Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001755.1 Hibiscus syriacus cultivar Beakdansim tig00003551_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 88219
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3013 original size:3 final size:3
Alignment explanation
Indices: 3005--3094 Score: 105
Period size: 3 Copynumber: 30.7 Consensus size: 3
2995 TTCATTTAAA
*
3005 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TA- TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
3051 AAT TAC TAT TAT T-T TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
3095 CAAACGGGCC
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
2 6 0.08
3 65 0.88
4 3 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:4077 original size:2 final size:2
Alignment explanation
Indices: 4070--4099 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4060 CCTTATCAGA
4070 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4100 TTAGGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12103 original size:83 final size:83
Alignment explanation
Indices: 11955--12135 Score: 294
Period size: 83 Copynumber: 2.2 Consensus size: 83
11945 AATGGAACAA
* *
11955 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAAAACC
12020 AATCATTGAATTTAGAAG
66 AATCATTGAATTTAGAAG
* *
12038 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACATAAC
1 ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGG-CAAAAC
*
12102 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTAGAAG
12121 ATGAA-TTGCTCATAG
1 ATGAATTTGCTCATAG
12136 TAGAAATAAG
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
82 13 0.14
83 78 0.86
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (83 bp):
ATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAAAACC
AATCATTGAATTTAGAAG
Found at i:13606 original size:22 final size:22
Alignment explanation
Indices: 13577--13631 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
13567 ATCTACACTC
**
13577 TTCAAAGATGGTAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
13599 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
13621 TTCAAAGATGA
1 TTCAAAGATGA
13632 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:14227 original size:113 final size:113
Alignment explanation
Indices: 14029--14538 Score: 905
Period size: 113 Copynumber: 4.5 Consensus size: 113
14019 TTAGCAAAGA
* * * * *
14029 TTCAAATCCATCATATGATGGATCAGCTTTTCCAGAAAAGGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
14094 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
14142 TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
14207 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
14255 TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
1 TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
*
14320 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
** * *
14368 TTTGAATTCATCA-CTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCT
1 TTCAAATCCATCATC-TGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCT
14432 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
65 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
*
14481 TTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAAC
1 TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAAC
14539 CAACCTTTTG
Statistics
Matches: 381, Mismatches: 14, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
112 1 0.00
113 379 0.99
114 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
TTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTG
Found at i:14554 original size:68 final size:68
Alignment explanation
Indices: 14471--14606 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
14461 AGAATTTGTT
14471 CAACCTTTTGTTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
14536 AAC
66 AAC
14539 CAACCTTTTGTTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
14604 AAC
66 AAC
14607 TCATCTGAAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (68 bp):
CAACCTTTTGTTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
AAC
Found at i:14587 original size:181 final size:180
Alignment explanation
Indices: 14383--14718 Score: 620
Period size: 181 Copynumber: 1.9 Consensus size: 180
14373 ATTCATCACT
14383 TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
14448 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCA-TCTGATGGATTATCATTG
66 ATTCATAATGAGAAGAATTTGTTCAACC-TTTGTTCAAATCCATCACT-TGATGGATTATCATTG
14512 CCAGAGAAGGTTCATAATGAGAAGAACCAACCTTTTGTTCAAATCCATCATC
129 CCAGAGAAGGTTCATAATGAGAAGAACCAACCTTTTGTTCAAATCCATCATC
14564 TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
1 TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
** *
14629 ATTCATAATGAGAAGAATTTGTTCAACCTTTGTTTGAATTCATCACTTGATGGATTATCATTGCC
66 ATTCATAATGAGAAGAATTTGTTCAACCTTTGTTCAAATCCATCACTTGATGGATTATCATTGCC
