Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003413.1 Hibiscus syriacus cultivar Beakdansim tig00007190_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: 66413
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:6734 original size:33 final size:33
Alignment explanation
Indices: 6672--6734 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
6662 TTTTTCAAAA
*
6672 AAATGATTTAAAAACATTATATTAGTTTTTTTT
1 AAATGATTTAAAAACATTATATTAATTTTTTTT
*
6705 AAATGATTT-TAAACATTATATTATATTTTT
1 AAATGATTTAAAAACATTATATTA-ATTTTT
6735 CAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (33 bp):
AAATGATTTAAAAACATTATATTAATTTTTTTT
Found at i:6850 original size:34 final size:35
Alignment explanation
Indices: 6646--6873 Score: 129
Period size: 34 Copynumber: 6.5 Consensus size: 35
6636 CAAGTTTTCC
6646 AAACTATATA-T-TATAGTTTTTCAAAAAAATGATTTAA
1 AAACTATATATTATATAG-TTTTC---AAAATGATTTAA
** *
6683 AAAC-AT-TA-TAT-TAGTTTTTTTTAAATGATTT-T
1 AAACTATATATTATATAG--TTTTCAAAATGATTTAA
**
6715 AAAC-ATTATATTATAT--TTTTCAAAAAAAAATTT-A
1 AAACTA-TATATTATATAGTTTTC--AAAATGATTTAA
* * *
6749 AAACTATATTTTATATACGTTTTTTCAAAAGGTTTTAAA
1 AAACTATATATTATATA-G--TTTTCAAAATGATTT-AA
* * *
6788 GAAATTATATATTATATATTTTTCAAAATGATTTCA
1 -AAACTATATATTATATAGTTTTCAAAATGATTTAA
*
6824 AAACTATATATTATA-AGTTTTCAAAATGTTTTAA
1 AAACTATATATTATATAGTTTTCAAAATGATTTAA
*
6858 AAACCATATATTATAT
1 AAACTATATATTATAT
6874 TTTTAAAATT
Statistics
Matches: 150, Mismatches: 23, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
32 9 0.06
33 10 0.07
34 52 0.35
35 24 0.16
36 10 0.07
37 24 0.16
39 6 0.04
40 15 0.10
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
AAACTATATATTATATAGTTTTCAAAATGATTTAA
Found at i:6890 original size:14 final size:14
Alignment explanation
Indices: 6867--6901 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
6857 AAAACCATAT
6867 ATTATATTTTTAAA
1 ATTATATTTTTAAA
*
6881 ATTATTTTTTTAAA
1 ATTATATTTTTAAA
6895 ATTATAT
1 ATTATAT
6902 ACTATATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATATTTTTAAA
Found at i:11245 original size:3 final size:3
Alignment explanation
Indices: 11229--11325 Score: 97
Period size: 3 Copynumber: 31.7 Consensus size: 3
11219 TTTGGGCTTG
* * * *
11229 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAG TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * *
11276 TTA TAA TTA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
11321 TAA TA
1 TAA TA
11326 TTTAAATGAA
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
2 2 0.03
3 68 0.88
4 7 0.09
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:11617 original size:36 final size:40
Alignment explanation
Indices: 11580--11660 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 40
11570 TCATTGTGAA
* *
11580 CTTCTTCTTTTTCAGAT-TAGTTCTTCTCATTATGAACTT
1 CTTCTTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTT
11619 CTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT
1 CTTCTT-CTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACT
11661 CTACCTGGCA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
39 6 0.17
40 10 0.28
43 20 0.56
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (40 bp):
CTTCTTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTT
Found at i:11953 original size:113 final size:113
Alignment explanation
Indices: 11600--12617 Score: 1181
Period size: 113 Copynumber: 8.9 Consensus size: 113
11590 TTCAGATTAG
11600 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* * * *
11665 CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
63 CTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
11716 TTCTTCTCATTATGAACTTCTTCTTCCTTCTT-AGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* * * *
11780 CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAG
63 CTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
*
11831 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* *
11896 GCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
66 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
* * *
11944 TTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
* * * * * * * *
12008 AGAAAAGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAGCAAA
65 GGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
* * *
12057 TTCTTCTCATTATGAATTTCTTTTTCTTTCTTCAGATGGCGAGTTCTTCTCATTATGAACTCT--
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* * * * *
12120 CTGGAAAAGCTGATGATCCATCAAATGATGAATTCAAGCCAAAGGGTTAAACAAA
63 CTGG-AAA--TGTTGATCCATCAAATGATGAATTTAA-ACAAAAGGTTGAACAAA
* * *
12175 TTCTTCTTATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
* * * * * * *
12239 GGAAAGGCTGATCCATCAAATGATGGATTTGAGCAAAAGATTGAGCAAA
65 GGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
*
12288 TTCTTCTCATTATGAATTTCTT-TTCCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT-
1 TTCTTCTCATTATGAACTTCTTCTTCC-TTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTA
* * * * *
12351 CTCTGGAAAAGCTGATGATCCATCAAATGATGAATTCAAGCCAAAGGGTTAAACAAA
62 C-CTGG-AAA--TGTTGATCCATCAAATGATGAATTTAA-ACAAAAGGTTGAACAAA
* * *
12408 TTCTTCTTATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CT
* * * * * *
12472 GGCAAA-GCTAATCCATCAAATGATGGATTTGAGCGAAAGGTTGAACAAA
65 GG-AAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
* * *
12521 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* ** *
12586 GAAAAGTTGATCCATTGAATGATGGATTTAAA
66 GAAATGTTGATCCATCAAATGATGAATTTAAA
12618 TCTTTGCCAA
Statistics
Matches: 788, Mismatches: 88, Indels: 55
0.85 0.09 0.06
Matches are distributed among these distances:
112 9 0.01
113 335 0.43
114 46 0.06
115 138 0.18
116 88 0.11
117 61 0.08
