Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004795.1 Hibiscus syriacus cultivar Beakdansim tig00010806_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: 56566
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:38 original size:17 final size:17
Alignment explanation
Indices: 16--65 Score: 75
Period size: 16 Copynumber: 3.0 Consensus size: 17
6 CGTTAAAAAA
*
16 CATAAAATATGACTTTT
1 CATAAAATTTGACTTTT
33 CAT-AAATTTGACTTTT
1 CATAAAATTTGACTTTT
*
49 CATAAATTTTGACTTTT
1 CATAAAATTTGACTTTT
66 TTTGTCAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (17 bp):
CATAAAATTTGACTTTT
Found at i:153 original size:19 final size:19
Alignment explanation
Indices: 129--174 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
119 TATGCTAAAA
* *
129 GTCAATGGTTTAGGTTCAG
1 GTCAATGGTTCAGGTTAAG
148 GTCAATGGTTCAGGTTAAG
1 GTCAATGGTTCAGGTTAAG
167 GTCAATGG
1 GTCAATGG
175 GTCATATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.33
Consensus pattern (19 bp):
GTCAATGGTTCAGGTTAAG
Found at i:3031 original size:12 final size:12
Alignment explanation
Indices: 3014--3049 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
3004 AGAGGCGAGG
3014 GTATCACCTTTT
1 GTATCACCTTTT
*
3026 GTATCACCTTTA
1 GTATCACCTTTT
*
3038 GAATCACCTTTT
1 GTATCACCTTTT
3050 CCACAGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.44
Consensus pattern (12 bp):
GTATCACCTTTT
Found at i:8466 original size:21 final size:21
Alignment explanation
Indices: 8428--8467 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
8418 TGAAATCCAA
*
8428 ATTTTATTTAATTAATTTATT
1 ATTTTATTTAATAAATTTATT
8449 ATTTTA-TTAATAATATTTA
1 ATTTTATTTAATAA-ATTTA
8468 CTTTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTATTTAATAAATTTATT
Found at i:10040 original size:14 final size:14
Alignment explanation
Indices: 9979--10059 Score: 55
Period size: 14 Copynumber: 6.1 Consensus size: 14
9969 AACATAGGTC
*
9979 TCGTTCGTTCAT-T
1 TCGTTCGTTTATGT
*
9992 TACGTTCGATTATGT
1 T-CGTTCGTTTATGT
* *
10007 TCATTCGGTTATG-
1 TCGTTCGTTTATGT
10020 T--TT-GTTTATGT
1 TCGTTCGTTTATGT
10031 TCGTTCGTTTATGT
1 TCGTTCGTTTATGT
** *
10045 TATTTCATTTATGT
1 TCGTTCGTTTATGT
10059 T
1 T
10060 TAATCCAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 6 0.11
11 3 0.06
13 4 0.07
14 39 0.72
15 2 0.04
ACGTcount: A:0.14, C:0.12, G:0.17, T:0.57
Consensus pattern (14 bp):
TCGTTCGTTTATGT
Found at i:11058 original size:10 final size:10
Alignment explanation
Indices: 11040--11098 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
11030 GGGTCTCCAA
*
11040 CGTTGATGTT
1 CGTTTATGTT
11050 CGTTTATGTT
1 CGTTTATGTT
11060 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* *
11071 ATGTTCATGTT
1 -CGTTTATGTT
11082 CGTTTATGTT
1 CGTTTATGTT
11092 CGTTTAT
1 CGTTTAT
11099 TTATTAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
10 29 0.73
11 7 0.17
12 4 0.10
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:11071 original size:16 final size:16
Alignment explanation
Indices: 11046--11102 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
11036 CCAACGTTGA
*
11046 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
*
11062 TGTTCATTTATGTTCA
1 TGTTCATTTATGTTCG
*
11078 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
11094 T-TT-ATTTAT
1 TGTTCATTTAT
11103 TAAATGAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
14 5 0.14
15 2 0.06
16 29 0.81
ACGTcount: A:0.12, C:0.11, G:0.18, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:13109 original size:2 final size:2
Alignment explanation
Indices: 13097--13126 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13087 TTGATAATTT
*
13097 TA TA CA 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
13127 CGTCGAGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:14715 original size:20 final size:20
Alignment explanation
Indices: 14668--14708 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
14658 GTTAATGTTG
*
14668 ATATTATTTATTTTTATAATT
1 ATATT-TTTATTTTTAAAATT
14689 ATATTTTTATTTTTAAAATT
1 ATATTTTTATTTTTAAAATT
14709 CAATTTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATTTTTATTTTTAAAATT
Found at i:18160 original size:19 final size:19
Alignment explanation