14694 AGAGAAGGTTCATAATGAGAAGAAC
131 AGAGAAGGTTCATAATGAGAAGAAC
14719 TCATCTGAAG
Statistics
Matches: 151, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
180 57 0.38
181 94 0.62
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (180 bp):
TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA
ATTCATAATGAGAAGAATTTGTTCAACCTTTGTTCAAATCCATCACTTGATGGATTATCATTGCC
AGAGAAGGTTCATAATGAGAAGAACCAACCTTTTGTTCAAATCCATCATC
Found at i:14644 original size:294 final size:292
Alignment explanation
Indices: 14245--14830 Score: 1102
Period size: 294 Copynumber: 2.0 Consensus size: 292
14235 AGAATTTGTT
14245 CAACCTTTTGTTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAG
14310 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTCGTTTGAAT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT-GTTTGAAT
14375 TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
130 TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
14440 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTCAAATCCATCA-TCTGATGGAT
195 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTGTTCAAATCCATCACT-TGATGGAT
14504 TATCATTGCCAGAGAAGGTTCATAATGAGAAGAAC
258 TATCATTGCCAGAGAAGGTTCATAATGAGAAGAAC
*
14539 CAACCTTTTGTTCAAATCCATCATCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAG
14604 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTGTTTGAATT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTGTTTGAATT
14669 CATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
131 CATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
** *
14734 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTGTTTGAATTCATCACTTGATGGATTAT
196 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTGTTCAAATCCATCACTTGATGGATTAT
14799 CATTGCCAGAGAAGGTTCATAATGAGAAGAAC
261 CATTGCCAGAGAAGGTTCATAATGAGAAGAAC
14831 TCATCTGAAG
Statistics
Matches: 287, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
292 57 0.20
293 110 0.38
294 120 0.42
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (292 bp):
CAACCTTTTGTTCAAATCCATCATCTGATGGATCATCATTGCCAGAGAAGGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTGTTTGAATT
CATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTGTTCAAATCCATCACTTGATGGATTAT
CATTGCCAGAGAAGGTTCATAATGAGAAGAAC
Found at i:14940 original size:225 final size:226
Alignment explanation
Indices: 14539--15324 Score: 1375
Period size: 225 Copynumber: 3.5 Consensus size: 226
14529 TGAGAAGAAC
** *
14539 CAACCTTTTGTTCAAATCCATCA-TCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAA
1 CAACCTTTTGTTTGAATTCATCACT-TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAA
14603 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACC-TTTGTTTGAA
65 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAA
14667 TTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAG
130 TTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAG
14732 GAAGAAGAAATTCATAATGAGAAGAATTTGTT
195 GAAGAAGAAATTCATAATGAGAAGAATTTGTT
14764 CAACC-TTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
14828 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
14893 TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
131 TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
14958 AAGAAGAAATTCATAATGAGAAGAA-TTGTT
196 AAGAAGAAATTCATAATGAGAAGAATTTGTT
14988 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
15053 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
* *
15118 TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAATAAAG
131 TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
15183 AAGAAGAAATTCATAATGAGAAGAATTTGTT
196 AAGAAGAAATTCATAATGAGAAGAATTTGTT
* * * * *
15214 CAAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGA
1 C-AACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAG-GTTCATAATGAGA
* *
15278 AGAACTCGTCATCTGAAGAAGGAGGAAGAAGTTCATAATGAGAAGAA
64 AGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
15325 CTCATCAAGA
Statistics
Matches: 540, Mismatches: 12, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
224 117 0.22
225 319 0.59
226 9 0.02
227 57 0.11
229 1 0.00
230 37 0.07
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (226 bp):
CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAAT
TCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
AAGAAGAAATTCATAATGAGAAGAATTTGTT
Found at i:14967 original size:113 final size:113
Alignment explanation
Indices: 14539--15324 Score: 1375
Period size: 112 Copynumber: 6.9 Consensus size: 113
14529 TGAGAAGAAC
** *
14539 CAACCTTTTGTTCAAATCCATCA-TCTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAA
1 CAACCTTTTGTTTGAATTCATCACT-TGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAA
14603 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
65 GAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
