Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006272.1 Hibiscus syriacus cultivar Beakdansim tig00014954_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: 63435
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:8003 original size:16 final size:19
Alignment explanation
Indices: 7963--8007 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 19
7953 AAAAGGATAA
7963 TATCGATACCGAATGAGTAG
1 TATCGATACCGAATGAG-AG
7983 TATCGATACC-AA-GAG-G
1 TATCGATACCGAATGAGAG
7999 TATCGATAC
1 TATCGATAC
8008 TAATGAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.40
18 3 0.12
19 2 0.08
20 10 0.40
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (19 bp):
TATCGATACCGAATGAGAG
Found at i:8620 original size:45 final size:45
Alignment explanation
Indices: 8526--8625 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 45
8516 CATTTCATCC
* * * * * * *
8526 TATGTGATTACATGAAAATGTGAGGTAAGCTATGTAGCATTTATT
1 TATGTGATTACATAAAAATATGAGATAAGCTATGTAGAAATGATA
*
8571 TATGTGATTACATAAAAATATGATATAAGCTATGT-GAAAATGATA
1 TATGTGATTACATAAAAATATGAGATAAGCTATGTAG-AAATGATA
8616 TATGTGATTA
1 TATGTGATTA
8626 TATGTCTATA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 1 0.02
45 45 0.98
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (45 bp):
TATGTGATTACATAAAAATATGAGATAAGCTATGTAGAAATGATA
Found at i:8763 original size:23 final size:23
Alignment explanation
Indices: 8737--8818 Score: 69
Period size: 23 Copynumber: 3.6 Consensus size: 23
8727 GTTCTGCGCG
8737 GTCCTTCTAGG-CAATTCTACGTA
1 GTCCTTC-AGGACAATTCTACGTA
* **
8760 GTCCTTCAGGACATTTCTACGCG
1 GTCCTTCAGGACAATTCTACGTA
* * *
8783 GTCCTT-AGGTACAATACTATGTG
1 GTCCTTCAGG-ACAATTCTACGTA
*
8806 GTCCTTCGGGACA
1 GTCCTTCAGGACA
8819 TTTTTATGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.12
23 40 0.83
24 2 0.04
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (23 bp):
GTCCTTCAGGACAATTCTACGTA
Found at i:8853 original size:24 final size:24
Alignment explanation
Indices: 8826--8874 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
8816 ACATTTTTAT
*
8826 GTGGCACTTCGGTGTAATTTCTAC
1 GTGGCACTTCGGTGCAATTTCTAC
*
8850 GTGGCACTTTGGTGCAATTTCTAC
1 GTGGCACTTCGGTGCAATTTCTAC
8874 G
1 G
8875 AGCTGTGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (24 bp):
GTGGCACTTCGGTGCAATTTCTAC
Found at i:8937 original size:11 final size:11
Alignment explanation
Indices: 8921--8946 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8911 TTTATATGAT
8921 TTTATAAAATG
1 TTTATAAAATG
8932 TTTATAAAATG
1 TTTATAAAATG
8943 TTTA
1 TTTA
8947 AGTGTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTATAAAATG
Found at i:22318 original size:11 final size:11
Alignment explanation
Indices: 22302--22329 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
22292 TCCTACTTGA
22302 CATTTTCTTAC
1 CATTTTCTTAC
22313 CATTTTCTTAC
1 CATTTTCTTAC
22324 CATTTT
1 CATTTT
22330 TACTTGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.25, G:0.00, T:0.57
Consensus pattern (11 bp):
CATTTTCTTAC
Found at i:28070 original size:76 final size:76
Alignment explanation
Indices: 27977--28238 Score: 425
Period size: 76 Copynumber: 3.4 Consensus size: 76
27967 GGATGAAATA
* * * * **
27977 TTGAAATCATCATGCACTGAAGGGCTTACAGATGACCCAAAGATTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
* *
28042 CCCAAGGCATT
66 CCGAAGGCTTT
28053 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
28118 CCGAAGGCTTT
66 CCGAAGGCTTT
* *
28129 TTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTATGGCTTTGAAAACATCAAAAAGCTC
1 TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
28194 CCGAAGGCTTT
66 CCGAAGGCTTT
*
28205 TTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCATGCACTGCAGGACTTACAGATG
28239 TGGGAAATAG