118 44 0.06
119 22 0.03
120 41 0.05
121 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
Found at i:12467 original size:233 final size:227
Alignment explanation
Indices: 11600--12609 Score: 1358
Period size: 231 Copynumber: 4.4 Consensus size: 227
11590 TTCAGATTAG
*
11600 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG-CGAGTTCTTCTCATTATGAACTCTAC
* * * * *
11665 CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
65 CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATG
* * * *
11730 AACTTCTTCTTCCTTCTT-AGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGA
130 AACTTATTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TTCTCTGG-AAAGCTGA
* ** * *
11793 TCCATCAAATGATGAATTCAAACAAAA-AGTTGAACAAG
190 TCCATCAAATGATGGATTTGAGCAAAAGA-TTGAACAAA
* *
11831 TTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGAT--GAGTTCTTCTCATTATGAACTCTACC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGCGAGTTCTTCTCATTATGAACTCTACC
* * * * *
11894 TGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
66 TGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGA
* *
11959 ACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTAGAAAAGCTGATCCAT
131 ACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT-GGAAAGCTGATCCAT
*
12024 CAAATGATGGATTTGAGCAAAAGATTGAGCAAA
195 CAAATGATGGATTTGAGCAAAAGATTGAACAAA
* *
12057 TTCTTCTCATTATGAATTTCTTTTTCTTTCTTCAGATGGCGAGTTCTTCTCATTATGAACTCT--
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT-GCGAGTTCTTCTCATTATGAACTCTAC
* * *
12120 CTGGAAAAGCTGATGATCCATCAAATGATGAATTCAAGCCAAAGGGTTAAACAAATTCTTCTTAT
65 CTGG-AAA--TGATGATCCATCAAATGATGAATTCAA-ACAAAAGGTTAAACAAATTCTTCTCAT
12185 TATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGCTGA
126 TATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA-GCTGA
*
12250 TCCATCAAATGATGGATTTGAGCAAAAGATTGAGCAAA
190 TCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAA
12288 TTCTTCTCATTATGAATTTCTT-TTCCTTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT-
1 TTCTTCTCATTATGAATTTCTTCTTCC-TTCTTCAGATG-CGAGTTCTTCTCATTATGAACTCTA
* * *
12351 CTCTGGAAAAGCTGATGATCCATCAAATGATGAATTCAAGCCAAAGGGTTAAACAAATTCTTCTT
64 C-CTGG-AAA--TGATGATCCATCAAATGATGAATTCAA-ACAAAAGGTTAAACAAATTCTTCTC
12416 ATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGCAAAGCT
124 ATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGCT
* * *
12481 AATCCATCAAATGATGGATTTGAGCGAAAGGTTGAACAAA
188 GATCCATCAAATGATGGATTTGAGCAAAAGATTGAACAAA
* *
12521 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGAT--GAGTTCTTCTCATTATGAACTCGAAC
1 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGCGAGTTCTTCTCATTATGAACTCTACC
* * **
12584 TGGAAAAGTTGATCCATTGAATGATG
66 TGGAAATGATGATCCATCAAATGATG
12610 GATTTAAATC
Statistics
Matches: 719, Mismatches: 41, Indels: 42
0.90 0.05 0.05
Matches are distributed among these distances:
225 2 0.00
226 92 0.13
227 22 0.03
228 105 0.15
229 30 0.04
230 58 0.08
231 211 0.29
233 192 0.27
234 7 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (227 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGCGAGTTCTTCTCATTATGAACTCTACC
TGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAGGTTAAACAAATTCTTCTCATTATGA
ACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGCTGATCCATC
AAATGATGGATTTGAGCAAAAGATTGAACAAA
Found at i:13588 original size:83 final size:83
Alignment explanation
Indices: 13449--13921 Score: 829
Period size: 83 Copynumber: 5.7 Consensus size: 83
13439 GGGGTTCATA
* *
13449 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
13514 TTTCAATAATTGGTTCTG
66 TTTCAATAATTGGTTCTG
*
13532 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGAGCACATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
* *
13597 ATTCAATAACTGGTTCTG
66 TTTCAATAATTGGTTCTG
13615 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
* * * *
13680 ATTCAATAACTGGTTTTA
66 TTTCAATAATTGGTTCTG
13698 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
*
13763 TTTCAATGATTGGTTCTG
66 TTTCAATAATTGGTTCTG
*
13781 CCACACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
*
13846 TTTCAATGATTGGTTCTG
66 TTTCAATAATTGGTTCTG
*
13864 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGGTGCTATGAGCACATTCAT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCAT
13922 TTGTTCCAGT
Statistics
Matches: 374, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 374 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAA
TTTCAATAATTGGTTCTG
Found at i:14740 original size:16 final size:16
Alignment explanation
Indices: 14704--14741 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
14694 TGAATTTTCG
14704 AAAATAAATTGAATCT
1 AAAATAAATTGAATCT
*
14720 CAAATAAATTGAA-CTT
1 AAAATAAATTGAATC-T
14736 AAAATA
1 AAAATA
14742 GATAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 1 0.05
16 18 0.95
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (16 bp):
AAAATAAATTGAATCT
Found at i:15080 original size:8 final size:8
Alignment explanation
Indices: 15064--15124 Score: 68
Period size: 8 Copynumber: 7.2 Consensus size: 8
15054 GACCCCCCCA
*
15064 TTTTCTTC
1 TTTTTTTC
15072 TTTTTTTC
1 TTTTTTTC
15080 TTTTTTTC
1 TTTTTTTC
15088 TTTTTTTTC
1 -TTTTTTTC
*
15097 TTTTTCTC
1 TTTTTTTC
*
15105 TTTTCTCTTT
1 TTTT-T-TTC
15115 TTTTTTTC
1 TTTTTTTC
15123 TT
1 TT
15125 CAAGCATAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
8 30 0.67
9 10 0.22
10 5 0.11
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:15085 original size:7 final size:7
Alignment explanation
Indices: 15073--15124 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
15063 ATTTTCTTCT
15073 TTTTTTC
1 TTTTTTC
15080 TTTTTTTC
1 -TTTTTTC
*
