Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017664.1 Corchorus olitorius cultivar O-4 contig17697, 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: 39765
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:10834 original size:21 final size:21
Alignment explanation
Indices: 10765--10845 Score: 99
Period size: 22 Copynumber: 3.8 Consensus size: 21
10755 AGAATATTTT
*
10765 TATGAAATTTTGATAACCACCC
1 TATGAAATTTTGATAATCA-CC
* *
10787 TATTAAATTTTAATAATCACGC
1 TATGAAATTTTGATAATCAC-C
*
10809 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAATCACC
*
10830 TATGAAATTGTGATAA
1 TATGAAATTTTGATAA
10846 ACTCCCTATA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.33
22 34 0.67
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
TATGAAATTTTGATAATCACC
Found at i:11773 original size:45 final size:45
Alignment explanation
Indices: 11693--11828 Score: 218
Period size: 45 Copynumber: 3.0 Consensus size: 45
11683 GGCAATCTAA
* * * *
11693 TCCGATTTAGCTCTTATAGTATGAGTATACGTTTAAAAATTCAAC
1 TCCGGTTTAGTTCTTATAGTATGACTATACATTTAAAAATTCAAC
*
11738 TCCGGTTTAGTTCTTATAGTATGACTCTACATTTAAAAATTCAAC
1 TCCGGTTTAGTTCTTATAGTATGACTATACATTTAAAAATTCAAC
*
11783 TCCGGTTTAGTTCTTATAGTATGATTATACATTTAAAAATTCAAC
1 TCCGGTTTAGTTCTTATAGTATGACTATACATTTAAAAATTCAAC
11828 T
1 T
11829 GCTTCGAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 84 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (45 bp):
TCCGGTTTAGTTCTTATAGTATGACTATACATTTAAAAATTCAAC
Found at i:14428 original size:22 final size:22
Alignment explanation
Indices: 14403--14452 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
14393 TGAAATACTG
14403 ATAACTTAACTATGAAATTTTA
1 ATAACTTAACTATGAAATTTTA
** *
14425 ATAAACTTTTCTATGAAATTTTG
1 AT-AACTTAACTATGAAATTTTA
14448 ATAAC
1 ATAAC
14453 CTCCATATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (22 bp):
ATAACTTAACTATGAAATTTTA
Found at i:14492 original size:23 final size:22
Alignment explanation
Indices: 14325--14555 Score: 96
Period size: 22 Copynumber: 10.4 Consensus size: 22
14315 TAAATATTTT
* * *
14325 TATGAAATTTTGATAAACACGC
1 TATGAAATTTTGATAACCTCTC
* * * *
14347 TATGAAATTTTGATGA-TTATTT
1 TATGAAATTTTGATAACCT-CTC
* * *
14369 TATGAAATTGTGATAAACTCCC
1 TATGAAATTTTGATAACCTCTC
* ** * **
14391 AATGAAATACTGATAACTTAAC
1 TATGAAATTTTGATAACCTCTC
* * *
14413 TATGAAATTTTAATAAACTTTTC
1 TATGAAATTTTGAT-AACCTCTC
14436 TATGAAATTTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCTC
**
14457 ATATGATTTTTTTGATAACCCTCTC
1 -TATGA-AATTTTGATAA-CCTCTC
* *
14482 TATGAAATTTT-ATTAATCTCCC
1 TATGAAATTTTGA-TAACCTCTC
**
14504 TAT-AAATTTTTGAT-ACCAT-AG
1 TATGAAA-TTTTGATAACC-TCTC
** *
14525 TATGAAATTTCAATAATCTCTC
1 TATGAAATTTTGATAACCTCTC
14547 TATGAAATT
1 TATGAAATT
14556 ATATATCATT
Statistics
Matches: 153, Mismatches: 42, Indels: 28
0.69 0.19 0.13
Matches are distributed among these distances:
21 15 0.10
22 91 0.59
23 37 0.24
24 9 0.06
25 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCTC
Found at i:15394 original size:43 final size:45
Alignment explanation
Indices: 15346--15435 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 45
15336 ATTTTAATAA
*
15346 TGGCAATTTTATATA-TTT-TAATAGTGACATAATTAAAATATAT
1 TGGCAATTTTATATATTTTATAATAATGACATAATTAAAATATAT
*
15389 TGGCAATTTTATATATTTTAATAATAATGGCATAATTAAAATATAT
1 TGGCAATTTTATATATTTT-ATAATAATGACATAATTAAAATATAT
15435 T
1 T
15436 TTAATAATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
43 15 0.36
44 3 0.07
46 24 0.57
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.44
