Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011469.1 Corchorus capsularis cultivar CVL-1 contig11490, 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: 63752
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:14291 original size:34 final size:36
Alignment explanation
Indices: 14231--14302 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 36
14221 GTTTCAACAA
*
14231 AATACATTTTTACCCTTTAATTGGTGATTTTCTTTC
1 AATACATTTTTACCCTTTAATCGGTGATTTTCTTTC
14267 AATACATTTTTA-CC-TTAATCGGTGATTTTCTTTC
1 AATACATTTTTACCCTTTAATCGGTGATTTTCTTTC
14301 AA
1 AA
14303 ATTGATAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 21 0.60
35 2 0.06
36 12 0.34
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (36 bp):
AATACATTTTTACCCTTTAATCGGTGATTTTCTTTC
Found at i:15400 original size:275 final size:276
Alignment explanation
Indices: 14902--15442 Score: 987
Period size: 276 Copynumber: 2.0 Consensus size: 276
14892 ATTGTTTTAA
14902 TGAATGTAAGCCTATACTTCTTGACCAAATTATTGAATTAAAATATCTTTCTTTTTACTAAAGGG
1 TGAATGTAAGCCTATACTTCTTGACCAAATTATTGAATTAAAATATCTTTCTTTTTACTAAAGGG
14967 AAATTATATTGAAAGATATATTTAAAAATTGATAAATTAATTTAATCTTACCAATTTATTTTGAA
66 AAATTATATTGAAAGATATATTTAAAAATTGATAAATTAATTTAATCTTACCAATTTATTTTGAA
* *
15032 TTAAATGTGATAAATACTCCATCTGTTCCTATTTATTTGTCATCACTCTGACCAAACAATTTCAA
131 TTAAATGTGAGAAATACTCCATCTGTTCCTATTTATTTGTCATCACTCTGACCAAACAACTTCAA
*
15097 CTTTGACCATCTTTTAAAAAATATATATAAACCAAAATAAAATTTT-AAATAATACTTATAAACT
196 CTTTGACCATCTTTTAAAAAATATATATAAACCAAAATAAAATTTTAAAATAATACTCATAAACT
15161 TTGGAACACATTATTT
261 TTGGAACACATTATTT
15177 TGAATGTAAGCCTATACTTCTTGACCAAATTATTGAATTAAAATATCTTTCTTTTTACTAAAGGG
1 TGAATGTAAGCCTATACTTCTTGACCAAATTATTGAATTAAAATATCTTTCTTTTTACTAAAGGG
*
15242 AAATTATATTGAAAGATATATTTAAAAAATTGATAAATTAGTTTAATCTTACCAATTTATTTTGA
66 AAATTATATTGAAAGATATATTT-AAAAATTGATAAATTAATTTAATCTTACCAATTTATTTTGA
* * *
15307 ATTAAATGTGAGATATACTCCCTCTGTTCCTATTTATTTGTCATCACTCTGATCAAACAACTTCA
130 ATTAAATGTGAGAAATACTCCATCTGTTCCTATTTATTTGTCATCACTCTGACCAAACAACTTCA
*
15372 ACTTTGACCATCTTTTTAAAAA-ATATATAAACCAAAATAAAATTTTAAAATAATACTCATAAAC
195 ACTTTGACCATCTTTTAAAAAATATATATAAACCAAAATAAAATTTTAAAATAATACTCATAAAC
15436 TTTGGAA
260 TTTGGAA
15443 TACAAGTTTT
Statistics
Matches: 256, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
275 112 0.44
276 144 0.56
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (276 bp):
TGAATGTAAGCCTATACTTCTTGACCAAATTATTGAATTAAAATATCTTTCTTTTTACTAAAGGG
AAATTATATTGAAAGATATATTTAAAAATTGATAAATTAATTTAATCTTACCAATTTATTTTGAA
TTAAATGTGAGAAATACTCCATCTGTTCCTATTTATTTGTCATCACTCTGACCAAACAACTTCAA
CTTTGACCATCTTTTAAAAAATATATATAAACCAAAATAAAATTTTAAAATAATACTCATAAACT
TTGGAACACATTATTT
Found at i:16583 original size:20 final size:20
Alignment explanation
Indices: 16558--16599 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
16548 TTTGGCCATA
16558 CATAAACCCTCCCTTTACCT
1 CATAAACCCTCCCTTTACCT
16578 CATAAACCCTCCCTTTACCT
1 CATAAACCCTCCCTTTACCT
16598 CA
1 CA
16600 ACTTTCATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.45, G:0.00, T:0.29
Consensus pattern (20 bp):
CATAAACCCTCCCTTTACCT
Found at i:19736 original size:20 final size:20
Alignment explanation
