Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014074.1 Corchorus capsularis cultivar CVL-1 contig14095, 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: 3223
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1083 original size:30 final size:31
Alignment explanation
Indices: 1019--1083 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1009 AACTTTATGT
* *
1019 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
*
1050 TTTCCAATTGTACCCTT-TTTTAAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
1080 TTTC
1 TTTC
1084 TAAATTGCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:1090 original size:31 final size:31
Alignment explanation
Indices: 1025--1090 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1015 ATGTTTTCCG
* *
1025 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCAA
*
1056 ATTGTACCCTT-TTTTAAAAATATATTTCTAA
1 ATTGTACCCTTATTTTAAAAACATATTTC-AA
1087 ATTG
1 ATTG
1091 CCATTACTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCAA
Found at i:1250 original size:44 final size:44
Alignment explanation
Indices: 1197--1280 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
1187 TCATGAGGAG
* *
1197 GTTATCAAAA-TTCTATAGTGTGGTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTC-ATAGAGTGGTTACCAAAATTTCATAGTGTA
1241 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG
1 GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAG
1281 GATCCGGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 34 0.92
45 3 0.08
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (44 bp):
GTTACCAAAATTTCATAGAGTGGTTACCAAAATTTCATAGTGTA
Found at i:1314 original size:22 final size:22
Alignment explanation
Indices: 1173--1334 Score: 121
Period size: 22 Copynumber: 7.3 Consensus size: 22
1163 TATTTTACTT
*
1173 TGGTTATTATAATTTCAT-GAGG
1 TGGTTATTAAAATTTCATAG-GG
* * *
1195 AGGTTATCAAAA-TTCTATAGTG
1 TGGTTATTAAAATTTC-ATAGGG
** *
1217 TGGTTACCAAAATTTCATAGTG
1 TGGTTATTAAAATTTCATAGGG
* ** *
1239 TAGTTACCAAAATTTCATAGAG
1 TGGTTATTAAAATTTCATAGGG
** *
1261 TGGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGG
* *
1283 TCCGGTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGG
*
1307 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGG
1329 TGGTTA
1 TGGTTA
1335 ATTATCACAA
Statistics
Matches: 117, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
21 3 0.03
22 92 0.79
23 4 0.03
24 18 0.15
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGG
Found at i:1502 original size:22 final size:22
Alignment explanation
Indices: 1398--1740 Score: 117
Period size: 22 Copynumber: 15.4 Consensus size: 22
1388 AGGTTATACG
* *
1398 AATTTCATA-GTATGGTTAACAA
1 AATTTCATATG-AAGGTTATCAA
1420 AATTTCAT-TAGAAGGTTA-CTAA
1 AATTTCATAT-GAAGGTTATC-AA
* * ** *
1442 TACTTCATCGGGAGGTTATCAA
1 AATTTCATATGAAGGTTATCAA
* *
1464 AATTTTATAGTG-TGGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
1486 AATTTCATATGAAGGTTAT-AA
1 AATTTCATATGAAGGTTATCAA
* * *
1507 AAGTCTCAATTTCAT-AAGGAGTACCAA
1 AA-TTTC-A--T-ATGAAGG-TTATCAA
*
1534 AATTTGATA-GAAGGTTATC-A
1 AATTTCATATGAAGGTTATCAA
* *
1554 AATCTCATA-G-AGTGATTATCGA
1 AATTTCATATGAAG-G-TTATCAA
* *
1576 AATTTCATAAAGATATGATTATCAA
1 AATTTCAT-ATGA-A-GGTTATCAA
*
1601 AATTT-ATATGAAGATTATCAA
1 AATTTCATATGAAGGTTATCAA
**
1622 AATTTCATAGTG-TTGTTATCAA
1 AATTTCATA-TGAAGGTTATCAA
* *
1644 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATATG-AAGGTTATCAA
* * *
1666 AATTACATAATG-TGATTATCAA
1 AATTTCAT-ATGAAGGTTATCAA
* * *
1688 AATTTCATA-GAGGGGTCAACAA
1 AATTTCATATGA-AGGTTATCAA
*
1710 AATTT--TATAAAGATGTTATCAA
1 AATTTCATATGAAG--GTTATCAA
1732 AATTTCATA
1 AATTTCATA
1741 AAGAGTTTAT
Statistics
Matches: 240, Mismatches: 45, Indels: 70
0.68 0.13 0.20
Matches are distributed among these distances:
19 2 0.01
20 15 0.06
21 32 0.13
22 144 0.60
23 11 0.05
24 7 0.03
25 17 0.07
26 7 0.03
27 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
AATTTCATATGAAGGTTATCAA
Found at i:1611 original size:18 final size:19
Alignment explanation
Indices: 1588--1626 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
1578 TTTCATAAAG
1588 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
1606 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
1627 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:1685 original size:44 final size:44
Alignment explanation
Indices: 1547--1760 Score: 159
Period size: 44 Copynumber: 4.8 Consensus size: 44
1537 TTGATAGAAG
* * * * * *
1547 GTTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAAAGATAT
1 GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG--AT
* * * *
1592 GATTATCAAAATTT-ATATGA-AGATTATCAAAATTTCATAGTGTT
