Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001557.1 Hibiscus syriacus cultivar Beakdansim tig00003078_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: 71938
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:2045 original size:3 final size:3
Alignment explanation
Indices: 2032--2072 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2022 GGACCTGTCT
*
2032 TTA TT- TTA TTA TTA TTA TTA TTA TT- TAA TTA -TA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2073 TTGTTTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.15
3 28 0.85
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2068 original size:16 final size:17
Alignment explanation
Indices: 2042--2073 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2032 TTATTTTATT
2042 ATTATTATTATTATTTA
1 ATTATTATTATTATTTA
2059 ATTA-TATTATTATTT
1 ATTATTATTATTATTT
2074 TGTTTTTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTATTATTATTATTTA
Found at i:8875 original size:7 final size:7
Alignment explanation
Indices: 8817--8917 Score: 51
Period size: 7 Copynumber: 13.1 Consensus size: 7
8807 GATAAAGATG
8817 AGAGAAA
1 AGAGAAA
*
8824 AGAAAAA
1 AGAGAAA
*
8831 AGAGGACA
1 AGA-GAAA
8839 AGAGGAAAA
1 AGA-G-AAA
*
8848 AGGGAAA
1 AGAGAAA
8855 AGGTAGAAA
1 A-G-AGAAA
8864 A-AGAAA
1 AGAGAAA
8870 AGAGAAAA
1 AGAG-AAA
* *
8878 ATAGTAA
1 AGAGAAA
8885 AGAAGAAGA
1 AG-AGAA-A
*
8894 AGAAAAA
1 AGAGAAA
8901 AGAAGAAAA
1 AG-AG-AAA
8910 AGAGAAA
1 AGAGAAA
8917 A
1 A
8918 AAATAGAAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
6 6 0.08
7 25 0.35
8 24 0.33
9 17 0.24
ACGTcount: A:0.69, C:0.01, G:0.27, T:0.03
Consensus pattern (7 bp):
AGAGAAA
Found at i:8876 original size:22 final size:21
Alignment explanation
Indices: 8845--8928 Score: 66
Period size: 22 Copynumber: 4.0 Consensus size: 21
8835 GACAAGAGGA
*
8845 AAAAGGGAAAAGGTAGAAAAAG
1 AAAAGAGAAAA-GTAGAAAAAG
*
8867 AAAAGAGAAAAATAGTAAAGAAG
1 AAAAGAGAAAAGTAG-AAA-AAG
* *
8890 AAGAAGAAAAAAGAAGAAAAAG
1 AA-AAGAGAAAAGTAGAAAAAG
*
8912 AGAA-A-AAAA-TAGAAAAA
1 AAAAGAGAAAAGTAGAAAAA
8929 AGTAATCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
18 7 0.13
19 4 0.08
20 1 0.02
21 5 0.10
22 17 0.33
23 8 0.15
24 10 0.19
ACGTcount: A:0.73, C:0.00, G:0.23, T:0.05
Consensus pattern (21 bp):
AAAAGAGAAAAGTAGAAAAAG
Found at i:8902 original size:16 final size:17
Alignment explanation
Indices: 8827--8928 Score: 63
Period size: 16 Copynumber: 6.3 Consensus size: 17
8817 AGAGAAAAGA
* * *
8827 AAAAAGAGGACAAGAGG
1 AAAAAGAGAAAAAGAAG
* * *
8844 AAAAAGGGAAAAGGTAG
1 AAAAAGAGAAAAAGAAG
8861 -AAAA-AG-AAAAG-AG
1 AAAAAGAGAAAAAGAAG
* *
8874 AAAAATAG-TAAAGAAG
1 AAAAAGAGAAAAAGAAG
*
8890 AAGAAGA-AAAAAGAAG
1 AAAAAGAGAAAAAGAAG
*
8906 AAAAAGAGAAAAAAATAG
1 AAAAAGAGAAAAAGA-AG
8924 AAAAA
1 AAAAA
8929 AGTAATCAAA
Statistics
Matches: 65, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
13 2 0.03
14 8 0.12
15 7 0.11
16 24 0.37
17 17 0.26
18 7 0.11
ACGTcount: A:0.71, C:0.01, G:0.25, T:0.04
Consensus pattern (17 bp):
AAAAAGAGAAAAAGAAG
Found at i:8905 original size:10 final size:10
Alignment explanation
Indices: 8890--8930 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
8880 AGTAAAGAAG
8890 AAGAAGAAAA
1 AAGAAGAAAA
8900 AAGAAG-AAA
1 AAGAAGAAAA
8909 AAG-AGAAAA
1 AAGAAGAAAA
8918 AA-ATAGAAAA
1 AAGA-AGAAAA
8928 AAG
1 AAG
8931 TAATCAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 2 0.07
9 11 0.41
10 14 0.52
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:8930 original size:19 final size:22
Alignment explanation
Indices: 8858--8929 Score: 73
Period size: 21 Copynumber: 3.4 Consensus size: 22
8848 AGGGAAAAGG
8858 TAGAAAAAGAA-AAG-AGAAAAA
1 TAGAAAAA-AAGAAGAAGAAAAA
* *
8879 TAGTAAAGAAGAAGAAGAAAAA
1 TAGAAAAAAAGAAGAAGAAAAA
