Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1043
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: 71140
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3186 original size:19 final size:19
Alignment explanation
Indices: 3162--3224 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
3152 AAACAGTAAC
3162 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
3181 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
3194 TGTAGCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
3213 TGTATCGATACA
1 TGTATCGATACA
3225 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:3208 original size:32 final size:32
Alignment explanation
Indices: 3162--3229 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
3152 AAACAGTAAC
*
3162 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTAGCGATACATAAGTGTTGTATCGATACAA
3194 TGTAGCGATACATAAGTGTTGTATCGATACAA
1 TGTAGCGATACATAAGTGTTGTATCGATACAA
3226 TGTA
1 TGTA
3230 TCGCTACAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (32 bp):
TGTAGCGATACATAAGTGTTGTATCGATACAA
Found at i:3294 original size:13 final size:13
Alignment explanation
Indices: 3276--3301 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3266 CATTACTCAA
3276 TGTATCGATACAT
1 TGTATCGATACAT
3289 TGTATCGATACAT
1 TGTATCGATACAT
3302 GGATCTTTGT
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:10487 original size:9 final size:9
Alignment explanation
Indices: 10473--10499 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
10463 AAATGACTTC
10473 AAATCATCA
1 AAATCATCA
10482 AAATCATCA
1 AAATCATCA
10491 AAATCATCA
1 AAATCATCA
10500 CAATAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
AAATCATCA
Found at i:11449 original size:19 final size:18
Alignment explanation
Indices: 11425--11487 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
11415 AGCGATACAT
11425 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
11444 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
11457 TGTGTCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
11476 TGTATCGATACA
1 TGTATCGATACA
11488 GTTACGGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
14 1 0.03
16 2 0.06
18 1 0.03
19 22 0.61
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:11458 original size:32 final size:32
Alignment explanation
Indices: 11417--11487 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
11407 AGCTTCGTAG
11417 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
11449 CGATACATTGTGTCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
11481 CGATACA
1 CGATACA
11488 GTTACGGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:14571 original size:13 final size:13
Alignment explanation
Indices: 14521--14579 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
14511 TGCCAATCTC
14521 ATGTATCGATACA
1 ATGTATCGATACA
*
14534 ATATATCGATAC-
1 ATGTATCGATACA
14546 A---AT-GA-AC-
1 ATGTATCGATACA
14553 ATGTATCGATACA
1 ATGTATCGATACA
14566 ATGTATCGATACA
1 ATGTATCGATACA
14579 A
1 A
14580 AGCATAATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
9 2 0.05
10 2 0.05
11 2 0.05
12 3 0.08
13 25 0.64
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:16013 original size:2 final size:2
Alignment explanation
Indices: 16006--16046 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
15996 AAAACGCTAA
16006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16047 CATCAATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26150 original size:16 final size:15
Alignment explanation
Indices: 26131--26175 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
26121 AATATTATTC
26131 ATAAAAAAAGAGAAAA
1 ATAAAAAAAGA-AAAA
*
26147 AT-AAAAAA-AATAA
1 ATAAAAAAAGAAAAA
26160 ATAAAAAAAGAAAAA
1 ATAAAAAAAGAAAAA
26175 A
1 A
26176 ATCGAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 5 0.20
14 7 0.28
15 11 0.44
16 2 0.08
ACGTcount: A:0.84, C:0.00, G:0.07, T:0.09
Consensus pattern (15 bp):
ATAAAAAAAGAAAAA
Found at i:26177 original size:16 final size:16
Alignment explanation
Indices: 26131--26177 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
26121 AATATTATTC
*
26131 ATAAAAAAAGAGAAAA
1 ATAAAAAAAGAAAAAA
*
26147 AT--AAAAA-AAATAA
1 ATAAAAAAAGAAAAAA
26160 ATAAAAAAAGAAAAAA
1 ATAAAAAAAGAAAAAA
26176 AT
1 AT
26178 CGAATGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 6 0.24
14 5 0.20
15 5 0.20
16 9 0.36
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (16 bp):
ATAAAAAAAGAAAAAA
Found at i:27882 original size:42 final size:42
Alignment explanation
Indices: 27763--28411 Score: 308
Period size: 42 Copynumber: 15.5 Consensus size: 42
27753 CTGCCTATTA
* * * * *
27763 GCTTTGACCCTA-GAGACTGCCTCATCTAAAGTCTACCTGTCA
1 GCTTTGACCCTAGGAGACT-CCTTACCTTAAGTCTGCCTGTCG
* * * * * *
27805 ACTTTAACCCTA-AAGACTTTCCTTACTTTCAGTCTGCTTGTCG
1 GCTTTGACCCTAGGAGAC--TCCTTACCTTAAGTCTGCCTGTCG
* * **
27848 GCTTTGACCCTAGAAGACTCCTCACCTTAAGTCTGGTTGTCG
1 GCTTTGACCCTAGGAGACTCCTTACCTTAAGTCTGCCTGTCG
* ** * *
27890 GCTTTGACCAT-GGAGACTTTTTTACCCTCAAGTCTGCCTATCG
1 GCTTTGACCCTAGGAGAC-TCCTTA-CCTTAAGTCTGCCTGTCG
* * * * *
27933 GCTTTGACCCTA-GAGACTTTCTTACCTTCAGTTTGCTTGTCA
1 GCTTTGACCCTAGGAGAC-TCCTTACCTTAAGTCTGCCTGTCG
* * * * *
27975 ACTTTGACCCT-GTAGACTACCTTACCTCAATTCTGTCTGTCG
1 GCTTTGACCCTAGGAGACT-CCTTACCTTAAGTCTGCCTGTCG
* * * * * * **
28017 ACTTTGACCGTA-GAAATATTCTTA-CTCTCAGTCTGCCTGTTA
1 GCTTTGACCCTAGGAGA-CTCCTTACCT-TAAGTCTGCCTGTCG
* * *
28059 GCTTTGACCCT-GGAGACTGCCTCACCTCAAGTCTGCCTGTTG
1 GCTTTGACCCTAGGAGACT-CCTTACCTTAAGTCTGCCTGTCG
** * * * *
28101 ATTTTGACCTTA-GAGACTTTCTTACCCTAAGTCTGCCTATCG
1 GCTTTGACCCTAGGAGAC-TCCTTACCTTAAGTCTGCCTGTCG
* * * *
28143 ACTTTGACCCTA-GAGACTGCTTTACCTCAAATCTGCCTGTCG
1 GCTTTGACCCTAGGAGACT-CCTTACCTTAAGTCTGCCTGTCG
* * * * * *
28185 GCTTTGA-CCTTGGAGACTTTCTTACCCTCAGTCTGGCTGTTG
1 GCTTTGACCCTAGGAGAC-TCCTTACCTTAAGTCTGCCTGTCG
* * * * *
28227 GCTTTGA-CCTTGGAGACTGCCTCATCTTAAGTCTGCCTATCA
1 GCTTTGACCCTAGGAGACT-CCTTACCTTAAGTCTGCCTGTCG
* * * * * *
28269 GCTTTGATCCTA-GAAACTTTCTTACCTTCAGTCTGCCTATCA
1 GCTTTGACCCTAGGAGAC-TCCTTACCTTAAGTCTGCCTGTCG
* * * * * * *
28311 GCTTTGA-CCTTGGAGATTGCCTGACCTCAAATTTGCTTGTCG
1 GCTTTGACCCTAGGAGACT-CCTTACCTTAAGTCTGCCTGTCG
* * *
28353 GCTTTGA--CTATGGAGATTTCC-TACCTCAAGTCTGCCTGTTG
1 GCTTTGACCCTA-GGAGA-CTCCTTACCTTAAGTCTGCCTGTCG
28394 GCTTTGACCCTA-GAGACT
1 GCTTTGACCCTAGGAGACT
28412 TTTTCACCTT
Statistics
