genome.fa.s12.2.7.7.80.10.50.1000.37.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   

This is table  37  of  120  ( 14336 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10075419--10075452	8	4.4	8	92	3	52	55	2	0	41	1.15
10075418--10075474	16	3.4	17	77	20	57	54	3	0	42	1.17
10075505--10075580	19	3.9	19	68	28	54	60	3	0	35	1.15
10075614--10075699	27	3.1	26	76	14	84	65	2	3	29	1.22
10076073--10076103	16	1.9	16	100	0	62	77	0	0	22	0.77
10076284--10076334	21	2.4	22	84	12	70	33	0	5	60	1.21
10076349--10076434	38	2.3	39	81	6	104	33	2	2	61	1.21
10076350--10076450	28	3.6	27	71	20	82	33	1	1	62	1.18
10077077--10077127	2	25.5	2	100	0	102	49	0	0	50	1.00
10081035--10081098	31	2.0	32	93	3	112	37	18	10	32	1.86
10082750--10082792	18	2.4	18	88	0	59	9	13	6	69	1.35
10083284--10083340	27	2.1	28	86	3	80	40	7	7	45	1.58
10085015--10085061	16	3.0	15	79	14	51	74	6	6	12	1.20
10085159--10085199	16	2.5	17	80	11	50	80	7	0	12	0.90
10091529--10091673	47	3.1	47	70	16	140	45	2	3	48	1.33
10091592--10091729	44	3.1	43	68	20	111	47	3	3	44	1.37
10091515--10091720	91	2.3	91	95	0	367	47	3	3	45	1.36
10091545--10091688	47	3.1	47	66	20	122	45	2	2	48	1.31
10091747--10092175	59	7.2	59	68	12	311	43	3	4	48	1.39
10092097--10092131	18	2.0	17	88	5	52	45	0	0	54	0.99
10092217--10092251	18	2.0	17	88	5	52	45	0	0	54	0.99
10091736--10092265	120	4.4	120	99	0	1026	43	2	4	48	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10092408--10092505	45	2.2	44	83	5	126	35	27	4	32	1.76
10095171--10095588	46	9.3	46	91	3	656	33	14	22	29	1.93
10095171--10095588	178	2.3	181	90	5	657	33	14	22	29	1.93
10096569--10096598	13	2.3	13	100	0	60	60	6	6	26	1.47
10097484--10097517	16	2.1	16	94	0	59	32	0	41	26	1.56
10098899--10098934	3	12.0	3	100	0	72	66	0	0	33	0.92
10098899--10098963	9	6.9	10	81	16	61	69	0	3	27	1.03
10112260--10112297	20	1.9	20	88	0	58	50	13	7	28	1.69
10112246--10112312	34	1.9	35	87	3	100	47	13	7	31	1.70
10114764--10114793	11	2.8	11	95	5	53	50	0	0	50	1.00
10126931--10126969	19	2.0	20	90	5	62	43	2	0	53	1.14
10132534--10132634	52	1.9	53	82	7	127	32	0	9	56	1.39
10134229--10134294	21	3.3	21	71	16	77	21	6	21	51	1.69
10134226--10134301	38	2.0	38	100	0	152	21	7	21	50	1.74
10137746--10137804	29	2.0	29	90	0	91	45	1	8	44	1.44
10138386--10138468	29	3.0	28	84	12	100	54	2	25	18	1.56
10138387--10138468	27	3.0	27	87	7	103	53	2	25	18	1.56
10138839--10139212	198	1.9	199	82	3	468	34	10	14	39	1.82
10141832--10141876	21	2.1	21	91	0	72	35	42	8	13	1.75
10146444--10146484	6	6.8	6	91	0	55	29	39	31	0	1.57
10146924--10147015	48	1.9	48	97	0	175	48	14	6	30	1.68
10146953--10147200	62	4.0	62	97	1	455	47	10	6	35	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10153816--10153857	6	7.0	6	94	0	66	78	4	0	16	0.91
10153971--10154036	27	2.4	27	82	0	69	28	25	21	24	1.99
10159450--10159591	34	4.2	34	85	1	151	55	14	9	20	1.66
10159478--10159572	33	2.8	34	95	3	165	58	12	8	20	1.59
10159749--10160013	144	1.8	144	85	3	372	23	21	26	27	1.99
10159727--10159983	72	3.6	73	82	3	297	23	22	25	27	2.00
10175595--10175625	3	10.3	3	100	0	62	67	0	0	32	0.91
10177353--10177701	94	3.7	95	79	5	327	30	22	16	30	1.96
10177436--10177755	94	3.4	94	78	5	310	29	20	17	31	1.96
10182109--10182553	158	2.8	156	73	14	419	30	11	6	51	1.64
10182882--10183064	10	17.9	10	67	16	83	1	28	0	69	0.97
10182910--10183079	44	4.0	44	80	12	194	1	29	0	69	0.96
10182928--10183062	38	3.3	39	79	17	134	0	28	0	71	0.92
10182951--10183050	34	2.8	35	80	19	118	0	28	0	72	0.86