Indices: 18106--18165 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
18096 GGATTTTAGG
18106 CCAAGAGTATCGATACTTT
1 CCAAGAGTATCGATACTTT
*
18125 ACCTCAA-AGTATTGATACTTT
1 --C-CAAGAGTATCGATACTTT
18146 CCAAGAGTATCGATACTTT
1 CCAAGAGTATCGATACTTT
18165 C
1 C
18166 AGCAACAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.09
19 15 0.43
21 14 0.40
22 3 0.09
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.33
Consensus pattern (19 bp):
CCAAGAGTATCGATACTTT
Found at i:21223 original size:29 final size:29
Alignment explanation
Indices: 21181--21242 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
21171 TTCCTTCCTA
21181 ACAATACCTTTGTAGTGGCGCACGCACAT
1 ACAATACCTTTGTAGTGGCGCACGCACAT
21210 ACAATACCTTTGTAGTGGCGCACGCACAT
1 ACAATACCTTTGTAGTGGCGCACGCACAT
21239 ACAA
1 ACAA
21243 ATTAGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (29 bp):
ACAATACCTTTGTAGTGGCGCACGCACAT
Found at i:31207 original size:30 final size:29
Alignment explanation
Indices: 31173--31247 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
31163 TAAGGTACTT
**
31173 AAATAATAAAAATAGATAGTTTAA-AGACTA
1 AAATAATAAAAATAGA-AAATTAAGA-ACTA
31203 AAATAATAAAAAGTAGAAAATTAAGTAACTA
1 AAATAATAAAAA-TAGAAAATTAAG-AACTA
31234 AAATAATAAAAATA
1 AAATAATAAAAATA
31248 TATAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 19 0.47
31 20 0.50
32 1 0.03
ACGTcount: A:0.65, C:0.03, G:0.08, T:0.24
Consensus pattern (29 bp):
AAATAATAAAAATAGAAAATTAAGAACTA
Found at i:32914 original size:6 final size:6
Alignment explanation
Indices: 32903--33007 Score: 50
Period size: 6 Copynumber: 16.0 Consensus size: 6
32893 TAACATATAT
* * * *
32903 TAATAA TAATAA TATTAT TATTAA TAATAG TAATAA TAATATA TATATATA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATA-A TA-ATA-A
* * *
32954 TATATATA TTATAA T-ATAA TACATATA TATATATA TATATAT TAATAC
1 TA-ATA-A TAATAA TAATAA TA-ATA-A TA-ATA-A TA-ATAA TAATAA
33002 TAATAA
1 TAATAA
33008 AAAAATGGAT
Statistics
Matches: 83, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
5 5 0.06
6 39 0.47
7 11 0.13
8 28 0.34
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
TAATAA
Found at i:32948 original size:2 final size:2
Alignment explanation
Indices: 32941--32995 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
32931 AGTAATAATA
*
32941 AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT AT A- AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32980 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
32996 TAATACTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:33341 original size:135 final size:135
Alignment explanation
Indices: 33197--33450 Score: 483
Period size: 135 Copynumber: 1.9 Consensus size: 135
33187 CATTGAAAGA
33197 CGTCACTGATTCGAAATG-TCGTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACT
1 CGTCACTGATTCGAAATGCT-GTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACT
33261 TCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGATCCCTCAA
65 TCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGATCCCTCAA
33326 GCGAGG
130 GCGAGG
*
33332 CGTCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTT
1 CGTCACTGATTCGAAATGCTGTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTT
33397 CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTT
66 CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTT
33451 AAGTCACCTC
Statistics
Matches: 117, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
135 116 0.99
136 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (135 bp):
CGTCACTGATTCGAAATGCTGTGAACCAAGTGATAGGTCGAACAAGCTCTTCTCATTATGAACTT
CTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTTGATCCCTCAAG
CGAGG
Found at i:33613 original size:247 final size:247
Alignment explanation
Indices: 33120--33694 Score: 763
Period size: 247 Copynumber: 2.3 Consensus size: 247
33110 TTGTTGGATT
* * * *
33120 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTGTTGGATGAGTTCTTCTCATTCTGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * *
33185 TCCATTG-AAAGACGTCACTGATTCGAAATGTCGTGAACCAAGTGATAGGTCGAACAAGCTCTTC
66 TCCATTGAAAAGAAGTCACTCATTC---ATGTCGTGAACC-AGTGATAAG-CGAACAAGCTCTTC
*
