Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold275
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: 1025155
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 7
Found at i:593959 original size:33 final size:32
Alignment explanation
Indices: 593922--593997 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
593912 GCTCTCTTCC
* *
593922 TTTTTTTGTGTGTATTTTTTGTTTTTGTTTTTG
1 TTTTTTTGTGTGT-GTTGTTGTTTTTGTTTTTG
*
593955 -TTTTTTGTGT-TGTTGTTGTTTTTGTTTTTT
1 TTTTTTTGTGTGTGTTGTTGTTTTTGTTTTTG
*
593985 TTTTTTTTTGTGT
1 TTTTTTTGTGTGT
593998 TTGCACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 16 0.43
31 10 0.27
32 11 0.30
ACGTcount: A:0.01, C:0.00, G:0.18, T:0.80
Consensus pattern (32 bp):
TTTTTTTGTGTGTGTTGTTGTTTTTGTTTTTG
Found at i:593967 original size:24 final size:22
Alignment explanation
Indices: 593936--594000 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 22
593926 TTTGTGTGTA
593936 TTTTTTGTTTTTGTTTTTGTTT
1 TTTTTTGTTTTTGTTTTTGTTT
*
593958 TTTGTGTTGTTGTTGTTTTTGTTT
1 TTT-T-TTGTTTTTGTTTTTGTTT
* *
593982 TTTTTTTTTTTTGTGTTTG
1 TTTTTTGTTTTTGTTTTTG
594001 CACTTTTGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.41
23 2 0.05
24 20 0.54
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (22 bp):
TTTTTTGTTTTTGTTTTTGTTT
Found at i:593991 original size:15 final size:15
Alignment explanation
Indices: 593922--593992 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 15
593912 GCTCTCTTCC
* * *
593922 TTTTTTTGTGTGTAT
1 TTTTTTTTTTTGTTT
*
593937 TTTTTGTTTTTGTTT
1 TTTTTTTTTTTGTTT
* * *
593952 TTGTTTTTTGTGTTG
1 TTTTTTTTTTTGTTT
* *
593967 TTGTTGTTTTTGTTT
1 TTTTTTTTTTTGTTT
593982 TTTTTTTTTTT
1 TTTTTTTTTTT
593993 TGTGTTTGCA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.01, C:0.00, G:0.17, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTGTTT
Found at i:600963 original size:13 final size:13
Alignment explanation
Indices: 600945--600970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
600935 ACAAAGATCC
600945 ATGTATCGATACA
1 ATGTATCGATACA
600958 ATGTATCGATACA
1 ATGTATCGATACA
600971 TTTCATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:600982 original size:20 final size:20
Alignment explanation
Indices: 600957--600994 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
600947 GTATCGATAC
600957 AATGTATCGATACATTTCAT
1 AATGTATCGATACATTTCAT
600977 AATGTATCGATACATTTC
1 AATGTATCGATACATTTC
600995 CTTGGCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTCAT
Found at i:601032 original size:13 final size:13
Alignment explanation
Indices: 601014--601065 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
601004 AGCTTCGTAG
601014 CGATACATTGTAT
1 CGATACATTGTAT
601027 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
601046 CGATACATTGTAT
1 CGATACATTGTAT
601059 CGATACA
1 CGATACA
601066 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:601046 original size:19 final size:19
Alignment explanation
Indices: 601022--601082 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
601012 AGCGATACAT
601022 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
601041 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
601054 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
601073 TGTATCGATA
1 TGTATCGATA
601083 TAGTGTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.25
14 1 0.03
16 6 0.17
18 1 0.03
19 19 0.53
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:601055 original size:32 final size:32
Alignment explanation
Indices: 601014--601098 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
601004 AGCTTCGTAG
601014 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
601046 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* * *
601078 CGATATAGTGTATCAATACAA
1 CGATACATTGTATCGATACAA
601099 ATTGTTGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:602443 original size:55 final size:55
Alignment explanation
Indices: 602289--602880 Score: 618
Period size: 55 Copynumber: 10.5 Consensus size: 55
602279 TCAGCCCTTT
* * *
602289 AGTCCTCAAAGAGCATGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTT--
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* **
602341 AGTCCTCAAAAAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGAAATTTTCC
1 AGTCCTCAAAGAGCAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
602402 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACATAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * * * **
602457 AGTCCTTAAAGAACATGATGCCTTTCAAAGCCCACACAAGTTGGTGGGATTTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * *
602513 TGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
** * * * *
602568 AGTCCTCAAAGAATAGGACACCTTTCAAAGCCCACACGAGTTGGTGGTATTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
602623 AGTCCTCAAAGAGCAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCC-TTTC-----AAAGCCCACACAAGTTGGTGGCATTTTCC
* *
602684 AGTCTTCAAAGAGTAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * *
602739 AGTCTTCAAAGAGCAGGACACCTTTCATAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* * ** *
602794 AGTCCTCAAAAAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCT
1 AGTCCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTCC
*
602855 AGTCCTCAAAGAGCAGGACACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTC
602881 CTTTTCAAAG
Statistics
Matches: 452, Mismatches: 63, Indels: 47
0.80 0.11 0.08
Matches are distributed among these distances:
52 18 0.04
54 2 0.00
55 234 0.52
56 53 0.12
57 2 0.00
58 26 0.06
59 4 0.01
60 5 0.01
61 108 0.24
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:602681 original size:27 final size:27
Alignment explanation
Indices: 602651--602736 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
602641 CACCTTTTCT
602651 TTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
** * ** * * ** *
602678 TTTTCCAGTCTTCAAAGAGTAGGACGCC
1 TTTTAAAGCCCACACA-AGTTGGTGGCA
*
602706 TCTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTAAAGCCCACACAAGTTGGTGGCA
602733 TTTT
1 TTTT
602737 CCAGTCTTCA
Statistics
Matches: 36, Mismatches: 22, Indels: 2
0.60 0.37 0.03
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (27 bp):
TTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:602693 original size:116 final size:113
Alignment explanation
Indices: 602288--602933 Score: 596
Period size: 116 Copynumber: 5.7 Consensus size: 113
602278 TTCAGCCCTT
* * *
602288 TAGTCCTCAAAGAGCATGACGCC--T-TTTAAAGCCCACACAAGTTGGTGGCA-CTT--AGTCCT
1 TAGTCCTCAAAGAGCAGGACACCTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
**
602347 CAAA-AAGCAGGACGCCTTTTCCTTTCAAAGCCCACACAAGTTGGTGAAATTTTC
66 CAAAGAA-CAGGACG------CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * * *
602401 CAGTCCTCAAAGAGCAGGACGCCTTTC---AAAGCCCACATAAGTTGGTGGCACCTTT-CAGTCC
1 TAGTCCTCAAAGAGCAGGACACCTTTCTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCC
* * * * *
602462 TTAAAGAACATGATGCCTTTCAAAGCCCACACAAGTTGGTGGGATTTTTT
65 TCAAAGAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
* * * *
602512 TTGTCCTCAAAGAGCAGGACGCC--T-TTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCT
1 TAGTCCTCAAAGAGCAGGACACCTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
* * * *
602574 CAAAGAATAGGACACCTTTCAAAGCCCACACGAGTTGGTGGTATTTTC
66 CAAAGAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
*
602622 TAGTCCTCAAAGAGCAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 TAGTCCTCAAAGAGCAGGACACC-TTTC--TTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
* **
602687 CTTCAAAGAGTAGGACGCCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTC
63 CCTCAAAGAACAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
* * *
602738 CAGTCTTCAAAGAGCAGGACACCTTTC---ATAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
1 TAGTCCTCAAAGAGCAGGACACCTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
* **
602800 CAAA-AAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
66 CAAAGAA-CAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCATTTTC
* *
602854 TAGTCCTCAAAGAGCAGGACACCTTTCCTTTTCAAAGCCCACA-AGAGTCGGTGGCACTTTT-TA
1 TAGTCCTCAAAGAGCAGGACACCTTT-C-TTT-AAAGCCCACACA-AGTTGGTGGCA-TTTTCCA
* *
602917 GCCCTCAAAGAGCAGGA
61 GTCCTCAAAGAACAGGA
602934 TGCACTTTAT
Statistics
Matches: 448, Mismatches: 49, Indels: 63
0.80 0.09 0.11
Matches are distributed among these distances:
109 2 0.00
110 95 0.21
111 90 0.20
112 1 0.00
113 44 0.10
114 3 0.01
115 9 0.02
116 160 0.36
117 5 0.01
121 1 0.00
122 33 0.07
123 5 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (113 bp):
TAGTCCTCAAAGAGCAGGACACCTTTCTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
CAAAGAACAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
Found at i:602729 original size:171 final size:169
Alignment explanation
Indices: 602311--602873 Score: 640
Period size: 171 Copynumber: 3.3 Consensus size: 169
602301 GCATGACGCC
*
602311 TTTTAAAGCCCACACAAGTTGGTGGCA-C-T-TAGTCCTCAAAAAGCAGGACGCCTTTTCCTTTC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCAGGACGCC---T-C-TT-
** *
602373 AAAGCCCACACAAGTTGGTGAAATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACA
60 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACA
* * * * * *
602438 TAAGTTGGTGGCACCTTTCAGTCCTTAAAGAACATGATGCC-TTTC-
125 CAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAAGA-ACCTTTTCT
* * * * *
602483 ----AAAGCCCACACAAGTTGGTGGGATTTTTTTTGTCCTCAAAGAGCAGGACGCCTTTTAAAGC
1 TTTTAAAGCCCACACAAGTTGGTGGCA-TCTTCTAGTCCTCAAAGAGCAGGACGCCTCTTAAAGC
* * ** *
602544 CCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAATAGGACACCTTTCAAAGCCCACACGAGT
65 CCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGT
*
602609 TGGTGGTATTTTCTAGTCCTCAAAGAGCAAGACACCTTTTCT
130 TGGTGGCATTTTC-AGTCCTCAAAGAGCAAGA-ACCTTTTCT
* * * *
602651 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGTAGGACGCCTCTTAAAGCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCAGGACGCCTCTTAAAGCC
* *
602716 CACACAAGTTGGTGGCATTTTCCAGTCTTCAAAGAGCAGGACACCTTTCATAGCCCACACAAGTT
66 CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTT
* * **
602781 GGTGGCATTTTCCAGTCCTCAAAAAGCAGGATGCTTTCTCT
131 GGTGGCATTTT-CAGTCCTCAAAGAGCAAGAACCTTT-TCT
** *
602822 TTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGAC
1 TTTTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCAGGAC
602874 ACCTTTCCTT
Statistics
Matches: 331, Mismatches: 47, Indels: 27
0.82 0.12 0.07
Matches are distributed among these distances:
165 4 0.01
166 85 0.26
167 6 0.02
168 22 0.07
169 1 0.00
170 4 0.01
171 165 0.50
172 44 0.13
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (169 bp):
TTTTAAAGCCCACACAAGTTGGTGGCATCTTCTAGTCCTCAAAGAGCAGGACGCCTCTTAAAGCC
CACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTT
GGTGGCATTTTCAGTCCTCAAAGAGCAAGAACCTTTTCT
Found at i:602947 original size:61 final size:61
Alignment explanation
Indices: 602310--602947 Score: 419
Period size: 55 Copynumber: 11.1 Consensus size: 61
602300 AGCATGACGC
* *
602310 CTTTT-AAAGCCCACACAAGTTGGTGGCAC---TTAGTCCTCAAAAAGCAGGACGC-CTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCAC-TTT
* * * * *
602367 CCTTTCAAAGCCCACACAAGTTGGT-GAAATTTTCCAGTCCTCAAAGAGCAGGA--CGC---
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCACTTT
* * * * * *
602423 C-TTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCTTAAAGAACATGATG--C---
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCACTTT
* * * *
602478 C-TTTCAAAGCCCACACAAGTTGGTGGGATTTTTTTTGTCCTCAAAGAGCAGGA--CGC---
1 CTTTTCAAAGCCCACACAAGTTGGTGGCA-CTTTTTAGTCCTCAAAGAGCAGGATGCACTTT
*** **
602534 CTTTT-AAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAATAGGA--CAC---
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCACTTT
* * *
602589 C-TTTCAAAGCCCACACGAGTTGGTGGTA-TTTTCTAGTCCTCAAAGAGCAAGA--CACCTTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCA-C-TTT
* * * * *
602649 CTTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCTTCAAAGAGTAGGACGC-C--T
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCACTTT
* *
602707 C--TT-AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCTTCAAAGAGCAGGA--CAC---
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCACTTT
* * *
602760 C-TTTCATAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAAAGCAGGATG--CTTT
1 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGATGCACTTT
* *
602818 CTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGA--CACCTTT
1 CT-TTT-CAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCA-CTTT
* *
602880 CCTTTTCAAAGCCCACA-AGAGTCGGTGGCACTTTTTAGCCCTCAAAGAGCAGGATGCACTTT
1 -CTTTTCAAAGCCCACACA-AGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCACTTT
*
602942 ATTTTC
1 CTTTTC
602948 CTCTTTCTTT
Statistics
Matches: 480, Mismatches: 59, Indels: 80
0.78 0.10 0.13
Matches are distributed among these distances:
53 2 0.00
54 8 0.02
55 214 0.45
56 50 0.10
