Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001092.1 Hibiscus syriacus cultivar Beakdansim tig00002159_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: 62011
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:9 original size:4 final size:4
Alignment explanation
Indices: 1--3660 Score: 6047
Period size: 4 Copynumber: 927.5 Consensus size: 4
*
1 CATA CATA CATA CATA CATA CATA CCTA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
49 CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATA -ATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
142 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATC
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
190 CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CAT- CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
236 CATA CATA CATA CATA CATA CAGA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
284 CATA CATTA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAGA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
333 CATA CATA CATA CATA CATA CATA CATA CATA -ACTA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA CATA
*
381 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATAGA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT--A CATA
*
431 CATA CATA CATA CATA CATA CATA CATA CATA CAGA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
478 CATA CATA CAT- CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
525 CATA CATA CATA CATA CATA CATA CATA CATC CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
573 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CCTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
621 CATA CATA CATA CATA CATA CATA CAGA C-TA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
666 CATAA CATA CATA CATA CA-A CATA CATCA CATA -ATA CATA CATA CATA
1 CAT-A CATA CATA CATA CATA CATA CAT-A CATA CATA CATA CATA CATA
*
714 CATA CATA CATA CATTA CATA CATA CATA CTAAA CATA CATA C--A CATA
1 CATA CATA CATA CA-TA CATA CATA CATA C-ATA CATA CATA CATA CATA
762 CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CA-A CATTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-TA
809 CATA CAT- CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
856 CATA CATA CATA CATA C--A CATA CATA -ATA CATA CCTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
901 CA-A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
948 CATA CATA CATA C-TA CATA C-TA CATA CAATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA CATA
995 CATTA CATA CATA CATA CATA CATA CATA CATA CATA -ATA CATA C--A
1 CA-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1041 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1089 CATA C-TA CATA CAGA C-TA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1135 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1183 C-TA CATA CATA CATA CATC CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1230 CAT- -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1276 CATA CATA CATA CATA CATA CATA CATAA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CAT-A CATA CATA CATA CATA CATA
1325 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1373 CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1419 CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1465 CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1511 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1559 CATA CATA CATA -ATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1606 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1654 CATA CATA CATA CATA CATA CATA CA-A CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1701 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1748 CATA C-TA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
