Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008216.1 Corchorus capsularis cultivar CVL-1 contig08237, 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: 26865
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:1476 original size:16 final size:16
Alignment explanation
Indices: 1457--1495 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1447 TCTCTTCGAC
*
1457 TCTTTAACTATTCAAT
1 TCTTCAACTATTCAAT
*
1473 TCTTCAATTATTCAAT
1 TCTTCAACTATTCAAT
*
1489 ACTTCAA
1 TCTTCAA
1496 TTTATCTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (16 bp):
TCTTCAACTATTCAAT
Found at i:1477 original size:53 final size:53
Alignment explanation
Indices: 1414--1548 Score: 174
Period size: 53 Copynumber: 2.6 Consensus size: 53
1404 TCTTCAATGC
*
1414 TTCAACTCTTCCATTATTCAA-ATCTTCAATTTATCTCTTCGACTCTTTAACTA
1 TTCAACTCTTCAATTATTCAATA-CTTCAATTTATCTCTTCGACTCTTTAACTA
* * *
1467 TTCAATTCTTCAATTATTCAATACTTCAATTTATCTCTTCGGCTCTTTAATTA
1 TTCAACTCTTCAATTATTCAATACTTCAATTTATCTCTTCGACTCTTTAACTA
*
1520 TT---CTC--CAATTCTTCAATACTTCAATTTAT
1 TTCAACTCTTCAATTATTCAATACTTCAATTTAT
1549 TTCCTCAATT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
48 23 0.31
50 2 0.03
53 49 0.65
54 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (53 bp):
TTCAACTCTTCAATTATTCAATACTTCAATTTATCTCTTCGACTCTTTAACTA
Found at i:1496 original size:16 final size:16
Alignment explanation
Indices: 1465--1497 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1455 ACTCTTTAAC
*
1465 TATTCAATTCTTCAAT
1 TATTCAATACTTCAAT
1481 TATTCAATACTTCAAT
1 TATTCAATACTTCAAT
1497 T
1 T
1498 TATCTCTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTCAATACTTCAAT
Found at i:1614 original size:8 final size:8
Alignment explanation
Indices: 1519--1614 Score: 53
Period size: 8 Copynumber: 12.4 Consensus size: 8
1509 CTCTTTAATT
*
1519 ATTCTCCA
1 ATTCTTCA
1527 ATTCTTCA
1 ATTCTTCA
*
1535 ATACTTCA
1 ATTCTTCA
1543 A-T-TT-A
1 ATTCTTCA
* *
1548 TTTCCTCA
1 ATTCTTCA
1556 ATTCTT-A
1 ATTCTTCA
1563 GATTACTT--
1 -ATT-CTTCA
1571 ATTGCTTCA
1 ATT-CTTCA
1580 ATTCTTCA
1 ATTCTTCA
*
1588 CTTAC-TCA
1 ATT-CTTCA
*
1596 ATGCTTCA
1 ATTCTTCA
1604 ATTCTTCA
1 ATTCTTCA
1612 ATT
1 ATT
1615 TACTTCAATG
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 9 0.13
8 47 0.70
9 7 0.10
ACGTcount: A:0.26, C:0.24, G:0.03, T:0.47
Consensus pattern (8 bp):
ATTCTTCA
Found at i:1683 original size:22 final size:22
Alignment explanation
Indices: 1651--1878 Score: 204
Period size: 22 Copynumber: 10.5 Consensus size: 22
1641 CTTCCATTCC
* *
1651 TCAATTATTCAATGCCTCAATT
1 TCAATTCTTCAATGCTTCAATT
*
1673 TCAAATT-TTCAATGCTTCAAAT
1 TC-AATTCTTCAATGCTTCAATT
*
1695 TCAATTCTTCAATGTTTC--TT
1 TCAATTCTTCAATGCTTCAATT
*
1715 TCAATTCTTCAATGTTTC--TT
1 TCAATTCTTCAATGCTTCAATT
*
1735 TCGATTCTTCAATGCTTCAATT
1 TCAATTCTTCAATGCTTCAATT
*
1757 TCAATAT-TTCAATGCTTCCATT
1 TCAAT-TCTTCAATGCTTCAATT
*
1779 TCAATAT-TTCAATGTTTCAATT
1 TCAAT-TCTTCAATGCTTCAATT
* *
1801 TCAATTATTCAATGTTTCAATGCT
1 TCAATTCTTCAATGCTTCAAT--T
* * *
1825 TCAA-T-TTCAATTCTCCAAAT
1 TCAATTCTTCAATGCTTCAATT
* *
1845 TCAATCCTTCAATGTTTCAATT
1 TCAATTCTTCAATGCTTCAATT
*
1867 TCAATTCCTCAA
1 TCAATTCTTCAA
1879 ATTCAATTCT
Statistics
Matches: 175, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