14652 CAACC-TTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
14716 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
14764 CAACC-TTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
14828 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
14876 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
14941 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA-TTGTT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
14988 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
15053 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
15101 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
1 CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
* *
15166 AACTCATCTGAATAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTT
66 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * * * *
15214 CAAACCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGA
1 C-AACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAG-GTTCATAATGAGA
* *
15278 AGAACTCGTCATCTGAAGAAGGAGGAAGAAGTTCATAATGAGAAGAA
64 AGAA--C-TCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
15325 CTCATCAAGA
Statistics
Matches: 651, Mismatches: 14, Indels: 12
0.96 0.02 0.02
Matches are distributed among these distances:
112 331 0.51
113 227 0.35
114 57 0.09
116 1 0.00
117 35 0.05
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
CAACCTTTTGTTTGAATTCATCACTTGATGGATTATCATTGCCAGAGAAGGTTCATAATGAGAAG
AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
Found at i:15581 original size:3 final size:3
Alignment explanation
Indices: 15573--15666 Score: 100
Period size: 3 Copynumber: 30.7 Consensus size: 3
15563 TTCATTTAAA
* * *
15573 TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
15621 TACT AAT T-T TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT TA
1 TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT TA
15667 CAAACGGGCC
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.03
3 66 0.87
4 8 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:16080 original size:18 final size:18
Alignment explanation
Indices: 16054--16088 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16044 AGAGAGACAG
* *
16054 AGAACAAAAATAGAAAAC
1 AGAAAAAAAAAAGAAAAC
16072 AGAAAAAAAAAAGAAAA
1 AGAAAAAAAAAAGAAAA
16089 AAAAAACGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAAAGAAAAC
Found at i:18176 original size:2 final size:2
Alignment explanation
Indices: 18169--18199 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18159 ATAAGGGATA
18169 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 A
18200 ATTTAAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18562 original size:24 final size:24
Alignment explanation
Indices: 18535--18581 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18525 GATAAAATTT
*
18535 ATCATAGGTCC-ATAAATTATTTTA
1 ATCATAGG-CCAACAAATTATTTTA
18559 ATCATAGGCCAACAAATTATTTT
1 ATCATAGGCCAACAAATTATTTT
18582 TAAGCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (24 bp):
ATCATAGGCCAACAAATTATTTTA
Found at i:18621 original size:20 final size:21
Alignment explanation
Indices: 18596--18640 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
18586 CATTAACTTT
18596 TTAAAAATTAT-AAATAATTA
1 TTAAAAATTATGAAATAATTA
*
18616 TT-AAAATTATGAAATGATTA
1 TTAAAAATTATGAAATAATTA
18636 -TAAAA
1 TTAAAA
18641 TAATCATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TTAAAAATTATGAAATAATTA
Found at i:18623 original size:19 final size:19
Alignment explanation
Indices: 18599--18641 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18589 TAACTTTTTA
18599 AAAATTAT-AAATAATTATT
1 AAAATTATGAAATAATTA-T
*
18618 AAAATTATGAAATGATTAT
1 AAAATTATGAAATAATTAT
18637 AAAAT
1 AAAAT
18642 AATCATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAATTATGAAATAATTAT
Found at i:19121 original size:59 final size:55
Alignment explanation
Indices: 19018--19140 Score: 133
Period size: 58 Copynumber: 2.1 Consensus size: 55
19008 GACCATTTTG
* *
19018 TAACTTTTAATAGTCGAGGGACTTAAAAAATAATGTCTCATAGTTAGGGGATCATTGA
1 TAACTTTTAATAGTC-AGGGACTCAAAAAATAATATCTCATAGTT--GGGATCATTGA
*
19076 TAACTTTTAATAGT-AGGATGACTCAATAAAATAATATC-CTATAGTTGGGATCATTTA
1 TAACTTTTAATAGTCAGG--GACTCAA-AAAATAATATCTC-ATAGTTGGGATCATTGA
19133 TATACTTT
1 TA-ACTTT
19141 ACCTCGATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
56 3 0.05
57 12 0.21
58 26 0.46
59 16 0.28
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (55 bp):
TAACTTTTAATAGTCAGGGACTCAAAAAATAATATCTCATAGTTGGGATCATTGA
Found at i:25176 original size:25 final size:28
Alignment explanation
Indices: 25132--25192 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
25122 ATGACAAGGC
25132 GAATCA-T-CAGGTTCAACAGC-CAC-AG
1 GAATCACTGCAGGTTC-ACAGCTCACGAG
25157 GAATCACTGCAGGTTC-CAGCTCACGAG
