Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012369.1 Corchorus olitorius cultivar O-4 contig12402, 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: 30090
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Found at i:991 original size:54 final size:54
Alignment explanation
Indices: 919--1062 Score: 189
Period size: 54 Copynumber: 2.7 Consensus size: 54
909 GTACAGGTGT
* * *
919 TTAAAATGACCCAATGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
***
973 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAGTTGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
* * * * *
1027 TTAAGTTGACCTAGTGCGGTCATTCAAAGAAGTTTT
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTT
1063 TATGATCAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (54 bp):
TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAAATCTAAACAGATC
Found at i:1092 original size:35 final size:34
Alignment explanation
Indices: 1053--1895 Score: 882
Period size: 35 Copynumber: 23.8 Consensus size: 34
1043 CGGTCATTCA
1053 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTCC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTT-C
***
1088 AAGAAGATTCCGATGATCAGAGTTGATCTCATTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
*
1123 AAGAAGTTTTT-T-AT-A-A-TCAGA---CATTTCC
1 AAGAAGTTTTTATGATCAGAGT-TGATCTCATTT-C
* * *
1151 AAGAAGTTTTCGATGATTAGAGTTGATCTTATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
**
1186 AAGAAGATTTTTATGATCAGAGTTGATCTCGGTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
1221 AAGAAGTTTTTATGATCAGAGTTGATCTCATTTCC
1 AAGAAGTTTTTATGATCAGAGTTGATCTCATTT-C
*
1256 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
*
1291 AATAAGTTTTTTATGATCAGAGTTGATCTCATTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
* * *
1326 CATAAGTTTTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAG----TTTTTATGATCAGAGTTGATCTCATTTC
*
1364 AAGAAGTTTTCGT-TGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
*
1399 AAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
*
1434 AAGAAGTTTTTCGTTGATCAGAGTTGATCTCA-TTC
1 AAGAAGTTTTT--ATGATCAGAGTTGATCTCATTTC
* *
1469 AAGAAGTTTTTTTTATGATCAGAGTTGATCTCGTATC
1 AAGAAG---TTTTTATGATCAGAGTTGATCTCATTTC
* *
1506 AAGAAGTTTTTTATGATTAGAGTTGATCTCCTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
1541 AAGAAGTTTTCGT-TGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT--TATGATCAGAGTTGATCTCATTTC
*
1576 AAGAAGTTTTTTTATGATCAGAGTTGATCT-AGTTCC
1 AAGAAG--TTTTTATGATCAGAGTTGATCTCA-TTTC
1612 AAGAAGCTTTTTATGATCAGAGTTGATCTCATTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
*
1647 AAGAAGTTTTTTATGATCAGAGTTGATCTCTTTTC
1 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTC
* * *
1682 AAGAAGTTTTTTTTTAGGATCAGAGTTTATCACATTACTCGTTTC
1 AAGAAG----TTTTTATGATCAGAG--T-T--GA-T-CTCATTTC
*
1727 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
* * *
1762 AAGAAGTTTTCGATGACCAGAGTTGATCTCGTTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
* *
1797 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
* *
1832 AAGAAGTTTTCGATGATCAGAGTTGATCTTATTTC
1 AAGAAGTTTT-TATGATCAGAGTTGATCTCATTTC
*
1867 AAGAAGTTTTCGATGATCAGAGTTGATCT
1 AAGAAGTTTT-TATGATCAGAGTTGATCT
1896 TCACATTGAT
Statistics
Matches: 708, Mismatches: 53, Indels: 94
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.01
28 11 0.02
29 1 0.00
30 4 0.01
31 3 0.00
32 3 0.00
33 4 0.01
34 42 0.06
35 413 0.58
36 125 0.18
37 13 0.02
38 52 0.07
39 1 0.00
40 2 0.00
41 5 0.01
42 9 0.01
43 1 0.00
44 1 0.00
45 13 0.02
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (34 bp):
