Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001987.1 Hibiscus syriacus cultivar Beakdansim tig00004056_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: 51713
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:734 original size:17 final size:17
Alignment explanation
Indices: 712--750 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
702 AAAATTGAAA
712 TAAAAAATAT-TAATTTT
1 TAAAAAATATATAA-TTT
729 TAAAAAATATATAATTT
1 TAAAAAATATATAATTT
746 TAAAA
1 TAAAA
751 TATTATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAAAAATATATAATTT
Found at i:757 original size:16 final size:16
Alignment explanation
Indices: 715--757 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
705 ATTGAAATAA
*
715 AAAATATTA-ATTTTT
1 AAAATATTATAATTTT
*
730 AAAAAATATATAATTTT
1 AAAATAT-TATAATTTT
747 AAAATATTATA
1 AAAATATTATA
758 TACCTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 6 0.26
16 6 0.26
17 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATATTATAATTTT
Found at i:1732 original size:20 final size:20
Alignment explanation
Indices: 1707--1753 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1697 AAATTCAGTA
*
1707 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1727 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1747 TTGCGAT
1 TTGCGAT
1754 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1763 original size:20 final size:20
Alignment explanation
Indices: 1740--1873 Score: 169
Period size: 20 Copynumber: 6.7 Consensus size: 20
1730 CGATAGTCAG
* *
1740 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
1760 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
1780 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1800 ATTCACATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
1820 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
1841 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1861 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1874 ATTAGGAAAT
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 81 0.84
21 16 0.16
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1904 original size:21 final size:21
Alignment explanation
Indices: 1870--1955 Score: 140
Period size: 21 Copynumber: 4.2 Consensus size: 21
1860 TATTCGCATT
*
1870 GCGAA-TTAGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
1890 GCGAATTTGGGAAATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
1911 GCGAATTTGGG-AATCGCAAC
1 GCGAATTTGGGAAATCGCAAC
*
1931 GCGAATTTGGGAAATCGCAAT
1 GCGAATTTGGGAAATCGCAAC
1952 GCGA
1 GCGA
1956 TAGTCAAAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
20 25 0.40
21 37 0.60
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (21 bp):
GCGAATTTGGGAAATCGCAAC
Found at i:1908 original size:41 final size:41
Alignment explanation
Indices: 1863--1955 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
1853 ATTTACGTAT
*
1863 TCGCATTGCGAATTAGGAAATCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAATCGCAACGCGAATTTGGGAAA
* * *
1904 TCGCAACGCGAATTTGGGAATCGCAACGCGAATTTGGGAAA
1 TCGCAATGCGAATTAGGAAATCGCAACGCGAATTTGGGAAA
1945 TCGCAATGCGA
1 TCGCAATGCGA
1956 TAGTCAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.32, C:0.19, G:0.28, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTAGGAAATCGCAACGCGAATTTGGGAAA
Found at i:6284 original size:15 final size:15
Alignment explanation
Indices: 6264--6293 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6254 ATAATTATTA
6264 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
6279 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
6294 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:7495 original size:24 final size:23
Alignment explanation
Indices: 7467--7545 Score: 65
Period size: 27 Copynumber: 3.3 Consensus size: 23
7457 ATGTAATTTG
7467 TAATATATATATATATATATTTAA
1 TAATA-ATATATATATATATTTAA
7491 TAATAA-ATAATAATATTATTATATTAA
1 TAATAATAT-AT-ATA-TA-TAT-TTAA
* *
7518 TAATAATATTTATA-ATA-ATAA
1 TAATAATATATATATATATTTAA
7539 TAATAAT
1 TAATAAT
7546 TTTAATAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