Indices: 19711--19748 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
19701 GGCTAAATCT
19711 TTTTTATTGATAGGTGTTCA
1 TTTTTATTGATAGGTGTTCA
*
19731 TTTTTATTGATAGTTGTT
1 TTTTTATTGATAGGTGTT
19749 AAAGATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (20 bp):
TTTTTATTGATAGGTGTTCA
Found at i:20621 original size:22 final size:23
Alignment explanation
Indices: 20592--20637 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
20582 TTGAGAAGAA
*
20592 GAAAAAAATGAGATAATGGTGTG
1 GAAAAAAAAGAGATAATGGTGTG
20615 GAAAAAAAAAGAGATAATGGTGT
1 G-AAAAAAAAGAGATAATGGTGT
20638 AAATAGGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.52, C:0.00, G:0.28, T:0.20
Consensus pattern (23 bp):
GAAAAAAAAGAGATAATGGTGTG
Found at i:21832 original size:13 final size:13
Alignment explanation
Indices: 21814--21839 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21804 ATTAGTCATG
21814 GTATGGGAATGTT
1 GTATGGGAATGTT
21827 GTATGGGAATGTT
1 GTATGGGAATGTT
21840 ACATTCCCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
GTATGGGAATGTT
Found at i:23910 original size:27 final size:27
Alignment explanation
Indices: 23859--23910 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
23849 TACTCAACTT
* **
23859 TTCCTACTCCTTTACATTACCAAACGA
1 TTCCTACTCCTTAACAACACCAAACGA
*
23886 TTCCTACTCCTTAACAACACTAAAC
1 TTCCTACTCCTTAACAACACCAAAC
23911 TACACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACGA
Found at i:25547 original size:33 final size:33
Alignment explanation
Indices: 25505--25592 Score: 122
Period size: 33 Copynumber: 2.7 Consensus size: 33
25495 AGTTAAAGGA
25505 TCATGTGGCCGGTTATGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTATGGCCGGGCATGGCCGAG
* **
25538 TCATGTGGCCGGTTGTGGCCGGGCATGGCCTTG
1 TCATGTGGCCGGTTATGGCCGGGCATGGCCGAG
** *
25571 TCGCGTGGCCGGTGATGGCCGG
1 TCATGTGGCCGGTTATGGCCGG
25593 ACATCTCCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.08, C:0.25, G:0.44, T:0.23
Consensus pattern (33 bp):
TCATGTGGCCGGTTATGGCCGGGCATGGCCGAG
Found at i:29958 original size:49 final size:49
Alignment explanation
Indices: 29901--30000 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
29891 ACGCTTACCA
29901 CACATAAAGGAATACTTATTTGTTTCACCATCATGATGGACCTTGTTGT
1 CACATAAAGGAATACTTATTTGTTTCACCATCATGATGGACCTTGTTGT
29950 CACATAAAGGAATACTTATTTGTTTCACCATCATGATGGACCTTGTTGT
1 CACATAAAGGAATACTTATTTGTTTCACCATCATGATGGACCTTGTTGT
29999 CA
1 CA
30001 TATTGCCATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (49 bp):
CACATAAAGGAATACTTATTTGTTTCACCATCATGATGGACCTTGTTGT
Found at i:39241 original size:31 final size:31
Alignment explanation
Indices: 39206--39267 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
39196 CACAAGAGAA
*
39206 CTCTTGATTCATGAATAATTACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
39237 CTCTTGATTCATGAATAATCACAATATTCAT
1 CTCTTGATTCATGAATAATCACAATATTCAT
39268 TAATGACTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.40
Consensus pattern (31 bp):
CTCTTGATTCATGAATAATCACAATATTCAT
Found at i:46167 original size:67 final size:66
Alignment explanation
Indices: 46060--46194 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 66
