Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024366.1 Corchorus olitorius cultivar O-4 contig24399, 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: 21963
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Found at i:831 original size:20 final size:20
Alignment explanation
Indices: 781--832 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
771 AGAATATCAG
781 ATTTAATATTATT--TTTTGA
1 ATTTAATATT-TTACTTTTGA
800 ATTTAATATTTTACTTTT-A
1 ATTTAATATTTTACTTTTGA
*
819 ATTTCAATTTTTTA
1 ATTT-AATATTTTA
833 ATGTCAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 15 0.52
20 12 0.41
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTAATATTTTACTTTTGA
Found at i:2976 original size:3 final size:3
Alignment explanation
Indices: 2968--2995 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2958 AAGCTCAATT
2968 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
1 ACC ACC ACC ACC ACC ACC ACC ACC ACC A
2996 AGGGGAGGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (3 bp):
ACC
Found at i:9537 original size:38 final size:38
Alignment explanation
Indices: 9485--9565 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
9475 TCAGAGATAT
* * **
9485 AAGTTGATCTCCAGATGATCCGGTACGGTCATTTTAAG
1 AAGTTGATCCCCAGATGATCCAGTACGGTCATTCCAAG
* *
9523 AAGTTGATCCCCAGATGATCTAGTGCGGTCATTCCAAG
1 AAGTTGATCCCCAGATGATCCAGTACGGTCATTCCAAG
9561 AAGTT
1 AAGTT
9566 TTAGAGATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (38 bp):
AAGTTGATCCCCAGATGATCCAGTACGGTCATTCCAAG
Found at i:9582 original size:53 final size:55
Alignment explanation
Indices: 9524--9639 Score: 191
Period size: 53 Copynumber: 2.1 Consensus size: 55
9514 CATTTTAAGA
9524 AGTTGATCCCCAGATGATCTAGTGCGGTCATTCC-AAGAAGTTTT-AGAGATCAG
1 AGTTGATCCCCAGATGATCTAGTGCGGTCATTCCAAAGAAGTTTTCAGAGATCAG
* * *
9577 AGTTGATCCCTAGATGATCTAGTGTGGTCATTCCAAAGAAGTTTTCAGTGATCAG
1 AGTTGATCCCCAGATGATCTAGTGCGGTCATTCCAAAGAAGTTTTCAGAGATCAG
9632 AGTTGATC
1 AGTTGATC
9640 TCCTTTCAAG
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
53 32 0.55
54 10 0.17
55 16 0.28
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (55 bp):
AGTTGATCCCCAGATGATCTAGTGCGGTCATTCCAAAGAAGTTTTCAGAGATCAG
Found at i:9651 original size:35 final size:35
Alignment explanation
Indices: 9612--9970 Score: 560
Period size: 35 Copynumber: 10.3 Consensus size: 35
9602 GGTCATTCCA
*
9612 AAGAAGTTTTC-AGTGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTCGA-TGATCAGAGTTGATCTCGTTTC
* *
9647 AAGAAGTTTTTGATGATCAGAGTTGATCTAGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
* * *
9682 AAGCAGTTTTCGATGATCATAGTTGATCTAGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
9717 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
* * *
9752 AAGAAGTTTTTGATGATCAAAGTTGATCTCCTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
9787 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
*
9822 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
*
9857 AAGAAGTTTT-GATGATCAGAGTTGATCTCCTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
* *
9891 AAGAAGTTTTCGAAGATCATAGTTGATCTCGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
* *
9926 AAGAAGTTTTTGATGATTAGAGTTGATCTCGTTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
9961 AAGAAGTTTT
1 AAGAAGTTTT
9971 TTTCAAGAAG
Statistics
Matches: 298, Mismatches: 24, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
34 33 0.11
35 264 0.89
36 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (35 bp):
AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
Found at i:9795 original size:105 final size:105
Alignment explanation
Indices: 9612--10528 Score: 1322
Period size: 105 Copynumber: 8.6 Consensus size: 105
9602 GGTCATTCCA
* *
9612 AAGAAGTTTTC-AGTGATCAGAGTTGATCTCCTTTCAAGAAGTTTTTGATGATCAGAGTTGATCT
1 AAGAAGTTTTCGA-TGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCT
** * *
9676 AGTTTCAAGCAGTTTTCGATGATCATAGTTGATCT-AGTTTC
65 CCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA-TTTC
* * *
9717 AAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTTGATGATCAAAGTTGATCTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
*
9782 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTC
66 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
9822 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-GATGATCAGAGTTGATCTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * *
9886 CTTTCAAGAAGTTTTCGAAGATCATAGTTGATCTCGTTTC
66 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* * *
9926 AAGAAGTTTTTGATGATTAGAGTTGATCTCGTTTCAAGAAGTTTTTTTCAAGAAGTTTTTGATGA
1 AAGAAGTTTTCGATGATCAGAGTTGA--TC---TC----A-----TTTCAAGAAGTTTTCGATGA
9991 TCAGAGTTGATC-CCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
52 TCAGAGTTGATCTCC-TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
10045 AAGAAGTTTTCAATGATCAGAGTTGATCTCATTTTAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* *
10110 ATTTCAAGAAGTTTTCAATGATC-GAAGTTGATCTCATTTC
66 CTTTCAAGAAGTTTTCGATGATCAG-AGTTGATCTCATTTC
*
10150 AAGAAGTTTTCAATGATCAGAGTTGATCTCATTTCAAGGAAGTTTTCGATGATCAGAGTTGATCT
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAA-GAAGTTTTCGATGATCAGAGTTGATCT
*
10215 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
65 CCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
10256 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCATGAAAGTTTTCAATGATCAGAGTTGATCT
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG-AAGTTTTCGATGATCAGAGTTGATCT
*
10321 CATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
65 CCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
10362 AGGAAAGTTTTCGATGATCAGAGTTGATCTCATTTTAAGAAAGTTTTCGATGATCAGAGTTGATC
1 AAG-AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAG-AAGTTTTCGATGATCAGAGTTGATC
**
10427 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTGTTTC
64 TCCTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
**
10469 AAGAAGTTTTCGATGATCAGAGTTGATCTTGTTTCAAGAAGTTTTCGATGATCAGAGTTG
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTG
10529 GTCTTCACAT
Statistics
Matches: 749, Mismatches: 39, Indels: 48
0.90 0.05 0.06
Matches are distributed among these distances:
104 81 0.11
105 264 0.35
106 204 0.27
107 100 0.13
109 2 0.00
110 1 0.00
113 1 0.00
114 2 0.00
117 2 0.00
118 16 0.02
119 76 0.10
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (105 bp):
AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
Found at i:9976 original size:14 final size:14
Alignment explanation
Indices: 9957--9985 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9947 GTTGATCTCG
9957 TTTCAAGAAGTTTT
1 TTTCAAGAAGTTTT
9971 TTTCAAGAAGTTTT
1 TTTCAAGAAGTTTT
9985 T
1 T
9986 GATGATCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (14 bp):
TTTCAAGAAGTTTT
Found at i:9997 original size:49 final size:49
Alignment explanation
Indices: 9922--10019 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 49
9912 GTTGATCTCG
* *
9922 TTTCAAGAAGTTTTTGATGATTAGAGTTGATCTCGTTTCAAGAAGTTTT