21 10 0.21
22 2 0.04
23 5 0.11
24 9 0.19
25 2 0.04
26 6 0.13
27 11 0.23
28 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TAATAATATATATATATATTTAA
Found at i:7496 original size:3 final size:3
Alignment explanation
Indices: 7488--7559 Score: 65
Period size: 3 Copynumber: 24.0 Consensus size: 3
7478 TATATATATT
* * * * *
7488 TAA TAA TAAA TAA TAA T-A TTA TTA TAT TAA TAA TAA TAT TTA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
7533 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
7560 ACGAAAAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:7536 original size:18 final size:18
Alignment explanation
Indices: 7483--7559 Score: 93
Period size: 18 Copynumber: 4.1 Consensus size: 18
7473 ATATATATAT
7483 ATATTTAATAATAAATAATA
1 ATATTT-ATAAT-AATAATA
*
7503 ATATTATTATATTAATAATA
1 ATA-T-TTATAATAATAATA
7523 ATATTTATAATAATAATA
1 ATATTTATAATAATAATA
7541 ATAATTT-TAATAATAATA
1 AT-ATTTATAATAATAATA
7559 A
1 A
7560 ACGAAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 27 0.52
19 5 0.10
20 13 0.25
21 5 0.10
22 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATTTATAATAATAATA
Found at i:7551 original size:15 final size:16
Alignment explanation
Indices: 7488--7559 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 16
7478 TATATATATT
* *
7488 TAATAATAAATAATAA
1 TAATAATTATTAATAA
* *
7504 TATTATTATATTAATAA
1 TAATAAT-TATTAATAA
*
7521 TAATATTTATAATAATAA
1 TAATAATTAT--TAATAA
7539 TAATAATT-TTAATAA
1 TAATAATTATTAATAA
7554 TAATAA
1 TAATAA
7560 ACGAAAAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
15 12 0.26
16 8 0.17
17 14 0.30
18 13 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAATTATTAATAA
Found at i:7866 original size:76 final size:76
Alignment explanation
Indices: 7704--8415 Score: 1284
Period size: 76 Copynumber: 9.4 Consensus size: 76
7694 GAGGTCTTAA
* *
7704 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTG-AAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
7767 AGGCTTTTTGG
66 AGGCTTTTTGG
*
7778 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
7843 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
7854 AAACATCATGCACTGTAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
7919 AGGCTTTTTGG
66 AGGCTTTTTGG
*
7930 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
7995 AGGCTTTTTGG
66 AGGCTTTTTGG
**
8006 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
8071 AGGCTTTTTGG
66 AGGCTTTTTGG
*
8082 AAACATCATGCACTGCAGGACTTACAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
8147 AGGCTTTTTGG
66 AGGCTTTTTGG
*
8158 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
8223 AGGCTTTTTGA
66 AGGCTTTTTGG
*
8234 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTTAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
8299 AGGCTTTTTGG
66 AGGCTTTTTGG
*
8310 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCAA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
8375 AGGCTTTTTGG
66 AGGCTTTTTGG
*
8386 AAACATCATGCACTGCAGGACTCACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
8416 TGGGAAATAG
Statistics
Matches: 614, Mismatches: 22, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
74 42 0.07
75 7 0.01
76 565 0.92
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:11650 original size:31 final size:31
Alignment explanation
Indices: 11615--11677 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
11605 AGAGATGTGG
11615 TCTGAATTCATCAATTACAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
*
11646 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
11677 T
1 T
11678 TTATATGTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (31 bp):
TCTGAATTCATCAATTACAGAGTTGACAGAT
Found at i:12059 original size:114 final size:114
Alignment explanation
Indices: 11857--12069 Score: 356
Period size: 114 Copynumber: 1.9 Consensus size: 114
11847 CATGCAGTTT
* *
11857 ATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
11922 CTTCCAAAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAATTC
66 CTTCCAAAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAATTC
* *