Consensus pattern (45 bp):
TGGCAATTTTATATATTTTATAATAATGACATAATTAAAATATAT
Found at i:15619 original size:22 final size:22
Alignment explanation
Indices: 15593--15671 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
15583 TATTTTTATG
15593 AAATTTTGAAAACTACTCTATT
1 AAATTTTGAAAACTACTCTATT
* * *
15615 AAATTTTGACAACCACCCTATT
1 AAATTTTGAAAACTACTCTATT
* * *
15637 AAATTTTGATAATTA-TCTATG
1 AAATTTTGAAAACTACTCTATT
*
15658 AAATTGTGATAAAC
1 AAATTTTGA-AAAC
15672 GCCATATGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
21 12 0.27
22 33 0.73
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGAAAACTACTCTATT
Found at i:15662 original size:43 final size:43
Alignment explanation
Indices: 15589--15708 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
15579 TGAATATTTT
* * * *
15589 TATGAAATTTTGAAAACTACTCTATTAAATTTTGACAACCACCC
1 TATGAAATTTTGATAACTA-TCTATGAAATTTTGACAAACACCA
* * * * *
15633 TATTAAATTTTGATAATTATCTATGAAATTGTGATAAACGCCA
1 TATGAAATTTTGATAACTATCTATGAAATTTTGACAAACACCA
* *
15676 TATGAAACTTTGATAAGCTAACTATGAAATTTT
1 TATGAAATTTTGATAA-CTATCTATGAAATTTT
15709 AATAAACCTT
Statistics
Matches: 61, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
43 32 0.52
44 29 0.48
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (43 bp):
TATGAAATTTTGATAACTATCTATGAAATTTTGACAAACACCA
Found at i:15726 original size:23 final size:21
Alignment explanation
Indices: 15697--15773 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
15687 GATAAGCTAA
15697 CTATGAAATTTTAATAAACCTTC
1 CTATGAAATTTT-AT-AACCTTC
* *
15720 CTATGAAATTTTGTAATCTTC
1 CTATGAAATTTTATAACCTTC
*
15741 CTATG-AATTTTGATAACCTCC
1 CTATGAAATTTT-ATAACCTTC
* *
15762 CTGTGAGATTTT
1 CTATGAAATTTT
15774 GTTAATCTCC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 6 0.13
21 21 0.47
22 6 0.13
23 12 0.27
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.43
Consensus pattern (21 bp):
CTATGAAATTTTATAACCTTC
Found at i:15773 original size:42 final size:44
Alignment explanation
Indices: 15697--15793 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 44
15687 GATAAGCTAA
* *
15697 CTATGAAATTTTAATAAACCTTCCTATGAAATTTTG-TAATCTTC
1 CTATG-AATTTTAATAAACCTCCCTATGAAATTTTGTTAATCTCC
* * *
15741 CTATGAATTTTGAT-AACCTCCCTGTGAGATTTTGTTAATCTCC
1 CTATGAATTTTAATAAACCTCCCTATGAAATTTTGTTAATCTCC
15784 CTAT-AATTTT
1 CTATGAATTTT
15794 TTATACTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 23 0.49
43 19 0.40
44 5 0.11
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (44 bp):
CTATGAATTTTAATAAACCTCCCTATGAAATTTTGTTAATCTCC
Found at i:15783 original size:22 final size:20
Alignment explanation
Indices: 15719--15793 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
15709 AATAAACCTT
*
15719 CCTATGAAATTTTGTAATCTT
1 CCTATG-AATTTTGTAATCTC
*
15740 CCTATGAATTTTGATAACCTC
1 CCTATGAATTTTG-TAATCTC
*
15761 CCTGTGAGATTTTGTTAATCTC
1 CCTATGA-ATTTTG-TAATCTC
15783 CCTAT-AATTTT
1 CCTATGAATTTT
15794 TTATACTATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
20 12 0.26
21 18 0.39
22 16 0.35
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (20 bp):
CCTATGAATTTTGTAATCTC
Found at i:16599 original size:2 final size:2
Alignment explanation
Indices: 16592--16619 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
16582 AAAGCCACAC
16592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16620 GTGAGAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22660 original size:32 final size:32
Alignment explanation