8901 -AGAAGAAAAAG-AGAA-AAAAA
1 TAGAA-AAAAAGAAGAAGAAAAA
8921 TAGAAAAAA
1 TAGAAAAAA
8930 GTAATCAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 11 0.26
21 20 0.47
22 12 0.28
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (22 bp):
TAGAAAAAAAGAAGAAGAAAAA
Found at i:10822 original size:38 final size:38
Alignment explanation
Indices: 10777--11503 Score: 818
Period size: 38 Copynumber: 19.1 Consensus size: 38
10767 TCATTCTATC
* * *
10777 TTGTTATTCTTGGCTTCCCCATGAAGAGAAGTCAATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * * * * *
10815 TTATTATTCCTAACTCCCTCGCGAAGAGAATTCAATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * *
10853 TTGTTATTCTTGACTTTCTCATGAAGAGAAGTCAATAT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* *
10891 TTGTTATTCTTGACTTCCTAGTGAAGAGAAGGCAATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* *
10929 TTTTTATTATTGACTTCCTCGT-ATAGAGAAGTC-ATCT
1 TTGTTATTCTTGACTTCCTCGTGA-AGAGAAGTCAATCT
* * * * *
10966 TTGTTATT-TTGACTTCCTCATTAAGAAAAATCGATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * *
11003 TTTTTATTCTTGACTTCCTCGTGAAGAGAAATCGATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
*
11041 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* *
11079 TTGTTATTCTTGACTTCCTCGTGAAGATAAGTCGATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
*
11117 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * *
11155 TTGCTATTCTTGACTTCCTCGTGAAGATAAGTCGATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* *
11193 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTTAATGT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
*
11231 TTGTTATTCTTGACTTCCCCGTGAAGAGAAG-CTAATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC-AATCT
* *
11269 TTGTCATTCTTGACTTCCTTGTGAAGAGAAGTCAATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * * * *
11307 TTGTTATTCCTGACTCCCTTGCGAAGAGGAGTCAATCGT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-T
* * ** *
11346 CCCAATGTCATTCTTGACTTCCTTATGAAGAGGAGTCAATCT
1 ----TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * * *
11388 TTATCATTAC-TGA-TTCCCTCGTGGAGAGAAGTCATTCT
1 TTGTTATT-CTTGACTT-CCTCGTGAAGAGAAGTCAATCT
* *
11426 TTGTTATTCTTGACTTCCTCGAGAAGAGAAGTCAATAT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
* * * * *
11464 CTGTTATTCCTGAATTTCTTGTGAAGAGAAGTCAATCT
1 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
11502 TT
1 TT
11504 CAGTGTTATA
Statistics
Matches: 590, Mismatches: 84, Indels: 30
0.84 0.12 0.04
Matches are distributed among these distances:
36 19 0.03
37 27 0.05
38 507 0.86
39 5 0.01
42 1 0.00
43 31 0.05
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (38 bp):
TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCT
Found at i:11604 original size:45 final size:45
Alignment explanation
Indices: 11469--11735 Score: 251
Period size: 45 Copynumber: 6.1 Consensus size: 45
11459 AATATCTGTT
* * * * *
11469 ATTCCTGAATTTCTTGTGAAGAGAAGTCAATCTTTCAG---TGTT
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * * ** *
11511 ATACTAGACTTTCTCGTGATGATAAGTCAATC--TCTGTATTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * * * * *
11554 ATTCTTGATTTTCTCGTAAAGAGGAGTTAATATTTTAGTGTTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * * *
11599 CTTCTTGACTTTCTCGCGAAGAGCAGTCAATCTTTCAATATTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
*
11644 A-ACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
* * *
11688 ATTCTTGATTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGA-TGTC
1 ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGT-ATTGTC
11733 ATT
1 ATT
11736 TTCAACTTGA
Statistics
Matches: 178, Mismatches: 40, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
