Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015378.1 Corchorus olitorius cultivar O-4 contig15411, 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: 65026
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:794 original size:28 final size:28
Alignment explanation
Indices: 754--811 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
744 TAATCGAAAT
*
754 AACCAATAGGAAACGATGGCTTTTAGCC
1 AACCAACAGGAAACGATGGCTTTTAGCC
782 AACCAACAGGAAACGATGGCTTTTAGCC
1 AACCAACAGGAAACGATGGCTTTTAGCC
810 AA
1 AA
812 GGCGAGGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (28 bp):
AACCAACAGGAAACGATGGCTTTTAGCC
Found at i:1920 original size:15 final size:15
Alignment explanation
Indices: 1896--1925 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1886 CTTTCAAAAT
1896 ATAATAATACATCGA
1 ATAATAATACATCGA
*
1911 ATAATCATACATCGA
1 ATAATAATACATCGA
1926 GAACCAGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.27
Consensus pattern (15 bp):
ATAATAATACATCGA
Found at i:2437 original size:31 final size:31
Alignment explanation
Indices: 2390--2766 Score: 504
Period size: 31 Copynumber: 12.7 Consensus size: 31
2380 ATATGGAGTA
* *
2390 ACCTAAGAGTGAACTATATGCTATAACGATAG
1 ACCTAA-AATGAACTATATGCAATAACGATAG
*
2422 ACCTAAAATGAACTATATGCTATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
2453 ACCT--AA--AACTATATGCAAT-ACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
*
2479 ACCT--AA--AACTATATGCAATAACGGTAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
2506 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
*
2537 ACCTAAAAAGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
2568 ACCT--AA--AACTATATGCAATAACG--AG
1 ACCTAAAATGAACTATATGCAATAACGATAG
2593 ACCT--AA--AACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
* *
2620 ACCTATAATGAACTATATGCAATAACAATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
*
2651 ACCTATAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
2682 ACCTAAAATGAACTATATGCAATAACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
* * *
2713 ACCAAAAATGAACTATATGCTATGACGATAG
1 ACCTAAAATGAACTATATGCAATAACGATAG
2744 ACCTAAAAATGAACTATATGCAA
1 ACCT-AAAATGAACTATATGCAA
2767 CAGCCATACT
Statistics
Matches: 320, Mismatches: 13, Indels: 24
0.90 0.04 0.07
Matches are distributed among these distances:
25 25 0.08
26 26 0.08
27 45 0.14
29 8 0.03
31 193 0.60
32 23 0.07
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (31 bp):
ACCTAAAATGAACTATATGCAATAACGATAG
Found at i:2652 original size:114 final size:115
Alignment explanation
Indices: 2390--2766 Score: 533
Period size: 114 Copynumber: 3.2 Consensus size: 115
2380 ATATGGAGTA
* * *
2390 ACCTAAGAGTGAACTATATGCTATAACGATAGACCTAAAATGAACTATATGCTATAACGATAGAC
1 ACCTAA-AATGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGAC
*
2455 CTAAAACTATATGCAAT-ACGATAGACCTAAAACTATATGCAATAACGGTAG
65 CTAAAACTATATGCAATAACGA-AGACCTAAAACTATATGCAATAACGATAG
*
2506 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAAAGAACTATATGCAATAACGATAGACC
1 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACC
2571 TAAAACTATATGCAATAACG-AGACCTAAAACTATATGCAATAACGATAG
66 TAAAACTATATGCAATAACGAAGACCTAAAACTATATGCAATAACGATAG
* * *
2620 ACCTATAATGAACTATATGCAATAACAATAGACCTATAATGAACTATATGCAATAACGATAGACC
1 ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACC
* * *
2685 TAAAATGAACTATATGCAATAACGATAGACCAAAAATGAACTATATGCTATGACGATAG
66 T--AA--AACTATATGCAATAACGA-AGACC--TAA--AACTATATGCAATAACGATAG
2744 ACCTAAAAATGAACTATATGCAA
1 ACCT-AAAATGAACTATATGCAA
2767 CAGCCATACT
Statistics
Matches: 236, Mismatches: 13, Indels: 15
0.89 0.05 0.06
Matches are distributed among these distances:
114 90 0.38
115 71 0.30
116 11 0.05
118 17 0.07
120 5 0.02
122 2 0.01
124 23 0.10
125 17 0.07
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (115 bp):
ACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACC
TAAAACTATATGCAATAACGAAGACCTAAAACTATATGCAATAACGATAG
Found at i:2664 original size:145 final size:141