1794 CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CCTA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1840 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1888 CATA CATA CATA CATA C--A CATA CAT- -ATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1930 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1978 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2026 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2073 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2121 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2169 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2217 CATA CATA CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2263 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2311 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2359 CATA CCATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA -CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2408 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2456 CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
2500 CATA CATA CATA CAGA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2548 C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2594 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2642 CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT- -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2688 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2736 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2784 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2832 CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2878 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2926 CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
2972 CATA CATA CATA CATA CA-A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3019 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
3067 CATA CATA CATA CATA CGTA CGTA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
3115 CATA CATA CGTA CATA CATA CGTA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3163 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
3211 CATA CATA CATA CATA CATA CATA CATA CGTA CGTA CGTA CGTA CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
3259 TATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3307 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * *
3355 CATA CATA CATA CGTA CGTA CGTATA TATA CGTA CGTA CATA CATA TATA
1 CATA CATA CATA CATA CATA C--ATA CATA CATA CATA CATA CATA CATA
* * ** * * *
3405 CGTA TATA CATA TGTA -AGTA TATA CGTA CATA CATA CGTA CATA CATA
1 CATA CATA CATA CATA CA-TA CATA CATA CATA CATA CATA CATA CATA
** * *
3453 TGTA CATA CATA CATA CGTA CATA CATA CGTA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * ** *
3501 CATA CATA CATA TC-TA CGTA CATA CATA TGTATA CGTA TGTA CATA CGTA
1 CATA CATA CATA -CATA CATA CATA CATA --CATA CATA CATA CATA CATA
* * * ** * * *
3551 TATA CATA CATG CATA TC-TA CGTA CATA CATA TGTA CGTA TATA CGTA
1 CATA CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * * *
3599 TATG CGTA TATA CATA CATG CATA CATA CGTA CATA CGTA TATG CGTA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
3647 CATA CGTA CATA CA
1 CATA CATA CATA CA
3661 AAGTTGCACA
Statistics
Matches: 3454, Mismatches: 112, Indels: 180
0.92 0.03 0.05
Matches are distributed among these distances:
2 40 0.01
3 78 0.02
4 3286 0.95
5 42 0.01
6 8 0.00
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:5753 original size:60 final size:59
Alignment explanation
Indices: 5680--5814 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 59
5670 TTTTTAGAGT
*
5680 AAAGTACACAAATG-GTC-CCATGACTATA-ATATATTGCTTTATTAAGTCCCTTGACTATTA
1 AAAGTACA-AAATGAGTCTCC--GACTATAGA-ATATTGCTTTATTAAGTCCCTCGACTATTA
* * * * *
5740 AAAGTTACAAAATGATTCTCCGACTATAGAGTGTTGCTTTGTTGAGTCCCTCGACTATTA
1 AAAG-TACAAAATGAGTCTCCGACTATAGAATATTGCTTTATTAAGTCCCTCGACTATTA
5800 AAAGCTACAAAATGA
1 AAAG-TACAAAATGA
5815 TCACCCGACT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
60 55 0.86
61 7 0.11
62 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (59 bp):
AAAGTACAAAATGAGTCTCCGACTATAGAATATTGCTTTATTAAGTCCCTCGACTATTA
Found at i:5823 original size:60 final size:60
Alignment explanation
Indices: 5713--5826 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
5703 CTATAATATA
* * *
5713 TTGCTTTATTAAGTCCCTTGACTATTAAAAGTTACAAAATGATTCTCCGACTATAGAGTG
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTCCCCGACTATAGAGTG
* *
5773 TTGCTTTGTTGAGTCCCTCGACTATTAAAAGCTACAAAATGA-TCACCCGACTAT
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTC-CCCGACTAT
5827 TCATTATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (60 bp):
TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTCCCCGACTATAGAGTG
Found at i:7362 original size:12 final size:12