11971 ATCTTTCAAATT-TAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
1 ATCTTTC-AATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAAC
* *
12035 ACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCT
65 ACTTCCAAAAGATGCTATTAGGTCTCCTTATTTCT
12070 GCTACGAGAA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
114 88 0.96
115 4 0.04
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
ATCTTTCAATTCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAAAAGATGCTATTAGGTCTCCTTATTTCTACTATGAGCAAATTC
Found at i:16188 original size:36 final size:35
Alignment explanation
Indices: 16109--16189 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 35
16099 ATGTAAATGC
* *
16109 GAAAATGCATAAATGCAAAAATAAGAATGCAAACT
1 GAAAATGCATAAATGCAAAAATAAGAATACAAAAT
** *
16144 GTGTAATGCA-AAGATGTAAAAAGTAAGAATACAAAAT
1 G-AAAATGCATAA-ATGCAAAAA-TAAGAATACAAAAT
16181 GAAAATGCA
1 GAAAATGCA
16190 CAAAAACAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
35 3 0.08
36 20 0.56
37 13 0.36
ACGTcount: A:0.56, C:0.09, G:0.17, T:0.19
Consensus pattern (35 bp):
GAAAATGCATAAATGCAAAAATAAGAATACAAAAT
Found at i:19566 original size:15 final size:15
Alignment explanation
Indices: 19546--19575 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19536 ATAATTATTA
19546 ATCAATGATTAAAAT
1 ATCAATGATTAAAAT
*
19561 ATCAATTATTAAAAT
1 ATCAATGATTAAAAT
19576 TAAGAAATCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (15 bp):
ATCAATGATTAAAAT
Found at i:20795 original size:3 final size:3
Alignment explanation
Indices: 20782--20853 Score: 74
Period size: 3 Copynumber: 24.0 Consensus size: 3
20772 ATATATTTAT
* * * *
20782 TAA TAAA TAA TAA TAA TAA T-A TTA TAT TAA TAA TAA TAT TTA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
20827 TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
20854 ACGAAAAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:28814 original size:20 final size:20
Alignment explanation
Indices: 28789--28835 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
28779 GGAAAGGCTC
*
28789 GGGTTCGGGAGAAGCGGTCA
1 GGGTTCAGGAGAAGCGGTCA
28809 GGGTTCAGGAGAAGCGGTCA
1 GGGTTCAGGAGAAGCGGTCA
*
28829 GGCTTCA
1 GGGTTCA
28836 TCGGTGATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.45, T:0.17
Consensus pattern (20 bp):
GGGTTCAGGAGAAGCGGTCA
Found at i:29831 original size:42 final size:42
Alignment explanation
Indices: 29740--29866 Score: 123
Period size: 43 Copynumber: 3.0 Consensus size: 42
29730 ACCAAAGGAC
* * *
29740 AAAAAGAGAAAATAAATAAAAATAAAATAAATAATTAAAAAAGT
1 AAAAAGAGAAAA-AAA-AATAATAAAATAAAAAATAAAAAAAGT
* *
29784 CAAAAG-GAAAAAAAGAATAATAAAATAAAAAAAAAGAAAAAG-
1 AAAAAGAGAAAAAAA-AATAATAAAATAAAAAATAA-AAAAAGT
** *
29826 AAAAAGTCAAAAGAAAATAAATAAAATAAAAAATAAAAAAA
1 AAAAAGAGAAAAAAAAAT-AATAAAATAAAAAATAAAAAAA
29867 TATCATAATA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
42 32 0.46
43 33 0.47
44 5 0.07
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.13
Consensus pattern (42 bp):
AAAAAGAGAAAAAAAAATAATAAAATAAAAAATAAAAAAAGT
Found at i:29834 original size:49 final size:52
Alignment explanation
Indices: 29733--29884 Score: 145
Period size: 52 Copynumber: 2.9 Consensus size: 52
29723 ATAATAAACC
*
29733 AAAGGACAAAAAGAGAA-AAT-AAATAAAAATAAAATAAATAATTAAAAAAGTCA
1 AAAGGA-AAAAAGAGAATAATAAAATAAAAA-AAAAGAAATAA-TAAAAAAGTCA
*
29786 AAAGGAAAAAA-AGAATAATAAAATAAAAAAAAAGAAA-AA-GAAAAAGTCA
1 AAAGGAAAAAAGAGAATAATAAAATAAAAAAAAAGAAATAATAAAAAAGTCA
* * * **
29835 AAAGAAAATAAATAAAATAA-AAAATAAAAAAATATCATAATAATAAAAAA
1 AAAGGAAA-AAAGAGAATAATAAAATAAAAAAA-AAGA-AATAATAAAAAA
29885 ATAAAAAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
49 16 0.19
50 15 0.18
51 14 0.17
52 17 0.20
53 17 0.20
54 5 0.06
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.14
Consensus pattern (52 bp):
AAAGGAAAAAAGAGAATAATAAAATAAAAAAAAAGAAATAATAAAAAAGTCA
Found at i:29920 original size:9 final size:8
Alignment explanation
Indices: 29839--29940 Score: 84
Period size: 8 Copynumber: 12.5 Consensus size: 8
29829 AAGTCAAAAG
29839 AAAATAAAT
1 AAAAT-AAT
29848 AAAATAA-
1 AAAATAAT
*
29855 AAAATAAA