40 3 0.02
42 25 0.14
43 26 0.15
44 40 0.22
45 83 0.47
46 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.40
Consensus pattern (45 bp):
ATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTC
Found at i:11666 original size:89 final size:90
Alignment explanation
Indices: 11547--11722 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 90
11537 TCAATCTCTG
* * * * * *
11547 TATTGTCATTCTTGATTTTCTCGTAAAGAGGAGTTAATATTTTAGTGTTGTCCTTCTTGACTTTC
1 TATTGTCATACTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAGTATTGTCATTCTTGACTTTC
*
11612 TCGCGAAGAGCAGTCAATCTTTCAA
66 TCGCGAAGAGCAGTCAACCTTTCAA
* * *
11637 TATTGTCA-ACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGTATTGTCATTCTTGATTTTC
1 TATTGTCATACTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAGTATTGTCATTCTTGACTTTC
* *
11701 TCGTGAAGAGGAGTCAACCTTT
66 TCGCGAAGAGCAGTCAACCTTT
11723 TAGTGATGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
89 66 0.89
90 8 0.11
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (90 bp):
TATTGTCATACTTGACTTTCTCGTAAAGAGGAGTCAATATTTCAGTATTGTCATTCTTGACTTTC
TCGCGAAGAGCAGTCAACCTTTCAA
Found at i:11714 original size:134 final size:130
Alignment explanation
Indices: 11486--11732 Score: 332
Period size: 134 Copynumber: 1.9 Consensus size: 130
11476 AATTTCTTGT
* * * * *
11486 GAAGAGAAGTCAATCTTTCAGTGTTATACTAGACTTTCTCGTGATGATAAGTCAATCTCTGTATT
1 GAAGAGAAGTCAATCTTTCAATATTATACTAGACTTTCTCGTGAAGAGAAGTCAATCTCAGTATT
* * *
11551 GTCATTCTTGATTTTCTCGTAAAGAGGAGTTAATATTTTAGTGTTGTCCTTCTTGACTTTCTCGC
66 GTCATTCTTGATTTTCTCGTAAAGAGGAGTCAACATTTTAGTGATGTCCTTCTTGACTTTCTCGC
* * * *
11616 GAAGAGCAGTCAATCTTTCAATATTGTCAACTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAG
1 GAAGAGAAGTCAATCTTTCAATATTAT--ACTAGACTTTCTCGTGAAGAGAAGTCAATC--TCAG
* *
11681 TATTGTCATTCTTGATTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTC
62 TATTGTCATTCTTGATTTTCTCGTAAAGAGGAGTCAACATTTTAGTGATGTC
11733 ATTTTCAACT
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
130 23 0.23
132 26 0.26
134 50 0.51
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (130 bp):
GAAGAGAAGTCAATCTTTCAATATTATACTAGACTTTCTCGTGAAGAGAAGTCAATCTCAGTATT
GTCATTCTTGATTTTCTCGTAAAGAGGAGTCAACATTTTAGTGATGTCCTTCTTGACTTTCTCGC
Found at i:11816 original size:50 final size:48
Alignment explanation
Indices: 11602--11822 Score: 203
Period size: 50 Copynumber: 4.7 Consensus size: 48
11592 TGTTGTCCTT
* *
11602 CTTGACTTTCTCGCGAAGAGCAGTCAATCTTTCA---A--T-ATTGTCAA
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGATGTCATT-TCAA
* *
11646 CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTCAGT-ATTGTCA-TT---
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGA-TGTCATTTCAA
* *
11691 CTTGATTTTCTCGTGAAGAGGAGTCAACCTTTTAGTGATGTCATTTTCAA
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGATGTCA-TTTCAA
* * *
11741 CTTGACTTTCTCACAAAGAGAAGTCAAGCTTTTAGTGATGTCATTCTCAA
1 CTTGACTTTCTCGCGAAGAGGAGTCAA-CTTTTAGTGATGTCATT-TCAA
*
11791 CTTGACTTTCTCGCGGAGAGGAGTCAACTTTT
1 CTTGACTTTCTCGCGAAGAGGAGTCAACTTTT
11823 CAGTAGTATT
Statistics
Matches: 149, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
44 32 0.21
45 38 0.26
46 2 0.01
47 2 0.01
48 1 0.01
49 9 0.06
50 65 0.44
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (48 bp):
CTTGACTTTCTCGCGAAGAGGAGTCAACTTTTAGTGATGTCATTTCAA
Found at i:12736 original size:133 final size:132
Alignment explanation
Indices: 12377--12974 Score: 710
Period size: 133 Copynumber: 4.5 Consensus size: 132
12367 AATGTTTGAT
* * * * *
12377 TTTCAGATTTGGTCTTCTTGAAGA-CAAGAGAAGCAAACCAAATTC-AATTCAATCTTCCCTGAA
1 TTTCAGATTTGGTCTTCCTGAAGAGC-AGTGAAGCAAATC-GATTCTGATTCAATCTTCCCTGAA
* * * *
12440 GAGCACTGAAGTGGATCAAAGTTTACTCGAGTCTGATCTCTCCTAAAGAGTAG-ATGAGTAGATT