1 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCGTTTCAAGAAGTTTT
9971 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCGTTTCAAGAAGTTTT
1 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCGTTTCAAGAAGTTTT
10020 CGATGATCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (49 bp):
TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCGTTTCAAGAAGTTTT
Found at i:10010 original size:35 final size:35
Alignment explanation
Indices: 9971--10528 Score: 920
Period size: 35 Copynumber: 15.8 Consensus size: 35
9961 AAGAAGTTTT
* * *
9971 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10006 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
10041 TTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
10076 TTTTAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
10111 TTTCAAGAAGTTTTCAATGATC-GAAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAG-AGTTGATCTCA
*
10146 TTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10181 TTTCAAGGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAA-GAAGTTTTCGATGATCAGAGTTGATCTCA
10217 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10252 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
10287 TTTCATGAAAGTTTTCAATGATCAGAGTTGATCTCA
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCA
10323 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
10358 TTTCAGGAAAGTTTTCGATGATCAGAGTTGATCTCA
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCA
* *
10394 TTTTAAGAAAGTTTTCGATGATCAGAGTTGATCTCC
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCA
**
10430 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
**
10465 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10500 TTTCAAGAAGTTTTCGATGATCAGAGTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTG
10529 GTCTTCACAT
Statistics
Matches: 498, Mismatches: 20, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
34 1 0.00
35 362 0.73
36 135 0.27
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (35 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:10032 original size:84 final size:84
Alignment explanation
Indices: 9887--10054 Score: 273
Period size: 84 Copynumber: 2.0 Consensus size: 84
9877 GTTGATCTCC
* * * *
9887 TTTCAAGAAGTTTTCGAAGATCATAGTTGATCTCGTTTCAAGAAGTTTTTGATGATTAGAGTTGA
1 TTTCAAGAAGTTTTCGAAGATCAGAGTTGATCCCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
*
9952 TCTCGTTTCAAGAAGTTTT
66 TCTCATTTCAAGAAGTTTT
* *
9971 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGAAGATCAGAGTTGATCCCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
10036 TCTCATTTCAAGAAGTTTT
66 TCTCATTTCAAGAAGTTTT
10055 CAATGATCAG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (84 bp):
TTTCAAGAAGTTTTCGAAGATCAGAGTTGATCCCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
TCTCATTTCAAGAAGTTTT
Found at i:10272 original size:106 final size:105
Alignment explanation
Indices: 9971--10528 Score: 920
Period size: 106 Copynumber: 5.3 Consensus size: 105
9961 AAGAAGTTTT
* * *
9971 TTTCAAGAAGTTTTTGATGATCAGAGTTGATCCCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGA
*
10036 TCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCA
66 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
10076 TTTTAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCAATGATC-GAAGTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAG-AGTTG
*
10140 ATCTCATTTCAAGAAGTTTTCAATGATCAGAGTTGATCTCA
