CCCACCTCCACCACCACCTCCAACAGACTCAACACC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
* ** * *
35377 ACCACCACCACCTTC-GTCTTCAAATAACTCAACC-CCACGTCCACCTCCAAGGAAT
66 ACCACCACCTCCAACAG-ATTC-AA-CAC-C-ACCACCACGTCCACCTCCAAGGAAT
*
35432 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCACCTCCAACAGATTCAAC
1 CCACCACCACCACCTCCTCCAACAGAATT-A-A-CACCACCACCACCACCTCCAACAGACTCAAC
** * * *
35497 ACCACCACCACCTTCGCCTTCA-AAT-AAC-TCAACACCACGTCCACCTCCAAGGAAT
63 ACCACCACCACC-T--CCAACAGATTCAACACCACCACCACGTCCACCTCCAAGGAAT
*
35552 CCACCACCACCATCTCCTCCAACAGAATTAACACCACCACCACCACCGTCTTCAACAGACTCAAC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACC-TC--CAACAGACTCAAC
* * * * **
35617 ACCACCACCACCTCCAACAGATTCAACACCACCACCACCTTCGCCTTCAAATAA-
63 ACCACCACCACCTCCAACAGATTCAACACCACCACCACGTCCACCTCCAAGGAAT
* * * * * ** * * *
35671 -CTCGA-CACCACGTCCACC-AC-CAAGGAAC-CCACCGCCACCACCTCCTATAACAGAATTAAC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCC---AACAGACTCAAC
* * ** * * *
35731 ACCACCACCACCTCC-A-AG---GAAC-CCACCGCCACCACCTCCTACAACAGAAT
63 ACCACCACCACCTCCAACAGATTCAACACCACCACCACGTCCACCTCCAA-GGAAT
* * * * ** * *
35781 -TAACACCACCACCACCTCCAA-GGAA--CCCACCACCGCCACCACCTCCAACAGAGTCAACACC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
* * * * * * *
35842 ACTACCACCTCCACCTTCGAAT-AACTCGA-CACCACGTCCACCTCCAAGGAAC
66 ACCACCACCTCCAAC--AGATTCAACACCACCACCACGTCCACCTCCAAGGAAT
* * * * * *
35894 CCA-CGCCACCACCACCTCCAATAG-ATTCAACACCACCACCACCTACGCCTTCAA-ATAACTCG
1 CCACCACCACCACCTCCTCCAACAGAATT-AACACCACCACCACC-A--CCTCCAACA-GACTCA
* ** * * * * ** * *
35956 ACTCCACGTCCACCTCCAA-GGA-AC-CCACCACCGCCACCACCTCCTCCAACAGAA-
61 ACACCACCACCACCTCCAACAGATTCAACACCACCACCACGTCCACCTCCAA-GGAAT
* * * * ** * * * *
36010 CTAACACCACCACCACCTCCAA-GGAA--CCCACCACCGCCACCACCTCAAACAGATTCAACATC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
* * * *
36072 ACCACCACCTCCACCATCA-AAT-AACTCTA-CACCACGTCCACCTCCAAGGAAC
66 ACCACCACCTCCA--A-CAGATTCAACACCACCACCACGTCCACCTCCAAGGAAT
* * * *
36124 CCACCGCCACCACCAT-CTCCAACAG-ACT--CAACACCACCACCACCTCC-A-AG----GA-A-
1 CCACCACCACCACC-TCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACAC
* * *
36177 C-CCACCACCTCCAACAGATTCAACACCACCACCA---CCTCCTCAAACCGAAT
65 CACCACCACCTCCAACAGATTCAACACCACCACCACGTCCACCTCCAA-GGAAT
** * * ** * *
36227 TAACC-CCACCACCTCCACCAA-GGAA--CCCACCGCCACCACCACCTCCAACAGACTTAACACC
1 CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
* * * * * *
36288 ACCACCACCTCC-GC--CTTCAAATAACTCAACTCCACGTCCACCTCCAAGGAAC
66 ACCACCACCTCCAACAGATTC-AA-CAC-CACCACCACGTCCACCTCCAAGGAAT
* *
36340 CCACCACCACCACCAT-CTCCAACAGATTTAACACCACCACCACCTCCTCC
1 CCACCACCACCACC-TCCTCCAACAGAATTAACACCACCACCACCACCTCC
36390 TTCAAATAAC
Statistics
Matches: 1037, Mismatches: 253, Indels: 251
