Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006383.1 Hibiscus syriacus cultivar Beakdansim tig00015372_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: 102756
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:3900 original size:17 final size:17
Alignment explanation
Indices: 3871--3912 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
3861 CTTTTAAGGG
*
3871 GCATGGACTTATATGTA
1 GCATGGACATATATGTA
*
3888 GCTTGGACATATATGTA
1 GCATGGACATATATGTA
3905 GCATGGAC
1 GCATGGAC
3913 GAACCAGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (17 bp):
GCATGGACATATATGTA
Found at i:18128 original size:19 final size:19
Alignment explanation
Indices: 18104--18154 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
18094 TATTGAAGGT
18104 ATGCATCGATGCACTACCC
1 ATGCATCGATGCACTACCC
18123 ATGCATCGATGCACTACCC
1 ATGCATCGATGCACTACCC
*
18142 ATGCATCGGTGCA
1 ATGCATCGATGCA
18155 TAAATCCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (19 bp):
ATGCATCGATGCACTACCC
Found at i:18231 original size:64 final size:64
Alignment explanation
Indices: 18124--18285 Score: 190
Period size: 64 Copynumber: 2.5 Consensus size: 64
18114 GCACTACCCA
* * *
18124 TGCATCGATGCACTACC-CATGCATCGGTGCATAAATCCTATTCGATGTT-TGT-ATTTTAA-GC
1 TGCATCGATGCACT-CCTTATGCATCGATGCATAAATCCTATTCGATGTTAT-TAATTTAAATG-
18185 AGG
63 A-G
*
18188 TGCATCGATGCACTCCTTATGCATCGATGCATAAATGGC-ATTCGATGTTCAATTAATTTAAATG
1 TGCATCGATGCACTCCTTATGCATCGATGCATAAAT-CCTATTCGATGTT--ATTAATTTAAATG
18252 AG
63 AG
18254 TGCATCGATGCACTCCTTATGCATCGATGCAT
1 TGCATCGATGCACTCCTTATGCATCGATGCAT
18286 CTTCAACAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
63 2 0.02
64 41 0.47
65 1 0.01
66 34 0.39
67 8 0.09
68 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (64 bp):
TGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTATTAATTTAAATGAG
Found at i:28805 original size:18 final size:18
Alignment explanation
Indices: 28782--28821 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
28772 ATTCAATGGG
28782 ATTTTAAACCGAGGCTTC
1 ATTTTAAACCGAGGCTTC
*
28800 ATTTTAAACCGAGGCTTT
1 ATTTTAAACCGAGGCTTC
28818 ATTT
1 ATTT
28822 GAAAACAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (18 bp):
ATTTTAAACCGAGGCTTC
Found at i:43020 original size:12 final size:12
Alignment explanation
Indices: 43003--43030 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42993 CAAATATGTA
43003 CAATTAATAGTG
1 CAATTAATAGTG
43015 CAATTAATAGTG
1 CAATTAATAGTG
43027 CAAT
1 CAAT
43031 CTGGGATCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (12 bp):
CAATTAATAGTG
Found at i:47937 original size:3 final size:3
Alignment explanation
Indices: 47929--47954 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47919 CTCCTTTTAT
47929 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
47955 TAAAATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:63793 original size:24 final size:24
Alignment explanation
Indices: 63761--63817 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
63751 GTATTGTAGA
*
63761 ATTCTCATGGGGTGGGAATCCTAC
1 ATTCTCATGGGGTGGGAATCATAC
63785 ATTCTCATGGGGTGGGAATCATAC
1 ATTCTCATGGGGTGGGAATCATAC
63809 ATTCTCATG
1 ATTCTCATG
63818 TTTGATTGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (24 bp):
ATTCTCATGGGGTGGGAATCATAC
Found at i:64217 original size:37 final size:37
Alignment explanation
Indices: 64141--64217 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
64131 TTTTTATATT
*
64141 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
64178 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
64215 TTT
1 TTT
64218 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:64384 original size:20 final size:20