Statistics
Matches: 176, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 176 1.00
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
TTGAAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTC
CCGAAGGCTTT
Found at i:29107 original size:22 final size:22
Alignment explanation
Indices: 29082--29158 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
29072 AATAAAGCTT
29082 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
29104 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
29126 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
29148 TCATCTTTGAA
1 TCATCTTTGAA
29159 GAGTGTAGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:30686 original size:76 final size:75
Alignment explanation
Indices: 30513--30687 Score: 242
Period size: 76 Copynumber: 2.3 Consensus size: 75
30503 GATGTGGGCC
* * * * *
30513 TTCAGCATGCCCCAACAATTGCTGATACGAACGTTCAAAATACATCAACATTCTTCATTCTGATT
1 TTCAGCATGCCCCAACATTTGCTGAAACAAACATTCAAAATACATCAACATTCCTCATTCTGATT
30578 GAAAAAGGCT
66 GAAAAAGGCT
* ** *
30588 TTCAGCATGCCCCAACATTTTGCTGAAATAAACATTCAGGATACATCAACATTCCTGATTCTGAT
1 TTCAGCATGCCCCAACA-TTTGCTGAAACAAACATTCAAAATACATCAACATTCCTCATTCTGAT
*
30653 TGAAAAAGGGTT
65 TGAAAAA-GGCT
30665 TTCAGCATGCCCCAACATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
30688 TCTTGTTAAT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 17 0.19
76 51 0.58
77 20 0.23
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTGAAACAAACATTCAAAATACATCAACATTCCTCATTCTGATT
GAAAAAGGCT
Found at i:31653 original size:31 final size:31
Alignment explanation
Indices: 31618--31680 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
31608 AGAGATATGG
*
31618 TCTGAATTCATCAATTGCAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
31649 TCTGAATTCATCAATTACAGAGTTGACAGAT
1 TCTGAATTCATCAATTACAGAGTTGACAGAT
31680 T
1 T
31681 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:34172 original size:30 final size:30
Alignment explanation
Indices: 34129--34189 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
34119 TTCTTTTTCC
34129 TTTTTTTTCTTTCTTTCTTTCTTTGCTGGA
1 TTTTTTTTCTTTCTTTCTTTCTTTGCTGGA
34159 TTTTTCTTT-TTTCTTTCTTTCTTTGCTGGA
1 TTTTT-TTTCTTTCTTTCTTTCTTTGCTGGA
34189 T
1 T
34190 GAGTATAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 27 0.90
31 3 0.10
ACGTcount: A:0.03, C:0.16, G:0.10, T:0.70
Consensus pattern (30 bp):
TTTTTTTTCTTTCTTTCTTTCTTTGCTGGA
Found at i:44489 original size:2 final size:2
Alignment explanation
Indices: 44482--44515 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
44472 TTAGATGGTC
44482 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
44516 TGATTAAGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44861 original size:10 final size:10
Alignment explanation
Indices: 44844--44891 Score: 55
Period size: 10 Copynumber: 4.8 Consensus size: 10
44834 AACACGCTGG
44844 GCATCCGAGA
1 GCATCCGAGA
*
44854 GTATCCGAG-
1 GCATCCGAGA
44863 GCCATCCGAGA
1 G-CATCCGAGA
44874 GCATCCGAG-
1 GCATCCGAGA
44883 GCCATCCGA
1 G-CATCCGA
44892 CCGAGGCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 30 0.91
11 1 0.03
ACGTcount: A:0.25, C:0.33, G:0.29, T:0.12
Consensus pattern (10 bp):
GCATCCGAGA
Found at i:44870 original size:20 final size:20
Alignment explanation
Indices: 44845--44891 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
44835 ACACGCTGGG
*
44845 CATCCGAGAGTATCCGAGGC
1 CATCCGAGAGCATCCGAGGC
44865 CATCCGAGAGCATCCGAGGC
1 CATCCGAGAGCATCCGAGGC
44885 CATCCGA
1 CATCCGA
44892 CCGAGGCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.34, G:0.28, T:0.13
Consensus pattern (20 bp):
CATCCGAGAGCATCCGAGGC
Found at i:44897 original size:14 final size:14
Alignment explanation