Alignment explanation
Indices: 7345--7371 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7335 GATTGTTGGG
7345 AAGAATTTTAAT
1 AAGAATTTTAAT
7357 AAGAATTTTAAT
1 AAGAATTTTAAT
7369 AAG
1 AAG
7372 TGAATGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
AAGAATTTTAAT
Found at i:7797 original size:16 final size:16
Alignment explanation
Indices: 7773--7835 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
7763 AATGAATGAA
*
7773 CAAACATAAATAACTT
1 CAAAAATAAATAACTT
**
7789 CAAAAATAAATAAACGAA
1 CAAAAATAAAT-AAC-TT
*
7807 CAAACATAAATAACTT
1 CAAAAATAAATAACTT
7823 CAAAAATAAATAA
1 CAAAAATAAATAA
7836 ACGAACACGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 22 0.58
17 6 0.16
18 10 0.26
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (16 bp):
CAAAAATAAATAACTT
Found at i:7808 original size:34 final size:34
Alignment explanation
Indices: 7761--7851 Score: 146
Period size: 34 Copynumber: 2.6 Consensus size: 34
7751 TCACAAACAC
* *
7761 TAAATGAATGAACAAACATAAATAACTTCAAAAA
1 TAAATAAACGAACAAACATAAATAACTTCAAAAA
7795 TAAATAAACGAACAAACATAAATAACTTCAAAAA
1 TAAATAAACGAACAAACATAAATAACTTCAAAAA
7829 TAAATAAACGAACACGAACATAA
1 TAAATAAACGAACA--AACATAA
7852 TTTGATTGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
34 46 0.87
36 7 0.13
ACGTcount: A:0.63, C:0.14, G:0.05, T:0.18
Consensus pattern (34 bp):
TAAATAAACGAACAAACATAAATAACTTCAAAAA
Found at i:10563 original size:50 final size:50
Alignment explanation
Indices: 10471--10569 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
10461 TATAAACTTT
* *
10471 TGAAATTCTAATTTCATCCTCAAAATATGATACTCATTCTAAATTAGTCC
1 TGAAATTCCAATTTCATCCTCAAAATATGACACTCATTCTAAATTAGTCC
* * * *
10521 TGAACATTCCAATTTTATCCTC-AACTATGACCCTTATTCTAAATTAGTC
1 TGAA-ATTCCAATTTCATCCTCAAAATATGACACTCATTCTAAATTAGTC
10570 TCTAGACTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 27 0.64
51 15 0.36
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.38
Consensus pattern (50 bp):
TGAAATTCCAATTTCATCCTCAAAATATGACACTCATTCTAAATTAGTCC
Found at i:11927 original size:122 final size:122
Alignment explanation
Indices: 11720--11981 Score: 310
Period size: 122 Copynumber: 2.1 Consensus size: 122
11710 ATTTAATATA
* * ** * ** * * *
11720 TAAACTATCAATTTAGATATGTTTTTATTACCTAAACATTCATTTCTTTCAAAATTATATTTAAA
1 TAAACTATCAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTCTTTCAAAATCAAATCTAAA
* * *
11785 GTTTAGTTTTGGTTGCATTTTAGTATCCGCCGTTAAAAACTTAATGCATCTAGCACC
66 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
*
11842 TAAACTATTAGTTTTGATCCGTTTTTATCATTTAAACATTCATTT-TTTCCAAAATCAAATCTAA
1 TAAACTATCAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTCTTT-CAAAATCAAATCTAA
* * * * * * *
11906 AGTTTAGTTTTTGTTGTATTTTAGTATCCATCATTAAAAACTTAGCGCGTTTAGTACC
65 AGTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
*
11964 TAAACTATCATTTTTGAT
1 TAAACTATCAGTTTTGAT
11982 ATATTTTAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
121 3 0.03
122 113 0.97
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (122 bp):
TAAACTATCAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTCTTTCAAAATCAAATCTAAA
GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
Found at i:12009 original size:122 final size:120
Alignment explanation
Indices: 11720--12016 Score: 306
Period size: 122 Copynumber: 2.4 Consensus size: 120
11710 ATTTAATATA
* * * * * *
11720 TAAACTATCAATTTAGATATGTTTTTATTACCTAAACATTCATTTCTTTCAAAATTATATTTAAA
1 TAAACTATCAATTTTGATAT-ATTTTAATACCTAAACATTCATTT-TTTCAAAATCAAATCTAAA
* * *
11785 GTTTAGTTTTGGTTGCATTTTAGTATCCGCCGTTAAAAACTTAATGCATCTAGCACC
64 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
* * *** * **
11842 TAAACTATTAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTTTTCCAAAATCAAATCTAAA
1 TAAACTATCAATTTTGATATATTTTAAT-ACCTAAACATTCATTTTTT-CAAAATCAAATCTAAA
* * * * * * *
11907 GTTTAGTTTTTGTTGTATTTTAGTATCCATCATTAAAAACTTAGCGCGTTTAGTACC
64 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
* **
11964 TAAACTATCATTTTTGATATATTTTAATACCTAAATTTTCAATTTTTTCAAAA
1 TAAACTATCAATTTTGATATATTTTAATACCTAAACATTC-ATTTTTTCAAAA
12017 CATGGCGACG
Statistics
Matches: 139, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
121 21 0.15
122 118 0.85
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (120 bp):
TAAACTATCAATTTTGATATATTTTAATACCTAAACATTCATTTTTTCAAAATCAAATCTAAAGT
TTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
Found at i:12297 original size:21 final size:21
Alignment explanation
Indices: 12258--12312 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
12248 ATCCTAAACC
12258 TTAAACCCTAAACTATAAGCT
1 TTAAACCCTAAACTATAAGCT
*
12279 TTAACCCCTAAACCT-TAAG-T
1 TTAAACCCTAAA-CTATAAGCT
*
12299 CATAAACCCTAAAC
1 -TTAAACCCTAAAC
12313 AATAGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.42, C:0.29, G:0.04, T:0.25
Consensus pattern (21 bp):
TTAAACCCTAAACTATAAGCT
Found at i:14026 original size:122 final size:122
Alignment explanation
Indices: 13819--14080 Score: 310
Period size: 122 Copynumber: 2.1 Consensus size: 122
13809 ATTTAATATA
* * ** * ** * * *
13819 TAAACTATCAATTTAGATATGTTTTTATTACCTAAACATTCATTTCTTTCAAAATTATATTTAAA
1 TAAACTATCAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTCTTTCAAAATCAAATCTAAA
* * *
13884 GTTTAGTTTTGGTTGCATTTTAGTATCCGCCGTTAAAAACTTAATGCATCTAGCACC
66 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
*
13941 TAAACTATTAGTTTTGATCCGTTTTTATCATTTAAACATTCATTT-TTTCCAAAATCAAATCTAA
1 TAAACTATCAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTCTTT-CAAAATCAAATCTAA
* * * * * * *
14005 AGTTTAGTTTTTGTTGTATTTTAGTATCCATCATTAAAAACTTAGCGCGTTTAGTACC
65 AGTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
*
14063 TAAACTATCATTTTTGAT
1 TAAACTATCAGTTTTGAT
14081 ATATTTTAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
121 3 0.03
122 113 0.97
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (122 bp):
TAAACTATCAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTCTTTCAAAATCAAATCTAAA
GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
Found at i:14108 original size:122 final size:120
Alignment explanation
Indices: 13819--14115 Score: 306
Period size: 122 Copynumber: 2.4 Consensus size: 120
13809 ATTTAATATA
* * * * * *
13819 TAAACTATCAATTTAGATATGTTTTTATTACCTAAACATTCATTTCTTTCAAAATTATATTTAAA
1 TAAACTATCAATTTTGATAT-ATTTTAATACCTAAACATTCATTT-TTTCAAAATCAAATCTAAA
* * *
13884 GTTTAGTTTTGGTTGCATTTTAGTATCCGCCGTTAAAAACTTAATGCATCTAGCACC
64 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
* * *** * **
13941 TAAACTATTAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTTTTCCAAAATCAAATCTAAA
1 TAAACTATCAATTTTGATATATTTTAAT-ACCTAAACATTCATTTTTT-CAAAATCAAATCTAAA
* * * * * * *
14006 GTTTAGTTTTTGTTGTATTTTAGTATCCATCATTAAAAACTTAGCGCGTTTAGTACC
64 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
* **
14063 TAAACTATCATTTTTGATATATTTTAATACCTAAATTTTCAATTTTTTCAAAA
1 TAAACTATCAATTTTGATATATTTTAATACCTAAACATTC-ATTTTTTCAAAA
14116 CATGGCGACG
Statistics
Matches: 139, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
121 21 0.15
122 118 0.85
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.45
Consensus pattern (120 bp):
TAAACTATCAATTTTGATATATTTTAATACCTAAACATTCATTTTTTCAAAATCAAATCTAAAGT
TTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
Found at i:17570 original size:18 final size:18
Alignment explanation
Indices: 17549--17605 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 18
17539 ATGAACGAAT
17549 AAATATAAATAACTTC-A
1 AAATATAAATAACTTCAA
*
17566 AAA-ATAAATAAAC--GAA
1 AAATATAAAT-AACTTCAA
*
17582 CAAACATAAATAACTTCAA
1 -AAATATAAATAACTTCAA
17601 AAATA
1 AAATA
17606 AATAAACGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
16 7 0.23
17 12 0.39
18 10 0.32
19 2 0.06
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATATAAATAACTTCAA
Found at i:17574 original size:16 final size:16
Alignment explanation
Indices: 17553--17610 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
17543 ACGAATAAAT
17553 ATAAATAACTTCAAAA
1 ATAAATAACTTCAAAA
** *
17569 ATAAATAAACGAACAAAC
1 ATAAAT-AAC-TTCAAAA
17587 ATAAATAACTTCAAAA
1 ATAAATAACTTCAAAA
17603 ATAAATAA
1 ATAAATAA
17611 ACGAACACGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 18 0.53
17 6 0.18
18 10 0.29
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.21
Consensus pattern (16 bp):
ATAAATAACTTCAAAA
Found at i:17574 original size:34 final size:34
Alignment explanation
Indices: 17536--17617 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
17526 TCACAAACAC
* * *
17536 TAAATGAACGAATAAATATAAATAACTTCAAAAA
1 TAAATAAACGAACAAACATAAATAACTTCAAAAA
17570 TAAATAAACGAACAAACATAAATAACTTCAAAAA