1 AAAATAAT
29863 AAAAT-AT
1 AAAATAAT
*
29870 CATAATAAT
1 -AAAATAAT
*
29879 AAAAAAAT
1 AAAATAAT
*
29887 AAAAAAAT
1 AAAATAAT
* *
29895 AGAGATAAA
1 A-AAATAAT
29904 AAAATAAT
1 AAAATAAT
29912 AACAATAAT
1 AA-AATAAT
29921 AATAATAAT
1 AA-AATAAT
29930 AAAATAA-
1 AAAATAAT
29937 AAAA
1 AAAA
29941 GGTTAAATAA
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
7 12 0.15
8 38 0.49
9 28 0.36
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:29951 original size:48 final size:46
Alignment explanation
Indices: 29834--29978 Score: 127
Period size: 48 Copynumber: 3.0 Consensus size: 46
29824 AGAAAAAGTC
*
29834 AAAAGAAAATAAATAAA-ATAAAAAATAAAAAAATATCATAATAATAAA
1 AAAATAAAA-AAATAAATA-AAAAAATAAAAAAATA-CATAATAATAAA
* *
29882 AAAATAAAAAAATAGAGATAAAAAAATAATAACAATA-ATAATAATAAT
1 AAAATAAAAAAATA-A-ATAAAAAAATAA-AAAAATACATAATAATAAA
* * *
29930 AAAATAAAAAAGGTTAAATAAAAAACTAAAATAAATAAAT-A-AATAAA
1 AAAATAAAAAA--ATAAATAAAAAAATAAAA-AAATACATAATAATAAA
29977 AA
1 AA
29979 GGGACTAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
47 14 0.17
48 46 0.56
49 13 0.16
50 9 0.11
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.19
Consensus pattern (46 bp):
AAAATAAAAAAATAAATAAAAAAATAAAAAAATACATAATAATAAA
Found at i:29961 original size:13 final size:12
Alignment explanation
Indices: 29799--29978 Score: 81
Period size: 12 Copynumber: 14.7 Consensus size: 12
29789 GGAAAAAAAG
29799 AATAATAAAATAA
1 AATAA-AAAATAA
29812 AA-AAAAAGA-AA
1 AATAAAAA-ATAA
* *
29823 AAGAAAAAGTCAA
1 AATAAAAAAT-AA
*
29836 AAGAAAATAAATAA
1 AA-TAAA-AAATAA
29850 AATAAAAAAT-A
1 AATAAAAAATAA
* *
29861 AA-AAAATATCAT
1 AATAAAAAAT-AA
*
29873 AATAATAAA-AA
1 AATAAAAAATAA
29884 AATAAAAAAATAGA
1 AAT-AAAAAATA-A
* *
29898 GATAAAAAA-AT
1 AATAAAAAATAA
*
29909 AAT-AACAATAA
1 AATAAAAAATAA
*
29920 TAAT-AATAATAA
1 -AATAAAAAATAA
*
29932 AATAAAAAAGGTTA
1 AATAAAAAA--TAA
29946 AATAAAAAACTAA
1 AATAAAAAA-TAA
29959 AATAAATAAAT-A
1 AATAAA-AAATAA
29971 AATAAAAA
1 AATAAAAA
29979 GGGACTAAAT
Statistics
Matches: 129, Mismatches: 20, Indels: 38
0.69 0.11 0.20
Matches are distributed among these distances:
10 10 0.08
11 22 0.17
12 41 0.32
13 29 0.22
14 24 0.19
15 3 0.02
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (12 bp):
AATAAAAAATAA
Found at i:29966 original size:17 final size:17
Alignment explanation
Indices: 29840--29977 Score: 74
Period size: 17 Copynumber: 7.7 Consensus size: 17
29830 AGTCAAAAGA
29840 AAATAAATAAAATAAA-
1 AAATAAATAAAATAAAT
*
29856 AAATAAA-AAAATATCAT
1 AAATAAATAAAATA-AAT
*
29873 AATAATAAA-AAAATAAAA
1 -A-AATAAATAAAATAAAT
29891 AAATAGAGATAAAA-AAAT
1 AAATA-A-ATAAAATAAAT
29909 -AATAACAATAATAATAATAAT
1 AAAT-A-AATAA-AAT-A-AAT
*
29930 AAAATAAA-AAAGGTTAAAT
1 -AAATAAATAAA--ATAAAT
29949 AAA-AAACTAAAATAAAT
1 AAATAAA-TAAAATAAAT
29966 AAATAAATAAAA
1 AAATAAATAAAA
29978 AGGGACTAAA
Statistics
Matches: 96, Mismatches: 7, Indels: 37
0.69 0.05 0.26
Matches are distributed among these distances:
15 6 0.06
16 12 0.12
17 25 0.26
18 16 0.17
19 23 0.24
20 4 0.04
21 6 0.06
22 1 0.01
23 3 0.03
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATAAAATAAAT
Found at i:30816 original size:3 final size:3
Alignment explanation
Indices: 30808--30847 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
30798 ATAAAAAAGT
*
30808 ATA ATA ATA ATA ATA ATA AT- ATA CTA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30848 TAAACTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:30837 original size:14 final size:13
Alignment explanation
Indices: 30808--30861 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 13
30798 ATAAAAAAGT
30808 ATAATAATA-ATA
1 ATAATAATATATA
30820 ATAATAATATACTA
1 ATAATAATATA-TA
30834 ATAATAATATA-A
1 ATAATAATATATA
*
30846 TATAA-ACTATATA
1 -ATAATAATATATA
30859 ATA
1 ATA
30862 TATATATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
12 18 0.49
13 6 0.16
14 13 0.35
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAATATATA
Found at i:31005 original size:39 final size:39
Alignment explanation
Indices: 30889--31226 Score: 137
Period size: 36 Copynumber: 9.3 Consensus size: 39