Alignment explanation
Indices: 64359--64413 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
64349 AGTAATCCTA
64359 TTCACTGATAATCTTTTATT
1 TTCACTGATAATCTTTTATT
64379 TTCACTGATAATCTTTTATT
1 TTCACTGATAATCTTTTATT
* *
64399 CTCACTGGTAATCTT
1 TTCACTGATAATCTT
64414 ACATTCCGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (20 bp):
TTCACTGATAATCTTTTATT
Found at i:65969 original size:2 final size:2
Alignment explanation
Indices: 65962--65986 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65952 ACCGCTTTAT
65962 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
65987 TACATATGAA
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:66274 original size:18 final size:18
Alignment explanation
Indices: 66235--66279 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
66225 ACCCACCAGA
*
66235 TGAACTGGATGAAGAGGC
1 TGAACTTGATGAAGAGGC
66253 TGAACTTGATGAAGA-GC
1 TGAACTTGATGAAGAGGC
66270 TTGAACTTGA
1 -TGAACTTGA
66280 ACCCCACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.33, C:0.11, G:0.31, T:0.24
Consensus pattern (18 bp):
TGAACTTGATGAAGAGGC
Found at i:67233 original size:36 final size:36
Alignment explanation
Indices: 67193--67267 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
67183 AAAATTGATG
* *
67193 TTATTTATAATAAGTCACATCACTTAGTGAATGGAC
1 TTATTAATAATAAGTCACATCACTTAGTGAATAGAC
* * *
67229 TTATTAATAATACGTCATATCACTTGGTGAATAGAC
1 TTATTAATAATAAGTCACATCACTTAGTGAATAGAC
67265 TTA
1 TTA
67268 ATTTTTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.37
Consensus pattern (36 bp):
TTATTAATAATAAGTCACATCACTTAGTGAATAGAC
Found at i:68168 original size:3 final size:3
Alignment explanation
Indices: 68162--68224 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
68152 CGGGTCTTCT
* **
68162 TTA TTA TTA TTT TTA TCG TTA TT- TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
68207 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
68225 ATTTACAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:68366 original size:26 final size:26
Alignment explanation
Indices: 68312--68383 Score: 128
Period size: 26 Copynumber: 2.8 Consensus size: 26
68302 AACCCATCAT
68312 ATTAGGGTTTCAAACCCT-AAAACAG
1 ATTAGGGTTTCAAACCCTAAAAACAG
*
68337 ATTAGGGTTTCAAACCCTAAAAATAG
1 ATTAGGGTTTCAAACCCTAAAAACAG
68363 ATTAGGGTTTCAAACCCTAAA
1 ATTAGGGTTTCAAACCCTAAA
68384 TGTTCCAGCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 18 0.40
26 27 0.60
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (26 bp):
ATTAGGGTTTCAAACCCTAAAAACAG
Found at i:75664 original size:4 final size:4
Alignment explanation
Indices: 75655--75722 Score: 63
Period size: 4 Copynumber: 17.2 Consensus size: 4
75645 TCACAAATCA
* *
75655 ACAT ACAT ACAT -CAAT ACAA ACAT ATAT -CAAT ACAT ACAT ACAT -CAAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT
75703 ACAT ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
75723 AAATTTGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 5 0.09
4 45 0.85
5 3 0.06
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:75684 original size:16 final size:16
Alignment explanation
Indices: 75655--75722 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
75645 TCACAAATCA
75655 ACATACATACATCAAT
1 ACATACATACATCAAT
* *
75671 ACAAACATATATCAAT
1 ACATACATACATCAAT
75687 ACATACATACATCAAT
1 ACATACATACATCAAT
75703 ACATACATACAT-AAT
1 ACATACATACATCAAT
75718 ACATA
1 ACATA
75723 AAATTTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
15 8 0.17
16 40 0.83
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (16 bp):
ACATACATACATCAAT
Found at i:76048 original size:35 final size:35
Alignment explanation