Matches: 454, Mismatches: 125, Indels: 58
0.71 0.20 0.09
Matches are distributed among these distances:
40 1 0.00
41 46 0.10
42 327 0.72
43 74 0.16
44 6 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (42 bp):
GCTTTGACCCTAGGAGACTCCTTACCTTAAGTCTGCCTGTCG
Found at i:28048 original size:84 final size:82
Alignment explanation
Indices: 27764--28411 Score: 406
Period size: 84 Copynumber: 7.7 Consensus size: 82
27754 TGCCTATTAG
** * * * * * * *
27764 CTTTGACCCTAGAGACTGCCTCATCTAAAGTCTACCTGTCAACTTTAACCCTAAAGACTTTCCTT
1 CTTTGACCCTAGAGACTTTCTTACCT-CAGTCTGCCTGTCAACTTTGACCCT-GAGAC-TGCCTT
* * *
27829 ACTTTC-AGTCTGCTTGTCGG
63 AC-CTCAAGTCTGCCTGTCGA
* * * ** ** * ***
27849 CTTTGACCCTAGAAGAC-TCCTCACCTTAAGTCTGGTTGTCGGCTTTGACCATGGAGACTTTTTT
1 CTTTGACCCTAG-AGACTTTCTTACC-TCAGTCTGCCTGTCAACTTTGACCCT-GAGACTGCCTT
* *
27913 ACCCTCAAGTCTGCCTATCGG
63 A-CCTCAAGTCTGCCTGTCGA
* * *
27934 CTTTGACCCTAGAGACTTTCTTACCTTCAGTTTGCTTGTCAACTTTGACCCTGTAGACTACCTTA
1 CTTTGACCCTAGAGACTTTCTTACC-TCAGTCTGCCTGTCAACTTTGACCCTG-AGACTGCCTTA
* *
27999 CCTCAATTCTGTCTGTCGA
64 CCTCAAGTCTGCCTGTCGA
* * * * *
28018 CTTTGACCGTAGA-AATATTCTTACTCTCAGTCTGCCTGTTAGCTTTGACCCTGGAGACTGCCTC
1 CTTTGACCCTAGAGACT-TTCTTAC-CTCAGTCTGCCTGTCAACTTTGACCCT-GAGACTGCCTT
*
28082 ACCTCAAGTCTGCCTGTTGA
63 ACCTCAAGTCTGCCTGTCGA
* * * * * *
28102 TTTTGACCTTAGAGACTTTCTTACCCTAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCTTTA
1 CTTTGACCCTAGAGACTTTCTTA-CCTCAGTCTGCCTGTCAACTTTGACCCT-GAGACTGCCTTA
* *
28167 CCTCAAATCTGCCTGTCGG
64 CCTCAAGTCTGCCTGTCGA
* * * *** * *
28186 CTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGGCTGTTGGCTTTGACCTTGGAGACTGCCTCA
1 CTTTGACCCTAGAGACTTTCTTA-CCTCAGTCTGCCTGTCAACTTTGACCCT-GAGACTGCCTTA
* * *
28251 TCTTAAGTCTGCCTATC-A
64 CCTCAAGTCTGCCTGTCGA
* * * * * * *
28269 GCTTTGATCCTAGAAACTTTCTTACCTTCAGTCTGCCTATCAGCTTTGACCTTGGAGATTGCCTG
1 -CTTTGACCCTAGAGACTTTCTTACC-TCAGTCTGCCTGTCAACTTTGACCCT-GAGACTGCCTT
* * * *
28334 ACCTCAAATTTGCTTGTCGG
63 ACCTCAAGTCTGCCTGTCGA
** * * ***
28354 CTTTGACTATGGAGA-TTTCCTACCTCAAGTCTGCCTGTTGGCTTTGACCCTAGAGACT
1 CTTTGACCCTAGAGACTTTCTTACCTC-AGTCTGCCTGTCAACTTTGACCCT-GAGACT
28412 TTTTCACCTT
Statistics
Matches: 447, Mismatches: 101, Indels: 32
0.77 0.17 0.06
Matches are distributed among these distances:
82 2 0.00
83 37 0.08
84 298 0.67
85 105 0.23
86 5 0.01
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (82 bp):
CTTTGACCCTAGAGACTTTCTTACCTCAGTCTGCCTGTCAACTTTGACCCTGAGACTGCCTTACC
TCAAGTCTGCCTGTCGA
Found at i:28107 original size:126 final size:122
Alignment explanation
Indices: 27975--28407 Score: 345
Period size: 126 Copynumber: 3.4 Consensus size: 122
27965 TTGCTTGTCA
* * * *
27975 ACTTTGACCCTGTAGACTACCTTACCTCAATTCTGTCTGTCGACTTTGACCGTAGAAATATTCTT
1 ACTTTGACCTTG-AGACTACCTTACCTCAAGTCTGCCTATCGACTTTGACC-TAGAAAT-TTCTT
* *
28040 ACTCTCAGTCTGCCTGTTAGCTTTGACCCTGGAGACTGCCTCACCTCAAGTCTGCCTGTTG
63 AC-CTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTGTTG
* ** * * *
28101 ATTTTGACCTTAGAGACTTTCTTACC-CTAAGTCTGCCTATCGACTTTGACCCTAGAGACTGCTT
1 ACTTTGACCTT-GAGACTACCTTACCTC-AAGTCTGCCTATCGACTTTGA-CCTAGAAATTTC-T
* * ** * *
28165 TACCTCAAATCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCTC-AGTCTGGCTGTTG
62 TACCTC-AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCA-CCTCAAGTCTGCCTGTTG
* * * * *
28227 GCTTTGACCTTGGAGACTGCCTCATCTTAAGTCTGCCTATC-AGCTTTGATCCTAGAAACTTTCT
1 ACTTTGACCTT-GAGACTACCTTACCTCAAGTCTGCCTATCGA-CTTTGA-CCTAGAAA-TTTCT
* * * * * * *
28291 TACCTTCAGTCTGCCTATCAGCTTTGACCTTGGAGATTGCCTGACCTCAAATTTGCTTGTCG
62 TACC-TCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTGTTG
* * * * * *
28353 GCTTTGA-CTATGGAGATTTCC-TACCTCAAGTCTGCCTGTTGGCTTTGACCCTAGA
1 ACTTTGACCT-T-GAGACTACCTTACCTCAAGTCTGCCTATCGACTTTGA-CCTAGA
28408 GACTTTTTCA
Statistics
Matches: 243, Mismatches: 51, Indels: 27
0.76 0.16 0.08
Matches are distributed among these distances:
125 39 0.16
126 193 0.79
127 11 0.05
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (122 bp):
ACTTTGACCTTGAGACTACCTTACCTCAAGTCTGCCTATCGACTTTGACCTAGAAATTTCTTACC
TCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTGTTG
Found at i:28117 original size:168 final size:162
Alignment explanation
Indices: 27915--28411 Score: 528
Period size: 168 Copynumber: 3.0 Consensus size: 162
27905 ACTTTTTTAC
* * * * *
27915 CCTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCTTACCTTCAGTTTGCTTGTCAACTTT
1 CCTCAAGTCTGCCT-TTGACTTTGA-CCTAGAGACTTTCTTACCTTCAGTCTGCCTATCAACTTT
* * * *
27980 GACCCTGTAGACTACCTTACCTCAATTCTGTCTGTCGACTTTGACCGTAGAAATATTCTTACTCT
64 GACCCTG-AGACTGCCTTACCTCAATTCTG-CTGTCGGCTTTGACCATGGAAAT-TTCTTAC-CT
*
28045 CAGTCTGCCTGTTAGCTTTGACCCTGGAGACTGCCTCA
125 CAGTCTGCCTGTTGGCTTTGACCCTGGAGACTGCCTCA
* * * *
28083 CCTCAAGTCTGCCTGTTGATTTTGACCTTAGAGACTTTCTTACCCTAAGTCTGCCTATCGACTTT
1 CCTCAAGTCTGCCT-TTGACTTTGACC-TAGAGACTTTCTTACCTTCAGTCTGCCTATCAACTTT
* * * *
28148 GACCCTAGAGACTGCTTTACCTCAAATCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTTACCCT
64 GACCCT-GAGACTGCCTTACCTCAATTCTG-CTGTCGGCTTTGACCATGGA-AATTTCTTA-CCT
* *
28213 CAGTCTGGCTGTTGGCTTTGACCTTGGAGACTGCCTCA
125 CAGTCTGCCTGTTGGCTTTGACCCTGGAGACTGCCTCA
* * * * * *
28251 TCTTAAGTCTGCCTATCAGCTTTGATCCTAGAAACTTTCTTACCTTCAGTCTGCCTATCAGCTTT
1 CCTCAAGTCTGCCTTTGA-CTTTGA-CCTAGAGACTTTCTTACCTTCAGTCTGCCTATCAACTTT
* * * * * *
28316 GACCTTGGAGATTGCCTGACCTCAAATT-TGCTTGTCGGCTTTGACTATGGAGATTTCCTACCTC
64 GACCCT-GAGACTGCCTTACCTC-AATTCTGC-TGTCGGCTTTGACCATGGAAATTTCTTACCTC
*
28380 AAGTCTGCCTGTTGGCTTTGACCCTAGAGACT
126 -AGTCTGCCTGTTGGCTTTGACCCTGGAGACT
28412 TTTTCACCTT
Statistics
Matches: 275, Mismatches: 45, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
166 4 0.01
167 39 0.14
168 223 0.81
169 9 0.03
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (162 bp):
CCTCAAGTCTGCCTTTGACTTTGACCTAGAGACTTTCTTACCTTCAGTCTGCCTATCAACTTTGA
CCCTGAGACTGCCTTACCTCAATTCTGCTGTCGGCTTTGACCATGGAAATTTCTTACCTCAGTCT
GCCTGTTGGCTTTGACCCTGGAGACTGCCTCA
Found at i:29015 original size:11 final size:11
Alignment explanation
Indices: 28986--29039 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
28976 ATTTAACATG
28986 AATAATAAAA-
1 AATAATAAAAT
*
28996 AACAATAAAAT
1 AATAATAAAAT
29007 AATAATAAAAATAT
1 AATAAT--AAA-AT
29021 AATAATAAAAT
1 AATAATAAAAT
*
29032 AGTAATAA
1 AATAATAA
29040 TTTATTAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.24
11 14 0.38
12 3 0.08