30879 ATCTTTAAAC
* * *
30889 TATATATTATAT--T-TTT-AAAAAAAAGTTTTCAAAAC
1 TATATATTATATAATGTTTCAAAAAAATGTTTTTAAAAT
* * *
30924 TATATATCATATAGT-TTTC--AAAAATG-ATTTAAAA-
1 TATATATTATATAATGTTTCAAAAAAATGTTTTTAAAAT
*
30958 -AAATATTATATAA-GTTTCAAAAAAATGTTTTTTAAAAT
1 TATATATTATATAATGTTTCAAAAAAATG-TTTTTAAAAT
* *
30996 TATATATTATATAATTTTTCAAAAAAATGTTTTTAGAAT
1 TATATATTATATAATGTTTCAAAAAAATGTTTTTAAAAT
* ** * *
31035 TATATA--A-GT--T-TTTC-AAAATGTTTTTTTAAAAAC
1 TATATATTATATAATGTTTCAAAAAAATGTTTTT-AAAAT
* * * *
31068 TATATATTATAT-ATATTT----AAAATGATTTCAAAAC
1 TATATATTATATAATGTTTCAAAAAAATGTTTTTAAAAT
* * *
31102 TATATATTATAT-AGGTTTTC---AAAATGTTTTAAAAACC
1 TATATATTATATAATG-TTTCAAAAAAATGTTTTTAAAA-T
** * *
31139 T-TATATTATAT-AT-TTTC-AAAATGTTTTTTTAAAAC
1 TATATATTATATAATGTTTCAAAAAAATGTTTTTAAAAT
* * *
31174 TATATATTATATATAT-TTTTAAAAATATGTTTTCAAAACT
1 TATATATTATATA-ATGTTTCAAAAAAATGTTTTTAAAA-T
31214 ATATATATTATAT
1 -TATATATTATAT
31227 GTATTTCAAA
Statistics
Matches: 238, Mismatches: 37, Indels: 50
0.73 0.11 0.15
Matches are distributed among these distances:
32 10 0.04
33 27 0.11
34 23 0.10
35 36 0.15
36 53 0.22
37 15 0.06
38 8 0.03
39 41 0.17
40 13 0.05
41 12 0.05
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (39 bp):
TATATATTATATAATGTTTCAAAAAAATGTTTTTAAAAT
Found at i:31102 original size:34 final size:35
Alignment explanation
Indices: 31058--31237 Score: 179
Period size: 36 Copynumber: 4.9 Consensus size: 35
31048 CAAAATGTTT
*
31058 TTTTAAAAACTATATATTATATATATTT-AAAATG
1 TTTTCAAAACTATATATTATATATATTTCAAAATG
*
31092 ATTTCAAAACTATATATTATATAGGT-TTTCAAAATG
1 TTTTCAAAACTATATATTATATA--TATTTCAAAATG
*
31128 TTTTAAAAACCT-TATATTATATAT-TTTCAAAATG
1 TTTTCAAAA-CTATATATTATATATATTTCAAAATG
* *
31162 TTTTTTTAAAACTATATATTATATATATTTTTAAAAATATG
1 --TTTTCAAAACTATATATTATATATA--TTT-CAAA-ATG
*
31203 TTTTCAAAACTATATATATTATATGTATTTCAAAA
1 TTTTCAAAAC--TATATATTATATATATTTCAAAA
31238 ACATTTGCAG
Statistics
Matches: 123, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
34 32 0.26
35 5 0.04
36 45 0.37
37 3 0.02
38 3 0.02
39 15 0.12
40 3 0.02
41 17 0.14
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (35 bp):
TTTTCAAAACTATATATTATATATATTTCAAAATG
Found at i:31110 original size:106 final size:108
Alignment explanation
Indices: 30991--31237 Score: 285
Period size: 106 Copynumber: 2.3 Consensus size: 108
30981 AATGTTTTTT
* * * *
30991 AAAATTATATATTATATAATTTTTCAAAAAAATGTTTTTAGAA-TTATA-TA-AGT-TTTTCAAA
1 AAAACTATATATTATATAAGTTTTC---AAAATGTTTTAAAAACTTATATTATA-TATTTTCAAA
31052 ATGTTTTTTTAAAAACTATATATTATATATA-TTT-AAA-ATGATTTC
62 ATGTTTTTTT-AAAACTATATATTATATATATTTTAAAATATGATTTC
*
31097 AAAACTATATATTATATAGGTTTTCAAAATGTTTTAAAAACCTTATATTATATATTTTCAAAATG
1 AAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAA-CTTATATTATATATTTTCAAAATG
*
31162 TTTTTTTAAAACTATATATTATATATATTTTTAAAAATATGTTTTC
65 TTTTTTTAAAACTATATATTATATATA-TTTT-AAAATATGATTTC
*
31208 AAAACTATATA-TATTATATGTATTTCAAAA
1 AAAACTATATATTA-TATAAGT-TTTCAAAA
31238 ACATTTGCAG
Statistics
Matches: 122, Mismatches: 7, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
103 13 0.11
105 5 0.04
106 45 0.37
107 19 0.16
108 3 0.02
110 5 0.04
111 24 0.20
112 8 0.07
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.47
Consensus pattern (108 bp):
AAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTTATATTATATATTTTCAAAATGT
TTTTTTAAAACTATATATTATATATATTTTAAAATATGATTTC
Found at i:31185 original size:178 final size:175
Alignment explanation
Indices: 30885--31206 Score: 429
Period size: 178 Copynumber: 1.8 Consensus size: 175
30875 AAACATCTTT
*
30885 AAACTATATATTATATTTTTAAAAAAAAGTTTTCAAAACTATATATCATATAGTTTTCAAAAATG
1 AAACTATATATTATATTTTT--AAAAAAGATTTCAAAACTATATATCATATAGTTTTCAAAAATG
*
30950 ATTTAAAAAAATATTATATAAGTTTCAAAAAAATGTTTTTTAAAATTATATATTATATA-ATTTT
64 ATTTAAAAAAATATTATATAAGTTTC--AAAAATGTTTTTTAAAACTATATATTATATATATTTT
31014 TCAAAAAAATGTTTTTAGAATTATATAAGTTTTTCAAAATGTTTTTTTAA
127 T-AAAAAAATGTTTTTAGAATTATATAAGTTTTTCAAAATGTTTTTTTAA
* *
31064 AAACTATATATTATATATATTT-AAAATGATTTCAAAACTATATATTATATAGGTTTTC-AAAAT
