Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000006.1 Hibiscus syriacus cultivar Beakdansim tig00000012_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: 133993
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:9672 original size:41 final size:40
Alignment explanation
Indices: 9411--9814 Score: 264
Period size: 41 Copynumber: 9.9 Consensus size: 40
9401 CATTTCTAGA
* * * *
9411 ACAAACGCCGGTAAAGACTCGT-ATTATAGCGACGTTTTAAT
1 ACAAACGCCGCTAAAGACT-GTAATT-TAGTGGCGTTTTTAT
* *
9452 AAAAACGCCGCTAAAGAC--TAATTTAGTGGCGTTTTTGT
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAT
* * * **
9490 ACAAACGCCGCTATAGTACGAGT-CTTTACCGGCGTTTTTTAT
1 ACAAACGCCGCTAAAG-AC-TGTAATTTAGTGGCG-TTTTTAT
* * * *
9532 ACAAACGCCGCTATAA-ACT-CATTCTATAGCGGCGTTTTTAC
1 ACAAACGCCGCTA-AAGACTGTAAT-T-TAGTGGCGTTTTTAT
* * * * *
9573 AGAAACGCCGCTAAATAATTTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAT
* * *
9613 ACAAACGCTGCGAAAGACTGTAATTTAGTGGCGTTTTTAGA
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTA-T
* * *
9654 ACAAACGCCGCTATAGACTCGTGATTTAGTGGCATTTTTAT
1 ACAAACGCCGCTAAAGACT-GTAATTTAGTGGCGTTTTTAT
* * * * *
9695 ACAAACACCGCTATAGTACGAGT-CTTTAGCGGCGTGTTTTAT
1 ACAAACGCCGCTAAAG-AC-TGTAATTTAGTGGCGT-TTTTAT
* * *
9737 ACAAACGCCGCTAAATACTCGTACTATAGTGGCGTTTTTAT
1 ACAAACGCCGCTAAAGACT-GTAATTTAGTGGCGTTTTTAT
* * * * * * *
9778 ATAAATGCCTCAAAATAATGTACTTTAGTGGCGTTTT
1 ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTT
9815 AAGCATAAAC
Statistics
Matches: 289, Mismatches: 55, Indels: 39
0.75 0.14 0.10
Matches are distributed among these distances:
38 26 0.09
39 5 0.02
40 65 0.22
41 112 0.39
42 80 0.28
43 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (40 bp):
ACAAACGCCGCTAAAGACTGTAATTTAGTGGCGTTTTTAT
Found at i:9860 original size:12 final size:12
Alignment explanation
Indices: 9843--9868 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9833 ATACTCGTAC
9843 ATTTTAAAATTA
1 ATTTTAAAATTA
9855 ATTTTAAAATTA
1 ATTTTAAAATTA
9867 AT
1 AT
9869 ATTGACCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:13822 original size:21 final size:21
Alignment explanation
Indices: 13798--13856 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
13788 TGATTTATTA
**
13798 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
13819 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
13840 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
13857 ATTGGAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:14072 original size:42 final size:43
Alignment explanation
Indices: 14046--14228 Score: 235
Period size: 43 Copynumber: 4.3 Consensus size: 43
14036 ACCAGATCTT
*
14046 TTGCGGTGTTTG-TGGGAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGGG-AAAACGCCGCTAAATCTCAACACCTA
14089 TTGCGGCGTTTGTTGGGAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGGGAAAACGCCGCTAAATCTCAACACCTA
* * * *
14132 TTGTGGCGTTTGTT-GGAGAAATGCCGCCAAATATCAACACCTA
1 TTGCGGCGTTTGTTGGGA-AAACGCCGCTAAATCTCAACACCTA
* * * ***
14175 TTGCGGCGTTTGTTGGAAAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTGGGAAAACGCCGCTAAATCTCAACACCTA
14218 TTGCGGCGTTT
1 TTGCGGCGTTT
14229 TTGTTACCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
42 3 0.02
43 115 0.93
44 6 0.05
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (43 bp):
TTGCGGCGTTTGTTGGGAAAACGCCGCTAAATCTCAACACCTA
Found at i:15991 original size:68 final size:69
Alignment explanation
Indices: 15850--16030 Score: 174
Period size: 68 Copynumber: 2.6 Consensus size: 69
15840 CAAGACACTC
** * *
15850 TAATCCTTCGGGGCTTCCATGCGAG--ACATCCAGAATAATTATGAATAGGTGCTCCCGTACGAA
1 TAATCCTTTAGGGCTCCCATGCGAGACACAT-C-GAATAATTATGAATAGGTGCTCCCATACGAA
* *
15913 TTAATC
64 TCAATA
* * * * *
15919 TAATCTTTTAGGG-TCCCGTGGGAGACAC-TCGAAATAATTATGACTAGGTGCTCCCATGC-AAG
1 TAATCCTTTAGGGCTCCCATGCGAGACACATCG-AATAATTATGAATAGGTGCTCCCATACGAA-
*
15981 TCACTA
64 TCAATA
*
15987 TAATCCTTTAGGGCTCCCATGCGAGACACATTGAATAATTATGA
1 TAATCCTTTAGGGCTCCCATGCGAGACACATCGAATAATTATGA
16031 TTATATCAAG
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
67 3 0.03
68 48 0.53
69 35 0.39
70 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (69 bp):
TAATCCTTTAGGGCTCCCATGCGAGACACATCGAATAATTATGAATAGGTGCTCCCATACGAATC
AATA
Found at i:22328 original size:11 final size:11
Alignment explanation
Indices: 22314--22344 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
22304 CAAAATAATT
22314 GAACTATAAAG
1 GAACTATAAAG
22325 GAACTATAAAG
1 GAACTATAAAG
*
22336 GAAATATAA
1 GAACTATAA
22345 TATTTTGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (11 bp):
GAACTATAAAG
Found at i:25881 original size:14 final size:14
Alignment explanation
Indices: 25855--25974 Score: 123
Period size: 14 Copynumber: 8.6 Consensus size: 14
25845 AACTTGGTTC
*
25855 GAGTCAACCCATCT
1 GAGTCAACTCATCT
* *
25869 GATTCAATTCATCT
1 GAGTCAACTCATCT
* *
25883 GAGTCAACCCGTCT
1 GAGTCAACTCATCT
* *
25897 CAGTCAACTCATCC
1 GAGTCAACTCATCT
*
25911 GAGTCAACCCATCT
1 GAGTCAACTCATCT
* *
25925 GATTCAATTCATCT
1 GAGTCAACTCATCT
* *
25939 GAGTCAACCCGTCT
1 GAGTCAACTCATCT
*
25953 CAGTCAACTCATCT
1 GAGTCAACTCATCT
25967 GAGTCAAC
1 GAGTCAAC
25975 CCGCTGACTT
Statistics
Matches: 81, Mismatches: 25, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 81 1.00
ACGTcount: A:0.28, C:0.33, G:0.13, T:0.27
Consensus pattern (14 bp):
GAGTCAACTCATCT
Found at i:25922 original size:56 final size:56
Alignment explanation
Indices: 25854--25976 Score: 237
Period size: 56 Copynumber: 2.2 Consensus size: 56
25844 CAACTTGGTT
25854 CGAGTCAACCCATCTGATTCAATTCATCTGAGTCAACCCGTCTCAGTCAACTCATC
1 CGAGTCAACCCATCTGATTCAATTCATCTGAGTCAACCCGTCTCAGTCAACTCATC
25910 CGAGTCAACCCATCTGATTCAATTCATCTGAGTCAACCCGTCTCAGTCAACTCATC
1 CGAGTCAACCCATCTGATTCAATTCATCTGAGTCAACCCGTCTCAGTCAACTCATC
*
25966 TGAGTCAACCC
1 CGAGTCAACCC