13 3 0.08
14 8 0.22
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:29024 original size:14 final size:13
Alignment explanation
Indices: 29005--29040 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
28995 AAACAATAAA
29005 ATAATAATAAAAAT
1 ATAATAAT-AAAAT
29019 ATAATAATAAAAT
1 ATAATAATAAAAT
29032 AGTAATAAT
1 A-TAATAAT
29041 TTATTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
ATAATAATAAAAT
Found at i:29517 original size:28 final size:28
Alignment explanation
Indices: 29458--29533 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 28
29448 AAGTAACAGT
* *
29458 AGCTGCAATAAGGAG-AGAAATCGATGC
1 AGCTGCAATGAGGAGAAGAAACCGATGC
29485 AGCTGCAATGAGGAGAAGAAACCGATGC
1 AGCTGCAATGAGGAGAAGAAACCGATGC
* *
29513 TGCTGCAATGAAGAGAAGAAA
1 AGCTGCAATGAGGAGAAGAAA
29534 TGGCAACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 14 0.32
28 30 0.68
ACGTcount: A:0.42, C:0.14, G:0.30, T:0.13
Consensus pattern (28 bp):
AGCTGCAATGAGGAGAAGAAACCGATGC
Found at i:29709 original size:20 final size:20
Alignment explanation
Indices: 29684--29721 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29674 CGAAATTAAA
*
29684 GCTGCAATTAAAAAGAAATG
1 GCTGCAAATAAAAAGAAATG
*
29704 GCTGCAAATGAAAAGAAA
1 GCTGCAAATAAAAAGAAA
29722 AAGCAGCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (20 bp):
GCTGCAAATAAAAAGAAATG
Found at i:31353 original size:19 final size:18
Alignment explanation
Indices: 31310--31352 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31300 AGACTTAATG
31310 AAAAAAATAATATAAAAC
1 AAAAAAATAATATAAAAC
*
31328 TAAAAAATAA-AGTAAAAC
1 AAAAAAATAATA-TAAAAC
31346 AAAAAAA
1 AAAAAAA
31353 AATTACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (18 bp):
AAAAAAATAATATAAAAC
Found at i:31443 original size:5 final size:5
Alignment explanation
Indices: 31435--31521 Score: 76
Period size: 5 Copynumber: 17.2 Consensus size: 5
31425 AATAAATCAA
*
31435 ATATT ATATGT -TATAT ATATT ATATT ATATT ATATT ATA-T ATATT CCCTA-T
1 ATATT ATAT-T ATAT-T ATATT ATATT ATATT ATATT ATATT ATATT --ATATT
31486 ATA-T ATTATT ATATT ATATT ATA-T ATTATT ATATT A
1 ATATT A-TATT ATATT ATATT ATATT A-TATT ATATT A
31522 ATATATATAG
Statistics
Matches: 70, Mismatches: 3, Indels: 18
0.77 0.03 0.20
Matches are distributed among these distances:
4 10 0.14
5 49 0.70
6 9 0.13
7 2 0.03
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:31453 original size:2 final size:2
Alignment explanation
Indices: 31446--31599 Score: 87
Period size: 2 Copynumber: 87.0 Consensus size: 2
31436 TATTATATGT
* **
31446 TA TA TA TA T- TA TA T- TA TA T- TA TA T- TA TA TA TA T- TC CC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31483 TA TA TA TA T- TA T- TA TA T- TA TA T- TA TA TA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * * *
31519 T- TA -A TA TA TA TA GC TG TT TA TA TA TA TT TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
31557 TA TA -A TA TA TA TA -A TA TA TA -A CA TA -A TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31594 TA TA TA
1 TA TA TA
31600 AAAAAAACAT
Statistics
Matches: 120, Mismatches: 12, Indels: 40
0.70 0.07 0.23
Matches are distributed among these distances:
1 20 0.17
2 100 0.83
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31527 original size:40 final size:39
Alignment explanation
Indices: 31446--31569 Score: 132
Period size: 40 Copynumber: 3.2 Consensus size: 39
31436 TATTATATGT
**
31446 TATATA-TATTATATTATA-TTATATTATATATATTCCCTA
1 TATATATTATTATATTATATTTATATTAT-TATATT-AATA
31485 TATATATTATTATATTATATTATATATTATTATATTAATA
1 TATATATTATTATATTATATT-TATATTATTATATTAATA
*
31525 TATATAGCTGT-TTATA-TATATTTATATTAATATA-TAATA
1 TATATA--T-TATTATATTATATTTATATTATTATATTAATA
31564 TATATA
1 TATATA
31570 ATATATAACA
Statistics
Matches: 76, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
39 17 0.22
40 31 0.41
41 13 0.17
42 14 0.18
43 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (39 bp):
TATATATTATTATATTATATTTATATTATTATATTAATA
Found at i:31574 original size:30 final size:31
Alignment explanation
Indices: 31447--31599 Score: 104
Period size: 32 Copynumber: 4.9 Consensus size: 31
31437 ATTATATGTT
*
31447 ATATATATTATATT-ATATTATATTATATATA
1 ATATATATTATATTAATA-TATAATATATATA
* * * *
31478 TTCCCTATA-TATATTATTATATTATAT-TAT-
1 AT--ATATATTATATTAATATATAATATATATA
* *
31508 ATAT-TATTATATTAATATAT-ATAGCTGT-TT
1 ATATATATTATATTAATATATAATA--TATATA
31538 ATATATATTTATATTAATATATAATATATATA
1 ATATATA-TTATATTAATATATAATATATATA
** *
31570 ATATATAACATAATATATATATAATATATA
1 ATATATATTATATTA-ATATATAATATATA
31600 AAAAAAACAT
Statistics
Matches: 96, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
27 5 0.05
28 13 0.14
29 2 0.02
30 6 0.06
31 13 0.14
32 48 0.50
33 9 0.09
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (31 bp):
ATATATATTATATTAATATATAATATATATA
Found at i:31596 original size:7 final size:7
Alignment explanation
Indices: 31547--31600 Score: 54
Period size: 7 Copynumber: 7.0 Consensus size: 7
31537 TATATATATT
31547 TATATTAA
1 TATA-TAA
31555 TATATAATA
1 TATAT-A-A
31564 TATATAA
1 TATATAA
31571 TATATAA
1 TATATAA
*
31578 CATAATATA
1 TAT-ATA-A
31587 TATATAA
1 TATATAA
31594 TATATAA
1 TATATAA
31601 AAAAAACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 19 0.47
8 12 0.30
9 9 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (7 bp):
TATATAA
Found at i:31841 original size:12 final size:12
Alignment explanation
Indices: 31786--31844 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
31776 AAAAAATTAT
*
31786 AATATTCATATA
1 AATATTTATATA
*
31798 AA-A-TTATCAAA
1 AATATTTAT-ATA
31809 AATATTTATAT-
1 AATATTTATATA
*
31820 AATAAATTATATA
1 AAT-ATTTATATA
31833 AATATTTATATA
1 AATATTTATATA
31845 TAATCTATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
10 3 0.08
11 8 0.22
12 19 0.51
13 7 0.19
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATTTATATA
Found at i:31848 original size:26 final size:25
Alignment explanation
Indices: 31786--31844 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 25
31776 AAAAAATTAT
*
31786 AATATTCATAT-A-AAATTATCAAA
1 AATATTTATATAATAAATTATCAAA
*
31809 AATATTTATATAATAAATTAT-ATA
1 AATATTTATATAATAAATTATCAAA
31833 AATATTTATATA
1 AATATTTATATA
31845 TAATCTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 10 0.31
24 15 0.47
25 7 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATTTATATAATAAATTATCAAA
Found at i:31853 original size:23 final size:22
Alignment explanation
Indices: 31786--31855 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
31776 AAAAAATTAT
* *
31786 AATATTCATATAAAATTATCAAA
1 AATATTTATATATAATTAT-AAA
*
31809 AATATTTATATAATAAATTATATA
1 AATATTTATAT-AT-AATTATAAA
31833 AATATTTATATATAATCTATAAA
1 AATATTTATATATAAT-TATAAA
31856 TAAAAAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 3 0.08
23 17 0.43
24 14 0.35
25 6 0.15
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
AATATTTATATATAATTATAAA
Found at i:32961 original size:14 final size:14
Alignment explanation
Indices: 32937--32986 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
32927 ATAATTTTTT
32937 TAAATAATTCATAAA
1 TAAA-AATTCATAAA
32952 TAAAAATTCATAAA
1 TAAAAATTCATAAA
* *
32966 TGAAAATTTA-AAA
1 TAAAAATTCATAAA
32979 TAATAAAT
1 TAA-AAAT
32987 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 5 0.16
14 22 0.71
15 4 0.13
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (14 bp):
TAAAAATTCATAAA
Found at i:33962 original size:19 final size:19
Alignment explanation
Indices: 33927--33964 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
33917 TCTTCTCATG
*
33927 GTTATAAATTTTGTTAATA
1 GTTATAAATTTTATTAATA
33946 GTTATATAA-TTTATTAATA
1 GTTATA-AATTTTATTAATA
33965 AAATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
GTTATAAATTTTATTAATA
Found at i:34130 original size:22 final size:23
Alignment explanation
Indices: 34102--34169 Score: 68
Period size: 22 Copynumber: 2.9 Consensus size: 23
34092 AATTCGAATC
**
34102 ATTTAATTTAATTTAAAT-TATT
1 ATTTAATTTAATAAAAATATATT
*
34124 ATTTAA-TTAATAAAAATATTTT
1 ATTTAATTTAATAAAAATATATT
34146 ATTTAAATTTAATATATAAATATA
1 ATTT-AATTTAATA-A-AAATATA
34170 ATATAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 9 0.24
22 13 0.35
23 2 0.05
24 6 0.16
25 1 0.03
26 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTAATTTAATAAAAATATATT
Found at i:36093 original size:13 final size:13
Alignment explanation
Indices: 36075--36099 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36065 ATTACTCAAA
36075 TGTATCGATACAT
1 TGTATCGATACAT
36088 TGTATCGATACA
1 TGTATCGATACA
36100 CTGATCTTTG
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:36152 original size:52 final size:52
Alignment explanation
Indices: 36108--36233 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
36098 CACTGATCTT
36108 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
36160 TGTATCGATACATACAGACAAATTTGCTCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
36212 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
36234 ATTTTATATT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:43986 original size:32 final size:32
Alignment explanation
Indices: 43948--44011 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
43938 ATTTGTATGA
*
43948 GATATAGATGATCATTAGAACTGATTAATTAT
1 GATATAGATGATCATTAGAACTAATTAATTAT
*
43980 GATATAGATGATCATTAGAAGTAATTAATTAT
1 GATATAGATGATCATTAGAACTAATTAATTAT
44012 ACCATACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.38
Consensus pattern (32 bp):
GATATAGATGATCATTAGAACTAATTAATTAT
Found at i:50292 original size:33 final size:34
Alignment explanation
Indices: 50228--50294 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
50218 ATCAATCTAT
50228 TATTATTTTATATATTTTTTATTTTTAAGAGATA
1 TATTATTTTATATATTTTTTATTTTTAAGAGATA
50262 TATTATTATTATATA-TTTTTATTTTT-AGAGATA
1 TATTATT-TTATATATTTTTTATTTTTAAGAGATA
50295 AAGTTATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
33 7 0.22
34 18 0.56
35 7 0.22
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (34 bp):
TATTATTTTATATATTTTTTATTTTTAAGAGATA
Found at i:50302 original size:34 final size:34
Alignment explanation
Indices: 50229--50302 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
50219 TCAATCTATT
*
50229 ATTATTTTATATATTTTTTATTTTTAAGAGATAT
1 ATTATTTTATATATTTTTTATTTTTAAGAGATAA
50263 ATTATTATTATATA-TTTTTATTTTT-AGAGATAA
1 ATTATT-TTATATATTTTTTATTTTTAAGAGATAA
50296 AGTTATT
1 A-TTATT
50303 GATGTAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
33 8 0.22
34 22 0.59
35 7 0.19
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (34 bp):
ATTATTTTATATATTTTTTATTTTTAAGAGATAA
Found at i:51407 original size:14 final size:15
Alignment explanation
Indices: 51390--51422 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
51380 ATTTAAATTT
51390 TTATTTGAT-TTTAA
1 TTATTTGATATTTAA
51404 TTATTTGATATTTAA
1 TTATTTGATATTTAA
51419 TTAT
1 TTAT
51423 AATTTTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (15 bp):
TTATTTGATATTTAA
Found at i:51584 original size:9 final size:9
Alignment explanation
Indices: 51570--51605 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
51560 TTATATCTCA
51570 TTAAAAATT
1 TTAAAAATT
*
51579 TTAAAAATA
1 TTAAAAATT
*
51588 TAAAAAATT
1 TTAAAAATT
51597 TTAAAAATT
1 TTAAAAATT
51606 AAAATATCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (9 bp):
TTAAAAATT
Found at i:51595 original size:18 final size:17
Alignment explanation
Indices: 51572--51609 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
51562 ATATCTCATT
51572 AAAAATTTTAAAAATATA
1 AAAAATTTTAAAAAT-TA
51590 AAAAATTTTAAAAATTA
1 AAAAATTTTAAAAATTA
51607 AAA
1 AAA
51610 TATCTTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAAATTTTAAAAATTA
Found at i:52247 original size:14 final size:15
Alignment explanation
Indices: 52228--52260 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
52218 ATTTTGATTT
52228 TTATTTGAT-TTTAA
1 TTATTTGATATTTAA
*
52242 TTATTTGGTATTTAA
1 TTATTTGATATTTAA
52257 TTAT
1 TTAT
52261 AATTCCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (15 bp):
TTATTTGATATTTAA
Found at i:52273 original size:838 final size:840
Alignment explanation
Indices: 49949--52357 Score: 3440
Period size: 829 Copynumber: 2.9 Consensus size: 840
49939 AACAAATCAT
49949 TTGAAAAGAGGACAATGGCCATAACAACTCTAAGAAAAGTAGAAAAGTGGTACTTTCATTGATGC
1 TTGAAAAGAGGACAATGGCCATAACAACTCTAAGAAAAGTAGAAAAGTGGTACTTTCATTGATGC
50014 TGACTTTTTTGCATTGAAAGCATCAGCCACGTTGATTCTTCTAACGTGGACCCAAAAAAAAAATG
66 TGACTTTTTTGCATTGAAAGCATCAGCCACGTTGATTCTTCTAACGTGGACCCAAAAAAAAAATG
* *
50079 TTATGTAGGCAAAAATAGCAATATTTAAAAAATAGTTTAAAAAAATAGTATTTGAGCAATTTGTT
131 TCATGTAGGCAAAAATAGCAATATTTGAAAAATAGTTTAAAAAAATAGTATTTGAGCAATTTGTT
*
50144 TGTGAATTGGTGTTGCAATATGGTCTGGATATGAATCCAGACCAGCAACTTAAAAGGTCTATATT