Indices: 44878--44910 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
44868 CCGAGAGCAT
44878 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
44892 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
44906 ACGAG
1 CCGAG
44911 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:44905 original size:10 final size:10
Alignment explanation
Indices: 44856--44891 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
44846 ATCCGAGAGT
44856 ATCCGAGGCC
1 ATCCGAGGCC
44866 ATCCGAGAG-C
1 ATCCGAG-GCC
44876 ATCCGAGGCC
1 ATCCGAGGCC
44886 ATCCGA
1 ATCCGA
44892 CCGAGGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 1 0.04
10 22 0.92
11 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.28, T:0.11
Consensus pattern (10 bp):
ATCCGAGGCC
Found at i:44944 original size:33 final size:33
Alignment explanation
Indices: 44892--44964 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
44882 GGCCATCCGA
* * *
44892 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAACGAGCTATGCGAGGGAAT
*
44925 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAACGAGCTATGCGAGGGAAT
*
44958 CCAAGGG
1 CCGAGGG
44965 AAGCCAAGCG
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:0.26, C:0.27, G:0.37, T:0.10
Consensus pattern (33 bp):
CCGAGGGCAACCGAACGAGCTATGCGAGGGAAT
Found at i:44975 original size:33 final size:33
Alignment explanation
Indices: 44907--44976 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
44897 GCCATCCGAA
* * *
44907 CGAGCTATGCGAGGGCATCCGAGGGCAACCGAG
1 CGAGCTATGCGAGGGAATCCAAGGGCAACCAAG
44940 CGAGCTATGCGAGGGAATCCAAGGG-AAGCCAAG
1 CGAGCTATGCGAGGGAATCCAAGGGCAA-CCAAG
44973 CGAG
1 CGAG
44977 GGTAGGTCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 2 0.06
33 31 0.94
ACGTcount: A:0.29, C:0.24, G:0.39, T:0.09
Consensus pattern (33 bp):
CGAGCTATGCGAGGGAATCCAAGGGCAACCAAG
Found at i:45110 original size:29 final size:29
Alignment explanation
Indices: 45065--45121 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
45055 GAGCAAGGGT
* *
45065 AGGTCGCCCGGAGTGCATGGTGACCTACA
1 AGGTCGCCCGGAATGCATGGCGACCTACA
45094 AGGTCGCCCGGAATGCATGGCGACCTAC
1 AGGTCGCCCGGAATGCATGGCGACCTAC
45122 GGCACCCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.33, T:0.16
Consensus pattern (29 bp):
AGGTCGCCCGGAATGCATGGCGACCTACA
Found at i:46196 original size:3 final size:3
Alignment explanation
Indices: 46188--46212 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
46178 TATCTTTTCG
46188 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
46213 ATAAGTAAAA
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):
TTA
Found at i:47354 original size:15 final size:15
Alignment explanation
Indices: 47316--47453 Score: 217
Period size: 15 Copynumber: 9.3 Consensus size: 15
47306 AAATAATTTT
47316 AAATAATTTA--ATA
1 AAATAATTTATTATA
* * *
47329 AGATTATTTATTTTA
1 AAATAATTTATTATA
*
47344 AAATAATTTATTTTA
1 AAATAATTTATTATA
47359 AAATAATTTATTATA
1 AAATAATTTATTATA
47374 AAATAATTTATTATA
1 AAATAATTTATTATA
47389 AAATAATTTATTATA
1 AAATAATTTATTATA
47404 AAATAATTTATTATA
1 AAATAATTTATTATA
47419 AAATAATTTATTATA
1 AAATAATTTATTATA
*
47434 AAATAAATTATTATA
1 AAATAATTTATTATA
47449 AAATA
1 AAATA
47454 TGGATTGATT
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
13 8 0.07
15 108 0.93
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (15 bp):
AAATAATTTATTATA
Found at i:47518 original size:32 final size:32
Alignment explanation
Indices: 47477--47572 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
47467 TTAAAAAAAA
47477 TTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
47509 TTA-TTT---TAA---A--A-TATGGATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
* *
47531 TGATTTTAAATAATTTATTAGTATTGATTGAT
