Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009005.1 Corchorus capsularis cultivar CVL-1 contig09026, 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: 39159
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:826 original size:25 final size:25
Alignment explanation
Indices: 775--827 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
765 ATTTCCATTA
* *
775 TTAAAATTTAGTATAATTTTATTAT
1 TTAAAATTTAGTAAAATTTTATAAT
*
800 TTAAAATTTAATTAAAATTTT-TAAT
1 TTAAAATTT-AGTAAAATTTTATAAT
825 TTA
1 TTA
828 GACCGAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAAAATTTAGTAAAATTTTATAAT
Found at i:921 original size:19 final size:20
Alignment explanation
Indices: 894--931 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
884 TACTATTATT
894 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
914 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
932 AATGTTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:1125 original size:22 final size:22
Alignment explanation
Indices: 1097--1258 Score: 150
Period size: 22 Copynumber: 7.3 Consensus size: 22
1087 GGTCTCTATG
*
1097 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
1119 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
1142 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
1163 TGGTTACCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
1185 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* * *
1207 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGGA
** *
1231 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAGGA
1253 TGGTTA
1 TGGTTA
1259 ATTATCACAA
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
21 3 0.03
22 95 0.80
23 3 0.03
24 18 0.15
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:1319 original size:22 final size:21
Alignment explanation
Indices: 1294--1642 Score: 138
Period size: 22 Copynumber: 15.7 Consensus size: 21
1284 ATCAAAGAGA
*
1294 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
1316 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
1338 TTAAT-AAAATTTCATTAGGAGG
1 TT-ATCAAAATTTCA-TAGGAGG
* *
1360 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
*
1382 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
1404 TTATAAAAGTCTGAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATA-GGAGG
* * *
1431 -TACCAAAATTTGATAGAAGG
1 TTATCAAAATTTCATAGGAGG
* *
1451 TTATC-AAATCTCATA-GAGTAA
1 TTATCAAAATTTCATAGGAG--G
*
1472 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAG-GA--GG
**
1496 ATTATCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAG-GAGG
* *
1519 TTATCAAAATTTCAAAACGAGG
1 TTATCAAAATTTC-ATAGGAGG
* * * *
1541 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
*
1563 TTAT-AAGAATTTCATAGAGGGG
1 TTATCAA-AATTTCATAG-GAGG
* * ** *
1585 TCAACAAAATTTTGTAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
1607 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
1629 TTATCAAATTTTCA
1 TTATCAAAATTTCA
1643 AAATGTGATT
Statistics
Matches: 246, Mismatches: 51, Indels: 60
0.69 0.14 0.17
Matches are distributed among these distances:
19 4 0.02
20 17 0.07
21 16 0.07
22 157 0.64
23 16 0.07
24 2 0.01
25 19 0.08
26 3 0.01
27 1 0.00
28 11 0.04
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:1360 original size:44 final size:42
Alignment explanation
Indices: 1294--2219 Score: 163
Period size: 44 Copynumber: 21.4 Consensus size: 42
1284 ATCAAAGAGA
* * *
1294 TTATCAAAATGTCATAGCGAGGTTATAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTATAA-AATTTCATAGGGAGG
* *
1338 TTAAT-AAAATTTCATTAGGAGGTTACTAATATTTCATGGGGAGG
1 TT-ATCAAAATTTCA-TAGGAGGTTA-TAAAATTTCATAGGGAGG
* *
1382 TTATCAAAATTTCATATGAAGGTTATAAAAGTCTGAATTTCATAAGGA-G
1 TTATCAAAATTTCATA-GGAGGTTAT--AA-----AATTTCATAGGGAGG
* * * * * * *
1431 -TACCAAAATTTGATAGAAGGTTATCAAATCTCATAGAGTA-A
1 TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAG-GGAGG
* * **
1472 TTATCGAAATTTCATAGAGATCGGATTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GA--GG-TTAT-AAAATTTCATAGGGAGG
* * * ** * *
1519 TTATCAAAATTTCAAAACGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTC-ATAGGAGGTTAT-AAAATTTCATAGGGAGG
* * * ** **
1563 TTAT-AAGAATTTCATAGAGGGGTCAACAAAATTTTGTAAAGAGG
1 TTATCAA-AATTTCATAG-GAGGT-TATAAAATTTCATAGGGAGG
* * * ** * *
1607 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCAT-AGGAGGTTAT-AAAATTTCATAGGGAGG
* *
1651 TTA-CAAAAATTTCATA-GTGG---T---ATTTC-TGGGGAGG
1 TTATC-AAAATTTCATAGGAGGTTATAAAATTTCATAGGGAGG
* * * *
1685 TTATCAAAATTTCATAGTATGGTTGTCAAA--T--TAGGAAGG
1 TTATCAAAATTTCATAGGA-GGTTATAAAATTTCATAGGGAGG
* * * *
1724 TTATTAAACTTTTATTATGGA-GTAATCAAAATTTC--AGGGAGG
1 TTATCAAAATTTCA-TA-GGAGGTTAT-AAAATTTCATAGGGAGG
* * **
1766 ATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTA-G
1 TTATCAAAATTTCATA-GGAGGTTAT-AAAATTTCATAG-GGAGG
* * * *
1810 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATG
1 TTATCAAAATTTCATAGGA-GGTTAT-AAAATTTCATAGGGAGG
* * * * **
1853 TAGATCAAAATTTGATAGGGAGATTAACAAAATTTCATAATGAGG
1 T-TATCAAAATTTCATA-GGAGGTT-ATAAAATTTCATAGGGAGG
** * * *
1898 TTATCAAAAAAATCACAGGAAGCTTATCAAAA-TT--T--GTA-G
1 TTATC-AAAATTTCATAGG-AGGTTAT-AAAATTTCATAGGGAGG
* * * *
1937 TTATCAAGATTTCATAAGAAAGTTATTAAAATTTTATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTA-TAAAATTTCATAGGGAGG
* * * *
1981 TTTATCAAAA-TTCTATAAGAAGATTTATCAGAATTTCATAGCGAGG
1 -TTATCAAAATTTC-AT-AGGAG-GTTAT-AAAATTTCATAGGGAGG
* * * * * * *
2027 TTATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGAGTGA
1 TTATCAAAATTTCATAG-GAGGTTAT-AAAATTTCATAGGGAGG
* * * ** *
2071 TTAAT-AACAA-TTCATATGGAGGTTTTTAAATTTTTATAACGTGG
1 TT-ATCAA-AATTTCATA-GGAGG-TTATAAAATTTCATAGGGAGG
* * * * * **
2115 TTAACAATATATCATATGGAGGTTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATA-GGAGGTTAT-AAAATTTCATAG-GGAGG
* * * *
2160 TTATCCAAATTTCATTGGGAAGTTATCAAAA-TTCTTTAGGGAGG
1 TTATCAAAATTTCA-TAGGAGGTTAT-AAAATTTC-ATAGGGAGG
*
2204 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
2220 AGAAAGTTAA
Statistics
Matches: 638, Mismatches: 164, Indels: 161
0.66 0.17 0.17
Matches are distributed among these distances:
34 16 0.03
35 5 0.01
36 2 0.00
38 14 0.02
39 33 0.05
40 15 0.02
41 10 0.02
42 50 0.08
43 24 0.04
44 281 0.44
45 104 0.16
46 25 0.04
47 33 0.05
48 15 0.02
49 1 0.00
50 10 0.02
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.35
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATAAAATTTCATAGGGAGG
Found at i:1574 original size:66 final size:66
Alignment explanation
Indices: 1495--1642 Score: 156
Period size: 66 Copynumber: 2.2 Consensus size: 66
1485 ATAGAGATCG
* ** * *
1495 GATTATCAAAATTTCATAGTGTTGTTATCAAAA-TTTCAAAACGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTCAAAA-GAGGTTATCAAAATTACATAAT
1559 GT
65 GT
** * *
1561 GATTAT-AAGAATTTCATAGAGGGGTCAACAAAATTTTGTAAAGAGGTTATCAAAATTTCATAAA
1 GATTATCAA-AATTTCATAGAGGGGTCAACAAAATTTTCAAAAGAGGTTATCAAAATTACATAAT
*
1625 GA
65 GT
* *
1627 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
1643 AAATGTGATT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
65 2 0.03
66 57 0.85
67 8 0.12
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTCAAAAGAGGTTATCAAAATTACATAATG
T
Found at i:1795 original size:22 final size:22
Alignment explanation
Indices: 1767--2062 Score: 130
Period size: 22 Copynumber: 13.6 Consensus size: 22
1757 TCAGGGAGGA
1767 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
1789 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
1811 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
1833 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * * *
1854 AGATCAAAATTTGATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
1877 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
1899 TATCAAAAAAATCACAGGAAGCT
1 TATC-AAAATTTCATATGAAGGT
*
1922 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
1938 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * * *
1960 TATTAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* *
1983 TATCAAAA-TTCTATAAGAAGATT
1 TATCAAAATTTC-ATATGAAG-GT
* *
2006 TATCAGAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