57 9 0.02
58 22 0.05
59 1 0.00
60 7 0.01
61 149 0.31
62 13 0.03
63 5 0.01
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.26
Consensus pattern (61 bp):
CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGATGCACTTT
Found at i:603852 original size:13 final size:13
Alignment explanation
Indices: 603834--603859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
603824 CATTATTCAA
603834 TGTATCGATACAT
1 TGTATCGATACAT
603847 TGTATCGATACAT
1 TGTATCGATACAT
603860 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:603923 original size:20 final size:20
Alignment explanation
Indices: 603898--604024 Score: 119
Period size: 20 Copynumber: 6.7 Consensus size: 20
603888 TTTACCCAGA
*
603898 TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTGCT-CAT
*
603918 TGTATCGATAAATTGCTCAT
1 TGTATCGATACATTGCTCAT
603938 TGTATCGAT--A-----CAT
1 TGTATCGATACATTGCTCAT
603951 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
603971 TGTATCGATACATTGCTCAT
1 TGTATCGATACATTGCTCAT
* * * *
603991 TATATCAATACATT-TTACAA
1 TGTATCGATACATTGCT-CAT
604011 TGTATCGATACATT
1 TGTATCGATACATT
604025 CAGGCATTTT
Statistics
Matches: 90, Mismatches: 8, Indels: 18
0.78 0.07 0.16
Matches are distributed among these distances:
13 12 0.13
15 1 0.01
18 1 0.01
19 1 0.01
20 74 0.82
21 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTGCTCAT
Found at i:603957 original size:33 final size:33
Alignment explanation
Indices: 603915--603985 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
603905 ATACATTTTG
603915 CATTGTATCGATAAATTGCTCATTGTATCGATA
1 CATTGTATCGATAAATTGCTCATTGTATCGATA
*
603948 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATAAATTGCTCATTGTATCGATA
603981 CATTG
1 CATTG
603986 CTCATTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (33 bp):
CATTGTATCGATAAATTGCTCATTGTATCGATA
Found at i:603964 original size:53 final size:53
Alignment explanation
Indices: 603898--604004 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 53
603888 TTTACCCAGA
* * *
603898 TGTATCGATACATT-TTGCATTGTATCGATAAATTGCTCATTGTATCGATACAT
1 TGTATCGATACATTGCT-CATTGTATCGATAAATTGCTCATTATATCAATACAT
*
603951 TGTATCGATACATTGCTCATTGTATCGATACATTGCTCATTATATCAATACAT
1 TGTATCGATACATTGCTCATTGTATCGATAAATTGCTCATTATATCAATACAT
604004 T
1 T
604005 TTACAATGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 48 0.98
54 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (53 bp):
TGTATCGATACATTGCTCATTGTATCGATAAATTGCTCATTATATCAATACAT
Found at i:603984 original size:13 final size:13
Alignment explanation
Indices: 603935--603965 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
603925 ATAAATTGCT
603935 CATTGTATCGATA
1 CATTGTATCGATA
603948 CATTGTATCGATA
1 CATTGTATCGATA
603961 CATTG
1 CATTG
603966 CTCATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:606403 original size:52 final size:51
Alignment explanation
Indices: 606342--606456 Score: 144
Period size: 52 Copynumber: 2.2 Consensus size: 51
606332 TTCATCTCGA
* *
606342 GGATACTCCAA-TCCCGATTTTATTTCTAAAACACCCA-TTTTCCATAATCAGG
1 GGATACTCCAACT-CCGATTTTATTTCCAAAACACCCACTTTT-CACAATC-GG
* * *
606394 GGATACTCCAACTCTGATTTTATTTCCAAAACATCGACTTTTCACAATCGG
1 GGATACTCCAACTCCGATTTTATTTCCAAAACACCCACTTTTCACAATCGG
606445 GGATACTCCAAC
1 GGATACTCCAAC
606457 CTCGTTATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
51 14 0.25
52 37 0.66
53 5 0.09
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
GGATACTCCAACTCCGATTTTATTTCCAAAACACCCACTTTTCACAATCGG
Found at i:606648 original size:76 final size:79
Alignment explanation
Indices: 606391--606691 Score: 378
Period size: 79 Copynumber: 3.8 Consensus size: 79
606381 TTCCATAATC
* * * *
606391 AGGGGATACTCCAACT-CTGATTTTATTTCCAAAACATCGACTTTTCACAATCGGGGATACTCCA
1 AGGGGACACTCCAACTCCAG-TTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCA
* *
606455 ACCTCGTTATTTCCG
65 ACCCCGTTATTTTCG
* * *
606470 AGGGGACACTCCAACTCCAATTTTATTTCTAAAAGATCGACTTTTCACAATCGGGGATACTCCAA
1 AGGGGACACTCCAACTCCAGTTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAA
*
606535 CCCCATTATTTTCG
66 CCCCGTTATTTTCG
* * * *
606549 GGGGGACACTCCAACCCCGGTTTTATTTCTAAAACATC-AATTTT-TC-ATCGGGGATACTCCAA
1 AGGGGACACTCCAACTCCAGTTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAA
*
606611 CCCCGTTATTTTTG
66 CCCCGTTATTTTCG
* * * *
606625 AGGGGATACTCTAACTCCAGTTTTATTTCTAAAACA-CTAATTCTCCACAATCGGGGATACTCCA
1 AGGGGACACTCCAACTCCAGTTTTATTTCTAAAACATCGAATT-TTCACAATCGGGGATACTCCA
606689 ACC
65 ACC
606692 TCGACTTTAT
Statistics
Matches: 193, Mismatches: 24, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
75 1 0.01
76 63 0.33
77 2 0.01
78 6 0.03
79 120 0.62
80 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
AGGGGACACTCCAACTCCAGTTTTATTTCTAAAACATCGAATTTTCACAATCGGGGATACTCCAA
CCCCGTTATTTTCG
Found at i:606677 original size:155 final size:158
Alignment explanation
Indices: 606392--606691 Score: 410
Period size: 155 Copynumber: 1.9 Consensus size: 158
606382 TCCATAATCA
* * * *
606392 GGGGATACTCCAACTCTGATTTTATTTCCAAAACATCGACTTTTCACAATCGGGGATACTCCAAC
1 GGGGACACTCCAACCCCGATTTTATTTCCAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
* * * *
606457 CTCGTTATTTCCGAGGGGACACTCCAACTCCAATTTTATTTCTAAAAGATCGACTTTTCACAATC
66 CCCGTTATTTCCGAGGGGACACTCCAACTCCAATTTTATTTCTAAAACATCGAATTTCCACAATC
606522 GGGGATACTCCAACCCCATTATTTTCGG
131 GGGGATACTCCAACCCCATTATTTTCGG
* * *
606550 GGGGACACTCCAACCCCGGTTTTATTTCTAAAACATC-AATTTT-TC-ATCGGGGATACTCCAAC
1 GGGGACACTCCAACCCCGATTTTATTTCCAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
** * * * *
606612 CCCGTTATTTTTGAGGGGATACTCTAACTCCAGTTTTATTTCTAAAACA-CTAATTCTCCACAAT
66 CCCGTTATTTCCGAGGGGACACTCCAACTCCAATTTTATTTCTAAAACATCGAATT-TCCACAAT
606676 CGGGGATACTCCAACC
130 CGGGGATACTCCAACC
606692 TCGACTTTAT
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
154 4 0.03
155 82 0.66
156 1 0.01
157 5 0.04
158 32 0.26
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (158 bp):
GGGGACACTCCAACCCCGATTTTATTTCCAAAACATCGAATTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTCCGAGGGGACACTCCAACTCCAATTTTATTTCTAAAACATCGAATTTCCACAATC
GGGGATACTCCAACCCCATTATTTTCGG
Found at i:606702 original size:51 final size:51
Alignment explanation
Indices: 606646--606795 Score: 176
Period size: 51 Copynumber: 2.9 Consensus size: 51
606636 TAACTCCAGT
* * * *
606646 TTTATTTCTAAAACACT-AATTCTCCACAATCGGGGATACTCCAACCTCGAC
1 TTTATTTCTAAAATATTGATTTCT-CACAATCGGGGATACTCCAACCCCGAC
* * * * *
606697 TTTATTTCCAAAATATTGATTTCTTACAATCAGGGATACTTCAACCCCGGC
1 TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCCGAC
* * *
606748 CTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCC
1 TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCC
606796 ATTCTTTTCA
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
51 77 0.94
52 5 0.06
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
TTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAACCCCGAC
Found at i:606885 original size:181 final size:181
Alignment explanation
Indices: 606551--606926 Score: 392
Period size: 181 Copynumber: 2.1 Consensus size: 181
606541 TATTTTCGGG
* ** * ** * *
606551 GGGACACTCCAACCCCGGTTTTATTTCTAAAACATCAATTT-T--TCATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
* * * *
606613 CCGTTATTTTTGAGGGGATACTCTAACTCCAGTTTTATTTCTAAAACACTAATTCTCCACAATCG
66 CCATTACTTTTCAGGGGATACTCCAACTCCAGTTTTATTTCTAAAACACTAATTCTCCACAATCG
* * *
606678 GGGATACTCCAACCTCGACTTTATTTCCAAAAT-ATTGATTTCTT-ACAATCA
131 GGGACACTCCAACCTCGACCTTATTT-CAAAATCATCG-TTTCTTCACAATCA
*
606729 GGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
1 GGGATACTCCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
* * * * * *
606794 CCATT-CTTTTCACGGGGATACTCCAA-TCCCGATTTTATTTTTGAAACATCT-ATTTTCTATAA
66 CCATTACTTTTCA-GGGGATACTCCAACTCCAG-TTTTATTTCTAAAACA-CTAATTCTCCACAA
* * * * *
606856 TCGGGGACACTTCAACCCTTG-CCTTATTTCTAAATCATCGTTTTTTCACAATCG
128 TCGGGGACACTCCAA-CCTCGACCTTATTTCAAAATCATCGTTTCTTCACAATCA
606910 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
606927 TTATTTTCGA
Statistics
Matches: 161, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
178 34 0.21
179 1 0.01
180 19 0.12
181 101 0.63
182 6 0.04
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (181 bp):
GGGATACTCCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACC
CCATTACTTTTCAGGGGATACTCCAACTCCAGTTTTATTTCTAAAACACTAATTCTCCACAATCG
GGGACACTCCAACCTCGACCTTATTTCAAAATCATCGTTTCTTCACAATCA
Found at i:606981 original size:130 final size:129
Alignment explanation
Indices: 606676--606981 Score: 330
Period size: 130 Copynumber: 2.3 Consensus size: 129
606666 TCTCCACAAT
* * * * *
606676 CGGGGATACTCCAACCTCGACTTTATTTCCAAAATATTGATTTCTTACAATCAGGGATACTTCAA
1 CGGGGATACTCCAACCCCGTCTTTATTTCTAAAATATTAATTTC-TACAATCAGGGACACTTCAA
* * * *
606741 CCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCATTCTTTTCA
65 CCCCGGCCTTATTTCTAAAATATCGATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTCA
* * * * * * *
606806 CGGGGATACTCCAATCCCGAT-TTTATTTTTGAAACATCTATTTTCTATAATCGGGGACACTTCA
1 CGGGGATACTCCAACCCCG-TCTTTATTTCTAAAATAT-TAATTTCTACAATCAGGGACACTTCA
** * * *
606870 ACCCTTGCCTTATTTCT-AAATCATCGTTTTTTCACAATCGGGGATACTCCAACCCCGTTATTTT
64 ACCCCGGCCTTATTTCTAAAAT-ATCGATTTCTCACAATCGGGGATACTCCAACCCCATTATTTT
606934 CGA
128 C-A
* *
606937 -GGGGATACTCCAACCCCGTCATTATCTCTAAAATATTAAATTTCT
1 CGGGGATACTCCAACCCCGTCTTTATTTCTAAAATATT-AATTTCT
606982 CGTCAGGAGA
Statistics
Matches: 142, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
129 6 0.04
130 130 0.92
131 6 0.04
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (129 bp):
CGGGGATACTCCAACCCCGTCTTTATTTCTAAAATATTAATTTCTACAATCAGGGACACTTCAAC
CCCGGCCTTATTTCTAAAATATCGATTTCTCACAATCGGGGATACTCCAACCCCATTATTTTCA
Found at i:609345 original size:27 final size:27
Alignment explanation
Indices: 609326--610172 Score: 785
Period size: 27 Copynumber: 31.2 Consensus size: 27
609316 CCATGATTCT
* *
609326 GTGGCACTCTTTTAAGTCCACAACTCT
1 GTGGCACCCTTTTAAGTCCACAACTCC
** *
609353 GTGGCACCCTTTTAAGTCTGCAAGTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* *
609380 GTGGCATCCTTTTAAGTCCACAAGTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* *
609407 GTGACACCCTTTTAAGTCCACAAGTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* * *
609434 GTGGCATCGTTTTAAGTCCACAACTCT
1 GTGGCACCCTTTTAAGTCCACAACTCC
*
609461 GTGGCACCCTTTTAAAGTCCACAACTTC
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* * *
609489 GTGGCACACTTTTAAGTCCATAACTCT
1 GTGGCACCCTTTTAAGTCCACAACTCC
* * *
609516 GTGGCATCCTTTTAAGTCTACAAGTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
609543 GTGGCACCCTTTTAAGTCCACAACTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* * *
609570 GTGACACCTTTTTAAAGTCCACAACTCT
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* *
609598 GTAGCACCTTTTTAAAGTCCAC-A----
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* * *
609621 ----CACCCTTTTAAGTCTACAAGTCT
1 GTGGCACCCTTTTAAGTCCACAACTCC
* * *
609644 GTGGCATCCTTTTAAGTTCACAAGTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* *
609671 GTGGCATCCTTTTAAGTCCACAACTCT
1 GTGGCACCCTTTTAAGTCCACAACTCC
*
609698 GTGGCACCCTTTTAAAGTCCACAACTTC
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* *
609726 GTGGCACCCTTTTAAGTCCATAAGTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
609753 GTGGCACCCTTTTAAGTCCACAACTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* *
609780 GTGGCACCCTTTTAAAGTCCATAACTCT
1 GTGGCACCCTTTT-AAGTCCACAACTCC
609808 GTGGCACCCTTTTAAAGTCCACAACTCC
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* *
609836 GTGGCACTCTTTTAAGTCCACAATTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
*
609863 GTGGCACCCTTTTAAGTCCACAACTTC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* *
609890 GTGGTATCCTTTTAAAGTCCACAACTCC
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* * *
609918 GTGGCATCCTTTTAAAGTCTATAACTCC
1 GTGGCACCCTTTT-AAGTCCACAACTCC
* * *
609946 GTGGCATCCTTTTAAGTCCATAACTTC
1 GTGGCACCCTTTTAAGTCCACAACTCC
* * *
609973 GTGGCATCCTTTCATGTCCACAACTCC
1 GTGGCACCCTTTTAAGTCCACAACTCC
** * * **
610000 GTGGCATTCTTTTAAGCCCACAAGTTA
1 GTGGCACCCTTTTAAGTCCACAACTCC
** * * *
610027 GTGGCACCCTTCCAAAGCCCACAAGTCA
1 GTGGCACCCTT-TTAAGTCCACAACTCC
* * * *
610055 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTT-TAAGTCCACAACTCC
* * * * * **
610083 GTGGCATCATTTCAAAGCCCACAAGTTA
1 GTGGCACCCTTT-TAAGTCCACAACTCC
* * * *
610111 GTGGCACCCTTTCAAAGCCCACAAGTCA
1 GTGGCACCCTTT-TAAGTCCACAACTCC
* * * *
610139 GTGGCATCCTTTCAAAGTCCACAAGTCA
1 GTGGCACCCTTT-TAAGTCCACAACTCC
610167 GTGGCA
1 GTGGCA
610173 TCTTTTCAAA
Statistics
Matches: 708, Mismatches: 96, Indels: 31
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.01
19 9 0.01
27 388 0.55
28 304 0.43
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (27 bp):
GTGGCACCCTTTTAAGTCCACAACTCC
Found at i:609486 original size:28 final size:28
Alignment explanation