64 GAGAAC-GAAGTGGATCAAAATTT-CTCGAGTCTGATCTCCCCTAAAGAGTAGTA-GAGCAGATT
12504 CTTCTTC
126 CTTCTTC
* *
12511 TTTCAGATTTGGTATTCCTTAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
** * * *
12576 GCAACGAAGTATATCAAAGTTATCTCGAGTCTGATATCCCCTAAAGAGTAGTAGAGCATATTCTT
66 G-AACGAAGTGGATCAAAATT-TCTCGAGTCTGATCTCCCCTAAAGAGTAGTAGAGCAGATTCTT
*
12641 CTTA
129 CTTC
* *
12645 TTTTAGATTTGGTCTTCCTGAAGAGCA-TGAAGTAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* *
12709 GAAACGAAGTGGATCAAAATTTCCTCGAGTCTGATCTCCCATAAAGAGTAGTGGAGCAGATTCTT
66 G-AACGAAGTGGATCAAAATTT-CTCGAGTCTGATCTCCCCTAAAGAGTAGTAGAGCAGATTCTT
12774 CTTC
129 CTTC
* *
12778 TATCAGATTTGGTCTTCTTGAAGAGCAGTGAAGC-AATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* *
12842 GTA-GTAAAGTGGAT-AAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCAGATTC
66 GAACG--AAGTGGATCAAAA--TTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTAGAGCAGATTC
*
12905 TTCCTC
127 TTCTTC
* * * * * * *
12911 TTTTAGATTTGGTCTTCCTGATA-AGTAATAAAGCAAATCGATTCCGATTC-ATCTTTCCTAAAG
1 TTTCAGATTTGGTCTTCCTGA-AGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAG
12974 A
65 A
12975 ATAATGAATA
Statistics
Matches: 407, Mismatches: 44, Indels: 27
0.85 0.09 0.06
Matches are distributed among these distances:
131 1 0.00
132 6 0.01
133 243 0.60
134 152 0.37
135 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (132 bp):
TTTCAGATTTGGTCTTCCTGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
GAACGAAGTGGATCAAAATTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTAGAGCAGATTCTTCT
TC
Found at i:12951 original size:267 final size:267
Alignment explanation
Indices: 12375--12974 Score: 784
Period size: 267 Copynumber: 2.2 Consensus size: 267
12365 GTAATGTTTG
* * * * * *
12375 ATTTTCAGATTTGGTCTTCTTGAAGACAAGAGAAGCAAACCAAATT-CAATTCAATCTTCCCTGA
1 ATTTT-AGATTTGGTCTTCCTGAAGAGAATA-AAGCAAATC-GATTCCGATTCAATCTTCCCTGA
* * *
12439 AGAGCACTGAAGTGGATCAAAGTTTACTCGAGTCTGATCTCTCCTAAAGAGTAGATGAGTAGATT
63 AGAGAACTGAAGTGGATCAAAATTTACTCGAGTCTGATCTCTCCTAAAGAGTAGATGAGCAGATT
*
12504 CTTCTTCTTTCAGATTTGGTATTCCTTAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCC
128 CTTCTTCTATCAGATTTGGTATTCCTTAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCC
* * *
12569 CTGAAGAGCAACGAAGTATATCAAAGTTATCTCGAGTCTGATATCCCCTAAAGAGTAGTAGAGCA
193 CTGAAGAGCAACAAAGTAGATAAAAGTTATCTCGAGTCTGATATCCCCTAAAGAGTAGTAGAGCA
* *
12634 TATTCTTCTT
258 GATTCTTCCT
* * * *
12644 ATTTTAGATTTGGTCTTCCTGAAGAGCATGAAGTAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 ATTTTAGATTTGGTCTTCCTGAAGAGAATAAAGCAAATCGATTCCGATTCAATCTTCCCTGAAGA
*
12709 GAAAC-GAAGTGGATCAAAATTTCCTCGAGTCTGATCTC-CCATAAAGAGTAG-TGGAGCAGATT
66 G-AACTGAAGTGGATCAAAATTTACTCGAGTCTGATCTCTCC-TAAAGAGTAGAT-GAGCAGATT
*
12771 CTTCTTCTATCAGATTTGGTCTT-CTTGAAGAGCAGTGAAGC-AATCGATTCTGATTCAATCTTC
128 CTTCTTCTATCAGATTTGGTATTCCTT-AAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTC
* ** * * * *
12834 CCTGAAGAGTAGTAAAGTGGATAAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGC
192 CCTGAAGAGCAACAAAGTAGATAAAAGTTATCTCGAGTCTGATATCCCCTAAAGAGTAGTAGAGC
12899 AGATTCTTCCT
257 AGATTCTTCCT
* * *
12910 CTTTTAGATTTGGTCTTCCTGATA-AGTAATAAAGCAAATCGATTCCGATTC-ATCTTTCCTAAA
1 ATTTTAGATTTGGTCTTCCTGA-AGAG-AATAAAGCAAATCGATTCCGATTCAATCTTCCCTGAA
12973 GA
64 GA
12975 ATAATGAATA
Statistics
Matches: 289, Mismatches: 35, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
266 130 0.45
267 132 0.46
268 22 0.08
269 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (267 bp):
ATTTTAGATTTGGTCTTCCTGAAGAGAATAAAGCAAATCGATTCCGATTCAATCTTCCCTGAAGA
GAACTGAAGTGGATCAAAATTTACTCGAGTCTGATCTCTCCTAAAGAGTAGATGAGCAGATTCTT
CTTCTATCAGATTTGGTATTCCTTAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTG
AAGAGCAACAAAGTAGATAAAAGTTATCTCGAGTCTGATATCCCCTAAAGAGTAGTAGAGCAGAT
TCTTCCT
Found at i:13195 original size:17 final size:16
Alignment explanation
Indices: 13166--13198 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
13156 CGGAACTGTC
13166 TTTATTTATTATTATT
1 TTTATTTATTATTATT
13182 TTTATTTAATTATTATT
1 TTTATTT-ATTATTATT
13199 AATATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTATTATTATT
Found at i:13204 original size:17 final size:16
Alignment explanation
Indices: 13168--13210 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
13158 GAACTGTCTT
**
13168 TATTTATTATTATTTT
1 TATTTATTATTATTAA
13184 TATTTAATTATTATTAA
1 TATTT-ATTATTATTAA
13201 TA-TTATTATT
1 TATTTATTATT
13211 TTGTTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTATTATTAA
Found at i:13206 original size:20 final size:20
Alignment explanation
Indices: 13166--13207 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13156 CGGAACTGTC
* * *
13166 TTTATTTATTATTATTTTTA
1 TTTAATTATTATTAATATTA
13186 TTTAATTATTATTAATATTA
1 TTTAATTATTATTAATATTA
13206 TT
1 TT
13208 ATTTTGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTAATTATTATTAATATTA
Found at i:17787 original size:87 final size:87
Alignment explanation
Indices: 17641--17813 Score: 229
Period size: 87 Copynumber: 2.0 Consensus size: 87
17631 GCTCTATTCC
* * * * *
17641 ACATGATCTAGCTAAAACTAAAAATGATTAATTATCATCCAATGGACCGAACAGTAATGAGGAAA
1 ACATGATATAACTAAAACAAAAAATGATTAACTATCATCCAAAGGACCGAACAGTAATGAGGAAA
17706 GAATACAAACAAAAGATGCTTA
66 GAATACAAACAAAAGATGCTTA
* ** **
17728 ACATGATATAACTAAAAGAAAAAATGATTAACTATCATCCAAAGGATTGAGTAGTAATGAGGAAA
1 ACATGATATAACTAAAACAAAAAATGATTAACTATCATCCAAAGGACCGAACAGTAATGAGGAAA
* * *
17793 GAATACATATAAAAGGTGCTT
66 GAATACAAACAAAAGATGCTT
17814 GTCAATCAAA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (87 bp):
ACATGATATAACTAAAACAAAAAATGATTAACTATCATCCAAAGGACCGAACAGTAATGAGGAAA
GAATACAAACAAAAGATGCTTA
Found at i:24999 original size:27 final size:27
Alignment explanation
Indices: 24950--25019 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
24940 TCGCTGCACC
* * *
24950 ATTTGAA-TTTTATTAATTGTACTTTA
1 ATTTGAATTTTTATTATTTATACTCTA
24976 ATTTGAATTTTTATTATTTATACTCTA
1 ATTTGAATTTTTATTATTTATACTCTA
* *
25003 ATTT-TATTTTTAATATT
1 ATTTGAATTTTTATTATT
25020 AATTAAAACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
26 18 0.47
27 20 0.53
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (27 bp):
ATTTGAATTTTTATTATTTATACTCTA
Found at i:28325 original size:26 final size:28
Alignment explanation
Indices: 28263--28325 Score: 76
Period size: 31 Copynumber: 2.2 Consensus size: 28
28253 CGAGCCTAGT
28263 CGAGCTCGACTCGACTCGAAAACTCTGAAA
1 CGAGCTCGACTCGACTCGAAAACTCTG--A
*
28293 TGAAGCTCGACTCGACTCGAAAACTC-G-
1 CG-AGCTCGACTCGACTCGAAAACTCTGA
28320 CGAGCT
1 CGAGCT
28326 TAAAATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (28 bp):
CGAGCTCGACTCGACTCGAAAACTCTGA
Found at i:28650 original size:17 final size:17
Alignment explanation
Indices: 28630--28662 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28620 AATTCGAATC
28630 GAGCTCGAGTTCGAGTT
1 GAGCTCGAGTTCGAGTT
28647 GAGCTCGAGTTCGAGT
1 GAGCTCGAGTTCGAGT
28663 CGAGTCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (17 bp):
GAGCTCGAGTTCGAGTT
Found at i:30924 original size:24 final size:23
Alignment explanation
Indices: 30893--30939 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
30883 AATTTTATGG
** *
30893 TTTATTCAATTTTAAATACCTTA
1 TTTATTCAAAGTTAAATAACTTA
30916 TTTATTTCAAAGTTAAATAACTTA
1 TTTA-TTCAAAGTTAAATAACTTA
30940 CTCCCTCGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (23 bp):
TTTATTCAAAGTTAAATAACTTA
Found at i:31015 original size:24 final size:24
Alignment explanation