20 42 0.24
21 5 0.03
22 117 0.67
23 6 0.03
24 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.46
Consensus pattern (22 bp):
TCAATTCTTCAATGCTTCAATT
Found at i:1705 original size:8 final size:8
Alignment explanation
Indices: 1639--1893 Score: 54
Period size: 8 Copynumber: 33.1 Consensus size: 8
1629 AGGGTGGTCT
*
1639 TTCTTCCA
1 TTCTTCAA
*
1647 TTCCTCAA
1 TTCTTCAA
*
1655 TTATTCAA
1 TTCTTCAA
* *
1663 TGCCTCAA
1 TTCTTCAA
1671 -T-TTCAAA
1 TTCTTC-AA
1678 TT-TTCAA
1 TTCTTCAA
*
1685 TGCTTCAA
1 TTCTTCAA
*
1693 --ATTCAA
1 TTCTTCAA
1699 TTCTTCAA
1 TTCTTCAA
1707 TGTTTCTTTCAA
1 ---TTC-TTCAA
1719 TTCTTCAA
1 TTCTTCAA
*
1727 TGTTTCTTTCGA
1 ---TTC-TTCAA
1739 TTCTTCAA
1 TTCTTCAA
*
1747 TGCTTCAA
1 TTCTTCAA
1755 -T-TTCAA
1 TTCTTCAA
1761 TAT-TTCAA
1 T-TCTTCAA
* *
1769 TGCTTCCA
1 TTCTTCAA
1777 -T-TTCAA
1 TTCTTCAA
1783 TAT-TTCAA
1 T-TCTTCAA
1791 TGT-TTCAA
1 T-TCTTCAA
1799 -T-TTCAA
1 TTCTTCAA
*
1805 TTATTCAA
1 TTCTTCAA
1813 TGT-TTCAA
1 T-TCTTCAA
*
1821 TGCTTCAA
1 TTCTTCAA
1829 -T-TTCAA
1 TTCTTCAA
*
1835 TTCTCCAA
1 TTCTTCAA
*
1843 --ATTCAA
1 TTCTTCAA
*
1849 TCCTTCAA
1 TTCTTCAA
1857 TGT-TTCAA
1 T-TCTTCAA
1865 -T-TTCAA
1 TTCTTCAA
*
1871 TTCCTCAA
1 TTCTTCAA
*
1879 --ATTCAA
1 TTCTTCAA
1885 TTCTTCAA
1 TTCTTCAA
1893 T
1 T
1894 GTGTCAATTT
Statistics
Matches: 184, Mismatches: 32, Indels: 62
0.66 0.12 0.22
Matches are distributed among these distances:
6 41 0.22
7 8 0.04
8 113 0.61
9 7 0.04
11 6 0.03
12 9 0.05
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (8 bp):
TTCTTCAA
Found at i:1719 original size:20 final size:21
Alignment explanation
Indices: 1651--1936 Score: 163
Period size: 22 Copynumber: 13.6 Consensus size: 21
1641 CTTCCATTCC
* **
1651 TCAATTATTCAATGCCTCAATT
1 TCAATTCTTCAATGTTTC-ATT
* *
1673 TCAAATT-TTCAATGCTTCAAAT
1 TC-AATTCTTCAATGTTTC-ATT
1695 TCAATTCTTCAATGTTTC-TT
1 TCAATTCTTCAATGTTTCATT
1715 TCAATTCTTCAATGTTTC-TT
1 TCAATTCTTCAATGTTTCATT
* *
1735 TCGATTCTTCAATGCTTCAATT
1 TCAATTCTTCAATGTTTC-ATT
*
1757 TCAATAT-TTCAATGCTTCCATT
1 TCAAT-TCTTCAATG-TTTCATT
1779 TCAATAT-TTCAATGTTTCAATT
1 TCAAT-TCTTCAATGTTTC-ATT
*
1801 TCAATTATTCAATGTTTCAATGCT
1 TCAATTCTTCAATGTTTC-AT--T
* *
1825 TCAA-T-TTCAAT-TCTCCAAAT
1 TCAATTCTTCAATGT-TTC-ATT
*
1845 TCAATCCTTCAATGTTTCAATT
1 TCAATTCTTCAATGTTTC-ATT
*
1867 TCAATTCCTCAA------A-T
1 TCAATTCTTCAATGTTTCATT
*
1881 TCAATTCTTCAATGTGTCAATT
1 TCAATTCTTCAATGTTTC-ATT
*
1903 TCAATAT-TTCAATGCTTCAATT
1 TCAAT-TCTTCAATGTTTC-ATT
*
1925 TCAATTCCTCAA
1 TCAATTCTTCAA
1937 ATTCAATTTT
Statistics
Matches: 219, Mismatches: 21, Indels: 48
0.76 0.07 0.17
Matches are distributed among these distances:
14 12 0.05
15 1 0.00
20 42 0.19
21 11 0.05
22 138 0.63
23 10 0.05
24 5 0.02
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (21 bp):
TCAATTCTTCAATGTTTCATT
Found at i:1782 original size:36 final size:36
Alignment explanation
Indices: 1742--1949 Score: 137
Period size: 36 Copynumber: 5.7 Consensus size: 36
1732 CTTTCGATTC
* *
1742 TTCAATGCTTCAATTTCAATATTTCAATGCTTCCAT
1 TTCAATGCTTCAATTTCAATATTTCAATGATTCAAT
** *
1778 TTCAATATTTCAATGTTTC-A-ATTTCAATTATTCAATGT
1 TTCAATGCTTCAA--TTTCAATATTTCAATGATTCAA--T
*
1816 TTCAATGCTTCAATTTCAAT-TCTCCAA--ATTCAAT
1 TTCAATGCTTCAATTTCAATAT-TTCAATGATTCAAT