1 TTATTTTAAATAATTTATTAGTATGGATTGAT
47563 TTATTTTAAA
1 TTATTTTAAA
47573 ATATAGATTG
Statistics
Matches: 51, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
22 13 0.25
23 4 0.08
25 1 0.02
26 3 0.06
28 3 0.06
29 1 0.02
31 4 0.08
32 22 0.43
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:47523 original size:22 final size:22
Alignment explanation
Indices: 47498--47540 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
47488 AATTTATTAG
*
47498 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTGATTTTAAAA
47520 TATGGATTGATTGATTTTAAA
1 TATGGATTGATTGATTTTAAA
47541 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTGATTTTAAAA
Found at i:47542 original size:54 final size:54
Alignment explanation
Indices: 47479--47604 Score: 225
Period size: 54 Copynumber: 2.3 Consensus size: 54
47469 AAAAAAAATT
*
47479 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTG
1 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTG
* *
47533 ATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATAGATTGATTT
1 ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTG
47587 ATTTTAAATAATTTATTA
1 ATTTTAAATAATTTATTA
47605 TTGTAGTTGT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.52
Consensus pattern (54 bp):
ATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTG
Found at i:47810 original size:10 final size:10
Alignment explanation
Indices: 47795--47823 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
47785 ACTTTTCTGT
47795 TGCAGATGTC
1 TGCAGATGTC
47805 TGCAGATGTC
1 TGCAGATGTC
47815 TGCAGATGT
1 TGCAGATGT
47824 GGTCCGCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (10 bp):
TGCAGATGTC
Found at i:50980 original size:21 final size:21
Alignment explanation
Indices: 50956--51001 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
50946 AATTTACGCA
50956 TTTAGTA-TCTAAA-TTATTAAT
1 TTTAGTACT-TAAACTT-TTAAT
50977 TTTAGTACTTAAACTTTTAAT
1 TTTAGTACTTAAACTTTTAAT
50998 TTTA
1 TTTA
51002 TGTTGATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTAGTACTTAAACTTTTAAT
Found at i:51091 original size:21 final size:22
Alignment explanation
Indices: 51060--51104 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
51050 AAAAATTCGG
*
51060 ATTCGGATCCGGATATTCGGAT
1 ATTCGGATCCGAATATTCGGAT
*
51082 ATTC-GATCCGAATTTTCGGAT
1 ATTCGGATCCGAATATTCGGAT
51103 AT
1 AT
51105 CCGAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (22 bp):
ATTCGGATCCGAATATTCGGAT
Found at i:51108 original size:16 final size:17
Alignment explanation
Indices: 51087--51119 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
51077 CGGATATTCG
51087 ATCCGAA-TTTTCGGAT
1 ATCCGAATTTTTCGGAT
51103 ATCCGAATTTTTCGGAT
1 ATCCGAATTTTTCGGAT
51120 CGGATACGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (17 bp):
ATCCGAATTTTTCGGAT
Found at i:52521 original size:19 final size:18
Alignment explanation
Indices: 52473--52560 Score: 83
Period size: 19 Copynumber: 4.8 Consensus size: 18
52463 AGGGTGTCAA
*
52473 AGTGCATCCATGCACCCCG
1 AGTGCATCCATGCA-CCTG
*
52492 TAGTCCATCCATGCACCTG
1 -AGTGCATCCATGCACCTG
52511 CAGTGCATCCATGCA-CT-
1 -AGTGCATCCATGCACCTG
* *
52528 -GTGCATCGATGCAACTTG
1 AGTGCATCCATGC-ACCTG
52546 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
52561 TCCATTTCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
15 11 0.19
16 1 0.02
17 1 0.02
18 4 0.07
19 27 0.47
20 13 0.23
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (18 bp):
AGTGCATCCATGCACCTG
Found at i:54227 original size:2 final size:2
Alignment explanation
Indices: 54220--54244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54210 TGTTGAACTT
54220 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
54245 CATCCCTTCA