Indices: 609304--610396 Score: 599
Period size: 28 Copynumber: 39.6 Consensus size: 28
609294 AGTAGTGTAA
** *
609304 CCTTTTCAAAGTCCATGATTCTGTGGCAC
1 CCTTTT-AAAGTCCACAACTCTGTGGCAC
*
609333 TCTTTT-AAGTCCACAACTCTGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
** * * *
609360 CCTTTT-AAGTCTGCAAGTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
609387 CCTTTT-AAGTCCACAAGTCCGTGACAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
609414 CCTTTT-AAGTCCACAAGTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
*
609441 CGTTTT-AAGTCCACAACTCTGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
609468 CCTTTTAAAGTCCACAACT-TCGTGGCAC
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
* * *
609496 ACTTTT-AAGTCCATAACTCTGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
609523 CCTTTT-AAGTCTACAAGTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* *
609550 CCTTTT-AAGTCCACAACTCCGTGACAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* *
609577 CTTTTTAAAGTCCACAACTCTGTAGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
*
609605 CTTTTTAAAGTCCAC-A--------CAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
** * * * ***
609624 CCTTTTAAGTCTACA-AGTCTGTG-GCATC
1 CCTTTTAA-AGTCCACA-ACTCTGTGGCAC
* * ***** *** * *
609652 CTTTTAAGTTCACAAGTCC--GTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
609678 CCTTTT-AAGTCCACAACTCTGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
609705 CCTTTTAAAGTCCACAACT-TCGTGGCAC
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
* * *
609733 CCTTTT-AAGTCCATAAGTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
*
609760 CCTTTT-AAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
*
609787 CCTTTTAAAGTCCATAACTCTGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
*
609815 CCTTTTAAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
609843 TCTTTT-AAGTCCACAATTCCGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* *
609870 CCTTTT-AAGTCCACAACT-TCGTGGTAT
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
* *
609897 CCTTTTAAAGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * * *
609925 CCTTTTAAAGTCTATAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* *
609953 CCTTTT-AAGTCCATAACT-TCGTGGCAT
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
* * * *
609980 CC-TTTCATGTCCACAACTCCGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
610007 TCTTTT-AAGCCCACAAGT-TAGTGGCAC
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
** * * *
610034 CCTTCCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * * * *
610062 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * * *
610090 CATTTCAAAGCCCACAAGT-TAGTGGCAC
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
* * * * *
610118 CCTTTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
610146 CCTTTCAAAGTCCACAAGTCAGTGGCA-
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
610173 TCTTTTCAAAAG-CTCACAAGTTTGTGGCATC
1 CCTTTT--AAAGTC-CACAACTCTGTGGCA-C
* * * * * *
610204 TTCTTTTTCAAAGCCCATAAGTCAGTGACAC
1 --CCTTTT-AAAGTCCACAACTCTGTGGCAC
* * *
610235 CCTTTCAAAGTCCACAAGTCAGTGGCATC
1 CCTTTTAAAGTCCACAACTCTGTGGCA-C
*
610264 CCTTTT-AAGTCCACAACTCTGTGGCTC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * * * * *
610291 TCTTTCAAAGCCCATAAGT-TAGTGGCAT
1 CCTTTTAAAGTCCACAACTCT-GTGGCAC
* * * *
610319 CCTTTCAAAGCCCACAAGTCAGTGGCAC
1 CCTTTTAAAGTCCACAACTCTGTGGCAC
* * *
610347 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTT-T-TAAAG-TC-CACAACTCTGTGGC-AC
*
610380 CCTTTCCAAAGTCCACA
1 CCTTT-TAAAGTCCACA
610397 CAAGTCGGTG
Statistics
Matches: 867, Mismatches: 146, Indels: 101
0.78 0.13 0.09
Matches are distributed among these distances:
19 10 0.01
20 3 0.00
25 4 0.00
26 8 0.01
27 364 0.42
28 388 0.45
29 33 0.04
30 8 0.01
31 4 0.00
32 34 0.04
33 11 0.01
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (28 bp):
CCTTTTAAAGTCCACAACTCTGTGGCAC
Found at i:609520 original size:82 final size:81
Alignment explanation
Indices: 609304--610178 Score: 777
Period size: 82 Copynumber: 10.7 Consensus size: 81
609294 AGTAGTGTAA
** * *
609304 CCTTTTCAAAGTCCATGA-TTCTGTGGCACTCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAA
1 CCTTTT-AAAGTCCACAACTTC-GTGGCAC-CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAA
** * *
609368 GTCTGCAAGTCCGTGGCAT
63 GTCCACAACTCCGTGGCAC
* * * * *
609387 CCTTTT-AAGTCCACAAGTCCGTGACACCCTTTTAAGTCCACAAGTCCGTGGCATCGTTTTAAGT
1 CCTTTTAAAGTCCACAACTTCGTGGCA-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGT
*
609451 CCACAACTCTGTGGCAC
65 CCACAACTCCGTGGCAC
* *
609468 CCTTTTAAAGTCCACAACTTCGTGGCACACTTTTAAGTCCATAACTCTGTGGCATCCTTTTAAGT
1 CCTTTTAAAGTCCACAACTTCGTGGCAC-CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGT
* *
609533 CTACAAGTCCGTGGCAC
65 CCACAACTCCGTGGCAC
* * * *
609550 CCTTTT-AAGTCCACAACTCCGTGACACCTTTTTAAAGTCCACAACTCTGTAGCA-CCTTTTTAA
1 CCTTTTAAAGTCCACAACTTCGTGGCACC-TTTT-AAGTCCACAACTCCGTGGCATCC-TTTT-A
609613 AGTCCAC-A--------CAC
62 AGTCCACAACTCCGTGGCAC
* * * *
609624 CCTTTT-AAGTCTACAA-GTCTGTGGCATCCTTTTAAGTTCACAAGTCCGTGGCATCCTTTTAAG
1 CCTTTTAAAGTCCACAACTTC-GTGGCA-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAG
*
609687 TCCACAACTCTGTGGCAC
64 TCCACAACTCCGTGGCAC
* * *
609705 CCTTTTAAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCATAAGTCCGTGGCACCCTTTTAAGT
1 CCTTTTAAAGTCCACAACTTCGTGGCA-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGT
609770 CCACAACTCCGTGGCAC
65 CCACAACTCCGTGGCAC
*
609787 CCTTTTAAAGTCCATAAC-TCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CTCTTTTA
1 CCTTTTAAAGTCCACAACTTC-GTGGCA-CCTTTT-AAGTCCACAACTCCGTGGCATC-CTTTTA
*
609850 AGTCCACAATTCCGTGGCAC
62 AGTCCACAACTCCGTGGCAC
*
609870 CCTTTT-AAGTCCACAACTTCGTGGTATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTTTAAA
1 CCTTTTAAAGTCCACAACTTCGTGGCA-CCTTTT-AAGTCCACAACTCCGTGGCATCCTTTT-AA
* * *
609934 GTCTATAACTCCGTGGCAT
63 GTCCACAACTCCGTGGCAC
* * * * *
609953 CCTTTT-AAGTCCATAACTTCGTGGCATCCTTTCATGTCCACAACTCCGTGGCATTCTTTTAAGC
1 CCTTTTAAAGTCCACAACTTCGTGGCA-CCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGT
* **
610017 CCACAAGTTAGTGGCAC
65 CCACAACTCCGTGGCAC
** * * * * * * * *
610034 CCTTCCAAAGCCCACAA-GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAA
1 CCTTTTAAAGTCCACAACTTC-GTGGCA-CCTTT-TAAGTCCACAACTCCGTGGCATCCTTT-TA
* * **
610098 AGCCCACAAGTTAGTGGCAC
62 AGTCCACAACTCCGTGGCAC
* * * * * *
610118 CCTTTCAAAGCCCACAA-GTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCAT-CTTTT
1 CCTTTTAAAGTCCACAACTTC-GTGGCA-CCTTT-TAAGTCCACAACTCCGTGGCATCCTTTT
610179 CAAAAGCTCA
Statistics
Matches: 675, Mismatches: 85, Indels: 65
0.82 0.10 0.08
Matches are distributed among these distances:
72 8 0.01
73 22 0.03
74 29 0.04
75 2 0.00
80 1 0.00
81 120 0.18
82 282 0.42
83 137 0.20
84 74 0.11
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (81 bp):
CCTTTTAAAGTCCACAACTTCGTGGCACCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTC
CACAACTCCGTGGCAC
Found at i:610112 original size:84 final size:85
Alignment explanation
Indices: 609636--610433 Score: 447
Period size: 82 Copynumber: 9.4 Consensus size: 85
609626 TTTTAAGTCT
* * * ** * * * *
609636 ACAAGTCTGTGGCATCCTTT-TAAGTTCACAAGTCCGTGGCATCCTTT--TAAGTCCACAACTCT
1 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGT-T
* *
609698 -GTGGCACCCTTTTAAAGTCC
65 AGTGGCACCCTTTCAAAGCCC
* * * * * * * * * *
609718 ACAACTTC-GTGGCACCCTTT-TAAGTCCATAAGTCCGTGGCACCCTTT--TAAGTCCACAACTC
1 ACAA-GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTT
* * *
609779 CGTGGCACCCTTTTAAAGTCC
65 AGTGGCACCCTTTCAAAGCCC
* * * * * * * * *
609800 ATAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCA-CTCTTT--TAAGTCCACAA-TT
1 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAAGCCCACAAGTT
* * *
609861 CCGTGGCACCCTTT-TAAGTCC
65 -AGTGGCACCCTTTCAAAGCCC
* * * * * * * * * * * * *
609882 ACAACTTC-GTGGTATCCTTTTAAAGTCCACAACTCCGTGGCATCCTTT-TAAAGTCTATAACTC
1 ACAA-GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTT
* * * *
609945 CGTGGCATCCTTT-TAAGTCC
65 AGTGGCACCCTTTCAAAGCCC
* * * * * * * * *
609965 ATAACTTC-GTGGCATCCTTTC-ATGTCCACAACTCCGTGGCATTCTTT--TAAGCCCACAAGTT
1 ACAA-GTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTT
*
610026 AGTGGCACCCTTCCAAAGCCC
65 AGTGGCACCCTTTCAAAGCCC
*
610047 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCATTTC-AAAGCCCACAAGTTA
1 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTTA
610111 GTGGCACCCTTTCAAAGCCC
66 GTGGCACCCTTTCAAAGCCC
* * * * *
610131 ACAAGTCAGTGGCATCCTTTCAAAGTCCACAAGTCAGTGGCATCTTTTCAAAAGCTCACAAGTTT
1 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTTA
*
610196 GTGGCATCTTCTTTTTCAAAGCCC
66 GTGGCA-C--C-CTTTCAAAGCCC
* * * * * *
610220 ATAAGTCAGTGACACCCTTTCAAAGTCCACAAGTCAGTGGCATCCCTTT--TAAGTCCACAACTC
1 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAT-CCTTTCAAAAGCCCACAAGT-
* *
610283 T-GTGGCTCTCTTTCAAAGCCC
64 TAGTGGCACCCTTTCAAAGCCC
* * * * *
610304 ATAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTCTCTAAAGCCCACACAAG
1 ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAAG-CC-CACAAG
**
610369 TCGGTGGCAACCCTTTCCAAAGTCCAC
63 TTAGTGGC-ACCCTTT-CAAAG-CC-C
*
610396 ACAAGTCGGTGGCAAACCCTTTCAAAGCTCACACAAGT
1 ACAAGTCAGTGGC--ACCCTTTCAAAGC-C-CACAAGT
610434 TTATGGCATT
Statistics
Matches: 600, Mismatches: 81, Indels: 56
0.81 0.11 0.08
Matches are distributed among these distances:
81 22 0.04
82 178 0.30
83 120 0.20
84 130 0.22
85 19 0.03
86 4 0.01
87 2 0.00
88 26 0.04
89 57 0.09
90 9 0.01
91 2 0.00
92 11 0.02
94 12 0.02
95 1 0.00
96 7 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (85 bp):
ACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAAGCCCACAAGTTA
GTGGCACCCTTTCAAAGCCC
Found at i:610229 original size:145 final size:144
Alignment explanation
Indices: 609973--610337 Score: 397
Period size: 145 Copynumber: 2.6 Consensus size: 144
609963 CCATAACTTC
* * * * * * *
609973 GTGGCAT-CCTTTCATGTCCACAACTCCGTGGCAT-TCTTT-TAAGCCCACAAGTTAGTGGCACC
1 GTGGCATCCCTTTAAAGCCCACAACTCAGTGGC-TCTCTTTCAAAGCCCACAAGTCAGTGGCATC
* ** * * *
610035 CTTCCAAAGCCCACAAGTCAGTGGCA-C--C-CTTTCAAAGCCCACAAGTCAGTGGCATCATTTC
65 CTTTCAAAGCCCACAAGTTTGTGGCATCTTCTTTTTCAAAGCCCACAAGTCAGTGACACCATTTC
*
610096 AAAGCCCACAAGTTA
130 AAAGCCCACAAGTCA
* *
610111 GTGGCA-CCCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGTCCACAAGTCAGTGGCAT
1 GTGGCATCCCTTT-AAAGCCCACAACTCAGTGGC-TCTCTTTCAAAGCCCACAAGTCAGTGGCAT
* * * *
610174 CTTTTCAAAAGCTCACAAGTTTGTGGCATCTTCTTTTTCAAAGCCCATAAGTCAGTGACACCCTT
64 CCTTTC-AAAGCCCACAAGTTTGTGGCATCTTCTTTTTCAAAGCCCACAAGTCAGTGACACCATT
*
610239 TCAAAGTCCACAAGTCA
128 TCAAAGCCCACAAGTCA
* * * * *
610256 GTGGCATCCCTTTTAAGTCCACAACTCTGTGGCTCTCTTTCAAAGCCCATAAGTTAGTGGCATCC
1 GTGGCATCCCTTTAAAGCCCACAACTCAGTGGCTCTCTTTCAAAGCCCACAAGTCAGTGGCATCC
610321 TTTCAAAGCCCACAAGT
66 TTTCAAAGCCCACAAGT
610338 CAGTGGCACC
Statistics
Matches: 186, Mismatches: 30, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
138 11 0.06
139 21 0.11
140 22 0.12
141 18 0.10
142 1 0.01
144 15 0.08
145 92 0.49
146 6 0.03
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (144 bp):
GTGGCATCCCTTTAAAGCCCACAACTCAGTGGCTCTCTTTCAAAGCCCACAAGTCAGTGGCATCC
TTTCAAAGCCCACAAGTTTGTGGCATCTTCTTTTTCAAAGCCCACAAGTCAGTGACACCATTTCA
AAGCCCACAAGTCA
Found at i:610441 original size:32 final size:32
Alignment explanation
Indices: 610319--610433 Score: 134
Period size: 32 Copynumber: 3.7 Consensus size: 32
610309 TTAGTGGCAT
*
610319 CCTTTCAAAGC-C-CACAAGTCAGTGGC--AC
1 CCTTTCAAAGCTCACACAAGTCGGTGGCAAAC
*
610347 CCTTCTCTAAAGCCCACACAAGTCGGTGGC-AAC
1 CCTT-TC-AAAGCTCACACAAGTCGGTGGCAAAC
610380 CCTTTCCAAAG-TCCACACAAGTCGGTGGCAAAC
1 CCTTT-CAAAGCT-CACACAAGTCGGTGGCAAAC
610413 CCTTTCAAAGCTCACACAAGT
1 CCTTTCAAAGCTCACACAAGT
610434 TTATGGCATT
Statistics
Matches: 76, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
28 4 0.05
29 2 0.03
30 5 0.07
31 1 0.01
32 48 0.63
33 16 0.21
ACGTcount: A:0.30, C:0.35, G:0.17, T:0.19
Consensus pattern (32 bp):
CCTTTCAAAGCTCACACAAGTCGGTGGCAAAC
Found at i:611807 original size:11 final size:11
Alignment explanation
Indices: 611791--611826 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
611781 AGGTTCAACT
611791 AAAAAAAAGAA
1 AAAAAAAAGAA
611802 AAAAAAAGAGAA
1 AAAAAAA-AGAA
611814 AAAAAAAAGAA
1 AAAAAAAAGAA
611825 AA
1 AA
611827 GAGAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:611808 original size:12 final size:12
Alignment explanation
Indices: 611791--611826 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
611781 AGGTTCAACT
611791 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
611803 AAAAAAGAG-AA
1 AAAAAAAAGAAA
611814 AAAAAAAAGAAA
1 AAAAAAAAGAAA
611826 A
1 A
611827 GAGAGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:611821 original size:18 final size:19
Alignment explanation
Indices: 611793--611830 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
611783 GTTCAACTAA