* *
1850 CCTTCAATGTTTCAATTTCAAT-TCCTCAA--ATTCAATT
1 --TTCAATGCTTCAATTTCAATAT-TTCAATGATTCAA-T
*
1887 CTTCAATG-TGTCAATTTCAATATTTCAATGCTTCAAT
1 -TTCAATGCT-TCAATTTCAATATTTCAATGATTCAAT
* * * *
1924 TTCAATTCCTCAAATTCAATTTTTCA
1 TTCAATGCTTCAATTTCAATATTTCA
1950 GTGCTTTAAT
Statistics
Matches: 140, Mismatches: 17, Indels: 30
0.75 0.09 0.16
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 107 0.76
37 6 0.04
38 25 0.18
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.45
Consensus pattern (36 bp):
TTCAATGCTTCAATTTCAATATTTCAATGATTCAAT
Found at i:1832 original size:44 final size:41
Alignment explanation
Indices: 1658--2089 Score: 103
Period size: 44 Copynumber: 10.0 Consensus size: 41
1648 TCCTCAATTA
** * *
1658 TTCAATGCCTCAATTTCAAATTTTCAATGCTTCAA-ATTCAATTC
1 TTCAATGTTTCAATTTC-AA-TTTCAAT-TTTCAATCTTCAA-TC
*
1702 TTCAATGTTTC--TTTCAATTCTTCAATGTTTC--T-TTCGATTC
1 TTCAATGTTTCAATTTCAA-T-TTCAAT-TTTCAATCTTC-AATC
* * * *
1742 TTCAATGCTTCAATTTCAATATTTCAATGCTTCCAT-TTCAATAT
1 TTCAATGTTTCAATTTC-A-ATTTCAAT-TTTCAATCTTCAAT-C
1786 TTCAATGTTTCAATTTCAATTATTCAATGTTTCAATGCTTCAAT-
1 TTCAATGTTTCAATTTCAA-T-TTCAAT-TTTCAAT-CTTCAATC
* *
1830 TTCAAT-TCTCCAAATTCAATCCTTCAATGTTTCAAT-TTCAATTC
1 TTCAATGT-TTCAATTTCAAT--TTCAAT-TTTCAATCTTCAA-TC
* * *
1874 CTCAA--ATTCAATTCTTCAATGTGTCAA-TTTCAATATTTCAATGC
1 TTCAATGTTTCAA-T-TTCAAT-T-TCAATTTTCAAT-CTTCAAT-C
* * *
1918 TTCAA--TTTCAATTCCTCAAATTCAATTTTTCAGTGCTTTAAT-
1 TTCAATGTTTCAATT--TCAATTTCAA-TTTTCAAT-CTTCAATC
* *
1960 TTTAATATTTCAATGTCTCAATTTCAATTTTTCGATAT-TTCAAT-
1 TTCAATGTTTCAAT-T-TCAATTTCAA-TTTTC-A-ATCTTCAATC
* * * **
2004 TTCAATATGTCAATGCTTCAATGTTTCAATTTCCCTTCTTCAATGC
1 TTCAATGTTTCAAT--TTCAA--TTTCAATTTTCAATCTTCAAT-C
* *
2050 TTCAA--TTTCAATCTCAATTTCAACTCTTCAATGCTTCAAT
1 TTCAATGTTTCAATTTCAATTTCAA-TTTTCAAT-CTTCAAT
2090 TTACTTTGAT
Statistics
Matches: 305, Mismatches: 42, Indels: 84
0.71 0.10 0.19
Matches are distributed among these distances:
40 21 0.07
41 9 0.03
42 65 0.21
43 14 0.05
44 171 0.56
45 7 0.02
46 18 0.06
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.46
Consensus pattern (41 bp):
TTCAATGTTTCAATTTCAATTTCAATTTTCAATCTTCAATC
Found at i:1892 original size:58 final size:58
Alignment explanation
Indices: 1830--1988 Score: 171
Period size: 58 Copynumber: 2.7 Consensus size: 58
1820 ATGCTTCAAT
* *
1830 TTCAAT-TCTCCAAATTCAATCCTTCAATGTTTCAATTTCAATTCCTCAAATTCAATTC
1 TTCAATGTCT-CAAATTCAATACTTCAATGCTTCAATTTCAATTCCTCAAATTCAATTC
* * * *
1888 TTCAATGTGTCAATTTCAATATTTCAATGCTTCAATTTCAATTCCTCAAATTCAATTT
1 TTCAATGTCTCAAATTCAATACTTCAATGCTTCAATTTCAATTCCTCAAATTCAATTC
* * * * *
1946 TTCAGTG-CTTTAATTTTAATATTTCAATG-TCTCAATTTCAATT
1 TTCAATGTC-TCAAATTCAATACTTCAATGCT-TCAATTTCAATT
1989 TTTCGATATT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
57 1 0.01
58 85 0.97
59 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.45
Consensus pattern (58 bp):
TTCAATGTCTCAAATTCAATACTTCAATGCTTCAATTTCAATTCCTCAAATTCAATTC
Found at i:1900 original size:22 final size:22
Alignment explanation
Indices: 1875--2089 Score: 89
Period size: 22 Copynumber: 9.9 Consensus size: 22
1865 TTTCAATTCC
* *
1875 TCAAATTCAATTCTTCAATGTG
1 TCAATTTCAATTCTTCAATGTT
*
1897 TCAATTTCAATAT-TTCAATGCT
1 TCAATTTCAAT-TCTTCAATGTT