AAGAAGTTTTTATGATCAGAGTTGATCTCATTTC
Found at i:1185 original size:63 final size:63
Alignment explanation
Indices: 1081--1206 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
1071 GAGTTGATCT
*
1081 CATTTCCAAGAAGATTCCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATAATCAGA
1 CATTTCCAAGAAGATTCCGATGATCAGAGTTGATCTCATTTCAAGAAGATTTTTATAATCAGA
* * * * *
1144 CATTTCCAAGAAGTTTTCGATGATTAGAGTTGATCTTATTTCAAGAAGATTTTTATGATCAGA
1 CATTTCCAAGAAGATTCCGATGATCAGAGTTGATCTCATTTCAAGAAGATTTTTATAATCAGA
1207 GTTGATCTCG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (63 bp):
CATTTCCAAGAAGATTCCGATGATCAGAGTTGATCTCATTTCAAGAAGATTTTTATAATCAGA
Found at i:1406 original size:19 final size:19
Alignment explanation
Indices: 1349--1406 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1339 TTATGATCAG
*
1349 AGTTGATCTCCTTTCAAGA
1 AGTTGATCTCGTTTCAAGA
1368 AGTT--T-TCGTTGATC-AG-
1 AGTTGATCTCGTT--TCAAGA
1384 AGTTGATCTCGTTTCAAGA
1 AGTTGATCTCGTTTCAAGA
1403 AGTT
1 AGTT
1407 TTTTATGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 14
0.67 0.02 0.30
Matches are distributed among these distances:
16 8 0.26
17 5 0.16
18 5 0.16
19 13 0.42
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (19 bp):
AGTTGATCTCGTTTCAAGA
Found at i:1789 original size:150 final size:140
Alignment explanation
Indices: 1053--1895 Score: 800
Period size: 142 Copynumber: 6.0 Consensus size: 140
1043 CGGTCATTCA
* * * *
1053 AAGAAG-TTTTTATGATCAGAGTTGATCTCATTTCCAAGAAGATTCCGATGATCAGAGTTGATCT
1 AAGAAGCTTTTGATGACCAGAGTTGATCTCATTT-CAAGAAGTTTTCGATGATCAGAGTTGATCT
* ** ** *
1117 CATTTCAAGAAGTTTTTTATAATC--A---GA-C--ATTTCCAAGAAGTTTTCGATGATTAGAGT
65 CGTTTCAAGAAGTTTTCGAGGATCAGAGTTGATCTTATTT-CAAGAAGTTTTCGATGATCAGAGT
*
1174 TGATCTTA-TTTC
129 TGATC-TAGTTCC
* * * ** *
1186 AAGAAGATTTTTATGATCAGAGTTGATCTCGGTTCAAGAAGTTTT-TATGATCAGAGTTGATCTC
1 AAGAAGCTTTTGATGACCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * * * **
1250 ATTTCCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAATAAGTTTTTTATGATCAGAGTT
66 GTTT-CAAGAAGTTTTCGAGGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGATGATCAGAGTT
*
1315 GATCTCATTTCC
130 GATCT-AGTTCC
* * * * * *
1327 -ATAAGTTTTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGAT
1 AAGAAG---CTTTTGATGACCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGAT
** * ** *
1391 CTCGTTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTCGTTGATCAGA
63 CTCGTTTCAAGAAGTTTTCGAGGATCAGAGTTGATCTTATTTCAAGAAG-TTTTCGATGATCAGA
1456 GTTGATCTCA-TT-C
127 GTTGATCT-AGTTCC
* * * * * ** *
1469 AAGAAGTTTTTTTTATGATCAGAGTTGATCTCGTATCAAGAAGTTTTTTATGATTAGAGTTGATC
1 AAGAAG--CTTTTGATGACCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATC
* ** * **
1534 TCCTTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTTATGATCAGAG
64 TCGTTTCAAGAAGTTTTCGAGGATCAGAGTTGATCTTATTTCAAGAAG-TTTTCGATGATCAGAG
1599 TTGATCTAGTTCC
128 TTGATCTAGTTCC
* * **
1612 AAGAAGCTTTTTATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTC
1 AAGAAGCTTTTGATGACCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* ** *
1677 TTTTCAAGAAGTTTTTTTTTAGGATCAGAGTTTATCACATTACTCGTTTCAAGAAGTTTTCGATG
66 GTTTCAAGAAG---TTTTCGAGGATCAGAGTTGAT--C-TTA----TTTCAAGAAGTTTTCGATG
*
1742 ATCAGAGTTGATCTCA-TTTC
121 ATCAGAGTTGATCT-AGTTCC
*
1762 AAGAAG-TTTTCGATGACCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
1 AAGAAGCTTTT-GATGACCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
*
1826 CGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGATGATCAGAGTT
65 CGTTTCAAGAAGTTTTCGAGGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGATGATCAGAGTT
1891 GATCT
130 GATCT