46050 CATCATACAA
*
46060 CAATTTAATTACAAACTAAGTTCCGCTGATGAGAAAGTAAATCATCGCAAGAGGATTTAGGGGGA
1 CAATTTAATTACAAACTAAGTTCCGCTGATGAAAAAGTAAATCATCGCAAGAGGATTTAGGGGGA
46125 G
66 G
46126 CAATTTAATTACAAAACTAAGTTCCGCTGATGAAAAAGTAAATCATCGCAAGAGGATTTAGGGGG
1 CAATTTAATTAC-AAACTAAGTTCCGCTGATGAAAAAGTAAATCATCGCAAGAGGATTTAGGGGG
46191 AG
65 AG
46193 CA
1 CA
46195 GGCAGGGGCC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
66 12 0.18
67 55 0.82
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (66 bp):
CAATTTAATTACAAACTAAGTTCCGCTGATGAAAAAGTAAATCATCGCAAGAGGATTTAGGGGGA
G
Found at i:48692 original size:31 final size:31
Alignment explanation
Indices: 48630--48695 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
48620 AAAAAACTGT
* *
48630 AAAAGTTAAATAAGGATATAATAGGTATTTC
1 AAAAGTTAAATAAGGATATAATAAGCATTTC
* *
48661 AAAAGTTAAATAAGGGTATAATAAGCGTTTC
1 AAAAGTTAAATAAGGATATAATAAGCATTTC
48692 AAAA
1 AAAA
48696 ATTTCTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.29
Consensus pattern (31 bp):
AAAAGTTAAATAAGGATATAATAAGCATTTC
Found at i:50889 original size:2 final size:2
Alignment explanation
Indices: 50882--50906 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50872 CAAATTATTT
50882 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 T
50907 GTAGAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51165 original size:7 final size:7
Alignment explanation
Indices: 51153--51178 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
51143 AATTTCTTTA
51153 TTTTTTC
1 TTTTTTC
51160 TTTTTTC
1 TTTTTTC
51167 TTTTTTC
1 TTTTTTC
51174 TTTTT
1 TTTTT
51179 GGTACCCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:52095 original size:24 final size:24
Alignment explanation
Indices: 52067--52117 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
52057 GGAAAAAAGG
*
52067 AAAAACTTCCACTAAGACAAGACT
1 AAAAACTTACACTAAGACAAGACT
* * *
52091 AAAAACTTACAGTATGGCAAGACT
1 AAAAACTTACACTAAGACAAGACT
52115 AAA
1 AAA
52118 GCTCTCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.18
Consensus pattern (24 bp):
AAAAACTTACACTAAGACAAGACT
Found at i:56425 original size:167 final size:166
Alignment explanation
Indices: 56134--56443 Score: 388
Period size: 167 Copynumber: 1.9 Consensus size: 166
56124 ATTTTAAACA
* * *
56134 AAATTGGCTTTCGTGTCTCATGTCTCCAACCGTTTATGTATAGGACAATTGCCGTTTGGATATCG
1 AAATTGGCTTTCGTATCTCATGTCTCCAACCGTTTATGTATAGAACAATTGCCGTTTGGATATCA
* * * * * * * *
56199 GAGATAGATATTCAATCCGTCAGAATCCGTTTATGGCGGATTTGGATTGTGATATATGGATATGG
66 AAGACAGATATTCAATCCGTCAGAATCCATTTAGGGCGGATTTGGATGGTCATATATGGATACGA
*
56264 AGTGAATTTGGATTTCCAAAATTTTTTCCATTTACT
131 AATGAATTTGGATTTCCAAAATTTTTTCCATTTACT
* * * * ** *
56300 AAATTGGACTTTTGTATCTCATGTCTCTAACCGTTTGTGTATCGAACAATTGTTGTTTGGATCTC
1 AAATTGG-CTTTCGTATCTCATGTCTCCAACCGTTTATGTATAGAACAATTGCCGTTTGGATATC
* * **
56365 AAAGGCGGATATTCAATTTGTCCA-AATCCATTTAGGGCGGATTTGGATGGTCATATATGGATAC
65 AAAGACAGATATTCAATCCGT-CAGAATCCATTTAGGGCGGATTTGGATGGTCATATATGGATAC
56429 GAAATGAATTTGGAT
129 GAAATGAATTTGGAT
56444 AGTGAAACTA
Statistics
Matches: 119, Mismatches: 23, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
166 7 0.06
167 110 0.92