65 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10181 TTTCAAGGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTG
1 TTTCAA-GAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTG
10246 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
65 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* *
10287 TTTCATGAAAGTTTTCAATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTG
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTG
*
10352 ATCTCATTTCAGGAAAGTTTTCGATGATCAGAGTTGATCTCA
65 ATCTCATTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCA
* *
10394 TTTTAAGAAAGTTTTCGATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTG
1 TTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTG
** **
10459 ATCTTGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTG
65 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
10500 TTTCAAGAAGTTTTCGATGATCAGAGTTG
1 TTTCAAGAAGTTTTCGATGATCAGAGTTG
10529 GTCTTCACAT
Statistics
Matches: 427, Mismatches: 21, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
104 1 0.00
105 126 0.30
106 200 0.47
107 100 0.23
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (105 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGA
TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:15762 original size:22 final size:21
Alignment explanation
Indices: 15728--15915 Score: 90
Period size: 22 Copynumber: 8.5 Consensus size: 21
15718 TTCACATCAT
* *
15728 GGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGGA
** *
15750 GGTTATCAAAATTGAATAGTGT
1 GGTTATCAAAATTTCATAG-GA
* * *
15772 GGTTACCAAAATTTGATATGAA
1 GGTTATCAAAATTTCATA-GGA
* * *
15794 AGTTATCAAAATTTCATACTGT
1 GGTTATCAAAATTTCATA-GGA
*
15816 GGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGG---A
* **
15840 GGTTATTAAAATTTTTTAGGAA
1 GGTTATCAAAATTTCATAGG-A
**
15862 GGTTATTGAAATTTCATAGTGTA
1 GGTTATCAAAATTTCATAG-G-A
* * *
15885 -GTTATCACAATTTTATAGATA
1 GGTTATCAAAATTTCATAG-GA
15906 GGTTATCAAA
1 GGTTATCAAA
15916 GAGATTATCA
Statistics
Matches: 122, Mismatches: 37, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
21 4 0.03
22 99 0.81
23 3 0.02
24 16 0.13
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (21 bp):
GGTTATCAAAATTTCATAGGA
Found at i:15956 original size:22 final size:21
Alignment explanation
Indices: 15920--16806 Score: 123
Period size: 22 Copynumber: 40.7 Consensus size: 21
15910 ATCAAAGAGA
* *
15920 TTATCAAAATATCATAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
*
15942 TTATAAGAATTTCATAGTGTGG
1 TTATAA-AATTTCATAGTGAGG
*
15964 TTAGCAAAATTTCATAAG-GAGG
1 TTA-TAAAATTTCAT-AGTGAGG
* *
15986 TTACTAATATTTCATAGGGAGG
1 TTA-TAAAATTTCATAGTGAGG
*
16008 TTATCAAAATTTCATAGTGTGG
1 TTAT-AAAATTTCATAGTGAGG
* ** *
16030 TTATTAAATTTTTTTAGTGTGG
1 TTA-TAAAATTTCATAGTGAGG
*
16052 TTATCAAAATTCCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
* *
16074 TTATAAAAGTCTTAATTTCA-TAAGG
1 TTATAAAA-T-TTCA--T-AGTGAGG
* * * *
16099 AGTACCAAAATTTGATAG-AAGG
1 -TTA-TAAAATTTCATAGTGAGG
* * * * *
16121 TTATCAAATCTCATAGAGTGC
1 TTATAAAATTTCATAGTGAGG
* *
16142 TTATCGAAATTTCATAGAGATCGG
1 TTAT-AAAATTTCATAGTGA--GG
*
16166 ATTATCAAAATTT-ATAG-GAAGT
1 -TTAT-AAAATTTCATAGTG-AGG
**
16188 TTATCAAAATTTCATAGTGTTG
1 TTAT-AAAATTTCATAGTGAGG
* *
16210 TTATCAAAATTTCAAAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
* * **
16232 TTATCAAAATTACATAATGAAA
1 TTAT-AAAATTTCATAGTGAGG
* * *
16254 ATATCAAAATTTCGTAGAG-GG
1 TTAT-AAAATTTCATAGTGAGG
* * * *
16275 TCAACAAAATTTTATAGAGAGG
1 T-TATAAAATTTCATAGTGAGG