196 TGTGGATTGGTGTTGCAATATGGTCTGGATATGAATCCAGACCAGCAACTTAAAAGG-C-ATA-T
* *
50209 ATTATATTTATCAATCTATTATTATTTTATATATTTTTTATTTTTAAGAGATATATTATTATTAT
258 ATTATATTTATCGATTTATTATTATTTTATATATTTTTTATTTTTAAGAGATATA-TATTATTAT
* *
50274 ATATTTTTATTTTTAGAGATAAAGTTATTGATGTAAATTACTTATTCGATTTAATTTTATTTGGA
322 ATATTTTTATTTTTAGAGATAAA-TTATTGATATAAATTACTTATTCGATTTAATTTTATTTGAA
* * * ** *
50339 GTCATCA-CTTATTTATTTCGATTAAATAAGATTAATCACATGTCAAAATTAATATTTTAAAGAT
386 GTCATCATC-AATTTATTTTGATCAAATAAGATTGGTCACATGTCGAAATTAATATTTTAAAGAT
* * *
50403 TACGAAA-CTCAAAAAATAAATTTTAATATCTGTAATAATATTAGAGATCACATGAAAATGTTTA
450 TACGAAATCT-AAAAAATAAATTTTGATATCTGTAATAATATTAGAGATTACAT-AAAAAGTTT-
50467 AAAATCAGTTACAATTATGAGTGACGATCGATCCCTTTCATGATATCTGAAAATCGATATTTTAT
512 AAAATC-GTTACAATTATGAGTGACGATCGATCCCTTTCATGATATCTGAAAATCGATATTTTAT
*
50532 TAATTATGTTTTAATTTAAATTTTGATTTTTATTTGATTTTAATTATTTAGTATTTAATTATAAT
576 TAATTATGTTTTAATTTAAATTTTGATTTTTATTTGATTTTAATTATTTGGTATTTAATTATAAT
*
50597 TTCATGCATTAAAAATAATATTTTAAATTTATTATTTTGTATAAAAAATTTAATTTTTAATATTT
641 TTCATGCATTAAAAATAATATTTTAAATTTATTATTTTGTATAAAAAATTAAATTTTTAATATTT
* *
50662 TTAAAAATTAAAATATCTTACGTACCTATCTAAAAAATAAAAAAAAATGTAAAAATTTTTTACCA
706 TTAAAAATTAAAATATCTTACGTACCTAACTAAAAAATAAAAAAAAATATAAAAATTTTTTACCA
50727 TTTTTTTATACCTCACTAAAAAATAAAAAAATATAAAAAATTTTAAAAATTAAAATATCTTTTAA
771 TTTTTTTATACCTCACTAAAAAATAAAAAAATATAAAAAATTTTAAAAATTAAAATATCTTTT--
*
50792 ACAAATAT
834 AC-AATAC
*
50800 TTAAAAAGAGGACAATGGCCATAACAACTCTAAGAAAAGTAGAAAAGTGGTACTTTCATTGATGC
1 TTGAAAAGAGGACAATGGCCATAACAACTCTAAGAAAAGTAGAAAAGTGGTACTTTCATTGATGC
* *
50865 TGACTTTTTTGCATTGGAAGCATCAGCCACGTTGATTCTTCTAACGTGGACCC--AAAAAGAATG
66 TGACTTTTTTGCATTGAAAGCATCAGCCACGTTGATTCTTCTAACGTGGACCCAAAAAAAAAATG
* **
50928 TCATGTAGGCAAAAATAGCAATATTTGAAAAATAGTTTAAAAAAACAGTATCCGAGCAATTTGTT
131 TCATGTAGGCAAAAATAGCAATATTTGAAAAATAGTTTAAAAAAATAGTATTTGAGCAATTTGTT
* * * *
50993 TGTGGATTGGTGTTGCAATATGGTCTGGATATGTATCCAGACCAGTCAACCTAGAA-GCTTATAT
196 TGTGGATTGGTGTTGCAATATGGTCTGGATATGAATCCAGACCAG-CAACTTAAAAGGCATATAT
*
51057 TATATTTATCGATTTATTATTATTTTATATATTTTTTTATTTTTAAGAGATATATAATTGTTATA
260 TATATTTATCGATTTATTATTATTTTATATA-TTTTTTATTTTTAAGAGATATAT-ATTATTATA
* * *
51122 TATTTTTATTTTTAGAGATAAAATTATTGATATAAATTACTTATTCAATTTAATTTTTTTTGAAA
323 TATTTTTATTTTTAGAGAT-AAATTATTGATATAAATTACTTATTCGATTTAATTTTATTTGAAG
* * *
51187 TCATCATCAATCTATTTTGATCAAGTAAGATTGGTCACATATCGAAATTAATATTTTAAAGATTA
387 TCATCATCAATTTATTTTGATCAAATAAGATTGGTCACATGTCGAAATTAATATTTTAAAGATTA
*
51252 CGAAATCTAAAAAATAAATTTTGATATCTGTAATAATATT-----TT---TAAAAA---T-CAA-
452 CGAAATCTAAAAAATAAATTTTGATATCTGTAATAATATTAGAGATTACATAAAAAGTTTAAAAT
* * * *
51304 --TTACAATTATGAGTGACGATCAATTCCTTTTATAATATCTGAAAATCGATATTTTATTAATTA
517 CGTTACAATTATGAGTGACGATCGATCCCTTTCATGATATCTGAAAATCGATATTTTATTAATTA
* ** * *
51367 TATTTTAATTTAAATTTAAATTTTTATTTGATTTTAATTATTTGATATTTAATTATAATTTTATG
582 TGTTTTAATTTAAATTTTGATTTTTATTTGATTTTAATTATTTGGTATTTAATTATAATTTCATG
*
51432 CATTAAAAATAATATTTTAAATTTATTATTTTATATAAAAAATTAAATTTTTAATATTTTTAAAA
647 CATTAAAAATAATATTTTAAATTTATTATTTTGTATAAAAAATTAAATTTTTAATATTTTTAAAA
* * * **
51497 ATTAAAATATCTTATGTACCTAACTAAAAGAT-TAAAAAAATATAAAAATTTTTTATTATTTTTT
712 ATTAAAATATCTTACGTACCTAACTAAAAAATAAAAAAAAATATAAAAATTTTTTACCATTTTTT
* * * **
51561 TATATCTCATTAAAAATTTTAAAAATATAAAAAATTTTAAAAATTAAAATATC-TTT-C-ATAC
777 TATACCTCACTAAAAAATAAAAAAATATAAAAAATTTTAAAAATTAAAATATCTTTTACAATAC
* * * *
51622 TTGAAAAGAGGACAATGACCATAA-TACTCTAAGAAAAGTAAAAAAGTGGTACTTTCATTAATGC
1 TTGAAAAGAGGACAATGGCCATAACAACTCTAAGAAAAGTAGAAAAGTGGTACTTTCATTGATGC
* * ** *
51686 TGACATTTTTGTAACGAAAGCATCAGCCACGTTGATTCTTCCAACGTGGACCCCAAAAAAAAAAA
66 TGACTTTTTTGCATTGAAAGCATCAGCCACGTTGATTCTTCTAACGTGGA-CCC--AAAAAAAAA
* * *
51751 AAGTCATGTAGGCAAAAATAGTAATATTTGAAAAATAGTTTAAAAAAATAGTATTTGAGTAATTT
128 ATGTCATGTAGGCAAAAATAGCAATATTTGAAAAATAGTTTAAAAAAATAGTATTTGAGCAATTT
* ** * *
51816 ATTTGTGGATTGGTGTTGCAATATGGTCCAGATATAAATCTAGACCAGCCAACTTAAAAGGCATA
193 GTTTGTGGATTGGTGTTGCAATATGGTCTGGATATGAATCCAGACCAG-CAACTTAAAAGGCATA
*
51881 TA-T-TATTTATCGATTTATTATTATTTTATATA-TTTTTATTTTTAA-A-AGATATATTATTAT
257 TATTATATTTATCGATTTATTATTATTTTATATATTTTTTATTTTTAAGAGATATATATTATTAT
* * * * *
51941 ATATGTTCATTTTTTGAGATAGAATTATTGATATGAATTA-TTCATTCGACTTAATTTTATTTGA
322 ATATTTTTATTTTTAGAGATA-AATTATTGATATAAATTACTT-ATTCGATTTAATTTTATTTGA
* * * * *
52005 AGTTACCATCAATTTATTTTGATCAAATGAGATTGGTCACATGTCGAAATTAATATTTCAAAAAT
385 AGTCATCATCAATTTATTTTGATCAAATAAGATTGGTCACATGTCGAAATTAATATTTTAAAGAT
*
52070 TACGAAATCTAAAAAATAAATTTTGATATCTGCAATAATATTAGAGATTACATAAAAAAGTTTGA
450 TACGAAATCTAAAAAATAAATTTTGATATCTGTAATAATATTAGAGATTACAT-AAAAAGTTT-A
** * * *
52135 AAATCGGTTACAATTATGAGTGACGATCGATCCCTCACATGATGTCCGAAAATCGATATCTTATT
513 AAATC-GTTACAATTATGAGTGACGATCGATCCCTTTCATGATATCTGAAAATCGATATTTTATT
*
52200 AATTATGTTTTAACTTAAATTTTGATTTTTATTTGATTTTAATTATTTGGTATTTAATTATAATT
577 AATTATGTTTTAATTTAAATTTTGATTTTTATTTGATTTTAATTATTTGGTATTTAATTATAATT
* * ** * * *
52265 CCATGCATTAAAAATAATATTCTAAATTTATTATTCCGCATGAAAAACTTAGATTTTTAATATTT
642 TCATGCATTAAAAATAATATTTTAAATTTATTATTTTGTAT-AAAAAATTAAATTTTTAATATTT
*
52330 TTAAAAATTAAAATATCTTACATACCTA
706 TTAAAAATTAAAATATCTTACGTACCTA
52358 TCTAGAAGAC
Statistics
Matches: 1393, Mismatches: 132, Indels: 78
0.87 0.08 0.05
Matches are distributed among these distances:
819 3 0.00
820 156 0.11
821 86 0.06
822 29 0.02
823 13 0.01
824 1 0.00
825 31 0.02
826 116 0.08
827 9 0.01
828 77 0.06
829 215 0.15
832 1 0.00
833 2 0.00
834 2 0.00
835 1 0.00
838 147 0.11
839 48 0.03
842 1 0.00
846 33 0.02
847 178 0.13
848 7 0.01
849 113 0.08
850 8 0.01
851 116 0.08
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (840 bp):
TTGAAAAGAGGACAATGGCCATAACAACTCTAAGAAAAGTAGAAAAGTGGTACTTTCATTGATGC
TGACTTTTTTGCATTGAAAGCATCAGCCACGTTGATTCTTCTAACGTGGACCCAAAAAAAAAATG
TCATGTAGGCAAAAATAGCAATATTTGAAAAATAGTTTAAAAAAATAGTATTTGAGCAATTTGTT
TGTGGATTGGTGTTGCAATATGGTCTGGATATGAATCCAGACCAGCAACTTAAAAGGCATATATT
ATATTTATCGATTTATTATTATTTTATATATTTTTTATTTTTAAGAGATATATATTATTATATAT
TTTTATTTTTAGAGATAAATTATTGATATAAATTACTTATTCGATTTAATTTTATTTGAAGTCAT
CATCAATTTATTTTGATCAAATAAGATTGGTCACATGTCGAAATTAATATTTTAAAGATTACGAA
ATCTAAAAAATAAATTTTGATATCTGTAATAATATTAGAGATTACATAAAAAGTTTAAAATCGTT
ACAATTATGAGTGACGATCGATCCCTTTCATGATATCTGAAAATCGATATTTTATTAATTATGTT
TTAATTTAAATTTTGATTTTTATTTGATTTTAATTATTTGGTATTTAATTATAATTTCATGCATT