611793 AAAAAAGAAAAAAAAAGAG
1 AAAAAAGAAAAAAAAAGAG
*
611812 AAAAAA-AAAAGAAAAGAG
1 AAAAAAGAAAAAAAAAGAG
611830 A
1 A
611831 GAAGAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAAAAAGAG
Found at i:613673 original size:97 final size:97
Alignment explanation
Indices: 613565--613798 Score: 335
Period size: 97 Copynumber: 2.4 Consensus size: 97
613555 CGGGATACTC
* * * *
613565 CAACCCTATTCCTCTGAGGGGATACTCCAACCTCGCTTTTAAACATATCAAAGTTTAAATCTTAT
1 CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
613630 TCTCACTTAAATTGTCACCATCGAGGACACTT-
66 TCTCACTTAAATTGTCACCATCGAGGACA-TTG
* *
613662 CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACGCATCAAAGTTTAAATTTTAT
1 CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
* *
613727 TCTCACTTAAATTGTCATCATCGGGGACATTG
66 TCTCACTTAAATTGTCACCATCGAGGACATTG
* * * * *
613759 TAGCCCCATTCCTCCGAGGGAATACTCTAACCCCGTTTTT
1 CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT
613799 TAATAAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
96 2 0.02
97 121 0.98
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.31
Consensus pattern (97 bp):
CAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTTAT
TCTCACTTAAATTGTCACCATCGAGGACATTG
Found at i:618549 original size:29 final size:28
Alignment explanation
Indices: 618517--618598 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
618507 TACATCATGA
618517 AAAATGACCTAAATGACCCCAACATTCAC
1 AAAATGACCTAAATGACCCCAACATT-AC
* * * * * *
618546 AAAATTACATAAAAT-TCCTACACCA-TAG
1 AAAATGACCT-AAATGACC-CCAACATTAC
618574 AAAATGACCTAAATGACCCCAACAT
1 AAAATGACCTAAATGACCCCAACAT
618599 ACATGAAATT
Statistics
Matches: 38, Mismatches: 11, Indels: 9
0.66 0.19 0.16
Matches are distributed among these distances:
27 8 0.21
28 11 0.29
29 11 0.29
30 8 0.21
ACGTcount: A:0.48, C:0.27, G:0.06, T:0.20
Consensus pattern (28 bp):
AAAATGACCTAAATGACCCCAACATTAC
Found at i:618596 original size:57 final size:57
Alignment explanation
Indices: 618430--618622 Score: 185
Period size: 58 Copynumber: 3.4 Consensus size: 57
618420 TAAAATATAT
* * * * * * * * *
618430 AAAATTGCACAAAAGTCCGTAAATCATAAAAAATAACCTAATTGACCCCAATATAT-A
1 AAAATTACATAAAAGTCCTTACACCATAGAAAATGACCTAAATGACCCCAACAT-TCA
* *
618487 AGAAATTGCATAAAAGTCCTTACATCAT-GAAAAATGACCTAAATGACCCCAACATTCA
1 A-AAATTACATAAAAGTCCTTACACCATAG-AAAATGACCTAAATGACCCCAACATTCA
* *
618545 CAAAATTACATAAAATTCC-TACACCATAGAAAATGACCTAAATGACCCCAACATACA
1 -AAAATTACATAAAAGTCCTTACACCATAGAAAATGACCTAAATGACCCCAACATTCA
* *
618602 TGAAATTACATAAATGTCCTT
1 -AAAATTACATAAAAGTCCTT
618623 TGAAAGCTCA
Statistics
Matches: 115, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
57 51 0.44
58 63 0.55
59 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.08, T:0.23
Consensus pattern (57 bp):
AAAATTACATAAAAGTCCTTACACCATAGAAAATGACCTAAATGACCCCAACATTCA
Found at i:619398 original size:13 final size:13
Alignment explanation
Indices: 619357--619410 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
619347 CCGTTAAAAG
619357 CAATGTATCGATA
1 CAATGTATCGATA
*
619370 CAAT-T-TC-CT-
1 CAATGTATCGATA
619379 C-ATGTATCGATA
1 CAATGTATCGATA
619391 CAATGTATCGATA
1 CAATGTATCGATA
*
619404 CATTGTA
1 CAATGTA
619411 CCATGTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
8 2 0.06
9 2 0.06
10 3 0.09
11 3 0.09
12 2 0.06
13 21 0.64
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:619421 original size:33 final size:34
Alignment explanation
Indices: 619357--619426 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 34
619347 CCGTTAAAAG
*
619357 CAATGTATCGATACAATTTCCTCATGTATCGATA
1 CAATGTATCGATACAATTTACTCATGTATCGATA
619391 CAATGTATCGATAC-ATTGTAC-CATGTATCGATA
1 CAATGTATCGATACAATT-TACTCATGTATCGATA
619424 CAA
1 CAA
619427 ATAGTGATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 18 0.53
34 16 0.47
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGTATCGATACAATTTACTCATGTATCGATA
Found at i:619479 original size:20 final size:21
Alignment explanation
Indices: 619451--619489 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
619441 TCTACTACTA
619451 ATCTCATGTATCGATACAATT
1 ATCTCATGTATCGATACAATT
619472 ATCT-ATGTATCGATACAA
1 ATCTCATGTATCGATACAA
619490 AGCATAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (21 bp):
ATCTCATGTATCGATACAATT
Found at i:621977 original size:13 final size:13
Alignment explanation
Indices: 621959--621987 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
621949 AAATAGTACC
621959 CAATGTATCGATA
1 CAATGTATCGATA
621972 CAATGTATCGATA
1 CAATGTATCGATA
621985 CAA
1 CAA
621988 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:629760 original size:13 final size:13
Alignment explanation
Indices: 629742--629768 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
629732 AAAATTCCCA
629742 AATGTATCGATAC
1 AATGTATCGATAC
629755 AATGTATCGATAC
1 AATGTATCGATAC
629768 A
1 A
629769 TGGAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:629828 original size:13 final size:13
Alignment explanation
Indices: 629806--629895 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
629796 GGCAGTAGCT
*
629806 TTGTAGCGATACA
1 TTGTATCGATACA
629819 TTGTATCGATACAAAA
1 TTGTATCGATAC---A
629835 CTTATGTATCGATACA
1 --T-TGTATCGATACA
629851 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
629867 CTTATGTATCGATACA
1 --T-TGTATCGATACA
629883 TTGTATCGATACA
1 TTGTATCGATACA
629896 AATTGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 32 0.50
14 2 0.03
16 8 0.12
18 2 0.03
19 20 0.31
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:629844 original size:19 final size:18
Alignment explanation
Indices: 629820--629882 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
629810 AGCGATACAT
629820 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
629839 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
629852 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
629871 TGTATCGATACA
1 TGTATCGATACA
629883 TTGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:629853 original size:32 final size:32
Alignment explanation
Indices: 629807--629897 Score: 164
Period size: 32 Copynumber: 2.8 Consensus size: 32
629797 GCAGTAGCTT
*
629807 TGTAGCGATACATTGTATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
*
629839 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
629871 TGTATCGATACATTGTATCGATACAAA
1 TGTATCGATACATTGTATCGATACAAA
629898 TTGTTGAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:630779 original size:49 final size:49
Alignment explanation
Indices: 630644--631242 Score: 517
Period size: 49 Copynumber: 12.2 Consensus size: 49
630634 CAGCGTCATA
* * ** * *
630644 GACTTGAAGAAGAA--TGCCAATGTGCTGAGACAAGGCCAACGACATTG
1 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* ** *
630691 GGCTTTAAAGATGACGAAGGCACCAATATGCTGATTCAAGGCCAACGATATTG
1 GAC-TTAAAGA--A-GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * * * *
630744 GACTTAAAGAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAACGACATTA
1 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * * *
630793 GACTTAAATAAGAA--TGCCAATGTGTTGATTCAAGGCC-GACGACATTGG
1 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAG-CGATATT-G
** *
630841 GTTTTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTG
1 GACTTAAAGA--A-GAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * * * * *
630893 GACTTAAAGATGAAGGTGTCAATGTGCTGAGTCAAGGCCAGCGAGATTA
1 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * *
630942 GTCTTAAAGATA-AAGGTGTCAATATGCTGATTCAAGGCCAGCGTTATTG
1 GACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * *
630991 GACTTAAAGGAAAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTG
1 GACTTAAA-GAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * * *
631041 GTCTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCCAGCAATATTG
1 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * * *
631090 GGCTT-----A-AAGGTGCCAATGTGCTGATTCAAGGCCAACGACATTG
1 GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
* * * *
631133 GTCTCAAAGACA-AA-GTGTCAGTATGCTGATTCAAGGCCAGCGATATTGG
1 GACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT-G
** *
631182 GTTTTAAAGATA-AAGGTGCCAATATGCTGGTTCAAGGCCAGCGATATTG
1 GACTTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
631231 GACTTAGAAGAA
1 GACTTA-AAGAA
631243 AACGCCACAA
Statistics
Matches: 449, Mismatches: 77, Indels: 50
0.78 0.13 0.09
Matches are distributed among these distances:
43 35 0.08
47 30 0.07
48 41 0.09
49 186 0.41
50 79 0.18
51 6 0.01
52 16 0.04
53 55 0.12
54 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
GACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTG
Found at i:630835 original size:149 final size:148
Alignment explanation
Indices: 630615--631236 Score: 599
Period size: 149 Copynumber: 4.2 Consensus size: 148
630605 AAAATGATGT
* * * * * * **
630615 CAATGTGCTGATTCACGGTCAGCGTCA-TAGACTTGAAGAAGAATGCCAATGTGCTGAGACAAGG
1 CAATGTGCTGAGTCAAGGCCAGCGACATTAGACTTAAATAAGAATGCCAATGTGCTGATTCAAGG
* *
630679 CCAACGACATTGGGCTTTAAAGATGACGAAGGCACCAATATGCTGATTCAAGGCCAACGATATTG
66 CCAACGACATTGGGCTTTAAAGA-GACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTG
630744 GACTTAAAGAAGAAGGTGC
130 GACTTAAAGAAGAAGGTGC
* *
630763 CAATGTGCTGAGTCAAGGCCAACGACATTAGACTTAAATAAGAATGCCAATGTGTTGATTCAAGG
1 CAATGTGCTGAGTCAAGGCCAGCGACATTAGACTTAAATAAGAATGCCAATGTGCTGATTCAAGG
* * * *
630828 CCGACGACATTGGGTTTTAAAGATGACGAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTG
66 CCAACGACATTGGGCTTTAAAGA-GACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTG
* *
630893 GACTTAAAGATGAAGGTGT
130 GACTTAAAGAAGAAGGTGC
* * * * *
630912 CAATGTGCTGAGTCAAGGCCAGCGAGATTAGTCTTAAAGATAA-AGGTGTCAATATGCTGATTCA
1 CAATGTGCTGAGTCAAGGCCAGCGACATTAGACTT-AA-ATAAGA-ATGCCAATGTGCTGATTCA
* ** * * ** * *
630976 AGGCCAGCGTTATTGGAC-TTAAAG-GAAAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACAT
63 AGGCCAACGACATTGGGCTTTAAAGAGACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATAT
* *
631039 TGGTCTTAAAGATGAAGGTGC
128 TGGACTTAAAGAAGAAGGTGC
* * * * * * * *
631060 CAATATGTTGATTCAAGGCCAGCAATATTGGGCTT--A-AAG-GTGCCAATGTGCTGATTCAAGG
1 CAATGTGCTGAGTCAAGGCCAGCGACATTAGACTTAAATAAGAATGCCAATGTGCTGATTCAAGG
* * * *
631121 CCAACGACATT-GG-TCTCAA-AGACAAAGTG--TCAGTATGCTGATTCAAGGCCAGCGATATTG
66 CCAACGACATTGGGCTTTAAAGAGACAAAG-GCACCAATATGCTGATTCAAGGCCAGCGATATT-
**
631181 GGTTTTAAAGATA-AAGGTGC
129 GGACTTAAAGA-AGAAGGTGC
* * *
631201 CAATATGCTG-GTTCAAGGCCAGCGATATTGGACTTA
1 CAATGTGCTGAG-TCAAGGCCAGCGACATTAGACTTA
631237 GAAGAAAACG
Statistics
Matches: 400, Mismatches: 62, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
140 26 0.06
141 57 0.14
142 29 0.07
143 2 0.00
144 1 0.00
148 103 0.26
149 142 0.35
150 9 0.02
151 31 0.08
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (148 bp):
CAATGTGCTGAGTCAAGGCCAGCGACATTAGACTTAAATAAGAATGCCAATGTGCTGATTCAAGG
CCAACGACATTGGGCTTTAAAGAGACAAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGG
ACTTAAAGAAGAAGGTGC
Found at i:631207 original size:240 final size:242
Alignment explanation
Indices: 630661--631244 Score: 651
Period size: 240 Copynumber: 2.4 Consensus size: 242
630651 AGAAGAATGC
* * * * **
630661 CAATGTGCTGAGACAAGGCCAACGACATTGGGCTTTAAAGATGACGAAGGCACCAATATGCTGAT
1 CAATATGCTGAGTCAAGGCCAGCGACATTGGGTTTTAAAGAT-A--AAGGTGCCAATATGCTGAT
* * * *
630726 TCAAGGCCAACGATATTGGACTTAAAGAAGAAGGTGCCAATGTGCTGAGTCAAGGCCAACGACAT
63 TCAAGGCCAGCGATATTGGACTTAAAGAAAAAGGTGCCAATATGCTGAGTCAAAGCCAACGACAT
* * * *
630791 TAGACTTAAATAAGAATGCCAATGTGTTGATTCAAGGCCGACGACATTGGGTTTTAAAGATGACG
128 TAGACTTAAAGAAGAATGCCAATATGTTGATTCAAGGCCGACAACATTGGG-TCT----ATGAC-
* * * * *
630856 AAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGT
187 AAGGCGCCAATATGCTGATTCAAGGCCAACGACATTGGACTCAAAGATCAAAGTGT
* * * * *
630912 CAATGTGCTGAGTCAAGGCCAGCGAGATT-AGTCTTAAAGATAAAGGTGTCAATATGCTGATTCA
1 CAATATGCTGAGTCAAGGCCAGCGACATTGGGTTTTAAAGATAAAGGTGCCAATATGCTGATTCA
* * * *
630976 AGGCCAGCGTTATTGGACTTAAAGGAAAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTG
66 AGGCCAGCGATATTGGACTTAAA-GAAAAAGGTGCCAATATGCTGAGTCAAAGCCAACGACATTA
* * * *
631041 GTCTTAAAGATGAAGGTGCCAATATGTTGATTCAAGGCC-AGCAATATTGGG-CT-T-A-AAGGT
130 GACTTAAAGAAGAA--TGCCAATATGTTGATTCAAGGCCGA-CAACATTGGGTCTATGACAAGGC
* *
631101 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTCAAAGA-CAAAGTGT
192 GCCAATATGCTGATTCAAGGCCAACGACATTGGACTCAAAGATCAAAGTGT
* * * *
631151 CAGTATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAAGGTGCCAATATGCTGGTTCA
1 CAATATGCTGAGTCAAGGCCAGCGACATTGGGTTTTAAAGATAAAGGTGCCAATATGCTGATTCA
631216 AGGCCAGCGATATTGGACTTAGAAGAAAA
66 AGGCCAGCGATATTGGACTTA-AAGAAAA
631245 CGCCACAAAC
Statistics
Matches: 286, Mismatches: 41, Indels: 23
0.82 0.12 0.07
Matches are distributed among these distances:
239 31 0.11
240 97 0.34
241 2 0.01
242 1 0.00
243 1 0.00
247 40 0.14
248 47 0.16
249 2 0.01
250 39 0.14
251 26 0.09