Indices: 76009--76112 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 35
75999 TGAGGGTGTT
* **
76009 TTTCTTGAAACAAATTTTGTCTCGCTTGAGACAGC
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
* *
76044 TTTCTAAAAACAAATTTTGTCTCGTTTGAGACAAA
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
* *
76079 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 TT-TCTTAAAACAAATTTTGTCTCGCTTGAGACA
76113 TTTTTCCTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 32 0.54
36 27 0.46
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAAA
Found at i:76198 original size:105 final size:105
Alignment explanation
Indices: 76079--76275 Score: 290
Period size: 105 Copynumber: 1.9 Consensus size: 105
76069 TTGAGACAAA
* *
76079 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACC-AATTTTGAATTT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGAT-CCAAATTTCGAATTT
76143 GATTCAC-TTAAAACAAAATTAATCTCACCTTAGATTGTTGT
65 GATTCACATT-AAACAAAATTAATCTCACCTTAGATTGTTGT
* * *
76184 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
* * *
76249 TTTCACATTAAACAAAGTTGATCTCAC
66 ATTCACATTAAACAAAATTAATCTCAC
76276 TTGAGATCGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 2 0.02
105 78 0.95
106 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (105 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
ATTCACATTAAACAAAATTAATCTCACCTTAGATTGTTGT
Found at i:76660 original size:28 final size:28
Alignment explanation
Indices: 76597--76698 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 28
76587 TCTGGAGACA
* * *
76597 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGAAAAAAATCTTTGAGTCT
*
76625 GTTCCTTTTGAATAAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAAATCTTTGAGTCT
76653 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTGAAA-AAA-ATCTTTGAGTCT
*
76683 ATTTCTTTTGAAAAAA
1 GTTTCTTTTGAAAAAA
76699 TTTATCTCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 1 0.02
28 24 0.38
29 26 0.41
30 13 0.20
ACGTcount: A:0.28, C:0.12, G:0.14, T:0.46
Consensus pattern (28 bp):
GTTTCTTTTGAAAAAAATCTTTGAGTCT
Found at i:76753 original size:60 final size:63
Alignment explanation
Indices: 76654--76791 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
76644 CTTTGAGTTG
*
76654 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTG-AA-AAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTT-TCTCTCTAAAGACA
76716 A
63 A
* * **
76717 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
*
76779 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
76792 TACCCACCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
60 18 0.28
61 8 0.12
62 29 0.45
63 9 0.14
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
Found at i:76931 original size:15 final size:15
Alignment explanation
Indices: 76908--76951 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
76898 TTTTGAGTCG
*
76908 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
76923 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
76938 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
76952 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:77430 original size:40 final size:40
Alignment explanation
Indices: 77372--77562 Score: 143
Period size: 40 Copynumber: 4.5 Consensus size: 40
77362 CCAGTCGTCC
* * *
77372 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
* ** * *
77412 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTCATCCCCAG---ACCAGATC-TCT
* * * * * *
77455 TCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTCATC-CC--CAGA---CCAGATCTCT
77501 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCT
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGACCAGATCTCT
77541 TCATCACGTATGAGCCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
