Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007467.1 Hibiscus syriacus cultivar Beakdansim tig00020492_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: 71794
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10237 original size:22 final size:22
Alignment explanation
Indices: 10212--10270 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
10202 CTTTATACTA
*
10212 AGAGGTTATAAAACCCCTTTAT
1 AGAGGTTATAAAACCCCCTTAT
**
10234 AGAGGTTACGAAACCCCCTTAT
1 AGAGGTTATAAAACCCCCTTAT
10256 AGAGGTT-TAGAAACC
1 AGAGGTTATA-AAACC
10271 AGTAGAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (22 bp):
AGAGGTTATAAAACCCCCTTAT
Found at i:11720 original size:13 final size:13
Alignment explanation
Indices: 11702--11726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11692 TTATATTGAT
11702 GCTTTAGAGGCTA
1 GCTTTAGAGGCTA
11715 GCTTTAGAGGCT
1 GCTTTAGAGGCT
11727 CATTTCCTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (13 bp):
GCTTTAGAGGCTA
Found at i:20189 original size:229 final size:227
Alignment explanation
Indices: 19779--20296 Score: 533
Period size: 229 Copynumber: 2.3 Consensus size: 227
19769 ATTAGTTGCA
* **
19779 ACTAGACCTCCTCAACATGAATGAGCAATGT-TATCATCAGATTTGACATCAAGCAAATCACTCA
1 ACTAGATCTCCTCAACATGAAAAAGCAATGTCT-TCATCAGATTTGACATCAA-CAAATCACTCA
* * * * * * *
19843 AGAGCGATCAAATTTACTCATCACGTAGGAGAAGTGTCGTTTACAAAATCAAGTTATCTCTAAAC
64 AAAGCAACCAAATATACTCATCACATAGAAGAAGTGTCGTTTACAAAATCAAGTTATCTCCAAAC
** * * *
19908 AATCAAACTTGTTAAACGTAAAGGAATATTATTGTCTTCAGATGCAATCTCTCAAATACAACTAG
129 AATCAAACTTGCCAAACGTAAAGGAATAGTATTGTCTTCAAATACAATCTCTCAAATACAACTA-
* * * * *
19973 ACGTC-CTCAACATGAAGGAACATTTTC-ATCCATTG
193 ACATCTC-CAACACGAAGAAACAATGTCGA-CCATTG
* *
20008 ACTAGATCTCCTCAACATGAAAAAGCAATGTCTTTATCAGATTTGACATCGAA-AATATTACTCA
1 ACTAGATCTCCTCAACATGAAAAAGCAATGTCTTCATCAGATTTGACATC-AACAA-ATCACTCA
* * * * * * *
20072 AAAGCAACCAGATATCCTCATCACATAGAAGCAGTGTCGTTTATAGAATCAAGTTATCTCCAGAT
64 AAAGCAACCAAATATACTCATCACATAGAAGAAGTGTCGTTTACAAAATCAAGTTATCTCCAAAC
* * * * * ***
20137 ACTCAAACTT-CCACAACGTGAAGGAATAGTGTTGTCTTCAAATACGATCTCTCGAATGTGACTA
129 AATCAAACTTGCCA-AACGTAAAGGAATAGTATTGTCTTCAAATACAATCTCTCAAATACAACTA
20201 ACATCTCCAACACGAAGAAACAATGTCGACCATTG
193 ACATCTCCAACACGAAGAAACAATGTCGACCATTG
* * * * * *
20236 ACTAAATCTCTTCAACATGAAGAAGCAATGTCATCATTAGATTTGACATTAAGCAAATCAC
1 ACTAGATCTCCTCAACATGAAAAAGCAATGTCTTCATCAGATTTGACATCAA-CAAATCAC
20297 CTAAAGTGAC
Statistics
Matches: 236, Mismatches: 45, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
227 2 0.01
228 76 0.32
229 155 0.66
230 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.27
Consensus pattern (227 bp):
ACTAGATCTCCTCAACATGAAAAAGCAATGTCTTCATCAGATTTGACATCAACAAATCACTCAAA
AGCAACCAAATATACTCATCACATAGAAGAAGTGTCGTTTACAAAATCAAGTTATCTCCAAACAA
TCAAACTTGCCAAACGTAAAGGAATAGTATTGTCTTCAAATACAATCTCTCAAATACAACTAACA
TCTCCAACACGAAGAAACAATGTCGACCATTG
Found at i:20998 original size:3 final size:3
Alignment explanation
Indices: 20990--21015 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20980 TTTGTCCAAG
20990 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
21016 TACAGACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:21384 original size:20 final size:19
Alignment explanation
Indices: 21357--21394 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
21347 AAATAAAGAA
21357 GAAAGAAAGAAA-GAAAAGT
1 GAAAGAAA-AAATGAAAAGT
21376 GAAATGAAAAAATGAAAAG
1 GAAA-GAAAAAATGAAAAG
21395 AAAAGGGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GAAAGAAAAAATGAAAAGT
Found at i:21901 original size:2 final size:2
Alignment explanation
Indices: 21896--21981 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
21886 ACACACATAC
21896 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
21938 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
21980 AT
1 AT
21982 TTCCTTTCAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23747 original size:38 final size:38
Alignment explanation
Indices: 23691--23818 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 38
23681 TTGCAAATTG
*
23691 TTTTTGAAAATACATATATAATATATAGTTTAAAACAT
1 TTTTTGAAAATATATATATAATATATAGTTTAAAACAT
* ***
23729 TTTTTGAAAATATGTATAT--TATATAGTTTTTCA-AT
1 TTTTTGAAAATATATATATAATATATAGTTTAAAACAT
*
23764 ATTTTTG-AAA-AT-TATATAATATAGT-TTTTGAAAACA-