* *
1919 TCAATTTCAATTCCTCAA--AT
1 TCAATTTCAATTCTTCAATGTT
* * *
1939 TCAATTTTTCAGTGCTTTAAT-TT
1 TCAA--TTTCAATTCTTCAATGTT
*
1962 TAATATTTCAATGTC-TCAA--TT
1 TCA-ATTTCAAT-TCTTCAATGTT
*
1983 TCAATTTTTCGATAT-TTCAA--TT
1 TCAA--TTTCAAT-TCTTCAATGTT
*
2005 TCAATATGTCAATGCTTCAATGTT
1 TCAAT-T-TCAATTCTTCAATGTT
** *
2029 TCAATTTCCCTTCTTCAATGCT
1 TCAATTTCAATTCTTCAATGTT
2051 TCAATTTCAA-TC-TCAA--TT
1 TCAATTTCAATTCTTCAATGTT
*
2069 TCAACTCTTCAATGCTTCAAT
1 TCAA-T-TTCAATTCTTCAAT
2090 TTACTTTGAT
Statistics
Matches: 146, Mismatches: 27, Indels: 39
0.69 0.13 0.18
Matches are distributed among these distances:
18 5 0.03
19 1 0.01
20 16 0.11
21 9 0.06
22 101 0.69
23 6 0.04
24 8 0.05
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.46
Consensus pattern (22 bp):
TCAATTTCAATTCTTCAATGTT
Found at i:2017 original size:30 final size:28
Alignment explanation
Indices: 1756--2091 Score: 122
Period size: 30 Copynumber: 11.6 Consensus size: 28
1746 ATGCTTCAAT
* **
1756 TTCAATATTTCAATGCTTCCATTTCAATAT
1 TTCAATATTTCAAT--TTCAATTTCAATGC
* *
1786 TTCAATGTTTCAATTTCAATTATTCAATGT
1 TTCAATATTTCAATTTCAA-T-TTCAATGC
** *
1816 TTCAATGCTTCAATTTCAATTCTCCAA--A
1 TTCAATATTTCAATTTCAATT-T-CAATGC
** *
1844 TTCAATCCTTCAATGTTTCAATTTCAATTC
1 TTCAATATTTCAA--TTTCAATTTCAATGC
*
1874 CTCAA-A-TTCAATTCTTCAATGTGTCAAT--
1 TTCAATATTTCAA-T-TTCAAT-T-TCAATGC
*
1902 TTCAATATTTCAATGCTTCAATTTCAATTC
1 TTCAATATTTCAAT--TTCAATTTCAATGC
* * *
1932 CTCAA-A-TTCAATTTTTCAGTGCTTTAAT--
1 TTCAATATTTCAA--TTTCAAT--TTCAATGC
* **
1960 TTTAATATTTCAATGTCTCAATTTCAATTT
1 TTCAATATTTCAAT-T-TCAATTTCAATGC
*
1990 TTCGATATTTCAATTTCAATATGTCAATGC
1 TTCAATATTTCAATTTCAAT-T-TCAATGC
* **
2020 TTCAATGTTTCAATTTCCCTTCTTCAATGC
1 TTCAATATTTCAATTT-CAAT-TTCAATGC
*
2050 TTC-A-ATTTCAATCTCAATTTCAACT-C
1 TTCAATATTTCAATTTCAATTTCAA-TGC
**
2076 TTCAATGCTTCAATTT
1 TTCAATATTTCAATTT
2092 ACTTTGATGA
Statistics
Matches: 240, Mismatches: 34, Indels: 66
0.71 0.10 0.19
Matches are distributed among these distances:
26 9 0.04
27 5 0.02
28 79 0.33
29 14 0.06
30 130 0.54
31 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.46
Consensus pattern (28 bp):
TTCAATATTTCAATTTCAATTTCAATGC
Found at i:2052 original size:8 final size:7
Alignment explanation
Indices: 2040--2089 Score: 52
Period size: 8 Copynumber: 7.1 Consensus size: 7
2030 CAATTTCCCT
2040 TCTTCAA
1 TCTTCAA
2047 TGCTTCAA
1 T-CTTCAA
2055 T-TTCAA
1 TCTTCAA
2061 TC-TCAA
1 TCTTCAA
2067 T-TTCAA
1 TCTTCAA
2073 CTCTTCAA
1 -TCTTCAA
2081 TGCTTCAA
1 T-CTTCAA
2089 T
1 T
2090 TTACTTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
6 15 0.41
7 3 0.08
8 19 0.51
ACGTcount: A:0.28, C:0.26, G:0.04, T:0.42
Consensus pattern (7 bp):
TCTTCAA
Found at i:2152 original size:50 final size:50
Alignment explanation
Indices: 2068--2181 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
2058 CAATCTCAAT
* ** **
2068 TTCAACTCTTCAATGCTTCAATTTACTTTGATGATCCAGGGTGATCTTTC
1 TTCAATTCTTCAATAATTCAATTTACTTCAATGATCCAGGGTGATCTTTC
* * * *
2118 TTCATTTCTTCAATAATTCAATTTACTTCAATGATCTAGGGTGGTTTTTC
1 TTCAATTCTTCAATAATTCAATTTACTTCAATGATCCAGGGTGATCTTTC
*
2168 TTCAATTATTCAAT
1 TTCAATTCTTCAAT
2182 TAGTCCATGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.46
Consensus pattern (50 bp):