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (242 bp):
CAATATGCTGAGTCAAGGCCAGCGACATTGGGTTTTAAAGATAAAGGTGCCAATATGCTGATTCA
AGGCCAGCGATATTGGACTTAAAGAAAAAGGTGCCAATATGCTGAGTCAAAGCCAACGACATTAG
ACTTAAAGAAGAATGCCAATATGTTGATTCAAGGCCGACAACATTGGGTCTATGACAAGGCGCCA
ATATGCTGATTCAAGGCCAACGACATTGGACTCAAAGATCAAAGTGT
Found at i:631323 original size:28 final size:28
Alignment explanation
Indices: 631258--631323 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
631248 CACAAACTTG
*
631258 TGTGGGCTTTTGAAAAGGTTGCATTAACT
1 TGTGGGCTTTTG-AAAGGTTGCACTAACT
* *
631287 TGTGTGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTG-CACTAACT
631315 TGTGGGCTT
1 TGTGGGCTT
631324 ACAGGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.22
28 14 0.44
29 11 0.34
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.39
Consensus pattern (28 bp):
TGTGGGCTTTTGAAAGGTTGCACTAACT
Found at i:631377 original size:30 final size:32
Alignment explanation
Indices: 631315--631391 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 32
631305 GCCACTGACT
* *
631315 TGTGGGCTTACAGGAAAAAGGGATGCCACAGAGG
1 TGTGGGCTTA-A-AAAAAAAGGATGCCACAGAGG
*
631349 TGTGGGCTTAAAAAAAAAGG-TGCC-CAGAGT
1 TGTGGGCTTAAAAAAAAAGGATGCCACAGAGG
*
631379 TGTGGACTTAAAA
1 TGTGGGCTTAAAA
631392 GGGTGCCACG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 17 0.44
31 4 0.10
32 7 0.18
33 1 0.03
34 10 0.26
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.19
Consensus pattern (32 bp):
TGTGGGCTTAAAAAAAAAGGATGCCACAGAGG
Found at i:631398 original size:26 final size:27
Alignment explanation
Indices: 631330--631420 Score: 94
Period size: 27 Copynumber: 3.2 Consensus size: 27
631320 GCTTACAGGA
* *
631330 AAAAGGGATGCCACAGAGGTGTGGGCTT
1 AAAAGGG-TGCCACAGAGTTGTGGACTT
*
631358 AAAAAAAAAGGTGCC-CAGAGTTGTGGACTT
1 ----AAAAGGGTGCCACAGAGTTGTGGACTT
*
631388 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTT
631415 AAAAGG
1 AAAAGG
631421 ACAAAGAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
26 10 0.19
27 20 0.38
30 13 0.25
31 4 0.08
32 6 0.11
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (27 bp):
AAAAGGGTGCCACAGAGTTGTGGACTT
Found at i:631399 original size:91 final size:94
Alignment explanation
Indices: 631299--631479 Score: 217
Period size: 91 Copynumber: 1.9 Consensus size: 94
631289 TGTGCTTTTG
* * * * * *
631299 AAGGTTGCCACTGACTTGTGGGCTT-ACAGGAAAAAGGGATGCCACAGAGGTGTGGGCTT-AA-A
1 AAGGGTGCCACGGACTTGTGGACTTAAAAGGAAAAAGAG-TGCCACAGAGGTATGGGCTTAAAGA
*
631361 AAAAAAGGTGCC-CAGAGTTGTGGACTTAA
65 AAAAAAAGTGCCACAGAGTTGTGGACTTAA
* * *
631390 AAGGGTGCCACGGAGTTGTGGACTTAAAAGGACAAAGAGTGCCACAGAGTTATGGGCTTAAAAGG
1 AAGGGTGCCACGGACTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGGTATGGGCTT-AAA-G
631455 AAAAAAAAGTGCCACAGAGTTGTGG
64 AAAAAAAAGTGCCACAGAGTTGTGG
631480 GCTTTCAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
91 39 0.53
92 10 0.14
93 2 0.03
95 12 0.16
96 11 0.15
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.19
Consensus pattern (94 bp):
AAGGGTGCCACGGACTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGGTATGGGCTTAAAGAA
AAAAAAGTGCCACAGAGTTGTGGACTTAA
Found at i:631473 original size:35 final size:34
Alignment explanation
Indices: 631394--631512 Score: 134
Period size: 34 Copynumber: 3.5 Consensus size: 34
631384 ACTTAAAAGG
* * * *
631394 GTGCCACGGAGTTGTGGACTTAAAAGGACAAAGA
1 GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAAA
*
631428 GTGCCACAGAGTTATGGGCTTAAAAGGAAAAAAAA
1 GTGCCACAGAGTTGTGGGCTTAAAAGG-AAAAAAA
631463 GTGCCACAGAGTTGTGGGCTTTCAAAA-G-AAAAAA
1 GTGCCACAGAGTTGTGGGC-TT-AAAAGGAAAAAAA
* *
631497 GTGCCACTGACTTGTG
1 GTGCCACAGAGTTGTG
631513 AACTTTTGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
34 44 0.59
35 23 0.31
36 3 0.04
37 4 0.05
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.20
Consensus pattern (34 bp):
GTGCCACAGAGTTGTGGGCTTAAAAGGAAAAAAA
Found at i:631538 original size:28 final size:28
Alignment explanation
Indices: 631498--631581 Score: 107
Period size: 29 Copynumber: 3.0 Consensus size: 28
631488 AAGAAAAAAG
** *
631498 TGCCACTGACTTGTGAACTTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGA
*
631526 TGCCACTGACTTGTGGGC-TTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG--AAGGA
631555 TGCCACTGACTTGTGGGCTTTTGAAGG
1 TGCCACTGACTTGTGGGCTTTTGAAGG
631582 GTGAGGAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 4 0.08
28 19 0.40
29 21 0.44
30 4 0.08
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGA
Found at i:633032 original size:1 final size:1
Alignment explanation
Indices: 633028--633080 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
633018 TGTTTGTTTG
** * * * *
633028 TTTTTTTTTTGGTTTTTTTTCTTCTTTTTTTTCTTCTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
633081 GCAGAGGACG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.89
Consensus pattern (1 bp):
T
Found at i:633038 original size:11 final size:11
Alignment explanation
Indices: 633011--633080 Score: 70
Period size: 12 Copynumber: 6.2 Consensus size: 11
633001 ATCCGGACCC
*
633011 TTTTTGTTGTT
1 TTTTTGTTTTT
*
633022 TGTTTGTTTTT
1 TTTTTGTTTTT
633033 TTTTTGGTTTTT
1 TTTTT-GTTTTT
*
633045 TTTCTTCTTTTT
1 TTT-TTGTTTTT
*
633057 TTTCTTCTTTTT
1 TTT-TTGTTTTT
633069 TTTTT-TTTTT
1 TTTTTGTTTTT
633079 TT
1 TT
633081 GCAGAGGACG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
10 7 0.13
11 15 0.28
12 29 0.55
13 2 0.04
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.86
Consensus pattern (11 bp):
TTTTTGTTTTT
Found at i:646790 original size:13 final size:13
Alignment explanation
Indices: 646772--646797 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
646762 CAAAAAATCC
646772 ATGTATCGATACA
1 ATGTATCGATACA
646785 ATGTATCGATACA
1 ATGTATCGATACA
646798 TGGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:648750 original size:19 final size:19
Alignment explanation
Indices: 648706--648761 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
648696 CTGCTAATCT
*
648706 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAC
*
648726 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAC
648745 CATGTATCGATACAATG
1 CATGTATCGATACAATG
648762 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:648764 original size:13 final size:13
Alignment explanation
Indices: 648746--648777 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
648736 TACAATGAGC
648746 ATGTATCGATACA
1 ATGTATCGATACA
648759 ATGTATCGATACA
1 ATGTATCGATACA
*
648772 AAGTAT
1 ATGTAT
648778 AATGTATCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:649297 original size:57 final size:56
Alignment explanation
Indices: 649120--649298 Score: 157
Period size: 57 Copynumber: 3.1 Consensus size: 56
649110 CCCCAACATT
* * * * *
649120 CATAAAAGTCTC-TAGATCATGGAAAAATGACTTAAATGGCCTAAAAATATATGAAATTG
1 CATAAAAGTCTCTTA-AACAT-GAAAAATAACTAAAATGACCT-AAAATACATGAAA-TG
* * * * *
649179 CATAATAGTCTCTTAAACATTAAAAATAACTAAAATGATTCTAAAATACATGAATTA
1 CATAAAAGTCTCTTAAACATGAAAAATAACTAAAATGA-CCTAAAATACATGAAATG
* *
649236 CATAAAAGTCT-TTAAAACATGACAAATTAC-AAGAATGACCTAAAATACATGAGAATG
1 CATAAAAGTCTCTT-AAACATGAAAAATAACTAA-AATGACCTAAAATACATGA-AATG
649293 CATAAA
1 CATAAA
649299 TGGTCCTGAA
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
56 17 0.17
57 37 0.38
58 25 0.26
59 17 0.17
60 2 0.02
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.27
Consensus pattern (56 bp):
CATAAAAGTCTCTTAAACATGAAAAATAACTAAAATGACCTAAAATACATGAAATG
Found at i:650204 original size:13 final size:13
Alignment explanation
Indices: 650166--650210 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
650156 GAAACTCTCT
650166 TTTTTCCTTTGTT-
1 TTTTTCCTTT-TTA
*
650179 TTTCTCTCTTTTTA
1 TTTTTC-CTTTTTA
650193 TTTTTCCTTTTTA
1 TTTTTCCTTTTTA
650206 TTTTT
1 TTTTT
650211 TGGTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTCCTTTTTA
Found at i:656978 original size:22 final size:22
Alignment explanation
Indices: 656953--657028 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
656943 AATCAACATC
656953 ATATTAGGATATAATTAGCATA
1 ATATTAGGATATAATTAGCATA
* * * *
656975 ATATTAGAGATTGTAATCAACATC
1 ATATTAG-GA-TATAATTAGCATA
*
656999 ACATTAGGATATAATTAGCATA
1 ATATTAGGATATAATTAGCATA
657021 ATATTAGG
1 ATATTAGG
657029 GATTCTTTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 23 0.55
23 4 0.10
24 15 0.36
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.34
Consensus pattern (22 bp):
ATATTAGGATATAATTAGCATA
Found at i:656990 original size:46 final size:46
Alignment explanation
Indices: 656938--657032 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
656928 GCTAATTAAT
*
656938 ATTGTAATCAACATCATATTAGGATATAATTAGCATAATATTAGAG
1 ATTGTAATCAACATCACATTAGGATATAATTAGCATAATATTAGAG
*
656984 ATTGTAATCAACATCACATTAGGATATAATTAGCATAATATTAGGG
1 ATTGTAATCAACATCACATTAGGATATAATTAGCATAATATTAGAG
657030 ATT
1 ATT
657033 CTTTTCTAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (46 bp):
ATTGTAATCAACATCACATTAGGATATAATTAGCATAATATTAGAG
Found at i:663280 original size:52 final size:52
Alignment explanation
Indices: 663202--663329 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
663192 CGAAATATGA
*
663202 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTAGGC
*
663254 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTAGGC
663306 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
663330 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTAGGC
Found at i:663356 original size:13 final size:13
Alignment explanation
Indices: 663338--663362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
663328 CAAAGATCAG
663338 TGTATCGATACAA
1 TGTATCGATACAA
663351 TGTATCGATACA
1 TGTATCGATACA
663363 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:663440 original size:33 final size:33
Alignment explanation
Indices: 663403--663469 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
663393 AGTAGCTTAA
663403 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
663436 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
663469 A
1 A
663470 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:663443 original size:13 final size:13
Alignment explanation
Indices: 663425--663449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
663415 CAAAAAAATA
663425 TGTATCGATACAT
1 TGTATCGATACAT
663438 TGTATCGATACA
1 TGTATCGATACA
663450 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:664236 original size:13 final size:13
Alignment explanation
Indices: 664218--664243 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
664208 CATTATTCAA
664218 TGTATCGATACAT
1 TGTATCGATACAT
664231 TGTATCGATACAT
1 TGTATCGATACAT
664244 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:664307 original size:20 final size:20
Alignment explanation
Indices: 664282--664355 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
664272 TTTACCTAGA
664282 TGTATCGATACATTTTGTAT
1 TGTATCGATACATTTTGTAT
664302 TGTATCGATACA--TTGCTCAT
1 TGTATCGATACATTTTG-T-AT
* ** *
664322 TGTATCGATATATTTTACAA
1 TGTATCGATACATTTTGTAT
664342 TGTATCGATACATT
1 TGTATCGATACATT
664356 CAGGCATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 39 0.87
22 2 0.04
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTTGTAT
Found at i:666818 original size:51 final size:50
Alignment explanation
Indices: 666679--666820 Score: 153
Period size: 49 Copynumber: 2.8 Consensus size: 50
666669 TCCCGGTTCC
* * * *
666679 ATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTTCAACTCCGATTT
1 ATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCAATTT
* ** **
666729 -TTTT-AAAAGCATCGATTTACCGCAATCGGGGATACTCCAACTCCAATTTT
1 ATTTTCAAAA-CATCAATTTTTCATAATCGGGGATACTCCAACTCCAA-TTT
* *
666779 ATTTTCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 ATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
666821 CCCGTTATTT
Statistics
Matches: 73, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
48 4 0.05
49 33 0.45
50 3 0.04
51 29 0.40
52 4 0.05
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.35
Consensus pattern (50 bp):
ATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTCCAATTT
Found at i:667006 original size:51 final size:51
Alignment explanation
Indices: 666944--667061 Score: 168
Period size: 51 Copynumber: 2.3 Consensus size: 51
666934 TTATTTTTGA
*
666944 GGGGATACTCCAACCCCAATTTTA-TTTCTAAAATACCAAATTTTC-ATAATC
1 GGGGATACTCCAACCCCAATTTTATTTTC-AAAACACC-AATTTTCTATAATC
* *
666995 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATC
1 GGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTATAATC
*
667046 AGGGATACTCCAACCC
1 GGGGATACTCCAACCC
667062 TGTTATTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 7 0.12
51 49 0.82
52 4 0.07
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAATTTTATTTTCAAAACACCAATTTTCTATAATC
Found at i:667158 original size:131 final size:130
Alignment explanation
Indices: 666917--667158 Score: 326
