Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012915.1 Corchorus olitorius cultivar O-4 contig12948, 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: 75911
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:64 original size:2 final size:2
Alignment explanation
Indices: 7--46 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 ATTATG
7 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
47 ACAACAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2137 original size:22 final size:22
Alignment explanation
Indices: 2109--2178 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
2099 CATCTAGTTA
2109 CAACATAAGCATAGTAATGCTT
1 CAACATAAGCATAGTAATGCTT
* * *
2131 CATCATATTGCAGTATAGTAATGTTT
1 CAACATA----AGCATAGTAATGCTT
2157 CAACATAAGCATAGTAATGCTT
1 CAACATAAGCATAGTAATGCTT
2179 ACATTTCATT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
22 19 0.50
26 19 0.50
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (22 bp):
CAACATAAGCATAGTAATGCTT
Found at i:5655 original size:46 final size:46
Alignment explanation
Indices: 5530--5980 Score: 457
Period size: 46 Copynumber: 9.9 Consensus size: 46
5520 GTTTTCCCTC
*
5530 TTTCCAAAAATGCCCCTTTCCCGGTCGGAAGGTCCTAGTTTTCAATGTC-
1 TTTCCAAAAATGCCCC-TTCCTGGTCGGAAGGTCCTAGTTTTC--T-TCA
*
5579 TCTTCAAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
1 T-TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
* *
5626 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTCA
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
*
5672 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCAGTTTTCTTTCA
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTC-TTCA
* *
5719 -TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCT--TATT-TTCA
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
* * *
5761 TTTCAAAAAATGCCCCTTCCTGGTTGGGAGGT-CT--TTTT-TTCCA
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTT-CA
* * *
5804 -TTCCCAAAATGCCCCTTCCTGGTTGGAAGGTCC---TTATCTTCA
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
*** * *
5846 TTTCCAAAAATGCCCCTTCCCAATCGGAAGGTCCCAGTTTTCGATATCTC
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTC--T-TC-A
* ** *
5896 TTTCCAAAATTGCCCCTTCCCAGTCGGAAGGTCCT--TGTT-TTCA
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
* * * *
5939 TTTCTAAAAATACCCCTTCCTAGTCGGAAGGTCCCAGTTTTC
1 TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTC
5981 CTTCGATAAT
Statistics
Matches: 350, Mismatches: 34, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
42 44 0.13
43 92 0.26
44 5 0.01
45 4 0.01
46 121 0.35
47 6 0.02
48 4 0.01
49 28 0.08
50 46 0.13
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.34
Consensus pattern (46 bp):
TTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTAGTTTTCTTCA
Found at i:5700 original size:92 final size:90
Alignment explanation
Indices: 5530--5980 Score: 474
Period size: 93 Copynumber: 4.9 Consensus size: 90
5520 GTTTTCCCTC
* *
5530 TTTCCAAAAATGCCCCTTTCCCGGTCGGAAGGTCCTAGTTTTCAATGTC-TCTTCAAAAAATGCC
1 TTTCCAAAAATGCCCC-TTCCTGGTTGGAAGGTCC---TTTTC--T-TCAT-TTCAAAAAATGCC
*
5594 CCTTCCTGGTCGGAAGGTCCTAGTTTTC-TTCA
58 CCTTCCTGGTCGGAAGGTCCCAGTTTTCATTCA
*
5626 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCTTCATTTCCAAAAATGCCCCTTC
1 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGT-CC--TTTTCTTCATTTCAAAAAATGCCCCTTC
*
5691 CTGGTCGGAAGGTCCCAGTTTTCTTTCA
63 CTGGTCGGAAGGTCCCAGTTTTCATTCA
5719 -TTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATT-TTCATTTCAAAAAATGCCCCTTCCT
1 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTT-TTCTTCATTTCAAAAAATGCCCCTTCCT
* * *
5782 GGTTGGGAGGT--C--TTTT-TTTCCA
65 GGTCGGAAGGTCCCAGTTTTCATT-CA
* * * **
5804 -TTCCCAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATCTTCATTTCCAAAAATGCCCCTTCCCA
1 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTTTCTTCATTTCAAAAAATGCCCCTTCCTG
* *
5868 ATCGGAAGGTCCCAGTTTTCGATATCTC
66 GTCGGAAGGTCCCAGTTTTC-AT-TC-A
* ** * * *
5896 TTTCCAAAATTGCCCCTTCCCAGTCGGAAGGTCCTTGTT-TTCATTTCTAAAAATACCCCTTCCT
1 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTT-TTCTTCATTTCAAAAAATGCCCCTTCCT
*
5960 AGTCGGAAGGTCCCAGTTTTC
65 GGTCGGAAGGTCCCAGTTTTC
5981 CTTCGATAAT
Statistics
Matches: 312, Mismatches: 27, Indels: 35
0.83 0.07 0.09
Matches are distributed among these distances:
84 4 0.01
85 70 0.22
87 2 0.01
89 39 0.12
90 2 0.01
91 4 0.01
92 73 0.23
93 78 0.25
94 1 0.00
95 21 0.07
96 18 0.06
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.34
Consensus pattern (90 bp):
TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTTTCTTCATTTCAAAAAATGCCCCTTCCTG
GTCGGAAGGTCCCAGTTTTCATTCA
Found at i:6100 original size:48 final size:47
Alignment explanation
Indices: 6037--6732 Score: 871
Period size: 48 Copynumber: 14.6 Consensus size: 47
6027 AAATTCCCAG
* *
6037 TTTGCCCTTCCCGGTCGGAAGGTGTCGTTTTCAATGAGTTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTATTCCTGT
* * *
6085 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCGATATTTCACTCCCG-
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT-ATTCCTGT
* *
6132 TTTGCCTTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCCGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA-TTTATTCCTGT
* * * * **
6180 TTTGCCCTTCGCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCCAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTATTCCTGT
* * *
6228 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCAGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTATTCCTGT
* * **
6276 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTATTCCTGT
6324 TTTGCCCTTCCCGGTCGGAAGGTGTTG-TTTCAATATTTTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA-TTTATTCCTGT
*
6371 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTT-TATCCTCAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTAT-TCCT-GT
* * * **
6419 TTTGCCCTTCCCGGTCGGAAGGTGTTCTCTTCAATGTTTTATTCCCAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTATTCCTGT
* *
6467 TTTGCCCTTCCCGGACGGAAGGTGTTGTTTTCAATATTTTATTCATGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA-TTTATTCCTGT
* * *
6515 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATT-CTCAT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAT-ATTTATTCCT-GT
*
6563 TTTGCCCTTCCCGGTCAGAAGGTGTTGTTTTCAATATTTTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA-TTTATTCCTGT
* *
6611 TTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAACGT-TTTATTCCCGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAA--TATTTATTCCTGT
* * *
6659 TTTGCCATTCCCAGTCGGAAGGTGTTGTTTTCAATATTTTATTCTTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATA-TTTATTCCTGT
6707 TTTGCCCTTCCCGGTCGGAAGGTGTT
1 TTTGCCCTTCCCGGTCGGAAGGTGTT
6733 TGATCGAGCT
Statistics
Matches: 574, Mismatches: 55, Indels: 38
0.86 0.08 0.06
Matches are distributed among these distances:
46 2 0.00
47 93 0.16
48 469 0.82
49 8 0.01
50 2 0.00
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (47 bp):
TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTATTCCTGT
Found at i:6268 original size:96 final size:96
Alignment explanation
Indices: 6029--6732 Score: 1027
Period size: 96 Copynumber: 7.4 Consensus size: 96
6019 TGTTGTTTAA
* * * ** *
6029 ATTCCCAGTTTGCCCTTCCCGGTCGGAAGGTGTCGTTTTCAATGAGTTATTCCTGTTTTGCCCTT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
* *
6094 CCCGGTCGGAAGGTGTTGTTTTCGATATTTC
66 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
* * * * *
6125 ACTCCC-GTTTGCCTTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCCGTTTTGCCCTT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
* * *
6189 CGCGGTCGGAAGGTGTTGTCTTCAATGTTTT
66 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
* *
6220 ATACCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCAGTTTTGCCCTT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
* *
6285 CCCGGTCGGAAGGTGTTGTCTTCAATGTTTT
66 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
* *
6316 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGT-TTCAATATTTTATTCCTGTTTTGCCCTT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
6380 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
66 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
* *
6411 A-TCCTCATTTTGCCCTTCCCGGTCGGAAGGTGTTCTCTTCAATGTTTTATTCCCATTTTGCCCT
1 ATTCC-CATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCT
*
6475 TCCCGGACGGAAGGTGTTGTTTTCAATATTTT
65 TCCCGGTCGGAAGGTGTTGTTTTCAATATTTT
*** * *
6507 ATTCATGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCTCATTTTGCCCTT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
*
6572 CCCGGTCAGAAGGTGTTGTTTTCAATATTTT
66 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
** * *
6603 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAACGTTTTATTCCCGTTTTGCCATT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
*
6668 CCCAGTCGGAAGGTGTTGTTTTCAATATTTT
66 CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
***
6699 ATTCTTGTTTTGCCCTTCCCGGTCGGAAGGTGTT
1 ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTT
6733 TGATCGAGCT
Statistics
Matches: 559, Mismatches: 45, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