33249 TCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATG
126 TCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATG
** * *
33314 TTGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTC
191 TCAATCCCTCAAGAGAGGCATCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTC
33371 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * * *
33436 TCCATTGAAAATGTTAAGTCACCTCTTTC-TGTGGTGGA-C-TTGA-AAG-GAACAAGTTCTTCT
66 TCCATTGAAAA-G--AAGTCA-CTCATTCATGTCGTGAACCAGTGATAAGCGAACAAGCTCTTCT
*
33496 CATTATGAACTTCTTCTCCCTC-TATCGGATGAGTTCTTCTCATTATGAACTCTCCATTGGAAAT
127 CATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAAT
*
33560 GTCAATCCCTCAAGAGAGGCATCACTGATTCGAAATG-TCGTGAATCGAGTGATAGGTC
190 GTCAATCCCTCAAGAGAGGCATCACTGATTCGAAATGCT-GTGAATCAAGTGATAGGTC
*
33618 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-TATCGGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGT-T-GGATGAGTTCTTCTCATTATGAAC
*
33682 TCTCTATTTGAAA
64 TCTCCA-TTGAAA
33695 TACTGATGCG
Statistics
Matches: 292, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
245 1 0.00
246 37 0.13
247 124 0.42
248 31 0.11
249 9 0.03
251 69 0.24
252 10 0.03
253 1 0.00
255 5 0.02
256 5 0.02
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (247 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAAGAAGTCACTCATTCATGTCGTGAACCAGTGATAAGCGAACAAGCTCTTCTCATT
ATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCTCCATTGAAAATGTCAAT
CCCTCAAGAGAGGCATCACTGATTCGAAATGCTGTGAATCAAGTGATAGGTC
Found at i:33724 original size:92 final size:90
Alignment explanation
Indices: 33613--33784 Score: 254
Period size: 92 Copynumber: 1.9 Consensus size: 90
33603 ATCGAGTGAT
* *
33613 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTAT
1 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCT-TATCGGATGAATTCTTCTCATTAT
*
33678 GAACTCTCTATTTGAAATACTGATGCG
65 GAACTCTCCA-TTGAAATACTGATGCG
* * * * *
33705 AGGTCAAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTGTTGGATGAATTCTTCTCATTATG
1 AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAATTCTTCTCATTATG
33770 AACTCTCCATTGAAA
66 AACTCTCCATTGAAA
33785 ATGTTGATCC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
90 6 0.08
91 30 0.42
92 36 0.50
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (90 bp):
AGGTCAAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTATCGGATGAATTCTTCTCATTATG
AACTCTCCATTGAAATACTGATGCG
Found at i:33842 original size:111 final size:105
Alignment explanation
Indices: 33711--33910 Score: 274
Period size: 107 Copynumber: 1.8 Consensus size: 105
33701 TGCGAGGTCA
** * *
33711 AACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTGTTGGATGAATTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAAC--TTTC-TCCTT-TAAGACGAACTCTTCTCATTATGAACTCT
33776 CCATTGAAAATGTTGATCCACCTCCTTTTGTGATGGACTCGAAAGG
62 CC--TGAAAATGTTGATCCACCTCCTTTTGTGATGGACTCGAAAGG
* *
33822 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAGCTCTTCTCATTATGAACTCTTCTG
1 AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAACTCTTCTCATTATGAACTCTCCTG
**
33887 GTAATGTTGATCCACCTCCTTTTG
66 AAAATGTTGATCCACCTCCTTTTG
33911 CAGTGAATCT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
105 24 0.30
107 25 0.31
108 5 0.06
109 4 0.05
111 23 0.28
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.40
Consensus pattern (105 bp):
AACAAGTTCTTCTCATTATGAACTTTCTCCTTTAAGACGAACTCTTCTCATTATGAACTCTCCTG
AAAATGTTGATCCACCTCCTTTTGTGATGGACTCGAAAGG
Found at i:33884 original size:16 final size:16
Alignment explanation
Indices: 33829--33885 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
33819 AGGAACAAGT
33829 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
33845 T-TTCTCCTTTAAGACGAGC
1 TCTTCT-CATTATGA--A-C
33864 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
33880 TCTTCT
1 TCTTCT
33886 GGTAATGTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 14 0.44
17 1 0.03
18 1 0.03
19 8 0.25
20 4 0.12
ACGTcount: A:0.21, C:0.26, G:0.09, T:0.44
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:34783 original size:17 final size:17
Alignment explanation
Indices: 34763--34828 Score: 73
Period size: 16 Copynumber: 3.9 Consensus size: 17
34753 AACCCTCCTT
*
34763 TTTCTCTTCATTTTTTA