Period size: 131 Copynumber: 1.9 Consensus size: 130
666907 TATGCCATCG
* * * * *
666917 GGGATACTCCAATCCTGTTATTTTTGAGGGGATACTCCAACCCCAATTTTATTTCTAAAATACCA
1 GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAATTTTACTTCCAAAACACCA
* * * *
666982 AATTTTCATAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCA
66 AATTTTCATAATCGGGGATACCCCAACCCCGATTTTATCTCCAAAACACCAATTTTCTATAATCA
*
667047 GGGATACTCCAACCCTGTTATTTTCCGAGGGGATACTCCAACCCCGATTTTACTTCCAAAACA-C
1 GGGATACTCCAACCCTGTTATTTT-CGAGGGGATACTCCAACCCCAATTTTACTTCCAAAACACC
** *
667111 TGATTTTCCATAATCGGGGATACCCCAGCCCCG-TTGTTATCTCCAAAA
65 AAATTTT-CATAATCGGGGATACCCCAACCCCGATT-TTATCTCCAAAA
667159 TATTAGATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
130 31 0.32
131 65 0.68
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (130 bp):
GGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAATTTTACTTCCAAAACACCA
AATTTTCATAATCGGGGATACCCCAACCCCGATTTTATCTCCAAAACACCAATTTTCTATAATCA
Found at i:674468 original size:20 final size:20
Alignment explanation
Indices: 674424--674468 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
674414 AGTAATATCA
*
674424 AATTAAAAAAAATTATCAAAT
1 AATTAAAAAAAATTAT-AAAC
674445 AATTAAAAAAATATTAT-AAC
1 AATTAAAAAAA-ATTATAAAC
674465 AATT
1 AATT
674469 GTGAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTAAAAAAAATTATAAAC
Found at i:675047 original size:16 final size:18
Alignment explanation
Indices: 675028--675060 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
675018 ACTTAACTCA
675028 TATTTTA-T-TTAAAAAT
1 TATTTTACTATTAAAAAT
675044 TATTTTACTATTAAAAA
1 TATTTTACTATTAAAAA
675061 AATCTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (18 bp):
TATTTTACTATTAAAAAT
Found at i:676290 original size:14 final size:15
Alignment explanation
Indices: 676262--676297 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
676252 AAACTTTATA
676262 TATTAATATAAATTT
1 TATTAATATAAATTT
676277 TATTAATA-AAATTT
1 TATTAATATAAATTT
*
676291 TTTTAAT
1 TATTAAT
676298 TAATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTAATATAAATTT
Found at i:676826 original size:28 final size:24
Alignment explanation
Indices: 676793--676888 Score: 87
Period size: 28 Copynumber: 4.0 Consensus size: 24
676783 TTTTACCTTT
676793 TTTTTAATATAAATAATATTTTAATAA
1 TTTTTAATATAAAT-ATATTTT--TAA
676820 TTATTTAATATAAATATATTTTTAA
1 TT-TTTAATATAAATATATTTTTAA
676845 TTTTT-A-AT-AA-ATA--TTTAA
1 TTTTTAATATAAATATATTTTTAA
* *
676863 TTATTTAATGTAAATATAATTTTAA
1 TT-TTTAATATAAATATATTTTTAA
676888 T
1 T
676889 AATTTTTATT
Statistics
Matches: 60, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
18 7 0.12
19 3 0.05
20 4 0.07
21 3 0.05
22 4 0.07
23 4 0.07
24 3 0.05
25 11 0.18
27 9 0.15
28 12 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
TTTTTAATATAAATATATTTTTAA
Found at i:676867 original size:43 final size:39
Alignment explanation
Indices: 676817--676955 Score: 131
Period size: 43 Copynumber: 3.4 Consensus size: 39
676807 AATATTTTAA
676817 TAATTATTTAATATAAATATATTTTTAATTTTTAATAAATATT
1 TAATTATTTAATATAAATATATTTTTAATTTTT-AT---TATT
* * *
676860 TAATTATTTAATGTAAATATAATTTTAATAATTT-TTATT
1 TAATTATTTAATATAAATATATTTTTAAT-TTTTATTATT
* *
676899 T-ACTATTTAATATAAATATAATTTTTAATTATTTATTATA
1 TAATTATTTAATATAAATAT-ATTTTTAATT-TTTATTATT
676939 TATATTATATTAA-ATAA
1 TA-ATTAT-TTAATATAA
676956 TTTTTTTATT
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
38 16 0.20
39 16 0.20
40 5 0.06
42 9 0.11
43 31 0.39
44 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (39 bp):
TAATTATTTAATATAAATATATTTTTAATTTTTATTATT
Found at i:676876 original size:21 final size:20
Alignment explanation
Indices: 676817--676879 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
676807 AATATTTTAA
676817 TAATTATTTAATATAAATATATTTT
1 TAATTATTTAAT-T-AA-ATA--TT
676842 TAATT-TTTAA-TAAATATT
1 TAATTATTTAATTAAATATT
676860 TAATTATTTAATGTAAATAT
1 TAATTATTTAAT-TAAATAT
676880 AATTTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 7 0.20
19 5 0.14
20 3 0.09
21 9 0.26
22 1 0.03
24 5 0.14
25 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATTATTTAATTAAATATT
Found at i:676915 original size:38 final size:37
Alignment explanation
Indices: 676864--676960 Score: 112
Period size: 38 Copynumber: 2.6 Consensus size: 37
676854 AATATTTAAT
*
676864 TATTTAATGTAAATATAATTTTAATAATT-TTTATT-TA
1 TATTTAATATAAATATAATTTT--TAATTATTTATTATA
676901 CTATTTAATATAAATATAATTTTTAATTATTTATTATA
1 -TATTTAATATAAATATAATTTTTAATTATTTATTATA
*
676939 TATATT-ATATTAA-ATAATTTTT
1 TAT-TTAATATAAATATAATTTTT
676961 TTATTCTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
36 14 0.26
37 15 0.28
38 25 0.46
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (37 bp):
TATTTAATATAAATATAATTTTTAATTATTTATTATA
Found at i:677077 original size:21 final size:20
Alignment explanation
Indices: 677017--677077 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
677007 TCTTATAAAT
*
677017 TAAT-TTTAATTTTATTAT-
1 TAATATTTAATTTTATTTTA
* *
677035 TAATATTTAATCTCATTATTA
1 TAATATTTAATTTTATT-TTA
677056 TAATATTTAATTTTATTGTTA
1 TAATATTTAATTTTATT-TTA
677077 T
1 T
677078 TGCTATTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.12
19 10 0.29
20 1 0.03
21 19 0.56
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
TAATATTTAATTTTATTTTA
Found at i:677821 original size:2 final size:2
Alignment explanation
Indices: 677816--677852 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
677806 TGAAAAGGTG
677816 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
677853 AAGATGTGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:678273 original size:23 final size:24
Alignment explanation
Indices: 678240--678285 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
678230 TTTTAATATT
*
678240 TAAATACTAAATTTAA-TATTAAA
1 TAAATACTAAATATAATTATTAAA
*
678263 TAAATATTAAATATAATTATTAA
1 TAAATACTAAATATAATTATTAA
678286 TTAATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATACTAAATATAATTATTAAA
Found at i:678291 original size:23 final size:22
Alignment explanation
Indices: 678240--678302 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
678230 TTTTAATATT
*
678240 TAAATACTAAATTTAATATTAAA
1 TAAATA-TAAATATAATATTAAA
678263 TAAATATTAAATATAATTATT-AA
1 TAAATA-TAAATATAA-TATTAAA
*
678286 TTAATA-AAATAT-ATATT
1 TAAATATAAATATAATATT
678303 TAATTGAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 6 0.17
23 21 0.58
24 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATAAATATAATATTAAA
Found at i:678295 original size:21 final size:21
Alignment explanation
Indices: 678282--678325 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
678272 AATATAATTA
678282 TTAATT-AATAAAATATATAT
1 TTAATTGAATAAAATATATAT
678302 TTAATTGAATAAAAT-TAT-T
1 TTAATTGAATAAAATATATAT
678321 TTAAT
1 TTAAT
678326 ATAAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 9 0.39
21 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAATTGAATAAAATATATAT
Found at i:678333 original size:21 final size:21
Alignment explanation
Indices: 678282--678335 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
678272 AATATAATTA
678282 TTAATT-AATAAAATATATAT
1 TTAATTAAATAAAATATATAT
*
678302 TTAATTGAATAAAAT-TAT-T
1 TTAATTAAATAAAATATATAT
678321 TTAATATAAAATAAA
1 TTAAT-T-AAATAAA
678336 GAAGTAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.20
20 10 0.33
21 14 0.47
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAATTAAATAAAATATATAT
Found at i:681496 original size:1 final size:1
Alignment explanation
Indices: 681490--681514 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
681480 GTTGAAACCA
681490 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
681515 GCGGCCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:687421 original size:11 final size:11
Alignment explanation
Indices: 687401--687440 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
687391 TTAACATATT
687401 TATT-TATTTA
1 TATTATATTTA
687411 TATTATATTTA
1 TATTATATTTA
*
687422 TATTAT-TTTT
1 TATTATATTTA
687432 TATTATATT
1 TATTATATT
687441 ATGTTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TATTATATTTA
Found at i:687421 original size:15 final size:15
Alignment explanation
Indices: 687396--687447 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
687386 AAATTTTAAC
687396 ATATTTATTTAT-TT
1 ATATTTATTTATATT
687410 ATATTATATTTATATT
1 ATATT-TATTTATATT
*
687426 AT-TTTTTATTATATT
1 ATATTTAT-TTATATT
*
687441 ATGTTTA
1 ATATTTA
687448 AAATTATTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 7 0.22
15 18 0.56
16 7 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
ATATTTATTTATATT
Found at i:687435 original size:21 final size:19
Alignment explanation
Indices: 687396--687440 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
687386 AAATTTTAAC
687396 ATATTTATTTATTTATATT
1 ATATTTATTTATTTATATT
*
687415 ATATTTATATTATTTTTTATT
1 ATATTTAT-TTA-TTTATATT
687436 ATATT
1 ATATT
687441 ATGTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
20 3 0.13
21 12 0.52
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
ATATTTATTTATTTATATT
Found at i:701777 original size:20 final size:20
Alignment explanation
Indices: 701747--701795 Score: 73
Period size: 20 Copynumber: 2.4 Consensus size: 20
701737 TTAATTTCTT
701747 TCAAAATTCATCT-TTTTCATA
1 TCAAAA-TCATCTATTTTCA-A
701768 TCAAAATCATCTATTTTCAA
1 TCAAAATCATCTATTTTCAA
701788 TCAAAATC
1 TCAAAATC
701796 TTCATCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (20 bp):
TCAAAATCATCTATTTTCAA
Found at i:704201 original size:19 final size:20
Alignment explanation
Indices: 704177--704229 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
704167 ATCGATATAA
704177 TGTATCGATACATGCTC-AT
1 TGTATCGATACATGCTCAAT
*
704196 TGTATCGATACATACTCAAT
1 TGTATCGATACATGCTCAAT
704216 TGTATCGATACATG
1 TGTATCGATACATG
704230 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGCTCAAT
Found at i:704204 original size:32 final size:33
Alignment explanation
Indices: 704142--704205 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
704132 TACATATCCA
* *
704142 AATGTATCGATACATTATGCTTTGTATCGATAT
1 AATGTATCGATACATGATGCATTGTATCGATAT
*
704175 AATGTATCGATACATGCT-CATTGTATCGATA
1 AATGTATCGATACATGATGCATTGTATCGATA
704206 CATACTCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (33 bp):
AATGTATCGATACATGATGCATTGTATCGATAT
Found at i:704301 original size:20 final size:20
Alignment explanation
Indices: 704256--704310 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
704246 CCCTAAGTGA
*
704256 AATGTATCGATACATGGGAC
1 AATGTATCGATACATGAGAC
704276 AATGTATCGATACATGAAGA-
1 AATGTATCGATACATG-AGAC
* *
704296 ATTGTATTGATACAT
1 AATGTATCGATACAT
704311 CATGCCCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 29 0.94
21 2 0.06
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (20 bp):
AATGTATCGATACATGAGAC
Found at i:712213 original size:15 final size:15
Alignment explanation
Indices: 712193--712244 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
712183 CGATGATTTT
712193 GTGGTGGGTAATTAG
1 GTGGTGGGTAATTAG
* **
712208 GTGGTGGGTGATTTT
1 GTGGTGGGTAATTAG
712223 GTGGTGGGTAATTAG
1 GTGGTGGGTAATTAG
712238 GTGGTGG
1 GTGGTGG
712245 ATGATTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.13, C:0.00, G:0.50, T:0.37
Consensus pattern (15 bp):
GTGGTGGGTAATTAG
Found at i:712222 original size:30 final size:30
Alignment explanation
Indices: 712184--712259 Score: 143
Period size: 30 Copynumber: 2.5 Consensus size: 30
712174 GCGGTGTATC
712184 GATGATTTTGTGGTGGGTAATTAGGTGGTG
1 GATGATTTTGTGGTGGGTAATTAGGTGGTG
*
712214 GGTGATTTTGTGGTGGGTAATTAGGTGGTG
1 GATGATTTTGTGGTGGGTAATTAGGTGGTG
712244 GATGATTTTGTGGTGG
1 GATGATTTTGTGGTGG
712260 ATTTGGCGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (30 bp):
GATGATTTTGTGGTGGGTAATTAGGTGGTG
Found at i:712256 original size:15 final size:15
Alignment explanation
Indices: 712184--712261 Score: 75
Period size: 15 Copynumber: 5.2 Consensus size: 15
712174 GCGGTGTATC
712184 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
* * **
712199 GGTAATTAGGTGGTG
1 GATGATTTTGTGGTG
*
712214 GGTGATTTTGTGGTG
1 GATGATTTTGTGGTG
* * **
712229 GGTAATTAGGTGGTG
1 GATGATTTTGTGGTG
712244 GATGATTTTGTGGTG
1 GATGATTTTGTGGTG
712259 GAT
1 GAT
712262 TTGGCGGAAT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.41
Consensus pattern (15 bp):
GATGATTTTGTGGTG
Found at i:721519 original size:19 final size:19
Alignment explanation
Indices: 721492--721547 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
721482 TGTATCGATA
* *
721492 CATTATATCGATACATGTT
1 CATTGTATCGATACATGCT
*
721511 CATTGTATCGATACATACT
1 CATTGTATCGATACATGCT
*
721530 CAATTGTATTGATACATG
1 C-ATTGTATCGATACATG
721548 AAATTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGCT
Found at i:723880 original size:17 final size:18
Alignment explanation
Indices: 723860--723900 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