94 3 0.01
95 168 0.30
96 386 0.69
97 2 0.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.42
Consensus pattern (96 bp):
ATTCCCATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTTTGCCCTT
CCCGGTCGGAAGGTGTTGTTTTCAATATTTT
Found at i:6298 original size:239 final size:240
Alignment explanation
Indices: 6033--6732 Score: 1070
Period size: 239 Copynumber: 2.9 Consensus size: 240
6023 GTTTAAATTC
* * ** *
6033 CCAG-TTTGCCCTTCCCGGTCGGAAGGTGTCGTTTTCAATGAGTTATTCCTGTTTTGCCCTTCCC
1 CCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCTATTTTGCCCTTCCC
* * * * *
6097 GGTCGGAAGGTGTTGTTTTCGATATTTCACTCCCG-TTTGCCTTTCCCGGTCGGAAGGTGTTGTT
66 GGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* *
6161 TTCAATATTTTATTCCCGTTTTGCCCTTCGCGGTCGGAAGGTGTTGTCTTCAATGTTTTATACCC
131 TTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCC
*
6226 ATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATT
196 ATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATT
*
6271 CCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCATTTTGCCCTTCCC
1 CCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCTATTTTGCCCTTCCC
6336 GGTCGGAAGGTGTTG-TTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
66 GGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
* *
6400 TTCAATATTTTA-TCCTCATTTTGCCCTTCCCGGTCGGAAGGTGTTCTCTTCAATGTTTTATTCC
131 TTCAATATTTTATTCC-CGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCC
* *
6464 CATTTTGCCCTTCCCGGACGGAAGGTGTTGTTTTCAATATTTTATT
195 CATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATT
6510 -CATGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATT-CTCATTTTGCCCTTC
1 CCA-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCT-ATTTTGCCCTTC
*
6573 CCGGTCAGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
64 CCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG
* ** * * * *
6638 TCTTCAACGTTTTATTCCCGTTTTGCCATTCCCAGTCGGAAGGTGTTGTTTTCAATATTTTATTC
129 TTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTC
***
6703 TTGTTTTGCCCTTCCCGGTCGGAAGGTGTT
194 CCATTTTGCCCTTCCCGGTCGGAAGGTGTT
6733 TGATCGAGCT
Statistics
Matches: 422, Mismatches: 33, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
238 25 0.06
239 269 0.64
240 125 0.30
241 3 0.01
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (240 bp):
CCAGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCTATTTTGCCCTTCCC
GGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTT
TTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCC
ATTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATATTTTATT
Found at i:7599 original size:11 final size:11
Alignment explanation
Indices: 7583--7608 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7573 AGATAATTTC
7583 TTTTCTTCTAG
1 TTTTCTTCTAG
7594 TTTTCTTCTAG
1 TTTTCTTCTAG
7605 TTTT
1 TTTT
7609 TTAGGGCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:8689 original size:28 final size:28
Alignment explanation
Indices: 8641--8696 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
8631 TTTCTTAGTC
8641 TCTGCGTTTCTGTCCTAAAAAAAAAAAT
1 TCTGCGTTTCTGTCCTAAAAAAAAAAAT
* *
8669 TCTGCGTTT-TTTTCTATAAAAAAAAAAT
1 TCTGCGTTTCTGTCCTA-AAAAAAAAAAT
8697 ATATTTTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (28 bp):
TCTGCGTTTCTGTCCTAAAAAAAAAAAT
Found at i:10308 original size:48 final size:48
Alignment explanation
Indices: 10237--10841 Score: 772
Period size: 48 Copynumber: 12.9 Consensus size: 48
10227 CTCCAAGCCG
* *
10237 TGCCCTTCCCCGTCGGAAGGTGTTGTTTTCAATATTTTATTCATGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * *
10285 TGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTATTCCCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * *
10333 TGCCCTTCCCAGTCGGAAGGTGTTGTTTTCAATATATTATTCTTGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * *
10381 TGCCCTTCCTGGTCGGAAGATGTTGTTTTCAATATTTTATTCATGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* *
10429 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATT-CTCATTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCT-GTTT
* *
10477 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* *
10525 TGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTTTTA--------T
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * *
10565 T-CCCTTCCTGGTCGGAAGGTG-AGATTTTCAATATTTTATTCCCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTG-TTTTCAATATTTTATTCCTGTTT
*
10612 TTCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * * *
10660 TGCCCGTCCCGGTCGGAA-G-G-TGTCTTCAATGTTTTATTCCCGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * *
10705 TACCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTATTCATGTTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * * *
10753 TGCCCTTCCCAGTCAGAAGGTGTTGTTTTCAATGTTTTATTCCTATTT
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
* * *
10801 TG-ACTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTCATTC
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTC
10842 ATGCCTTCAA
Statistics
Matches: 483, Mismatches: 58, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.00
39 31 0.06
40 2 0.00
45 38 0.08
46 2 0.00
47 38 0.08
48 369 0.76
49 2 0.00
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (48 bp):
TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTT
Found at i:10578 original size:39 final size:39
Alignment explanation
Indices: 10527--10607 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
10517 TCCCGTTTTG
* *
10527 CCCTTCCCGGTCGGAAGGTGTTG-TCTTCAATGTTTTATT
1 CCCTTCCCGGTCGGAAGGTG-AGATCTTCAATATTTTATT
* *
10566 CCCTTCCTGGTCGGAAGGTGAGATTTTCAATATTTTATT
1 CCCTTCCCGGTCGGAAGGTGAGATCTTCAATATTTTATT
10605 CCC
1 CCC
10608 GTTTTTCCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (39 bp):
CCCTTCCCGGTCGGAAGGTGAGATCTTCAATATTTTATT
Found at i:10593 original size:87 final size:85
Alignment explanation
Indices: 10479--10746 Score: 322
Period size: 87 Copynumber: 3.0 Consensus size: 85
10469 TCTCATTTTG
* * *
10479 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAG
1 CCCTTCCTGGTCGGAAGGTG--GTTTTCAATATTTTATTCCCGTTTTACCCTTCCCGGTCGGAAG
* *
10544 GTGTTGTCTTCAATGTTTTATT
64 GTGTTGTTTTCAATATTTTATT
*
10566 CCCTTCCTGGTCGGAAGGTGAGATTTTCAATATTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAG
1 CCCTTCCTGGTCGGAAGGTG-G-TTTTCAATATTTTATTCCCGTTTTACCCTTCCCGGTCGGAAG
10631 GTGTTGTTTTCAATATTTTATT
64 GTGTTGTTTTCAATATTTTATT
* * *
10653 CCTGTTTTGCCCGTCCCGGTCGGAAGGT-GTCTTCAATGTTTTATTCCCGTTTTACCCTTCCCGG
1 CC---CTT--CC-T---GGTCGGAAGGTGGTTTTCAATATTTTATTCCCGTTTTACCCTTCCCGG
*
10717 TCGGAAGGTGTTGTTTTCAAAATTTTATT
57 TCGGAAGGTGTTGTTTTCAATATTTTATT
10746 C
1 C
10747 ATGTTTTGCC
Statistics
Matches: 160, Mismatches: 11, Indels: 14
0.86 0.06 0.08
Matches are distributed among these distances:
86 1 0.01
87 81 0.51
90 2 0.01
92 2 0.01
93 62 0.39
94 1 0.01
96 11 0.07
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.42
Consensus pattern (85 bp):
CCCTTCCTGGTCGGAAGGTGGTTTTCAATATTTTATTCCCGTTTTACCCTTCCCGGTCGGAAGGT
GTTGTTTTCAATATTTTATT
Found at i:10673 original size:135 final size:135
Alignment explanation
Indices: 10431--10841 Score: 508
Period size: 135 Copynumber: 3.0 Consensus size: 135
10421 TCATGTTTTG
* * * *
10431 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTCATTCTCATTTTGCCCTTCCCGGTCGGAAG
1 CCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTTATTCACGTTTTGCCCTTCCCGGTCGGAAG
* *
10496 GTGTTGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTT
66 GTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTT
10561 TTATT
131 TTATT
* * *
10566 CCCTTCCTGGTCGGAAGGTG-AGATTTTCAATATTTTATTCCCGTTTTTCCCTTCCCGGTCGGAA
1 CCCTTCCTGGTCGGAAGGTGTTG-TTTTCAATATTTTATTCACGTTTTGCCCTTCCCGGTCGGAA
*
10630 GGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCGTCCCGGTCGGAA-G-G-TGTCTTCAATGT
65 GGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGT
10692 TTTATT
130 TTTATT
* *
10698 CCCGTTTTACCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTATTCATGTTTTGCCCTTCCC
1 CCC---TT--CC-T---GGTCGGAAGGTGTTGTTTTCAATATTTTATTCACGTTTTGCCCTTCCC
* * * * * * *
10763 AGTCAGAAGGTGTTGTTTTCAATGTTTTATTCCTATTTTG-ACTTCCCGGTAGGAAGGTGTTGTT
57 GGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTC
* *
10827 TTCAATATTTCATT
122 TTCAATGTTTTATT
10841 C
1 C
10842 ATGCCTTCAA
Statistics
Matches: 238, Mismatches: 24, Indels: 20
0.84 0.09 0.07
Matches are distributed among these distances:
132 21 0.09
133 1 0.00
134 2 0.01
135 103 0.43
137 2 0.01
138 1 0.00
140 12 0.05
141 78 0.33
142 2 0.01
143 16 0.07
ACGTcount: A:0.15, C:0.22, G:0.20, T:0.43
Consensus pattern (135 bp):
CCCTTCCTGGTCGGAAGGTGTTGTTTTCAATATTTTATTCACGTTTTGCCCTTCCCGGTCGGAAG
GTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTCTTCAATGTT
TTATT
Found at i:10724 original size:93 final size:96
Alignment explanation
Indices: 10591--10844 Score: 356
Period size: 93 Copynumber: 2.7 Consensus size: 96
10581 AGGTGAGATT
* * *
10591 TTCAATATTTTATTCCCGTTTTTCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCT
1 TTCAATGTTTTATTCCCGTTTTACCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCAT
* *
10656 GTTTTGCCCGTCCCGGTCGGAA-G-G-TGTC
66 GTTTTGCCCGTCCCAGTCAGAAGGTGTTGTC
*
10684 TTCAATGTTTTATTCCCGTTTTACCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTATTCAT
1 TTCAATGTTTTATTCCCGTTTTACCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCAT
* *
10749 GTTTTGCCCTTCCCAGTCAGAAGGTGTTGTT
66 GTTTTGCCCGTCCCAGTCAGAAGGTGTTGTC
** * *
10780 TTCAATGTTTTATTCCTATTTTGA--CTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTCATTCA
1 TTCAATGTTTTATTCCCGTTTT-ACCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCA
10843 TG
65 TG
10845 CCTTCAATGT
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
93 80 0.56
94 1 0.01
95 39 0.27
96 23 0.16
97 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.44
Consensus pattern (96 bp):
TTCAATGTTTTATTCCCGTTTTACCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCAT
GTTTTGCCCGTCCCAGTCAGAAGGTGTTGTC
Found at i:20382 original size:11 final size:11
Alignment explanation
Indices: 20366--20391 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20356 AGATAATTTC
20366 TTTTCTTCTAG
1 TTTTCTTCTAG
20377 TTTTCTTCTAG
1 TTTTCTTCTAG
20388 TTTT
1 TTTT
20392 TAGGCAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:21181 original size:15 final size:15
Alignment explanation
Indices: 21151--21192 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
21141 TTACTCTGCT
21151 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
21167 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
21182 TTGCTTTCTGT
1 TTGTTTTCTGT
21193 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:36292 original size:2 final size:2
Alignment explanation
Indices: 36285--36316 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
36275 ACATTAACAT
36285 TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
36317 CATAAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40493 original size:22 final size:22
Alignment explanation
Indices: 40424--40529 Score: 54
Period size: 22 Copynumber: 4.8 Consensus size: 22
40414 TACTAACAAT
* *
40424 TCATATGGAGGTTATTAAAATT
1 TCATATGGAGGTTATCAAAATA
* * * *
40446 TTATAAT-GTGGTTATCGATATA
1 TCAT-ATGGAGGTTATCAAAATA
* *
40468 TCATATGGAGGTTATCAACATC
1 TCATATGGAGGTTATCAAAATA
** * *
40490 TCATAGTGTTGGTTGTCAAAATT
1 TCATA-TGGAGGTTATCAAAATA
*
40513 TCAT-TGGGAAGTTATCA
1 TCATAT-GGAGGTTATCA
40530 TCATAGTGAG
Statistics
Matches: 60, Mismatches: 20, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
21 3 0.05
22 39 0.65
23 18 0.30
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (22 bp):
TCATATGGAGGTTATCAAAATA
Found at i:40594 original size:21 final size:22
Alignment explanation
Indices: 40546--40595 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
40536 TGAGGTCTTT
* * *
40546 AAAATTCCTTAAGGAGGTTAAC
1 AAAATTTCATAAGAAGGTTAAC
40568 AAAATTTCATAAGAAGGTTAA-
1 AAAATTTCATAAGAAGGTTAAC
40589 AAAATTT
1 AAAATTT
40596 AAAAAAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTTAAC
Found at i:40681 original size:22 final size:22
Alignment explanation
Indices: 40634--40681 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
40624 TATCGTTATT
* *
40634 AAAATTTTATAGCAAGGTTATC
1 AAAATTTTATAGCAAGGTCATA
*
40656 AAAATTTTATAAG-GAGGTCATA
1 AAAATTTTAT-AGCAAGGTCATA
40678 AAAA
1 AAAA
40682 AATATTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (22 bp):
AAAATTTTATAGCAAGGTCATA
Found at i:47933 original size:20 final size:19
Alignment explanation
Indices: 47904--47941 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
47894 AATGCCAACT
47904 AAAAACATAGCTTTTATAA
1 AAAAACATAGCTTTTATAA
47923 AAAAGACATAGCTTTTATA
1 AAAA-ACATAGCTTTTATA
47942 TTTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (19 bp):
AAAAACATAGCTTTTATAA
Found at i:48818 original size:29 final size:30
Alignment explanation
Indices: 48767--48824 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
48757 TAAAAGCAAA
*
48767 TAAGGGCCTGACCTTTAGGGAAAAGGTCATT
1 TAAGGGCCTGAACTTTA-GGAAAAGGTCATT
48798 TAAGGGCCTGAACTTTA-GAAAAGGTCA
1 TAAGGGCCTGAACTTTAGGAAAAGGTCA
48825 AATCAGTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.38
31 16 0.62
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24
Consensus pattern (30 bp):
TAAGGGCCTGAACTTTAGGAAAAGGTCATT
Found at i:50678 original size:15 final size:15
Alignment explanation
Indices: 50645--50678 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
50635 AGTTAGAATC
* *
50645 TATATCTATATTATC
1 TATATCTATACTATA
50660 TATATCTATACTATA
1 TATATCTATACTATA
50675 TATA
1 TATA
50679 AAAGTACGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