Indices: 30983--31040 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
30973 CATGTAGTTT
*
30983 ACCCTAATTTTTTTCACTAGCTTC
1 ACCCTAATTCTTTTCACTAGCTTC
31007 ACCCTAATTCTTTTCACTAGCTTC
1 ACCCTAATTCTTTTCACTAGCTTC
31031 ACCCTAATTC
1 ACCCTAATTC
31041 ATTGGCTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.22, C:0.33, G:0.03, T:0.41
Consensus pattern (24 bp):
ACCCTAATTCTTTTCACTAGCTTC
Found at i:33614 original size:2 final size:2
Alignment explanation
Indices: 33609--33636 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
33599 TTTTCTAACC
33609 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
33637 TCTTTTCACA
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:34343 original size:11 final size:11
Alignment explanation
Indices: 34327--34351 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34317 TGCCCTAACA
34327 ACATGTAGAAT
1 ACATGTAGAAT
34338 ACATGTAGAAT
1 ACATGTAGAAT
34349 ACA
1 ACA
34352 GCAAAAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (11 bp):
ACATGTAGAAT
Found at i:35982 original size:74 final size:74
Alignment explanation
Indices: 35852--36008 Score: 287
Period size: 74 Copynumber: 2.1 Consensus size: 74
35842 GGTATGTTGT
*
35852 CTACGATGGCTAATGTTGTTTTTACTTTTATGTCTGAATTAAGGCTCAAAACCTTATAGAAAGAT
1 CTAC-ATGACTAATGTTGTTTTTACTTTTATGTCTGAATTAAGGCTCAAAACCTTATAGAAAGAT
35917 GTCTTAAACG
65 GTCTTAAACG
*
35927 CTACATGACTAATGTTGTTTTTACTTTTATGTCTGAATTCAGGCTCAAAACCTTATAGAAAGATG
1 CTACATGACTAATGTTGTTTTTACTTTTATGTCTGAATTAAGGCTCAAAACCTTATAGAAAGATG
35992 TCTTAAACG
66 TCTTAAACG
36001 CTACATGA
1 CTACATGA
36009 TGAAGAAGGA
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
74 76 0.95
75 4 0.05
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (74 bp):
CTACATGACTAATGTTGTTTTTACTTTTATGTCTGAATTAAGGCTCAAAACCTTATAGAAAGATG
TCTTAAACG
Found at i:54483 original size:44 final size:44
Alignment explanation
Indices: 54365--54897 Score: 647
Period size: 44 Copynumber: 12.0 Consensus size: 44
54355 AAATGAATGA
* * *
54365 ATAAATGAAAATGTATAACGGTGCATTATTGGCAAAAAAGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGC-AGAAAGGTGCC
* * * * *
54410 ATAAATGAAAATGTATAATGTTACGTTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
54454 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* *
54498 ATAAATGAAAATGCATAACGTTGTATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
54542 ATAAATGAAAATGCATAACGGGGCATTATTGGAAGAAATGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
54586 ATAAAAGAAAATGCATAACAGTGCCTTATTGGCAGAAAGGT-TC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * *
54629 AAAAATGAAAATGCATAACGTTTCATTATTGGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
54673 ATAAATGAAAATGCATAACAGTGTATTATTGGCAGAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * * * *
54717 ATAAATAAAAATGCATAATGTTGCATTATTAGCAGAAATGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
54761 ATAAATGAAAATGCATAATGGTGCATTATTGGCTGACAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
*
54805 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
** * *
54849 ACCAATGAAAATTAAATGCATAATGGTGCATT-TTGGCAAAAAGGTGCC
1 ATAAATG---A--AAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
54897 A
1 A
54898 CTCCTGGTTT
Statistics
Matches: 423, Mismatches: 59, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
43 37 0.09
44 321 0.76
45 29 0.07
47 1 0.00
48 16 0.04
49 19 0.04
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:54791 original size:219 final size:220
Alignment explanation
Indices: 54365--54860 Score: 690
Period size: 219 Copynumber: 2.3 Consensus size: 220
54355 AAATGAATGA
* * * * * *
54365 ATAAATGAAAATGTATAACGGTGCATTATTGGCAAAAAAGATGCCATAAATGAAAATGTATAATG