1 -TTTTTGAAAATATATATATAATATA-TAGTTT-AAAACAT
23800 TTTTT-AAAATATATATATA
1 TTTTTGAAAATATATATATA
23819 TACTTTTGAA
Statistics
Matches: 72, Mismatches: 9, Indels: 19
0.72 0.09 0.19
Matches are distributed among these distances:
33 5 0.07
34 2 0.03
35 20 0.28
36 21 0.29
37 7 0.10
38 17 0.24
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (38 bp):
TTTTTGAAAATATATATATAATATATAGTTTAAAACAT
Found at i:23813 original size:33 final size:33
Alignment explanation
Indices: 23691--23831 Score: 108
Period size: 38 Copynumber: 4.0 Consensus size: 33
23681 TTGCAAATTG
*
23691 TTTTTGAAAATACATATATAATATATAGTTTAAAACA
1 TTTTTGAAAAT--ATATAT-ATATAT-TTTTAAAACA
* *
23728 TTTTTTGAAAATATGTATATTATATAGTTTTT-CAATA
1 -TTTTTGAAAATA--TATA-TATATA-TTTTTAAAACA
23765 TTTTTGAAAAT-TATATAATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATAT-ATATA-TTTTT-AAAACA
*
23800 TTTTT-AAAATATATATATATACTTTTGAAAAC
1 TTTTTGAAAATATATATATATA-TTTTTAAAAC
23832 GTTATGAAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
32 1 0.01
33 20 0.23
34 14 0.16
35 13 0.15
36 12 0.14
37 3 0.03
38 23 0.26
39 2 0.02
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (33 bp):
TTTTTGAAAATATATATATATATTTTTAAAACA
Found at i:23938 original size:26 final size:25
Alignment explanation
Indices: 23874--23940 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
23864 TAAAAAAACC
* *
23874 ATTTTGAAAATATATTTTTTTGAAA
1 ATTTTTAAAATATATGTTTTTGAAA
* *
23899 A-TTATATAATATATAGTTTTTGAAA
1 ATTTTTAAAATATAT-GTTTTTGAAA
23924 ACGTTTTTAAAATATAT
1 A--TTTTTAAAATATAT
23941 AATATATACT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 10 0.31
25 11 0.34
28 11 0.34
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (25 bp):
ATTTTTAAAATATATGTTTTTGAAA
Found at i:23993 original size:102 final size:100
Alignment explanation
Indices: 23891--24074 Score: 273
Period size: 100 Copynumber: 1.8 Consensus size: 100
23881 AAATATATTT
* *
23891 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACGTTTTTAAAA-TATATAATATATACTTTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATTATATAATATATACTTTT
*
23954 GAAAATGTTTATATAATATATAATTTTTAAAAACCA
66 GAAAACGTTTATAT-ATATATAATTTTTAAAAACCA
* * **
23990 TTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTTAAAAATTTATATATTATATGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAA-TTATATAATATATACTTT
24055 TGAAAACGTTTATATATATA
65 TGAAAACGTTTATATATATA
24075 ATATTATTAC
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
99 10 0.13
100 32 0.43
101 5 0.07
102 28 0.37
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (100 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATTATATAATATATACTTTT
GAAAACGTTTATATATATATAATTTTTAAAAACCA
Found at i:24011 original size:38 final size:37
Alignment explanation
Indices: 23963--24049 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 37
23953 TGAAAATGTT
*
23963 TATATAATATATAATTTTTAAAAACCATTTTGAAAATA
1 TATATAATATATAATTTTTAAAAA-CATTTTAAAAATA
* * *
24001 TATATAATATATAGTTTTTTAAAACATTTTAAAAATT
1 TATATAATATATAATTTTTAAAAACATTTTAAAAATA
*
24038 TATATATTATAT
1 TATATAATATAT
24050 GTTTTTGAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
37 22 0.50
38 22 0.50
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (37 bp):
TATATAATATATAATTTTTAAAAACATTTTAAAAATA
Found at i:24092 original size:4 final size:4
Alignment explanation
Indices: 24085--24151 Score: 74
Period size: 4 Copynumber: 18.2 Consensus size: 4
24075 ATATTATTAC
* *
24085 TATT TA-T T-TT TATT T-TT AATT TA-T TACT TA-T T-TT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
24127 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
24152 TCTTTTCTTC
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
3 13 0.24
4 42 0.76
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:25402 original size:27 final size:28
Alignment explanation
Indices: 25371--25435 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
25361 TTTTATCCCG
25371 TTTTTCATTTTATTTCATT-TCATT-TTA
1 TTTTTCATTTTA-TTCATTATCATTATTA
* * *
25398 TTTTTTAATTTATTCCTTATCATTATTA
1 TTTTTCATTTTATTCATTATCATTATTA
*
25426 TTTTTGATTT
1 TTTTTCATTT
25436 CCTTCTCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.16
27 15 0.48
28 11 0.35
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (28 bp):
TTTTTCATTTTATTCATTATCATTATTA
