Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004163.1 Hibiscus syriacus cultivar Beakdansim tig00009104_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: 65719
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:8500 original size:2 final size:2
Alignment explanation
Indices: 8493--8542 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
8483 TTCCTTAATG
8493 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
8535 AT AT AT AT
1 AT AT AT AT
8543 TTGACTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29018 original size:3 final size:3
Alignment explanation
Indices: 29010--29068 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
29000 GTATTTGTAT
* * **
29010 TAA TAA TAA TAA TAA TAC CAA TAA TAA T-A TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29057 TAA TAA -AA TAA T
1 TAA TAA TAA TAA T
29069 GGAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:29047 original size:26 final size:26
Alignment explanation
Indices: 29018--29067 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
29008 ATTAATAATA
* *
29018 ATAATAATACCAATAATAATATAACG
1 ATAATAATAACAATAATAAAATAACG
*
29044 ATAATAATAATAATAATAAAATAA
1 ATAATAATAACAATAATAAAATAA
29068 TGGAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAATAATAACAATAATAAAATAACG
Found at i:29453 original size:40 final size:41
Alignment explanation
Indices: 29357--29463 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 41
29347 CAAGGTGATA
29357 ACACGGTTCCTACGTGATGAGGACTACTGGTTATCTAAGGGTG
1 ACACGGTTCCTACGTGATGAGGACTACTGG-T-TCTAAGGGTG
* * * *
29400 ACACAGCTCCTACGTGATGAGGAGGT-CTGG-TC-GAGGGATG
1 ACACGGTTCCTACGTGATGAGGA-CTACTGGTTCTAAGGG-TG
29440 ACACGGTTCCTACGTGATGAGGAC
1 ACACGGTTCCTACGTGATGAGGAC
29464 GGCTGGCCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 4 0.07
40 25 0.45
43 25 0.45
44 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.33, T:0.23
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGACTACTGGTTCTAAGGGTG
Found at i:29519 original size:51 final size:51
Alignment explanation
Indices: 29443--29570 Score: 256
Period size: 51 Copynumber: 2.5 Consensus size: 51
29433 AGGGATGACA
29443 CGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACT
1 CGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACT
29494 CGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACT
1 CGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACT
29545 CGGTTCCTACGTGATGAGGACGGCTG
1 CGGTTCCTACGTGATGAGGACGGCTG
29571 ATTATCTAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 77 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (51 bp):
CGGTTCCTACGTGATGAGGACGGCTGGCCATCTTTAGGAGTGGTGATAACT
Found at i:29856 original size:31 final size:28
Alignment explanation
Indices: 29764--29859 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 28
29754 GGAGTTATGA
* * *
29764 TTTCAAGAGAAACCGATTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
29792 TTTCAAAAGAAACAGACTCAAAGATTTG
1 TTTCAAAAGAAACAGACTCAAAGATTTG
29820 TTTCAAGAA-AAACA-AGCTCAAAGATAATGTG
1 TTTCAA-AAGAAACAGA-CTCAAAGAT--T-TG
29851 TTTCAAAAG
1 TTTCAAAAG
29860 CAACTGTCTC
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 1 0.02
28 45 0.76
29 2 0.03
30 3 0.05
31 8 0.14
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTG
Found at i:30050 original size:66 final size:63
Alignment explanation
Indices: 29861--30043 Score: 152
Period size: 66 Copynumber: 2.8 Consensus size: 63
29851 TTTCAAAAGC
* ** * *
29861 AACTGTCTCGAAAGAGACAAAATTCGTTTCAAATGAAAC-AACTCAAAAGATGACGTTTAAAGGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATCTC-AAAGATGATGTTTAAAGGG
* * * ** * * * * * *
29925 AATTGTCTCAAGCGAGATAAAATTTGTTTTTAAGGGAAACGTTCTCAAATATCGGTGTTTCATGG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATCTCAAAGAT-GATGTTTAAAGG
29990 G
63 G
29991 AAACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
1 -AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATG
30044 TTTGTTTTGT
Statistics
Matches: 90, Mismatches: 23, Indels: 11
0.73 0.19 0.09
Matches are distributed among these distances:
63 2 0.02
64 16 0.18
65 18 0.20
66 36 0.40
67 18 0.20
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (63 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATGATGTTTAAAGGG
Found at i:30892 original size:37 final size:37
Alignment explanation