168 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (166 bp):
AAATTGGCTTTCGTATCTCATGTCTCCAACCGTTTATGTATAGAACAATTGCCGTTTGGATATCA
AAGACAGATATTCAATCCGTCAGAATCCATTTAGGGCGGATTTGGATGGTCATATATGGATACGA
AATGAATTTGGATTTCCAAAATTTTTTCCATTTACT
Found at i:61787 original size:8 final size:8
Alignment explanation
Indices: 61770--61851 Score: 87
Period size: 8 Copynumber: 10.5 Consensus size: 8
61760 TGAAATAAAC
*
61770 TGAATAAT
1 TGAAGAAT
*
61778 TGAAGGAT
1 TGAAGAAT
61786 TGAAGAAT
1 TGAAGAAT
*
61794 TGAATAAT
1 TGAAGAAT
*
61802 TGAAAAAT
1 TGAAGAAT
*
61810 TGAAGCAT
1 TGAAGAAT
*
61818 TGAATAAT
1 TGAAGAAT
*
61826 TGAAGTAT
1 TGAAGAAT
61834 TG-A-AAT
1 TGAAGAAT
61840 TGAAGAAT
1 TGAAGAAT
61848 TGAA
1 TGAA
61852 TTTGAAACAT
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
6 4 0.07
7 2 0.03
8 54 0.90
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.30
Consensus pattern (8 bp):
TGAAGAAT
Found at i:61794 original size:16 final size:16
Alignment explanation
Indices: 61770--61852 Score: 98
Period size: 16 Copynumber: 5.3 Consensus size: 16
61760 TGAAATAAAC
*
61770 TGAATAATTGAAGGAT
1 TGAATAATTGAAGAAT
* *
61786 TGAAGAATTGAATAAT
1 TGAATAATTGAAGAAT
* *
61802 TGAAAAATTGAAGCAT
1 TGAATAATTGAAGAAT
*
61818 TGAATAATTGAAGTAT
1 TGAATAATTGAAGAAT
61834 TG-A-AATTGAAGAAT
1 TGAATAATTGAAGAAT
61848 TGAAT
1 TGAAT
61853 TTGAAACATT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.21
15 2 0.04
16 42 0.75
ACGTcount: A:0.47, C:0.01, G:0.20, T:0.31
Consensus pattern (16 bp):
TGAATAATTGAAGAAT
Found at i:61798 original size:24 final size:24
Alignment explanation
Indices: 61770--61851 Score: 105
Period size: 24 Copynumber: 3.5 Consensus size: 24
61760 TGAAATAAAC
*
61770 TGAATAATTGAAGGATTGAAGAAT
1 TGAATAATTGAAGAATTGAAGAAT
* *
61794 TGAATAATTGAAAAATTGAAGCAT
1 TGAATAATTGAAGAATTGAAGAAT
*
61818 TGAATAATTGAAGTATTG-A-AAT
1 TGAATAATTGAAGAATTGAAGAAT
*
61840 TGAAGAATTGAA
1 TGAATAATTGAA
61852 TTTGAAACAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 13 0.25
23 1 0.02
24 37 0.73
ACGTcount: A:0.48, C:0.01, G:0.21, T:0.30
Consensus pattern (24 bp):
TGAATAATTGAAGAATTGAAGAAT
Found at i:61937 original size:42 final size:42
Alignment explanation
Indices: 61838--61930 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
61828 AAGTATTGAA
* *
61838 ATTGAAGAATTGAATTTGAAACATTGAAATATAGAGATTGAAGC
1 ATTGAAGAATTGAA--AGAAACATTGAAATATAGAAATTGAAGC
* * *
61882 ATTTAAGAATTGAAAGAAACATTGAAGA-ATTGAAATTGAGGC
1 ATTGAAGAATTGAAAGAAACATTGAA-ATATAGAAATTGAAGC
61924 ATTGAAG
1 ATTGAAG
61931 CGTTGAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
42 28 0.67
43 1 0.02
44 13 0.31
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (42 bp):
ATTGAAGAATTGAAAGAAACATTGAAATATAGAAATTGAAGC
Found at i:62015 original size:22 final size:21
Alignment explanation
Indices: 61990--62038 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
61980 ATACATTGAA
61990 ATTGAAACATTGAAATTGAAGC
1 ATTGAAA-ATTGAAATTGAAGC
*
62012 ATTGAAAATTGAAATTGAGGC
1 ATTGAAAATTGAAATTGAAGC
62033 ATTGAA
1 ATTGAA
62039 TAATGGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (21 bp):
ATTGAAAATTGAAATTGAAGC
Found at i:62024 original size:21 final size:22
Alignment explanation