Indices: 22623--22687 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
22613 GCAGACACTA
*
22623 TCCTGAGATCTAC-GTGATTACCCAGTGTTCCT
1 TCCTGAAATCT-CTGTGATTACCCAGTGTTCCT
*
22655 TCCTGAAATCTCTGTGATTTCCCAGTGTTCCT
1 TCCTGAAATCTCTGTGATTACCCAGTGTTCCT
22687 T
1 T
22688 GAAAGCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 1 0.03
32 29 0.97
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (32 bp):
TCCTGAAATCTCTGTGATTACCCAGTGTTCCT
Found at i:22740 original size:55 final size:55
Alignment explanation
Indices: 22656--22796 Score: 210
Period size: 55 Copynumber: 2.6 Consensus size: 55
22646 AGTGTTCCTT
22656 CCTGAAATCTCTGTGATTTCCCAGTGTTCCTTGAAAGCTTCAATGCTGACACTCG
1 CCTGAAATCTCTGTGATTTCCCAGTGTTCCTTGAAAGCTTCAATGCTGACACTCG
* * * * * **
22711 CCTGAGATCTCCGTGATTTCCCAGTGTTCCCTGAAAGCTTCAATGTTGTCGTTCG
1 CCTGAAATCTCTGTGATTTCCCAGTGTTCCTTGAAAGCTTCAATGCTGACACTCG
*
22766 CCTGAAATCTCTGTGATCTCCCAGTGTTCCT
1 CCTGAAATCTCTGTGATTTCCCAGTGTTCCT
22797 GTGACGCTTC
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.34
Consensus pattern (55 bp):
CCTGAAATCTCTGTGATTTCCCAGTGTTCCTTGAAAGCTTCAATGCTGACACTCG
Found at i:24816 original size:438 final size:438
Alignment explanation
Indices: 24014--24827 Score: 1093
Period size: 438 Copynumber: 1.9 Consensus size: 438
24004 CGCGTTGGCT
24014 TTTATTTTTGTATTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
1 TTTATTTTTGTATTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
* * ** * ** *
24079 TTGATGATCTGCAATTTTCATTAAGAACTCAAAAGCCAATTTTAATGTTTTGATCTAAAAAATGC
66 TTCATGATCTACAACCTTCATGAAGAACTCAAAAGCCAA-TTTAATGTTTCAATCAAAAAAATGC
* * * * * * * *
24144 TTCCGAAATTTTGTGGTTTTGATTGCCGGTTAATTTAATATCGTATAATTTTTTGTCCACATGTC
130 TTCCGAAATTTGGTCGTTTTGATTGCCAGTTAATTTAATACCATATAAATGTTCGTCCACATGTC
* * * * * * *
24209 CGATTGAAGTTATTGAAGAGTCGATTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACC
195 CAATTAAAGTTATTGAAGAGTCGATTAAAAGGTTACTACATAATCTACGACTTTCATGAAGAACC
*
24274 CCAAAGCTCAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGAT
260 CCAAAGCTCAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGAT
* * *
24339 CTCCATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCATGCTTTTCTCTTTAT
325 CTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATGCTTTTCTCTTTAT
24404 ATTATTTAGTCCTTTACAAATTCTATCTTAATTAATTTAACGTTTAAGC
390 ATTATTTAGTCCTTTACAAATTCTATCTTAATTAATTTAACGTTTAAGC
* * * *
24453 TTTATTTTTTTATTTTTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTAAAATGTAA
1 TTTATTTTTGTATTTTTT-TTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAA
* *
24518 TTTCATGAGT-TACAACCTTCATGAAGGACTCAAAAG-TAA-TT-ATGTTTCAATTCAAAAAAAT
65 TTTCATGA-TCTACAACCTTCATGAAGAACTCAAAAGCCAATTTAATGTTTCAA-TCAAAAAAAT
* * ** *
24579 GCTTGCTAAATTTGGTCGTTTTGATTGTTAGTCT-ATTTAATACCATATATAATGTTCGATCTAC
128 GCTTCCGAAATTTGGTCGTTTTGATTGCCAGT-TAATTTAATACCATATA-AATGTTCG-TCCAC
* * *
24643 ATGTCCAATTAAAGTTATTTAA-ATGTCGGTTAAAAGGTTACTATATAATCTACGACTTTCATGA
190 ATGTCCAATTAAAGTTATTGAAGA-GTCGATTAAAAGGTTACTACATAATCTACGACTTTCATGA
** * *
24707 AGAACCCGGAAG-TTAATTTGATCTATGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTT
254 AGAACCCCAAAGCTCAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTT
*
24771 CAAGATCTCCATTAACAAATATTTTCTTATTTGAATTAGTTATCAAATCACCCTCAT
319 CAAGATCTCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCAT
24828 TAACTAAAGC
Statistics
Matches: 322, Mismatches: 46, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
436 7 0.02
437 49 0.15
438 109 0.34
439 85 0.26
440 71 0.22