1 G-TTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGAT
* *
1636 GTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG-T
1 GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
* * * * * *
1679 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAT
1 G-TTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
* *
1724 GTTATCAAAATTTCATAA-AGAGTTTATCAAATTTTCA
1 GTTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCA
1761 AAATCTGATT
Statistics
Matches: 133, Mismatches: 28, Indels: 17
0.75 0.16 0.10
Matches are distributed among these distances:
43 16 0.12
44 82 0.62
45 4 0.03
46 24 0.18
47 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGAT
Found at i:1711 original size:66 final size:66
Alignment explanation
Indices: 1612--1760 Score: 165
Period size: 66 Copynumber: 2.3 Consensus size: 66
1602 ATTTATATGA
* ** * * *
1612 AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAA
*
1676 TG
65 AG
* * * *
1678 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
1743 G
66 G
* *
1744 AGTTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
1761 AAATCTGATT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 66 0.97
67 2 0.03
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.36
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
G
Found at i:1713 original size:88 final size:88
Alignment explanation
Indices: 1619--1785 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
1609 TGAAGATTAT
** * * * *
1619 CAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATCTGATT
1683 ATC-AAAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
* * * *
1707 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGTTTATCAAATTTTCAAAATCTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
1772 CAAAAATTTCATAG
66 CAAAAATTTCATAG
1786 TGGTCTGGGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.01
88 64 0.96
89 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.35
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:1757 original size:21 final size:22
Alignment explanation
Indices: 1514--1760 Score: 140
Period size: 22 Copynumber: 11.3 Consensus size: 22
1504 TAAAAGTCTC
* *
1514 AATTTCATAAGGA-G-TACCAA
1 AATTTCATAAAGATGTTATCAA
*
1534 AATTTGATAGAAG--GTTATC-A
1 AATTTCATA-AAGATGTTATCAA
* * *
1554 AATCTCATAGAG-TGATTATCGA
1 AATTTCATAAAGATG-TTATCAA
1576 AATTTCATAAAGATATGATTATCAA
1 AATTTCATAAAG--ATG-TTATCAA
1601 AATTT-ATATGAAGA--TTATCAA
1 AATTTCATA--AAGATGTTATCAA
** *
1622 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGATGTTATCAA
* *
1644 AATTTCA-AAGCGAGGTTATCAA
1 AATTTCATAA-AGATGTTATCAA
* *
1666 AATTACATAATG-TGATTATCAA
1 AATTTCATAAAGATG-TTATCAA
* ** * *
1688 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGATGTTATCAA
*
1710 AATTTTATAAAGATGTTATCAA
1 AATTTCATAAAGATGTTATCAA
1732 AATTTCATAAAGA-GTTTATCAA
1 AATTTCATAAAGATG-TTATCAA
*
1754 ATTTTCA
1 AATTTCA
1761 AAATCTGATT
Statistics
Matches: 176, Mismatches: 33, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
19 2 0.01
20 19 0.11
21 25 0.14
22 106 0.60
23 3 0.02
24 4 0.02
25 14 0.08
26 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
AATTTCATAAAGATGTTATCAA
Found at i:1892 original size:19 final size:19
Alignment explanation
Indices: 1864--1930 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
1854 ACGGAGTAAT
1864 CAAAATTTCAGGGAGGATAC
1 CAAAA-TTCAGGGAGGATAC
1884 CAAAATTCAGGGAGGATATC
1 CAAAATTCAGGGAGGATA-C
* *
1904 ACAAAATTCAGTGAGGATAT
1 -CAAAATTCAGGGAGGATAC
1924 CAAAATT
1 CAAAATT
1931 TCATATGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
19 20 0.47
20 6 0.14
21 17 0.40
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (19 bp):
CAAAATTCAGGGAGGATAC
Found at i:1910 original size:21 final size:21
Alignment explanation
Indices: 1864--1933 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
1854 ACGGAGTAAT
1864 CAAAATTTCAGGGAGGATA-C-
1 CAAAA-TTCAGGGAGGATATCA
1884 CAAAATTCAGGGAGGATATCA
1 CAAAATTCAGGGAGGATATCA
*
1905 CAAAATTCAGTGAGGATATCA
1 CAAAATTCAGGGAGGATATCA
*
1926 -AAATTTCA
1 CAAAATTCA
1934 TATGAAGGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.28
20 13 0.28
21 20 0.43
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (21 bp):
CAAAATTCAGGGAGGATATCA
Found at i:1949 original size:22 final size:22
Alignment explanation
Indices: 1921--2480 Score: 119
Period size: 22 Copynumber: 25.7 Consensus size: 22
1911 TCAGTGAGGA
1921 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
1943 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1965 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