1 AAACTATATATTATAT-T-TTTAAAAAAGATTTCAAAACTATATATCATATA-GTTTTCAAAAAT
* * *
31127 GTTTTAAAAACCTTATATTATAT-ATTTTC-AAAATGTTTTTTTAAAACTATATATTATATATAT
63 GATTTAAAAA---AATATTATATAAGTTTCAAAAATG-TTTTTTAAAACTATATATTATATATAT
*
31190 TTTTAAAAATATGTTTT
124 TTTTAAAAAAATGTTTT
31207 CAAAACTATA
Statistics
Matches: 127, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
177 6 0.05
178 75 0.59
179 28 0.22
180 6 0.05
181 12 0.09
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (175 bp):
AAACTATATATTATATTTTTAAAAAAGATTTCAAAACTATATATCATATAGTTTTCAAAAATGAT
TTAAAAAAATATTATATAAGTTTCAAAAATGTTTTTTAAAACTATATATTATATATATTTTTAAA
AAAATGTTTTTAGAATTATATAAGTTTTTCAAAATGTTTTTTTAA
Found at i:31263 original size:2 final size:2
Alignment explanation
Indices: 31256--31314 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
31246 AGATTATGTA
31256 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
31298 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
31315 AAATCGGACG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31936 original size:35 final size:35
Alignment explanation
Indices: 31888--31959 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
31878 AAAAGAAGAA
*
31888 TTGGATTAGGACTCAAATACTAGTCTAAAATAGAG
1 TTGGATTAAGACTCAAATACTAGTCTAAAATAGAG
31923 TTGGATTAAGACTCAAATACTAGTCTAAAATAGAG
1 TTGGATTAAGACTCAAATACTAGTCTAAAATAGAG
31958 TT
1 TT
31960 TTTTAGTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (35 bp):
TTGGATTAAGACTCAAATACTAGTCTAAAATAGAG
Found at i:32356 original size:17 final size:18
Alignment explanation
Indices: 32330--32369 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
32320 ATTATATGGA
32330 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
32346 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
32364 TATTAT
1 TATTAT
32370 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:32625 original size:2 final size:2
Alignment explanation
Indices: 32620--32652 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
32610 CTTATAACTT
32620 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32653 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:32913 original size:38 final size:40
Alignment explanation
Indices: 32862--32941 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
32852 AGTGAAAGGG
*
32862 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
32900 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
32940 TA
1 TA
32942 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:32937 original size:2 final size:2
Alignment explanation
Indices: 32930--32970 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
32920 TACTTTGATG
32930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32971 TCCTTTTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33068 original size:15 final size:14
Alignment explanation
Indices: 33026--33058 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
33016 TTTCCTTATC
*
33026 TTATTTATTT-ATT
1 TTATTTATTTCCTT
33039 TTATTTATTTCCTT
1 TTATTTATTTCCTT
33053 TTATTT
1 TTATTT
33059 TATTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (14 bp):
TTATTTATTTCCTT
Found at i:41589 original size:106 final size:106
Alignment explanation
Indices: 41329--42202 Score: 1166
Period size: 106 Copynumber: 8.3 Consensus size: 106
41319 GCCATCAGCG
* * *
41329 ATTTCAACTTCAC-GACGGAGGATATCGCGCTACTCGAGATAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATATTG-G--ACTCGAGACAACACAAGTTCAACTTCACAACGA
* * *
41393 AGGGACGGCTGGTTGTCAACAAACCACTTT-TCAGTTTCATTCAGAGCCA
62 AGGGACGGCTGGTTGTCAACAAA-CAATTTCCCA--AT--TTCAGAGCCA
*
41442 ATTTCAACTTCACAGCGAAGGATATTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
41507 ATGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
41548 ATTTCAACTTCACATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * *
41613 ACGACTGGTTGTCAACAAACAATTTCCCAATTTCATAGTCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
**
41654 ATTTCAACTTCACAGCGAAGGATATTGGACTTAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
*
41719 ACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAG-C-