1 GAATCACTGCAGGTTCACAGCTCACGAG
*
25184 GAACCACTG
1 GAATCACTG
25193 GTGGCTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 10 0.32
26 4 0.13
27 17 0.55
ACGTcount: A:0.31, C:0.30, G:0.23, T:0.16
Consensus pattern (28 bp):
GAATCACTGCAGGTTCACAGCTCACGAG
Found at i:25344 original size:3 final size:3
Alignment explanation
Indices: 25336--25420 Score: 143
Period size: 3 Copynumber: 28.3 Consensus size: 3
25326 TACCCATATC
* *
25336 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
25384 ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
25421 AATATATTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:25463 original size:21 final size:21
Alignment explanation
Indices: 25419--25463 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
25409 TTATTATTAT
* *
25419 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
25440 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
25461 TAA
1 TAA
25464 TTACAGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:26808 original size:19 final size:19
Alignment explanation
Indices: 26770--26805 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26760 TAATTTAGTC
26770 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
26789 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
26806 TAAATATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:26872 original size:22 final size:21
Alignment explanation
Indices: 26833--26875 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
26823 AGAATTTTTC
**
26833 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
26854 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
26876 ATATAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:38220 original size:5 final size:5
Alignment explanation
Indices: 38210--38270 Score: 51
Period size: 5 Copynumber: 13.0 Consensus size: 5
38200 ATGCTTGAAG
* *
38210 AGAAA AGAAA A-AAG A-AAA AGAAA A-AAA A-AAA A-AAA AAAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
*
38255 AGAGA AGAAAA AGAAA
1 AGAAA AG-AAA AGAAA
38271 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
4 18 0.38
5 26 0.54
6 4 0.08
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:38222 original size:7 final size:7
Alignment explanation
Indices: 38207--38270 Score: 58
Period size: 7 Copynumber: 8.9 Consensus size: 7
38197 ATTATGCTTG
*
38207 AAGAGAA
1 AAGAAAA
38214 AAGAAAA
1 AAGAAAA
38221 AAG-AAA
1 AAGAAAA
38227 AAGAAAAA
1 AAG-AAAA
*
38235 AAAAAAA
1 AAGAAAA
*
38242 AAAAAAA
1 AAGAAAA
38249 AAGAAAA
1 AAGAAAA
*
38256 GAGAAGAAA
1 AAG-A-AAA
38265 AAGAAA
1 AAGAAA
38271 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
6 6 0.12
7 30 0.62
8 7 0.15
9 5 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:38227 original size:6 final size:6
Alignment explanation
Indices: 38207--38270 Score: 64
Period size: 6 Copynumber: 11.0 Consensus size: 6
38197 ATTATGCTTG
*
38207 AAGAGAA AAGAAAA AAGAAA AAGAAA AA-AAA AA-AAA AAAAAA AAG-AA
1 AAGA-AA AAG-AAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
*
38254 AAG-AG AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA
38271 GGGGGTCAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
5 19 0.37
6 23 0.45
7 8 0.16
8 1 0.02
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:38266 original size:1 final size:1
Alignment explanation
Indices: 38212--38255 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
38202 GCTTGAAGAG
* * * *
38212 AAAAGAAAAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38256 GAGAAGAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:39919 original size:84 final size:84
Alignment explanation
Indices: 39413--39900 Score: 922
Period size: 84 Copynumber: 5.8 Consensus size: 84
39403 GAACAAATAT
*
39413 AATGTGCTCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
39478 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
39497 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
39562 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
39581 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
39646 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
39665 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
* *
39730 TCATTGAATTTAGAAAATAT
66 TCATTGAATTTAGAAGAT-G
39750 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
39815 TCATTGAATTTAGAAGATG
66 TCATTGAATTTAGAAGATG
* *
39834 AATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAACCAA
1 AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
39899 TC
66 TC
39901 GAGGGAATTA
Statistics
Matches: 396, Mismatches: 7, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
84 314 0.79
85 82 0.21
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.35
Consensus pattern (84 bp):
AATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAA
TCATTGAATTTAGAAGATG