77563 ACCATAGATA
Statistics
Matches: 117, Mismatches: 22, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
40 54 0.46
42 1 0.01
43 29 0.25
44 1 0.01
46 29 0.25
47 3 0.03
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (40 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGACCAGATCTCT
Found at i:77519 original size:46 final size:43
Alignment explanation
Indices: 77401--77603 Score: 175
Period size: 40 Copynumber: 4.7 Consensus size: 43
77391 TCATCCCCAG
*
77401 ACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
* * * * * * * *
77444 ACCAG-CCGTCCTCATCACATAGGAACCGTGTTATCACCTTTAGATG
1 ACCAGAAC-TCTTCATCACGTATGAGCCGTGTCA--ACC-ATAGATA
* * **
77490 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CCG---
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTCA-ACCATAGATA
*
77530 ACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
* *
77573 ACCA-AACTCTTCATCACGTACGAGCAGTGTC
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTC
77604 GTCCCCAACA
Statistics
Matches: 124, Mismatches: 27, Indels: 19
0.73 0.16 0.11
Matches are distributed among these distances:
39 2 0.02
40 32 0.26
42 25 0.20
43 30 0.24
45 5 0.04
46 29 0.23
47 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (43 bp):
ACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
Found at i:77760 original size:3 final size:3
Alignment explanation
Indices: 77754--77819 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
77744 CGGGTCTTCT
* **
77754 TTA TTA TTA TTT TTA TCG TTA TT- TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
77799 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
77820 ATTTACAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:77936 original size:25 final size:25
Alignment explanation
Indices: 77907--77977 Score: 142
Period size: 25 Copynumber: 2.8 Consensus size: 25
77897 AACCCATCAT
77907 ATTAGGGTTTCAAACCCTAAAACAG
1 ATTAGGGTTTCAAACCCTAAAACAG
77932 ATTAGGGTTTCAAACCCTAAAACAG
1 ATTAGGGTTTCAAACCCTAAAACAG
77957 ATTAGGGTTTCAAACCCTAAA
1 ATTAGGGTTTCAAACCCTAAA
77978 TGTTCCAGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.25
Consensus pattern (25 bp):
ATTAGGGTTTCAAACCCTAAAACAG
Found at i:90132 original size:63 final size:63
Alignment explanation
Indices: 90065--90341 Score: 299
Period size: 63 Copynumber: 4.4 Consensus size: 63
90055 TACTTCATCT
* * * * *
90065 ATGAAGGAGATGAATTTGCAGTGCCACCGGA-ATCCGATTACGACTTAGTCCTTGACTACTATC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGAT-GGATTACGACTTAGGCCTTGACTACAACC
* * * * *
90128 ATGAAGGAGATGAATTTGCGGTGCCACTGGAGGTGGATTACGACTCAGGCCTTGACTACAACC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGATGGATTACGACTTAGGCCTTGACTACAACC
* * *
90191 ATGAAGAAGATGAATTTGCGGTGCCACCGGAGGTGGATTACAACTTAGGCCTTGACTACAACC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGATGGATTACGACTTAGGCCTTGACTACAACC
* * * * * * *
90254 ATGAAGAAGATGAATTTGCACTCCCACCAGA-ATCTGATTACGACTTAAGACTTTGAATACAACC
1 ATGAAGAAGATGAATTTGCAGTGCCACCGGAGAT-GGATTACGACTT-AGGCCTTGACTACAACC
*
90318 ATGAA-ATATTATGAATTTGCAGTG
1 ATGAAGA-A-GATGAATTTGCAGTG
90342 GCGGATATTC
Statistics
Matches: 184, Mismatches: 25, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
62 1 0.01
63 150 0.82
64 21 0.11
65 12 0.07
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (63 bp):
ATGAAGAAGATGAATTTGCAGTGCCACCGGAGATGGATTACGACTTAGGCCTTGACTACAACC
Found at i:91546 original size:69 final size:69
Alignment explanation
Indices: 91432--91573 Score: 178
Period size: 69 Copynumber: 2.1 Consensus size: 69
91422 GATGTAGGAC
* * * * *
91432 CTGACTACGACGGTGAAGGAGATGAATTCGAAGTGCCAACGGAGGCGGATTTTGCTCTTCCACCA