441 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (438 bp):
TTTATTTTTGTATTTTTTTTCTATTTGTCCGATTAAGGTGATTCAAGTGTCTATTAAAAGGTAAT
TTCATGATCTACAACCTTCATGAAGAACTCAAAAGCCAATTTAATGTTTCAATCAAAAAAATGCT
TCCGAAATTTGGTCGTTTTGATTGCCAGTTAATTTAATACCATATAAATGTTCGTCCACATGTCC
AATTAAAGTTATTGAAGAGTCGATTAAAAGGTTACTACATAATCTACGACTTTCATGAAGAACCC
CAAAGCTCAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATC
TCCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCATGCTTTTCTCTTTATA
TTATTTAGTCCTTTACAAATTCTATCTTAATTAATTTAACGTTTAAGC
Found at i:24856 original size:12 final size:12
Alignment explanation
Indices: 24839--24891 Score: 88
Period size: 12 Copynumber: 4.4 Consensus size: 12
24829 AACTAAAGCG
24839 TTTATTTGAATT
1 TTTATTTGAATT
*
24851 TTTATTAGAATT
1 TTTATTTGAATT
*
24863 CTTATTTGAATT
1 TTTATTTGAATT
24875 TTTATTTGAATT
1 TTTATTTGAATT
24887 TTTAT
1 TTTAT
24892 GTTTCAAGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.26, C:0.02, G:0.08, T:0.64
Consensus pattern (12 bp):
TTTATTTGAATT
Found at i:26709 original size:51 final size:50
Alignment explanation
Indices: 26630--26769 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 50
26620 GTTCATCAAA
*
26630 TTTTCCTTGTTT-AGATCTTGTCTCAGGACAATCAAACATTCTTTTAGTGT
1 TTTTCCTTGTTTCA-ATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
*
26680 TTTTCCTTTGTTTCAATCTTGTCTTAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCC-TTGTTTCAATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
*
26731 TTTTCCCTTGTTTCAATCTTGTCTCCGGAC-ATACAAACA
1 TTTT-CCTTGTTTCAATCTTGTCTCAGGACAAT-CAAACA
26770 ATGTACACGT
Statistics
Matches: 82, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
50 8 0.10
51 71 0.87
52 3 0.04
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.44
Consensus pattern (50 bp):
TTTTCCTTGTTTCAATCTTGTCTCAGGACAATCAAACACTCTTTTAGTGT
Found at i:26782 original size:51 final size:51
Alignment explanation
Indices: 26630--26786 Score: 160
Period size: 51 Copynumber: 3.1 Consensus size: 51
26620 GTTCATCAAA
* * **
26630 TTTT-CCTTGTTT-AGATCTTGTCTCAGGACAATCAAACATTCTTTTAGTGT
1 TTTTCCCTTGTTTCA-ATCTTGTCTCAGGACAATCAAACAATCGTACAGTGT
* * * * **
26680 TTTTCCTTTGTTTCAATCTTGTCTTAGGACAATCAAACACTCTTTTAGTGT
1 TTTTCCCTTGTTTCAATCTTGTCTCAGGACAATCAAACAATCGTACAGTGT
*
26731 TTTTCCCTTGTTTCAATCTTGTCTCCGGAC-ATACAAACAAT-GTACACGTGT
1 TTTTCCCTTGTTTCAATCTTGTCTCAGGACAAT-CAAACAATCGTACA-GTGT
26782 TTTTC
1 TTTTC
26787 ATTCAAAAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
50 8 0.09
51 84 0.90
52 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.45
Consensus pattern (51 bp):
TTTTCCCTTGTTTCAATCTTGTCTCAGGACAATCAAACAATCGTACAGTGT
Found at i:28052 original size:2 final size:2
Alignment explanation
Indices: 28045--28070 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28035 TTGCATAGTC
28045 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
28071 GTAGGGGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28499 original size:15 final size:16
Alignment explanation
Indices: 28476--28509 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28466 AATTGAAAAA
28476 AAAAATAATTT-ATTT
1 AAAAATAATTTAATTT
*
28491 AAAATTAATTTAATTT
1 AAAAATAATTTAATTT
28507 AAA
1 AAA
28510 CAGAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAAATAATTTAATTT
Found at i:29719 original size:21 final size:21
Alignment explanation
Indices: 29695--29790 Score: 102
Period size: 21 Copynumber: 4.3 Consensus size: 21
29685 GAATATGAGA
29695 TTGAAAATCCAGTTGATGGAG
1 TTGAAAATCCAGTTGATGGAG
29716 TTGAAAATCCAGTTGATGATGAAG