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
41758 ----CAA--T---AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * *
41814 ATGACTGGTTGTCAATAAACAATTTCCCAATTTCAGGGTCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
**
41855 ATTTCAACTTCACATTGAAGGATATTGGACTCGAGAC--CACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
*
41918 ACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
41959 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
42024 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGGGTCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * * * *
42065 ATTTCAACTTCGCATCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * * *
42130 GCGGTTGGCTGTCAACAAACAATTTTCCAGTTTCAGTGCCA
66 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* *
42171 ATTTCAACTTCACGGCGGAGGATATTGGACTC
1 ATTTCAACTTCACAGCGAAGGATATTGGACTC
42203 AGAACAATAC
Statistics
Matches: 684, Mismatches: 62, Indels: 37
0.87 0.08 0.05
Matches are distributed among these distances:
95 82 0.12
96 1 0.00
98 1 0.00
100 3 0.00
101 3 0.00
103 1 0.00
104 96 0.14
105 1 0.00
106 411 0.60
108 1 0.00
109 5 0.01
110 54 0.08
112 1 0.00
113 23 0.03
114 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (106 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:42019 original size:305 final size:306
Alignment explanation
Indices: 41455--42202 Score: 1084
Period size: 305 Copynumber: 2.4 Consensus size: 306
41445 TCAACTTCAC
*
41455 AGCGAAGGATATTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTC
* *
41520 AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATGTTGGACTCGGGAC
66 AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC
*
41585 AACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCATA
131 -ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGA
* *
41650 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTTAAGACAACACAAGTTCAACTTCACAACGA
195 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGA
41715 AGGGACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAAT
260 AGGGACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAAT
*
41762 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTC
* * * *
41827 AATAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATTGAAGGATATTGGACTCGAGAC
66 AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC
* *
41892 -CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAG
131 ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAG
* *
41956 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAA
196 CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
* *
42021 GGGACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTT
261 GGGACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAG-C-----CAA--T
* * * * * ** ** *
42075 CGCATCGAAGGATATTAGACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCT
1 ---AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTT
* * * ** *
42140 GTCAACAAACAATTTTCCAGTTTCAGTGCCAATTTCAACTTCACGGCGGAGGATATTGGACTC
63 GTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTC
42203 AGAACAATAC
Statistics
Matches: 393, Mismatches: 37, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
305 161 0.41
306 1 0.00
307 122 0.31
311 3 0.01
313 1 0.00
316 105 0.27
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (306 bp):
AGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTC
AACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC
ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAG
CCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAA
GGGACGGCTGGTTGTCAACAAACAATCTCCCAATTTCAGAGCCAAT
Found at i:42779 original size:35 final size:35
Alignment explanation
Indices: 42687--42758 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
42677 CCAAAAAAGA
42687 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
42722 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
42757 AG
1 AG
42759 GGTTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:43158 original size:17 final size:18
Alignment explanation