Indices: 61784--62038 Score: 101
Period size: 22 Copynumber: 11.6 Consensus size: 22
61774 TAATTGAAGG
*
61784 ATTGAAGAATTGAATA-ATTGAAAA
1 ATTGAAGCATTGAA-ACATTG--AA
61808 ATTGAAGCATTGAATA-ATTGAA
1 ATTGAAGCATTGAA-ACATTGAA
61830 GTATTGAA--ATTGAAGA-ATTGAA
1 --ATTGAAGCATTGAA-ACATTGAA
* * * * *
61852 TTTGAAACATTGAAATATAGAG
1 ATTGAAGCATTGAAACATTGAA
*
61874 ATTGAAGCATTTAAGA-ATTGAA
1 ATTGAAGCATTGAA-ACATTGAA
*
61896 A--GAAACATTGAAGA-ATTGAA
1 ATTGAAGCATTGAA-ACATTGAA
* * *
61916 ATTGAGGCATTGAAGCGTTGAAGA
1 ATTGAAGCATTGAAACATTG-A-A
* * *
61940 ATGGAA--ATTGAAGCATCGAATA
1 ATTGAAGCATTGAAACATTG-A-A
* * *
61962 ATT-AA-AATTGAAGCACTGATA
1 ATTGAAGCATTGAAACATTGA-A
61983 CATTGAA--ATTGAAACATTGAA
1 -ATTGAAGCATTGAAACATTGAA
62004 ATTGAAGCATTGAAA-ATTGAA
1 ATTGAAGCATTGAAACATTGAA
*
62025 ATTGAGGCATTGAA
1 ATTGAAGCATTGAA
62039 TAATGGAGAA
Statistics
Matches: 188, Mismatches: 27, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
20 29 0.15
21 26 0.14
22 99 0.53
23 4 0.02
24 30 0.16
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTGAAGCATTGAAACATTGAA
Found at i:62038 original size:14 final size:14
Alignment explanation
Indices: 61982--62025 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
61972 AAGCACTGAT
61982 ACATTGAAATTGAA
1 ACATTGAAATTGAA
61996 ACATTGAAATTGAA
1 ACATTGAAATTGAA
*
62010 GCATTGAAAATTGAA
1 ACATTG-AAATTGAA
62025 A
1 A
62026 TTGAGGCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (14 bp):
ACATTGAAATTGAA
Found at i:62175 original size:14 final size:14
Alignment explanation
Indices: 62156--62203 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
62146 AATTGAGTCA
*
62156 TGAAGAATTGAATT
1 TGAAGAATTGAAAT
62170 TGAAGAATTGAAAT
1 TGAAGAATTGAAAT
*
62184 TGAAGCATTGTAGAAT
1 TGAAGAATTG-A-AAT
62200 TGAA
1 TGAA
62204 ATTGAAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 22 0.73
15 1 0.03
16 7 0.23
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (14 bp):
TGAAGAATTGAAAT
Found at i:62209 original size:36 final size:35
Alignment explanation
Indices: 62134--62224 Score: 107
Period size: 36 Copynumber: 2.6 Consensus size: 35
62124 AAATCAGGAG
62134 AATTG-AAATTGAAATTG-AGTCATGAAGAATTGA
1 AATTGAAAATTGAAATTGAAGTCATGAAGAATTGA
* *
62167 ATTTGAAGAATTGAAATTGAAG-CATTGTAGAATTGA
1 AATTGAA-AATTGAAATTGAAGTCA-TGAAGAATTGA
*
62203 AATTGAAAGATTGAAACTGAAG
1 AATTGAAA-ATTGAAATTGAAG
62225 AATGACCAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
33 4 0.08
34 1 0.02
35 14 0.29
36 30 0.61
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (35 bp):
AATTGAAAATTGAAATTGAAGTCATGAAGAATTGA
Found at i:62283 original size:215 final size:214
Alignment explanation
Indices: 61961--62448 Score: 501
Period size: 215 Copynumber: 2.3 Consensus size: 214
61951 AGCATCGAAT
* * * * * *
61961 AATTAAAATTGAAGCACTGATA-CATTGAAATTGAAACATTGAAATTGAAGCATTGAAAATTGAA
1 AATTGAAATTGAAGCATTG-TAGAATTGAAATTGAAACATTGAAACTGAAGCAATGAAAAGTGAA
* * **
62025 ATTGAGGCATTGAATAATGGAGAAATGGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAG
65 ATTGAAGCATGGAATAATAAAGAAATGGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAG
* *** * * *
62090 CGTTGACATCTTGAAAAT-GAAACATTGAAGGATTAAATCAGGAGAATTGAAATTGAAATTG-AG