1 TTGAAAATCCAGTTGATG--G-AG
*
29740 TTGAAAATCCAGTAGATGATGGTG
1 TTGAAAATCCAGT---TGATGGAG
* * *
29764 TTGGAAATCCAGTTGAAGAAG
1 TTGAAAATCCAGTTGATGGAG
29785 TTGAAA
1 TTGAAA
29791 TGCCTGGAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
21 28 0.44
23 1 0.02
24 28 0.44
25 1 0.02
27 5 0.08
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.28
Consensus pattern (21 bp):
TTGAAAATCCAGTTGATGGAG
Found at i:29741 original size:24 final size:23
Alignment explanation
Indices: 29695--29790 Score: 110
Period size: 24 Copynumber: 4.3 Consensus size: 23
29685 GAATATGAGA
29695 TTGAAAATCCAGTTGATG-G-AG
1 TTGAAAATCCAGTTGATGAGAAG
29716 TTGAAAATCCAGTTGATGATGAAG
1 TTGAAAATCCAGTTGATGA-GAAG
* **
29740 TTGAAAATCCAGTAGATGATGGTG
1 TTGAAAATCCAGTTGATGA-GAAG
*
29764 TTGGAAATCCAGTTGA--AGAAG
1 TTGAAAATCCAGTTGATGAGAAG
29785 TTGAAA
1 TTGAAA
29791 TGCCTGGAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 25 0.39
22 1 0.02
23 1 0.02
24 37 0.58
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.28
Consensus pattern (23 bp):
TTGAAAATCCAGTTGATGAGAAG
Found at i:29785 original size:45 final size:44
Alignment explanation
Indices: 29695--29790 Score: 124
Period size: 45 Copynumber: 2.1 Consensus size: 44
29685 GAATATGAGA
29695 TTGAAAATCCAGTTGATGGAGTTGAAAATCCAGTTGATGATGAAG
1 TTGAAAATCCAGTTGATGGAGTTGAAAATCCAGTTGA-GATGAAG
* *
29740 TTGAAAATCCAGTAGATGATGGTGTTGGAAATCCAGTTGA-A-GAAG
1 TTGAAAATCCAGT---TGATGGAGTTGAAAATCCAGTTGAGATGAAG
29785 TTGAAA
1 TTGAAA
29791 TGCCTGGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
45 23 0.50
46 1 0.02
48 22 0.48
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.28
Consensus pattern (44 bp):
TTGAAAATCCAGTTGATGGAGTTGAAAATCCAGTTGAGATGAAG
Found at i:29858 original size:15 final size:15
Alignment explanation
Indices: 29838--29881 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
29828 TGATGATGCA
29838 GTCAATGTAGAGGAT
1 GTCAATGTAGAGGAT
* *
29853 GTCAATGTACATGAT
1 GTCAATGTAGAGGAT
29868 GTCAATGTAGAGGA
1 GTCAATGTAGAGGA
29882 GGATGTCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.27
Consensus pattern (15 bp):
GTCAATGTAGAGGAT
Found at i:31171 original size:16 final size:17
Alignment explanation
Indices: 31127--31178 Score: 61
Period size: 16 Copynumber: 3.0 Consensus size: 17
31117 TAACATATTT
31127 ATGGTTTCATAAGTTTAGG
1 ATGGTTTCATAAG-TTA-G
* *
31146 TTGTTTTCATAAGTTA-
1 ATGGTTTCATAAGTTAG
31162 ATGGTTTCATAAGTTAG
1 ATGGTTTCATAAGTTAG
31179 CTAACTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.50
18 3 0.11
19 11 0.39
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (17 bp):
ATGGTTTCATAAGTTAG
Found at i:33730 original size:21 final size:21
Alignment explanation
Indices: 33691--33731 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
33681 AGGCAGTGAA
**
33691 GGATTTATGTATTTTGTATTC
1 GGATTTATGTATTCAGTATTC
33712 GGATTTATGTATTCAGTATT
1 GGATTTATGTATTCAGTATT
33732 TATTTGGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.20, T:0.54
Consensus pattern (21 bp):
GGATTTATGTATTCAGTATTC
Found at i:35271 original size:22 final size:22
Alignment explanation
Indices: 35214--35262 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
35204 TTCTTTTTTA
*
35214 TTTTAAGTAATTAAAAATTACTT
1 TTTTAA-TAATTAAAAAATACTT
35237 TTTTAATAATTAAAAAATA-TT
1 TTTTAATAATTAAAAAATACTT
35258 TTTTA
1 TTTTA
35263 TTCACTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.28
22 12 0.48
23 6 0.24
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTAATAATTAAAAAATACTT
Done.