25977 GCTGACTTTG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26
Consensus pattern (56 bp):
CGAGTCAACCCATCTGATTCAATTCATCTGAGTCAACCCGTCTCAGTCAACTCATC
Found at i:25977 original size:28 final size:28
Alignment explanation
Indices: 25855--25977 Score: 165
Period size: 28 Copynumber: 4.4 Consensus size: 28
25845 AACTTGGTTC
* * * *
25855 GAGTCAACCCATCTGATTCAATTCATCT
1 GAGTCAACCCGTCTCAGTCAACTCATCT
*
25883 GAGTCAACCCGTCTCAGTCAACTCATCC
1 GAGTCAACCCGTCTCAGTCAACTCATCT
* * * *
25911 GAGTCAACCCATCTGATTCAATTCATCT
1 GAGTCAACCCGTCTCAGTCAACTCATCT
25939 GAGTCAACCCGTCTCAGTCAACTCATCT
1 GAGTCAACCCGTCTCAGTCAACTCATCT
25967 GAGTCAACCCG
1 GAGTCAACCCG
25978 CTGACTTTGA
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 81 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (28 bp):
GAGTCAACCCGTCTCAGTCAACTCATCT
Found at i:30648 original size:14 final size:14
Alignment explanation
Indices: 30589--30651 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
30579 AATTGGTTCA
* *
30589 AGTCAACCCATCTG
1 AGTCAACTCATCCG
*
30603 ATTCAACTCATCCG
1 AGTCAACTCATCCG
* *
30617 AGTTAACTCGTCTC-
1 AGTCAACTCATC-CG
30631 AGTCAACTCATCCG
1 AGTCAACTCATCCG
30645 AGTCAAC
1 AGTCAAC
30652 CAATTGACTT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
13 1 0.03
14 37 0.95
15 1 0.03
ACGTcount: A:0.29, C:0.33, G:0.13, T:0.25
Consensus pattern (14 bp):
AGTCAACTCATCCG
Found at i:32798 original size:103 final size:102
Alignment explanation
Indices: 32574--32790 Score: 380
Period size: 103 Copynumber: 2.1 Consensus size: 102
32564 GTCGAGGGTC
*
32574 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTTGAAGTCTGGTGAGACACATACT
* *
32639 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
32676 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGT-TGAAGTCTGGTGAGACACATAC
* *
32741 TTGATCCCTAGTATATGTATATGGTTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
32779 TATGTGGTCCTT
1 TATGTGGTCCTT
32791 ATGGACATTA
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 41 0.38
103 68 0.62
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:32874 original size:23 final size:23
Alignment explanation
Indices: 32797--32873 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
32787 CCTTATGGAC
32797 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATATGGCACTACGGTGCA
* * * *
32821 ATTCTACACGGCACTCCGGTGCA
1 ATTATATATGGCACTACGGTGCA
* *
32844 ATTATATGTGGCACTTCGGTGCA
1 ATTATATATGGCACTACGGTGCA
32867 ATTATAT
1 ATTATAT
32874 GAGTTGTGGT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
ATTATATATGGCACTACGGTGCA
Found at i:38506 original size:103 final size:103
Alignment explanation
Indices: 38281--38498 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
38271 GTCGAGGGTC
38281 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
38346 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
38384 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
38449 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
38487 TATGTGGTCCTT
1 TATGTGGTCCTT
38499 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:38543 original size:23 final size:23
Alignment explanation
Indices: 38515--38580 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
38505 ATTATTATAT
38515 GGCACTACGGTGCAATTATACGC
1 GGCACTACGGTGCAATTATACGC
* *
38538 GGCACTCCGGTGCAATTATACGT
1 GGCACTACGGTGCAATTATACGC
* *
38561 GGCACTTCGATGCAATTATA
1 GGCACTACGGTGCAATTATA
38581 TGAGCTGTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:41129 original size:31 final size:31
Alignment explanation
Indices: 41091--41178 Score: 124
Period size: 31 Copynumber: 2.8 Consensus size: 31
41081 TAAGGCAACC
*
41091 CTTGGGTAGGCTCTGAGGCCTCAAGAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCAAGAACTTT
* *
41122 CTTGGGTAGGCCCCGAGGCCCCGAA-AACTTT
1 CTTGGGTAGGCTCTGAGGCCCC-AAGAACTTT
*
41153 CTTGGGTAGGCTCTTAGGCCCCAAGA
1 CTTGGGTAGGCTCTGAGGCCCCAAGA
41179 TTCTCCCTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 45 0.92
32 2 0.04
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.24
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGAGGCCCCAAGAACTTT
Found at i:49255 original size:76 final size:77
Alignment explanation
Indices: 49126--49334 Score: 289
Period size: 76 Copynumber: 2.8 Consensus size: 77
49116 CCGTTGTACA
* * * *
49126 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
**
49190 -AAAAACTGTTT
66 CAAAAACCATTT
* *
49201 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
*
49266 CCAAAACCATTT
66 CAAAAACCATTT
* * *
49278 AGGGGGG-ATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
49335 TTTGGCTTTG
Statistics
Matches: 119, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 19 0.16
76 85 0.71
77 15 0.13
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAG
CAAAAACCATTT
Found at i:51966 original size:21 final size:22
Alignment explanation
Indices: 51916--51979 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 22
51906 TTCCCCCTGT
51916 GGGGGGAATCGGTTCCTCTTCAAA
1 GGGGGGAATCGGTTCC-C-TCAAA
*
51940 GGGGGGAATCGGTTCCCTC-AG
1 GGGGGGAATCGGTTCCCTCAAA
* *
51961 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGGTTCCCTC
51980 TGCACCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.49
22 2 0.05
23 1 0.03
24 16 0.43
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.22
Consensus pattern (22 bp):
GGGGGGAATCGGTTCCCTCAAA
Found at i:55833 original size:22 final size:21
Alignment explanation
Indices: 55791--55830 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55781 GAGTTTGTTT
*
55791 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
55812 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
55831 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:57862 original size:75 final size:76
Alignment explanation
Indices: 57755--57951 Score: 254
Period size: 75 Copynumber: 2.6 Consensus size: 76