1 TAAATAAACGAACAAACATAAATAACTTCAAAAA
17604 TAAATAAACGAACA
1 TAAATAAACGAACA
17618 CGAATATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.63, C:0.12, G:0.05, T:0.20
Consensus pattern (34 bp):
TAAATAAACGAACAAACATAAATAACTTCAAAAA
Found at i:20030 original size:60 final size:59
Alignment explanation
Indices: 19957--20091 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 59
19947 TTTTTAGGGT
*
19957 AAAGTACACAAATG-GTC-CCATGACTATA-ATATATTGCTTTATTAAGTCCCTTGACTATTA
1 AAAGTACA-AAATGAGTCTCC--GACTATAGA-ATATTGCTTTATTAAGTCCCTCGACTATTA
* * * * *
20017 AAAGTTACAAAATGATTCTCCGACTATAGAGTGTTGCTTTGTTGAGTCCCTCGACTATTA
1 AAAG-TACAAAATGAGTCTCCGACTATAGAATATTGCTTTATTAAGTCCCTCGACTATTA
20077 AAAGCTACAAAATGA
1 AAAG-TACAAAATGA
20092 TCACCCGACT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
60 55 0.86
61 7 0.11
62 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (59 bp):
AAAGTACAAAATGAGTCTCCGACTATAGAATATTGCTTTATTAAGTCCCTCGACTATTA
Found at i:20100 original size:60 final size:60
Alignment explanation
Indices: 19990--20103 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
19980 CTATAATATA
* * *
19990 TTGCTTTATTAAGTCCCTTGACTATTAAAAGTTACAAAATGATTCTCCGACTATAGAGTG
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTCCCCGACTATAGAGTG
* *
20050 TTGCTTTGTTGAGTCCCTCGACTATTAAAAGCTACAAAATGA-TCACCCGACTAT
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTC-CCCGACTAT
20104 TCATTATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (60 bp):
TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTCCCCGACTATAGAGTG
Found at i:20591 original size:2 final size:2
Alignment explanation
Indices: 20586--20639 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
20576 TTTTTTTTAA
20586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20626 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
20640 TAAAAAATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21659 original size:12 final size:12
Alignment explanation
Indices: 21642--21668 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
21632 GATTGTTGGG
21642 AAGAATTTTAAT
1 AAGAATTTTAAT
21654 AAGAATTTTAAT
1 AAGAATTTTAAT
21666 AAG
1 AAG
21669 TGAATGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
AAGAATTTTAAT
Found at i:23954 original size:51 final size:50
Alignment explanation
Indices: 23864--23963 Score: 137
Period size: 51 Copynumber: 2.0 Consensus size: 50
23854 TATAAACTTT
* *
23864 TGAAATTCTAATTTCATCCTCAAAATATGATACTCATTCTAAATTAGTCC
1 TGAAATTCCAATTTCATCCTCAAAATATGACACTCATTCTAAATTAGTCC
* * * *
23914 TGAACATTCCAATTTTATCCTCAAACTATGACCCTTATTCTAAATTAGTC
1 TGAA-ATTCCAATTTCATCCTCAAAATATGACACTCATTCTAAATTAGTC
23964 TCTAGACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 4 0.09
51 39 0.91
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (50 bp):
TGAAATTCCAATTTCATCCTCAAAATATGACACTCATTCTAAATTAGTCC
Found at i:25323 original size:121 final size:122
Alignment explanation
Indices: 25146--25372 Score: 305
Period size: 121 Copynumber: 1.9 Consensus size: 122
25136 TTTATTACCT
* * * * *
25146 AACATTCATTTCTTTCAAAATTATATTTAAAGTTTAGTTTTGGTTGCATTTTAGTATCCGCCGTT
1 AACATTCATTTCTTTCAAAATCAAATCTAAAGTTTAGTTTTGGTTGCATTTTAGTATCCACCATT
* *
25211 AAAAACTTAATGCATCTAGCACCTAAACTATTAGTTTTGATCCGTTTTTATCATTTA
66 AAAAACTTAACGCATCTAGCACCTAAACTATCAGTTTTGATCCGTTTTTATCATTTA
* *
25268 AACATTCATTT-TTTCCAAAATCAAATCTAAAGTTTAGTTTT-GTTGTATTTTAGTATCCATCAT
1 AACATTCATTTCTTT-CAAAATCAAATCTAAAGTTTAGTTTTGGTTGCATTTTAGTATCCACCAT
* * * * *
25331 TAAAAACTTAGCGCGTTTAGTACCTAAACTATCATTTTTGAT
65 TAAAAACTTAACGCATCTAGCACCTAAACTATCAGTTTTGAT
25373 ATATTTTAAT
Statistics
Matches: 90, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
121 56 0.62
122 34 0.38
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (122 bp):
AACATTCATTTCTTTCAAAATCAAATCTAAAGTTTAGTTTTGGTTGCATTTTAGTATCCACCATT
AAAAACTTAACGCATCTAGCACCTAAACTATCAGTTTTGATCCGTTTTTATCATTTA
Found at i:25400 original size:121 final size:118
Alignment explanation
Indices: 25113--25407 Score: 277
Period size: 121 Copynumber: 2.4 Consensus size: 118
25103 ATTTAATATA
* * * * * *
25113 TAAACTATCAATTTAGATATGTTTTTATTACCTAACATTCATTTCTTTCAAAATTATATTTAAAG
1 TAAACTATCAATTTTGATAT-ATTTTAATACCTAA-ATTCATTT-TTTCAAAATCAAATCTAAAG
* * *
25178 TTTAGTTTTGGTTGCATTTTAGTATCCGCCGTTAAAAACTTAATGCATCTAGCACC