2028 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
2050 TATCAAAATTTCA
1 TATCAAAATTTCA
2063 GAGAGTGATT
Statistics
Matches: 202, Mismatches: 52, Indels: 40
0.69 0.18 0.14
Matches are distributed among these distances:
16 8 0.04
17 2 0.01
18 1 0.00
20 2 0.01
21 5 0.02
22 132 0.65
23 48 0.24
24 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:1860 original size:66 final size:66
Alignment explanation
Indices: 1762--1906 Score: 161
Period size: 66 Copynumber: 2.2 Consensus size: 66
1752 AAATTTCAGG
* * ** **
1762 GAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAG-TTTTCAAAATTTCATA
1 GAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAG-GGAGATTAACAAAATTTCATA
1826 A-
65 AT
* * *
1827 GAGGGTTATCAAAATTTCATA-GTATGTAGATCAAAATTTGATAGGGAGATTAACAAAATTTCAT
1 GA-GGTTATCAAAATTTCATATGAAGGT-GATCAAAATTTCATAGGGAGATTAACAAAATTTCAT
1891 AAT
64 AAT
1894 GAGGTTATCAAAA
1 GAGGTTATCAAAA
1907 AAATCACAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
65 8 0.12
66 57 0.85
67 2 0.03
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (66 bp):
GAGGTTATCAAAATTTCATATGAAGGTGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAA
T
Found at i:2001 original size:45 final size:45
Alignment explanation
Indices: 1743--2042 Score: 173
Period size: 44 Copynumber: 6.9 Consensus size: 45
1733 TTTTATTATG
* * * *
1743 GAGTAATCAAAATTTC--AGGGAGGATATCAAAATTTCATATGAA
1 GAGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAA
** *
1786 G-GTTATCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAAG-A
1 GAGTTATCAAAATTTCATAG-CGAGGTTATCAAAATTTCATAAGAA
* * * * * * *
1829 GGGTTATCAAAATTTCATAG-TATGTAGATCAAAATTTGATAGGGA
1 GAGTTATCAAAATTTCATAGCGAGGT-TATCAAAATTTCATAAGAA
* ** ** * *
1874 GA-TTAACAAAATTTCATAATGAGGTTATCAAAAAAATCACAGGAA
1 GAGTTATCAAAATTTCATAGCGAGGTTATC-AAAATTTCATAAGAA
* * *
1919 G-CTTATCAAAA-TT--T-G-TA-GTTATCAAGATTTCATAAGAA
1 GAGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAA
* * *
1957 -AGTTATTAAAATTTTATAGGGAGGTTTATCAAAA-TTCTATAAGAA
1 GAGTTATCAAAATTTCATAGCGAGG-TTATCAAAATTTC-ATAAGAA
* * *
2002 GATTTATCAGAATTTCATAGCGAGGTTATCACAATTTCATA
1 GAGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATA
2043 GTGTGATTAT
Statistics
Matches: 197, Mismatches: 39, Indels: 40
0.71 0.14 0.14
Matches are distributed among these distances:
38 18 0.09
39 8 0.04
40 1 0.01
41 1 0.01
42 17 0.09
43 6 0.03
44 73 0.37
45 51 0.26
46 22 0.11
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (45 bp):
GAGTTATCAAAATTTCATAGCGAGGTTATCAAAATTTCATAAGAA
Found at i:2070 original size:22 final size:22
Alignment explanation
Indices: 2027--2073 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2017 CATAGCGAGG
* * *
2027 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGAGTGA
2049 TTATCAAAATTTCAGAGAGTGA
1 TTATCAAAATTTCAGAGAGTGA
2071 TTA
1 TTA
2074 ATAACAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGAGTGA
Found at i:2191 original size:22 final size:23
Alignment explanation
Indices: 2159--2218 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
2149 CATAGTGTTG
*
2159 GTTATCCAAATTTCATT-GGGAA
1 GTTATCAAAATTTCATTAGGGAA
* *
2181 GTTATCAAAA-TTCTTTAGGGAG
1 GTTATCAAAATTTCATTAGGGAA
*
2203 GTTAACAAAATTTCAT
1 GTTATCAAAATTTCAT
2219 AAGAAAGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 5 0.16
22 22 0.71
23 4 0.13
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (23 bp):
GTTATCAAAATTTCATTAGGGAA
Found at i:2874 original size:1 final size:1
Alignment explanation
Indices: 2868--2894 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2858 ACATAGTTTT
2868 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2895 CTAAGTTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6756 original size:2 final size:2
Alignment explanation
Indices: 6749--6775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6739 ATAATTTTCC
6749 TA 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 TA T
6776 TTATTTTCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8135 original size:13 final size:14
Alignment explanation