Found at i:40801 original size:113 final size:113
Alignment explanation
Indices: 40603--41838 Score: 1949
Period size: 113 Copynumber: 11.0 Consensus size: 113
40593 CAAAGATTCA
* * *
40603 AATCCATCACTTGATGGATAAAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTAATGGAT-CATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
40667 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
** ****
40716 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
40781 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
*
40829 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
40894 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
** ****
40942 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
41007 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
*
41055 AATCCATCATTTAATGGATAAAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCATTTAATGGAT-CATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
41119 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
** ****
41168 AATCCATCATTTGGTGGATCATC-TTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
41232 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
*
41280 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
41345 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
** ****
41393 AATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
41458 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
*
41506 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
41571 AGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
*
41619 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
41684 AGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
* * * * *
41732 AATTCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
41796 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
41839 GCATAATTCT
Statistics
Matches: 1033, Mismatches: 86, Indels: 9
0.92 0.08 0.01
Matches are distributed among these distances:
112 176 0.17
113 855 0.83
114 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AATCCATCATTTAATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
Found at i:40997 original size:226 final size:226
Alignment explanation
Indices: 40603--41838 Score: 2179
Period size: 226 Copynumber: 5.5 Consensus size: 226
40593 CAAAGATTCA
* * * **
40603 AATCCATCACTTGATGGATAAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
40668 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
40733 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
40798 AATGAGAAGAATTTGTTCAACCTTTTATATG
196 AATGAGAAGAATTTGTTCAACCTTTTATATG
40829 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
40894 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
40959 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
41024 AATGAGAAGAATTTGTTCAACCTTTTATATG
196 AATGAGAAGAATTTGTTCAACCTTTTATATG
* **
41055 AATCCATCATTTAATGGATAAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
41120 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
41185 ATCATC-TTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
41249 AATGAGAAGAATTTGTTCAACCTTTTATATG
196 AATGAGAAGAATTTGTTCAACCTTTTATATG
41280 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
41345 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
41410 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
131 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
41475 AATGAGAAGAATTTGTTCAACCTTTTATATG
196 AATGAGAAGAATTTGTTCAACCTTTTATATG
41506 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* ** **
41571 AGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTATATGAATCCATCATTTAATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
* **** *
41636 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
131 ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
**
41701 AATGAGAAGAATTTGTTCAACCTTTTACCTG
196 AATGAGAAGAATTTGTTCAACCTTTTATATG
* * * * * *
41732 AATTCATCAATTGATGGATTATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
41796 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
41839 GCATAATTCT
Statistics
Matches: 974, Mismatches: 35, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
225 291 0.30
226 683 0.70
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (226 bp):
AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGG
ATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAATTTGTTCAACCTTTTATATG
Found at i:41340 original size:564 final size:564
Alignment explanation
Indices: 40603--41838 Score: 2010
Period size: 564 Copynumber: 2.2 Consensus size: 564
40593 CAAAGATTCA
* * *
40603 AATCCATCACTTGATGGATAAAT-TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCAATTGATGGAT-CATCTTTTCCGGAG-AAGTTCATAATGAGAAGAACTCATCTGAAG
* **
40667 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTG
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATGAATCCATCATTTAATG
* ****
40732 GATCATCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
129 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
*
40797 TAATGAGAAGAATTTGTTCAACCTTTTATATGAATCCATCATTTAATGGATCAGCTTTTCCAGAG
194 TAATGAGAAGAATTTGTTCAACCTTTTACATGAATCCATCATTTAATGGATCAGCTTTTCCAGAG
40862 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
259 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* ** * ****
40927 TCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGTTCGAGTTCATAATGAGAA
324 TCAACCTTTTACATGAATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
40992 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATGAA
389 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATGAA
*
41057 TCCATCATTTAATGGATAAATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
454 TCCATCATTTAATGGATAAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
*
41122 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
519 GAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* * **
41168 AATCCATCATTTGGTGGATCATC-TTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAAG
1 AATCCATCAATTGATGGATCATCTTTTCC-G-GAGAAGTTCATAATGAGAAGAACTCATCTGAAG
*
41231 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATGAATCCATCATTTAATG
64 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATGAATCCATCATTTAATG
41296 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
129 GATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* ** * **
41361 TAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGTT
194 TAATGAGAAGAATTTGTTCAACCTTTTACATGAATCCATCATTTAATGGATCAGCTTTTCCAGAG
**
41426 CGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
259 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
41491 TCAACCTTTTATATGAATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
324 TCAACCTTTTACATGAATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
*
41556 GAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTATATGAA
389 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATGAA
* *
41621 TCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
454 TCCATCATTTAATGGATAAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
41686 GAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
519 GAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
* *
41732 AATTCATCAATTGATGGATTATCTTTTCCGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AATCCATCAATTGATGGATCATCTTTTCCGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
* * * *
41797 GAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
66 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
41839 GCATAATTCT
Statistics
Matches: 618, Mismatches: 48, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
563 1 0.00
564 594 0.96
565 22 0.04
566 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (564 bp):
AATCCATCAATTGATGGATCATCTTTTCCGGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAA
GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATGAATCCATCATTTAATGGA
TCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAATTTGTTCAACCTTTTACATGAATCCATCATTTAATGGATCAGCTTTTCCAGAGAA
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTACATGAATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
ACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATGAATC
CATCATTTAATGGATAAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AAAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
Found at i:42168 original size:3 final size:3
Alignment explanation
Indices: 42160--42260 Score: 175
Period size: 3 Copynumber: 33.3 Consensus size: 3
42150 TACCCATATC
42160 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
* *
42206 ATT ATT ATC ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42254 ATT ATT A
1 ATT ATT A
42261 AATATATTAA
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
3 90 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:42303 original size:21 final size:21
Alignment explanation
Indices: 42259--42303 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
42249 TTATTATTAT
* *
42259 TAAATATATTAAATACATATA
1 TAAATATATTAAAAAAATATA
42280 TAAATATTATTAAAAAAATA-A
1 TAAATA-TATTAAAAAAATATA
42301 TAA
1 TAA
42304 TTACAGGCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATATTAAAAAAATATA
Found at i:43653 original size:19 final size:19
Alignment explanation
Indices: 43615--43650 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43605 TAATTTAGTC
43615 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
43634 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
43651 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:43718 original size:22 final size:21
Alignment explanation
Indices: 43679--43721 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