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:54438 original size:29 final size:29
Alignment explanation
Indices: 54383--54441 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
54373 AATTCATTAT
* * * *
54383 TCTTTTATTCAACAGTGTTTTACCGTTCA
1 TCTTTTACTCAACAATATTTAACCGTTCA
*
54412 TCTTTTACTCAACAATATTTAATCGTTCA
1 TCTTTTACTCAACAATATTTAACCGTTCA
54441 T
1 T
54442 TTAACTGGCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (29 bp):
TCTTTTACTCAACAATATTTAACCGTTCA
Found at i:54619 original size:68 final size:68
Alignment explanation
Indices: 54510--54677 Score: 230
Period size: 68 Copynumber: 2.5 Consensus size: 68
54500 ACCCAACGGT
* * * * *
54510 ACTTAACCGTTCATCTAACTTGCATAATTGACACCTTTCTGTCAAATACACAGCTAGGCCTCAAA
1 ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATACACAGCTAGGCCTCAAA
*
54575 GGC
66 GAC
* * * *
54578 ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCATATGCACAGTTAGGCCTTAAA
1 ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATACACAGCTAGGCCTCAAA
54643 GAC
66 GAC
*
54646 ACTTAGCCTTTCATCTAACTGGCAT-AATGACA
1 ACTTAGCCTTTCATCTAACTAGCATAAATGACA
54678 TAAATGACAC
Statistics
Matches: 89, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 7 0.08
68 82 0.92
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.30
Consensus pattern (68 bp):
ACTTAGCCTTTCATCTAACTAGCATAAATGACACATTTCTGTCAAATACACAGCTAGGCCTCAAA
GAC
Found at i:54876 original size:225 final size:225
Alignment explanation
Indices: 54483--54942 Score: 713
Period size: 225 Copynumber: 2.1 Consensus size: 225
54473 AATGCACCGC
*
54483 TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTTGCATAATTGACACCTTT
1 TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
* * *
54548 CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAAATGACACA
66 CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTAGAAAAAATGACACA
54613 TTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGACA
131 TTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGACA
54678 TAAATGACACATTTCTTTCATCTGCACAGT
196 TAAATGACACATTTCTTTCATCTGCACAGT
* *
54708 TAGGCCATTATTGTTTTACTCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
1 TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
* * * *
54773 CTGTCAAATGCACAGCTAGGCTTCAAAGGCATTTAATCTTTCATCTAA-TAGGAAAAAATGACAC
66 CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTA-GAAAAAATGACAC
* *
54837 CTTTCTGTCATATGCACAGTTAGGCCTTAAAGGCACTTAGCCTTTCATCTAACTGGCAT-A--A-
130 ATTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGAC
* *
54898 AT--A--ACACATTTCTGTCATATGCACAGT
195 ATAAATGACACATTTCTTTCATCTGCACAGT
*
54925 TAGTCCATTATTCTTTTA
1 TAGGCCATTATTCTTTTA
54943 TTTTGAAATA
Statistics
Matches: 218, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
217 38 0.17
219 1 0.00
221 2 0.01
222 1 0.00
224 3 0.01
225 173 0.79
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (225 bp):
TAGGCCATTATTCTTTTACCCAACGGTACTTAACCGTTCATCTAACTGGCATAATTGACACCTTT
CTGTCAAATACACAGCTAGGCCTCAAAGGCACTTAACCTTTCATCTAACTAGAAAAAATGACACA
TTTCTGTCATATGCACAGTTAGGCCTTAAAGACACTTAGCCTTTCATCTAACTGGCATAATGACA
TAAATGACACATTTCTTTCATCTGCACAGT
Found at i:54924 original size:68 final size:68
Alignment explanation
Indices: 54735--54927 Score: 255
Period size: 68 Copynumber: 2.8 Consensus size: 68
54725 ACTCAACGGT
* * * *
54735 ACTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTTCAAA
1 ACTTAACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCTTCAAA
54800 GGC
66 GGC
* * * *
54803 ATTTAATCTTTCATCTAA-TAGGAAAAAATGACACCTTTCTGTCATATGCACAGTTAGGCCTT-A
1 ACTTAACCTTTCATCTAACT-GGCATAAATGACACCTTTCTGTCATATGCACAGTTAGG-CTTCA
54866 AAGGC
64 AAGGC
* * *
54871 ACTTAGCCTTTCATCTAACTGGCATAAATAACACATTTCTGTCATATGCACAGTTAG
1 ACTTAACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAG
54928 TCCATTATTC
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
67 1 0.01
68 102 0.95
69 4 0.04
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (68 bp):
ACTTAACCTTTCATCTAACTGGCATAAATGACACCTTTCTGTCATATGCACAGTTAGGCTTCAAA
GGC
Found at i:55280 original size:59 final size:59
Alignment explanation
Indices: 55216--55377 Score: 243
Period size: 59 Copynumber: 2.7 Consensus size: 59
55206 TTCCCCTATG
* * * *
55216 GAAATTCATACATTTAGTATGAATCTCTTATCATTTTAGCACACAAGGTGCCCAATACA
1 GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCAATACA
* * *
55275 GAAATTCATACACTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCTATACG
1 GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCAATACA
* *
55334 GTAATTCATACATTGAGTATGAATTTCCTAACATTTTAGCACAC
1 GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACAC
55378 TTAGTGCCAT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 93 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (59 bp):
GAAATTCATACATTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCAATACA
Found at i:55828 original size:94 final size:95
Alignment explanation
Indices: 55666--55885 Score: 257
Period size: 94 Copynumber: 2.3 Consensus size: 95
55656 TCCAGTTCAA
* * * * * * * *
55666 TAGTATCGATACTAC-TACCCTGGTACCGATACTTCTATACTATGGTATCGATACTCCTTTATGG
1 TAGTATCGATAC-CCTTACCATGGTATCGATACTTCTATACTATGATACCGATACCCCCTTACGG
* *
55730 TATCGATATCAATTTTAGGTTTGAAGTTGCC
65 TATCGATATCAATTTTAGATTCGAAGTTGCC
* * *
55761 TAGTATTGATA-CCTTATCATGGTATCGATACTATC-ATACTATGATACCGATACCCCCTTCCGG
1 TAGTATCGATACCCTTACCATGGTATCGATACT-TCTATACTATGATACCGATACCCCCTTACGG
* *
55824 TATCGATATCAATTTTAGATTCGATGTTGCT
65 TATCGATATCAATTTTAGATTCGAAGTTGCC
*
55855 TGGTATCGATACCCTTACCATGGTATCGATA
1 TAGTATCGATACCCTTACCATGGTATCGATA
55886 TTACCTCGTT
Statistics
Matches: 104, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
93 1 0.01
94 73 0.70
95 30 0.29
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (95 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTTCTATACTATGATACCGATACCCCCTTACGGT
ATCGATATCAATTTTAGATTCGAAGTTGCC
Found at i:59650 original size:2 final size:2
Alignment explanation
Indices: 59587--59637 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
59577 TGTTGAACAT
59587 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59629 TA TA TA TA T
1 TA TA TA TA T
59638 CATCCCTATA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59888 original size:110 final size:110
Alignment explanation
Indices: 59718--59917 Score: 256
Period size: 110 Copynumber: 1.8 Consensus size: 110
59708 GGTATTTAGC
* * * * * * **
59718 CTTTCATCTAACTTGCATATTTGACACTTTTCTGTCAAATGTATAGCTAATTCATTATTCTTTTA
1 CTTTCATCTAACTGGCATAATTAACACTTTTCTATCAAATGCACAGCTAAGCCATTATTCTTTTA
* ** *
59783 TTCAACAGTGTTTTACCGTTCATCTTTTACTCAACAATATTTAAT
66 CTCAACAGTACTTAACCGTTCATCTTTTACTCAACAATATTTAAT
* * *
59828 CTTTCATTTAACTGGCATAATTAACACTTTTCTATCAAATGCACCGCTAGGCCATTATTCTTTTA
1 CTTTCATCTAACTGGCATAATTAACACTTTTCTATCAAATGCACAGCTAAGCCATTATTCTTTTA
*
59893 CTCAACGGTACTTAACCGTTCATCT
66 CTCAACAGTACTTAACCGTTCATCT
59918 AATTGGCATA
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
110 74 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (110 bp):
CTTTCATCTAACTGGCATAATTAACACTTTTCTATCAAATGCACAGCTAAGCCATTATTCTTTTA
CTCAACAGTACTTAACCGTTCATCTTTTACTCAACAATATTTAAT
Found at i:59941 original size:81 final size:81
Alignment explanation
Indices: 59805--59961 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
59795 TTACCGTTCA
* * * * *
59805 TCTTTTACTCAACAATATTTAATCTTTCATTTAACTGGCATAATTAACACTTTTCTATCAAATGC
1 TCTTTTACTCAACAATACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGC
*
59870 ACCGCTAGGCCATTAT