AAAAATAATATTTTAAATTTATTATTTTGTATAAAAAATTAAATTTTTAATATTTTTAAAAATTA
AAATATCTTACGTACCTAACTAAAAAATAAAAAAAAATATAAAAATTTTTTACCATTTTTTTATA
CCTCACTAAAAAATAAAAAAATATAAAAAATTTTAAAAATTAAAATATCTTTTACAATAC
Found at i:53629 original size:167 final size:167
Alignment explanation
Indices: 53431--53838 Score: 457
Period size: 169 Copynumber: 2.4 Consensus size: 167
53421 ATGGGTTTAA
* *
53431 AATTTTAAAAATTCATCAGATATATTTATTTAATTCATATTAAATCCGTTTTCAAAAATTCATT-
1 AATTTTTAAAATTCATCA-ATAT-TTTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTC
* ** * *
53495 TTTGTTCACAAAAT-TTTC-ATTTTTTTCCTTAAAATTTTCC-TATTTAAAAAATACGGAGTTTT
64 ATT-TTCA-AAAATATTTCAATTTTTTTCCTTAAAATTCCCCTTATTTAAAAAACACGAAGTTTT
* * * *
53557 CTACTCCGTAAATATTTTTTA-GGGGATTTTTCTTGGTTTTT
127 CTACTACGTAAAT-GTTTTTAGGGGGATTTTTATTGGTTCTT
* * * *
53598 AATTTTTAAAATTTATGCAATATTCTTATTTAATTTAAATTAAATCAGTTTTTAAAAATTCATTC
1 AATTTTTAAAATTCAT-CAATATT-TTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTC
* * ***
53663 ATTTTCATAAATATTTCAATTTTTTTCCTTGAAATTCCCCTTATTTCCGAAACACGAAGTTTTCT
64 ATTTTCAAAAATATTTCAATTTTTTTCCTTAAAATTCCCCTTATTTAAAAAACACGAAGTTTTCT
53728 ACTACGTAAATGTTTTTAGGGGGATTTTTATTGGTTCTT
129 ACTACGTAAATGTTTTTAGGGGGATTTTTATTGGTTCTT
* * * * * * *
53767 GATTTTTAAAACTCATCAAATATTTTAGTTTGATTCATATTAAATTAGTTTTAAAAAAATAATTC
1 AATTTTTAAAATTCATC-AATATTTTA-TTTAATTCATATTAAATCAGTTTTCAAAAATTCATTC
53832 ATTTTCA
64 ATTTTCA
53839 TAAGTTTTGG
Statistics
Matches: 202, Mismatches: 30, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
166 5 0.02
167 61 0.30
168 33 0.16
169 103 0.51
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.48
Consensus pattern (167 bp):
AATTTTTAAAATTCATCAATATTTTATTTAATTCATATTAAATCAGTTTTCAAAAATTCATTCAT
TTTCAAAAATATTTCAATTTTTTTCCTTAAAATTCCCCTTATTTAAAAAACACGAAGTTTTCTAC
TACGTAAATGTTTTTAGGGGGATTTTTATTGGTTCTT
Found at i:54546 original size:12 final size:14
Alignment explanation
Indices: 54504--54549 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 14
54494 AGGCTCAGTT
54504 GAAA-AAAAAGAGA
1 GAAAGAAAAAGAGA
54517 GAAA-AAAAAGAGA
1 GAAAGAAAAAGAGA
54530 GAAAGAAAAA-A-A
1 GAAAGAAAAAGAGA
54542 GAAAGAAA
1 GAAAGAAA
54550 TAGGGTGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.28
13 18 0.56
14 5 0.16
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
GAAAGAAAAAGAGA
Found at i:55775 original size:13 final size:13
Alignment explanation
Indices: 55757--55787 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
55747 ACATTTCTTC
55757 ATGTATCGATACA
1 ATGTATCGATACA
55770 ATGTATCGATACA
1 ATGTATCGATACA
*
55783 TTGTA
1 ATGTA
55788 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:55775 original size:33 final size:33
Alignment explanation
Indices: 55737--55803 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
55727 GTTACAAGCT
55737 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
55770 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
55803 A
1 A
55804 ATAGTGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:55876 original size:19 final size:20
Alignment explanation
Indices: 55832--55887 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
55822 CTGCCAGTTT
* **
55832 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATGGAA
55852 CATGTATCGATACAA-GGAA
1 CATGTATCGATACAATGGAA
55871 CATGTATCGATACAATG
1 CATGTATCGATACAATG
55888 TATCGATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (20 bp):
CATGTATCGATACAATGGAA
Found at i:55890 original size:13 final size:13
Alignment explanation
Indices: 55872--55898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55862 TACAAGGAAC
55872 ATGTATCGATACA
1 ATGTATCGATACA
55885 ATGTATCGATACA
1 ATGTATCGATACA
55898 A
1 A
55899 AGCAGCATGT
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):
ATGTATCGATACA
Found at i:55913 original size:33 final size:32
Alignment explanation
Indices: 55853--55917 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 32
55843 ACAATTGTCC
*
55853 ATGTATCGATACAAGGAACATGTATCGATACA
1 ATGTATCGATACAAGCAACATGTATCGATACA
*
55885 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATAC-AAGCAACATGTATCGATACA
55918 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (32 bp):
ATGTATCGATACAAGCAACATGTATCGATACA
Found at i:56842 original size:19 final size:20
Alignment explanation
Indices: 56808--56855 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
56798 ACATTTTGAA
*
56808 AAATAAATCGAAATAAAATT
1 AAATAAATCGAAATAAAAAT
*
56828 AAATAAAT-TAAATAAAAAT
1 AAATAAATCGAAATAAAAAT
*
56847 GAATAAATC
1 AAATAAATC
56856 CTAATTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AAATAAATCGAAATAAAAAT
Found at i:57243 original size:28 final size:28
Alignment explanation
Indices: 57203--57260 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
57193 CCTTCACGTA
57203 TTCAAATCCCTTAGGGGTATC-GAGTACT
1 TTCAAATCCCTTAGGGGTATCAG-GTACT
57231 TTCAAATCCCTTAGGGGTATCAGGTACT
1 TTCAAATCCCTTAGGGGTATCAGGTACT
57259 TT
1 TT
57261 TACATCGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (28 bp):
TTCAAATCCCTTAGGGGTATCAGGTACT
Found at i:57574 original size:156 final size:153
Alignment explanation
Indices: 57289--57856 Score: 596
Period size: 155 Copynumber: 3.7 Consensus size: 153
57279 TAGGAGTATG
* * * *
57289 TTCATAATTTCTTA-AAACTGAGTCCTAGGTTGTCACAGGGT-TGCTTTTATGCTGAAGGT-AGA
1 TTCATAATTTTTTAGAACCT-AGTCCTAGGTTATCAC-TGGTCTGCTTTTATGCTGAAGGTGAG-
* * * *
57351 TATTTAGGATAAGTTCATCCAT-TTTAATATCCTTTTTAAGTTTTTTAGGGTTACT-GGATACTT
63 TATTTAGGATAGGTTCATCCATCTCT-A-AT-CTTTTTAAGTCTTTTAGGGTTATTGGGATACTT
57414 TCATGTCGTAGGAATACCTATAAGGGCATT
125 TCATGTCG-AGGAATACCTATAAGGGCATT
*
57444 TTCATAATTTTTTAGAACCTAGTCCTAGGTTATCATTGAGTCTGCTTTTATGCTGAAGGTGAGTA
1 TTCATAATTTTTTAGAACCTAGTCCTAGGTTATCACTG-GTCTGCTTTTATGCTGAAGGTGAGTA
* *
57509 TTTAGGATAGGTTGATCTCGTCTCTAATCTTTTTAAGTCTTTTAGGGTTATTGGGATACTTTCAT
65 TTTAGGATAGGTTCATC-CATCTCTAATCTTTTTAAGTCTTTTAGGGTTATTGGGATACTTTCAT
*
57574 GTCGAAGATATACCTAT-AGGGACATT
129 GTCGAGGA-ATACCTATAAGGG-CATT
* * * * *
57600 TTCATAATTTTTTAGAACCTAGTCCTAGGTTGTCAC-CGTGCTCGCTTTTATGTTGAAAGTG-GG
1 TTCATAATTTTTTAGAACCTAGTCCTAGGTTATCACTGGT-CT-GCTTTTATGCTGAAGGTGAGT
* * *
57663 ATTTAGGATAGGTTCATCCCATCTCTAATCTTTTTAAGTCCTTTAGGGTTATTGAGATATTTTCA
64 ATTTAGGATAGGTTCAT-CCATCTCTAATCTTTTTAAGTCTTTTAGGGTTATTGGGATACTTTCA
* * *
57728 TGTCGAAGGTATATCC-ACAAAGGCATT
128 TGTCG-AGGAATA-CCTATAAGGGCATT