1987 TATCAAAATTCCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * **
2008 AGATCAAAATTTCATAGGGACAT
1 -TATCAAAATTTCATATGAAGGT
* *
2031 TAACAAAATTTCATAATG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * **
2053 TATCAAAAAATCATAGGGAA-CA
1 TATCAAAATTTCATA-TGAAGGT
*
2075 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
2091 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
2113 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
2136 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
*
2159 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2181 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
2203 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
2225 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
2247 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
2269 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
2291 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
2314 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
2336 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
2358 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
2380 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
2402 TA-AAAAATTTTATA-AAAGGAT
1 TATCAAAATTTCATATGAAGG-T
* ** * **
2423 TCTTGAAATTCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2445 TATTATAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
2466 TATCAAAATTTCATA
1 TATCAAAATTTCATA
2481 ATGGGATCAT
Statistics
Matches: 387, Mismatches: 112, Indels: 79
0.67 0.19 0.14
Matches are distributed among these distances:
16 9 0.02
18 2 0.01
20 11 0.03
21 43 0.11
22 247 0.64
23 69 0.18
24 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:2143 original size:23 final size:23
Alignment explanation
Indices: 2112--2215 Score: 95
Period size: 23 Copynumber: 4.6 Consensus size: 23
2102 CATAAGAAAG
*
2112 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAGAGGT
* * *
2135 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAGAGGT
* *
2158 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGAGAGGT
* * * * *
2180 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGAGAGGT
2202 TTATCAAAATTTTA
1 TTATCAAAATTTTA
2216 AAGTGTGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
21 1 0.02
22 29 0.44
23 36 0.55
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAGAGGT
Found at i:2338 original size:45 final size:45
Alignment explanation
Indices: 2265--2350 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
2255 TTTTATAAAG
* * *
2265 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
2310 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
2351 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Found at i:2699 original size:30 final size:31
Alignment explanation
Indices: 2640--2704 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2630 AACTTTATGT
*
2640 TTTCCAATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
2671 TTTCCAATTGTACCCTT-TTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
2701 TTTC
1 TTTC
2705 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.31, C:0.20, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:2919 original size:38 final size:37
Alignment explanation
Indices: 2829--2919 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 37
2819 AACTTTTTGT
* * * *
2829 TTCCAACGTCCT-GTTTAATTTTGCCTTTTGTCTTTG
1 TTCCAACGTCCTATTTTAATTTTACATTTTGTCTTCG
* **
2865 TTTCAATCGTTGTATTTTAATTTTACATTTTGTCTTCG
1 TTCCAA-CGTCCTATTTTAATTTTACATTTTGTCTTCG
2903 TCTCCAACGTCCTATTT
1 T-TCCAACGTCCTATTT
2920 GGCCTTAGAT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
36 5 0.12
37 4 0.10
38 29 0.69
39 4 0.10
ACGTcount: A:0.15, C:0.21, G:0.11, T:0.53
Consensus pattern (37 bp):
TTCCAACGTCCTATTTTAATTTTACATTTTGTCTTCG
Found at i:3005 original size:22 final size:22
Alignment explanation
Indices: 2973--3033 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
2963 TGAATGGTCC
2973 AATT-TCAAAATTTCA-AAT-T
1 AATTATCAAAATTTCATAATGT
*
2992 GAAGTTATCAAAATTACATAATGT
1 -AA-TTATCAAAATTTCATAATGT
*
3016 CATTATCAAAATTTCATA
1 AATTATCAAAATTTCATA
3034 GAGGGGTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 25 0.74
23 4 0.12
24 1 0.03
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (22 bp):
AATTATCAAAATTTCATAATGT
Found at i:3072 original size:21 final size:22
Alignment explanation
Indices: 3046--3088 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
3036 GGGGTCAACA
*
3046 AAAATTT-ATAGAGAGGTTATT
1 AAAATTTAATAAAGAGGTTATT
3067 AAAATTTACATAAAGAGGTTAT
1 AAAATTTA-ATAAAGAGGTTAT
3089 CAAATTTTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (22 bp):
AAAATTTAATAAAGAGGTTATT
Done.