43669 AGAATTTTTC
**
43679 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
43700 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
43722 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:49737 original size:183 final size:182
Alignment explanation
Indices: 49427--49788 Score: 571
Period size: 183 Copynumber: 2.0 Consensus size: 182
49417 TATCACAATG
* * * *
49427 AACGGATTAATATTCAACTTAGAATATAGTCTATTTTTAGTGAAAAATGATGAGTTTGGAATATA
1 AACGGATTAATATTCAAATCAGAATATAGTCTATTTTTAGCGAAAAATGACGAGTTTGGAATATA
* * * *
49492 ATGAATAGTCTAATGACAATCTTGTAACTTTTAATAATCAAATGACTCAACAACGCAACACTATA
66 ATGAATAGTCGAATGACAATCTTGTAACTTTTAATAATCAAACGACTCAACAAAGAAACACTATA
49557 TAATCAGAGTAGCATTATGTAACTTTTAATAATTGAAAAACTTAATAAAATT
131 TAATCAGAGTAGCATTATGTAACTTTTAATAATTGAAAAACTTAATAAAATT
* * *
49609 AACGGATTAATATTCAAATCAGAATATCGTCTATTTTTTAGCGGAAAATGACGGGTTTGGAATAT
1 AACGGATTAATATTCAAATCAGAATATAGTCTA-TTTTTAGCGAAAAATGACGAGTTTGGAATAT
*
49674 AATGAATAGTCGAATGATAATCTTGTAACTTTTAATAATCAAACGACTCAACAAAGAAACACTAT
65 AATGAATAGTCGAATGACAATCTTGTAACTTTTAATAATCAAACGACTCAACAAAGAAACACTAT
* * * *
49739 ATAATCAGAGTAGCATTTTTTAACTTTTAATAATTGAAGAACTTGATAAA
130 ATAATCAGAGTAGCATTATGTAACTTTTAATAATTGAAAAACTTAATAAA
49789 TTAGTATCCT
Statistics
Matches: 163, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
182 30 0.18
183 133 0.82
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (182 bp):
AACGGATTAATATTCAAATCAGAATATAGTCTATTTTTAGCGAAAAATGACGAGTTTGGAATATA
ATGAATAGTCGAATGACAATCTTGTAACTTTTAATAATCAAACGACTCAACAAAGAAACACTATA
TAATCAGAGTAGCATTATGTAACTTTTAATAATTGAAAAACTTAATAAAATT
Found at i:60323 original size:2 final size:2
Alignment explanation
Indices: 60316--60345 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60306 GTTTTTATTT
60316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
60346 CATAATGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61416 original size:91 final size:92
Alignment explanation
Indices: 61256--61440 Score: 354
Period size: 91 Copynumber: 2.0 Consensus size: 92
61246 AGAGGTCCCC
*
61256 TGTTGGGCCCTTTTTGTATTTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATT
1 TGTTGGGCCCTTTTTGTATTTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATC
61321 CTTTAGGAATTGAGTCTATATCTCAAG
66 CTTTAGGAATTGAGTCTATATCTCAAG
61348 TGTTGGGCCCTTTTTGTA-TTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATC
1 TGTTGGGCCCTTTTTGTATTTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATC
61412 CTTTAGGAATTGAGTCTATATCTCAAG
66 CTTTAGGAATTGAGTCTATATCTCAAG
61439 TG
1 TG
61441 GTAGAGCATA
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 74 0.80
92 18 0.20
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (92 bp):
TGTTGGGCCCTTTTTGTATTTTTTTTTTAAATTAGAAACAATTTTTATATACATAAAATTGAATC
CTTTAGGAATTGAGTCTATATCTCAAG
Found at i:62072 original size:36 final size:36
Alignment explanation
Indices: 62023--62093 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
62013 ATTAAAAATG
*
62023 ATCTTTAGATAAAC-AAA-AAATAAATTCCTCAAACA
1 ATCTTTAGATAAACAAAATAAATAAA-TACTCAAACA
*
62058 ATCTCTTATATAAACAAAATAAATAAATACTCAAAC
1 ATCT-TTAGATAAACAAAATAAATAAATACTCAAAC
62094 TATTGGTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 4 0.13
36 9 0.29
37 11 0.35
38 7 0.23
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (36 bp):
ATCTTTAGATAAACAAAATAAATAAATACTCAAACA
Found at i:65652 original size:14 final size:14
Alignment explanation
Indices: 65630--65677 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
65620 TTTTTTTATC
*
65630 AAAAGTAAAATATT
1 AAAATTAAAATATT
65644 AAAATTAAAATATT
1 AAAATTAAAATATT
*
65658 ----TTAAAAAATT
1 AAAATTAAAATATT
65668 AAAATTAAAA
1 AAAATTAAAA
65678 AAATTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.32
14 19 0.68
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AAAATTAAAATATT
Found at i:65716 original size:2 final size:2
Alignment explanation
Indices: 65711--65762 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
65701 TTTTTGTCAT
65711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65753 TA TA TA TA TA
1 TA TA TA TA TA
65763 AATGATTCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66119 original size:26 final size:25
Alignment explanation
Indices: 66076--66138 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
66066 CATATCAATT
66076 TAAT-TTTA-AAAATAATATATAAC
1 TAATATTTATAAAATAATATATAAC
66099 -AATTATTTAATAAAATAATATATAAC
1 TAA-TATTT-ATAAAATAATATATAAC
66125 TAATATTTATAAAA
1 TAATATTTATAAAA
66139 AATCATTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 3 0.09
25 7 0.20
26 20 0.57
27 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (25 bp):
TAATATTTATAAAATAATATATAAC
Found at i:66558 original size:84 final size:83
Alignment explanation
Indices: 66416--66581 Score: 215