Found at i:30840 original size:84 final size:85
Alignment explanation
Indices: 30666--31196 Score: 579
Period size: 84 Copynumber: 6.4 Consensus size: 85
30656 TAAACAAACT
* * * * * ** *
30666 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAGGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
* *
30727 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCCAAGGCACATC
* * *
30747 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
30812 CTCAGC-TCCAAGGCACATC
66 CTCAGCTTCCAAGGCACATC
* * * * ** *
30831 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
* *
30892 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCCAAGGCACATC
* * *
30912 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
30977 CTCAGC-TCCAAGGCACATC
66 CTCAGCTTCCAAGGCACATC
** * * * ** *
30996 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATC--TG-CC-AAAGACCCCCGAGTTCGATTACA
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
* *
31057 CTCAGCTTCGAGGGCACATC
66 CTCAGCTTCCAAGGCACATC
* * *
31077 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
31142 CTCAGC-TCCAAGGCACATC
66 CTCAGCTTCCAAGGCACATC
* * * *
31161 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG
1 ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTG
31197 CCAAAGACTC
Statistics
Matches: 367, Mismatches: 69, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
80 50 0.14
81 109 0.30
82 4 0.01
83 6 0.02
84 124 0.34
85 74 0.20
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (85 bp):
ATTTACAGCATAACTCAAGGCGAGAAGGGCTATCTGTGACCAAAAGACCTTCGAGTTCGACTACA
CTCAGCTTCCAAGGCACATC
Found at i:31256 original size:81 final size:79
Alignment explanation
Indices: 30666--31274 Score: 588
Period size: 81 Copynumber: 7.4 Consensus size: 79
30656 TAAACAAACT
* * * *
30666 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACCCCCGAGTTCGATTACACTCA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCA
30731 GCTTCGAGGGCACATC
65 GCTTCGAGGG-ACATC
* * * * * *
30747 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATC--TG-CC-AAAGACC-CCGAGTTCGATTACA
* * *
30812 CTCAGCTCCAAGGCACATC
61 CTCAGCTTCGAGGGACATC
* * *
30831 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCA
30896 GCTTCGAGGGCACATC
65 GCTTCGAGGG-ACATC
* * * * * *
30912 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATC--TG-CC-AAAGACC-CCGAGTTCGATTACA
* * *
30977 CTCAGCTCCAAGGCACATC
61 CTCAGCTTCGAGGGACATC
** * *
30996 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCA
31061 GCTTCGAGGGCACATC
65 GCTTCGAGGG-ACATC
* * * * * *
31077 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACG
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATC--TG-CC-AAAGACC-CCGAGTTCGATTACA
* * *
31142 CTCAGCTCCAAGGCACATC
61 CTCAGCTTCGAGGGACATC
* * *
31161 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCCCGAGTTCGATTACACTCA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAGAC-CCCGAGTTCGATTACACTCA
* *
31226 ACTTCGAGGTGATATC
65 GCTTCGAGG-GACATC
** * *
31242 ATTTACAATATAGCTCATGGCAAGAAGGGCTAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTAT
31275 TTGTCAATAA
Statistics
Matches: 423, Mismatches: 84, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
80 84 0.20
81 134 0.32
82 6 0.01
83 6 0.01
84 110 0.26
85 83 0.20
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.23
Consensus pattern (79 bp):
ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
CTTCGAGGGACATC
Found at i:31270 original size:165 final size:165
Alignment explanation
Indices: 30666--31248 Score: 1105
Period size: 165 Copynumber: 3.5 Consensus size: 165
30656 TAAACAAACT
*
30666 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAGGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
30731 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
30796 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
30831 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
30896 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
30961 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
30996 ATTTGTAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
31061 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
31126 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
31161 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* *
31226 ACTTCGAGGTG-ATATCATTTACA
66 GCTTCGAGG-GCACATCATTTACA