57745 GTTGTACAAG
* * * *
57755 GGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCAGAG-A
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAGCA
**
57818 AAAACTGTTTA
66 AAAACCATTTA
* * * * *
57829 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTTCCTCCGAGCATTCTGGAAATCTCGGGGCC
1 GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAGCA
57894 AAAACCATTTA
66 AAAACCATTTA
* *
57905 GGGGGGATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 GGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
57952 ATCTGTAATT
Statistics
Matches: 106, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
74 17 0.16
75 37 0.35
76 29 0.27
77 23 0.22
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (76 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCAGAGCA
AAAACCATTTA
Found at i:65418 original size:21 final size:21
Alignment explanation
Indices: 65393--65440 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
65383 CCTAATATTG
*
65393 CAATGTCAAAATTATGTGCAA
1 CAATGTCAAAATTAGGTGCAA
65414 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
65435 TAATGT
1 CAATGT
65441 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:70076 original size:21 final size:21
Alignment explanation
Indices: 70051--70098 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
70041 CCTAATATTG
70051 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
70072 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
70093 TAATGT
1 CAATGT
70099 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:76589 original size:2 final size:2
Alignment explanation
Indices: 76582--76612 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
76572 ATCAATTTTA
76582 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76613 CTTATACTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:76924 original size:7 final size:7
Alignment explanation
Indices: 76907--76974 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
76897 CATAATCGGA
*
76907 TTTAGGG
1 TTTAGGT
*
76914 TTTATGT
1 TTTAGGT
*
76921 TTTATGT
1 TTTAGGT
*
76928 TTTAGGA
1 TTTAGGT
76935 TTTAGGT
1 TTTAGGT
76942 TTTAGGAT
1 TTTAGG-T
*
76950 TTAAGG-
1 TTTAGGT
*
76956 TTTAGGG
1 TTTAGGT
*
76963 TTTAGGG
1 TTTAGGT
76970 TTTAG
1 TTTAG
76975 ATATTAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.10
7 41 0.79
8 6 0.12
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.51
Consensus pattern (7 bp):
TTTAGGT
Found at i:76931 original size:14 final size:14
Alignment explanation
Indices: 76904--76974 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
76894 TCACATAATC
*
76904 GGATTTAGGGTTTA
1 GGATTTAGGTTTTA
* * *
76918 TGTTTTATGTTTTA
1 GGATTTAGGTTTTA
76932 GGATTTAGGTTTTA
1 GGATTTAGGTTTTA
76946 GGATTTAAGG-TTTA
1 GGATTT-AGGTTTTA
* *
76960 GGGTTTAGGGTTTA
1 GGATTTAGGTTTTA
76974 G
1 G
76975 ATATTAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
13 3 0.06
14 41 0.87
15 3 0.06
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
GGATTTAGGTTTTA
Found at i:76932 original size:21 final size:21
Alignment explanation
Indices: 76904--76974 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
76894 TCACATAATC
*
76904 GGATTTAGGGTTTATGTTTTA
1 GGATTTAGGGTTTAGGTTTTA
* * *
76925 TGTTTTAGGATTTAGGTTTTA
1 GGATTTAGGGTTTAGGTTTTA
* *
76946 GGATTTAAGGTTTAGGGTTTA
1 GGATTTAGGGTTTAGGTTTTA
*
76967 GGGTTTAG
1 GGATTTAG
76975 ATATTAATTA
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (21 bp):
GGATTTAGGGTTTAGGTTTTA
Found at i:76981 original size:28 final size:28
Alignment explanation
Indices: 76904--76974 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
76894 TCACATAATC
* * * *
76904 GGATTTAGGGTTTATGTTTTATGTTTTA
1 GGATTTAGGGTTTAGGATTTAAGGTTTA
*
76932 GGATTTAGGTTTTAGGATTTAAGGTTTA
1 GGATTTAGGGTTTAGGATTTAAGGTTTA
*
76960 GGGTTTAGGGTTTAG
1 GGATTTAGGGTTTAG
76975 ATATTAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (28 bp):
GGATTTAGGGTTTAGGATTTAAGGTTTA
Found at i:77057 original size:14 final size:14
Alignment explanation
Indices: 77040--77085 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
77030 TGATTTAGAA
77040 TTTAAGGTTTATGG
1 TTTAAGGTTTATGG
* *
77054 TTTAAGATTTATTG
1 TTTAAGGTTTATGG
* *
77068 CTTATGGTTTATGG
1 TTTAAGGTTTATGG
77082 TTTA
1 TTTA
77086 GGGCTCATTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.54
Consensus pattern (14 bp):
TTTAAGGTTTATGG
Found at i:77063 original size:21 final size:21
Alignment explanation
Indices: 77017--77078 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
77007 AGGTAAGTAT
* *
77017 GATTTAGGGTTTATGATTT-A
1 GATTTAAGGTTTATGGTTTAA
77037 GAATTTAAGGTTTATGGTTTAA
1 G-ATTTAAGGTTTATGGTTTAA
** *
77059 GATTTATTGCTTATGGTTTA
1 GATTTAAGGTTTATGGTTTA
77079 TGGTTTAGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.03
21 32 0.91
22 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.23, T:0.50
Consensus pattern (21 bp):
GATTTAAGGTTTATGGTTTAA
Found at i:80170 original size:21 final size:20
Alignment explanation
Indices: 80084--80241 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
80074 AAATGACCAA
**
80084 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
80103 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
80123 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
80143 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
80164 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
80185 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
80205 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
80226 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
80242 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:80270 original size:20 final size:20
Alignment explanation
Indices: 80208--80401 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
80198 CGATTTTCCA
* ** *
80208 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