TTCAATTCTTCAATAATTCAATTTACTTCAATGATCCAGGGTGATCTTTC
Found at i:2181 original size:8 final size:8
Alignment explanation
Indices: 2168--2235 Score: 66
Period size: 8 Copynumber: 8.5 Consensus size: 8
2158 GTGGTTTTTC
2168 TTCAATTA
1 TTCAATTA
2176 TTCAATTA
1 TTCAATTA
* *
2184 GTCCATGT-
1 TTCAAT-TA
*
2192 TTCAATTC
1 TTCAATTA
*
2200 CTCAATTA
1 TTCAATTA
**
2208 TTCAATGC
1 TTCAATTA
2216 TTCAATTA
1 TTCAATTA
2224 TTCAATTA
1 TTCAATTA
2232 TTCA
1 TTCA
2236 TCTCTTCAGT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
7 1 0.02
8 45 0.96
9 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.46
Consensus pattern (8 bp):
TTCAATTA
Found at i:2232 original size:24 final size:24
Alignment explanation
Indices: 2167--2235 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
2157 GGTGGTTTTT
* *
2167 CTTCAATTATTCAATTAGTCCATG
1 CTTCAATTATTCAATTATTCAATG
* **
2191 TTTCAATTCCTCAATTATTCAATG
1 CTTCAATTATTCAATTATTCAATG
2215 CTTCAATTATTCAATTATTCA
1 CTTCAATTATTCAATTATTCA
2236 TCTCTTCAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.30, C:0.20, G:0.04, T:0.45
Consensus pattern (24 bp):
CTTCAATTATTCAATTATTCAATG
Found at i:2242 original size:24 final size:23
Alignment explanation
Indices: 2165--2243 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 23
2155 AGGGTGGTTT
*
2165 TTCTTCAATTATTCAATTAGTCCA
1 TTCTTCAATTATTCAATTA-TTCA
**
2189 TGT-TTCAATTCCTCAATTATTCAA
1 T-TCTTCAATTATTCAATTATTC-A
*
2213 TGCTTCAATTATTCAATTATTCA
1 TTCTTCAATTATTCAATTATTCA
2236 TCTCTTCA
1 T-TCTTCA
2244 GTACCTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
23 4 0.09
24 39 0.89
25 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.47
Consensus pattern (23 bp):
TTCTTCAATTATTCAATTATTCA
Found at i:5633 original size:16 final size:15
Alignment explanation
Indices: 5612--5647 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5602 AAGTTTTCAA
5612 AAAAATCCAAAAAAAT
1 AAAAATCC-AAAAAAT
*
5628 AAAAATTCAAAAAAT
1 AAAAATCCAAAAAAT
5643 AAAAA
1 AAAAA
5648 AGAATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATCCAAAAAAT
Found at i:5648 original size:16 final size:15
Alignment explanation
Indices: 5610--5648 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
5600 AAAAGTTTTC
5610 AAAAAAATCCAAAAA
1 AAAAAAATCCAAAAA
*
5625 AATAAAAATTCAAAAA
1 AA-AAAAATCCAAAAA
5641 ATAAAAAA
1 A-AAAAAA
5649 GAATTACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 18 0.86
17 1 0.05
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAAATCCAAAAA
Found at i:11237 original size:90 final size:90
Alignment explanation
Indices: 10937--11401 Score: 646
Period size: 90 Copynumber: 5.1 Consensus size: 90
10927 AAAGATAATC
* * * * *
10937 GATTCACCGAATCAATCTGAATTGTCTGAGAATGTGCTGCACCGAGCTCATTGAATCCAATCTTG
1 GATTCACCGAATCAACCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
* * *
11002 AAGAAATAAAGCACCGCATCAATTT
66 AAGAAATAAGGCACCGCCTCAACTT
* * * * * *
11027 CG-TTCTCCGAACCATCCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACCGATTTCCAACCT
1 -GATTCACCGAATCAACCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGA-ATCCAATC-
11091 TTGAAGAAATAAGGCACCGCCTCAACTT
63 TTGAAGAAATAAGGCACCGCCTCAACTT
* * *
11119 GATTCACCGAAT-AATCCTGATCTATTTGAAAATGTGCTGCACTGAGCTCACTGAATCCAATCTT