Indices: 30846--30961 Score: 104
Period size: 37 Copynumber: 3.3 Consensus size: 37
30836 TTAAAGATTT
30846 TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTG
1 TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTG
* * * *
30883 TTTCCAAAGAAACAGA-C-T--CAAAG----ATTTTTG
1 TTTCAAAAGAAA-ATATCTTAAGAAAGACAAAATTTTG
* *
30913 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTG
1 TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTG
*
30950 TTTCCAAAGAAA
1 TTTCAAAAGAAA
30962 CAGACTCAAA
Statistics
Matches: 59, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
29 1 0.02
30 18 0.31
31 1 0.02
33 3 0.05
34 4 0.07
36 1 0.02
37 29 0.49
38 2 0.03
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (37 bp):
TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTG
Found at i:30912 original size:30 final size:30
Alignment explanation
Indices: 30878--31008 Score: 115
Period size: 30 Copynumber: 4.1 Consensus size: 30
30868 AAAGACAAAA
*
30878 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
**
30908 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAA-A-
1 TTTTGTTTCAAAAG-AA--A-C-----AGACTCAAAGAT
*
30945 TTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGACTCAAAGAT
30975 TTTTGTTTCAAAAGAAACA-ATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAGA-CTCAAAGAT
31005 TTTT
1 TTTT
31009 TTTTTCACAA
Statistics
Matches: 82, Mismatches: 7, Indels: 24
0.73 0.06 0.21
Matches are distributed among these distances:
28 7 0.09
29 2 0.02
30 44 0.54
31 2 0.02
33 2 0.02
34 2 0.02
36 2 0.02
37 13 0.16
38 1 0.01
39 7 0.09
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:30931 original size:67 final size:67
Alignment explanation
Indices: 30846--30991 Score: 274
Period size: 67 Copynumber: 2.2 Consensus size: 67
30836 TTAAAGATTT
30846 TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT
1 TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT
30911 TG
66 TG
* *
30913 TTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT
1 TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT
30978 TG
66 TG
30980 TTTCAAAAGAAA
1 TTTCAAAAGAAA
30992 CAATCTCAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.30
Consensus pattern (67 bp):
TTTCAAAAGAAAATATCTTAAGAAAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT
TG
Found at i:31203 original size:28 final size:28
Alignment explanation
Indices: 31094--31195 Score: 109
Period size: 28 Copynumber: 3.6 Consensus size: 28
31084 GAGACAAAAC
* *
31094 TTTATTTCAAAAGAAATAGACTCAACGAT
1 TTTA-TTCAAAAGAAACAGACTCAAAGAT
*
31123 ATTTGTTTCAAAAGAAACA-ACTCAAAGAT
1 -TTT-ATTCAAAAGAAACAGACTCAAAGAT
*
31152 TTTATTCAAAAGGAACAGACTCAAAGA-
1 TTTATTCAAAAGAAACAGACTCAAAGAT
*
31179 TTTATCTCAAGAGAAAC
1 TTTAT-TCAAAAGAAAC
31196 TGTCTCAAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
27 17 0.27
28 21 0.34
29 9 0.15
30 15 0.24
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (28 bp):
TTTATTCAAAAGAAACAGACTCAAAGAT
Found at i:31524 original size:36 final size:36
Alignment explanation
Indices: 31440--31543 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
31430 GAGAAAATGA
* * *
31440 TGTCTCAAGCGAGACAAAAGTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
31474 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
31510 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
31544 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:31571 original size:36 final size:36
Alignment explanation
Indices: 31441--31559 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
31431 AGAAAATGAT
* * * *
31441 GTCTCAAGCGAGACAAAAGTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
31475 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
31511 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
31546 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
31560 TCAACTTTGT
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
34 19 0.28
35 12 0.17
36 38 0.55
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:31690 original size:105 final size:101
Alignment explanation
Indices: 31511--31743 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
31501 TAGAGAAATT
*
31511 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
31575 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
31613 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