1 TTTCTTTTCATTTTTTA
*
34780 TTTC-TTTCTTTTTTTA
1 TTTCTTTTCATTTTTTA
*
34796 TTT-TTTTCTTCTTTTTA
1 TTTCTTTTCAT-TTTTTA
*
34813 TTTTTTTTCATTTTTT
1 TTTCTTTTCATTTTTT
34829 TCTTCAAGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
16 19 0.44
17 18 0.42
18 6 0.14
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTCATTTTTTA
Found at i:34800 original size:35 final size:35
Alignment explanation
Indices: 34761--34829 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
34751 CGAACCCTCC
34761 TTTTTCTCTTCATTTTT-TATTTCTTTC-TTTTTTTA
1 TTTTTCTCTTC-TTTTTAT-TTTCTTTCATTTTTTTA
* *
34796 TTTTTTTCTTCTTTTTATTTTTTTTCATTTTTTT
1 TTTTTCTCTTCTTTTTATTTTCTTTCATTTTTTT
34830 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTTTCTCTTCTTTTTATTTTCTTTCATTTTTTTA
Found at i:34802 original size:9 final size:9
Alignment explanation
Indices: 34788--34829 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
34778 TATTTCTTTC
34788 TTTTTTTA-
1 TTTTTTTAT
*
34796 TTTTTTTCT
1 TTTTTTTAT
*
34805 TCTTTTTAT
1 TTTTTTTAT
34814 TTTTTTTCAT
1 TTTTTTT-AT
34824 TTTTTT
1 TTTTTT
34830 CTTCAAGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.25
9 13 0.46
10 8 0.29
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:46168 original size:30 final size:29
Alignment explanation
Indices: 46134--46208 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 29
46124 TAAGGTACTT
**
46134 AAATAATAAAAATAGATAGTTTAA-AGACTA
1 AAATAATAAAAATAGA-AAATTAAGA-ACTA
46164 AAATAATAAAAAATAGAAAATTAAGTAACTA
1 AAATAAT-AAAAATAGAAAATTAAG-AACTA
46195 AAATAATAAAAATA
1 AAATAATAAAAATA
46209 TATAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 19 0.47
31 20 0.50
32 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.24
Consensus pattern (29 bp):
AAATAATAAAAATAGAAAATTAAGAACTA
Found at i:47867 original size:3 final size:3
Alignment explanation
Indices: 47859--47938 Score: 63
Period size: 3 Copynumber: 25.0 Consensus size: 3
47849 TAACATATAT
* *
47859 TAA TAA TAA TAA T-A TTA TAA TAA TAG TAA TAA TAA TAA TATA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A
* *
47905 TATA TACA TAA TATA TATA TAT TAA TAC TAA TAA
1 TA-A TA-A TAA TA-A TA-A TAA TAA TAA TAA TAA
47939 AAAATGGATG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.03
3 43 0.65
4 21 0.32
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:47872 original size:26 final size:26
Alignment explanation
Indices: 47859--47937 Score: 83
Period size: 26 Copynumber: 3.0 Consensus size: 26
47849 TAACATATAT
47859 TAATAATAATAATATTATAATAATAG
1 TAATAATAATAATATTATAATAATAG
47885 TAATAATAATAATA-TAT-ATATATA-
1 TAATAATAATAATATTATAATA-ATAG
*
47909 TACATAATATATATATATTAATACTAATA
1 TA-ATAATA-ATA-ATATT-ATAATAATA
47938 AAAAATGGAT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
24 5 0.11
25 12 0.27
26 17 0.38
27 3 0.07
28 1 0.02
29 5 0.11
30 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (26 bp):
TAATAATAATAATATTATAATAATAG
Found at i:47873 original size:17 final size:17
Alignment explanation
Indices: 47853--47938 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
47843 AATATGTAAC
47853 ATATATTAATAATAATA
1 ATATATTAATAATAATA
*
47870 ATAT-TATAATAATAGTA
1 ATATAT-TAATAATAATA
47887 ATA-A-TAATAAT-ATA
1 ATATATTAATAATAATA
47901 TATATATATACATAAT-ATA
1 -ATATAT-TA-ATAATAATA
*
47920 TATATATTAATACTAATA
1 -ATATATTAATAATAATA
47938 A
1 A
47939 AAAATGGATG
Statistics
Matches: 58, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
14 2 0.03
15 10 0.17
16 2 0.03
17 22 0.38
18 7 0.12
19 15 0.26
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (17 bp):
ATATATTAATAATAATA
Found at i:47888 original size:23 final size:22
Alignment explanation
Indices: 47861--47938 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 22
47851 ACATATATTA
47861 ATAATAATAATATTATAATAAT
1 ATAATAATAATATTATAATAAT
*
47883 AGTAATAATAATAATATATATATAT
1 A-TAATAATAATATTATA-ATA-AT
*
47908 ATACATAAT-ATATATATATTAAT
1 ATA-ATAATAATAT-TATAATAAT
47931 ACTAATAA
1 A-TAATAA
47939 AAAATGGATG
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
22 1 0.02
23 22 0.47
24 12 0.26
25 12 0.26
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (22 bp):
ATAATAATAATATTATAATAAT
Done.