723850 ACCATGCCAC
723860 AAAAAAATTC-ATAATAT
1 AAAAAAATTCAATAATAT
*
723877 AAAAAATTTCAAATAATAT
1 AAAAAAATTC-AATAATAT
723896 AAAAA
1 AAAAA
723901 TATATACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAAAATTCAATAATAT
Found at i:723936 original size:25 final size:25
Alignment explanation
Indices: 723908--723957 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
723898 AAATATATAC
723908 TTATATATCATATCAAGTAGTTGAA
1 TTATATATCATATCAAGTAGTTGAA
723933 TTATATATCATATCAAGTAGTTGAA
1 TTATATATCATATCAAGTAGTTGAA
723958 CAATAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
TTATATATCATATCAAGTAGTTGAA
Found at i:724493 original size:15 final size:16
Alignment explanation
Indices: 724473--724505 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
724463 CCAACCTCTT
*
724473 TTTTTTTCTTC-TTTC
1 TTTTTTCCTTCATTTC
724488 TTTTTTCCTTCATTTC
1 TTTTTTCCTTCATTTC
724504 TT
1 TT
724506 CTTCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCCTTCATTTC
Found at i:724503 original size:16 final size:15
Alignment explanation
Indices: 724469--724505 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
724459 GCACCCAACC
724469 TCTTT-TTTTTT-CT
1 TCTTTCTTTTTTCCT
724482 TCTTTCTTTTTTCCT
1 TCTTTCTTTTTTCCT
724497 TCATTTCTT
1 TC-TTTCTT
724506 CTTCAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 4 0.19
16 6 0.29
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTTCTTTTTTCCT
Found at i:724985 original size:16 final size:17
Alignment explanation
Indices: 724959--724990 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
724949 GAAAGCTCTT
724959 TATAGAGGAACTCCTTA
1 TATAGAGGAACTCCTTA
724976 TATA-AGGAACTCCTT
1 TATAGAGGAACTCCTT
724991 TACAAACACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (17 bp):
TATAGAGGAACTCCTTA
Found at i:728652 original size:68 final size:66
Alignment explanation
Indices: 728557--728813 Score: 347
Period size: 68 Copynumber: 3.8 Consensus size: 66
728547 TTTTTTTACC
*
728557 AAAAGAAATCGATTCTCATG-TACAATTCATACATTAGTCTAATCCTTGCAGTCTTTCTTGTTTT
1 AAAA-AAATCGATTCTCA-GATATAATTCATACATTAGTCTAATCCTTGCAGTCTTTCTT-TTTT
728621 CTAT
63 CTAT
728625 AAAAAAATCTGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCT
1 AAAAAAATC-GATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGTCTTTCTTTTTTC-
728690 TAT
64 TAT
* * * *
728693 AAAAAAGAATCTGATTCTGAGATATAATTCATGCATTAATCTAATCCTTGCAGTTTTTCTTTTTT
1 -AAAAA-AATC-GATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGTCTTTCTTTTTT
728758 -TAT
63 CTAT
* * * *
728761 AAAAAAGTCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTTGTAGTCT
1 AAAAAAATCGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGTCT
728814 GACATTTACA
Statistics
Matches: 173, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
65 39 0.23
66 3 0.02
67 16 0.09
68 56 0.32
69 5 0.03
70 54 0.31
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (66 bp):
AAAAAAATCGATTCTCAGATATAATTCATACATTAGTCTAATCCTTGCAGTCTTTCTTTTTTCTA
T
Found at i:728975 original size:92 final size:91
Alignment explanation
Indices: 728743--728994 Score: 347
Period size: 92 Copynumber: 2.8 Consensus size: 91
728733 CTAATCCTTG
*
728743 CAGTTTTTC-TTTTTT-TATAAAAAAG--TCGATTCTCAGATATAATTCATGCATTAGTCTAATC
1 CAGTCTTTCTTTTTTTCTATAAAAAAGAATCGATTCTCAGATATAATTCATGCATTAGTCTAATC
* * *
728804 TTTGTAGTCTGACATTTACAATTAAT
66 CTTGCAGTCTGACATTTACAATCAAT
* * * * *
728830 TAGTC--T-TTTTTTTCTATAAAAAAGAATCCCATTCTTAAATATAATTCATGCATTAGTTTAAT
1 CAGTCTTTCTTTTTTTCTATAAAAAAGAAT-CGATTCTCAGATATAATTCATGCATTAGTCTAAT
728892 CCTTGCAGTCTGACATTTACAATCAAT
65 CCTTGCAGTCTGACATTTACAATCAAT
728919 CAGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
1 CAGTCTTTCTTTTTTTCTATAAAAAAGAATC-GATTCTCAGATATAATTCATGCATTAGTCTAAT
*
728984 TCTTGCAGTCT
65 CCTTGCAGTCT
728995 TTCTTTTTTC
Statistics
Matches: 141, Mismatches: 15, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
85 7 0.05
86 10 0.07
87 3 0.02
88 1 0.01
89 58 0.41
91 2 0.01
92 60 0.43
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.43
Consensus pattern (91 bp):
CAGTCTTTCTTTTTTTCTATAAAAAAGAATCGATTCTCAGATATAATTCATGCATTAGTCTAATC
CTTGCAGTCTGACATTTACAATCAAT
Found at i:729042 original size:68 final size:69
Alignment explanation
Indices: 728919--729060 Score: 225
Period size: 68 Copynumber: 2.1 Consensus size: 69
728909 TACAATCAAT
*
728919 CAGTCTTTCTTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAAT
1 CAGTCTTTCTTTTTTCCTATAAAAAAGAATCT-ATTCTCAGATATAATTCATGCATTAGTCTAAT
*
728984 TCTTG
65 CCTTG
*
728989 CAGTCTTTCTTTTTTCCTATAAAAAA-AATC-ATTTCTCAGATATAATTCGTGCATTAGTCTAAT
1 CAGTCTTTCTTTTTTCCTATAAAAAAGAATCTA-TTCTCAGATATAATTCATGCATTAGTCTAAT
729052 CCTTG
65 CCTTG
729057 CAGT
1 CAGT
729061 TTGACATTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
67 1 0.01
68 38 0.56
69 4 0.06
70 25 0.37
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.43
Consensus pattern (69 bp):
CAGTCTTTCTTTTTTCCTATAAAAAAGAATCTATTCTCAGATATAATTCATGCATTAGTCTAATC
CTTG
Found at i:729086 original size:160 final size:162
Alignment explanation
Indices: 728836--729154 Score: 511
Period size: 162 Copynumber: 2.0 Consensus size: 162
728826 TAATTAGTCT
* * *
728836 TTTTTTTCTATAAAAAAGAATCCCATTCTTAAATATAATTCATGCATTAGTTTAATCCTTGCAGT
1 TTTTTTCCTATAAAAAAGAAT-CCATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGT
*
728901 CTGACATTTACAATCAATCAGTCTTTC-TTTTTTTCTATAAAAAAGAATCTGATTCTCAGATATA
65 CTGACATTTACAATCAATCAGTCTTTCTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATA
728965 ATTCATGCATTAGTCTAAT-TCTTGCAGTCTTTC
130 ATTCATGCATTAGTCTAATCT-TTGCAGTCTTTC
* *
728998 TTTTTTCCTATAAAAAA-AAT-CATTTCTCAGATATAATTCGTGCATTAGTCTAATCCTTGCAGT
1 TTTTTTCCTATAAAAAAGAATCCA-TTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGT
*
729061 TTGACATTTACAATCAATCAGTCTTTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATAT
65 CTGACATTTACAATCAATCAGTCTTTC-TTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATAT
729126 AATTCATGCATTAGTCTAATCTTTGCAGT
129 AATTCATGCATTAGTCTAATCTTTGCAGT
729155 TTGACATTTA
Statistics
Matches: 146, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
159 2 0.01
160 62 0.42
161 3 0.02
162 78 0.53
163 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.42
Consensus pattern (162 bp):
TTTTTTCCTATAAAAAAGAATCCATTCTCAAATATAATTCATGCATTAGTCTAATCCTTGCAGTC
TGACATTTACAATCAATCAGTCTTTCTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAA
TTCATGCATTAGTCTAATCTTTGCAGTCTTTC
Found at i:729325 original size:91 final size:91
Alignment explanation
Indices: 728994--729398 Score: 450
Period size: 91 Copynumber: 4.5 Consensus size: 91
728984 TCTTGCAGTC
* *
728994 TTTCTTTTTTCCTATAAAAAA-AATC--ATTTCTCAGATATAATTCGTGCATTAGTCTAATCCTT
1 TTTCTTTTTT-TTATAAAAAAGAATCTGA-TTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * *
729056 GCAGTTTGACATTTACAATCAATCAGTCT
64 GCAGTCTAACATTTACAATCAATCA-ACT
* * *
729085 TTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTT
1 TT-TCTTTTTTT-TATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * * *
729150 GCAGTTTGACATTTACAATCAGTTAAC-
64 GCAGTCTAACATTTACAATCAATCAACT
* * * ** * *
729177 TTT-TTTTCTATATAAAAAA-AATCTGATTCTCAGCTATAATTCATATATTAGTCTAATCTTTAC
1 TTTCTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT-G
*
729240 CA-TCTAACATTTACAATCAGTCAACT
65 CAGTCTAACATTTACAATCAATCAACT
729266 TTTCTTTTGTTTTATAAAAAAGAAT-TGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
1 TTTCTTTT-TTTTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
729330 CAGTCTAACATTTACAATCAATCAACT
65 CAGTCTAACATTTACAATCAATCAACT
** * * *
729357 TTTCTTTTTTCCATAAAAAGGAAT-TCGATTTTAAGATATAAT
1 TTTCTTTTTTTTATAAAAAAGAATCT-GATTCTCAGATATAAT
729399 CACATTTATT
Statistics
Matches: 272, Mismatches: 30, Indels: 24
0.83 0.09 0.07
Matches are distributed among these distances:
88 58 0.21
89 14 0.05
90 25 0.09
91 92 0.34
92 21 0.08
93 5 0.02
94 56 0.21
95 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (91 bp):
TTTCTTTTTTTTATAAAAAAGAATCTGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTGC
AGTCTAACATTTACAATCAATCAACT
Found at i:729343 original size:179 final size:180
Alignment explanation
Indices: 728998--729359 Score: 475
Period size: 179 Copynumber: 2.0 Consensus size: 180
728988 GCAGTCTTTC
* * * * *
728998 TTTTTTCCTATAAAAAAAATCATTTCTCAGATATAATTCGTGCATTAGTCTAATCCTTGCAGTTT
1 TTTTTTCATATAAAAAAAATCATTTCTCAGATATAATTCATACATTAGTCTAATCCTTCCAGTCT
* * *
729063 GACATTTACAATCAATCAGTCTTTCTTTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAA
66 AACATTTACAATCAATCACTCTTTCTTTTTGTTTCTATAAAAAAGAATCCGATTCTCAGATATAA
* * * * *
729128 TTCATGCATTAGTCTAATCTTTGCAGTTTGACATTTACAATCAGTTAACT
131 TTCATGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATCAACT
* * *
729178 TTTTTTCTATATAAAAAAAATC-TGATTCTCAGCTATAATTCATATATTAGTCTAATCTTTACCA
1 TTTTTTC-ATATAAAAAAAATCAT--TTCTCAGATATAATTCATACATTAGTCTAATCCTT-CCA
* *
729242 -TCTAACATTTACAATCAGTCAACT-TTTC-TTTTGTTT-TATAAAAAAGAAT-TGATTCTCAGA
62 GTCTAACATTTACAATCAATC-ACTCTTTCTTTTTGTTTCTATAAAAAAGAATCCGATTCTCAGA
729302 TATAATTCATGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATCAACT
126 TATAATTCATGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATCAACT
729357 TTT
1 TTT
729360 CTTTTTTCCA
Statistics
Matches: 159, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
179 63 0.40
180 21 0.13
181 20 0.13
182 51 0.32
183 4 0.03
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (180 bp):
TTTTTTCATATAAAAAAAATCATTTCTCAGATATAATTCATACATTAGTCTAATCCTTCCAGTCT
AACATTTACAATCAATCACTCTTTCTTTTTGTTTCTATAAAAAAGAATCCGATTCTCAGATATAA
TTCATGCATTAGTCTAATCCTTGCAGTCTAACATTTACAATCAATCAACT
Found at i:730206 original size:19 final size:18
Alignment explanation
Indices: 730147--730206 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 18
730137 TTTTTAATAA
*
730147 AATTAAAAA-TAATATTT
1 AATTAAAAATTAAAATTT
* *
730164 AATT-AAATTTAAAAAATT
1 AATTAAAAATT-AAAATTT
730182 ACATTAACAAATTAAAATTT
1 A-ATTAA-AAATTAAAATTT
730202 AATTA
1 AATTA
730207 TTATGTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
18 6 0.18
19 7 0.21
20 8 0.24
21 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAAATTAAAATTT
Found at i:730312 original size:117 final size:116
Alignment explanation
Indices: 730009--730376 Score: 440
Period size: 117 Copynumber: 3.1 Consensus size: 116
729999 TAATGTATTA
* * *
730009 ATTATTATTTTTAATAAAAAATAATATTTAATTAACTTTAAAGAAATTTATATTAACAAATT-AA
1 ATTATAATTTTTAATAAAAAATAATATTTAATTAAATTT-AA-AAATTTACATTAACAAATTAAA
* *
730073 A--T-ATTAATTAT-TTTTTAATAATAAAAAATTTTAAATAAAAATAAAAAGGGTTTATT
64 ATTTAATT-ATTATGTTTTTAAAAATAAAAAA-TTT---T-AAAATAAAAA-GGTTTTTT
* *
730129 ATTATTATTTTTTAATAAAATTAAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAAT
1 ATTA-TAATTTTTAAT---A--AAAAATAATATTTAATTAAATTTAAAAATTTACATTAACAAAT
730194 TAAAATTTAATTATTATGTTTTTATAAAATAAAAAATTTTAAAATAAAAAGGTTTTTT
60 TAAAATTTAATTATTATGTTTTTA-AAAATAAAAAATTTTAAAATAAAAAGGTTTTTT
* * *
730252 CTTATAATTTTTAATAAAAAATAATATTTAATTCAGTTTAAAAATTTACATTAACAAATTAAAAT
1 ATTATAATTTTTAATAAAAAATAATATTTAATTAAATTTAAAAATTTACATTAACAAATTAAAAT
* *
730317 ATTAATTATTATGTTTTTAAAAATAAAAAATTTTAAATTAAAAAAGTTTTTT
66 -TTAATTATTATGTTTTTAAAAATAAAAAATTTTAAAATAAAAAGGTTTTTT
730369 ATTATAAT
1 ATTATAAT
730377 AATATTTTTT
Statistics
Matches: 220, Mismatches: 15, Indels: 29
0.83 0.06 0.11
Matches are distributed among these distances:
117 84 0.38
118 18 0.08
119 1 0.00
120 4 0.02
121 9 0.04
122 10 0.05
123 10 0.05
124 28 0.13
125 6 0.03
126 22 0.10
127 6 0.03
128 12 0.05
129 10 0.05
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (116 bp):
ATTATAATTTTTAATAAAAAATAATATTTAATTAAATTTAAAAATTTACATTAACAAATTAAAAT
TTAATTATTATGTTTTTAAAAATAAAAAATTTTAAAATAAAAAGGTTTTTT
Found at i:733719 original size:20 final size:20
Alignment explanation
Indices: 733694--733731 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
733684 GTAAAAAGAC
733694 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
733714 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
733732 TGGGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:734391 original size:28 final size:28
Alignment explanation
Indices: 734293--734946 Score: 703
Period size: 28 Copynumber: 22.7 Consensus size: 28
734283 TAAAAAAATG
*
734293 GTGCCACTAACTTGTGTGGGCTTTGAAAAGA
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAGA
734324 GTTGCCACTGACTCATGTGGGCTTTGAAAAGA
1 G-TGCCACTGACT--TGTGGGCTTTG-AAAGA
*
734356 GTGCCACTAACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* * * * *
734384 GTACCACTAACTTGTAGGTTTTAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
734411 GATGCCACTAACTTGTGGGCTTTGAAAAGA
1 G-TGCCACTGACTTGTGGGCTTTG-AAAGA
*
734441 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
734469 GTGCCACTGACTTGTGGGCTTT-AAAAA
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
734496 GGTGCCACTAACTTATGGGCTTTGAAAG-
1 -GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
734524 GATGCCACTAACTTGTGGGCTTTGAAAAA