15088 TTTTTTT
1 TTTTTTC
15095 TCTTTTTC
1 T-TTTTTC
*
15103 TCTTTTC
1 TTTTTTC
*
15110 TCTTTT-
1 TTTTTTC
15116 TTTTTTC
1 TTTTTTC
15123 TT
1 TT
15125 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 5 0.13
7 20 0.53
8 13 0.34
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:15092 original size:17 final size:17
Alignment explanation
Indices: 15072--15124 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
15062 CATTTTCTTC
15072 TTTTTTTCTTTTTTTCT
1 TTTTTTTCTTTTTTTCT
*
15089 TTTTTTTCTTTTTCTCT
1 TTTTTTTCTTTTTTTCT
15106 TTTCTCTTT-TTTTTTTCT
1 TTT-T-TTTCTTTTTTTCT
15124 T
1 T
15125 CAAGCATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
17 19 0.59
18 10 0.31
19 3 0.09
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTCT
Found at i:15120 original size:25 final size:25
Alignment explanation
Indices: 15064--15119 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
15054 GACCCCCCCA
* * *
15064 TTTTCTTCTTTTTTTCTTTTTTTCT
1 TTTTTTTCTTTTTCTCTTTTTCTCT
15089 TTTTTTTCTTTTTCTC-TTTTCTCT
1 TTTTTTTCTTTTTCTCTTTTTCTCT
15113 TTTTTTT
1 TTTTTTT
15120 TTCTTCAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTTTCTTTTTCTCTTTTTCTCT
Found at i:27888 original size:3 final size:3
Alignment explanation
Indices: 27872--27962 Score: 103
Period size: 3 Copynumber: 29.7 Consensus size: 3
27862 TTTGGGCTTG
* * * *
27872 TAA TAA TATT TAA TAA TAA TAT TAA TAA TAAA TAA TAA TAT TAG TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
27919 TTA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
27963 TTTAAATGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
2 2 0.03
3 66 0.88
4 7 0.09
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:38374 original size:44 final size:46
Alignment explanation
Indices: 38254--38379 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 46
38244 TATAAAATCT
*
38254 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
38299 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** * *
38346 CTTGTCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
38380 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 22 0.32
45 10 0.14
46 2 0.03
47 35 0.51
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:41984 original size:37 final size:36
Alignment explanation
Indices: 41943--42016 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
41933 GGATAAAGAT
*
41943 AAAAAGAAAATAG-ATAAATAAATGAGTAAAATATATA
1 AAAAAGAAAA-AGCATAAATAAATAAGTAAAATA-ATA
* * *
41980 AAAAAGTAAAAGCATATATATATAAGTAAAATAATA
1 AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
42016 A
1 A
42017 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.23
Consensus pattern (36 bp):
AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
Found at i:41998 original size:20 final size:20
Alignment explanation
Indices: 41973--42010 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41963 AATGAGTAAA
41973 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
41993 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
42011 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:42081 original size:2 final size:2
Alignment explanation
Indices: 42074--42104 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42064 AAAATAGGAA
42074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42105 ATAACACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46913 original size:15 final size:15
Alignment explanation
Indices: 46895--46995 Score: 54
Period size: 14 Copynumber: 6.9 Consensus size: 15
46885 CATCTCTCAT
46895 TTTTTTCTCTTTTTC
1 TTTTTTCTCTTTTTC
*
46910 TTTTCTTTCTCGTTTTC
1 -TTT-TTTCTCTTTTTC
*
46927 ATTTTTT-TCTTCTTC
1 -TTTTTTCTCTTTTTC
*
46942 --GTTT-TCTTTTTC
1 TTTTTTCTCTTTTTC
*
46954 -TTTTTCTATTTTT-
1 TTTTTTCTCTTTTTC
* *
46967 TTTCTTCTATTTTT-
1 TTTTTTCTCTTTTTC
*
46981 TTTTCTTCTATTTTT
1 TTTT-TTCTCTTTTT
46996 TTCTTCTTCT
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
12 10 0.14
13 3 0.04
14 21 0.30
15 16 0.23
16 6 0.09
17 14 0.20
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTTCTCTTTTTC
Found at i:46918 original size:9 final size:8
Alignment explanation
Indices: 46894--46987 Score: 50
Period size: 8 Copynumber: 11.2 Consensus size: 8
46884 TCATCTCTCA
46894 TTTTTTTC
1 TTTTTTTC
*
46902 TCTTTTTC
1 TTTTTTTC
46910 TTTTCTTTC
1 TTTT-TTTC
**
46919 TCGTTTTC
1 TTTTTTTC
46927 ATTTTTTTC
1 -TTTTTTTC
46936 TTCTTCGTTT-
1 TT-TT--TTTC
*
46946 TCTTTTTC
1 TTTTTTTC
46954 TTTTTCTAT-
1 TTTTT-T-TC
46963 TTTTTTTC
1 TTTTTTTC
* *
46971 TTCTATT-
1 TTTTTTTC
46978 TTTTTTTC
1 TTTTTTTC
46986 TT
1 TT
46988 CTATTTTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
7 9 0.14
8 28 0.44
9 22 0.34
10 2 0.03
11 3 0.05
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (8 bp):
TTTTTTTC
Found at i:46960 original size:21 final size:22
Alignment explanation
Indices: 46902--46960 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
46892 CATTTTTTTC
*
46902 TCTTTTTCTTTTCTTTCTCGTTT
1 TCTTTTTCTTTT-TCTCTCGTTT
*
46925 TCATTTTT-TTCTTCT-TCGTTT
1 TC-TTTTTCTTTTTCTCTCGTTT
46946 TCTTTTTCTTTTTCT
1 TCTTTTTCTTTTTCT
46961 ATTTTTTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 5 0.16
21 14 0.45
22 2 0.06
23 5 0.16
24 5 0.16
ACGTcount: A:0.02, C:0.20, G:0.03, T:0.75
Consensus pattern (22 bp):
TCTTTTTCTTTTTCTCTCGTTT
Found at i:46969 original size:12 final size:11
Alignment explanation
Indices: 46928--47000 Score: 56
Period size: 13 Copynumber: 5.9 Consensus size: 11
46918 CTCGTTTTCA
46928 TTTTTTTCTTCT
1 TTTTTTTCTT-T
**
46940 TCGTTTTCTTT
1 TTTTTTTCTTT
46951 TTCTTTTTCTATTT
1 TT-TTTTTC--TTT
46965 TTTTTCTTCTATT
1 TTTTT-TTCT-TT
46978 TTTTTTTCTTCT
1 TTTTTTTCTT-T