63 TTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
* * *** * **
25234 TAAACTATTAGTTTTGATCCGTTTTTATCATTTAAACATTCATTTTTTCCAAAATCAAATCTAAA
1 TAAACTATCAATTTTGATATATTTTAAT-ACCT-AA-ATTCATTTTTT-CAAAATCAAATCTAAA
* * * * * *
25299 GTTTAGTTTT-GTTGTATTTTAGTATCCATCATTAAAAACTTAGCGCGTTTAGTACC
62 GTTTAGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
*
25355 TAAACTATCATTTTTGATATATTTTAATACCTAAATTTTCAATTTTTTCAAAA
1 TAAACTATCAATTTTGATATATTTTAATACCTAAA--TTC-ATTTTTTCAAAA
25408 CATGGCGACG
Statistics
Matches: 138, Mismatches: 30, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
118 1 0.01
119 2 0.01
120 15 0.11
121 86 0.62
122 34 0.25
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (118 bp):
TAAACTATCAATTTTGATATATTTTAATACCTAAATTCATTTTTTCAAAATCAAATCTAAAGTTT
AGTTTTGGTTGCATTTTAGTATCCACCATTAAAAACTTAACGCATCTAGCACC
Found at i:28887 original size:16 final size:16
Alignment explanation
Indices: 28832--28891 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
28822 ATGAACGAAT
28832 AAATATAATAACTTC-A
1 AAATA-AATAACTTCAA
**
28848 AAATAAATAAACGAACAA
1 AAATAAAT-AAC-TTCAA
*
28866 ACATAAATAACTTCAA
1 AAATAAATAACTTCAA
28882 AAATAAATAA
1 AAATAAATAA
28892 ACGAACACGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 3 0.09
16 20 0.57
17 4 0.11
18 8 0.23
ACGTcount: A:0.65, C:0.12, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAAATAACTTCAA
Found at i:28890 original size:34 final size:32
Alignment explanation
Indices: 28819--28898 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 32
28809 TCACAAACAC
* * *
28819 TAAATGAACGAATAAATATAATAACTTCAAAA
1 TAAATAAACGAACAAACATAATAACTTCAAAA
28851 TAAATAAACGAACAAACATAAATAACTTCAAAAA
1 TAAATAAACGAACAAACAT-AATAACTTC-AAAA
28885 TAAATAAACGAACA
1 TAAATAAACGAACA
28899 CGAATATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 16 0.37
33 9 0.21
34 18 0.42
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.20
Consensus pattern (32 bp):
TAAATAAACGAACAAACATAATAACTTCAAAA
Found at i:31381 original size:60 final size:60
Alignment explanation
Indices: 31271--31384 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
31261 CTATAATATA
* * *
31271 TTGCTTTATTAAGTCCCTTGACTATTAAAAGTTACAAAATGATTCTCCGACTATAGAGTG
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTCCCCGACTATAGAGTG
* *
31331 TTGCTTTGTTGAGTCCCTCGACTATTAAAAGCTACAAAATGA-TCACCCGACTAT
1 TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTC-CCCGACTAT
31385 TCATTATGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 2 0.04
60 46 0.96
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (60 bp):
TTGCTTTATTAAGTCCCTCGACTATTAAAAGCTACAAAATGATTCCCCGACTATAGAGTG
Found at i:31872 original size:2 final size:2
Alignment explanation
Indices: 31867--31926 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
31857 TTTTTTTTAA
31867 AT AT AT AT AT AT 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 AT AT AT AT AT AT
31909 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
31927 TAAAAAATCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32952 original size:12 final size:12
Alignment explanation
Indices: 32935--32961 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32925 GATTGTTGGG
32935 AAGAATTTTAAT
1 AAGAATTTTAAT
32947 AAGAATTTTAAT
1 AAGAATTTTAAT
32959 AAG
1 AAG
32962 TGAATGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (12 bp):
AAGAATTTTAAT
Found at i:34337 original size:28 final size:30
Alignment explanation
Indices: 34270--34338 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 30
34260 TTTAACGGTC
34270 CAGTGGTATAATTGAACAAAAATCAAAGTT
1 CAGTGGTATAATTGAACAAAAATCAAAGTT
* * *
34300 CAATGTTATAATTG-AC-AAAATTAAAGTT
1 CAGTGGTATAATTGAACAAAAATCAAAGTT
*
34328 TAGTGGTATAA
1 CAGTGGTATAA
34339 ACGATACAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 19 0.58
29 2 0.06
30 12 0.36
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (30 bp):
CAGTGGTATAATTGAACAAAAATCAAAGTT
Found at i:36472 original size:17 final size:15
Alignment explanation
Indices: 36430--36464 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
36420 TTGTCCAACA
*
36430 TCGGGCTCGACAAGC
1 TCGGGCCCGACAAGC
36445 TCGGGCCCGACAAGC
1 TCGGGCCCGACAAGC
36460 TCGGG
1 TCGGG
36465 GCCCCGACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.34, G:0.37, T:0.11
Consensus pattern (15 bp):
TCGGGCCCGACAAGC