130 CATTGA-AGAATGAAAATCCAAACATTGAAGAATTAAATCAGAAGAATTGAAATTGAAATTGAAG
* *
62153 TC-ATGAAGAATTGAATTTGAA
194 -CGATGAAGAATGGAAATTGAA
*
62174 GAATTGAAATTGAAGCATTGTAGAATTGAAATTGAAAGATTGAAACTGAAG-AATGACCAGAAGT
1 -AATTGAAATTGAAGCATTGTAGAATTGAAATTGAAACATTGAAACTGAAGCAATGA--A-AAGT
* * *
62238 -AAATTGAAGCATGGAATAATTAAAG-AATTGAAGAAAGACCACCCTGGGTCCTTGAAGTAAATT
62 GAAATTGAAGCATGGAATAA-TAAAGAAATGGAAGAAAGACCACCCTGGATCATTGAAGTAAATT
* * * ** *
62301 GGAGCATTGAAGAATGAAAATCCAAGCATTGAAGAATTGAATTTGAAGATTTGAAATTGAAATTG
126 GAAGCATTGAAGAATGAAAATCCAAACATTGAAGAATTAAATCAGAAGAATTGAAATTGAAATTG
* *
62366 AAGCGTTGAATAATGGAAATTGAA
191 AAGCGATGAAGAATGGAAATTGAA
** *
62390 ACATTGAAGAATTGAA--ATTG-AGAATTGAAATTGAAACATTGAAGTTGAAGCATTGAAAA
1 A-ATTG-A-AATTGAAGCATTGTAGAATTGAAATTGAAACATTGAAACTGAAGCAATGAAAA
62449 CTTGAGGAAT
Statistics
Matches: 227, Mismatches: 35, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
213 8 0.04
214 51 0.22
215 125 0.55
216 35 0.15
217 1 0.00
218 7 0.03
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (214 bp):
AATTGAAATTGAAGCATTGTAGAATTGAAATTGAAACATTGAAACTGAAGCAATGAAAAGTGAAA
TTGAAGCATGGAATAATAAAGAAATGGAAGAAAGACCACCCTGGATCATTGAAGTAAATTGAAGC
ATTGAAGAATGAAAATCCAAACATTGAAGAATTAAATCAGAAGAATTGAAATTGAAATTGAAGCG
ATGAAGAATGGAAATTGAA
Found at i:62321 original size:22 final size:21
Alignment explanation
Indices: 62296--62418 Score: 99
Period size: 22 Copynumber: 5.8 Consensus size: 21
62286 TCCTTGAAGT
*
62296 AAATTGGAGCATTGAAGAATG
1 AAATTGAAGCATTGAAGAATG
**
62317 AAAATCCAAGCATTGAAGAATTG
1 -AAATTGAAGCATTGAAGAA-TG
* *
62340 AATTTGAAG-ATTTGAA-ATTG
1 AAATTGAAGCA-TTGAAGAATG
* *
62360 AAATTGAAGCGTTGAATAATGG
1 AAATTGAAGCATTGAAGAAT-G
*
62382 AAATTGAAACATTGAAGAATTG
1 AAATTGAAGCATTGAAGAA-TG
*
62404 AAATTG-AGAATTGAA
1 AAATTGAAGCATTGAA
62419 ATTGAAACAT
Statistics
Matches: 80, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
20 15 0.19
21 11 0.14
22 51 0.64
23 3 0.04
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.28
Consensus pattern (21 bp):
AAATTGAAGCATTGAAGAATG
Found at i:62348 original size:14 final size:14
Alignment explanation
Indices: 62328--62447 Score: 75
Period size: 14 Copynumber: 8.1 Consensus size: 14
62318 AAATCCAAGC
62328 ATTGAAGAATTGAA
1 ATTGAAGAATTGAA
* *
62342 TTTGAAGATTTGAA
1 ATTGAAGAATTGAA
62356 ATTGAAATTGAAGCGTTGAA
1 ATTG-AA--GAA---TTGAA
* *
62376 TAATGGA-AATTGAAA
1 -ATTGAAGAATTG-AA
62391 CATTGAAGAATTGAA
1 -ATTGAAGAATTGAA
62406 ATTG-AGAATTGAA
1 ATTGAAGAATTGAA
62419 ATTGAA-ACATTGAA
1 ATTGAAGA-ATTGAA
* *
62433 GTTGAAGCATTGAA
1 ATTGAAGAATTGAA
62447 A
1 A
62448 ACTTGAGGAA
Statistics
Matches: 82, Mismatches: 12, Indels: 24
0.69 0.10 0.20
Matches are distributed among these distances:
13 14 0.17
14 40 0.49
15 10 0.12
16 5 0.06
17 4 0.05
20 6 0.07
21 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (14 bp):
ATTGAAGAATTGAA
Found at i:62360 original size:6 final size:6
Alignment explanation
Indices: 62335--62425 Score: 56
Period size: 6 Copynumber: 13.3 Consensus size: 6
62325 AGCATTGAAG
* * *
62335 AATTGA ATTTGA AGATTTGA AATTGA AATTGA AGCGTTGAA TAATGGA
1 AATTGA AATTGA A-A-TTGA AATTGA AATTGA A--ATTG-A -AATTGA
