Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000688.1 Hibiscus syriacus cultivar Beakdansim tig00001344_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: 77558
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Found at i:2487 original size:12 final size:12
Alignment explanation
Indices: 2467--2500 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2457 CATTATTAGT
*
2467 GTTTTGGCTTCC
1 GTTTCGGCTTCC
2479 GTTTCGGCTTCC
1 GTTTCGGCTTCC
*
2491 GTTTCAGCTT
1 GTTTCGGCTT
2501 ATGCAGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.26, G:0.24, T:0.47
Consensus pattern (12 bp):
GTTTCGGCTTCC
Found at i:3724 original size:20 final size:20
Alignment explanation
Indices: 3684--3738 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
3674 TTATTTTTTT
**
3684 AAAATATTTAAAAAATCATA
1 AAAATATTTTTAAAATCATA
* *
3704 ATTAAT-TTTTTAAAATTATA
1 A-AAATATTTTTAAAATCATA
3724 AAAATATTTTTAAAA
1 AAAATATTTTTAAAA
3739 ATTAATTTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 3 0.11
20 22 0.79
21 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATATTTTTAAAATCATA
Found at i:6480 original size:34 final size:36
Alignment explanation
Indices: 6436--6505 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
6426 TATGTGCAGG
6436 GGGAACAGATTCCCCC-T-GGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
*
6470 GGGAATAGATTCCCCCTTGGGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
6506 CCTAAATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 15 0.45
35 1 0.03
36 17 0.52
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
Found at i:13253 original size:36 final size:36
Alignment explanation
Indices: 13206--13276 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
13196 TATGTGCAGG
13206 GGGAACAGATTCCCCC-TGGGAGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTTGGG-GGGTATCGATTCCCC
13242 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCC
1 GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCC
13277 TCTAAATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
36 30 0.88
37 4 0.12
ACGTcount: A:0.18, C:0.30, G:0.31, T:0.21
Consensus pattern (36 bp):
GGGAACAGATTCCCCCTTGGGGGGTATCGATTCCCC
Found at i:19962 original size:20 final size:20
Alignment explanation
Indices: 19937--20000 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
19927 AAGGGAAACA
19937 GATTCCCCCTGGGGGGTATC
1 GATTCCCCCTGGGGGGTATC
*
19957 GATT-CCCCT----GG-AAC
1 GATTCCCCCTGGGGGGTATC
*
19971 AGATTTCCCCTGGGGGGTATC
1 -GATTCCCCCTGGGGGGTATC
19992 GATTCCCCC
1 GATTCCCCC
20001 CTAAATGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
14 2 0.06
15 6 0.18
16 5 0.15
19 5 0.15
20 14 0.41
21 2 0.06
ACGTcount: A:0.14, C:0.33, G:0.28, T:0.25
Consensus pattern (20 bp):
GATTCCCCCTGGGGGGTATC
Found at i:19981 original size:35 final size:35
Alignment explanation
Indices: 19933--19999 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
19923 GTGCAAGGGA
19933 AACAGATTCCCCCTGGGGGGTATCGATTCCCCTGG
1 AACAGATTCCCCCTGGGGGGTATCGATTCCCCTGG
*
19968 AACAGATTTCCCCTGGGGGGTATCGATTCCCC
1 AACAGATTCCCCCTGGGGGGTATCGATTCCCC
20000 CCTAAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.24
Consensus pattern (35 bp):
AACAGATTCCCCCTGGGGGGTATCGATTCCCCTGG
Found at i:26363 original size:3 final size:3
Alignment explanation
Indices: 26348--26416 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
26338 GGTTAAAGAA
*
26348 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26395 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
26417 GTGTTTATAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 62 0.98
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:28036 original size:2 final size:2