1896 TCACATTGAT
Statistics
Matches: 612, Mismatches: 66, Indels: 57
0.83 0.09 0.08
Matches are distributed among these distances:
132 22 0.04
133 31 0.05
134 25 0.04
135 1 0.00
138 2 0.00
139 2 0.00
140 63 0.10
141 73 0.12
142 120 0.20
143 87 0.14
144 61 0.10
145 1 0.00
146 1 0.00
147 19 0.03
149 4 0.01
150 89 0.15
151 11 0.02
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (140 bp):
AAGAAGCTTTTGATGACCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
GTTTCAAGAAGTTTTCGAGGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGATGATCAGAGTTG
ATCTAGTTCC
Found at i:1902 original size:185 final size:184
Alignment explanation
Indices: 1053--1890 Score: 743
Period size: 178 Copynumber: 4.7 Consensus size: 184
1043 CGGTCATTCA
* * * **
1053 AAGAAGTTTTT--ATGATCAGAGTTGATCTCATTTCCAAGAAGATTCCGATGATCAGAGTTGATC
1 AAGAAGTTTTTCGATGACCAGAGTTGATCT-AGTTCCAAGAAGCTTTTGATGATCAGAGTTGATC
** * * * * *
1116 TCATTTCAAGAAGTTTTTTATAATC--A---GA-C-ATTTCCAAGAAG-TTTTCGATGATTAGAG
65 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCTTTTCAAGAAGTTTTTCGAGGATCAGAG
* * **
1173 TTGAT--C-TTA----TTTCAAGAAGATTTT-TATGATCAGAGTTGATCTCGGTTC
130 TTTATCACATTACTCGTTTCAAGAAG-TTTTCGATGATCAGAGTTGATCTCATTTC
* *
1221 AAGAAGTTTTT--ATGATCAGAGTTGATCTCATTTCCAAGAAG-TTTTCGATGATCAGAGTTGAT
1 AAGAAGTTTTTCGATGACCAGAGTTGATCT-AGTTCCAAGAAGCTTTT-GATGATCAGAGTTGAT
* ** * * * ** *
1283 CTCATTTCAATAAGTTTTTTATGATCAGAGTTGATCTCATTTCCATAAGTTTTTTTTTATGATCA
64 CTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCTTTTCAAGAAG--TTTTTCGAGGATCA
* * *
1348 GAGTTGAT--C--T-C-C-TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCGTTTC
127 GAGTTTATCACATTACTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* * ** * * *
1399 AAGAAGTTTTT-TATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTCGTTGATCAGAGTTGATC
1 AAGAAGTTTTTCGATGACCAGAGTTGATCTAGTTCCAAGAAGCTTTT-GATGATCAGAGTTGATC
** * * * * *
1463 TCA-TTCAAGAAGTTTTTTTTATGATCAGAGTTGATCTCGTATCAAGAAGTTTTT-TATGATTAG
65 TCATTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCTTTTCAAGAAGTTTTTCGAGGATCAG
* *
1526 AGTTGAT--C--T-C-C-TTTCAAGAAGTTTTCGTTGATCAGAGTTGATCTCATTTC
128 AGTTTATCACATTACTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
** * *
1576 AAGAAGTTTTTTTATGATCAGAGTTGATCTAGTTCCAAGAAGCTTTTTATGATCAGAGTTGATCT
1 AAGAAGTTTTTCGATGACCAGAGTTGATCTAGTTCCAAGAAGCTTTTGATGATCAGAGTTGATCT
** **
1641 CATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCTTTTCAAGAAGTTTTTTTTTAGGATCAGA
66 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCTTTTCAAGAAG--TTTTTCGAGGATCAGA
1706 GTTTATCACATTACTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
129 GTTTATCACATTACTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
1762 AAGAAG-TTTTCGATGACCAGAGTTGATCTCGTTTCAAGAAG-TTTTCGATGATCAGAGTTGATC
1 AAGAAGTTTTTCGATGACCAGAGTTGATCTAGTTCCAAGAAGCTTTT-GATGATCAGAGTTGATC
* *
1825 TCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCT-TATTTCAAGAAG-TTTTCGATGATCAGA
65 TCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCT-TTTCAAGAAGTTTTTCGAGGATCAGA
1888 GTT
129 GTT
1891 GATCTTCACA
Statistics
Matches: 588, Mismatches: 50, Indels: 50
0.85 0.07 0.07
Matches are distributed among these distances:
167 2 0.00
168 81 0.14
170 1 0.00
173 2 0.00
174 1 0.00
175 7 0.01
176 33 0.06
177 91 0.15
178 128 0.22
179 54 0.09
180 31 0.05
181 1 0.00
182 15 0.03
183 1 0.00
184 6 0.01
185 90 0.15
186 44 0.07
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (184 bp):
AAGAAGTTTTTCGATGACCAGAGTTGATCTAGTTCCAAGAAGCTTTTGATGATCAGAGTTGATCT
CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCTTTTCAAGAAGTTTTTCGAGGATCAGAGT
TTATCACATTACTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
Found at i:9417 original size:23 final size:23
Alignment explanation
Indices: 9387--9433 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
9377 ATCCGAAAAT
* *
9387 GGCCATGGTGCTGATCGCGACCC
1 GGCCATGGAGATGATCGCGACCC
*
9410 GGCCATGGAGATGGTCGCGACCC
1 GGCCATGGAGATGATCGCGACCC
9433 G
1 G
9434 CGTCGCGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.32, G:0.38, T:0.15
Consensus pattern (23 bp):
GGCCATGGAGATGATCGCGACCC
Found at i:9847 original size:16 final size:16
Alignment explanation
Indices: 9823--9864 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
9813 AATTCAGATT
*
9823 TTTTTTAGAATTTGGG
1 TTTTATAGAATTTGGG
9839 TTTTATAGAATTTGGG
1 TTTTATAGAATTTGGG
9855 TTTTAT-GAAT
1 TTTTATAGAAT
9865 GAAACACACG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (16 bp):
TTTTATAGAATTTGGG
Found at i:11280 original size:42 final size:43
Alignment explanation
Indices: 11232--11321 Score: 146
Period size: 45 Copynumber: 2.1 Consensus size: 43
11222 TATTATCTTA
*
11232 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
11274 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
11319 ATT
1 ATT
11322 AATTGTTGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
42 6 0.14
45 38 0.86
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAT
Found at i:15594 original size:22 final size:21
Alignment explanation
Indices: 15568--15652 Score: 73
Period size: 22 Copynumber: 4.0 Consensus size: 21
15558 AAAAAAAAAC
*
15568 CCTATTAAATTGTGATAACCA
1 CCTATGAAATTGTGATAACCA
* * **
15589 CGCTATGAAATTTTGATCATTA
1 C-CTATGAAATTGTGATAACCA
* *
15611 CCTATGAAATTGTGATAAACT
1 CCTATGAAATTGTGATAACCA
15632 CCATATGAAACTT-TGATAACC
1 CC-TATGAAA-TTGTGATAACC
15653 TAAATATAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
21 18 0.36
22 30 0.60
23 2 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (21 bp):
CCTATGAAATTGTGATAACCA
Found at i:15698 original size:21 final size:21
Alignment explanation
Indices: 15591--15734 Score: 71
Period size: 21 Copynumber: 6.7 Consensus size: 21
15581 GATAACCACG
* *
15591 CTATGAAATTTTG-ATCATTAC
1 CTATGAAATTTTGTAACCTT-C
* *
15612 CTATGAAATTGTGATAAAC-TC
1 CTATGAAATTTTG-TAACCTTC
* **
15633 CATATGAAACTTTGATAACCTAA
1 C-TATGAAATTTTG-TAACCTTC
* * *
15656 ATATAAAATTTTAATAAACCTTC
1 CTATGAAATTTT-GT-AACCTTC
15679 CTATGAAATTTTGTAACCTTC
1 CTATGAAATTTTGTAACCTTC
* *
15700 TTATG-ATTTTTGATAA-CTTCC
1 CTATGAAATTTTG-TAACCTT-C
*
15721 CTATGAGATTTTGT
1 CTATGAAATTTTGT
15735 TAATTTCCCT
Statistics
Matches: 91, Mismatches: 23, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
20 9 0.10
21 34 0.37
22 32 0.35
23 16 0.18
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (21 bp):
CTATGAAATTTTGTAACCTTC
Found at i:15754 original size:22 final size:22
Alignment explanation
Indices: 15706--15758 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
15696 CTTCTTATGA
*
15706 TTTTTGATAACTTCCCTATGAG
1 TTTTTGATAACTTCCCTATAAG
* * * *
15728 ATTTTGTTAATTTCCCTATAAT
1 TTTTTGATAACTTCCCTATAAG
15750 TTTTTGATA
1 TTTTTGATA
15759 TCATAGTATG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.25, C:0.13, G:0.09, T:0.53
Consensus pattern (22 bp):
TTTTTGATAACTTCCCTATAAG
Found at i:18436 original size:19 final size:18
Alignment explanation
Indices: 18403--18438 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18393 TTGAGATAAT
18403 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
18421 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
18439 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.