**
16297 TTATCAAAATTTCATAAAGAGG
1 TTAT-AAAATTTCATAGTGAGG
* * * * * *
16319 TTATCAATTTTCAAAATGTGA
1 TTATAAAATTTCATAGTGAGG
*
16340 TTACCAAAATTTCATAGT-ATGG
1 TTA-TAAAATTTCATAGTGA-GG
*
16362 TT-TCCAAA--T--TAG-GAAGG
1 TTAT-AAAATTTCATAGTG-AGG
*
16379 TTATTAAACCTTTACCAT-G-GA-G
1 TTA-TAAA-ATTT--CATAGTGAGG
* * *
16401 TAATCAAAATTTC--AGGGTGG
1 TTAT-AAAATTTCATAGTGAGG
*
16421 ATATCAAAATTTCATA-TGAAGG
1 TTAT-AAAATTTCATAGTG-AGG
*
16443 TTATCAAAATTTCATAGTTTA-G
1 TTAT-AAAATTTCATAG-TGAGG
* *
16465 TTTTCAAAATTTCATA-AGATGG
1 TTAT-AAAATTTCATAGTGA-GG
* * *
16487 TTATCAAAATTTAATAGGGAGA
1 TTAT-AAAATTTCATAGTGAGG
* *
16509 TTAACAAAATTTCATAATGAGG
1 TT-ATAAAATTTCATAGTGAGG
16531 TTATCAAAA-TT--T-GT-A-G
1 TTAT-AAAATTTCATAGTGAGG
*
16547 TTATCAAGATTTCATAAG-GAGG
1 TTAT-AAAATTTCAT-AGTGAGG
* *
16569 TTATCAAAATTTTATTAG-GAGCT
1 TTAT-AAAATTTCA-TAGTGAG-G
* *
16592 TTATCAAAATTTTATAGCGAGG
1 TTAT-AAAATTTCATAGTGAGG
* * * *
16614 TTATCACAATTTCATAGCGTGA
1 TTAT-AAAATTTCATAGTGAGG
* * *
16636 TTATCAAAATTTCAGAGTGTGA
1 TTAT-AAAATTTCATAGTGAGG
*
16658 TTACTAACAA-TTCATA-TGGAAGT
1 TTA-TAA-AATTTCATAGT-G-AGG
* * ** *
16681 TTTTAAATTTTCATAACGTGG
1 TTATAAAATTTCATAGTGAGG
* *
16702 TTATTAATATATCATA-TGGAGG
1 TTA-TAAAATTTCATAGT-GAGG
* * *
16724 TTATCAACATCTCATAGTGTTGG
1 TTAT-AAAATTTCATAGTG-AGG
16747 TTATCAAAATTTCATAGTGAGG
1 TTAT-AAAATTTCATAGTGAGG
* * *
16769 TCT-TCAAAATTCCTTAGGGAGG
1 T-TAT-AAAATTTCATAGTGAGG
*
16791 TTAACAAAATTTCATA
1 TT-ATAAAATTTCATA
16807 AGAAGGTTAA
Statistics
Matches: 640, Mismatches: 146, Indels: 158
0.68 0.15 0.17
Matches are distributed among these distances:
16 9 0.01
17 10 0.02
18 5 0.01
19 6 0.01
20 22 0.03
21 79 0.12
22 412 0.64
23 60 0.09
24 9 0.01
25 19 0.03
26 5 0.01
27 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.36
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:15972 original size:44 final size:43
Alignment explanation
Indices: 15920--16824 Score: 169
Period size: 44 Copynumber: 20.8 Consensus size: 43
15910 ATCAAAGAGA
*
15920 TTATCAAAATATCATAGCGAGGTTA-TAAGAATTTCATAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTACTAA-AATTTCATAGTGTGG
* * * *
15964 TTAGCAAAATTTCATAAGGAGGTTACTAATATTTCATAGGGAGG
1 TTATCAAAATTTCAT-AGGAGGTTACTAAAATTTCATAGTGTGG
* * * **
16008 TTATCAAAATTTCATAGTGTGGTTATTAAATTTTTTTAGTGTGG
1 TTATCAAAATTTCATAG-GAGGTTACTAAAATTTCATAGTGTGG
* * * **
16052 TTATCAAAATTCCATATGAAGGTTA-TAAAAGTCTTAATTTCA-TAAGG
1 TTATCAAAATTTCATA-GGAGGTTACTAAAA-T-TTCA--T-AGTGTGG
* * * * * * * *
16099 AGTACCAAAATTTGATAGAAGGTTA-TCAAATCTCATAGAGTGC
1 -TTATCAAAATTTCATAGGAGGTTACTAAAATTTCATAGTGTGG
* * *
16142 TTATCGAAATTTCATAGAGATCGGATTA-TCAAAATTT-ATAG-GAAGT
1 TTATCAAAATTTCATAG-GA--GG-TTACT-AAAATTTCATAGTG-TGG
** * * *
16188 TTATCAAAATTTCATAGTGTTGTTA-TCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGGTTACT-AAAATTTCATAGTGTGG
* * *** * *
16232 TTATCAAAATTACATAATGAAAATA-TCAAAATTTCGTAGAG-GG
1 TTATCAAAATTTCAT-AGGAGGTTACT-AAAATTTCATAGTGTGG
* * * ** *
16275 TCAACAAAATTTTATAGAGAGGTTA-TCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAG-GAGGTTACT-AAAATTTCATAGTGTGG
* * * * * * *
16319 TTATC-AATTTTCAAAATGTGATTACCAAAATTTCATAGTATGG
1 TTATCAAAATTTC-ATAGGAGGTTACTAAAATTTCATAGTGTGG
* * * *
16362 TT-TCCAAA--T--TAGGAAGGTTATTAAACCTTTACCAT-G-G-AG
1 TTATCAAAATTTCATAGG-AGGTTACTAAA-ATTT--CATAGTGTGG
* * * * *
16401 TAATCAAAATTTCA-GGGTGGATA-TCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGGAGGTTACT-AAAATTTCATAGTG-TGG
* * * *
16443 TTATCAAAATTTCATAGTTTAGTTTTC-AAAATTTCATAAG-ATGG