Alignment explanation
Indices: 28031--28067 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28021 ATTAATTCGA
28031 AT AT AT AT 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 AT AT AT AT A
28068 AATTTAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29206 original size:52 final size:52
Alignment explanation
Indices: 29145--29248 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
29135 TTGAAGTTTT
*
29145 TAATTGCTTCATTTTATTATTGTCTTACTAACATTTTTATCTTTGTTCTCAG
1 TAATTGCTTCATTTTATTATTGTCTTACTAACATCTTTATCTTTGTTCTCAG
29197 TAATTGCTTCATTTTATTATTGTCTTACTAACATCTTTATCTTTGTTCTCAG
1 TAATTGCTTCATTTTATTATTGTCTTACTAACATCTTTATCTTTGTTCTCAG
29249 ATTTGTCCAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (52 bp):
TAATTGCTTCATTTTATTATTGTCTTACTAACATCTTTATCTTTGTTCTCAG
Found at i:40006 original size:15 final size:15
Alignment explanation
Indices: 39972--40051 Score: 83
Period size: 16 Copynumber: 5.3 Consensus size: 15
39962 GCTTGAAGAA
* *
39972 AAAAAAGGAACAAAT
1 AAAAAATGAAAAAAT
39987 AAAAAGATGAAAAAAT
1 AAAAA-ATGAAAAAAT
*
40003 AAAAAATGAAAAAGAA
1 AAAAAATGAAAAA-AT
40019 AAAAAATG-AAAAA-
1 AAAAAATGAAAAAAT
*
40032 AAGAAATGAAAAAAT
1 AAAAAATGAAAAAAT
*
40047 GAAAA
1 AAAAA
40052 GAGAAAAAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
13 7 0.13
14 6 0.11
15 20 0.36
16 22 0.40
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (15 bp):
AAAAAATGAAAAAAT
Found at i:40046 original size:8 final size:8
Alignment explanation
Indices: 39972--40051 Score: 64
Period size: 8 Copynumber: 10.5 Consensus size: 8
39962 GCTTGAAGAA
*
39972 AAAAAAGG
1 AAAAAATG
*
39980 AACAAAT-
1 AAAAAATG
39987 AAAAAGATG
1 AAAAA-ATG
39996 AAAAAAT-
1 AAAAAATG
40003 AAAAAATG
1 AAAAAATG
*
40011 AAAAAGA-A
1 AAAAA-ATG
40019 AAAAAATG
1 AAAAAATG
40027 -AAAAA--
1 AAAAAATG
*
40032 AAGAAATG
1 AAAAAATG
40040 AAAAAATG
1 AAAAAATG
40048 AAAA
1 AAAA
40052 GAGAAAAAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
6 4 0.07
7 17 0.30
8 30 0.53
9 6 0.11
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:40050 original size:13 final size:13
Alignment explanation
Indices: 40017--40060 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
40007 AATGAAAAAG
40017 AAAAA-AAATGAA
1 AAAAAGAAATGAA
40029 AAAAAGAAATGAA
1 AAAAAGAAATGAA
* * *
40042 AAAATGAAAAGAG
1 AAAAAGAAATGAA
40055 AAAAAG
1 AAAAAG
40061 GAGGGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 5 0.19
13 22 0.81
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (13 bp):
AAAAAGAAATGAA
Found at i:40051 original size:31 final size:31
Alignment explanation
Indices: 39987--40044 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
39977 AGGAACAAAT
*
39987 AAAAAGATGAAAAAATAAAAAATGAAAAAGA
1 AAAAAAATGAAAAAATAAAAAATGAAAAAGA
*
40018 AAAAAAATG-AAAAA-AAGAAATGAAAAA
1 AAAAAAATGAAAAAATAAAAAATGAAAAA
40045 ATGAAAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.48
30 5 0.20
31 8 0.32
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (31 bp):
AAAAAAATGAAAAAATAAAAAATGAAAAAGA
Found at i:40057 original size:15 final size:16
Alignment explanation
Indices: 39987--40059 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 16
39977 AGGAACAAAT
*
39987 AAAAAGATGAAAAA-AT
1 AAAAA-ATGAAAAAGAG
*
40003 AAAAAATGAAAAAGAA
1 AAAAAATGAAAAAGAG
40019 AAAAAATGAAAAAAAGAAATG
1 AAAAAATG--AAAAAG--A-G
40040 AAAAAATG-AAAAGAG
1 AAAAAATGAAAAAGAG
40055 AAAAA
1 AAAAA
40060 GGAGGGTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
15 14 0.29
16 15 0.31
18 11 0.22
20 1 0.02
21 8 0.16
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (16 bp):
AAAAAATGAAAAAGAG
Found at i:41174 original size:136 final size:133