31249 ATATAGCTCA
Statistics
Matches: 411, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
165 410 1.00
166 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:31961 original size:36 final size:37
Alignment explanation
Indices: 31864--32240 Score: 181
Period size: 37 Copynumber: 10.0 Consensus size: 37
31854 TTGCAAATTG
31864 TTTTTGAAAATACATATATAATATATAG--TTTAAAACA
1 TTTTTGAAAAT--ATATATAATATATAGTTTTTAAAACA
* * * *
31901 TTTTTTGAAAATATGTATATTATATAGTTTTTCAAATA
1 -TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
31939 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTT-AAAACA
* *
31976 TTTTT-AAAATATATATAATATATACTTTTGAAAAC-
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * * * *
32011 GTTATGAAAACATTTATGTAATATATAATTTTTAAAAAAACCA
1 TTTTTG-AAA-ATATATATAATATATAGTTTTT---AAAA-CA
** * * * * *
32054 -TTTTGAAAATATAT-TTTTTTGAAAATTATATAATATATA
1 TTTTTGAAAATATATATAATAT-ATAGTT-TTTAA-A-ACA
* * * * * *
32093 GTTTTTGAAAACGTTTTTAAAATATATA--ATAT-ATAC-
1 -TTTTTGAAAA--TATATATAATATATAGTTTTTAAAACA
* *
32129 -TTTTGAAAATGTTTATATAATATATAATTTTTAAAAACCA
1 TTTTTGAAAA--TATATATAATATATAGTTTTT-AAAA-CA
32169 -TTTTGAAAATATATATAATATATAGTTTTTTAAAACA
1 TTTTTGAAAATATATATAATATATAG-TTTTTAAAACA
* * *
32206 -TTTTAAAAATTTATATATTATAT-GTTTTTGAAAAC
1 TTTTTGAAAATATATATAATATATAGTTTTT-AAAAC
32241 GTTTATATAT
Statistics
Matches: 265, Mismatches: 45, Indels: 60
0.72 0.12 0.16
Matches are distributed among these distances:
34 23 0.09
35 8 0.03
36 48 0.18
37 63 0.24
38 58 0.22
39 12 0.05
40 23 0.09
41 18 0.07
42 5 0.02
43 5 0.02
44 2 0.01
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:31974 original size:75 final size:72
Alignment explanation
Indices: 31838--32005 Score: 198
Period size: 75 Copynumber: 2.3 Consensus size: 72
31828 ATATATACAC
* *
31838 ATATATATTATGTAG-TTTGCAAATTGTTTTTGAAAATACATATATAATATATAGTTTAAAACAT
1 ATATATATTATATAGTTTTGCAAATTATTTTTGAAAAT--ATATATAATATATAGTTTAAAACA-
31902 TTTTTGAAAAT
63 TTTTT-AAAAT
* *
31913 ATGTATATTATATAGTTTTTCAAA-TATTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACA
1 ATATATATTATATAGTTTTGCAAATTATTTTTGAAAATATATATAATATATAG--TTT-AAAACA
31976 TTTTTAAAAT
63 TTTTTAAAAT
* *
31986 ATATATAATATATACTTTTG
1 ATATATATTATATAGTTTTG
32006 AAAACGTTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
72 14 0.17
73 21 0.26
74 8 0.10
75 31 0.38
76 7 0.09
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.48
Consensus pattern (72 bp):
ATATATATTATATAGTTTTGCAAATTATTTTTGAAAATATATATAATATATAGTTTAAAACATTT
TTAAAAT
Found at i:32117 original size:26 final size:25
Alignment explanation
Indices: 32053--32119 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
32043 TAAAAAAACC
* *
32053 ATTTTGAAAATATATTTTTTTGAAA
1 ATTTTTAAAATATATGTTTTTGAAA
* *
32078 A-TTATATAATATATAGTTTTTGAAA
1 ATTTTTAAAATATAT-GTTTTTGAAA
32103 ACGTTTTTAAAATATAT
1 A--TTTTTAAAATATAT
32120 AATATATACT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 10 0.31
25 11 0.34
28 11 0.34
ACGTcount: A:0.42, C:0.01, G:0.07, T:0.49
Consensus pattern (25 bp):
ATTTTTAAAATATATGTTTTTGAAA
Found at i:32151 original size:34 final size:35
Alignment explanation
Indices: 32075--32156 Score: 112
Period size: 34 Copynumber: 2.3 Consensus size: 35
32065 TATTTTTTTG
* *
32075 AAAATTATATAATATATAGTTTTTGAAAACGTTTTT
1 AAAA-TATATAATATATAGCTTTTGAAAACGTTTAT
*
32111 AAAATATATAATATATA-CTTTTGAAAATGTTTAT
1 AAAATATATAATATATAGCTTTTGAAAACGTTTAT
*
32145 ATAATATATAAT
1 AAAATATATAAT
32157 TTTTAAAAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
34 25 0.60
35 13 0.31
36 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.45
Consensus pattern (35 bp):
AAAATATATAATATATAGCTTTTGAAAACGTTTAT
Found at i:32172 original size:102 final size:100
Alignment explanation
Indices: 32070--32253 Score: 273
Period size: 100 Copynumber: 1.8 Consensus size: 100
32060 AAATATATTT
* *
32070 TTTTGAAAAT-TATATAATATATAGTTTTTGAAAACGTTTTTAAAA-TATATAATATATACTTTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATTATATAATATATACTTTT
*
32133 GAAAATGTTTATATAATATATAATTTTTAAAAACCA
66 GAAAACGTTTATAT-ATATATAATTTTTAAAAACCA
* * **
32169 TTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTTAAAAATTTATATATTATATGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAA-TTATATAATATATACTTT
32234 TGAAAACGTTTATATATATA
65 TGAAAACGTTTATATATATA
32254 ATATTATTAC