80228 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
80248 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
80268 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
80288 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
80308 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
80328 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
80348 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
80368 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
80389 AAATCGCAACGCG
1 AAATCGCAACGCG
80402 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:80292 original size:60 final size:60
Alignment explanation
Indices: 80208--80401 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
80198 CGATTTTCCA
* ** * *
80208 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
80268 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
80328 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
80389 AAATCGCAACGCG
1 AAATCGCAACGCG
80402 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:80821 original size:33 final size:33
Alignment explanation
Indices: 80782--80852 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
80772 TTCACTTAGA
* *
80782 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
80815 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
80848 TTTCA
1 TTTCA
80853 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:80976 original size:20 final size:20
Alignment explanation
Indices: 80932--81041 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
80922 TGCAGAAGAG
*
80932 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
80953 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
80973 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
80994 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
81008 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
81027 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
81042 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:80989 original size:41 final size:38
Alignment explanation
Indices: 80925--81041 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
80915 TTCAATTTGC
* *
80925 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
80963 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
81004 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
81037 AGAAT
1 AGAAT
81042 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:81011 original size:14 final size:14
Alignment explanation
Indices: 80992--81048 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
80982 GAGAAATGAA
80992 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
81006 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
81025 AATCGCAACGAGAG
1 AATCGCAACGAGAG
81039 AATCGCAACG
1 AATCGCAACG
81049 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:81024 original size:33 final size:33
Alignment explanation
Indices: 80984--81064 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
80974 CGCAACGAGA
80984 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
81017 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
81050 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
81065 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:81082 original size:19 final size:19
Alignment explanation
Indices: 81060--81157 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
81050 GAAACCAAAA
*
81060 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
81079 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
81093 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
81112 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
81126 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
81145 TCGCGTTGCGATT
1 TCGCGTTGCGATT
81158 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:81101 original size:14 final size:14
Alignment explanation
Indices: 81082--81171 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
81072 TTTCATTTCG
81082 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
81096 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
81115 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
81129 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
81146 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
81162 CGTTGCGATT
1 CGTTGCGATT
81172 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:81107 original size:33 final size:33
Alignment explanation
Indices: 81065--81179 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
81055 CAAAATCGCA
81065 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
81098 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
81131 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
81164 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
81180 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:83191 original size:185 final size:185
Alignment explanation
Indices: 82876--83440 Score: 1094
Period size: 185 Copynumber: 3.0 Consensus size: 185
82866 TAGATTGCTT
* *
82876 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
82941 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 -TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
83006 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
83062 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83127 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
*
83192 TGTATTCTATAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
83247 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83312 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
83377 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
83432 AGTAAATTT
1 AGTAAATTT
83441 ATCCATTCAA
Statistics
Matches: 375, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 312 0.83
186 63 0.17