31677 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
31718 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
31744 AAAATTCTCA
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 78 0.68
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:39275 original size:3 final size:3
Alignment explanation
Indices: 39267--39325 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
39257 GTATTTGTAT
* * **
39267 TAA TAA TAA TAA TAA TAC CAA TAA TAA T-A TAA CGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39314 TAA TAA -AA TAA T
1 TAA TAA TAA TAA T
39326 GAAAAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:39304 original size:26 final size:26
Alignment explanation
Indices: 39275--39324 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
39265 ATTAATAATA
* *
39275 ATAATAATACCAATAATAATATAACG
1 ATAATAATAACAATAATAAAATAACG
*
39301 ATAATAATAATAATAATAAAATAA
1 ATAATAATAACAATAATAAAATAA
39325 TGAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAATAATAACAATAATAAAATAACG
Found at i:41699 original size:2 final size:2
Alignment explanation
Indices: 41694--41744 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
41684 AGTATGTACC
41694 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
41736 AT AT AT AT A
1 AT AT AT AT A
41745 CTAGTACTAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:50608 original size:471 final size:472
Alignment explanation
Indices: 49186--50597 Score: 2654
Period size: 471 Copynumber: 3.0 Consensus size: 472
49176 TGCAATAGAC
*
49186 TGTTTGCATCAATGGAAACCAATGCATGTGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
49251 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATG-A-TGCC
66 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
49314 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCC-CACCCAATC-AAAAAATG
131 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
49377 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
196 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
49442 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
261 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
49507 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
326 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
49572 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
391 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
49637 TTTTGCATACATACTTT
456 TTTTGCATACATACTTT
49654 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
*
49719 AAGACAAGATCAAGGTCACGTAGGTTCAACCTCAATGCATTATCAGAATGTGGGGATGAATTGCC
66 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
* * *
49784 ATACCAGACAATATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACTCGATCAAAAAAATG
131 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
*
49849 TTCATGATTTCGAATGGTGTTTTGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
196 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
49914 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
261 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
49979 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
326 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
50044 CTGCTTAATAAGCAAGT-AACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
391 CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
50108 TTTTGCATACATACTTT
456 TTTTGCATACATACTTT
50125 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
1 TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
50190 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
66 AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
50255 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
131 ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
50320 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
196 TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
*
50385 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGGATAT
261 CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
* * ** * *
50450 TGGATTGATGCCTCGGTAAACCACAGAGATTATGGGGGCATAGGTGGCTGATTCCTTGTTTTGGC
326 TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
*
50515 CGTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGATCTTGGAAGTTGTTCATGTAGC
391 C-TGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGC
50580 CTTTTGCATACATACTTT
455 CTTTTGCATACATACTTT