Alignment explanation
Indices: 2400--2720 Score: 482
Period size: 145 Copynumber: 2.2 Consensus size: 141
2390 ACCTAAGAGT
* *
2400 GAACTATATGCTATAACGATAGACCTAAAATGAACTATATGCTATAACGATAGACCTAAAACTAT
1 GAACTATATGCAATAACGATAGACCT--AA--AACTATATGCAATAACGA-AGACCTAAAACTAT
**
2465 ATGCAATACGATAGACCTAAAACTATATGCAATAACGGTAGACCTAAAATGAACTATATGCAATA
61 ATGCAATACGATAGACCTAAAACTATATGCAATAACAATAGACCTAAAATGAACTATATGCAATA
2530 ACGATAGACCTAAAAA
126 ACGATAGACCTAAAAA
2546 GAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACG-AGACCTAAAACTATATGCA
1 GAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGAAGACCTAAAACTATATGCA
*
2610 ATAACGATAGACCTATAATGAACTATATGCAATAACAATAGACCTATAATGAACTATATGCAATA
66 AT-ACGATAGACC--TAA--AACTATATGCAATAACAATAGACCTAAAATGAACTATATGCAATA
*
2675 ACGATAGACCTAAAAT
126 ACGATAGACCTAAAAA
*
2691 GAACTATATGCAATAACGATAGACCAAAAA
1 GAACTATATGCAATAACGATAGACCTAAAA
2721 TGAACTATAT
Statistics
Matches: 163, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
140 21 0.13
141 10 0.06
142 16 0.10
143 3 0.02
144 2 0.01
145 86 0.53
146 25 0.15
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (141 bp):
GAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGAAGACCTAAAACTATATGCA
ATACGATAGACCTAAAACTATATGCAATAACAATAGACCTAAAATGAACTATATGCAATAACGAT
AGACCTAAAAA
Found at i:3420 original size:31 final size:31
Alignment explanation
Indices: 3366--3998 Score: 860
Period size: 31 Copynumber: 21.0 Consensus size: 31
3356 CAAATGAACT
3366 ATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3393 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
*
3424 ATAACGATAGACCT---A-GACCTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3451 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3482 ATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3509 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3540 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3571 ATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3598 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
* *
3629 ATAACGATAGACCTAAAACTAGACCTAAAATG-A
1 ATAACGATAGACCTAAAA-T-GAACT-ATATGCA
* *
3662 ACTATATGCAATA-ACGATAGACCAA-GAACTATATGCA
1 A-TA-A--CGATAGAC-CTA-A--AATGAACTATATGCA
3699 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3730 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3761 ATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3788 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3819 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3850 ATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3877 ATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
3908 ATAACGATAGACCT---A-GAACTATATGCA
1 ATAACGATAGACCTAAAATGAACTATATGCA
* *
3935 ATAACGATAGGCCTAAAATGAACTATATGCT
1 ATAACGATAGACCTAAAATGAACTATATGCA
* *
3966 ATGACGATAAACCTAAAAATGAACTATATGCA
1 ATAACGATAGACCT-AAAATGAACTATATGCA
3998 A
1 A
3999 CAGCCACACT
Statistics
Matches: 547, Mismatches: 16, Indels: 81
0.85 0.02 0.13
Matches are distributed among these distances:
27 164 0.30
28 2 0.00
29 18 0.03
30 4 0.01
31 295 0.54
32 19 0.03
33 12 0.02
34 8 0.01
35 2 0.00
36 8 0.01
37 12 0.02
38 1 0.00
40 2 0.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (31 bp):
ATAACGATAGACCTAAAATGAACTATATGCA
Found at i:3430 original size:58 final size:58
Alignment explanation
Indices: 3366--3983 Score: 849
Period size: 58 Copynumber: 10.3 Consensus size: 58
3356 CAAATGAACT
3366 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
* *
3424 ATAACGATAGACCTAGACCTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
3482 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
3540 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCT--AA--AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
3598 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTAGACCTAAAATGAA
1 ATAACGATAGACCT--AA--AACTATATGCAATAAC----G-------A-TAGACCTAAAATGAA
3663 CTATATGCA
50 CTATATGCA