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:83192 original size:92 final size:93
Alignment explanation
Indices: 82876--83440 Score: 1080
Period size: 93 Copynumber: 6.1 Consensus size: 93
82866 TAGATTGCTT
* *
82876 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
82941 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
82969 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83034 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
83062 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83127 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
83154 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83219 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
83247 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83312 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
83339 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
83404 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
83432 AGTAAATTT
1 AGTAAATTT
83441 ATCCATTCAA
Statistics
Matches: 467, Mismatches: 3, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
92 183 0.39
93 284 0.61
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:83509 original size:20 final size:20
Alignment explanation
Indices: 83484--83549 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 20
83474 TAGTTTACTT
* *
83484 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
*
83504 TCGCAACGTGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
83523 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
83542 TCGCAACG
1 TCGCAACG
83550 ACAGAATCGC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.45, C:0.26, G:0.17, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:83585 original size:19 final size:19
Alignment explanation
Indices: 83563--83690 Score: 132
Period size: 19 Copynumber: 7.2 Consensus size: 19
83553 GAATCGCAAC
83563 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
83582 GCGA--TTC-TTT--CGTT
1 GCGATTTTCATTTCGCGTT
*
83596 GCGATTTTCATTTCGCATT
1 GCGATTTTCATTTCGCGTT
*
83615 GCGA--TTC-TGT--CGTT
1 GCGATTTTCATTTCGCGTT
83629 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
**
83648 GCGATTTTGGTTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
83667 GCGATTTTAAGTTTCGCGTT
1 GCGATTTTCA-TTTCGCGTT
83687 GCGA
1 GCGA
83691 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
14 15 0.17
16 11 0.12
17 11 0.12
19 40 0.44
20 13 0.14
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:83595 original size:14 final size:14
Alignment explanation
Indices: 83578--83634 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
83568 TTTCATTTCG
83578 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
83592 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
83609 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
83625 CGTTGCGATT
1 CGTTGCGATT
83635 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:83605 original size:33 final size:33
Alignment explanation
Indices: 83563--83690 Score: 166
Period size: 33 Copynumber: 3.7 Consensus size: 33
83553 GAATCGCAAC
83563 GCGATTTTCATTTCGCGTTGCGATTCTTTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTTTCGTT
* *
83596 GCGATTTTCATTTCGCATTGCGATTCTGTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTTTCGTT
*
83629 GCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGTT
1 GCGATTTTCATTTCGCGTTGCGA--TT-CTTT--CGTT
*
83667 GCGATTTTAAGTTTCGCGTTGCGA
1 GCGATTTTCA-TTTCGCGTTGCGA
83691 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
33 53 0.64
35 2 0.02
36 2 0.02
38 13 0.16
39 13 0.16
ACGTcount: A:0.11, C:0.20, G:0.24, T:0.45
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTTTCGTT
Found at i:85632 original size:14 final size:14
Alignment explanation
Indices: 85613--85648 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
85603 ATTGTTTAAT
85613 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
85627 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
85641 TGATTTGT
1 TGATTTGT
85649 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:85809 original size:20 final size:19
Alignment explanation
Indices: 85755--85821 Score: 125
Period size: 19 Copynumber: 3.5 Consensus size: 19
85745 AAAATTGACT
85755 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
85774 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
85793 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
85813 ATCGCAATG
1 ATCGCAATG
85822 GGAGAATCGC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 29 0.62
20 18 0.38
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:85856 original size:19 final size:19
Alignment explanation
Indices: 85828--85995 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
85818 AATGGGAGAA
* *
85828 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
* *
85847 TCGCGTTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
85863 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
85880 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
85899 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
85915 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
85932 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
85951 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
85967 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
85984 TCCGCATTGCGA
1 T-CGCATTGCGA
85996 AATGTAATGG
Statistics
Matches: 124, Mismatches: 9, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.15
16 21 0.17
17 18 0.15
18 2 0.02
19 59 0.48
20 6 0.05
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:85881 original size:33 final size:33
Alignment explanation
Indices: 85834--85995 Score: 150
Period size: 33 Copynumber: 4.7 Consensus size: 33
85824 AGAATCGCAA
* *
85834 TGCGATTTTAATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