1 ATAAATGAAAATGCATAACGGTGCATTATTGGC-AGAAAGGTGCCAAAAATGAAAATGCATAACG
* *
54430 TTACGTTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGT
65 TTACATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGT
* * *
54495 GTCATAAATGAAAATGCATAACGTTGTATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAA
130 GTCATAAATAAAAATGCATAACGTTGCATTATTAGCAGAAAGGTGCCATAAATGAAAATGCATAA
* *
54560 CGGGGCATTATTGGAAGAAATGTGTC
195 CGGGGCATTATTGGAAGAAAGGTGCC
* * * *
54586 ATAAAAGAAAATGCATAACAGTGCCTTATTGGCAGAAAGGT-TCAAAAATGAAAATGCATAACGT
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCAAAAATGAAAATGCATAACGT
* * *
54650 TTCATTATTGGCAGAAAGGTGTCATAAATGAAAATGCATAACAGTGTATTATTGGCAGAAAGGT-
66 TACATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTG
* *
54714 TCCATAAATAAAAATGCATAATGTTGCATTATTAGCAGAAATGTGCCATAAATGAAAATGCATAA
131 T-CATAAATAAAAATGCATAACGTTGCATTATTAGCAGAAAGGTGCCATAAATGAAAATGCATAA
* * ** *
54779 TGGTGCATTATTGGCTGACAGGTGCC
195 CGGGGCATTATTGGAAGAAAGGTGCC
* **
54805 ATAAATGAAAATGCATAATGGTGCATTATTGGCAGAAAGGTGCCACCAATGAAAAT
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCAAAAATGAAAAT
54861 TAAATGCATA
Statistics
Matches: 239, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
218 1 0.00
219 192 0.80
220 17 0.07
221 29 0.12
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (220 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCCAAAAATGAAAATGCATAACGT
TACATTATTGGCAGAAAGGTGCCATAAATGAAAATGCATAACAGTGCATTATTGGCAGAAAGGTG
TCATAAATAAAAATGCATAACGTTGCATTATTAGCAGAAAGGTGCCATAAATGAAAATGCATAAC
GGGGCATTATTGGAAGAAAGGTGCC
Found at i:58205 original size:25 final size:27
Alignment explanation
Indices: 58159--58242 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
58149 TAAAATAGTG
* *
58159 TACA-TCATCTTCAATCTTTTACATAA
1 TACACTCATATTCAATCTTTTACACAA
*
58185 TACACTCAT-TTC-ATCTCTTACACAA
1 TACACTCATATTCAATCTTTTACACAA
*
58210 TACACTCATATTCGATCTTTTACACAA
1 TACACTCATATTCAATCTTTTACACAA
*
58237 CACACT
1 TACACT
58243 TCTTTTATCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
25 20 0.39
26 10 0.20
27 21 0.41
ACGTcount: A:0.33, C:0.29, G:0.01, T:0.37
Consensus pattern (27 bp):
TACACTCATATTCAATCTTTTACACAA
Found at i:71085 original size:4 final size:4
Alignment explanation
Indices: 71076--71143 Score: 57
Period size: 4 Copynumber: 15.8 Consensus size: 4
71066 TGAAAAATAA
*
71076 AAAT AAAT AAAT AAAT AATAT AAAT AATAT AAATT AATAT AAAT TAAT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AA-AT AAA-T AA-AT AAAT AAAT
*
71124 ATAT -AAT AATAT ATAAT AAA
1 AAAT AAAT AA-AT A-AAT AAA
71144 AACTATATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 2 0.04
4 29 0.55
5 20 0.38
6 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (4 bp):
AAAT
Found at i:71085 original size:10 final size:9
Alignment explanation
Indices: 71078--71142 Score: 87
Period size: 10 Copynumber: 6.9 Consensus size: 9
71068 AAAAATAAAA
71078 ATAAATAA-
1 ATAAATAAT
71086 ATAAATAAT
1 ATAAATAAT
71095 ATAAATAAT
1 ATAAATAAT
71104 ATAAATTAAT
1 ATAAA-TAAT
71114 ATAAATTAAT
1 ATAAA-TAAT
71124 ATATAATAAT
1 ATA-AATAAT
71134 ATATAATAA
1 ATA-AATAA
71143 AAACTATATA
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
8 8 0.15
9 14 0.26
10 30 0.56
11 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAAATAAT
Found at i:71130 original size:36 final size:35
Alignment explanation
Indices: 71078--71167 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 35
71068 AAAAATAAAA
* * *
71078 ATAAATAAATAAATAATATAAATAATATAAATTAAT
1 ATAAATAAATATATAATATAAATAATAAAAACT-AT
* *
71114 ATAAATTAATATATAATAATATATAATAAAAACTAT
1 ATAAATAAATATATAAT-ATAAATAATAAAAACTAT
71150 ATAAA-AAATTATATAATA
1 ATAAATAAA-TATATAATA
71168 CGTTTTGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
35 3 0.07