Alignment explanation
Indices: 40910--41257 Score: 481
Period size: 136 Copynumber: 2.6 Consensus size: 133
40900 AGAAAGAGAT
* *
40910 GGATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAG-AAGTTCA
1 GGATCAACATTTCC-ATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAGTTCA
* * * * *
40974 TAATGAGAAGAGCCTATTCGACCTATCACTCGATTCATGGCGTTTTGAATCAGTGACACCTCGCT
65 TAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCT
41039 TGAG
130 TGAG
41043 GGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAAAGTT
1 GGATCAACATTTCCA-TGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAG--AAAGTT
* * *
41108 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGTCATTTCGAATTAGTGATACCTCG
63 CATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCG
41173 CTTGAG
128 CTTGAG
** * * *
41179 GGATTGACATTTTCA-GAAGAGTTCATAATGAGAAGAACTCGTCC--TA-AAGGAGAAAGTTCAT
1 GGATCAACATTTCCATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAGTTCAT
*
41240 AATGAGAAGAACTTGTTC
66 AATGAGAAGAGCTTGTTC
41258 CTTCAAGTCC
Statistics
Matches: 195, Mismatches: 16, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
129 26 0.13
131 5 0.03
132 3 0.02
133 53 0.27
134 28 0.14
136 80 0.41
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (133 bp):
GGATCAACATTTCCATGAAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAGTTCAT
AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACGGCATTTCGAATCAGTGACACCTCGCTT
GAG
Found at i:41679 original size:331 final size:331
Alignment explanation
Indices: 41062--41701 Score: 1027
Period size: 331 Copynumber: 1.9 Consensus size: 331
41052 TTTCCAGTGA
* *
41062 AGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGT
1 AGAGCTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGT
* * *
41127 TCGACCTATCACTCGATTCACGTCATTTCGAATTAGTGATACCTCGCTTGAGGGATTGACATTTT
66 TCGACCTATCACTCGATTCACGTCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTC
* *
41192 CAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTT
131 CAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAAAAGAACTTGTT
* *
41257 CCTTCAAGTCCATCACAGAAAGAGATGGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAA
196 CCTTCAAGTCCACCACAGAAAGAGATGGATCAACATTTCCAATGAAGAGTTCATAATAAGAAGAA
* * *
41322 CTCATCCAACGAGAGAGAATAAGTTCATAATGAGAAGTACTTGTCCAATTTCACATCAACATTTT
261 CTCATCCAACGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAATTTCACATCAACATTTT
41387 AAATGG
326 AAATGG
* *
41393 AGAGCTCATAATGAGAAGAAGTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGCTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGT
*
41458 TCGACCTATCACTCGATTCACGAT-ATTTCGAATCAGTGACGCCTCG-TTAGAGGGATTGACATT
66 TCGACCTATCACTCGATTCACG-TCATTTCGAATCAGTGACACCTCGCTT-GAGGGATTGACATT
*
41521 TCCAAAAGAGTTCATAATGAGAAGAACTCGTCTTAAAGGAGAAAGTTCATAATGAAAAGAACTTG
129 TCCAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAAAAGAACTTG
* * * *
41586 TTCCTTTCAAGTCCACCACAGAAATAGGT-GACTCAACATTTTCAGTGAAGAGTTCATAATAAGA
194 TTCC-TTCAAGTCCACCACAGAAAGAGATGGA-TCAACATTTCCAATGAAGAGTTCATAATAAGA
*
41650 AGAACTCATCC-ACGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAT
257 AGAACTCATCCAACGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAAT
41702 CCAACGACGA
Statistics
Matches: 284, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
330 2 0.01
331 220 0.77
332 62 0.22
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (331 bp):
AGAGCTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAAAAGTTCATAATGAGAAGAGCTTGT
TCGACCTATCACTCGATTCACGTCATTTCGAATCAGTGACACCTCGCTTGAGGGATTGACATTTC
CAAAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATGAAAAGAACTTGTT
CCTTCAAGTCCACCACAGAAAGAGATGGATCAACATTTCCAATGAAGAGTTCATAATAAGAAGAA
CTCATCCAACGAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAATTTCACATCAACATTTT
AAATGG
Found at i:41844 original size:3 final size:3
Alignment explanation
Indices: 41829--41868 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
41819 GGTTAAAGAA
*
41829 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
41869 AGTGTGTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:42592 original size:2 final size:2
Alignment explanation
Indices: 42585--42614 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42575 AGGTTTTCGA
42585 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
42615 GCTAACTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43505 original size:2 final size:2
Alignment explanation
Indices: 43500--43526 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43490 ATTAATTCGA
43500 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 A
43527 ATTAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55453 original size:25 final size:25
Alignment explanation
Indices: 55406--55461 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
55396 TGTAACATTA
* ** * *
55406 ATTGTATTTAATATTATTTTTATTT
1 ATTGTATTTAAGAAAATTATTATAT
55431 ATTGTATTTAAGAAAATTATTATAT
1 ATTGTATTTAAGAAAATTATTATAT
55456 A-TGTAT
1 ATTGTAT
55462 AGTTTGGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (25 bp):
ATTGTATTTAAGAAAATTATTATAT
Found at i:63976 original size:31 final size:32
Alignment explanation
Indices: 63941--64010 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
63931 ATTTAGTCAA
* * *
63941 TGACCAAATTATAAGA-TTTTGTAAAGTTT-GG
1 TGACCAAAGTATAA-ACTTTGGAAAAGTTTAGG
63972 TGACCAAAGTATAAACTTTGGAAAAGTTTAGG
1 TGACCAAAGTATAAACTTTGGAAAAGTTTAGG
64004 -GACCAAA
1 TGACCAAA
64011 ATGGTAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.03
31 31 0.91
32 2 0.06
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (32 bp):
TGACCAAAGTATAAACTTTGGAAAAGTTTAGG
Found at i:66728 original size:22 final size:22
Alignment explanation
Indices: 66700--66752 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
66690 AGCATTTGGT
*
66700 ACTGTTCACGGTAATGTTCATC
1 ACTGTTCACGGTAATGTACATC
* * *
66722 ACTGTTCATGGTATTGTACATT
1 ACTGTTCACGGTAATGTACATC
*
66744 ACTTTTCAC
1 ACTGTTCAC
66753 AACACTGTTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.42
Consensus pattern (22 bp):
ACTGTTCACGGTAATGTACATC
Found at i:68257 original size:43 final size:42
Alignment explanation
Indices: 68200--68473 Score: 203
Period size: 44 Copynumber: 6.4 Consensus size: 42
68190 GCGTTTGTAC
* * * * *
68200 CCAAAAATGCCGCTATAGATCTAACCTTTTATGGCCTTTGTGT
1 CCAAAAACGACGCTATAGATCTAACCTTTTGTGACATTTGT-T
*
68243 CCAAAAACGACGCTATAGATCTAACCTTTTGCGACATTTGTGT
1 CCAAAAACGACGCTATAGATCTAACCTTTTGTGACATTTGT-T
* * * * **
68286 CAAAAAAATGTCGCTATATATCTAACCTTTTGTGATGTTTGTT
1 C-CAAAAACGACGCTATAGATCTAACCTTTTGTGACATTTGTT
* * * * * * *
68329 CCAAAAAAGTCGCTATAGATTTGACATTTTGCGGCATTTGTT
1 CCAAAAACGACGCTATAGATCTAACCTTTTGTGACATTTGTT
* ** *
68371 CCAAAAAAC-ACCGCTATAGATCTTGACCTTTTGCTG-TGTTTATAT
1 CC-AAAAACGA-CGCTATAGATC-TAACCTTTTG-TGACATTTGT-T
* *
68416 CCAAAAAC-ACCGCTATAGATATCAACCTTTTGTGACGTTTGTT
1 CCAAAAACGA-CGCTATAGATCT-AACCTTTTGTGACATTTGTT
*
68459 CCAAAAACGCCGCTA
1 CCAAAAACGACGCTA
68474 ACATTAGCGA
Statistics
Matches: 186, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
42 33 0.18
43 72 0.39
44 77 0.41
45 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (42 bp):
CCAAAAACGACGCTATAGATCTAACCTTTTGTGACATTTGTT
Found at i:70778 original size:20 final size:20
Alignment explanation
Indices: 70753--70842 Score: 69
Period size: 20 Copynumber: 4.5 Consensus size: 20