TATATCTATACTATA
Found at i:50756 original size:31 final size:31
Alignment explanation
Indices: 50700--50758 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
50690 TTTGTAAAAC
*
50700 TTTTGAAACGCCTATTGTAACCTTATTTAAT
1 TTTTGAAACGCCTATTATAACCTTATTTAAT
**
50731 TTTTGAAACGCCTATTATATTCTTATTT
1 TTTTGAAACGCCTATTATAACCTTATTT
50759 GTCTAACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (31 bp):
TTTTGAAACGCCTATTATAACCTTATTTAAT
Found at i:51859 original size:45 final size:45
Alignment explanation
Indices: 51792--51888 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
51782 AGCAACAATT
* * * *
51792 AATATTAACTTTATATTGATGAATTATCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATATTAATGAATTACCTAGAGATGGAGGACTAG
* * *
51837 AATATTAGTTTTATTTTAATGAATTACCTAGAGATGGAGTACTAG
1 AATATTAGCTTTATATTAATGAATTACCTAGAGATGGAGGACTAG
51882 AAT-TTAG
1 AATATTAG
51889 GTAATGTACT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 4 0.09
45 41 0.91
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (45 bp):
AATATTAGCTTTATATTAATGAATTACCTAGAGATGGAGGACTAG
Found at i:54996 original size:15 final size:16
Alignment explanation
Indices: 54978--55007 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
54968 TTTTTCTCTC
54978 TTTTCTTTTC-TTTTT
1 TTTTCTTTTCGTTTTT
54993 TTTTCTTTTCGTTTT
1 TTTTCTTTTCGTTTT
55008 GTAATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTCGTTTTT
Found at i:56362 original size:83 final size:84
Alignment explanation
Indices: 56270--56427 Score: 266
Period size: 84 Copynumber: 1.9 Consensus size: 84
56260 TATTTTTATT
56270 TAATTAAATCTAAT-TCTTTATAACTATTTTATTTTTACCA-TTTTAATATTTTAATTAAAAAAA
1 TAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTAATATTTTAATT-AAAAAA
56333 CTTAGATATATTAGAATTTA
65 CTTAGATATATTAGAATTTA
* * *
56353 TAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTACTATTTTAATTACATAAC
1 TAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTAATATTTTAATTAAAAAAC
56418 TTAGATATAT
66 TTAGATATAT
56428 ATTATAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
83 14 0.20
84 41 0.59
85 15 0.21
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (84 bp):
TAATTAAATCTAATCTCTTTATAACTATTTTATTTTTACCATTTTTAATATTTTAATTAAAAAAC
TTAGATATATTAGAATTTA
Found at i:56562 original size:50 final size:47
Alignment explanation
Indices: 56507--56613 Score: 119
Period size: 50 Copynumber: 2.2 Consensus size: 47
56497 TCTATTTTTA
* *
56507 TTTAATTAAAT-TCAATATTTTTATAAATATTTTATTTTTACCATTTTAAT
1 TTTAATAAAATATCAAT-TTTTTAAAAATA-TTTA--TTTACCATTTTAAT
***
56557 TTTAATAAAATATTGGTTTTTTAAAAATATTTATTTACCATTTTAAT
1 TTTAATAAAATATCAATTTTTTAAAAATATTTATTTACCATTTTAAT
56604 TTTAA-AAAAT
1 TTTAATAAAAT
56614 TGGAGACTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
46 5 0.10
47 19 0.37
49 4 0.08
50 21 0.41
51 2 0.04
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (47 bp):
TTTAATAAAATATCAATTTTTTAAAAATATTTATTTACCATTTTAAT
Found at i:67541 original size:45 final size:46
Alignment explanation
Indices: 67477--67607 Score: 205
Period size: 45 Copynumber: 2.9 Consensus size: 46
67467 TTTTTTTTTT
67477 TTTTTTTATATTCATTTTAGAAGTTGTGTGTAATTAGTTATG-TTG
1 TTTTTTTATATTCATTTTAGAAGTTGTGTGTAATTAGTTATGTTTG
* * *
67522 TTTTTTTATATTCATTTTAGGAGTTGTGTGT--TTAGTCATGTTTT
1 TTTTTTTATATTCATTTTAGAAGTTGTGTGTAATTAGTTATGTTTG
67566 TTTTTTGTATATTCATTTTAGAAGTTGTGTGTAATTAGTTAT
1 TTTTTT-TATATTCATTTTAGAAGTTGTGTGTAATTAGTTAT
67608 TTTAGATTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
43 8 0.10
44 8 0.10
45 54 0.70
47 7 0.09
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (46 bp):
TTTTTTTATATTCATTTTAGAAGTTGTGTGTAATTAGTTATGTTTG
Found at i:68112 original size:19 final size:19
Alignment explanation
Indices: 68088--68137 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 19
68078 CTAAAAGGGG
68088 CATTACTTCATCAAAAGCC
1 CATTACTTCATCAAAAGCC
* **
68107 CATTAC-CCATTGAAAGCC
1 CATTACTTCATCAAAAGCC
68125 CATTA-TTCA-CAAA
1 CATTACTTCATCAAA
68138 TGATTAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
17 2 0.08
18 16 0.67
19 6 0.25
ACGTcount: A:0.38, C:0.30, G:0.06, T:0.26
Consensus pattern (19 bp):
CATTACTTCATCAAAAGCC
Found at i:68573 original size:132 final size:133
Alignment explanation
Indices: 68349--68854 Score: 858
Period size: 132 Copynumber: 3.8 Consensus size: 133
68339 TAAACAAACT
* *
68349 ATTGTGGTGGTAACTCCAACAATGGTGGTCACCATTTGATTGTAAGAACCC-ATATATCAAGAGG
1 ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCCGATATATCAAGAGG
* *
68413 TAGCTTAAATCATGGTGGCCGACTTAGAATGGTAAATCCCCATGGTTTCCTTCTCCC-TTAAACG