66 ACAGCTAGGCCATTAT
** * * *
59886 TCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTTTCAAATGC
1 TCTTTTACTCAACAATACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGC
59951 ACAGCTAGGCC
66 ACAGCTAGGCC
59962 TCAAAGGCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACAATACTTAACCGTTCATCTAACTGGCATAATTAACACCTTTCTATCAAATGC
ACAGCTAGGCCATTAT
Found at i:60002 original size:68 final size:68
Alignment explanation
Indices: 59893--60029 Score: 166
Period size: 68 Copynumber: 2.0 Consensus size: 68
59883 TATTCTTTTA
* * * * * *
59893 CTCAACGGTACTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTTTCAAATGCACAGCTA
1 CTCAAAGGCACTTAACCGTTCATCGAACTGGCATAAATGACACATTTCTTTCAAATGCACAGCTA
59958 GGC
66 GGC
* * * * * *
59961 CTCAAAGGCACTTAGCCTTTCATCGAACTGGCATAAATGACACATTTTTTTCATATGCATAGTTA
1 CTCAAAGGCACTTAACCGTTCATCGAACTGGCATAAATGACACATTTCTTTCAAATGCACAGCTA
60026 GGC
66 GGC
60029 C
1 C
60030 ATTATTCTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 57 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAACCGTTCATCGAACTGGCATAAATGACACATTTCTTTCAAATGCACAGCTA
GGC
Found at i:60082 original size:149 final size:144
Alignment explanation
Indices: 59866--60173 Score: 420
Period size: 144 Copynumber: 2.1 Consensus size: 144
59856 TTTCTATCAA
* *
59866 ATGCACCGCTAGGCCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATT
1 ATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATT
* * **
59931 GACACCTTTCTTTCAAATGCACAGCTAGGCCTCAAAGGCACTTAGCCTTTCATCGAACTGGCATA
66 GACACCTTTC--T---ATGCACAGCAAGGCCTCAAAGGCACTCAGCCTTTCATCGAACCAGCATA
***
59996 AATGACACATTTTTTTCAT
126 AATGACACATTTCCGTCAT
* *
60015 ATGCATAGTTAGGCCATTATTCTTTTACTCAACGGTACTTAATCGTTCATCTAACTT-GCATAAT
1 ATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAA-TTGGCATAAT
* * *
60079 TGACACCTTTCTGTGCATAGCAAGGCCTCAAAGGCACTCAGCCTTTCATCTAACCAGCATAAATG
65 TGACACCTTTCTATGCACAGCAAGGCCTCAAAGGCACTCAGCCTTTCATCGAACCAGCATAAATG
*
60144 ACACCTTTCCGTCAT
130 ACACATTTCCGTCAT
60159 ATGCACAGTTAGGCC
1 ATGCACAGTTAGGCC
60174 TCAAAGACAC
Statistics
Matches: 142, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
144 71 0.50
147 1 0.01
149 68 0.48
150 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (144 bp):
ATGCACAGTTAGGCCATTATTCTTTTACTCAACGGTACTTAACCGTTCATCTAATTGGCATAATT
GACACCTTTCTATGCACAGCAAGGCCTCAAAGGCACTCAGCCTTTCATCGAACCAGCATAAATGA
CACATTTCCGTCAT
Found at i:60146 original size:63 final size:65
Alignment explanation
Indices: 60060--60230 Score: 179
Period size: 68 Copynumber: 2.6 Consensus size: 65
60050 TACTTAATCG
* * * *
60060 TTCATCTAACTTGCATAATTGACACCTTTCTGTGCATA-G-CA-AGGCCTCAAAGGCACTCAGCC
1 TTCATCTAACTAGCATAAATGACACCTTTCCGT-CATATGACATAGGCCTCAAAGACACTCAGCC
60122 T
65 T
* *
60123 TTCATCTAACCAGCATAAATGACACCTTTCCGTCATATGCACAGTTAGGCCTCAAAGACACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCCGTCATATG-ACA--TAGGCCTCAAAGACACTCAG
60188 CCT
63 CCT
* * * *
60191 TTCATCTAGCTGGTATAAATGACACC-GTCCTGTCATATGA
1 TTCATCTAACTAGCATAAATGACACCTTTCC-GTCATATGA
60231 ACAATTAGGC
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
62 4 0.04
63 30 0.33
65 2 0.02
67 4 0.04
68 50 0.56
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (65 bp):
TTCATCTAACTAGCATAAATGACACCTTTCCGTCATATGACATAGGCCTCAAAGACACTCAGCCT
Found at i:60195 original size:68 final size:68
Alignment explanation
Indices: 60101--60241 Score: 185
Period size: 68 Copynumber: 2.1 Consensus size: 68
60091 GTGCATAGCA
* * *
60101 AGGCCTCAAAGGCACTCAGCCTTTCATCTAACCAGCATAAATGACACCTTTCC-GTCATATGCAC
1 AGGCCTCAAAGACACTCAGCCTTTCATCTAACCAGCATAAATGACACC-GTCCTGTCATATGAAC
*
60165 AGTT
65 AATT
* * ** *
60169 AGGCCTCAAAGACACTTAGCCTTTCATCTAGCTGGTATAAATGACACCGTCCTGTCATATGAACA
1 AGGCCTCAAAGACACTCAGCCTTTCATCTAACCAGCATAAATGACACCGTCCTGTCATATGAACA