36 30 0.65
37 13 0.28
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (35 bp):
ATAAATAAATATATAATATAAATAATAAAAACTAT
Found at i:71349 original size:34 final size:34
Alignment explanation
Indices: 71240--71500 Score: 174
Period size: 35 Copynumber: 7.4 Consensus size: 34
71230 ATATATATCT
* *
71240 AAAACTATA-TATATATTTTCAAAATATGTTTTCA
1 AAAACTATATTATATGTTTTCAAAA-ATGATTTCA
* * **
71274 AAAATTATATTATATAGTTTTCAAAAATCATTTTT
1 AAAACTATATTATAT-GTTTTCAAAAATGATTTCA
* * *
71309 ATAACTATATTATATTTTTTCCAAAAA-GGTTTCA
1 AAAACTATATTATATGTTTT-CAAAAATGATTTCA
*
71343 AAAACTATATTATATGTTTTCAAAAACGTGTTTTC-
1 AAAACTATATTATATGTTTTCAAAAA--TGATTTCA
* * * * *
71378 AAAAC--CATTATGTATTTTCAAAAACCGATTTTA
1 AAAACTATATTATATGTTTTCAAAAA-TGATTTCA
* ** *
71411 AAAACTACATATTATATGCTTTCAAAACCCGTTTTCTA
1 AAAACT--ATATTATATGTTTTCAAAA-ATGATTTC-A
71449 AAAACTATATATTATATGTTTTCAAAAAAT-ATTTTCA
1 AAAAC--TATATTATATGTTTTC-AAAAATGA-TTTCA
*
71486 AAAAATATATTATAT
1 AAAACTATATTATAT
71501 TATATATATA
Statistics
Matches: 175, Mismatches: 35, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
32 4 0.02
33 27 0.15
34 33 0.19
35 44 0.25
36 14 0.08
37 24 0.14
38 24 0.14
39 4 0.02
40 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (34 bp):
AAAACTATATTATATGTTTTCAAAAATGATTTCA
Found at i:71394 original size:69 final size:66
Alignment explanation
Indices: 71239--71500 Score: 170
Period size: 69 Copynumber: 3.7 Consensus size: 66
71229 TATATATATC
* * * *
71239 TAAAACTATATATATATTTTCAAAATATGTTTTCAAAAATTATATTATATAGTTTTCAAAAATCA
1 TAAAACCATAT-TATATTTTCAAAA-ACGATTTCAAAAACTATATTATAT-GTTTTCAAAAATCA
71304 TTTT
63 TTTT
* * * *
71308 TATAACTATATTATATTTTTTCCAAAAA-GGTTTCAAAAACTATATTATATGTTTTCAAAAA-CG
1 TAAAACCATATTATA--TTTT-CAAAAACGATTTCAAAAACTATATTATATGTTTTCAAAAATCA
71371 TGTTT
63 T-TTT
* * * **
71376 TCAAAACCAT-TATGTATTTTCAAAAACCGATTTTAAAAACTACATATTATATGCTTTCAAAACC
1 T-AAAACCATAT-TATATTTTCAAAAA-CGATTTCAAAAACT--ATATTATATGTTTTCAAAAAT
*
71440 CGTTTT
61 CATTTT
* ** *
71446 CTAAAAACTATATATTATATGTTTTCAAAAAATATTTTCAAAAAATATATTATAT
1 -T-AAAAC--CATATTATA--TTTTCAAAAACGA-TTTCAAAAACTATATTATAT
71501 TATATATATA
Statistics
Matches: 157, Mismatches: 18, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
66 6 0.04
67 6 0.04
68 31 0.20
69 39 0.25
70 26 0.17
71 14 0.09
73 14 0.09
74 2 0.01
75 19 0.12
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (66 bp):
TAAAACCATATTATATTTTCAAAAACGATTTCAAAAACTATATTATATGTTTTCAAAAATCATTT
T
Found at i:71434 original size:37 final size:38
Alignment explanation
Indices: 71393--71476 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 38
71383 CATTATGTAT
71393 TTTCAAAAACCGATTT-TAAAAACTACATATTATATGC
1 TTTCAAAAACCGATTTCTAAAAACTACATATTATATGC
* * * *
71430 TTTCAAAACCCGTTTTCTAAAAACTATATATTATATGT
1 TTTCAAAAACCGATTTCTAAAAACTACATATTATATGC
71468 TTTCAAAAA
1 TTTCAAAAA
71477 ATATTTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 14 0.34
38 27 0.66
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.38
Consensus pattern (38 bp):
TTTCAAAAACCGATTTCTAAAAACTACATATTATATGC
Found at i:71485 original size:13 final size:13
Alignment explanation
Indices: 71467--71493 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
71457 ATATTATATG
71467 TTTTCAAAAAATA
1 TTTTCAAAAAATA
71480 TTTTCAAAAAATA
1 TTTTCAAAAAATA
71493 T
1 T
71494 ATTATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTTCAAAAAATA
Found at i:71512 original size:11 final size:11
Alignment explanation
Indices: 71490--71519 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
71480 TTTTCAAAAA
71490 ATATATTATATT
1 ATATA-TATATT
71502 ATATATATATT
1 ATATATATATT
71513 ATATATA
1 ATATATA
71520 AATAGCCCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATATATATATT
Done.