* * * * ** * *
57755 TTCATAATTTTTTAGAATCGAGTCCTAAGTTATCATCTGTTCCACTTTTATGCCGAAGGTGGGTA
1 TTCATAATTTTTTAGAACCTAGTCCTAGGTTATCA-CTGGTCTGCTTTTATGCTGAAGGTGAGTA
* * * *
57820 TTTAGGATAGGTTTACCCCATCTATTATCTTTTTAAG
65 TTTAGGATAGGTTCA-TCCATCTCTAATCTTTTTAAG
57857 CCCTTTGGGA
Statistics
Matches: 351, Mismatches: 43, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
154 3 0.01
155 177 0.50
156 163 0.46
157 6 0.02
158 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (153 bp):
TTCATAATTTTTTAGAACCTAGTCCTAGGTTATCACTGGTCTGCTTTTATGCTGAAGGTGAGTAT
TTAGGATAGGTTCATCCATCTCTAATCTTTTTAAGTCTTTTAGGGTTATTGGGATACTTTCATGT
CGAGGAATACCTATAAGGGCATT
Found at i:57852 original size:311 final size:311
Alignment explanation
Indices: 57289--57856 Score: 727
Period size: 311 Copynumber: 1.8 Consensus size: 311
57279 TAGGAGTATG
* * * *
57289 TTCATAATTTCTTAAAACTGAGTCCTAGGTTGTCACAGGGTTGCTTTTATGCTGAAGGTAGATAT
1 TTCATAATTTCTTAAAACTGAGTCCTAGGTTGTCACAGGCTCGCTTTTATGCTGAAAGTAGAGAT
* **
57354 TTAGGATAAGTTCATCCATTTTAATATCCTTTTTAAGTTTTTTAGGGTTACTGGATACTTTCATG
66 TTAGGATAAGTTCATCCATTCTAATATCCTTTTTAAGTCCTTTAGGGTTACTGGATACTTTCATG
* * * * *
57419 TCGTAGGAATACCTATAAGGGCATTTTCATAATTTTTTAGAACCTAGTCCTAGGTTATCATTGAG
131 TCGAAGGAATACCTACAAAGGCATTTTCATAATTTTTTAGAACCGAGTCCTAAGTTATCATTGAG
** * * * * *
57484 TCTGCTTTTATGCTGAAGGTGAGTATTTAGGATAGGTTGATCTCGTCTCTAATCTTTTTAAGTCT
196 TCCACTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTGACCCCATCTATAATCTTTTTAAGTCT
57549 TTTAGGGTTATTGGGATACTTTCATGTCGAAGATATACCTATAGGGACATT
261 TTTAGGGTTATTGGGATACTTTCATGTCGAAGATATACCTATAGGGACATT
* * * * *
57600 TTCATAATTTTTTAGAACCT-AGTCCTAGGTTGTCACCGTGCTCGCTTTTATGTTGAAAGT-GGG
1 TTCATAATTTCTTA-AAACTGAGTCCTAGGTTGTCACAG-GCTCGCTTTTATGCTGAAAGTAGAG
* * *
57663 ATTTAGGATAGGTTCATCCCATCTCT-A-AT-CTTTTTAAGTCCTTTAGGGTTATTGAGATATTT
64 ATTTAGGATAAGTTCAT-CCAT-TCTAATATCCTTTTTAAGTCCTTTAGGGTTACTG-GATACTT
* *
57725 TCATGTCGAAGGTATATCC-ACAAAGGCATTTTCATAATTTTTTAGAATCGAGTCCTAAGTTATC
126 TCATGTCGAAGGAATA-CCTACAAAGGCATTTTCATAATTTTTTAGAACCGAGTCCTAAGTTATC
* * * *
57789 ATCTG-TTCCACTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTTACCCCATCTATTATCTTTT
190 AT-TGAGTCCACTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTGACCCCATCTATAATCTTTT
57853 TAAG
254 TAAG
57857 CCCTTTGGGA
Statistics
Matches: 217, Mismatches: 33, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
310 22 0.10
311 163 0.75
312 30 0.14
313 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (311 bp):
TTCATAATTTCTTAAAACTGAGTCCTAGGTTGTCACAGGCTCGCTTTTATGCTGAAAGTAGAGAT
TTAGGATAAGTTCATCCATTCTAATATCCTTTTTAAGTCCTTTAGGGTTACTGGATACTTTCATG
TCGAAGGAATACCTACAAAGGCATTTTCATAATTTTTTAGAACCGAGTCCTAAGTTATCATTGAG
TCCACTTTTATGCCGAAGGTGAGTATTTAGGATAGGTTGACCCCATCTATAATCTTTTTAAGTCT
TTTAGGGTTATTGGGATACTTTCATGTCGAAGATATACCTATAGGGACATT
Found at i:59799 original size:21 final size:21
Alignment explanation
Indices: 59773--59849 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
59763 TTTTTATCCA
59773 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
* *
59794 AATGTATCGATAAATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
59815 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
59836 AATGTATCGATACA
1 AATGTATCGATACA
59850 AGGTCCCAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:59932 original size:19 final size:18
Alignment explanation
Indices: 59881--59970 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
59871 TTGAATTCCA
59881 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
* *
59898 ATTCAGTAAATGTATCGATAC
1 A-TAAGT--TTGTATCGATAC
59919 ATAAGTGTTGTATCGATAC
1 ATAAGT-TTGTATCGATAC
59938 --AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
59951 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
59970 A
1 A
59971 ATGTATCGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
13 11 0.19
15 2 0.03
17 3 0.05
18 2 0.03
19 24 0.41
20 4 0.07
21 12 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:59945 original size:13 final size:13
Alignment explanation
Indices: 59927--59951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59917 ACATAAGTGT
59927 TGTATCGATACAA
1 TGTATCGATACAA
59940 TGTATCGATACA
1 TGTATCGATACA
59952 TAAGTTTTGT
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:59947 original size:32 final size:32
Alignment explanation
Indices: 59906--59978 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
59896 ACATTCAGTA
59906 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
59938 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
59970 AATGTATCG
1 AATGTATCG
59979 TTAGGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:60040 original size:13 final size:13
Alignment explanation
Indices: 60022--60047 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60012 CATTTTTCTG
60022 TGTATCGATACAT
1 TGTATCGATACAT
60035 TGTATCGATACAT
1 TGTATCGATACAT
60048 ATATTCTTTG
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:60065 original size:34 final size:33
Alignment explanation
Indices: 60002--60068 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
59992 GCCAAGGAAA
*
60002 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATTATTCTGTGTATCGATACAT
*
60035 TGTATCGATACATATATTCTTTGTATCGATACAT
1 TGTATCGATACAT-TATTCTGTGTATCGATACAT
60069 CTAGGAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATTCTGTGTATCGATACAT
Found at i:62481 original size:53 final size:53
Alignment explanation
Indices: 62400--62534 Score: 161
Period size: 53 Copynumber: 2.5 Consensus size: 53
62390 TTGAGTTTCT
* * *
62400 CAATTCTTCGCAATCGGGGATA-TCCCAACTCCGATTTTATTTTC-AAAA-CAC
1 CAATTTTTCACAATCGGGGATACT-CCAACTCCGATTTTATTTCCAAAAAGCAC
* *
62451 TAA-TTTTCTATAATCGGGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCAC
1 CAATTTTTC-ACAATC--GGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCAC
62506 CAATTTTTCACAATCGGGGATACTCCAAC
1 CAATTTTTCACAATCGGGGATACTCCAAC
62535 CCCGTTATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
50 4 0.06
51 6 0.09
53 40 0.57
54 5 0.07
55 10 0.14
56 5 0.07
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (53 bp):
CAATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAGCAC
Found at i:62615 original size:79 final size:79
Alignment explanation
Indices: 62469--62692 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 79
62459 TATAATCGGG
* * * * * *