3672 ATAACGATAGACC-AAGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAA-AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
3730 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA--AACTATATGCA
1 ATAACGATAGACCT--AA--AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
3788 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCT--AA--AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
3850 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
1 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
* * *
3908 ATAACGATAGACCTAGAACTATATGCAATAACGATAGGCCTAAAATGAACTATATGCT
1 ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
* *
3966 ATGACGATAAACCTAAAA
1 ATAACGATAGACCTAAAA
3984 ATGAACTATA
Statistics
Matches: 522, Mismatches: 10, Indels: 56
0.89 0.02 0.10
Matches are distributed among these distances:
58 378 0.72
59 1 0.00
60 10 0.02
61 2 0.00
62 77 0.15
66 1 0.00
69 1 0.00
70 24 0.05
71 2 0.00
72 2 0.00
74 24 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (58 bp):
ATAACGATAGACCTAAAACTATATGCAATAACGATAGACCTAAAATGAACTATATGCA
Found at i:3488 original size:89 final size:87
Alignment explanation
Indices: 3366--3998 Score: 838
Period size: 89 Copynumber: 7.0 Consensus size: 87
3356 CAAATGAACT
3366 ATAACGATAGACCT--AA--AACTATATGCAATAACGATAGACCTAAAATGAACTATATGCAATA
1 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA--AACTATATGCAATA
*
3427 ACGATAGACCT-A-GACCTATATGCA
62 ACGATAGACCTAATGAACTATATGCA
3451 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
1 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
3516 TAGACCTAAAATGAACTATATGCA
66 TAGACCT--AATGAACTATATGCA
3540 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
1 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
3605 TAGACCTAAAATGAACTATATGCA
66 TAGACCT--AATGAACTATATGCA
3629 ATAACGATAGACCTAAAACTAGACCTAAAATGAACTATATGCAATAACGATAGACC-AAGAACTA
1 ATAAC----G-------A-TAGACCTAAAATGAACTATATGCAATAACGATAGACCTAA-AACTA
3693 TATGCAATAACGATAGACCTAAAATGAACTATATGCA
53 TATGCAATAACGATAGACCT--AATGAACTATATGCA
3730 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
1 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
3795 TAGACCTAAAATGAACTATATGCA
66 TAGACCT--AATGAACTATATGCA
3819 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
1 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
3884 TAGACCTAAAATGAACTATATGCA
66 TAGACCT--AATGAACTATATGCA
* * *
3908 ATAACGATAGACCT---A-GAACTATATGCAATAACGATAGGCCTAAAATGAACTATATGCTATG
1 ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCT--AA--AACTATATGCAATA
*
3969 ACGATAAACCTAAAAATGAACTATATGCA
62 ACGATAGACCT---AATGAACTATATGCA
3998 A
1 A
3999 CAGCCACACT
Statistics
Matches: 516, Mismatches: 5, Indels: 49
0.91 0.01 0.09
Matches are distributed among these distances:
85 64 0.12
86 1 0.00
87 6 0.01
88 1 0.00
89 334 0.65
90 21 0.04
93 1 0.00
97 1 0.00
100 3 0.01
101 84 0.16
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (87 bp):
ATAACGATAGACCTAAAATGAACTATATGCAATAACGATAGACCTAAAACTATATGCAATAACGA
TAGACCTAATGAACTATATGCA
Found at i:3666 original size:43 final size:43
Alignment explanation
Indices: 3605--3692 Score: 160
Period size: 43 Copynumber: 2.0 Consensus size: 43
3595 GCAATAACGA
3605 TAGACCTAAAATGAACTATATGCAATAACGATAGACCTAA-AAC
1 TAGACCTAAAATGAACTATATGCAATAACGATAGACC-AAGAAC
3648 TAGACCTAAAATGAACTATATGCAATAACGATAGACCAAGAAC
1 TAGACCTAAAATGAACTATATGCAATAACGATAGACCAAGAAC
3691 TA
1 TA
3693 TATGCAATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 2 0.05
43 42 0.95
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.20
Consensus pattern (43 bp):
TAGACCTAAAATGAACTATATGCAATAACGATAGACCAAGAAC
Found at i:21485 original size:2 final size:2
Alignment explanation
Indices: 21480--21524 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
21470 TAGAGAAAAA
21480 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21522 AG A
1 AG A