Found at i:39404 original size:60 final size:59
Alignment explanation
Indices: 39279--39405 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 59
39269 GTAGTTGAAT
* ** * * * * *
39279 GACCATTTTGTAACTTTTAATAGTCGAGTGAATCAACAAATCAATACCCTATAGTTGAG
1 GACCATTTTATAACTTTTAATAGTCGAAAGAATCAACAAAACAACAACCTATAATCGAG
*
39338 GAACCATTTTATAACTTTTAATAGTCGAAAGAATCAACAAAACAACAATCTATAATCGATG
1 G-ACCATTTTATAACTTTTAATAGTCGAAAGAATCAACAAAACAACAACCTATAATCGA-G
39399 GACCATT
1 GACCATT
39406 CGTGTACTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 1 0.02
60 54 0.95
61 2 0.04
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (59 bp):
GACCATTTTATAACTTTTAATAGTCGAAAGAATCAACAAAACAACAACCTATAATCGAG
Found at i:41146 original size:2 final size:2
Alignment explanation
Indices: 41139--41166 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41129 AAAATGATTA
41139 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
41167 CTGCATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43099 original size:2 final size:2
Alignment explanation
Indices: 43092--43153 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
43082 ATATGTAGAA
43092 AT AT AT AT AT AT 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 AT AT AT AT AT AT
43134 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
43154 TGATAATTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44153 original size:112 final size:112
Alignment explanation
Indices: 43952--44169 Score: 357
Period size: 112 Copynumber: 1.9 Consensus size: 112
43942 AATCATATCG
* *
43952 TCAAAAGAGACATAAAACTTCATTAATAACATTTAAAATAACTCAATAACATGAAAAAAGGACTT
1 TCAAAAGAGACATAAAACCTCATTAATAACATTCAAAATAACTCAATAACATGAAAAAAGGACTT
* *
44017 AACAAAAATTAGGTTAGAATTAGAG-ATGGCAATGGGACAAGATCTGA
66 AACAAAAATTAGGTTAGAAGTAGAGAAT-GCAACGGGACAAGATCTGA
* * *
44064 TCAAAAGCGACATAAAACCTCATTAATAACATTCAAAATAACTCAATAATATGAAAAAATGACTT
1 TCAAAAGAGACATAAAACCTCATTAATAACATTCAAAATAACTCAATAACATGAAAAAAGGACTT
44129 AACAAAAATTAGGTTAGAAGTAGAGAATGCAACGGGACAAG
66 AACAAAAATTAGGTTAGAAGTAGAGAATGCAACGGGACAAG
44170 TTAGATTTTT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
112 96 0.98
113 2 0.02
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (112 bp):
TCAAAAGAGACATAAAACCTCATTAATAACATTCAAAATAACTCAATAACATGAAAAAAGGACTT
AACAAAAATTAGGTTAGAAGTAGAGAATGCAACGGGACAAGATCTGA
Found at i:44664 original size:167 final size:167
Alignment explanation
Indices: 44383--44716 Score: 659
Period size: 167 Copynumber: 2.0 Consensus size: 167
44373 ACTGAGAGAA
*
44383 TTATGAAATGAAAGTCGACGACGTTAAGGAAAAATATTTTAGAATTAACCTAAATATTATATATA
1 TTATAAAATGAAAGTCGACGACGTTAAGGAAAAATATTTTAGAATTAACCTAAATATTATATATA
44448 TATATAGGATGACAATTTTGTAAATATCATAACTATAATAACATTTTCGTTAAGTATATTACGCA
66 TATATAGGATGACAATTTTGTAAATATCATAACTATAATAACATTTTCGTTAAGTATATTACGCA
44513 TCTCCTACTAAACTACTCTTTTTTCGATCAGATCTGT
131 TCTCCTACTAAACTACTCTTTTTTCGATCAGATCTGT
44550 TTATAAAATGAAAGTCGACGACGTTAAGGAAAAATATTTTAGAATTAACCTAAATATTATATATA
1 TTATAAAATGAAAGTCGACGACGTTAAGGAAAAATATTTTAGAATTAACCTAAATATTATATATA
44615 TATATAGGATGACAATTTTGTAAATATCATAACTATAATAACATTTTCGTTAAGTATATTACGCA
66 TATATAGGATGACAATTTTGTAAATATCATAACTATAATAACATTTTCGTTAAGTATATTACGCA
44680 TCTCCTACTAAACTACTCTTTTTTCGATCAGATCTGT
131 TCTCCTACTAAACTACTCTTTTTTCGATCAGATCTGT
44717 CAAAAGCTAC
Statistics
Matches: 166, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
167 166 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (167 bp):
TTATAAAATGAAAGTCGACGACGTTAAGGAAAAATATTTTAGAATTAACCTAAATATTATATATA
TATATAGGATGACAATTTTGTAAATATCATAACTATAATAACATTTTCGTTAAGTATATTACGCA
TCTCCTACTAAACTACTCTTTTTTCGATCAGATCTGT
Found at i:46818 original size:28 final size:28
Alignment explanation
Indices: 46782--46843 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
46772 ATGATATTTG
46782 CATGAGCATAGTTTCCATTCTGATTCTA
1 CATGAGCATAGTTTCCATTCTGATTCTA
* **
46810 CATGGGCATAGTTTCTGTTCTGATTCTA
1 CATGAGCATAGTTTCCATTCTGATTCTA
*
46838 TATGAG
1 CATGAG
46844 ATTATATCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (28 bp):
CATGAGCATAGTTTCCATTCTGATTCTA
Found at i:47075 original size:30 final size:29
Alignment explanation
Indices: 47027--47097 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 29
47017 ATCCGACCCT
47027 GGATTATATCCCGTTCTGACATCTGCATG
1 GGATTATATCCCGTTCTGACATCTGCATG
*