46990 ATTTTTTTCTT
1 -TTTTTTTCTT
47001 CTTCTTATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
11 3 0.06
12 19 0.38
13 20 0.40
14 8 0.16
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:46994 original size:28 final size:28
Alignment explanation
Indices: 46948--47002 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
46938 CTTCGTTTTC
46948 TTTTTCTTTTTCTATTTTTTTTCTTCTA
1 TTTTTCTTTTTCTATTTTTTTTCTTCTA
*
46976 TTTTTTTTTCTTCTA-TTTTTTTCTTCT
1 TTTTTCTTT-TTCTATTTTTTTTCTTCT
47003 TCTTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTTCTTTTTCTATTTTTTTTCTTCTA
Found at i:46996 original size:14 final size:14
Alignment explanation
Indices: 46948--47002 Score: 78
Period size: 13 Copynumber: 3.9 Consensus size: 14
46938 CTTCGTTTTC
46948 TTTTTCTTT-TTCTA
1 TTTTT-TTTCTTCTA
46962 TTTTTTTTCTTCTA
1 TTTTTTTTCTTCTA
46976 TTTTTTTTTCTTCTA
1 -TTTTTTTTCTTCTA
46991 -TTTTTTTCTTCT
1 TTTTTTTTCTTCT
47003 TCTTATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
13 15 0.38
14 10 0.26
15 14 0.36
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTTCTTCTA
Found at i:46996 original size:15 final size:16
Alignment explanation
Indices: 46876--47005 Score: 103
Period size: 15 Copynumber: 8.1 Consensus size: 16
46866 AAGTGAAATA
*
46876 TATTTTTTTCATC-TC
1 TATTTTTTTCTTCTTC
*
46891 TCATTTTTTTCTCTTTTTC
1 T-A-TTTTTT-TCTTCTTC
46910 T-TTTCTTTCTCGTT-TTC
1 TATTT-TTT-TC-TTCTTC
46927 -ATTTTTTTCTTCTTC
1 TATTTTTTTCTTCTTC
* *
46942 GTTTTCTTTTTCTTTTTC
1 -TATT-TTTTTCTTCTTC
46960 TA-TTTTTT-TTCTTC
1 TATTTTTTTCTTCTTC
46974 TATTTTTTT-TTCTTC
1 TATTTTTTTCTTCTTC
46989 TATTTTTTTCTTCTTC
1 TATTTTTTTCTTCTTC
47005 T
1 T
47006 TATAATATAT
Statistics
Matches: 96, Mismatches: 6, Indels: 25
0.76 0.05 0.20
Matches are distributed among these distances:
14 9 0.09
15 32 0.33
16 15 0.16
17 21 0.22
18 16 0.17
19 3 0.03
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (16 bp):
TATTTTTTTCTTCTTC
Found at i:49927 original size:44 final size:46
Alignment explanation
Indices: 49807--49932 Score: 141
Period size: 47 Copynumber: 2.8 Consensus size: 46
49797 TATAAAATCT
*
49807 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
49852 CTTACCATTTAAATTCCATAAGCTTGTAAGCTTATTTTTCCTATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** * *
49899 CTTGTCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
49933 GCATGGTTAC
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
44 22 0.32
45 10 0.14
46 2 0.03
47 35 0.51
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:53614 original size:2 final size:2
Alignment explanation
Indices: 53607--53631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53597 TAAATAGGAA
53607 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 A
53632 ATAACACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54079 original size:37 final size:36
Alignment explanation
Indices: 54038--54141 Score: 127
Period size: 36 Copynumber: 2.8 Consensus size: 36
54028 GTGCTTGTGG
* * *
54038 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGTAGAACTCT
** * *
54075 ATCCTATTTTAGGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGTAGAACTCT
54111 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAG
54142 GACGAAAAGG
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 28 0.50
37 28 0.50
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGTAGAACTCT
Found at i:55026 original size:106 final size:106
Alignment explanation
Indices: 54841--55891 Score: 1554
Period size: 106 Copynumber: 10.0 Consensus size: 106
54831 CATTGTTCCA
* * * *
54841 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACTGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
* * * * ** *
54905 CTAGCCGTCCCTTCATTGTGAAGTTGAACTTGTATTGTCTCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
54947 AGTTCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
55012 CAGCGGTCCATTCATCGTGAAGTTGAAGTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
55053 AGTCCAATATCCTTTGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
55118 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55159 AGTCCAATATCCTTCGCTGTGAAGTTAAAATT-G---TG-AA----G---TTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
55212 CAGCGGTCCCTTCATCATGAAGTTGAACTTGCGTTGTCTAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55253 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTAATT-ACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT-ATTGACAA
*
55317 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
55359 AGTCCAATATCCTTCGCTGTGGAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
55424 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
55465 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAATTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
55530 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * *
55571 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGGTCTAAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
55636 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
55677 AATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
* * *
55742 CAGCGGGCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
55783 AGTCCAATATCATTTGCTGTGAAGTTGAAATTAGCTCTAAAATTGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
*
55848 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
55889 AGT
1 AGT
55892 GGCACGATAT
Statistics
Matches: 860, Mismatches: 70, Indels: 30
0.90 0.07 0.03
Matches are distributed among these distances:
94 84 0.10
95 1 0.00
97 1 0.00
98 2 0.00
99 2 0.00
101 2 0.00
102 2 0.00
103 1 0.00
105 4 0.00
106 757 0.88
107 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:56511 original size:24 final size:24