85867 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
85905 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
85938 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
85971 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
85996 AATGTAATGG
Statistics
Matches: 103, Mismatches: 14, Indels: 23
0.74 0.10 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 48 0.47
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:85908 original size:52 final size:52
Alignment explanation
Indices: 85828--85995 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
85818 AATGGGAGAA
* * *
85828 TCGCAATGCGATTTTAATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
85880 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
85932 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
85984 TCCGCATTGCGA
1 T-CGCATTGCGA
85996 AATGTAATGG
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 102 0.91
53 10 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:86078 original size:19 final size:19
Alignment explanation
Indices: 86054--86151 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
86044 AAAATTGACT
86054 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
86073 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
86092 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
86106 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
86125 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
86145 ATCGCAA
1 ATCGCAA
86152 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:86183 original size:53 final size:53
Alignment explanation
Indices: 86054--86170 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
86044 AAAATTGACT
86054 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
86106 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
86159 ATCGCAATGCGA
1 ATCGCAATGCGA
86171 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:88504 original size:12 final size:12
Alignment explanation
Indices: 88487--88511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
88477 TCTTCGGGGA
88487 CTTTTTCTTCTT
1 CTTTTTCTTCTT
88499 CTTTTTCTTCTT
1 CTTTTTCTTCTT
88511 C
1 C
88512 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:88720 original size:24 final size:24
Alignment explanation
Indices: 88686--88732 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
88676 CTGAAACATC
88686 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
88710 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
88733 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:89442 original size:20 final size:20
Alignment explanation
Indices: 89414--89643 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
89404 AAATTTCAGT
* * *
89414 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
89434 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
89454 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
89474 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
89494 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
89514 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
89534 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
89554 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
89574 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
89594 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
89614 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
89634 GTTGCGATTT
1 GTTGCGATTT
89644 TGGAAAATCG
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:89660 original size:21 final size:21
Alignment explanation
Indices: 89630--89712 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
89620 ATTTTCATAT
*
89630 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
89651 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
89672 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
89693 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
89713 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:89703 original size:42 final size:43
Alignment explanation
Indices: 89610--89708 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
89600 ATTTATGTGT
* *
89610 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
89651 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
89693 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
89709 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:94659 original size:24 final size:24
Alignment explanation
Indices: 94632--94703 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
94622 GTAAACGGAG
*
94632 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
94656 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
94680 ATATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
94703 A
1 A
94704 GGTAACGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 15 0.35
24 28 0.65
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:94704 original size:12 final size:12
Alignment explanation
Indices: 94636--94704 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
94626 ACGGAGATAT
* *
94636 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
94648 CAGAATTCATAT
1 CAGAATTCAGAA
94660 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
94672 CAGAATCCATAT
1 CAGAATTCAGAA
94684 CAGAA-TCAGAA
1 CAGAATTCAGAA
94695 CAGAATTCAG
1 CAGAATTCAG
94705 GTAACGTATC
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
11 10 0.23
12 31 0.72
13 2 0.05
ACGTcount: A:0.49, C:0.19, G:0.13, T:0.19
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:97195 original size:3 final size:3
Alignment explanation
Indices: 97172--97216 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
97162 TCAAAGGAAA
97172 AAT AA- AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
97217 TTAAGATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:99129 original size:80 final size:84