70743 TTCAAAGAGG
70753 TATTATATTTAATTTTATAT
1 TATTATATTTAATTTTATAT
*
70773 TATTATATTTGATTTTA-AT
1 TATTATATTTAATTTTATAT
*
70792 T-TAATA-TTAATTTTTTATAT
1 TATTATATTTAA--TTTTATAT
* * * *
70812 AAATTAAATATTAATTTTTTAA
1 -TATTATAT-TTAATTTTATAT
70834 TATTATATT
1 TATTATATT
70843 ATAGATTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
17 3 0.06
18 4 0.08
19 8 0.15
20 19 0.36
21 6 0.11
22 9 0.17
24 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (20 bp):
TATTATATTTAATTTTATAT
Found at i:70801 original size:11 final size:11
Alignment explanation
Indices: 70773--70889 Score: 58
Period size: 11 Copynumber: 9.8 Consensus size: 11
70763 AATTTTATAT
*
70773 TATTATATTTGA
1 TATTA-ATTTAA
*
70785 TTTTAATTTAA
1 TATTAATTTAA
*
70796 TATTAATTTTTTA
1 TATTAA--TTTAA
* *
70809 TATAAATTAAA
1 TATTAATTTAA
70820 TATTAATTTTTTAA
1 TATTAA---TTTAA
70834 TATTATATTATAGA
1 TATTA-ATT-TA-A
70848 T-TTAATTTAA
1 TATTAATTTAA
70858 TATTAATTTTTAA
1 TATTAA--TTTAA
* *
70871 -ATAAATTAAA
1 TATTAATTTAA
70881 TATTAATTT
1 TATTAATTT
70890 TTTAATATTA
Statistics
Matches: 80, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
10 6 0.08
11 30 0.38
12 13 0.16
13 19 0.24
14 11 0.14
15 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:70868 original size:61 final size:62
Alignment explanation
Indices: 70761--70923 Score: 242
Period size: 61 Copynumber: 2.6 Consensus size: 62
70751 GGTATTATAT
* * *
70761 TTAATTTTATATTATTATATT-T-GATTTTAATTTAATATTAATTTTTTATATAAATTAAATA
1 TTAATTTTTTAATATTATATTATAGA-TTTAATTTAATATTAATTTTTTAAATAAATTAAATA
70822 TTAATTTTTTAATATTATATTATAGATTTAATTTAATATTAA-TTTTTAAATAAATTAAATA
1 TTAATTTTTTAATATTATATTATAGATTTAATTTAATATTAATTTTTTAAATAAATTAAATA
*
70883 TTAATTTTTTAATATTATATTATAGATATTTAATTTTATAT
1 TTAATTTTTTAATATTATATTATAG--ATTTAATTTAATAT
70924 CATATAAATT
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
61 62 0.66
62 17 0.18
63 15 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (62 bp):
TTAATTTTTTAATATTATATTATAGATTTAATTTAATATTAATTTTTTAAATAAATTAAATA
Found at i:70882 original size:23 final size:23
Alignment explanation
Indices: 70851--70896 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
70841 TTATAGATTT
*
70851 AATTTAATATTAATTTTTAAATA
1 AATTAAATATTAATTTTTAAATA
*
70874 AATTAAATATTAATTTTTTAATA
1 AATTAAATATTAATTTTTAAATA
70897 TTATATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTAAATATTAATTTTTAAATA
Found at i:70975 original size:20 final size:19
Alignment explanation
Indices: 70915--70976 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
70905 TAGATATTTA
*
70915 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
70934 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
70952 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
70972 ATTTT
1 ATTTT
70977 GATTTAAGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:71463 original size:31 final size:31
Alignment explanation
Indices: 71421--71480 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
71411 TAGTTGTATG
* * *
71421 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATATAAATCTCAGTATTGCAAAACTAA
71452 AATTATATAAATCTCAGTATTGCAAAACT
1 AATTATATAAATCTCAGTATTGCAAAACT
71481 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (31 bp):
AATTATATAAATCTCAGTATTGCAAAACTAA
Found at i:76645 original size:18 final size:18
Alignment explanation
Indices: 76632--76671 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
76622 TTCGAGATTG
*
76632 TATGTTTTGACGAGGTAT
1 TATGTTTTGACGAGATAT
*
76650 TATGTTTTGACGAGGTAT
1 TATGTTTTGACGAGATAT
76668 TATG
1 TATG
76672 GAACTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.45
Consensus pattern (18 bp):
TATGTTTTGACGAGATAT
Done.