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
99 10 0.13
100 32 0.43
101 5 0.07
102 28 0.37
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (100 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTAAAAATTATATAATATATACTTTT
GAAAACGTTTATATATATATAATTTTTAAAAACCA
Found at i:32271 original size:4 final size:4
Alignment explanation
Indices: 32264--32326 Score: 66
Period size: 4 Copynumber: 17.2 Consensus size: 4
32254 ATATTATTAC
* *
32264 TATT TA-T T-TT TATT T-TT AATT TA-T TACT TA-T T-TT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT TATT
32306 TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT T
32327 TCTTTTCTTC
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
3 13 0.25
4 38 0.75
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:33571 original size:27 final size:27
Alignment explanation
Indices: 33540--33603 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
33530 TTTTATCCCG
33540 TTTTTCATTTTATTTCATT-TCATT-TTA
1 TTTTT-ATTTTAT-TCATTATCATTATTA
* *
33567 TTTTTAATTTATTCCTTATCATTATTA
1 TTTTTATTTTATTCATTATCATTATTA
33594 TTTTTGATTT
1 TTTTT-ATTT
33604 CCTTCTCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 4 0.13
26 11 0.35
27 13 0.42
28 3 0.10
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTTTATTTTATTCATTATCATTATTA
Found at i:33577 original size:26 final size:27
Alignment explanation
Indices: 33548--33603 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
33538 CGTTTTTCAT
33548 TTTATTTCATT-TCATT-TTATTTTTAA
1 TTTA-TTCATTATCATTATTATTTTTAA
* *
33574 TTTATTCCTTATCATTATTATTTTTGA
1 TTTATTCATTATCATTATTATTTTTAA
33601 TTT
1 TTT
33604 CCTTCTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 5 0.19
26 9 0.35
27 12 0.46
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTATTCATTATCATTATTATTTTTAA
Found at i:34736 original size:21 final size:21
Alignment explanation
Indices: 34692--34736 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
34682 AGATTACACA
*
34692 TTTAGTACTTAAACTATCAGT
1 TTTAGTACTTAAACTATCAAT
* * *
34713 TTTAGTATTTAAACTTTTAAT
1 TTTAGTACTTAAACTATCAAT
34734 TTT
1 TTT
34737 TTCAAAATCA
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:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTAGTACTTAAACTATCAAT
Found at i:37597 original size:18 final size:17
Alignment explanation
Indices: 37568--37608 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
37558 TTAAATTTTA
*
37568 TAATATTATTTTTTAAT
1 TAATATTATTTTTAAAT
37585 TAATATATATTTTTAAAT
1 TAATAT-TATTTTTAAAT
37603 T-ATATT
1 TAATATT
37609 CGAAGAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.45
18 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATATTATTTTTAAAT
Found at i:40842 original size:17 final size:20
Alignment explanation
Indices: 40803--40849 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
40793 TTAAAAAACG
*
40803 ATAATAAAAATATATTAATA
1 ATAATATAAATATATTAATA
40823 ATAATATAAAT-TA-TAA-A
1 ATAATATAAATATATTAATA
*
40840 ATATTATAAA
1 ATAATATAAA
40850 AACATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
18 3 0.12
19 2 0.08
20 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATATAAATATATTAATA
Found at i:47536 original size:21 final size:21
Alignment explanation
Indices: 47512--47623 Score: 63
Period size: 20 Copynumber: 5.5 Consensus size: 21
47502 ACTCAGTTTC
47512 TAAATTCGCATCGCGAATATG
1 TAAATTCGCATCGCGAATATG
* *
47533 TAAA-TCGCATTGCG-AT-TT
1 TAAATTCGCATCGCGAATATG
* * * * *
47551 TACGAATTCGCGTTGCGATTTTC
1 TA--AATTCGCATCGCGAATATG
* * *
47574 CAAATTCACAACGCGAATATG
1 TAAATTCGCATCGCGAATATG
* *
47595 TAAA-TCGCAACGCGAATTTG
1 TAAATTCGCATCGCGAATATG
47615 T-AATTCGCA
1 TAAATTCGCA
47624 ACACAGAAGT
Statistics
Matches: 69, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
18 3 0.04
19 4 0.06
20 31 0.45
21 28 0.41
22 1 0.01
23 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (21 bp):
TAAATTCGCATCGCGAATATG
Found at i:47607 original size:20 final size:20
Alignment explanation
Indices: 47582--47625 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
47572 TCCAAATTCA
47582 CAACGCGAATATGTAAATCG
1 CAACGCGAATATGTAAATCG
* *
47602 CAACGCGAATTTGTAATTCG
1 CAACGCGAATATGTAAATCG
47622 CAAC
1 CAAC
47626 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (20 bp):
CAACGCGAATATGTAAATCG
Found at i:47639 original size:20 final size:20