0.67 0.16 0.16
Matches are distributed among these distances:
101 2 0.00
102 41 0.04
103 10 0.01
104 7 0.01
105 17 0.02
106 1 0.00
107 1 0.00
108 46 0.04
109 9 0.01
110 9 0.01
111 77 0.07
112 11 0.01
113 64 0.06
114 370 0.36
115 39 0.04
116 37 0.04
117 103 0.10
118 21 0.02
119 31 0.03
120 92 0.09
123 43 0.04
125 1 0.00
126 5 0.00
ACGTcount: A:0.33, C:0.48, G:0.07, T:0.12
Consensus pattern (117 bp):
CCACCACCACCACCTCCTCCAACAGAATTAACACCACCACCACCACCTCCAACAGACTCAACACC
ACCACCACCTCCAACAGATTCAACACCACCACCACGTCCACCTCCAAGGAAT
Found at i:35739 original size:30 final size:29
Alignment explanation
Indices: 35700--35799 Score: 102
Period size: 30 Copynumber: 3.6 Consensus size: 29
35690 CCAAGGAACC
*
35700 CACCGCCACCACCTCCTATAACAGAATTAA
1 CACCACCACCACCTCCTA-AACAGAATTAA
* **
35730 CACCACCACCACCTCC--AA-GGAA--CC
1 CACCACCACCACCTCCTAAACAGAATTAA
*
35754 CACCGCCACCACCTCCTACAACAGAATTAA
1 CACCACCACCACCTCCTA-AACAGAATTAA
35784 CACCACCACCACCTCC
1 CACCACCACCACCTCC
35800 AAGGAACCCA
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
24 15 0.27
26 3 0.05
27 4 0.07
28 3 0.05
30 30 0.55
ACGTcount: A:0.34, C:0.49, G:0.06, T:0.11
Consensus pattern (29 bp):
CACCACCACCACCTCCTAAACAGAATTAA
Found at i:36137 original size:87 final size:87
Alignment explanation
Indices: 36013--36171 Score: 246
Period size: 87 Copynumber: 1.8 Consensus size: 87
36003 AACAGAACTA
* * *
36013 ACACCACCACCACCTCCAAGGAACCCACCACCGCCACCACCTCAAACAGATTCAACATCACCACC
1 ACACCACCACCACCTCCAAGGAACCCACCACCACCACCACCTCAAACAGACTCAACACCACCACC
36078 ACCTCCACCATCAAATAACTCT
66 ACCTCCACCATCAAATAACTCT
** * * *
36100 ACACCACGTCCACCTCCAAGGAACCCACCGCCACCACCATCTCCAACAGACTCAACACCACCACC
1 ACACCACCACCACCTCCAAGGAACCCACCACCACCACCACCTCAAACAGACTCAACACCACCACC
36165 ACCTCCA
66 ACCTCCA
36172 AGGAACCCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.34, C:0.50, G:0.06, T:0.10
Consensus pattern (87 bp):
ACACCACCACCACCTCCAAGGAACCCACCACCACCACCACCTCAAACAGACTCAACACCACCACC
ACCTCCACCATCAAATAACTCT
Found at i:36254 original size:129 final size:130
Alignment explanation
Indices: 36046--36299 Score: 361
Period size: 129 Copynumber: 1.9 Consensus size: 130
36036 CCCACCACCG
* * * *
36046 CCACCACCTCAAACAGATTCAACATCACCACCACCTCCACCATCAAATAACTCTACACCACGTCC
1 CCACCACCTCAAACAGATTCAACACCACCACCACCTCCACAACCAAATAACTCTACACCACCTCC
*
36111 ACCTCCAAGGAACCCACCGCCACCACCATCTCCAACAGACTCAACACCACCACCACCTCCAAGGA
66 A-C-CCAAGGAACCCACCGCCACCACCACCTCCAACAGACTCAACACCACCACCACCTCCAAGGA
36176 AC
129 AC
* * * *
36178 CCACCACCTCCAACAGATTCAACACCACCACCACCTCCTCAAACCGAATTAAC-C-CCACCACCT
1 CCACCACCTCAAACAGATTCAACACCACCACCACCTCCAC-AACC-AAATAACTCTACACCACCT
*
36241 CCA-CCAAGGAACCCACCGCCACCACCACCTCCAACAGACTTAACACCACCACCACCTCC