21525 CAAGAAGTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26762 original size:23 final size:22
Alignment explanation
Indices: 26731--26788 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
26721 TGATCTCTAC
*
26731 AAAAGTTTGATAACCACATATAT
1 AAAATTTTGATAACCACA-ATAT
* * *
26754 GAAATTTTGATAATCTCAATAT
1 AAAATTTTGATAACCACAATAT
26776 AAAATTTTGATAA
1 AAAATTTTGATAA
26789 ATTTTCATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.36
Consensus pattern (22 bp):
AAAATTTTGATAACCACAATAT
Found at i:26780 original size:22 final size:22
Alignment explanation
Indices: 26731--26812 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
26721 TGATCTCTAC
* * *
26731 AAAAGTTTGATAACCACATATAT
1 AAAATTTTGATAATCTCA-ATAT
*
26754 GAAATTTTGATAATCTCAATAT
1 AAAATTTTGATAATCTCAATAT
*
26776 AAAATTTTGATAAATTTTC-ATAT
1 AAAATTTTGAT-AA-TCTCAATAT
*
26799 GAAATTTTGATAAT
1 AAAATTTTGATAAT
26813 TTCCTCATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 1 0.02
22 16 0.32
23 30 0.60
24 3 0.06
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAATCTCAATAT
Found at i:26803 original size:23 final size:23
Alignment explanation
Indices: 26750--26811 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
26740 ATAACCACAT
26750 ATATGAAATTTTGAT-AATCTCA
1 ATATGAAATTTTGATAAATCTCA
* *
26772 ATATAAAATTTTGATAAATTTTC-
1 ATATGAAATTTTGATAAA-TCTCA
26795 ATATGAAATTTTGATAA
1 ATATGAAATTTTGATAA
26812 TTTCCTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 14 0.40
23 18 0.51
24 3 0.09
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (23 bp):
ATATGAAATTTTGATAAATCTCA
Found at i:45706 original size:3 final size:3
Alignment explanation
Indices: 45698--45730 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
45688 CCGATAAAAG
*
45698 CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
45731 TATCTCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:49956 original size:26 final size:26
Alignment explanation
Indices: 49920--49972 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
49910 GGCCAAAACC
*
49920 CAAAATCATTTCTCCCACTTAATTAG
1 CAAAATCATTTCCCCCACTTAATTAG
49946 CAAAATCATTTCCCCCACTTAATTAG
1 CAAAATCATTTCCCCCACTTAATTAG
49972 C
1 C
49973 CTGAAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (26 bp):
CAAAATCATTTCCCCCACTTAATTAG
Found at i:51688 original size:32 final size:32
Alignment explanation
Indices: 51646--51715 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
51636 CTTCAAATAA
*
51646 AAAAAAACCATGTTCATACAATTTCAGAAATT
1 AAAAATACCATGTTCATACAATTTCAGAAATT
*
51678 AAAAATACCATGTTCATACAATTTTAGAAATT
1 AAAAATACCATGTTCATACAATTTCAGAAATT
51710 AAAAAT
1 AAAAAT
51716 GGTCATATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (32 bp):
AAAAATACCATGTTCATACAATTTCAGAAATT
Found at i:51782 original size:47 final size:47
Alignment explanation
Indices: 51728--51820 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
51718 TCATATTCCA
*
51728 ACACTTTTGAGTACCTAAATTCATGGCCAAATTTCGACACAAACCTT
1 ACACTTTTGAGTACCTAAATTCATGGCCAAATTTCAACACAAACCTT
*
51775 ACACTTTTGAGTACCTAAATTCATGGTCAAATTTCAACACAAACCT
1 ACACTTTTGAGTACCTAAATTCATGGCCAAATTTCAACACAAACCT
51821 ATTCCAGTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.35, C:0.25, G:0.10, T:0.30
Consensus pattern (47 bp):
ACACTTTTGAGTACCTAAATTCATGGCCAAATTTCAACACAAACCTT
Found at i:64765 original size:2 final size:2
Alignment explanation
Indices: 64760--64796 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
64750 CTTTTATAAG
64760 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64797 GATTGTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64958 original size:25 final size:25
Alignment explanation
Indices: 64930--64980 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
64920 AATTTTTATT
64930 TTTAAGGGTTAATAAATGATATCTC
1 TTTAAGGGTTAATAAATGATATCTC
64955 TTTAAGGGTTAATAAATGATATCTC
1 TTTAAGGGTTAATAAATGATATCTC
64980 T
1 T
64981 GCTCTCTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (25 bp):
TTTAAGGGTTAATAAATGATATCTC
Done.