1 TTATCAAAATTTCATAG--GAGGTTACTAAAATTTCAT-AGTGTGG
* * * *
16487 TTATCAAAATTTAATAGGGAGATTAAC-AAAATTTCATAATGAGG
1 TTATCAAAATTTCATA-GGAGGTT-ACTAAAATTTCATAGTGTGG
* * *
16531 TTATCAAAA-TT--T-GTA-GTTA-TCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCATAGGAGGTTACT-AAAATTTCAT-AGTGTGG
* * * * *
16569 TTATCAAAATTTTATTAGGAGCTTTA-TCAAAATTTTATAGCGAGG
1 TTATCAAAATTTCA-TAGGAG-GTTACT-AAAATTTCATAGTGTGG
* * * * *
16614 TTATCACAATTTCATAGCGTGATTA-TCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCATAG-GAGGTTACT-AAAATTTCATAGTGTGG
* ** * **
16658 TTA-CTAACAA-TTCATATGGAAGTTTTTAAATTTTCATAACGTGG
1 TTATC-AA-AATTTCATA-GGAGGTTACTAAAATTTCATAGTGTGG
* * * * *
16702 TTATTAATATATCATATGGAGGTTA-TCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATA-GGAGGTTACT-AAAATTTCATAGTG-TGG
* * * * *
16747 TTATCAAAATTTCATAGTGAGGTCTTC-AAAATTCCTTAGGGAGG
1 TTATCAAAATTTCATAG-GAGGT-TACTAAAATTTCATAGTGTGG
* * **
16791 TTAACAAAATTTCATAAGAAGGTTAAAAAAATTT
1 TTATCAAAATTTCAT-AGGAGGTTACTAAAATTT
16825 TATAAAAGGG
Statistics
Matches: 623, Mismatches: 165, Indels: 146
0.67 0.18 0.16
Matches are distributed among these distances:
37 1 0.00
38 26 0.04
39 17 0.03
40 9 0.01
41 7 0.01
42 43 0.07
43 95 0.15
44 277 0.44
45 86 0.14
46 28 0.04
47 21 0.03
48 13 0.02
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATAGGAGGTTACTAAAATTTCATAGTGTGG
Found at i:16191 original size:21 final size:22
Alignment explanation
Indices: 16167--16806 Score: 165
Period size: 22 Copynumber: 29.7 Consensus size: 22
16157 AGAGATCGGA
16167 TTATCAAAATTT-ATAG-GAAG
1 TTATCAAAATTTCATAGTGAAG
**
16187 TTTATCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAGTGAAG
* * *
16210 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAAG
* * *
16232 TTATCAAAATTACATAATGAAA
1 TTATCAAAATTTCATAGTGAAG
* * * *
16254 ATATCAAAATTTCGTAGAG-GG
1 TTATCAAAATTTCATAGTGAAG
* * * * *
16275 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAAG
** *
16297 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAAG
* *
16319 TTATC-AATTTTCAAAATGTG-A-
1 TTATCAAAATTTC-ATA-GTGAAG
* *
16340 TTACCAAAATTTCATAGT-ATGG
1 TTATCAAAATTTCATAGTGA-AG
*
16362 TT-TCCAAA--T--TAG-GAAGG
1 TTATCAAAATTTCATAGTGAA-G
* *
16379 TTATTAAACCTTTACCAT-G-G-AG
1 TTATCAAA-ATTT--CATAGTGAAG
* **
16401 TAATCAAAATTTCAGGGTG--G
1 TTATCAAAATTTCATAGTGAAG
*
16421 ATATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTGAA-G
**
16443 TTATCAAAATTTCATAGTTTAG
1 TTATCAAAATTTCATAGTGAAG
*
16465 TTTTCAAAATTTCATAAGATG--G
1 TTATCAAAATTTCAT-AG-TGAAG
* *
16487 TTATCAAAATTTAATAG-GGAG
1 TTATCAAAATTTCATAGTGAAG
* * *
16508 ATTAACAAAATTTCATAATGAGG
1 -TTATCAAAATTTCATAGTGAAG
16531 TTATCAAAA-TT--T-GT--AG
1 TTATCAAAATTTCATAGTGAAG
* *
16547 TTATCAAGATTTCATAAG-GAGG
1 TTATCAAAATTTCAT-AGTGAAG
*
16569 TTATCAAAATTTTATTAG-G-AG
1 TTATCAAAATTTCA-TAGTGAAG
* * *
16590 CTTTATCAAAATTTTATAGCGAGG
1 --TTATCAAAATTTCATAGTGAAG
*
16614 TTATCACAATTTCATAGCGTG-A-
1 TTATCAAAATTTCATA--GTGAAG
* *
16636 TTATCAAAATTTCAGAGTG-TG
1 TTATCAAAATTTCATAGTGAAG
16657 ATTA-CTAACAA-TTCATA-TGGAAG
1 -TTATC-AA-AATTTCATAGT-GAAG
* * *
16680 TTTTTAAATTTTCATAACGTG--G
1 TTATCAAAATTTCAT-A-GTGAAG
* * * *
16702 TTATTAATATATCATA-TGGAGG
1 TTATCAAAATTTCATAGT-GAAG
* * **
16724 TTATCAACATCTCATAGTGTTGG
1 TTATCAAAATTTCATAGTG-AAG
*
16747 TTATCAAAATTTCATAGTGAGG
1 TTATCAAAATTTCATAGTGAAG
* * * *
16769 TCT-TCAAAATTCCTTAGGGAGG
1 T-TATCAAAATTTCATAGTGAAG
*
16791 TTAACAAAATTTCATA
1 TTATCAAAATTTCATA
16807 AGAAGGTTAA
Statistics
Matches: 455, Mismatches: 101, Indels: 125