Alignment explanation
Indices: 98894--99216 Score: 377
Period size: 84 Copynumber: 3.9 Consensus size: 84
98884 ATATGCCGTT
* * * * * * * * * * *
98894 GAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGGTGACATATAACTCTTCTAGCCTTTAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* *
98959 CTGTAAATGATGTG-CCTTG
65 CTGCAAATGATGTGCCCTCG
* * * * * *
98978 GAGATGAGCGTAGTCGAACTCGAGGGTCTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
99043 CTGCAAATGATGTGCCCTCG
65 CTGCAAATGATGTGCCCTCG
* *
99063 GAGCTGAGGGTAATCAAACTCGAAGGTC-TT-TT-GCAGATAGCCC-TCTCGACTTAAGCTATGC
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
*
99124 TGCAAATGATGTGCCCTCA
66 TGCAAATGATGTGCCCTCG
*
99143 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
1 GAGCTGAGCGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAGCCCTTCTCGACTTAAGCTATG
99208 CTGCAAATG
65 CTGCAAATG
99217 TTGTCTTAAA
Statistics
Matches: 206, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
80 60 0.29
81 12 0.06
82 2 0.01
83 5 0.02
84 74 0.36
85 53 0.26
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAGCCCTTCTCGACTTAAGCTATGC
TGCAAATGATGTGCCCTCG
Found at i:100552 original size:105 final size:105
Alignment explanation
Indices: 99408--100550 Score: 1641
Period size: 106 Copynumber: 10.9 Consensus size: 105
99398 GCATTGTTTC
* ** * * **
99408 GAGTCCAATATCCTCCGTCATGAAGTTGAAATCGGCTCTGGAACCGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAA
* * * * * *
99473 CCAACCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
99514 GAGTCCAATATCTTTCGATGTGAAGTTGGAATTGACTCTG-AA-T--GAAAT-TTTGTTGACAAT
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
* * * *
99574 CAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
99615 GA-TCCAAGATCCTTCGTTGAGAAGTTAAAATTGGTTCTGAAGTTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAA
* *
99679 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
99720 GAGTCTAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAA
99785 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
99826 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TGTTTATTGACAA
99891 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
99932 GAGTCCAATATCCTTCACTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA-ATGTTTATTGACAA
* *
99997 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGTGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
100038 GAGTCCAATAACCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGTAGTTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTG-GGAAATGTTTATTGACAA
*
100103 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
100144 GAGTCCAATATCCTTCGTTCTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
100209 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
100249 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
100314 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
100354 GAGTCCAATACCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
*
100419 CAGCGGTCCCTTCGTCGTGAAGTTGAAATTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
100459 AAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
*
100524 CAACGGTCCCTTCGTCGTGAAGTTGAA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAA
100551 ATCCGCTCTC
Statistics
Matches: 945, Mismatches: 81, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
100 72 0.08
101 5 0.01
102 5 0.01
104 3 0.00
105 349 0.37
106 509 0.54
107 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:104309 original size:6 final size:5
Alignment explanation
Indices: 104270--104308 Score: 60
Period size: 5 Copynumber: 7.4 Consensus size: 5
104260 GAATCAAAGG
104270 AAAAT AAAAT AAAAT AAAAT AAAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
104309 TTTAAGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 22 0.67
6 11 0.33
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:105824 original size:13 final size:13
Alignment explanation
Indices: 105808--105843 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
105798 GTCAACAGGT
*
105808 CGGGTAGGGTAAA
1 CGGGTCGGGTAAA
105821 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
105834 CGGGTCGGGT
1 CGGGTCGGGT
105844 TGTGACCGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.50, T:0.17
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:105843 original size:18 final size:18
Alignment explanation
Indices: 105790--105831 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
105780 CAACGATCAA
* *
105790 CGGGTCGGGTCAACAGGT
1 CGGGTAGGGTAAACAGGT
*
105808 CGGGTAGGGTAAACGGGT
1 CGGGTAGGGTAAACAGGT
105826 CGGGTA
1 CGGGTA
105832 AACGGGTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTAGGGTAAACAGGT
Found at i:105966 original size:13 final size:13
Alignment explanation
Indices: 105948--105981 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
105938 CTGATTTCGG
105948 AAAATTCCCGGAA
1 AAAATTCCCGGAA
105961 AAAATTCCCGGAA
1 AAAATTCCCGGAA
105974 AAAATTCC
1 AAAATTCC
105982 TAAAAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (13 bp):
AAAATTCCCGGAA
Found at i:108703 original size:2 final size:2
Alignment explanation
Indices: 108696--108766 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
108686 ACAAGCTTCA
108696 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
108738 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
108767 ACTTCAAAAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112325 original size:2 final size:2
Alignment explanation
Indices: 112318--112360 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
112308 TAAATTTGTC
112318 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
112360 A
1 A
112361 ACTTTAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112418 original size:17 final size:19
Alignment explanation
Indices: 112377--112420 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