Indices: 8110--8148 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
8100 AATAAGCTGT
8110 ATTAATATCATTTA
1 ATTAATATCATTTA
8124 ATTAATAT-ATTTA
1 ATTAATATCATTTA
*
8137 TTTAATCATCAT
1 ATTAAT-ATCAT
8149 CATATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 10 0.45
14 10 0.45
15 2 0.09
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTAATATCATTTA
Found at i:8476 original size:3 final size:3
Alignment explanation
Indices: 8468--8527 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
8458 AATTGAATAG
8468 TAT TAT TAT TAT 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
8516 TAT TAT TAT TAT
1 TAT TAT TAT TAT
8528 ATAGTTGCTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:10605 original size:2 final size:2
Alignment explanation
Indices: 10598--10637 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
10588 ATATAATTTA
10598 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10638 GAGGAGTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12584 original size:6 final size:6
Alignment explanation
Indices: 12568--12602 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
12558 TCACTTTATT
12568 ATATAAA ATATAA ATATAA ATATAA ATAT-A ATATA
1 ATAT-AA ATATAA ATATAA ATATAA ATATAA ATATA
12603 TGCCGCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 18 0.67
7 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:12859 original size:33 final size:33
Alignment explanation
Indices: 12797--12890 Score: 95
Period size: 33 Copynumber: 2.9 Consensus size: 33
12787 TTTTTGCACT
** *
12797 GAGCCTCCCCACTATGACGG-TTCAGCCATGGCG
1 GAGCCTCCCCACTGGGGCGGCTTCAGCCATGG-G
12830 GAGCCTCCCCACTGGGGCGGCTTCA-CCATGGG
1 GAGCCTCCCCACTGGGGCGGCTTCAGCCATGGG
* **
12862 CAGGTTGCCCCACTGGGGCGGCTTC-GCCA
1 GAGCCT-CCCCACTGGGGCGGCTTCAGCCA
12891 CGGCAAGCCG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
32 4 0.08
33 44 0.85
34 4 0.08
ACGTcount: A:0.14, C:0.37, G:0.32, T:0.17
Consensus pattern (33 bp):
GAGCCTCCCCACTGGGGCGGCTTCAGCCATGGG
Found at i:12891 original size:17 final size:17
Alignment explanation
Indices: 12838--12891 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
12828 CGGAGCCTCC
12838 CCACTGGGGCGGCTTCA
1 CCACTGGGGCGGCTTCA
*
12855 CCA-T-GGGCAGG-TTGCC
1 CCACTGGGGC-GGCTT-CA
*
12871 CCACTGGGGCGGCTTCG
1 CCACTGGGGCGGCTTCA
12888 CCAC
1 CCAC
12892 GGCAAGCCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 6 0.20
16 7 0.23
17 11 0.37
18 6 0.20
ACGTcount: A:0.11, C:0.37, G:0.35, T:0.17
Consensus pattern (17 bp):
CCACTGGGGCGGCTTCA
Found at i:30220 original size:29 final size:29
Alignment explanation
Indices: 30188--30248 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
30178 TAAATTTAGC
**
30188 ATATA-TAAATAAACATCAATTGCAAGTCT
1 ATATATTAAATAAA-AAAAATTGCAAGTCT
*
30217 ATATATTATATAAAAAAAATTGCAAGTCT
1 ATATATTAAATAAAAAAAATTGCAAGTCT
30246 ATA
1 ATA
30249 CAATGGGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.33
Consensus pattern (29 bp):
ATATATTAAATAAAAAAAATTGCAAGTCT
Found at i:30271 original size:51 final size:54
Alignment explanation
Indices: 30213--30318 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
30203 TCAATTGCAA
30213 GTCTATATA-T-TATAT-AAAAAAAATTGCAAGTCTATACAATGGGAAATGAAT
1 GTCTATATATTATATATAAAAAAAAATTGCAAGTCTATACAATGGGAAATGAAT
*
30264 GTCTATATATTATATATAAAAAAAAATTGCAAGTCTATACAGTGGGAAATGAAT
1 GTCTATATATTATATATAAAAAAAAATTGCAAGTCTATACAATGGGAAATGAAT
30318 G
1 G
30319 CCGGTTCTCC
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
51 9 0.18
52 1 0.02
53 5 0.10
54 36 0.71
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (54 bp):
GTCTATATATTATATATAAAAAAAAATTGCAAGTCTATACAATGGGAAATGAAT
Found at i:34418 original size:24 final size:23
Alignment explanation
Indices: 34386--34432 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
34376 CAACCAATTC
*
34386 AAGAAATAGCAAAACAGACCTTGA
1 AAGAAATAG-AAAACACACCTTGA
*
34410 AAGAAATAGAAACCACACCTTGA
1 AAGAAATAGAAAACACACCTTGA
34433 GGATAACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.53, C:0.19, G:0.15, T:0.13
Consensus pattern (23 bp):
AAGAAATAGAAAACACACCTTGA
Done.