0.67 0.15 0.18
Matches are distributed among these distances:
16 9 0.02
17 9 0.02
18 4 0.01
19 9 0.02
20 20 0.04
21 59 0.13
22 285 0.63
23 51 0.11
24 7 0.02
25 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAAG
Found at i:16324 original size:65 final size:66
Alignment explanation
Indices: 16104--16325 Score: 168
Period size: 65 Copynumber: 3.4 Consensus size: 66
16094 TAAGGAGTAC
* * * * * *
16104 CAAAATTTGATAGAAG-G-TTATC-AAATCTCATAGAGTGCTTATCGAAATTTCATAGAGATCGG
1 CAAAATTTCATA-AAGAGATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCATAGAGA--GG
16166 ATTAT
63 -TTAT
* * * * * * * *
16171 CAAAATTT-AT-AGGAAGTTTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGGTT
1 CAAAATTTCATAAAG-AGATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCATAGAGAGGTT
16234 AT
65 AT
* * * * * *
16236 CAAAATTACATAATGAAAATATCAAAATTTCGTAGAG-GGTCAACAAAATTTTATAGAGAGGTTA
1 CAAAATTTCATAAAGAGATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCATAGAGAGGTTA
16300 T
66 T
*
16301 CAAAATTTCATAAAGAGGTTATCAA
1 CAAAATTTCATAAAGAGATTATCAA
16326 TTTTCAAAAT
Statistics
Matches: 123, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
64 2 0.02
65 53 0.43
66 24 0.20
67 15 0.12
68 29 0.24
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.32
Consensus pattern (66 bp):
CAAAATTTCATAAAGAGATTATCAAAATTTCATAGAGTGGTCAACAAAATTTCATAGAGAGGTTA
T
Found at i:16578 original size:82 final size:85
Alignment explanation
Indices: 16425--16625 Score: 216
Period size: 83 Copynumber: 2.4 Consensus size: 85
16415 GGGTGGATAT
*
16425 CAAAATTTCAT-ATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAAGATGGTT
1 CAAAATTTCATAATG-AGGTTATCAAAA-TT--TAG-TTAGTTATCAAAATTTCATAAGATGGTT
16489 ATCAAAA-TTTAATAGGGAG-ATTAA
61 ATCAAAATTTTAATA-GGAGCATTAA
*
16513 CAAAATTTCATAATGAGGTTATCAAAATTT-G-TAGTTATCAAGATTTCATAAGGA-GGTTATCA
1 CAAAATTTCATAATGAGGTTATCAAAATTTAGTTAGTTATCAAAATTTCATAA-GATGGTTATCA
* * *
16575 AAATTTTATTAGGAGCTTTAT
65 AAATTTTAATAGGAGCATTAA
* ** *
16596 CAAAATTTTATAGCGAGGTTATCACAATTT
1 CAAAATTTCATAATGAGGTTATCAAAATTT
16626 CATAGCGTGA
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
82 33 0.33
83 37 0.37
84 1 0.01
85 1 0.01
87 2 0.02
88 23 0.23
89 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (85 bp):
CAAAATTTCATAATGAGGTTATCAAAATTTAGTTAGTTATCAAAATTTCATAAGATGGTTATCAA
AATTTTAATAGGAGCATTAA
Found at i:16752 original size:23 final size:23
Alignment explanation
Indices: 16722--16765 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16712 ATCATATGGA
*
16722 GGTTATCAACATCTCATAGTGTT
1 GGTTATCAAAATCTCATAGTGTT
*
16745 GGTTATCAAAATTTCATAGTG
1 GGTTATCAAAATCTCATAGTG
16766 AGGTCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (23 bp):
GGTTATCAAAATCTCATAGTGTT
Found at i:16836 original size:22 final size:22
Alignment explanation
Indices: 16788--16833 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
16778 TTCCTTAGGG
*
16788 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAGA
*
16810 AGGTTAAAAAAATTTTATAA-A
1 AGGTTAAAAAAATTTCATAAGA
16831 AGG
1 AGG
16834 GTTCTCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.28
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAGA
Found at i:19088 original size:5 final size:6
Alignment explanation
Indices: 19073--19097 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19063 TTGTGAATTA
19073 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
19098 ATTTGATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Done.