62469 GGGATACTCCAACTCCGATTTTATTTCCAAAAAGCACCAATTTTTCACAATCGGGGATACTCCAA
1 GGGATACTCCAACCCCGCTTTCATTTCC-AAAA-CATCAATTTCTCATAATCGGGGATACTCCAA
*
62534 CCCCGTTATTTCCGAG
64 CCCCGTTATTTCCGAA
* * **
62550 GGGATACTCCAACCCCTGCTTT-A-TTCTTAAAATATTGATTTCTCATAATCGGGGATACTCCAA
1 GGGATACTCCAACCCC-GCTTTCATTTC-CAAAACATCAATTTCTCATAATCGGGGATACTCCAA
62613 CCCCGTTATTTCCGAA
64 CCCCGTTATTTCCGAA
* * * *
62629 GGGATACTCTAATCCCGGTTTCATTTCCAAAACATCAATTTCTCTTAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCGCTTTCATTTCCAAAACATCAATTTCTCATAATCGGGGATACTCCAAC
62693 TCTGATTTTA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
78 4 0.03
79 87 0.72
80 10 0.08
81 16 0.13
82 4 0.03
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCCGCTTTCATTTCCAAAACATCAATTTCTCATAATCGGGGATACTCCAACC
CCGTTATTTCCGAA
Found at i:62706 original size:51 final size:51
Alignment explanation
Indices: 62629--62787 Score: 162
Period size: 51 Copynumber: 3.1 Consensus size: 51
62619 TATTTCCGAA
* * * * *
62629 GGGATACTCTAA-TCCCGGTTTCATTTCCAAAACATCAA-TTTCTCTTAATCG
1 GGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTC-CATAATCG
* * *
62680 GGGATACTCCAACTCTGATTTTATTTCTAAAACACCCATTTTCCATAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAATCG
* * * *
62731 GGGATACTCCAACTCCGATTTTATTTTCAAAGCACCAACTTTT-CACAATCA
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAA-TTTTCCATAATCG
62782 GGGATA
1 GGGATA
62788 TTGCAACCCC
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
51 81 0.90
52 9 0.10
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCCATAATCG
Found at i:62904 original size:103 final size:106
Alignment explanation
Indices: 62778--63009 Score: 280
Period size: 103 Copynumber: 2.2 Consensus size: 106
62768 ACTTTTCACA
* * * *
62778 ATCA-GGGATATTGCAACCCCGTTA-TTTCTGAGGGGACACTCCAA-CCCCGGTTTTATTTCTAA
1 ATCAGGGGATACTCCAACCCCGTTATTTTC-GAGGGGACACTCCAACCCCCGGCTTTATTCCTAA
*
62840 AACT-TCAATTT-T-TCATCGGGGATACTCCAACCCCGTTAATC
65 AA-TATCAATTTCTATAATCGGGGATACTCCAACCCCGTT-ATC
*
62881 ATC-GGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAA
1 ATCAGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCCGGCTTTATTCCTAAA
** *
62945 ATATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATT
66 ATATCAATTTCT-ATAATCGGGGATACTCCAACCCCGTTATC
*
62987 TTCGAGGGGATACTCCAACCCCG
1 ATC-AGGGGATACTCCAACCCCG
63010 ACTTTATTTC
Statistics
Matches: 110, Mismatches: 10, Indels: 13
0.83 0.08 0.10
Matches are distributed among these distances:
103 36 0.33
104 27 0.25
105 1 0.01
106 4 0.04
107 24 0.22
108 18 0.16
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (106 bp):
ATCAGGGGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCAACCCCCGGCTTTATTCCTAAA
ATATCAATTTCTATAATCGGGGATACTCCAACCCCGTTATC
Found at i:62924 original size:28 final size:27
Alignment explanation
Indices: 62852--62928 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 27
62842 CTTCAATTTT
62852 TCATCGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
62879 TCATCGGGGATACTCCAACCCCGTT-A
1 TCATCGGGGATACTCCAACCCCGTTAA
**
62905 TTTTCGAGGGGATACTCCAACCCC
1 TCATC--GGGGATACTCCAACCCC
62929 CGGCTTTATT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
26 4 0.09
27 25 0.54
28 17 0.37
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:63055 original size:79 final size:80
Alignment explanation
Indices: 62881--63060 Score: 326
Period size: 79 Copynumber: 2.3 Consensus size: 80
62871 CCCGTTAATC
*
62881 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGGCTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGACTTTATTCCTAAAA
*
62946 TATTGATTTCTCATA
66 TATTAATTTCTCATA
*
62961 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCCCGACTTTATTTCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGACTTTATTCCTAAAA
63025 TATTAATTTCTCATA
66 TATTAATTTCTCATA
63040 ATCGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
63061 GTTTTATTTC
Statistics
Matches: 97, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
79 53 0.55
80 44 0.45
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (80 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCCGACTTTATTCCTAAAA
TATTAATTTCTCATA
Found at i:63068 original size:51 final size:51
Alignment explanation
Indices: 62992--63111 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
62982 TTATTTTCGA
* *
62992 GGGGATACTCCAACCCCGACTTTATTTCTAAAAT-ATTAATTTCTCATAATC
1 GGGGATACTCCAACCCCGACTTTATTTC-AAAATCATCAATTTCTCACAATC
** * *
63043 GGGGATACTCCAACCCCGGTTTTATTTCAAAATCATCGATTTTTCACAATC
1 GGGGATACTCCAACCCCGACTTTATTTCAAAATCATCAATTTCTCACAATC
*
63094 GAGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
63112 TTATTTTCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 5 0.08
51 56 0.92
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCAAAATCATCAATTTCTCACAATC
Found at i:63100 original size:130 final size:131
Alignment explanation
Indices: 62912--63169 Score: 380
Period size: 130 Copynumber: 2.0 Consensus size: 131
62902 TTATTTTCGA
* * *
62912 GGGGATACTCCAACCCCCGGCTTTATTCCTAAAATATTGATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCCGGCTTTATTCCTAAAATATCGATTTCTCACAATCGAGGATACTCCAA
* *
62977 CCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTT-TATTTCTAAAATATT-AATTTCTCATA
66 CCCCGTTATTTTCAAGGGGATACTCCAACCCCG--TTATATCTCTAAAATATTAAATTTCTCATA
63040 ATC
129 ATC
* * *
63043 GGGGATACTCCAA-CCCCGGTTTTATTTC-AAAATCATCGATTTTTCACAATCGAGGATACTCCA
1 GGGGATACTCCAACCCCCGGCTTTATTCCTAAAAT-ATCGATTTCTCACAATCGAGGATACTCCA
63106 ACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTACTATCTCTAAAATATTAAATTTCTCAT
65 ACCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTA-TATCTCTAAAATATTAAATTTCTCAT
63170 CGGGAAATAT
Statistics
Matches: 115, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
128 2 0.02
129 5 0.04
130 85 0.74
131 23 0.20
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (131 bp):
GGGGATACTCCAACCCCCGGCTTTATTCCTAAAATATCGATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTTCAAGGGGATACTCCAACCCCGTTATATCTCTAAAATATTAAATTTCTCATAAT
C
Found at i:65210 original size:4 final size:4
Alignment explanation
Indices: 65201--65230 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
65191 TTTTGAGGTG
*
65201 TTTA TTTA TTTA TTTA TTTA TTTG TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
65231 CTGTTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (4 bp):
TTTA
Done.