1 GATTCACCGAATCAA-CCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGAATCCAATCTT
* *
11183 GAAGAAATAAGGCACCACCTTAACTT
65 GAAGAAATAAGGCACCGCCTCAACTT
*
11209 GATTCACCGAATCAACCTAAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
1 GATTCACCGAATCAACCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
11274 AAGAAATAAGGCACCGCCTCAACTT
66 AAGAAATAAGGCACCGCCTCAACTT
** * * **
11299 GATTCACCGAATCATGCTAAACTGTTTGAAAGTGTGCTGCACCGAGCTCACCAAATCCAATCTTG
1 GATTCACCGAATCAACCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
11364 AAGAAATAAGGCACCGCCTCAACTT
66 AAGAAATAAGGCACCGCCTCAACTT
11389 GATTCACCGAATC
1 GATTCACCGAATC
11402 CAACTTTGAA
Statistics
Matches: 333, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
90 248 0.74
91 17 0.05
92 68 0.20
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (90 bp):
GATTCACCGAATCAACCTGAACTGTTTGAAAATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
AAGAAATAAGGCACCGCCTCAACTT
Found at i:11348 original size:180 final size:180
Alignment explanation
Indices: 10937--11401 Score: 648
Period size: 182 Copynumber: 2.6 Consensus size: 180
10927 AAAGATAATC
* * *
10937 GATTCACCGAATCAATCTGAATTGTCTGAGAATGTGCTGCACCGAGCTCATTGAATCCAATCTTG
1 GATTCACCGAATC-ATCTGAACTGTTTGA-AATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
* * * * * * *
11002 AAGAAATAAAGCACCGCATCAATTTCG-TTCTCCGAACCATCCTGAACTGTTTGAAAATGTGCTG
64 AAGAAATAAGGCACCGCCTCAACTT-GATTCACCGAATCAACCTAAACTGTTTGAAAATGTGCTG
*
11066 CACCGAGCTCACCGATTTCCAACCTTTGAAGAAATAAGGCACCGCCTCAACTT
128 CACCGAGCTCACCGATATCCAACCTTTGAAGAAATAAGGCACCGCCTCAACTT
* * * *
11119 GATTCACCGAATAATCCTGATCTATTTGAAAATGTGCTGCACTGAGCTCACTGAATCCAATCTTG
1 GATTCACCGAATCAT-CTGAACTGTTTG-AAATGTGCTGCACCGAGCTCACTGAATCCAATCTTG
* *
11184 AAGAAATAAGGCACCACCTTAACTTGATTCACCGAATCAACCTAAACTGTTTGAAAATGTGCTGC
64 AAGAAATAAGGCACCGCCTCAACTTGATTCACCGAATCAACCTAAACTGTTTGAAAATGTGCTGC
* *
11249 ACCGAGCTCACTGA-ATCCAATC-TTGAAGAAATAAGGCACCGCCTCAACTT
129 ACCGAGCTCACCGATATCCAACCTTTGAAGAAATAAGGCACCGCCTCAACTT
* **
11299 GATTCACCGAATCATGCTAAACTGTTTGAAAGTGTGCTGCACCGAGCTCACCAAATCCAATCTTG
1 GATTCACCGAATCAT-CTGAACTGTTTGAAA-TGTGCTGCACCGAGCTCACTGAATCCAATCTTG
11364 AAGAAATAAGGCACCGCCTCAACTTGATTCACCGAATC
64 AAGAAATAAGGCACCGCCTCAACTTGATTCACCGAATC
11402 CAACTTTGAA
Statistics
Matches: 250, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
179 3 0.01
180 117 0.47
181 9 0.04
182 120 0.48
183 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (180 bp):
GATTCACCGAATCATCTGAACTGTTTGAAATGTGCTGCACCGAGCTCACTGAATCCAATCTTGAA
GAAATAAGGCACCGCCTCAACTTGATTCACCGAATCAACCTAAACTGTTTGAAAATGTGCTGCAC
CGAGCTCACCGATATCCAACCTTTGAAGAAATAAGGCACCGCCTCAACTT
Found at i:11444 original size:43 final size:43
Alignment explanation
Indices: 11388--11954 Score: 759
Period size: 43 Copynumber: 13.3 Consensus size: 43
11378 CGCCTCAACT
11388 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
*
11431 TGATTCACCGAATCCAACTTTGAAGATGCTACACTGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
*
11474 TGATTCACCGAATCCAACTTTGAAGATGCTTCACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * *
11517 TGATT--TCGAATCCAACTTTAAAGATGCTACACCGAGTCACC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * * *
11558 TGATTCACCGAATCCAATTTTGGAGATGCTTCACCGAGTCACC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
*
11601 TGATTCACAGAATCCAACTTTGAAGATGCTACACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
** *
11644 TGATT--TTGAATCCAACTTTCAAGATGCTACACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * * * *
11685 TGATTCATCGAATCCAATTTTGGAGATGCTTCACCGAGTCACC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * *
11728 TGACTCACCGAATCCAACTTTGAAGAGGCTACACCAAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * * * *
11771 TGAATCACCGAATCCAATTTTGGAGATGCTTCACCGAGTCACC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
*
11814 TGACTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * **
11857 TGATTCACCGAATCCAATTTTGGAGATGCTTTACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
* * * * *
11900 TGATT--TCGGATCTAACTTAGAAGATGCTTCACCGAGTCATC
1 TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
*
11941 TGATTCACCAAATC
1 TGATTCACCGAATC
11955 ACTGAAAACT
Statistics
Matches: 457, Mismatches: 61, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
41 109 0.24
43 348 0.76
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (43 bp):
TGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATC
Found at i:11542 original size:127 final size:127
Alignment explanation
Indices: 11396--11954 Score: 769
Period size: 127 Copynumber: 4.4 Consensus size: 127
11386 CTTGATTCAC
*
11396 CGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCT
1 CGAATCCAACTTTAAAGATGCTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCT
* * *
11461 ACACTGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCTTCACCGAGTCATCTGATTT
66 ACACCGAGTCACCTGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGATTT
* * *
11523 CGAATCCAACTTTAAAGATGCTACACCGAGTCACCTGATTCACCGAATCCAATTTTGGAGATGCT
1 CGAATCCAACTTTAAAGATGCTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCT
* *
11588 TCACCGAGTCACCTGATTCACAGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGATTT
66 ACACCGAGTCACCTGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGATTT
* * * * *
11650 TGAATCCAACTTTCAAGATGCTACACCGAGTCATCTGATTCATCGAATCCAATTTTGGAGATGCT
1 CGAATCCAACTTTAAAGATGCTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCT
* * * * **
11715 TCACCGAGTCACCTGACTCACCGAATCCAACTTTGAAGAGGCTACACCAAGTCATCTGAATCAC
66 ACACCGAGTCACCTGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTG-AT-TT
* ** * * *
11779 CGAATCCAATTTTGGAGATGCTTCACCGAGTCACCTGACTCACCGAATCCAACTTTGAAGATGCT
1 CGAATCCAACTTTAAAGATGCTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCT
* * * **
11844 ACACCGAGTCATCTGATTCACCGAATCCAATTTTGGAGATGCTTTACCGAGTCATCTGATTT
66 ACACCGAGTCACCTGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGATTT
* * * *
11906 CGGATCTAAC-TTAGAAGATGCTTCACCGAGTCATCTGATTCACCAAATC
1 CGAATCCAACTTTA-AAGATGCTACACCGAGTCATCTGATTCACCGAATC
11955 ACTGAAAACT
Statistics
Matches: 381, Mismatches: 48, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
126 2 0.01
127 271 0.71
128 4 0.01
129 104 0.27
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (127 bp):
CGAATCCAACTTTAAAGATGCTACACCGAGTCATCTGATTCACCGAATCCAACTTTGAAGATGCT
ACACCGAGTCACCTGATTCACCGAATCCAACTTTGAAGATGCTACACCGAGTCATCTGATTT