62383 AATTGAA ACATTGAA GAATTGA AATTGA GAATTGA AATTGA AA
1 AATTG-A A-ATTG-A -AATTGA AATTGA -AATTGA AATTGA AA
62426 CATTGAAGTT
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
6 35 0.51
7 11 0.16
8 20 0.29
9 2 0.03
10 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.31
Consensus pattern (6 bp):
AATTGA
Found at i:62364 original size:64 final size:63
Alignment explanation
Indices: 62296--62425 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 63
62286 TCCTTGAAGT
* * * *
62296 AAATTGGAGCATTGAAGAATGAAAATCCAAGCATTGAAGAATTGAATTTGAAGATTTGAAATTG
1 AAATTGAAGCATTGAAGAATGAAAATCCAAACATTGAAGAATTGAAATTG-AGAATTGAAATTG
* * * **
62360 AAATTGAAGCGTTGAATAATGGAAATTGAAACATTGAAGAATTGAAATTGAGAATTGAAATTG
1 AAATTGAAGCATTGAAGAATGAAAATCCAAACATTGAAGAATTGAAATTGAGAATTGAAATTG
62423 AAA
1 AAA
62426 CATTGAAGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
63 15 0.26
64 42 0.74
ACGTcount: A:0.46, C:0.05, G:0.22, T:0.28
Consensus pattern (63 bp):
AAATTGAAGCATTGAAGAATGAAAATCCAAACATTGAAGAATTGAAATTGAGAATTGAAATTG
Found at i:62445 original size:35 final size:35
Alignment explanation
Indices: 62356--62445 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 35
62346 AAGATTTGAA
* * *
62356 ATTGAAATTGAAGCGTTGAATAATGGAAATTGAAAC
1 ATTGAAGTTGAAGCATTG-AGAATGGAAATTGAAAC
*
62392 ATTGAAGAATTGAA--ATTGAGAATTGAAATTGAAAC
1 ATTGAAG--TTGAAGCATTGAGAATGGAAATTGAAAC
62427 ATTGAAGTTGAAGCATTGA
1 ATTGAAGTTGAAGCATTGA
62446 AAACTTGAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
33 5 0.11
35 27 0.59
36 9 0.20
38 5 0.11
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (35 bp):
ATTGAAGTTGAAGCATTGAGAATGGAAATTGAAAC
Found at i:62519 original size:24 final size:26
Alignment explanation
Indices: 62480--62531 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
62470 CACCCTGGAT
62480 CATTGGAGTAAATTGAAAAATTGAAG
1 CATTGGAGTAAATTGAAAAATTGAAG
* *
62506 CATT-GAGT-AATTGAAGAATTTAAG
1 CATTGGAGTAAATTGAAAAATTGAAG
62530 CA
1 CA
62532 ATAAGTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 4 0.17
26 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (26 bp):
CATTGGAGTAAATTGAAAAATTGAAG
Found at i:62525 original size:8 final size:8
Alignment explanation
Indices: 62490--62661 Score: 67
Period size: 8 Copynumber: 22.2 Consensus size: 8
62480 CATTGGAGTA
*
62490 AATTGAAA
1 AATTGAAG
62498 AATTGAAG
1 AATTGAAG
*
62506 CATTG-AG
1 AATTGAAG
62513 TAATTGAAG
1 -AATTGAAG
*
62522 AATTTAAG
1 AATTGAAG
62530 CAA-T-AAG
1 -AATTGAAG
* *
62537 TGATCGAAG
1 -AATTGAAG
62546 AATTGAAG
1 AATTGAAG
*
62554 AAAT--A-
1 AATTGAAG
62559 AATTGAAG
1 AATTGAAG
* *
62567 TATTGAAT
1 AATTGAAG
*
62575 AATTAAAG
1 AATTGAAG
* *
62583 AGTCGAAG
1 AATTGAAG
62591 -A--GATA-
1 AATTGA-AG
*
62596 AATTGAAT
1 AATTGAAG
*
62604 CATTGAAG
1 AATTGAAG
*
62612 AATTGAAT
1 AATTGAAG
*
62620 AATTGAAT
1 AATTGAAG
*
62628 AATAGAAG
1 AATTGAAG
*
62636 AGTTGAAG
1 AATTGAAG
* *
62644 CATTGAAT
1 AATTGAAG
62652 AATTGAAG
1 AATTGAAG
62660 AA
1 AA
62662 AGAGACCATT
Statistics
Matches: 118, Mismatches: 33, Indels: 26
0.67 0.19 0.15
Matches are distributed among these distances:
5 5 0.04
6 3 0.03
7 8 0.07
8 95 0.81
9 7 0.06
ACGTcount: A:0.49, C:0.03, G:0.20, T:0.27