Alignment explanation
Indices: 56445--56526 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 24
56435 TTTTATTTTC
* *
56445 AAAGTTCTGAAA-AT-ATCAAT-A
1 AAAGTTTTGAAAGATAATTAATCA
*
56466 AAGAGTTTCGAAAGATAATTAATCA
1 AA-AGTTTTGAAAGATAATTAATCA
** ** *
56491 AGTGTTTTGAAAGATGTTTAATTA
1 AAAGTTTTGAAAGATAATTAATCA
56515 AAAGTTTTGAAA
1 AAAGTTTTGAAA
56527 ATATTGTCCC
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
21 2 0.04
22 8 0.17
23 2 0.04
24 32 0.70
25 2 0.04
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (24 bp):
AAAGTTTTGAAAGATAATTAATCA
Found at i:56744 original size:22 final size:22
Alignment explanation
Indices: 56718--56794 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
56708 TTATGTTTGG
56718 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
56740 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
56762 TCATAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
56784 TCAATGGTTTG
1 TCAAAGGTTTG
56795 ATGGGGTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:57441 original size:18 final size:18
Alignment explanation
Indices: 57414--57452 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
57404 TTCTTTTTGA
57414 TTTTTGTTC-TTTCTTTT
1 TTTTTGTTCTTTTCTTTT
57431 TTTTTGCTTCTTTTCTTTT
1 TTTTTG-TTCTTTTCTTTT
57450 TTT
1 TTT
57453 GTTTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 11 0.55
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTTTGTTCTTTTCTTTT
Found at i:57453 original size:17 final size:17
Alignment explanation
Indices: 57414--57455 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
57404 TTCTTTTTGA
*
57414 TTTTTGTTCTTTCTTTT
1 TTTTTGTTCTTTCTCTT
57431 TTTTTGCTTCTTT-TCTT
1 TTTTTG-TTCTTTCTCTT
57448 TTTTTGTT
1 TTTTTGTT
57456 TTTTTTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 2 0.09
17 15 0.65
18 6 0.26
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (17 bp):
TTTTTGTTCTTTCTCTT
Found at i:62122 original size:37 final size:36
Alignment explanation
Indices: 62081--62154 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
62071 GGATAAAGAT
*
62081 AAAAAGAAAATAG-ATAAATAAATGAGTAAAATATATA
1 AAAAAGAAAA-AGCATAAATAAATAAGTAAAATA-ATA
* * *
62118 AAAAAGTAAAAGCATATATATATAAGTAAAATAATA
1 AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
62154 A
1 A
62155 TAATAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 6 0.19
37 26 0.81
ACGTcount: A:0.66, C:0.01, G:0.09, T:0.23
Consensus pattern (36 bp):
AAAAAGAAAAAGCATAAATAAATAAGTAAAATAATA
Found at i:62136 original size:20 final size:20
Alignment explanation
Indices: 62111--62148 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62101 AATGAGTAAA
62111 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
62131 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
62149 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:62663 original size:37 final size:36
Alignment explanation
Indices: 62622--62718 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 36
62612 GTGCTTGTGG
* * ** *
62622 ATCCTATCTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTAT-TTTAGGAGTTTGAATCATAACAAAACTCT
* *
62659 ATCCTATTTTAGGAGTTTGAATCCTAACAAAATTCT
1 ATCCTATTTTAGGAGTTTGAATCATAACAAAACTCT
62695 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTA-TTTTAGGAGTTTGAATC
62719 CTACTAGGAC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
36 28 0.54
37 24 0.46
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCATAACAAAACTCT
Found at i:62932 original size:9 final size:8
Alignment explanation
Indices: 62914--63624 Score: 131
Period size: 8 Copynumber: 96.8 Consensus size: 8
62904 ATGATTCAAC
62914 ATACTTAT
1 ATACTTAT
62922 ATACTT-T
1 ATACTTAT
62929 ATA-TTAT
1 ATACTTAT
*
62936 ATAGTT-T
1 ATACTTAT
*
62943 AAAACTT-T
1 -ATACTTAT
*
62951 AT-TTTAT
1 ATACTTAT
62958 ATACTT-T
1 ATACTTAT
*
62965 AATA-TTTT
1 -ATACTTAT
62973 AATACTTAT
1 -ATACTTAT
*
62982 ATAATGTAT
1 ATACT-TAT
62991 AT--TTA-
1 ATACTTAT
62996 ATACTTAT
1 ATACTTAT
63004 AT--TTAT
1 ATACTTAT
63010 ATACTT-T
1 ATACTTAT
63017 AATACTT-T
1 -ATACTTAT
*
63025 ATATTTAT
1 ATACTTAT
63033 ATACTT-T
1 ATACTTAT
63040 AATACTTAT
1 -ATACTTAT
* *
63049 AT-C-CAA
1 ATACTTAT
*
63055 ACACTT-T
1 ATACTTAT
*
63062 ATTAATT-T
1 A-TACTTAT
63070 ATA-TTAT
1 ATACTTAT
63077 ATACTT-T
1 ATACTTAT
63084 ATA-TTAT
1 ATACTTAT
63091 ATACTT-T
1 ATACTTAT
*
63098 ATAGTT-T
1 ATACTTAT
63105 ATA-TATAT
1 ATACT-TAT
63113 ATAC-T-T
1 ATACTTAT
63119 ATACTT-T
1 ATACTTAT
*
63126 ATAGTTTTAT
1 ATA--CTTAT
*
63136 ATATGTATAT
1 ATA-CT-TAT
63146 ATACTT-T
1 ATACTTAT
63153 ATAC-TA-
1 ATACTTAT
*
63159 AAACTT-T
1 ATACTTAT
*
63166 ATAGTT-T
1 ATACTTAT
63173 ATA--TAT
1 ATACTTAT
63179 ATACTTAT
1 ATACTTAT
63187 ATACTTTAT
1 ATAC-TTAT
63196 ATTA-TTAT
1 A-TACTTAT
63204 ATA-TGTAT
1 ATACT-TAT
* *
63212 ATATATTTT
1 ATA-CTTAT
*
63221 ATAC-CA-
1 ATACTTAT
*
63227 AAACTT-T
1 ATACTTAT
63234 ATA--TAT
1 ATACTTAT
63240 ATACTT-T
1 ATACTTAT
63247 AATACTTAT
1 -ATACTTAT
63256 AT--TTAT
1 ATACTTAT
63262 ATACTT-T
1 ATACTTAT
63269 AATACTTAT
1 -ATACTTAT
* *
63278 AT-C-CAA
1 ATACTTAT
*
63284 ACACTT-T
1 ATACTTAT
63291 ATTACTT-T
1 A-TACTTAT
*
63299 TTA--TAT
1 ATACTTAT
63305 ATACTT-T
1 ATACTTAT
63312 AATACTTAT
1 -ATACTTAT
*
63321 GT--TTA-
1 ATACTTAT
63326 ATACTT-T
1 ATACTTAT
*
63333 ATATTTA-
1 ATACTTAT
63340 ATACTTAT
1 ATACTTAT
63348 AT--TTAT
1 ATACTTAT
63354 ATACTT-T
1 ATACTTAT
63361 AATACTTAT
1 -ATACTTAT
* *
63370 AT-C-CAA
1 ATACTTAT
*
63376 ACACTT-T
1 ATACTTAT
63383 ATTACTT-T
1 A-TACTTAT
*
63391 TTA-TTAT
1 ATACTTAT
63398 ATACTT-T
1 ATACTTAT
63405 AATACTT-T
1 -ATACTTAT
63413 ATA-TTAT
1 ATACTTAT
63420 ATACTT-T
1 ATACTTAT