Found at i:12086 original size:54 final size:54
Alignment explanation
Indices: 11954--12265 Score: 428
Period size: 54 Copynumber: 5.7 Consensus size: 54
11944 TTCACCAAAT
* * * * * *
11954 CACTGAAAACTTCCTTGACTGACCGCATTGGTTCACTTTAAAGATAAACTTAATAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAACTTAA-AC
* * * *
12010 AATTGAAAAACTTTCTTAATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
1 CACTG-GAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
**
12065 CACTGGAAACTTTCTTGATTGACCTTACTGGATCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
*
12119 CACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
* * *
12173 CACTAGAAACTTTCTTGATTGACCGCACTGGATCCCTTAAAGATAAACTTAATAC
1 CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAA-AC
12228 CACTGGAAAC-TTCTTTGATTGACCGCACTGGATCACTT
1 CACTGGAAACTTTC-TTGATTGACCGCACTGGATCACTT
12266 TGAAATTCGG
Statistics
Matches: 230, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
54 147 0.64
55 39 0.17
56 18 0.08
57 26 0.11
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (54 bp):
CACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAAC
Found at i:13507 original size:20 final size:20
Alignment explanation
Indices: 13482--13519 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
13472 CTTTTTTGAG
* *
13482 AAAAACACTTTTTCTTTTGC
1 AAAAACAATTTTTATTTTGC
13502 AAAAACAATTTTTATTTT
1 AAAAACAATTTTTATTTT
13520 AGGAACAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.03, T:0.47
Consensus pattern (20 bp):
AAAAACAATTTTTATTTTGC
Found at i:14701 original size:14 final size:13
Alignment explanation
Indices: 14649--14699 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
14639 ACTTAAAACC
14649 TTTTGAAAAACTCAT
1 TTTTG-AAAA-TCAT
*
14664 TTTTGAAAATCTT
1 TTTTGAAAATCAT
*
14677 TTCTTGAAAATAAT
1 TT-TTGAAAATCAT
14691 TTTTGAAAA
1 TTTTGAAAA
14700 ATGTTTCTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 12 0.38
14 15 0.47
15 5 0.16
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (13 bp):
TTTTGAAAATCAT
Found at i:17885 original size:68 final size:67
Alignment explanation
Indices: 17641--17902 Score: 285
Period size: 67 Copynumber: 3.8 Consensus size: 67
17631 CTAGACTCAG
* * * ** * **
17641 ATGCAAAAAGATGAAAATGACCCTTTGACCGGAAGGGTATTTTTTTTTGG-AAATGAAGATGGTA
1 ATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTA----TTTTTGGAAAAACAAAATACTA
*
17705 AACTTGA
61 AACTTAA
* * * *
17712 ATGCAAAAGAC-AACAATGACCCTTTGACCGAAAGGGTATTCTTGGGAAAAGAAAATACTAAACT
1 ATGCAAAAGACGAA-AATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAACAAAATACTAAACT
17776 TAA
65 TAA
* *
17779 ATGCAAAAGACGAAAATGACCCTTCCACCGAAAGGGTATTTTTGGAAAAACAAAATACTAGACTT
1 ATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAACAAAATACTAAACTT
17844 AA
66 AA
** *
17846 ATGCGAAAAGACGAAAATGACCCTTCGATTGAAAGGGTATTTTTGGAAATACAAAAT
1 ATGC-AAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAACAAAAT
17903 TAAGCTTTTC
Statistics
Matches: 169, Mismatches: 18, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
66 6 0.04
67 78 0.46
68 50 0.30
69 2 0.01
70 29 0.17
71 4 0.02
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (67 bp):
ATGCAAAAGACGAAAATGACCCTTCGACCGAAAGGGTATTTTTGGAAAAACAAAATACTAAACTT
AA
Done.