Alignment explanation
Indices: 47616--47664 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
47606 GCGAATTTGT
47616 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
*
47636 AATTCGCAACACATAAGTCA
1 AATTCGCAACACAGAAGTCA
47656 AATTCGCAA
1 AATTCGCAA
47665 AGCGCGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.18
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:47845 original size:22 final size:22
Alignment explanation
Indices: 47818--47864 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
47808 CTACGGCGAC
47818 ATCCGTCCCCATCTCTAACGAA
1 ATCCGTCCCCATCTCTAACGAA
**
47840 ATCCGTCCCCATCTCTGGCGAA
1 ATCCGTCCCCATCTCTAACGAA
47862 ATC
1 ATC
47865 AGTCTATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.40, G:0.13, T:0.23
Consensus pattern (22 bp):
ATCCGTCCCCATCTCTAACGAA
Found at i:48048 original size:20 final size:20
Alignment explanation
Indices: 48023--48068 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
48013 TTTACTGGTA
48023 ATTTCAGTAATAAATTAACC
1 ATTTCAGTAATAAATTAACC
48043 ATTTCAGTAATAAATTAACC
1 ATTTCAGTAATAAATTAACC
48063 ATTTCA
1 ATTTCA
48069 CTTAGATTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (20 bp):
ATTTCAGTAATAAATTAACC
Found at i:48291 original size:20 final size:20
Alignment explanation
Indices: 48256--48322 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
48246 AAATCGCAAC
* *
48256 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTCATTTTCGCATT
48275 GCGATTTTCATTTTCGCATT
1 GCGATTTTCATTTTCGCATT
48295 GCGATTTTCATTTTCGCATT
1 GCGATTTTCATTTTCGCATT
48315 GCGATTTT
1 GCGATTTT
48323 TAGTTTCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 8 0.18
20 37 0.82
ACGTcount: A:0.13, C:0.18, G:0.19, T:0.49
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCATT
Found at i:50025 original size:21 final size:21
Alignment explanation
Indices: 49998--50047 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
49988 GTTAGGTGAG
*
49998 TTACGTGATGAGGTCAATACT
1 TTACGTGAGGAGGTCAATACT
* **
50019 TTGCGTGAGGAGGTCGGTACT
1 TTACGTGAGGAGGTCAATACT
50040 TTACGTGA
1 TTACGTGA
50048 AGACAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGAGGAGGTCAATACT
Found at i:50483 original size:21 final size:21
Alignment explanation
Indices: 50455--50553 Score: 101
Period size: 21 Copynumber: 4.7 Consensus size: 21
50445 GTAGTACCTG
*
50455 TCATCATTCAAGAGGCCTCT-
1 TCATCATTCAAGAGGCCCCTA
*
50475 CCTATCATTCAAGAGGCCCCTA
1 TC-ATCATTCAAGAGGCCCCTA
* *
50497 TCATCATTCAAGAGACCCCTG
1 TCATCATTCAAGAGGCCCCTA
* * * *
50518 CCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTA
*
50539 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
50554 TCCATCCCAC
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
20 1 0.02
21 64 0.97
22 1 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.23
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTA
Found at i:50564 original size:42 final size:40
Alignment explanation
Indices: 50451--50573 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 40
50441 GCCCGTAGTA
* *
50451 CCTGTCATCATTCAAGAGGCCTCTCCTATCATTCAAGAGGCC
1 CCTGTCATCATTCAAGAGGCCTC-CC-ACCGTTCAAGAGGCC
* * *
50493 CCTATCATCATTCAAGAGACCCCTGCCACCGTTCAAGAGGCC
1 CCTGTCATCATTCAAGAG--GCCTCCCACCGTTCAAGAGGCC
* *
50535 CCTGTCATCGTTCAAGAGGTCCATCCCACCGTTCGAGAG
1 CCTGTCATCATTCAAGAGG-CC-TCCCACCGTTCAAGAG
50574 CCCGAATCAC
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
41 2 0.03
42 60 0.90
43 2 0.03
44 3 0.04
ACGTcount: A:0.24, C:0.35, G:0.19, T:0.23
Consensus pattern (40 bp):
CCTGTCATCATTCAAGAGGCCTCCCACCGTTCAAGAGGCC
Found at i:50567 original size:21 final size:21
Alignment explanation
Indices: 50503--50573 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
50493 CCTATCATCA
* * *
50503 TTCAAGAGACCCCTGCCACCG
1 TTCAAGAGGCCCATCCCACCG
* ** *
50524 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCATCCCACCG
*
50545 TTCAAGAGGTCCATCCCACCG
1 TTCAAGAGGCCCATCCCACCG
*
50566 TTCGAGAG
1 TTCAAGAG
50574 CCCGAATCAC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.20
Consensus pattern (21 bp):
TTCAAGAGGCCCATCCCACCG
Found at i:51600 original size:13 final size:14
Alignment explanation
Indices: 51575--51605 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
51565 AAATTGATGT
51575 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTG
51589 ATTTGT-AAAGTTG
1 ATTTGTAAAAGTTG
51602 ATTT
1 ATTT
51606 TTTAATTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (14 bp):
ATTTGTAAAAGTTG
Found at i:51688 original size:64 final size:64
Alignment explanation
Indices: 51584--51735 Score: 227
Period size: 64 Copynumber: 2.4 Consensus size: 64
51574 TATTTGTAAA
*
51584 AGTTGATTTGT-AAAGTTGATTT-TTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTT
1 AGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTCGTTT
* * ***
51646 AGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTCGTTT
1 AGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTCGTTT
*
51710 AATTGATTTGTAAAAGTTGATTTGTT
1 AGTTGATTTGTAAAAGTTGATTTGTT
51736 GTTTTAAATT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
62 11 0.14
63 11 0.14
64 59 0.73
ACGTcount: A:0.28, C:0.03, G:0.18, T:0.51
Consensus pattern (64 bp):
AGTTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTCGTTT
Found at i:52964 original size:18 final size:18
Alignment explanation
Indices: 52941--52977 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52931 CGAAATTTAT
52941 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
52959 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
52977 A
1 A
52978 CTTCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:53391 original size:25 final size:25
Alignment explanation
Indices: 53363--53412 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
53353 CATTATTTTC
*
53363 CAAATAATTTACCCATAACAATGTT
1 CAAATAATGTACCCATAACAATGTT
53388 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCATAACAATGTT
53413 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (25 bp):
CAAATAATGTACCCATAACAATGTT
Found at i:53516 original size:20 final size:20
Alignment explanation
Indices: 53487--53527 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
53477 TACACTTTCT
53487 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
*
53507 CAACGTGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
53527 C
1 C
53528 GTTGCGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:53622 original size:49 final size:49
Alignment explanation
Indices: 53541--53646 Score: 122
Period size: 49 Copynumber: 2.2 Consensus size: 49
53531 GCGATTTTCT
* ** * * *
53541 CGTTTCGATTGTTGTGATAGTCAAATTCGCAACGCGAAAGTAAAATTCG
1 CGTTGCGATTGTTACGAAAGTCAAATTCGCAACGCGAAACTAAAATTCA
* * *
53590 CGTTGCGATTGTTACGAAAGTCAAATTTGCAACGTGAAACTCAAATTCA
1 CGTTGCGATTGTTACGAAAGTCAAATTCGCAACGCGAAACTAAAATTCA
*
53639 CATTGCGA
1 CGTTGCGA
53647 ATTTGATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (49 bp):
CGTTGCGATTGTTACGAAAGTCAAATTCGCAACGCGAAACTAAAATTCA
Found at i:56209 original size:24 final size:24
Alignment explanation
Indices: 56182--56228 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
56172 CAAAATATGA
56182 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
56206 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
56229 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:56237 original size:24 final size:24
Alignment explanation
Indices: 56186--56237 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
56176 ATATGAGTAT
** *
56186 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
56210 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
56234 TGAC
1 TGAC
56238 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:57230 original size:20 final size:19
Alignment explanation
Indices: 57194--57311 Score: 87
Period size: 20 Copynumber: 5.9 Consensus size: 19
57184 GTGAATTCGA
* * *
57194 AAATCGAGTTACTAATTCAG
1 AAATCGAGTTGCGAATT-GG
*
57214 AAATCGAGTTGCGAATTTG
1 AAATCGAGTTGCGAATTGG
* *
57233 AAATTCAGTGTTGCGAATTTGT
1 AAA-TC-GAGTTGCGAA-TTGG
57255 AAATC-ACGTTGCGAATTTGG
1 AAATCGA-GTTGCGAA-TTGG
57275 AAATCGCA-TTGCGAATTTGG
1 AAATCG-AGTTGCGAA-TTGG
*
57295 AAATCGTGTTGCGAATT
1 AAATCGAGTTGCGAATT
57312 TGACTTCTGT
Statistics
Matches: 82, Mismatches: 9, Indels: 15
0.77 0.08 0.14
Matches are distributed among these distances:
19 6 0.07
20 59 0.72
21 11 0.13
22 6 0.07
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (19 bp):
AAATCGAGTTGCGAATTGG
Found at i:57312 original size:20 final size:20
Alignment explanation
Indices: 57213--57313 Score: 123
Period size: 20 Copynumber: 5.0 Consensus size: 20
57203 TACTAATTCA
*
57213 GAAATCGAGTTGCGAATTT-