Consensus pattern (8 bp):
AATTGAAG
Found at i:62615 original size:16 final size:16
Alignment explanation
Indices: 62596--62661 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 16
62586 CGAAGAGATA
*
62596 AATTGAATCATTGAAG
1 AATTGAATAATTGAAG
*
62612 AATTGAATAATTGAAT
1 AATTGAATAATTGAAG
* * *
62628 AATAGAAGAGTTGAAG
1 AATTGAATAATTGAAG
*
62644 CATTGAATAATTGAAG
1 AATTGAATAATTGAAG
62660 AA
1 AA
62662 AGAGACCATT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.29
Consensus pattern (16 bp):
AATTGAATAATTGAAG
Found at i:62624 original size:24 final size:24
Alignment explanation
Indices: 62596--62661 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
62586 CGAAGAGATA
* *
62596 AATTGAATCATTGAAGAATTGAAT
1 AATTGAATAATTGAAGAATTGAAG
* *
62620 AATTGAATAATAGAAGAGTTGAAG
1 AATTGAATAATTGAAGAATTGAAG
*
62644 CATTGAATAATTGAAGAA
1 AATTGAATAATTGAAGAA
62662 AGAGACCATT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.48, C:0.03, G:0.20, T:0.29
Consensus pattern (24 bp):
AATTGAATAATTGAAGAATTGAAG
Found at i:63701 original size:23 final size:23
Alignment explanation
Indices: 63675--63749 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
63665 ACCCTAGAGC
63675 TTTTCTCTTTTTCTTCTTCTTTT
1 TTTTCTCTTTTTCTTCTTCTTTT
* *
63698 TTTT-TCTTCTTTTTTCTT-TCTT
1 TTTTCTCTT-TTTCTTCTTCTTTT
*
63720 TTTTCCCTTCTTTTCTT-TTCTTTT
1 TTTTCTC-T-TTTTCTTCTTCTTTT
63744 TTTTCT
1 TTTTCT
63750 TTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 11 0.27
23 15 0.37
24 14 0.34
25 1 0.02
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTCTCTTTTTCTTCTTCTTTT
Found at i:63704 original size:13 final size:13
Alignment explanation
Indices: 63677--63723 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
63667 CCTAGAGCTT
*
63677 TTCTCTTTTTCTTC
1 TTCT-TTTTTTTTC
63691 TTCTTTTTTTTTC
1 TTCTTTTTTTTTC
63704 TTCTTTTTTCTTTC
1 TTCTTTTTT-TTTC
63718 TT-TTTT
1 TTCTTTT
63724 CCCTTCTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 21 0.68
14 10 0.32
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (13 bp):
TTCTTTTTTTTTC
Found at i:63710 original size:10 final size:10
Alignment explanation
Indices: 63691--63752 Score: 65
Period size: 10 Copynumber: 6.0 Consensus size: 10
63681 CTTTTTCTTC
*
63691 TTCTTTTTTT
1 TTCTTCTTTT
63701 TTCTTCTTTT
1 TTCTTCTTTT
63711 TTCTTTCTTTT
1 TTC-TTCTTTT
63722 TTCCCTTCTTTT
1 TT--CTTCTTTT
63734 CTT-TTCTTTT
1 -TTCTTCTTTT
63744 TT-TTCTTTT
1 TTCTTCTTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
9 9 0.19
10 19 0.40
11 9 0.19
12 7 0.15
13 3 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTCTTCTTTT
Found at i:63730 original size:36 final size:37
Alignment explanation
Indices: 63676--63751 Score: 111
Period size: 36 Copynumber: 2.1 Consensus size: 37
63666 CCCTAGAGCT
* *
63676 TTTCTCTTTTTCTTCTTCTTTTTTTTTCTTCTTTTTTC
1 TTTCTCTTTTTCTCCTTCTTTTCTTTTCTT-TTTTTTC
63714 TTTCT-TTTTTC-CCTTCTTTTCTTTTCTTTTTTTTC
1 TTTCTCTTTTTCTCCTTCTTTTCTTTTCTTTTTTTTC
63749 TTT
1 TTT
63752 T
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 10 0.28
36 15 0.42
37 6 0.17
38 5 0.14
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (37 bp):
TTTCTCTTTTTCTCCTTCTTTTCTTTTCTTTTTTTTC
Done.