Period size: 84 Copynumber: 2.0 Consensus size: 83
66406 ATATTACTTT
** * *
66416 CCATAATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTTTTCATTTTTATTTTGATCAC
1 CCATAATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTGATCATTTTCATTTTGACCAC
66481 CATATTTGAAATCTTACC
66 CATATTTGAAATCTTACC
* * * * *
66499 CCATAATTTTTTTGGATAAATTATAATAGTGATCACCTAATTCTTGATCCTTTTCATTTTGACCA
1 CCATAA-TTTTTTAGATAAATTATAACAGTGATCACCTAACTATTGATCATTTTCATTTTGACCA
* * *
66564 CTATTTTTGAAATTTTAC
65 CCATATTTGAAATCTTAC
66582 AAATTAGGTC
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
83 6 0.09
84 64 0.91
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (83 bp):
CCATAATTTTTTAGATAAATTATAACAGTGATCACCTAACTATTGATCATTTTCATTTTGACCAC
CATATTTGAAATCTTACC
Found at i:66771 original size:14 final size:14
Alignment explanation
Indices: 66747--66779 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
66737 TATCAAATTG
66747 GTTAA-AACTTTAA
1 GTTAATAACTTTAA
66760 GTTAATAACTTTAA
1 GTTAATAACTTTAA
*
66774 ATTAAT
1 GTTAAT
66780 TCAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
GTTAATAACTTTAA
Found at i:66931 original size:18 final size:19
Alignment explanation
Indices: 66895--66932 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
66885 TGCTACAAAC
66895 AATTATTATATTTTCTAAA
1 AATTATTATATTTTCTAAA
66914 AATTA-TATAATTTT-TAAA
1 AATTATTAT-ATTTTCTAAA
66932 A
1 A
66933 TCAAACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
AATTATTATATTTTCTAAA
Found at i:70386 original size:22 final size:18
Alignment explanation
Indices: 70338--70412 Score: 87
Period size: 18 Copynumber: 3.9 Consensus size: 18
70328 TCAGTATTTA
70338 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
70356 TCCCAAAGGACCACTGGATACG
1 TCCCGAAGGACCACT--AT--G
70378 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
**
70396 TCCCGAATAACCACTAT
1 TCCCGAAGGACCACTAT
70413 ACTCTCGACT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 30 0.61
20 4 0.08
22 15 0.31
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:73422 original size:223 final size:228
Alignment explanation
Indices: 73101--73517 Score: 627
Period size: 224 Copynumber: 1.9 Consensus size: 228
73091 CTTTATTTTG
*
73101 TTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAAATTACCTGACCCGACCCGAAAATATATATAA
1 TTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAAAATACCTGACCCGACCCGAAAATATATATAA
* *
73166 TTTTATCTTATATATTTAGGAATAATTACAATAATA-CCCTCTATATA-ATTTTTTTCAATTAAG
66 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAG
* * ** *
73229 TCA-TGTTTTTATTGAATAAAAATATTTTTTATTATTTCGGGTCGGGTCGGGTTTTTAATTCATA
131 TCACCGTTTTTATTGAATAAAAATA--TTTTATTATTTCGGCTAAGGTCGGGTTTCTAATTCATA
73293 TTCGTCGGGTTGGGTCGATTTTTTTAAGTGTGATA
194 TTCGTCGGGTTGGGTCGATTTTTTTAAGTGTGATA
**
73328 TTCGGGTCGGGTCGGGGTTC-GGTTTAGGGTGAAAAATACCCT-ACCCGA-CC-AAAA-A-ATAT
1 TTCGGGTCGGGTC-GAATTCGGGTTTAGGGTGAAAAATA-CCTGACCCGACCCGAAAATATATAT
*
73387 AATTTTGCCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTA
64 AATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTA
*
73452 AGTCACCGTTTTTATTGAATAAAAATATTTTATTATTTCGGCTAAGGTCGGGTTTCTAATTTATA
129 AGTCACCGTTTTTATTGAATAAAAATATTTTATTATTTCGGCTAAGGTCGGGTTTCTAATTCATA
73517 T
194 T
73518 ATTCGGGTCG
Statistics
Matches: 173, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
223 40 0.23
224 46 0.27
225 22 0.13
226 22 0.13
227 36 0.21
228 7 0.04
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (228 bp):
TTCGGGTCGGGTCGAATTCGGGTTTAGGGTGAAAAATACCTGACCCGACCCGAAAATATATATAA
TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTCAATTAAG
TCACCGTTTTTATTGAATAAAAATATTTTATTATTTCGGCTAAGGTCGGGTTTCTAATTCATATT
CGTCGGGTTGGGTCGATTTTTTTAAGTGTGATA
Found at i:74853 original size:29 final size:29
Alignment explanation
Indices: 74792--74853 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
74782 ATTTTTCTCT
* * * *
74792 TTTATTTTATTCATTGTATTTTTAATTTT
1 TTTAATTTATTCATTGTACTTTTAAATTG
74821 TTTAATTTATTCATT-TAACTTTTAAATTG
1 TTTAATTTATTCATTGT-ACTTTTAAATTG
74850 TTTA
1 TTTA
74854 TGATTGGATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTAATTTATTCATTGTACTTTTAAATTG
Found at i:75781 original size:12 final size:13
Alignment explanation
Indices: 75751--75780 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
75741 ACGTTCAATT
75751 TTTTTAAAAAATA
1 TTTTTAAAAAATA
*
75764 TTTTTAAATAATA
1 TTTTTAAAAAATA
75777 TTTT
1 TTTT
75781 ATTTTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTTAAAAAATA
Found at i:75907 original size:16 final size:15
Alignment explanation
Indices: 75882--75911 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
75872 AGATACTATT
75882 TTTAACAAAAAATTC
1 TTTAACAAAAAATTC
75897 TTTAGACAAAAAATT
1 TTTA-ACAAAAAATT
75912 TTAAGATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (15 bp):
TTTAACAAAAAATTC
Done.