*
63427 ATAGTT-T
1 ATACTTAT
63434 ATA-TATAT
1 ATACT-TAT
63442 ATA-TATAT
1 ATACT-TAT
63450 ATAC-T-T
1 ATACTTAT
63456 ATACTT-T
1 ATACTTAT
*
63463 ATAGTTTAT
1 ATA-CTTAT
63472 ATACTTAT
1 ATACTTAT
63480 ATACTT-T
1 ATACTTAT
63487 ATA-TTAT
1 ATACTTAT
63494 ATACTT-T
1 ATACTTAT
*
63501 AATTCTT-T
1 -ATACTTAT
63509 ATA-TTAT
1 ATACTTAT
63516 ATACTTAT
1 ATACTTAT
*
63524 A-ATTTAT
1 ATACTTAT
63531 ATA--TAT
1 ATACTTAT
63537 ATA--TAT
1 ATACTTAT
63543 ATA--TAT
1 ATACTTAT
63549 ATA-TATAT
1 ATACT-TAT
63557 ATA-TATAT
1 ATACT-TAT
63565 ATA-TTAT
1 ATACTTAT
63572 ATA--TAT
1 ATACTTAT
63578 ATA-TATAT
1 ATACT-TAT
63586 ATA-TATAT
1 ATACT-TAT
*
63594 ATACACT-T
1 ATAC-TTAT
63602 ATACTTTAT
1 ATAC-TTAT
63611 ATA-TATAT
1 ATACT-TAT
63619 ATACTT
1 ATACTT
63625 GTAATGTATT
Statistics
Matches: 543, Mismatches: 59, Indels: 202
0.68 0.07 0.25
Matches are distributed among these distances:
5 6 0.01
6 99 0.18
7 163 0.30
8 224 0.41
9 38 0.07
10 13 0.02
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.52
Consensus pattern (8 bp):
ATACTTAT
Found at i:62952 original size:22 final size:23
Alignment explanation
Indices: 62914--63100 Score: 138
Period size: 22 Copynumber: 8.0 Consensus size: 23
62904 ATGATTCAAC
62914 ATAC-TTATATACTTTATA-TTAT
1 ATACTTTA-ATACTTTATATTTAT
* *
62936 ATAGTTTAAAACTTTAT-TTTAT
1 ATACTTTAATACTTTATATTTAT
*
62958 ATACTTTAATATTTTAATACTTATAT
1 ATACTTTAATACTTT-ATA-TT-TAT
*
62984 AATGTATATTTAATAC-TTATATTTAT
1 -A--TA-CTTTAATACTTTATATTTAT
63010 ATACTTTAATACTTTATATTTAT
1 ATACTTTAATACTTTATATTTAT
** *
63033 ATACTTTAATAC-TTATATCCAA
1 ATACTTTAATACTTTATATTTAT
* * *
63055 ACACTTTATTAATTTATA-TTAT
1 ATACTTTAATACTTTATATTTAT
63077 ATACTTT-ATA-TTATATACTTTAT
1 ATACTTTAATACTT-TATA-TTTAT
63100 A
1 A
63101 GTTTATATAT
Statistics
Matches: 131, Mismatches: 19, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
20 2 0.02
21 6 0.05
22 58 0.44
23 39 0.30
25 3 0.02
26 6 0.05
27 3 0.02
28 3 0.02
29 4 0.03
30 7 0.05
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (23 bp):
ATACTTTAATACTTTATATTTAT
Found at i:62979 original size:52 final size:50
Alignment explanation
Indices: 62914--63034 Score: 147
Period size: 52 Copynumber: 2.4 Consensus size: 50
62904 ATGATTCAAC
62914 ATACTTATATACTTTATATTATATAGTTTAAAACTT-TATTTTATATACTTTA
1 ATACTT-TATACTTTATATTATATA-TTTAAAACTTATA-TTTATATACTTTA
* * * *
62966 ATATTTTAATACTTATATAATGTATATTTAATACTTATATTTATATACTTTA
1 ATACTTT-ATACTT-TATATTATATATTTAAAACTTATATTTATATACTTTA
63018 ATACTTTATA-TTTATAT
1 ATACTTTATACTTTATAT
63035 ACTTTAATAC
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
49 4 0.07
50 2 0.03
51 4 0.07
52 39 0.65
53 11 0.18
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.55
Consensus pattern (50 bp):
ATACTTTATACTTTATATTATATATTTAAAACTTATATTTATATACTTTA
Found at i:62996 original size:30 final size:30
Alignment explanation
Indices: 62914--62998 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
62904 ATGATTCAAC
* *
62914 ATACTTATATACTTTATA-TTATATAGTTTA
1 ATACTTATATAATATATATTTA-ATAGTTTA
* ** *
62944 AAACTT-TATTTTATATACTTTAATATTTTA
1 ATACTTATATAATATATA-TTTAATAGTTTA
*
62974 ATACTTATATAATGTATATTTAATA
1 ATACTTATATAATATATATTTAATA
62999 CTTATATTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 8 0.19
30 24 0.56
31 11 0.26
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (30 bp):
ATACTTATATAATATATATTTAATAGTTTA
Found at i:63006 original size:13 final size:14
Alignment explanation
Indices: 62978--63613 Score: 116
Period size: 14 Copynumber: 46.5 Consensus size: 14
62968 ATTTTAATAC
*
62978 TTATATAATGTATAT
1 TTATATACT-TATAT
62993 TTA-ATACTTATAT
1 TTATATACTTATAT
63006 TTATATACTTTAATACT
1 TTATATAC-TT-ATA-T
*
63023 TTATAT-TTATATACT
1 TTATATACT-TATA-T
63038 TTA-ATACTTATAT
1 TTATATACTTATAT
** * *
63051 CCAAACACTT-TA-
1 TTATATACTTATAT
63063 TTA-AT--TTATA-
1 TTATATACTTATAT
63073 TTATATACTT-TAT
1 TTATATACTTATAT
63086 ATTATATACTTTATAGT
1 -TTATATAC-TTATA-T
63103 TTATATA--TATAT
1 TTATATACTTATAT
*
63115 ACT-TATACTTTATAGT
1 -TTATATAC-TTATA-T
*
63131 TT-TATA--TATGT
1 TTATATACTTATAT
*
63142 ATATATACTT-TAT
1 TTATATACTTATAT
* *
63155 ACTA-AAACTTTATAGT
1 -TTATATAC-TTATA-T
*
63171 TTATATA--TATAC
1 TTATATACTTATAT
63183 TTATATACTTTATATT
1 TTATATAC-TTATA-T
*
63199 ATTATATATGTATATAT
1 -TTATATA-CT-TATAT
* ** *
63216 ATTTTATACCAAAACT
1 -TTATATACTTATA-T
63232 TTATATA--TATACT
1 TTATATACTTATA-T
63245 TTA-ATACTTATAT
1 TTATATACTTATAT
*
63258 TTATATACTTTAATAC
1 TTATATAC-TT-ATAT
* ** *
63274 TTATATCCAAACACT
1 TTATATACTTATA-T
63289 TTAT-TAC-T-T-T
1 TTATATACTTATAT
*
63299 TTATATA--TA-CT
1 TTATATACTTATAT
*
63310 TTA-ATACTTATGT
1 TTATATACTTATAT
63323 TTA-ATACTTTATAT
1 TTATATAC-TTATAT
63337 TTA-ATACTTATAT
1 TTATATACTTATAT
*
63350 TTATATACTTTAATAC
1 TTATATAC-TT-ATAT
* ** *
63366 TTATATCCAAACACT
1 TTATATACTTATA-T
63381 TTAT-TAC-T-T-T
1 TTATATACTTATAT
63391 TTAT-TA--TATACT
1 TTATATACTTATA-T
63403 TTA-ATACTT-TAT
1 TTATATACTTATAT
63415 ATTATATACTTTATAGT
1 -TTATATAC-TTATA-T
63432 TTATATA-TATATAT
1 TTATATACT-TATAT
*
63446 ATATATACTTATACT
1 TTATATACTTATA-T
63461 TTATAGT--TTATAT
1 TTATA-TACTTATAT
63474 ACTTATATACTT-TAT
1 --TTATATACTTATAT
63489 ATTATATACTT-TA-
1 -TTATATACTTATAT
63502 --AT-T-CTT-TAT
1 TTATATACTTATAT
63511 ATTATATACTTATAAT
1 -TTATATACTTAT-AT
63527 TTATATA--TATAT
1 TTATATACTTATAT
*
63539 ATATATA-TATATAT
1 TTATATACT-TATAT
*
63553 ATATATA-TATATAT
1 TTATATACT-TATAT
63567 ATTATATA--TATAT
1 -TTATATACTTATAT
*
63580 ATATATA--TATAT
1 TTATATACTTATAT
* *
63592 ATATACACTTATACT
1 TTATATACTTATA-T
63607 TTATATA
1 TTATATA
63614 TATATATACT
Statistics
Matches: 476, Mismatches: 58, Indels: 174
0.67 0.08 0.25
Matches are distributed among these distances:
8 5 0.01
9 4 0.01
10 24 0.05
11 11 0.02
12 61 0.13
13 71 0.15
14 125 0.26
15 94 0.20
16 52 0.11
17 25 0.05
18 4 0.01
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.52
Consensus pattern (14 bp):
TTATATACTTATAT
Found at i:63113 original size:27 final size:26
Alignment explanation
Indices: 63083--63155 Score: 94
Period size: 29 Copynumber: 2.7 Consensus size: 26
63073 TTATATACTT
63083 TATATTATATACTTTATAG-TTTATA
1 TATATTATATACTTTATAGTTTTATA
63108 TATATATACTTATACTTTATAGTTTTATA
1 TATAT-TA--TATACTTTATAGTTTTATA
*
63137 TATGTATATATACTTTATA
1 TATAT-TATATACTTTATA
63156 CTAAAACTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
25 5 0.12
26 2 0.05
27 11 0.26
28 12 0.28
29 13 0.30
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (26 bp):
TATATTATATACTTTATAGTTTTATA
Found at i:63191 original size:68 final size:67
Alignment explanation
Indices: 63074--63236 Score: 231
Period size: 68 Copynumber: 2.4 Consensus size: 67
63064 TAATTTATAT
* *
63074 TATATACTTTATATTATATACTTTATAGTTTATATATATATACTTATACTTTATAGTT-TTATAT
1 TATATACTTTATACTA-AAACTTTATAGTTTATATATATATAC-TATACTTTATA-TTATTATAT
63138 ATGTA
63 ATGTA
63143 TATATACTTTATACTAAAACTTTATAGTTTATATATATACTTA-TATACTTTATATTATTATATA
1 TATATACTTTATACTAAAACTTTATAGTTTATATATATA--TACTATACTTTATATTATTATATA
63207 TGTA
64 TGTA
* *
63211 TATATATTTTATACCAAAACTTTATA
1 TATATACTTTATACTAAAACTTTATA
63237 TATATACTTT
Statistics
Matches: 87, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
67 2 0.02
68 68 0.78
69 15 0.17
70 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (67 bp):
TATATACTTTATACTAAAACTTTATAGTTTATATATATATACTATACTTTATATTATTATATATG
TA
Found at i:63214 original size:27 final size:27
Alignment explanation
Indices: 63152--63223 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
63142 ATATATACTT
*
63152 TATACTA-AAACTTTATAGTTTATATA
1 TATACTATATACTTTATAGTTTATATA
*
63178 TATACTTATATACTTTATATTATTATATA
1 TATAC-TATATACTTTATAGT-TTATATA
* *
63207 TGTA-TATATATTTTATA
1 TATACTATATACTTTATA
63224 CCAAAACTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 5 0.13
27 14 0.36
28 10 0.26
29 10 0.26
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (27 bp):
TATACTATATACTTTATAGTTTATATA
Found at i:63265 original size:22 final size:22
Alignment explanation
Indices: 63229--63481 Score: 180
Period size: 22 Copynumber: 11.4 Consensus size: 22
63219 TTATACCAAA
*
63229 ACTT-TATATATATACTTTAAT
1 ACTTATATTTATATACTTTAAT
63250 ACTTATATTTATATACTTTAAT
1 ACTTATATTTATATACTTTAAT
** * * *
63272 ACTTATATCCAAACACTTTATT
1 ACTTATATTTATATACTTTAAT
63294 ACTT-T-TTATATATACTTTAAT
1 ACTTATATT-TATATACTTTAAT
* *
63315 ACTTATGTTTAATACTTTATATTTAAT
1 ACTTATATTT-ATA---TA-CTTTAAT
63342 ACTTATATTTATATACTTTAAT
1 ACTTATATTTATATACTTTAAT
** * * *
63364 ACTTATATCCAAACACTTTATT
1 ACTTATATTTATATACTTTAAT
*
63386 ACTT-TTTATTATATACTTTAAT
1 ACTTATAT-TTATATACTTTAAT
63408 ACTT-TATATTATATACTTT-AT
1 ACTTATAT-TTATATACTTTAAT
* * *
63429 AGTTTATATATATATA-TATATAT
1 A-CTTATATTTATATACTTTA-AT
* *
63452 ACTTATACTT-TATAGTTTATAT
1 ACTTATATTTATATACTTTA-AT
63474 ACTTATAT
1 ACTTATAT
63482 ACTTTATATT
Statistics
Matches: 183, Mismatches: 34, Indels: 29
0.74 0.14 0.12
Matches are distributed among these distances:
20 1 0.01
21 29 0.16
22 120 0.66
23 13 0.07
26 5 0.03
27 15 0.08
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.53
Consensus pattern (22 bp):
ACTTATATTTATATACTTTAAT
Found at i:63339 original size:27 final size:29
Alignment explanation
Indices: 63304--63489 Score: 111
Period size: 29 Copynumber: 6.1 Consensus size: 29
63294 ACTTTTTATA
*
63304 TATACTTTAATACTTATGTTTA-ATACTT
1 TATACTTTAATACTTATATTTATATACTT
63332 TATA-TTTAATACTTATATTTATATACTT
1 TATACTTTAATACTTATATTTATATACTT
*
63360 TAATACTTATATCCAAACACTTTATTACTTT-T-TA-TT
1 T-ATAC-T-T-T---AATAC-TTA-TA-TTTATATACTT
63396 ATATACTTTAATACTT-TATATTATATACTT
1 -TATACTTTAATACTTATAT-TTATATACTT
* *
63426 TATAGTTTATATA-TATATATATATATAC-T
1 TATACTTTA-ATACT-TATATTTATATACTT
*
63455 TATACTTT-ATAGTTTATATACTTATATACTT
1 TATACTTTAATA-CTTATAT--TTATATACTT
63486 TATA
1 TATA
63490 TTATATACTT
Statistics
Matches: 126, Mismatches: 7, Indels: 47
0.70 0.04 0.26
Matches are distributed among these distances:
26 1 0.01
27 23 0.18
28 17 0.13
29 25 0.20
30 24 0.19
31 9 0.07
32 1 0.01
33 2 0.02
34 1 0.01
35 1 0.01
36 10 0.08
37 6 0.05
38 3 0.02
39 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (29 bp):
TATACTTTAATACTTATATTTATATACTT
Found at i:63347 original size:92 final size:95
Alignment explanation
Indices: 63239--63547 Score: 377
Period size: 92 Copynumber: 3.3 Consensus size: 95
63229 ACTTTATATA
63239 TATACTTTAATACTTATATTTATATACTTTAATACTTATATCCAAACACTTTATTACTTTTTA-T
1 TATACTTTAATACTTATATTTATATACTTTAATACTTATATCCAAACACTTTATTACTTTTTATT
*
63303 ATATACTTTAATAC-TTATGTT-TAATACTT
66 ATATACTTTAATACTTTATATTAT-ATACTT
63332 TATA-TTTAATACTTATATTTATATACTTTAATACTTATATCCAAACACTTTATTACTTTTTATT
1 TATACTTTAATACTTATATTTATATACTTTAATACTTATATCCAAACACTTTATTACTTTTTATT
63396 ATATACTTTAATACTTTATATTATATACTT
66 ATATACTTTAATACTTTATATTATATACTT
* * ** * *
63426 TATAGTTTATATA-TATATATATATATAC-TT-ATACTTTATAGTTTATATAC-TTATATACTTT
1 TATACTTTA-ATACT-TATATTTATATACTTTAATAC-TTATA-TCCAAACACTTTAT-TACTTT
* *
63487 ATATTATATACTTTAATTCTTTATATTATATAC-T
61 TTATTATATACTTTAATACTTTATATTATATACTT
* *
63521 TATAATTTATATA-TATATATATATATA
1 TATACTTTA-ATACT-TATATTTATATA
63548 TATATATATA
Statistics
Matches: 198, Mismatches: 9, Indels: 16
0.89 0.04 0.07
Matches are distributed among these distances:
92 58 0.29
93 19 0.10
94 20 0.10
95 44 0.22
96 57 0.29
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.53
Consensus pattern (95 bp):