Indices: 43132--43171 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
43122 ATTATATGGA
43132 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
43148 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
43166 TATTAT
1 TATTAT
43172 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:43422 original size:2 final size:2
Alignment explanation
Indices: 43417--43441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43407 CTTATAACTT
43417 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
43442 TATTTTTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43728 original size:2 final size:2
Alignment explanation
Indices: 43723--43753 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43713 TTGATGTGTG
43723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43754 TTCCTTTTTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43846 original size:18 final size:18
Alignment explanation
Indices: 43794--43851 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
43784 ATTATTTTAC
43794 TATTTTTTTCC-TTATCTAT
1 TATTTTTTTCCTTTAT-T-T
* *
43813 TATTTATTT-ATTTATTT
1 TATTTTTTTCCTTTATTT
43830 TATTTTTTTCCTTTATTT
1 TATTTTTTTCCTTTATTT
43848 TATT
1 TATT
43852 CTCTTTATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 9 0.27
18 12 0.36
19 12 0.36
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTTTCCTTTATTT
Found at i:43859 original size:36 final size:37
Alignment explanation
Indices: 43794--43866 Score: 98
Period size: 36 Copynumber: 2.0 Consensus size: 37
43784 ATTATTTTAC
43794 TATTTTTTTCCTTATCTATTATTTATTTAT-TTATTT
1 TATTTTTTTCCTTATCTATTATTTATTTATCTTATTT
*
43830 TATTTTTTTCCTTTAT-T-TTATTCTCTTTATCTTATTT
1 TATTTTTTTCC-TTATCTATTATT-TATTTATCTTATTT
43867 GTTTTCTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
35 5 0.15
36 18 0.55
37 10 0.30
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (37 bp):
TATTTTTTTCCTTATCTATTATTTATTTATCTTATTT
Found at i:47268 original size:16 final size:15
Alignment explanation
Indices: 47249--47295 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
47239 TCTATAAAAA
47249 TATTTTATTATATTAT
1 TATTTTATT-TATTAT
47265 TA-TTTATTTATTAT
1 TATTTTATTTATTAT
*
47279 TATTATTATTTTTTAT
1 TATT-TTATTTATTAT
47295 T
1 T
47296 TATATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTATTTATTAT
Found at i:47276 original size:19 final size:18
Alignment explanation
Indices: 47251--47301 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 18
47241 TATAAAAATA
47251 TTTTATTATATTATTATT
1 TTTTATTATATTATTATT
47269 TATTTATTATTATTATTATT
1 T-TTTATTA-TATTATTATT
47289 TTTTATTTATATT
1 TTTTA-TTATATT
47302 TTTTTGTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 14 0.47
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTATTATATTATTATT
Found at i:47278 original size:14 final size:15
Alignment explanation
Indices: 47252--47298 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
47242 ATAAAAATAT
47252 TTTATTATATTATTA
1 TTTATTATATTATTA
47267 TTTATT-TATTATTA
1 TTTATTATATTATTA
*
47281 -TTATTAT-TTTTTA
1 TTTATTATATTATTA
47294 TTTAT
1 TTTAT
47299 ATTTTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.34
14 13 0.45
15 6 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:47293 original size:23 final size:22
Alignment explanation
Indices: 47253--47298 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
47243 TAAAAATATT
47253 TTATTATATTATTATTTATTTA
1 TTATTATATTATTATTTATTTA
*
47275 TTATTATTATTATTTTTTATTTA
1 TTATTA-TATTATTATTTATTTA
47298 T
1 T
47299 ATTTTTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATTATATTATTATTTATTTA
Found at i:47301 original size:16 final size:17
Alignment explanation
Indices: 47251--47306 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 17
47241 TATAAAAATA
47251 TTTTATTATATTATTATT
1 TTTTATT-TATTATTATT
47269 TATTTATTATTATTATTATT
1 T-TTTA-T-TTATTATTATT
47289 TTTTATTTA-TATT-TT
1 TTTTATTTATTATTATT
47304 TTT
1 TTT
47307 GTAGGTCTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.14
16 4 0.11
17 3 0.09
18 2 0.06
19 8 0.23
20 12 0.34
21 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTATTATTATT
Done.