1 CTGACTACGACCGTGAAGGAGAAGAATTCGAAGTGCCAACAGAGGCGGATTTCGCACTTCCACCA
91497 GACT
66 GACT
* * * *
91501 CTGACTACTACCGTGAAGTAGAAGAATTTGTAGTGCC-ACTAGAGGCGGATTTCGCACTTCCACC
1 CTGACTACGACCGTGAAGGAGAAGAATTCGAAGTGCCAAC-AGAGGCGGATTTCGCACTTCCACC
*
91565 GGACT
65 AGACT
91570 CTGA
1 CTGA
91574 TTACAACTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
68 2 0.03
69 60 0.97
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (69 bp):
CTGACTACGACCGTGAAGGAGAAGAATTCGAAGTGCCAACAGAGGCGGATTTCGCACTTCCACCA
GACT
Found at i:91655 original size:63 final size:63
Alignment explanation
Indices: 91549--91693 Score: 182
Period size: 63 Copynumber: 2.3 Consensus size: 63
91539 CTAGAGGCGG
* * * *
91549 ATTTCGCACTTCCACCGGACTCTGATTACAACTTAGGCTCTGACTATTACCATGAAGGAGATGA
1 ATTT-GCACTTCCACCAGACTCTGACTACAACTTAGGCCCTGACTACTACCATGAAGGAGATGA
* * * * *
91613 GTTTTCACTTCCACCAGACTCTGACTACGACTTAGGCCCTGACTACTACGATGAGGGAGATGA
1 ATTTGCACTTCCACCAGACTCTGACTACAACTTAGGCCCTGACTACTACCATGAAGGAGATGA
* *
91676 ATTTGCAGTGCCACCAGA
1 ATTTGCACTTCCACCAGA
91694 GGTGGATTTC
Statistics
Matches: 68, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
63 65 0.96
64 3 0.04
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (63 bp):
ATTTGCACTTCCACCAGACTCTGACTACAACTTAGGCCCTGACTACTACCATGAAGGAGATGA
Found at i:91764 original size:87 final size:88
Alignment explanation
Indices: 91618--91779 Score: 274
Period size: 87 Copynumber: 1.9 Consensus size: 88
91608 GATGAGTTTT
* *
91618 CACTTCCACCAGACTCTGACTACGACTTAGGCCCTGACTACTACGATGAGGGAGATGAA-TTTGC
1 CACTTCCACCAGACTCTGACTACGACTTAGGCCCTGACTACTACCATGAAGGAGATGAATTTTGC
91682 AGTGCCACCAGAGGTGGATTTCC
66 AGTGCCACCAGAGGTGGATTTCC
*
91705 CACTTCCACCAGACTCTGACTACGACTTAGGCCCT-ACCTTCTACCATGAAGGAGATGAATTTTG
1 CACTTCCACCAGACTCTGACTACGACTTAGGCCCTGA-CTACTACCATGAAGGAGATGAATTTTG
91769 CAGTGCCACCA
65 CAGTGCCACCA
91780 ATGGAGGATA
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
86 1 0.01
87 54 0.77
88 15 0.21
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (88 bp):
CACTTCCACCAGACTCTGACTACGACTTAGGCCCTGACTACTACCATGAAGGAGATGAATTTTGC
AGTGCCACCAGAGGTGGATTTCC
Found at i:92264 original size:28 final size:28
Alignment explanation
Indices: 92209--92265 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
92199 CATTGATGAA
** *
92209 TTTAATATTTAAATTAAATTTATGTTTT
1 TTTAATATTTAAATTAAATAGATATTTT
92237 TTTAATATTATAAATTAAA-AGATATTTT
1 TTTAATATT-TAAATTAAATAGATATTTT
92265 T
1 T
92266 AATTTGAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TTTAATATTTAAATTAAATAGATATTTT
Found at i:92265 original size:29 final size:28
Alignment explanation
Indices: 92209--92265 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
92199 CATTGATGAA
**
92209 TTTAATATTTAAATTAAATTTATGTTTT
1 TTTAATATTTAAATTAAAGATATGTTTT
92237 TTTAATATTATAAATTAAAAGATAT-TTTT
1 TTTAATATT-TAAATT-AAAGATATGTTTT
92266 AATTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 10 0.40
30 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
TTTAATATTTAAATTAAAGATATGTTTT
Found at i:92413 original size:64 final size:63
Alignment explanation
Indices: 92328--92447 Score: 172
Period size: 63 Copynumber: 1.9 Consensus size: 63
92318 ATTTGTTACC
*
92328 TATTTAACTTTGAATATTAAAGAT-AATTATATCCTTTTTAAATATTTTAAATTAAAATCATATA
1 TATTTAACTTTGAATAGTAAAGATGAATT-TATCC-TTTTAAATATTTTAAATTAAAATCATATA
* *
92392 TATTTAAGTTT-AAGTAGTAAAGATGACTTTATCCTTTTAAATATTTTAAATTAAAA
1 TATTTAACTTTGAA-TAGTAAAGATGAATTTATCCTTTTAAATATTTTAAATTAAAA
92448 GATATTATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
63 24 0.47
64 24 0.47
65 3 0.06
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (63 bp):
TATTTAACTTTGAATAGTAAAGATGAATTTATCCTTTTAAATATTTTAAATTAAAATCATATA
Done.