1 G-TGCCACTGACTTGTGGGCTTTGAAAGA
*
734553 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
734581 GTACCACTGACTTATGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTG-AAAGA
* * *
734610 GTGCCACTAATTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
* *
734638 GTGCCACTAACTTGCATCGGCTTTGAAAG-
1 GTGCCACTGACTTG--TGGGCTTTGAAAGA
*
734667 GATGCCACTGACTTGTGGGCTTTGAAAAAA
1 G-TGCCACTGACTTGTGGGCTTTG-AAAGA
734697 GT---ACTGACTTGTGGGCTTTGAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
734722 GTGCCACTGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
*
734750 GTGCCACTGACTTGCGTGGGCTTTGAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA
* *
734780 GTGCCACTGACTTACGTGGGCTTTGAGAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA
* *
734810 GTGCCACTAACTTGCGTGGGCTTTGAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA
*
734840 GTGCCACTGACTTGCGTGAGCTTTGAAAG-
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA
* * *
734869 GATTCCACTAACTTGTGGGTTTTGAAAAGA
1 G-TGCCACTGACTTGTGGGCTTTG-AAAGA
* *
734899 GTGCCAATGACTTGTGGGCTTTGAAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAGA
734927 GTGCCACTGACTTGTGGGCT
1 GTGCCACTGACTTGTGGGCT
734947 AATTTGTGGG
Statistics
Matches: 545, Mismatches: 55, Indels: 49
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.01
26 18 0.03
27 5 0.01
28 252 0.46
29 91 0.17
30 134 0.25
31 12 0.02
32 27 0.05
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGA
Found at i:734558 original size:141 final size:141
Alignment explanation
Indices: 734293--735196 Score: 831
Period size: 141 Copynumber: 6.4 Consensus size: 141
734283 TAAAAAAATG
*
734293 GTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACTGACTCATGTGGGCTTTGAAAAGAGT
1 GTGCCACTGAC-T-TGTGGGCTTTG-AAAGAG-TGCCACTGACT--TGTGGGCTTTGAAAAG-GT
* * * * * *
734358 GCCACTAACTTGTGGGCTTTGAAA-GAGTACCACTAACTTGTAGG-TTTTAAAAGGATGCCACTA
59 GCCACTAACTTATGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTGAAAAAG-TGCCACTG
734421 ACTTGTGGGCTTTGAAAAGA
122 ACTTGTGGGCTTTGAAAAGA
* *
734441 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTA
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTA
734506 ACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGG
66 ACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGG
*
734571 CTTTG-AAAGG
131 CTTTGAAAAGA
* * * * *
734581 GTACCACTGACTTATGGGCTTTGAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACT
* *
734646 AACTTGCATCGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAAAGT---ACTGACTTG
65 AACTT--ATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTG-AAAAAGTGCCACTGACTTG
734708 TGGGCTTTG-AAAGA
127 TGGGCTTTGAAAAGA
* *
734722 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCAC
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAAGGTGCCAC
* * * **
734787 TGACTTACGTGGGCTTTGAGAGGGTGCCACTAACTTGCGTGGGCTTTGAAAGGGTGCCACTGACT
64 TAACTTA--TGGGCTTTGAAAGGATGCCACTAACTT--GTGGGCTTTGAAAAAGTGCCACTGACT
* *
734852 TGCGTGAGCTTTGAAAGGA
125 T--GTGGGCTTTGAAAAGA
* * * * *
734871 -TTCCACTAACTTGTGGGTTTTGAAAAGAGTGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACT
* * **
734935 GAC-T-T--G---T----GG--G---CTAATTTGTGGGCTTTGAAAAGAGTAACACTGACTTGTG
65 AACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA-AGTGCCACTGACTTGTG
*
734984 GGCTTTG-AAAGG
129 GGCTTTGAAAAGA
* * * *
734996 GTGCCACTGGCTTGCGTAGGCTTTGAAA-AGGTGCCATTGACTTGTGGGCTTTGAAATGAGTGCC
1 GTGCCACTGACTT--GTGGGCTTTGAAAGA-GTGCCACTGACTTGTGGGCTTTGAAAAG-GTGCC
* * * * **
735060 ACTGACCTGTGGGCTTTG-AAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
62 ACTAACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGTGCCACTGACTTG
* *
735124 TGGAC-TTAAAAAGA
127 TGGGCTTTGAAAAGA
* * * * * * * * *
735138 -TGCCACGGAGTTATGGACTTTGAAAAGAAATGCCACTGAATCGTGGACTTTGAAGAGGT
1 GTGCCACTGACTTGTGGGCTTTG-AAAG-AGTGCCACTGACTTGTGGGCTTTGAAAAGGT
735197 CATAGTACTA
Statistics
Matches: 636, Mismatches: 76, Indels: 96
0.79 0.09 0.12
Matches are distributed among these distances:
125 3 0.00
126 19 0.03
127 42 0.07
128 30 0.05
129 7 0.01
130 1 0.00
132 2 0.00
134 2 0.00
135 1 0.00
138 3 0.00
139 7 0.01
140 47 0.07
141 178 0.28
142 96 0.15
143 60 0.09
144 28 0.04
145 5 0.01
146 20 0.03
147 27 0.04
148 38 0.06
149 20 0.03
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (141 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTA
ACTTATGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGG
CTTTGAAAAGA
Found at i:734601 original size:169 final size:169
Alignment explanation
Indices: 734292--735162 Score: 955
Period size: 169 Copynumber: 5.0 Consensus size: 169
734282 TTAAAAAAAT
* *
734292 GGTGCCACTAACTTGTGTGGGCTTTGAAAAGAGTTGCCACTGACTCATGTGGGCTTTGAAAAGAG
1 GGTGCCACTAAC-T-TGTGGGCTTT-AAAA-AGGTGCCACTGACT--TGTGGGCTTTGAAAGGA-
* * * * * * *
734357 TGCCACTAACTTGTGGGCTTTGAAAGAGTACCACTAACTTGTAGGTTTTAAAAGGATGCCACTAA
59 TGCCACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
734422 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
124 CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
734468 GGTGCCACTGACTTGTGGGCTTTAAAAAGGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACT
1 GGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT
* * *
734533 AACTTGTGGGCTTTGAAAAAGTGCCACTGACTTGTGGGCTTTGAAAGGGTACCACTGACTTATGG
66 AACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
* *
734598 GCTTTGAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAG
131 GCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
734637 GGTGCCACTAACTTGCATCGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTTTGAAA-AAAG-T
1 GGTGCCACTAACTTG--TGGGCTTTAAAAAGG-TGCCACTGACTTGTGGGCTTTGAAAGGATGCC
*
734699 ACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
63 ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT-
* *
734764 CGTGGGCTTTG-AAAGGGTGCCACTGACTTACGTGGGCTTTGAGAG
127 -GTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAG
* * * *
734809 GGTGCCACTAACTTGCGTGGGCTTTGAAAGGGTGCCACTGACTTGCGTGAGCTTTGAAAGGATTC
1 GGTGCCACTAACTT--GTGGGCTTTAAAAAGGTGCCACTGACTT--GTGGGCTTTGAAAGGATGC
* *
734874 CACTAACTTGTGGGTTTTGAAAAGAGTGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
62 CACTAACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA--
**
734939 TGTGGGCTAATTTGTGGGCTTTGAAAAGAGTAACACTGACTTGTGGGCTTTGAAAG
124 ------C----TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
** * * * *
734995 GGTGCCACTGGCTTGCGTAGGCTTTGAAAAGGTGCCATTGACTTGTGGGCTTTGAAATGAGTGCC
1 GGTGCCACTAACTT--GTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCC
* * *
735060 ACTGACCTGTGGGCTTTGAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
63 ACTAACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * * *
735124 TGGAC-TTAAAAAGA-TGCCACGGAGTTATGGACTTTGAAA
128 TGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAA
735163 AGAAATGCCA
Statistics
Matches: 597, Mismatches: 69, Indels: 65
0.82 0.09 0.09
Matches are distributed among these distances:
169 193 0.32
170 45 0.08
171 46 0.08
172 58 0.10
173 8 0.01
174 23 0.04
175 3 0.01
176 27 0.05
177 42 0.07
183 36 0.06
184 18 0.03
185 19 0.03
186 52 0.09
187 10 0.02
188 15 0.03
189 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (169 bp):
GGTGCCACTAACTTGTGGGCTTTAAAAAGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT
AACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG
GCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:734986 original size:41 final size:40
Alignment explanation
Indices: 734910--734987 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
734900 TGCCAATGAC
* **
734910 TTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTAAT
1 TTGTGGGCTTTGAAAGAGTAACACTGACTTGTGGGCTAAT
734950 TTGTGGGCTTTGAAAAGAGTAACACTGACTTGTGGGCT
1 TTGTGGGCTTTG-AAAGAGTAACACTGACTTGTGGGCT
734988 TTGAAAGGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 12 0.35
41 22 0.65
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.32
Consensus pattern (40 bp):
TTGTGGGCTTTGAAAGAGTAACACTGACTTGTGGGCTAAT
Found at i:734992 original size:29 final size:28
Alignment explanation
Indices: 734950--735191 Score: 220
Period size: 28 Copynumber: 8.5 Consensus size: 28
734940 GTGGGCTAAT
**
734950 TTGTGGGCTTTGAAAAGAGTAACACTGAC
1 TTGTGGGCTTTG-AAAGAGTGCCACTGAC
* *
734979 TTGTGGGCTTTGAAAGGGTGCCACTGGC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* *
735007 TTGCGTAGGCTTTGAAA-AGGTGCCATTGAC
1 TT--GTGGGCTTTGAAAGA-GTGCCACTGAC
735037 TTGTGGGCTTTGAAATGAGTGCCACTGAC
1 TTGTGGGCTTTGAAA-GAGTGCCACTGAC
* *
735066 CTGTGGGCTTTGAAGGA-TGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
*
735093 TTGTGGGCTTTGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* ** * *
735121 TTGTGGACTTAAAAAGA-TGCCACGGAG
1 TTGTGGGCTTTGAAAGAGTGCCACTGAC
* * * *
735148 TTATGGACTTTGAAAAGAAATGCCACTGAA
1 TTGTGGGCTTTG-AAAG-AGTGCCACTGAC
* *
735178 TCGTGGACTTTGAA
1 TTGTGGGCTTTGAA
735192 GAGGTCATAG
Statistics
Matches: 176, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
27 41 0.23
28 55 0.31
29 38 0.22
30 42 0.24
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (28 bp):
TTGTGGGCTTTGAAAGAGTGCCACTGAC
Found at i:734992 original size:69 final size:69
Alignment explanation
Indices: 734876--735009 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
734866 AAGGATTCCA
* **
734876 CTAACTTGTGGGTTTTGAAAAGAGTGCCAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
1 CTAACTTGTGGGCTTTGAAAAGAGTAACAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
734941 TGGG
66 TGGG
* * *
734945 CTAATTTGTGGGCTTTGAAAAGAGTAACACTGACTTGTGGGCTTTGAAAGGGTGCCACTGGCTTG
1 CTAACTTGTGGGCTTTGAAAAGAGTAACAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
735010 CGTAGGCTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.22, C:0.15, G:0.32, T:0.31
Consensus pattern (69 bp):
CTAACTTGTGGGCTTTGAAAAGAGTAACAATGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
TGGG
Found at i:735004 original size:28 final size:28
Alignment explanation
Indices: 734950--735126 Score: 221
Period size: 28 Copynumber: 6.2 Consensus size: 28
734940 GTGGGCTAAT
* **
734950 TTGTGGGCTTTGAAAAGAGTAACACTGAC
1 TTGTGGGCTTTG-AAAGGGTGCCACTGAC
*
734979 TTGTGGGCTTTGAAAGGGTGCCACTGGC
1 TTGTGGGCTTTGAAAGGGTGCCACTGAC
* * *
735007 TTGCGTAGGCTTTGAAAAGGTGCCATTGAC
1 TT--GTGGGCTTTGAAAGGGTGCCACTGAC
*
735037 TTGTGGGCTTTGAAATGAGTGCCACTGAC
1 TTGTGGGCTTTGAAA-GGGTGCCACTGAC
* *
735066 CTGTGGGCTTTG-AAGGATGCCACTGAC
1 TTGTGGGCTTTGAAAGGGTGCCACTGAC
735093 TTGTGGGCTTTGAAAGGGTGCCACTGAC
1 TTGTGGGCTTTGAAAGGGTGCCACTGAC
735121 TTGTGG
1 TTGTGG
735127 ACTTAAAAAG
Statistics
Matches: 127, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
27 22 0.17
28 48 0.38
29 33 0.26
30 24 0.19
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TTGTGGGCTTTGAAAGGGTGCCACTGAC
Found at i:735140 original size:55 final size:54
Alignment explanation
Indices: 734972--735162 Score: 202
Period size: 55 Copynumber: 3.4 Consensus size: 54
734962 AAAAGAGTAA
* * *
734972 CACTGACTTGTGGGCTTTGAAAGGGTGCCACTGGCTTGCGTAGGCTTTGAAAAGGTGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--GT-GGC-TTAAAAAGATGC
* * * ** *
735030 CATTGACTTGTGGGCTTTGAAATGAGTGCCACTGACCTGTGGGCTTTGAAGGATGC
1 CACTGACTTGTGGGCTTTGAAA-GGGTGCCACTGACTTGT-GGCTTAAAAAGATGC
735086 CACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGACTTAAAAAGATGC
1 CACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGG-CTTAAAAAGATGC
* * * *
735141 CACGGAGTTATGGACTTTGAAA
1 CACTGACTTGTGGGCTTTGAAA
735163 AGAAATGCCA
Statistics
Matches: 112, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
54 2 0.02
55 43 0.38
56 29 0.26
57 5 0.04
58 21 0.19
59 12 0.11
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (54 bp):
CACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGCTTAAAAAGATGC
Found at i:743534 original size:20 final size:20
Alignment explanation
Indices: 743511--743580 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
743501 AAAAAGACAG
743511 AATGTATCGATATATT-AAA
1 AATGTATCGATATATTCAAA
* *
743530 GAATGTATCGATACATTCATA
1 -AATGTATCGATATATTCAAA
* *
743551 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTCAAA
*
743571 ATTGTATCGA
1 AATGTATCGA
743581 CACATCTGGG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATATATTCAAA
Found at i:744029 original size:23 final size:23
Alignment explanation
Indices: 743982--744076 Score: 77
Period size: 23 Copynumber: 4.1 Consensus size: 23
743972 TTATTTGAAT
**
743982 AATGATAATTTTTTTAATTCCTTA
1 AATG-TAATTTTTTTAATTTATTA
*
744006 AATGTTATTTTTTTAATTTATT-
1 AATGTAATTTTTTTAATTTATTA
* *
744028 AATGTAAATTTTTTAAATATAATTA
1 AATGT-AATTTTTTTAAT-TTATTA
* * *
744053 AATATCA-TTTTTTATTTTATTA
1 AATGTAATTTTTTTAATTTATTA
744075 AA
1 AA
744077 AATAATGATA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
22 12 0.21
23 32 0.56
24 9 0.16
25 4 0.07
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (23 bp):
AATGTAATTTTTTTAATTTATTA
Done.