60234 ATT
66 ATT
60237 AGGCC
1 AGGCC
60242 ATTATTCTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
67 3 0.05
68 60 0.95
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (68 bp):
AGGCCTCAAAGACACTCAGCCTTTCATCTAACCAGCATAAATGACACCGTCCTGTCATATGAACA
ATT
Found at i:60597 original size:59 final size:60
Alignment explanation
Indices: 60528--60688 Score: 202
Period size: 59 Copynumber: 2.7 Consensus size: 60
60518 TCCCCTATGG
* * *
60528 AAATTCATACATTTAGTATGAATCTCTTATCATTTTAGCACACAAGGTGCCCAATA-AAT
1 AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACAAT
* * * * **
60587 AAATTTATACACTTAGTATGAATTTCCTAACATTTTAGCACACAAAGTGCCCTATACGGT
1 AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACAAT
*
60647 -AATTCATACATTGAGTATGAATTTCTTAACATATTT-GCACAC
1 AAATTCATACATTTAGTATGAATTTCTTAACAT-TTTAGCACAC
60689 TTAGTGCCAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 83 0.95
60 4 0.05
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (60 bp):
AAATTCATACATTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATACAAT
Found at i:61139 original size:94 final size:95
Alignment explanation
Indices: 60977--61199 Score: 252
Period size: 94 Copynumber: 2.4 Consensus size: 95
60967 TCCAGTTCAA
* * * * * * * * * *
60977 TAGTATCGATACTAC-TACCCTGGTACCGATACTTTTATACTATGGTATCGATACTCCTTTATGG
1 TAGTATCGATAC-CCTTACCATGGTATCGATACTATCATACTATGATACCGATACCCCCTTACGG
* * *
61041 TATCGATCTCAATTTTAGGTTTGAAGTTGCC
65 TATCGATATCAATTTTAGATTCGAAGTTGCC
* * *
61072 TAGTATTGATA-CCTTATCATGGTATCGATACTATCATACTATGATACCGATACCCCCTTCCGGT
1 TAGTATCGATACCCTTACCATGGTATCGATACTATCATACTATGATACCGATACCCCCTTACGGT
* *
61136 ATCGATATCAATTTTAGATTCGATGTTGCT
66 ATCGATATCAATTTTAGATTCGAAGTTGCC
*
61166 TGGTATCGATACCCTTACCATGGTATCGATACTA
1 TAGTATCGATACCCTTACCATGGTATCGATACTA
61200 CCTCGTTGGA
Statistics
Matches: 105, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
93 1 0.01
94 73 0.70
95 31 0.30
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (95 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTATCATACTATGATACCGATACCCCCTTACGGT
ATCGATATCAATTTTAGATTCGAAGTTGCC
Found at i:61295 original size:20 final size:19
Alignment explanation
Indices: 61266--61308 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
61256 CCATTTTAGC
61266 CTATAGTATCAGTACTGTT
1 CTATAGTATCAGTACTGTT
*
61285 CTATCAGTATCGGTACTGTT
1 CTAT-AGTATCAGTACTGTT
61305 CTAT
1 CTAT
61309 TAGAATCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (19 bp):
CTATAGTATCAGTACTGTT
Found at i:61316 original size:20 final size:20
Alignment explanation
Indices: 61277--61316 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
61267 TATAGTATCA
*
61277 GTACTGTTCTATCAGTATCG
1 GTACTGTTCTATCAGAATCG
*
61297 GTACTGTTCTATTAGAATCG
1 GTACTGTTCTATCAGAATCG
61317 ATACCCTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (20 bp):
GTACTGTTCTATCAGAATCG
Found at i:61797 original size:3 final size:3
Alignment explanation
Indices: 61789--61853 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
61779 CTACTCACGT
61789 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
61837 GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GA
61854 GAAATGCTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:62538 original size:32 final size:31
Alignment explanation
Indices: 62480--62539 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
62470 TCGGGGTGTT
62480 TTTCTTGTTATTGTTTTCAATCTTAATTACA
1 TTTCTTGTTATTGTTTTCAATCTTAATTACA
* * *
62511 TTTCTTTTTATTTTATTTCAATTTTAATT
1 TTTCTTGTTATTGT-TTTCAATCTTAATT
62540 CTTTATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.22, C:0.10, G:0.03, T:0.65
Consensus pattern (31 bp):
TTTCTTGTTATTGTTTTCAATCTTAATTACA
Done.