64 CCACCCAAGGAACCCACCGCCACCACCACCTCCAACAGACTCAACACCACCACCACCTCC
36300 GCCTTCAAAT
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
129 54 0.49
132 47 0.43
133 3 0.03
134 6 0.05
ACGTcount: A:0.34, C:0.50, G:0.06, T:0.11
Consensus pattern (130 bp):
CCACCACCTCAAACAGATTCAACACCACCACCACCTCCACAACCAAATAACTCTACACCACCTCC
ACCCAAGGAACCCACCGCCACCACCACCTCCAACAGACTCAACACCACCACCACCTCCAAGGAAC
Found at i:36293 original size:30 final size:29
Alignment explanation
Indices: 36178--36389 Score: 93
Period size: 30 Copynumber: 7.4 Consensus size: 29
36168 TCCAAGGAAC
36178 CCACCACCTCCAACAGATTCAACACCACCA
1 CCACCACCTCCAACAGATT-AACACCACCA
* * *
36208 CCACCTCCTCAAACCGAATT-A-ACC-CCA
1 CCACCACCTCCAACAG-ATTAACACCACCA
* * * * *
36235 CCACCTCCACCAA-GGA--ACCCACCGCCA
1 CCACCACCTCCAACAGATTA-ACACCACCA
36262 CCACCACCTCCAACAGACTTAACACCACCA
1 CCACCACCTCCAACAGA-TTAACACCACCA
* * ** * * *
36292 CCACCTCCGCCTTCA-AATAACTCAACTCCA
1 CCACCACCTCCAACAGATTAA--CACCACCA
** * *
36322 CGTCCACCTCCAA-GGA--ACCCACCACCA
1 CCACCACCTCCAACAGATTA-ACACCACCA
*
36349 CCACCATCTCCAACAGATTTAACACCACCA
1 CCACCACCTCCAACAGA-TTAACACCACCA
*
36379 CCACCTCCTCC
1 CCACCACCTCC
36390 TTCAAATAAC
Statistics
Matches: 129, Mismatches: 36, Indels: 34
0.65 0.18 0.17
Matches are distributed among these distances:
25 1 0.01
26 4 0.03
27 44 0.34
28 11 0.09
29 2 0.02
30 62 0.48
31 5 0.04
ACGTcount: A:0.32, C:0.50, G:0.05, T:0.12
Consensus pattern (29 bp):
CCACCACCTCCAACAGATTAACACCACCA
Found at i:36350 original size:87 final size:86
Alignment explanation
Indices: 36178--36506 Score: 382
Period size: 87 Copynumber: 3.8 Consensus size: 86
36168 TCCAAGGAAC
* * * **
36178 CCACCACCTCCAACAGATTCAACACCACCACCACCT---CC-TCAAACCGAA-TTAACCCCACCA
1 CCACCACCTCCAACAGATT-AACACCACCACCACCTCCGCCTTCAAA--TAACTCAACACCACGT
* *
36238 CCTCCACCAAGGAACCCACCGCCA
63 CCACCTCCAAGGAACCCACCGCCA
*
36262 CCACCACCTCCAACAGACTTAACACCACCACCACCTCCGCCTTCAAATAACTCAACTCCACGTCC
1 CCACCACCTCCAACAGA-TTAACACCACCACCACCTCCGCCTTCAAATAACTCAACACCACGTCC
*
36327 ACCTCCAAGGAACCCACCACCA
65 ACCTCCAAGGAACCCACCGCCA
* * *
36349 CCACCATCTCCAACAGATTTAACACCACCACCACCTCCTCCTTCAAATAACTCGACACCACGTCC
1 CCACCACCTCCAACAGA-TTAACACCACCACCACCTCCGCCTTCAAATAACTCAACACCACGTCC
* * *
36414 ACCTCCAAGGAATCCACCGTCG
65 ACCTCCAAGGAACCCACCGCCA
* * *
36436 CCACCACCTCCAACAGAATCT-ACACCACCACCACCTACGCCTTCAAATAATTCCGACACCACGT
1 CCACCACCTCCAACAG-AT-TAACACCACCACCACCTCCGCCTTCAAATAACT-CAACACCACGT
36500 CCACCTC
63 CCACCTC
Statistics
Matches: 215, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
84 33 0.15
85 2 0.01
86 2 0.01
87 153 0.71
88 25 0.12
ACGTcount: A:0.32, C:0.48, G:0.06, T:0.14
Consensus pattern (86 bp):
CCACCACCTCCAACAGATTAACACCACCACCACCTCCGCCTTCAAATAACTCAACACCACGTCCA
CCTCCAAGGAACCCACCGCCA
Done.