TATACTTTAATACTTATATTTATATACTTTAATACTTATATCCAAACACTTTATTACTTTTTATT
ATATACTTTAATACTTTATATTATATACTT
Found at i:63364 original size:36 final size:36
Alignment explanation
Indices: 63322--63499 Score: 116
Period size: 36 Copynumber: 4.6 Consensus size: 36
63312 AATACTTATG
63322 TTTAATACTTTATATTTAATACTTATA-TTTATATAC
1 TTTAATACTTTATA-TTAATACTTATAGTTTATATAC
* * *
63358 TTTAATAC-TTATATCCAAACACTTTATTACTTTTTATTATATAC
1 TTTAATACTTTATAT--TAATAC-TTA-TA----GT-TTATATAC
63402 TTTAATACTTTATATTATATACTTTATAGTTTATATA-
1 TTTAATACTTTATATTA-ATAC-TTATAGTTTATATAC
* *
63439 TATATATA-TATATACTT-ATACTTTATAGTTTATATAC
1 TTTA-ATACTTTATA-TTAATAC-TTATAGTTTATATAC
63476 -TTATATACTTTATATTATATACTT
1 TTTA-ATACTTTATATTA-ATACTT
63500 TAATTCTTTA
Statistics
Matches: 115, Mismatches: 9, Indels: 35
0.72 0.06 0.22
Matches are distributed among these distances:
34 1 0.01
35 5 0.04
36 39 0.34
37 18 0.16
38 18 0.16
39 1 0.01
43 4 0.03
44 23 0.20
45 6 0.05
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.54
Consensus pattern (36 bp):
TTTAATACTTTATATTAATACTTATAGTTTATATAC
Found at i:63438 original size:2 final size:2
Alignment explanation
Indices: 63433--63621 Score: 146
Period size: 2 Copynumber: 95.0 Consensus size: 2
63423 CTTTATAGTT
* *
63433 TA TA TA TA TA TA TA TA TA TA CT- TA TA CTT TA TA GTT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA
* * * *
63475 CT- TA TA TA CTT TA TA T- TA TA TA CTT TA -A T- TC TT TA TA T-
1 -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
63513 TA TA TA CT- TA TA -A TT TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63554 TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
63595 TA CA CT- TA TA CTT TA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA
63622 CTTGTAATGT
Statistics
Matches: 152, Mismatches: 16, Indels: 38
0.74 0.08 0.18
Matches are distributed among these distances:
1 10 0.07
2 134 0.88
3 8 0.05
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63516 original size:36 final size:35
Alignment explanation
Indices: 63406--63521 Score: 119
Period size: 36 Copynumber: 3.2 Consensus size: 35
63396 ATATACTTTA
*
63406 ATACTTTATATTATATACTTTATAGTTTATATATATAT
1 ATACTTTATATTATATACTTTA-A-TTTTTATAT-TAT
* * *
63444 ATA-TATATACT-TATACTTTATAGTTTATATACTTAT
1 ATACTTTATATTATATACTTTA-A-TTTTTATA-TTAT
63480 ATACTTTATATTATATACTTTAATTCTTTATATTAT
1 ATACTTTATATTATATACTTTAATT-TTTATATTAT
63516 ATACTT
1 ATACTT
63522 ATAATTTATA
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
36 38 0.55
37 19 0.28
38 12 0.17
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (35 bp):
ATACTTTATATTATATACTTTAATTTTTATATTAT
Found at i:63809 original size:20 final size:20
Alignment explanation
Indices: 63780--63817 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
63770 CAATTCAGTC
*
63780 CATTTTACAATTTTTTATCA
1 CATTTCACAATTTTTTATCA
63800 CATTTCACAATTTTTTAT
1 CATTTCACAATTTTTTAT
63818 TTGATCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (20 bp):
CATTTCACAATTTTTTATCA
Found at i:64339 original size:32 final size:32
Alignment explanation
Indices: 64289--64365 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
64279 ACCAAAAAAT
* **
64289 GATCCGACCTGAAATCAATTTGTA-TCTGGTAA
1 GATCCAACCTGAAATCAATCCGTATTC-GGTAA
64321 GATCCAACCT-AAAGTCAATCCGTATTCGGTAA
1 GATCCAACCTGAAA-TCAATCCGTATTCGGTAA
64353 GATCCAACCTGAA
1 GATCCAACCTGAA
64366 TTTTGTTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.08
32 32 0.82
33 4 0.10
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (32 bp):
GATCCAACCTGAAATCAATCCGTATTCGGTAA
Found at i:65145 original size:20 final size:21
Alignment explanation
Indices: 65120--65169 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
65110 TTCCCAATTT
*
65120 GCAATGCGAA-TAAGTAAATC
1 GCAATGCGAATTAAGAAAATC
**
65140 GCAATGCGAATTTGGAAAATC
1 GCAATGCGAATTAAGAAAATC
65161 GCAATGCGA
1 GCAATGCGA
65170 TACTGACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
GCAATGCGAATTAAGAAAATC
Found at i:65183 original size:20 final size:20
Alignment explanation
Indices: 65158--65333 Score: 167
Period size: 20 Copynumber: 8.7 Consensus size: 20
65148 AATTTGGAAA
*
65158 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
65178 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
65199 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
65220 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
65240 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
65260 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
65280 TTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
65300 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
65320 ATCGCAACGAGATA
1 ATCGCAACGCGATA
65334 ATACAGAATT
Statistics
Matches: 141, Mismatches: 12, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
19 2 0.01
20 101 0.72
21 36 0.26
22 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:65204 original size:21 final size:21
Alignment explanation
Indices: 65178--65233 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
65168 GATACTGACT
65178 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
65199 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
65220 ATCGCAACGCGATA
1 ATCGCAACGCGATA
65234 CTGACTTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:66101 original size:24 final size:24
Alignment explanation
Indices: 66074--66127 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
66064 GTATTCGAAA
*
66074 TTTGATCTTGGTCAATA-TCCGGAC
1 TTTGATATTGGTCAATACT-CGGAC
*
66098 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
66122 TTTGAT
1 TTTGAT
66128 GATTTTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Done.