66 TAGCTTAAATCATGGTGGCCGGCCTAGAATGGTAAATCCCCATGGTTTCCTTC-CCCTTTAAACG
68477 AG-C
130 AGTC
68480 AATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCC-ATATATCAAGAG
1 -ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCCGATATATCAAGAG
68544 GTAGCTTAAATCATGGTGGCCGGCCTAGAATGGTAAATCCCCATGGTTTCCTTCCCCTTTAAACG
65 GTAGCTTAAATCATGGTGGCCGGCCTAGAATGGTAAATCCCCATGGTTTCCTTCCCCTTTAAACG
68609 AGTC
130 AGTC
*
68613 ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATCTGATTGTAAGAACCCGTATATATCAAGAG
1 ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCCG-ATATATCAAGAG
* * *
68678 ATAACTTAAATCATGGTGGCTGGCCTAGAATGGTAAATCCCCCATGGTTTCCTTCCCCTTTAAAC
65 GTAGCTTAAATCATGGTGGCCGGCCTAGAATGGTAAAT-CCCCATGGTTTCCTTCCCCTTTAAAC
68743 GAGTC
129 GAGTC
68748 ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCCGTATATATCAAGAG
1 ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCCG-ATATATCAAGAG
*
68813 GTAGCTTAAATCAGGGTGGCCGGCCTAGAATGGTAAATCCCC
65 GTAGCTTAAATCATGGTGGCCGGCCTAGAATGGTAAATCCCC
68855 CCTGGTTCAT
Statistics
Matches: 356, Mismatches: 13, Indels: 8
0.94 0.03 0.02
Matches are distributed among these distances:
131 3 0.01
132 172 0.48
133 1 0.00
134 51 0.14
135 129 0.36
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (133 bp):
ATTGCGGTGGTAACTCCAACAATGGCGGTCACCATTTGATTGTAAGAACCCGATATATCAAGAGG
TAGCTTAAATCATGGTGGCCGGCCTAGAATGGTAAATCCCCATGGTTTCCTTCCCCTTTAAACGA
GTC
Found at i:68967 original size:64 final size:64
Alignment explanation
Indices: 68866--69134 Score: 486
Period size: 64 Copynumber: 4.2 Consensus size: 64
68856 CTGGTTCATC
* *
68866 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCAAGCATTACGTCTCTCACCTTATTT
1 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTT
*
68930 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCAATATGTCTCTCACCTTATTT
1 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTT
68994 ACAAAG-CCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTT
1 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTT
* *
69057 ACAAAGCCCACTATACTATGTGGCAAGATATTGGTTATCGAGCATTATGTCTCTCACCTTATTT
1 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTT
69121 ACAAAGCCCACTAT
1 ACAAAGCCCACTAT
69135 GTGGCAAGGC
Statistics
Matches: 198, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
63 62 0.31
64 136 0.69
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (64 bp):
ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTT
Found at i:69099 original size:127 final size:127
Alignment explanation
Indices: 68866--69153 Score: 485
Period size: 127 Copynumber: 2.3 Consensus size: 127
68856 CTGGTTCATC
68866 ACAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCAAGCATTACGTCTCTCACCTTATTTA
1 ACAAAG-CCACTATACTATGTGGCAAGACATTGGTGATCAAGCATTACGTCTCTCACCTTATTTA
68931 CAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCAATATGTCTCTCACCTTATTT
65 CAAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCAATATGTCTCTCACCTTATTT
* *
68994 ACAAAGCCACTATACTATGTGGCAAGACATTGGTGATCGAGCATTATGTCTCTCACCTTATTTAC
1 ACAAAGCCACTATACTATGTGGCAAGACATTGGTGATCAAGCATTACGTCTCTCACCTTATTTAC
* * *
69059 AAAGCCCACTATACTATGTGGCAAGATATTGGTTATCGAGCATTATGTCTCTCACCTTATTT
66 AAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCAATATGTCTCTCACCTTATTT
*
69121 ACAAAGCC-C---ACTATGTGGCAAGGCATTGGTGAT
1 ACAAAGCCACTATACTATGTGGCAAGACATTGGTGAT
69154 TGAGAAACCC
Statistics
Matches: 154, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
123 23 0.15
126 1 0.01
127 124 0.81
128 6 0.04
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (127 bp):
ACAAAGCCACTATACTATGTGGCAAGACATTGGTGATCAAGCATTACGTCTCTCACCTTATTTAC
AAAGCCCACTATACTATGTGGCAAGACATTGGTGATCGAGCAATATGTCTCTCACCTTATTT
Found at i:70009 original size:20 final size:21
Alignment explanation
Indices: 69984--70023 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
69974 TGAAGGGAAT
69984 CTTGT-CATAAGCATTAAATG
1 CTTGTCCATAAGCATTAAATG
* *
70004 CTTGTCCTTGAGCATTAAAT
1 CTTGTCCATAAGCATTAAAT
70024 TTTGATGGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
CTTGTCCATAAGCATTAAATG
Found at i:71337 original size:124 final size:124
Alignment explanation
Indices: 71162--71397 Score: 314
Period size: 124 Copynumber: 1.9 Consensus size: 124
71152 GTGGGACTGC
* * * ** *
71162 CTTGCTGACGTGTCACTCTGCCGAGGAGGAGTTTCCGTTGCTGGAAAGTGCTGCTGGGCACTTTC
1 CTTGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCTGCCAGAAAGTGCTGCTGGACAC-TTC
*
71227 -ACCAAAGTCTTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAAT
65 AACCAAAGTCCTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAAT
* *
71286 CTTGCTGATGTGTCACTCTGTCGAGGAAGAGGTTCCGCTGCCCAG-AAGTGCTGCTGGACACTTC
1 CTTGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCTG-CCAGAAAGTGCTGCTGGACACTTC
* * * * *
71350 AACCTAAGTCCTGTTCTTTATCAACAAAGGAGGTCAGTAGCGTGGCTA
65 AACCAAAGTCCTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTA
71398 CTATGGTACA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
123 3 0.03
124 91 0.95
125 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (124 bp):
CTTGCTGACGTGTCACTCTGCCGAGGAAGAGGTTCCGCTGCCAGAAAGTGCTGCTGGACACTTCA
ACCAAAGTCCTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAAT
Found at i:71419 original size:124 final size:124
Alignment explanation
Indices: 71164--71424 Score: 296
Period size: 124 Copynumber: 2.1 Consensus size: 124
71154 GGGACTGCCT
* * * * ** *
71164 TGCTGACGTGTCACTCTGCCGAGGAGGAGTTTCCGTTGCTGGAAAGTGCTGCTGGGCACTTTCAC
1 TGCTGATGTGTCACTCTGCCGAGGAAGAGGTTCCGCTGCCAGAAAGTGCTGCTGGACACTTTCAC
* * * *
71229 CAAAGTCTTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAACCTGGTGCAATCT
66 CAAAGTCCTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAACATGGTACAATCC
*
71288 TGCTGATGTGTCACTCTGTCGAGGAAGAGGTTCCGCTGCCCAG-AAGTGCTGCTGGACAC-TTCA
1 TGCTGATGTGTCACTCTGCCGAGGAAGAGGTTCCGCTG-CCAGAAAGTGCTGCTGGACACTTTC-
* * * * *
71351 ACCTAAGTCCTGTTCTTTATCAACAAAGGAGGTCAGTAGCGTGGCT-ACTATGGTACAA-CGC
64 ACCAAAGTCCTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAAC-ATGGTACAATC-C
*
71412 TGTTGATGTGTCA
1 TGCTGATGTGTCA
71425 TTCTACCAAG
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
123 6 0.05
124 107 0.93
125 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (124 bp):
TGCTGATGTGTCACTCTGCCGAGGAAGAGGTTCCGCTGCCAGAAAGTGCTGCTGGACACTTTCAC
CAAAGTCCTATCCTTTATCAACAAAGGAGGTCAGCAGCATGGCTAACATGGTACAATCC
Found at i:71586 original size:137 final size:137
Alignment explanation
Indices: 71330--71586 Score: 313
Period size: 137 Copynumber: 1.9 Consensus size: 137
71320 CCGCTGCCCA
* * * *
71330 GAAGTGCTGCTGGACACTTCAACCTAAGTCCTGTTCTTTATCAACAAAGGAGGTCAGTAGCGTGG
1 GAAGTGATGCTGGACACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGATCAGTAGCGTGG
* * * * *
71395 CTACTATGGTACAACGCTGTTGATGTGTCATTCTACCAAGAGGGAGGCACTTCTGTCGAGACACG
66 CTACGATGGTACAACACTGTTGAGGTGTCATCCTACCAAGAGGGAAGCACTTCTGTCGAGACACG
71460 CTGCTGG
131 CTGCTGG
* * * * *
71467 GAAGTGATGCTGGGCACTTCAATCGAAGTCCTTTTCTTCATCAACAAATGAGATCAGTAGTGTGG
1 GAAGTGATGCTGGACACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGATCAGTAGCGTGG
* * *
71532 TTCT-CGA-GGTGCAACACTGTTGAGGTGTCATCCTGCCAAG-GAGGAAGCATTTCTG
66 --CTACGATGGTACAACACTGTTGAGGTGTCATCCTACCAAGAG-GGAAGCACTTCTG
71587 CCTAGAGGTG
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
136 1 0.01
137 95 0.95
138 2 0.02
139 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (137 bp):
GAAGTGATGCTGGACACTTCAACCGAAGTCCTGTTCTTCATCAACAAAGGAGATCAGTAGCGTGG
CTACGATGGTACAACACTGTTGAGGTGTCATCCTACCAAGAGGGAAGCACTTCTGTCGAGACACG
CTGCTGG
Found at i:72277 original size:30 final size:31
Alignment explanation
Indices: 72241--72320 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 31
72231 ACATTTTCGT
*
72241 AACGTTATATCCTGAATTGTCA-CTTCA-TCA
1 AACGTTATATCCTGAATTG-CATCTTCAGGCA
* *
72271 AACGTTATATCCTGAATTGGATTTTCAGGCA
1 AACGTTATATCCTGAATTGCATCTTCAGGCA
*
72302 AACGTTATATCTTGAATTG
1 AACGTTATATCCTGAATTG
72321 ATCATTTAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 1 0.02
30 23 0.52
31 20 0.45
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (31 bp):
AACGTTATATCCTGAATTGCATCTTCAGGCA
Found at i:74850 original size:24 final size:24
Alignment explanation
Indices: 74822--74889 Score: 102
Period size: 24 Copynumber: 2.8 Consensus size: 24
74812 CTTTTTTTCT
74822 AATTTTTTAATT-TCTTAATTCCAA
1 AATTTTTTAATTAT-TTAATTCCAA
**
74846 AATTTTTTAATTATTTAATTCTGA
1 AATTTTTTAATTATTTAATTCCAA
74870 AATTTTTTAATTATTTAATT
1 AATTTTTTAATTATTTAATT
74890 TTTAATTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
24 40 0.98
25 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (24 bp):
AATTTTTTAATTATTTAATTCCAA
Found at i:74865 original size:16 final size:15
Alignment explanation
Indices: 74846--74897 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
74836 TTAATTCCAA
74846 AATTTTTTAATTATTT
1 AATTTTTTAATT-TTT
* **
74862 AATTCTGAAATTTTTT
1 AATTTTTTAA-TTTTT
*
74878 AATTATTTAATTTTT
1 AATTTTTTAATTTTT
74893 AATTT
1 AATTT
74898 AAAAATTTCC
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
15 9 0.32
16 17 0.61
17 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
AATTTTTTAATTTTT
Done.