112367 AAAAATAGTT
112377 TTTATTTTAACTTATTAAA
1 TTTATTTTAACTTATTAAA
* *
112396 TATATTTT-A-TTATTAAC
1 TTTATTTTAACTTATTAAA
112413 TTTATTTT
1 TTTATTTT
112421 TATTTTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 1 0.05
19 7 0.32
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTTAACTTATTAAA
Found at i:112564 original size:26 final size:25
Alignment explanation
Indices: 112481--112564 Score: 64
Period size: 30 Copynumber: 3.2 Consensus size: 25
112471 ATAAAAACAA
*
112481 AATATATTTAATAATTTAAAGTAATAATAT
1 AATATATTTAATAAATT-AA--AAT-A-AT
*
112511 AATATATTTAATAAATTAAGATAA-
1 AATATATTTAATAAATTAAAATAAT
*
112535 AATATACTTTTAA-AAGTTAAAATAAT
1 AATATA--TTTAATAAATTAAAATAAT
112561 AATA
1 AATA
112565 AAATATTTAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
24 6 0.13
25 11 0.23
26 10 0.21
27 2 0.04
29 2 0.04
30 16 0.34
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (25 bp):
AATATATTTAATAAATTAAAATAAT
Found at i:112583 original size:33 final size:33
Alignment explanation
Indices: 112536--112608 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
112526 TTAAGATAAA
* *
112536 ATATACTTTTAAAAGTTAAAATAATAATAAAAT
1 ATATATTTTTAAAAGTTAAAATAAGAATAAAAT
* *
112569 ATTTATTTTTAAAAGTTTAAATAAGAATAAAAT
1 ATATATTTTTAAAAGTTAAAATAAGAATAAAAT
112602 ATATATT
1 ATATATT
112609 CTAAAATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (33 bp):
ATATATTTTTAAAAGTTAAAATAAGAATAAAAT
Found at i:112704 original size:26 final size:26
Alignment explanation
Indices: 112637--112710 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
112627 ACTTTTAAAT
*
112637 TAAGTTAATA-ATAAAACATATTTAA
1 TAAGTTAATATATAAAAAATATTTAA
** * *
112662 TAAGTTAATATGGAAAATAATTTTTTA
1 TAAGTTAATATATAAAA-AATATTTAA
112689 -AAGTTAATATATAAAAAATATT
1 TAAGTTAATATATAAAAAATATT
112711 ATAAATTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
25 15 0.38
26 18 0.46
27 6 0.15
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (26 bp):
TAAGTTAATATATAAAAAATATTTAA
Found at i:114014 original size:17 final size:18
Alignment explanation
Indices: 113968--114016 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 18
113958 TATTTTATTT
113968 TAAT-TAAAATTT-ATAA
1 TAATATAAAATTTAATAA
** *
113984 TAATATAATTTTTAATGA
1 TAATATAAAATTTAATAA
114002 TAA-ATAAAATTTAAT
1 TAATATAAAATTTAAT
114017 CATACGAGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 4 0.15
17 16 0.62
18 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAATATAAAATTTAATAA
Found at i:117414 original size:24 final size:24
Alignment explanation
Indices: 117381--117428 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
117371 CATTAAAATT
117381 AAAATCAAAT-TAATAAAGTATACA
1 AAAATCAAATAT-ATAAAGTATACA
* *
117405 AAAATTAAATATATAAATTATACA
1 AAAATCAAATATATAAAGTATACA
117429 GATTTATTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAATCAAATATATAAAGTATACA
Found at i:119711 original size:15 final size:15
Alignment explanation
Indices: 119693--119749 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
119683 AAGAAATAGA
119693 GGAAGAAGAGGAAGT
1 GGAAGAAGAGGAAGT
** *
119708 GGAAGTTGAGGAAGA
1 GGAAGAAGAGGAAGT
** *
119723 GGTGGAAGAGGAGGT
1 GGAAGAAGAGGAAGT
119738 GGAAGAAGAGGA
1 GGAAGAAGAGGA
119750 TGAGGATGCT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.51, T:0.09
Consensus pattern (15 bp):
GGAAGAAGAGGAAGT
Found at i:119729 original size:24 final size:24
Alignment explanation
Indices: 119691--119749 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
119681 TGAAGAAATA
* * *
119691 GAGGAAGAAGAGGAAGTGGAAGTT
1 GAGGAAGAGGAGGAAGAGGAAGTG
* *
119715 GAGGAAGAGGTGGAAGAGGAGGTG
1 GAGGAAGAGGAGGAAGAGGAAGTG
*
119739 GAAGAAGAGGA
1 GAGGAAGAGGA
119750 TGAGGATGCT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.51, T:0.08
Consensus pattern (24 bp):
GAGGAAGAGGAGGAAGAGGAAGTG
Found at i:119738 original size:12 final size:12
Alignment explanation
Indices: 119718--119748 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
119708 GGAAGTTGAG
119718 GAAGAGGTGGAA
1 GAAGAGGTGGAA
*
119730 GAGGAGGTGGAA
1 GAAGAGGTGGAA
119742 GAAGAGG
1 GAAGAGG
119749 ATGAGGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.55, T:0.06
Consensus pattern (12 bp):
GAAGAGGTGGAA
Found at i:119749 original size:30 final size:30
Alignment explanation
Indices: 119697--119754 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
119687 AATAGAGGAA
**
119697 GAAGAGGAAGTGGAAGTTGAGGAAGAGGTG
1 GAAGAGGAAGTGGAAGAAGAGGAAGAGGTG
* *
119727 GAAGAGGAGGTGGAAGAAGAGGATGAGG
1 GAAGAGGAAGTGGAAGAAGAGGAAGAGG
119755 ATGCTGATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.52, T:0.10
Consensus pattern (30 bp):
GAAGAGGAAGTGGAAGAAGAGGAAGAGGTG
Found at i:124002 original size:3 final size:3
Alignment explanation
Indices: 123994--124018 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
123984 AGTTTTTTAC
123994 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
124019 TGGATTTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:126261 original size:12 final size:12
Alignment explanation
Indices: 126244--126282 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
126234 GAGTTCGAGT
*
126244 ATTTTAAATAAA
1 ATTTTAAATATA
*
126256 ATTTT-AATTTA
1 ATTTTAAATATA
126267 ATTTTAAATATA
1 ATTTTAAATATA
126279 ATTT
1 ATTT
126283 CATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTTTAAATATA
Found at i:133159 original size:24 final size:24
Alignment explanation
Indices: 133143--133195 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
133133 TATATATAAT
*
133143 TATTGAAACATTATTATTTAAATTG
1 TATTG-AACATTATTATATAAATTG
*
133168 TATTGAACATTATTATTTAAATTG
1 TATTGAACATTATTATATAAATTG
133192 TATT
1 TATT
133196 AAATATTGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.51
Consensus pattern (24 bp):
TATTGAACATTATTATATAAATTG
Done.