47056 GGATTATATCCTTGTTCTGACATCTGCATG
1 GGATTATATCC-CGTTCTGACATCTGCATG
*
47086 GGGTTATATCCC
1 GGATTATATCCC
47098 TGTCTTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 11 0.29
30 27 0.71
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (29 bp):
GGATTATATCCCGTTCTGACATCTGCATG
Found at i:48929 original size:29 final size:29
Alignment explanation
Indices: 48887--48945 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
48877 ATTTTCACCT
48887 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
48916 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
48945 A
1 A
48946 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:53613 original size:29 final size:29
Alignment explanation
Indices: 53571--53629 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
53561 ATTTTCACCT
53571 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
53600 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
53629 A
1 A
53630 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:53854 original size:2 final size:2
Alignment explanation
Indices: 53847--53908 Score: 51
Period size: 2 Copynumber: 32.0 Consensus size: 2
53837 AGTTAAGTAT
* * *
53847 TA TA TA TA TA TA TA TA TA TA TA TGA TG TA -A T- TT TCA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA T-A TA TA TA
53889 TA -A TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
53909 ATAACATTCT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
1 4 0.08
2 42 0.86
3 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:55895 original size:21 final size:21
Alignment explanation
Indices: 55862--55906 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55852 TGATTTTTAA
*
55862 AAAAATGAAAGTTTAGGTACT
1 AAAAATGAAAGTTTAAGTACT
* * *
55883 AAAACTGATAGTTTAAGTATT
1 AAAAATGAAAGTTTAAGTACT
55904 AAA
1 AAA
55907 TGTGTGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (21 bp):
AAAAATGAAAGTTTAAGTACT
Found at i:58877 original size:2 final size:2
Alignment explanation
Indices: 58827--58863 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
58817 GAGGATATCT
58827 TA TA TA -A 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
58864 CACACACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:61807 original size:160 final size:162
Alignment explanation
Indices: 61490--62010 Score: 710
Period size: 165 Copynumber: 3.2 Consensus size: 162
61480 TTCATCGTTT
* *
61490 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCGAACATACTCTCCTTTAATTTCGTGCTCTC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACA-ACTCTCCTTTAATTTCATG--CTC
*
61555 AGTCTTGACTTCCTCTAGAGATTCTTGCAGAT-AATTACCTTAGA-TCAACTTCCTTTAGGCTAT
63 AGTCTTGACTTCCTCTAGAG---CTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTAT
61618 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
125 CCTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* * * * * *
61656 TCTTGAATGACACTCTGCAACTCATTTTC-TTAGCCAACAACCTCTCGTCTAGTTTCATGCTCGG
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAA-CTCTCCTTTAATTTCATGCTCAG
* * * * *
61720 CCTTGACTTTCTCTAGAGCTTGCAGATAAATCACTTTATATTCAATTTCCTTTAGGCTATCCTTC
65 TCTTGACTTCCTCTAGAGCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCCTTC
61785 AA-CGAGTTTC-TCCTCCTTGGACTCAGAAGCC
130 AACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
** *
61816 TCCCGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAAACTTTCCTTTAATTTCATGCTCCC
1 TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAAC-AACTCTCCTTTAATTTCATGCT--C
*
61881 AGTCTTGACTTCCCCTAGAGCTTCTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATC
63 AGTCTTGACTTCCTCTAGAGC-T-TGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATC
*
61946 CTTCAACCGAGTTTCTTCCTCCTTGGACTCGGAAGCC
126 CTTCAACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
* *
61983 TCTTGAATGACACTCCGCAACTCGGTTT
1 TCTTGAATGACACTCTGCAACTCAGTTT
62011 T
Statistics
Matches: 310, Mismatches: 34, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
160 56 0.18
161 41 0.13
162 27 0.09
163 38 0.12
164 2 0.01
165 66 0.21
166 36 0.12
167 44 0.14
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.35
Consensus pattern (162 bp):
TCTTGAATGACACTCTGCAACTCAGTTTCTTTATCCAACAACTCTCCTTTAATTTCATGCTCAGT
CTTGACTTCCTCTAGAGCTTGCAGATAAATCACCTTAGATTCAACTTCCTTTAGGCTATCCTTCA
ACCGAGTTTCTTCCTCCTTGGACTCAGAAGCC
Done.