50598 GGATCATCAA
Statistics
Matches: 919, Mismatches: 19, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
468 121 0.13
469 1 0.00
470 49 0.05
471 450 0.49
472 235 0.26
473 63 0.07
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (472 bp):
TGTTTGCATCAATGGAAACCAATGCATGAGATGACAGCCCCAAAATTGTCAAAGTCGATACATTG
AAGACAAGATCAAGGTCACGTAGGTTCAACTTCAATGCATTATCAGAATGTGGGGATGAATTGCC
ATACCAGACAGTATCATCGCCCCTTCCGTGTCCTGTTCGATCATCCACACCCAATCAAAAAAATG
TTCATGATTTCGAATGGTGTTTCGCTGACAAGGAATGTAAGTTTTCTACTGCTCAGACCACTCCT
CGTTTCGGGCAGTAATGCCTTGAAATTTGACTAAGAAACTCTCCCATGTAAAGATTAGTGAATAT
TGGCTTGATGCCTCGGCAAACCACAGAGATTATGGGGGCATAGGTACCCGATTCCTTGTTTTGAC
CTGCTTAATAAGCAAGTAAACAAGAAAATGTTATACCCGAGAACTTGGAAGTTGTTCATGTAGCC
TTTTGCATACATACTTT
Found at i:57576 original size:2 final size:2
Alignment explanation
Indices: 57569--57597 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57559 GTCCCGATGC
57569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57598 TTTTAATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63909 original size:16 final size:16
Alignment explanation
Indices: 63888--63918 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
63878 TCGGGGGGAC
63888 AAAAGTCGGGGAAACA
1 AAAAGTCGGGGAAACA
63904 AAAAGTCGGGGAAAC
1 AAAAGTCGGGGAAAC
63919 GGCTGTCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.32, T:0.06
Consensus pattern (16 bp):
AAAAGTCGGGGAAACA
Found at i:64159 original size:21 final size:20
Alignment explanation
Indices: 64086--64160 Score: 53
Period size: 21 Copynumber: 3.6 Consensus size: 20
64076 CAGTTTCCAG
* **
64086 ATTCGCAACGCGATTATGACT
1 ATTCGCAATGCGATT-TTCCT
*
64107 A-TCGCAATGCGATTTTCCA
1 ATTCGCAATGCGATTTTCCT
***
64126 ATTTCGTGTTGCGATTTTCCCT
1 A-TTCGCAATGCGATTTT-CCT
64148 ATTCGCAATGCGA
1 ATTCGCAATGCGA
64161 ATAAGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 3 0.08
20 12 0.30
21 22 0.55
22 3 0.08
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (20 bp):
ATTCGCAATGCGATTTTCCT
Found at i:64192 original size:20 final size:20
Alignment explanation
Indices: 64169--64303 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
64159 GAATAAGTAA
* *
64169 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
*
64189 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATAATGAC--T
*
64210 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* *
64230 TTCGCAACGCGATAATAACT
1 ATCGCAACGCGATAATGACT
* **
64250 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATGACT
*
64270 ATCGCAACGAGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
64290 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
64304 TTTCAAAGTT
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.04
20 61 0.66
21 26 0.28
22 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:64212 original size:41 final size:41
Alignment explanation
Indices: 64167--64303 Score: 186
Period size: 41 Copynumber: 3.4 Consensus size: 41
64157 GCGAATAAGT
*
64167 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
*
64208 AAATCGCAACGCGATACTGACTTTCGCAACGCGATAATA-A
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
*** * *
64248 CTTTCGCAACGCGATTCTGACTATCGCAACGAGATAATACA
1 AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
* *
64289 TAATCGCAATGCGAT
1 AAATCGCAACGCGAT
64304 TTTCAAAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 34 0.41
41 49 0.59
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.22
Consensus pattern (41 bp):
AAATCGCAACGCGATACTGACTATCGCAACGCGATAATACA
Found at i:64453 original size:12 final size:12
Alignment explanation
Indices: 64434--64467 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
64424 CTCTCCGACG
64434 ACATCCGTTCCT
1 ACATCCGTTCCT
*
64446 ATATCCGTTCCT
1 ACATCCGTTCCT
64458 ACATCC-TTCC
1 ACATCCGTTCC
64468 CCATTCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:65041 original size:23 final size:23
Alignment explanation
Indices: 65014--65066 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
65004 AGTATTCGAA
*
65014 ATTTGATCTTGGTCAATAC-CGG
1 ATTTGATATTGGTCAATACTCGG
65036 ACTTTGATATTGGTCAATACTCGG
1 A-TTTGATATTGGTCAATACTCGG
65060 ATTTGAT
1 ATTTGAT
65067 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 1 0.04
23 23 0.82
24 4 0.14
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (23 bp):
ATTTGATATTGGTCAATACTCGG
Done.