1 GAAATCGCGTTGCGAATTTG
*
57232 GAAATTCAGTGTTGCGAATTTG
1 GAAA-TC-GCGTTGCGAATTTG
* *
57254 TAAATCACGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
*
57274 GAAATCGCATTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
*
57294 GAAATCGTGTTGCGAATTTG
1 GAAATCGCGTTGCGAATTTG
57314 ACTTCTGTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
19 4 0.06
20 49 0.70
21 14 0.20
22 3 0.04
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.34
Consensus pattern (20 bp):
GAAATCGCGTTGCGAATTTG
Found at i:57327 original size:40 final size:39
Alignment explanation
Indices: 57213--57413 Score: 133
Period size: 40 Copynumber: 5.0 Consensus size: 39
57203 TACTAATTCA
57213 GAAATCGAGTTGCGAATTTGAAATTCAGTGTTGCGAATTTG
1 GAAATCGAGTTGCGAATTTG-AATTC-GTGTTGCGAATTTG
* * **
57254 TAAATC-ACGTTGCGAATTTGGAAATCGCATTGCGAATTTG
1 GAAATCGA-GTTGCGAATTT-GAATTCGTGTTGCGAATTTG
* * *
57294 GAAATCGTGTTGCGAATTTGACTTCTGTGTTGCG-ATTTA
1 GAAATCGAGTTGCGAATTTGAATTC-GTGTTGCGAATTTG
* * * * *
57333 CAGATTCGCGTTGCG-ATTTACAAATT-GATGTTGCGAATTTA
1 GA-AATCGAGTTGCGAATTT--GAATTCG-TGTTGCGAATTTG
* * *
57374 GAAA-CTGAGTTGCGAAATTAGAGTTCGCGTTGCGAATTTG
1 GAAATC-GAGTTGCG-AATTTGAATTCGTGTTGCGAATTTG
57414 TTGGTCATTT
Statistics
Matches: 123, Mismatches: 24, Indels: 27
0.71 0.14 0.16
Matches are distributed among these distances:
39 15 0.12
40 74 0.60
41 30 0.24
42 4 0.03
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (39 bp):
GAAATCGAGTTGCGAATTTGAATTCGTGTTGCGAATTTG
Found at i:57328 original size:60 final size:61
Alignment explanation
Indices: 57161--57313 Score: 163
Period size: 61 Copynumber: 2.5 Consensus size: 61
57151 AATAAAACCT
* * * * * * * **
57161 GTTGCGAAATTAAAATTC-GTGTTGTGAATTCGAAAATCGA-GTTACTAATTCAGAAATCGA
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATC-ACGTTGCGAATTTGGAAATCGA
57221 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATCACGTTGCGAATTTGGAAATCGCA
1 GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATCACGTTGCGAATTTGGAAATCG-A
57283 -TTGCGAATTTGGAAA-TC-GTGTTGCGAATTTG
1 GTTGCGAATTT-GAAATTCAGTGTTGCGAATTTG
57314 ACTTCTGTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
60 31 0.39
61 44 0.55
62 5 0.06
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (61 bp):
GTTGCGAATTTGAAATTCAGTGTTGCGAATTTGTAAATCACGTTGCGAATTTGGAAATCGA
Found at i:57347 original size:60 final size:61
Alignment explanation
Indices: 57278--57413 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 61
57268 AATTTGGAAA
* * ** * *
57278 TCGCATTGCGAATTTGGAAATCG-TGTTGCGAATTT-GACTTCTGTGTTGCG-ATTTACAGAT
1 TCGCGTTGCGAATTTGCAAATCGATGTTGCGAATTTAGA-AACTGAGTTGCGAAATTACAG-T
* * *
57338 TCGCGTTGCG-ATTTACAAATTGATGTTGCGAATTTAGAAACTGAGTTGCGAAATTAGAGT
1 TCGCGTTGCGAATTTGCAAATCGATGTTGCGAATTTAGAAACTGAGTTGCGAAATTACAGT
57398 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
57414 TTGGTCATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
59 9 0.15
60 41 0.66
61 12 0.19
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (61 bp):
TCGCGTTGCGAATTTGCAAATCGATGTTGCGAATTTAGAAACTGAGTTGCGAAATTACAGT
Found at i:57365 original size:20 final size:20
Alignment explanation
Indices: 57321--57388 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
57311 TTGACTTCTG
*
57321 TGTTGCGATTTACAGATTCG-
1 TGTTGCGATTTACAAATT-GA
*
57341 CGTTGCGATTTACAAATTGA
1 TGTTGCGATTTACAAATTGA
* *
57361 TGTTGCGAATTTAGAAACTGA
1 TGTTGCG-ATTTACAAATTGA
57382 -GTTGCGA
1 TGTTGCGA
57389 AATTAGAGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.05
20 28 0.68
21 11 0.27
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (20 bp):
TGTTGCGATTTACAAATTGA
Found at i:57389 original size:20 final size:21
Alignment explanation
Indices: 57342--57395 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
57332 ACAGATTCGC
* *
57342 GTTGCG-ATTTACAAATTGAT
1 GTTGCGAATTTAGAAACTGAT
57362 GTTGCGAATTTAGAAACTGA-
1 GTTGCGAATTTAGAAACTGAT
*
57382 GTTGCGAAATTAGA
1 GTTGCGAATTTAGA
57396 GTTCGCGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (21 bp):
GTTGCGAATTTAGAAACTGAT
Found at i:64703 original size:2 final size:2
Alignment explanation
Indices: 64696--64724 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64686 CCAGTTCATC
64696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64725 GATAAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.