10182947--10183076	24	5.6	23	73	13	115	0	29	0	70	0.87
10183121--10183188	27	2.5	27	85	4	93	16	23	39	20	1.91
10184646--10184683	12	3.2	12	78	14	51	15	5	5	73	1.19
10194046--10194104	30	2.0	30	93	0	100	27	16	30	25	1.97
10208487--10208582	18	5.4	17	74	18	79	57	4	1	37	1.25
10208488--10208571	28	3.0	27	72	18	75	55	4	1	38	1.28
10208471--10208574	54	1.9	55	84	9	142	55	3	2	37	1.33
10208487--10208576	26	3.4	25	70	19	67	55	4	1	38	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10208487--10208582	9	10.9	8	75	15	50	57	4	1	37	1.25
10209222--10209254	11	3.2	11	83	16	52	27	0	0	72	0.85
10209213--10209254	20	2.1	20	90	0	66	26	2	0	71	0.98
10209222--10209324	9	10.8	9	73	14	73	27	4	2	65	1.27
10209213--10209296	29	2.9	30	78	8	84	28	4	2	64	1.26
10209232--10209291	19	3.3	18	77	11	59	28	5	1	65	1.23
10211450--10211493	22	2.0	22	86	0	61	25	4	6	63	1.38
10215510--10215555	23	2.0	23	100	0	92	21	4	4	69	1.24
10220074--10220119	24	1.9	24	86	8	67	28	8	21	41	1.83
10222741--10222774	12	2.8	12	90	0	50	44	11	5	38	1.65
10222895--10222919	13	1.9	13	100	0	50	32	0	0	68	0.90
10227103--10227148	23	2.0	24	82	4	58	73	6	4	15	1.19
10227728--10227759	15	2.1	15	100	0	64	53	18	12	15	1.73
10228014--10228055	6	6.7	6	94	5	66	71	0	14	14	1.15
10228007--10228056	12	3.8	13	89	7	75	74	0	12	14	1.09
10228007--10228062	14	4.3	13	78	13	53	73	0	12	14	1.11
10229324--10230992	44	38.6	44	75	7	1128	31	21	23	24	1.98
10229319--10229743	175	2.4	175	91	0	672	29	20	25	24	1.99
10229368--10230992	127	12.5	127	83	5	1371	31	20	23	24	1.98
10230099--10231040	351	2.7	349	86	3	1104	31	21	22	23	1.98
10231723--10231760	20	1.9	20	84	10	51	78	13	7	0	0.94
10232693--10232726	2	17.0	2	100	0	68	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10232796--10232829	12	2.8	12	90	0	50	44	11	5	38	1.65
10235266--10235319	27	2.2	24	80	12	56	35	11	12	40	1.79
10238778--10238818	21	1.9	22	85	14	59	78	4	2	14	1.03
10240279--10240304	3	8.7	3	100	0	52	34	0	0	65	0.93
10241238--10241340	6	17.2	6	98	0	161	33	0	11	54	1.37
10244521--10244616	35	2.7	35	76	13	90	29	22	16	31	1.96
10245535--10245713	42	4.3	42	79	2	162	38	18	17	24	1.93
10245535--10245767	84	2.8	84	79	1	216	37	17	19	25	1.93
10245573--10245767	42	4.6	42	79	1	158	36	15	20	27	1.93
10245604--10245770	42	4.0	42	82	0	190	34	15	22	28	1.94
10245743--10245793	26	2.0	26	92	0	84	37	19	23	19	1.94
10245659--10245880	110	2.0	110	83	3	277	35	17	21	25	1.95
10245699--10245838	68	2.1	68	82	2	165	36	15	22	25	1.94
10245782--10245947	42	4.0	41	74	3	125	36	16	19	26	1.93
10245622--10245919	152	2.0	152	82	1	364	36	16	21	25	1.94
10252150--10252366	91	2.4	91	82	1	238	42	13	9	34	1.77
10262050--10262093	4	11.0	4	95	0	79	0	0	27	72	0.85
10262182--10262216	2	17.5	2	100	0	70	51	0	0	48	1.00
10266176--10266203	12	2.3	12	100	0	56	28	0	17	53	1.44
10277991--10278016	12	2.2	12	100	0	52	0	23	42	34	1.54
10279796--10279835	3	13.3	3	100	0	80	67	0	0	32	0.91
10281825--10281868	19	2.2	21	84	8	56	31	4	0	63	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10285168--10285206	18	2.1	19	85	4	53	61	5	2	30	1.31
10294716--10294761	24	1.9	24	91	8	76	39	0	0	60	0.97
10294858--10294885	9	3.1	9	100	0	56	57	10	0	32	1.33
10294828--10294969	68	2.1	66	94	2	248	45	9	4	40	1.58
10294958--10294999	16	2.6	16	92	0	66	42	7	2	47	1.43
10294973--10295028	23	2.5	23	82	2	69	44	1	1	51	1.22
10294828--10294991	68	2.5	66	86	10	216	45	9	4	40	1.55
10295167--10295213	21	2.2	21	88	0	76	12	55	27	4	1.56
10296642--10296698	19	2.9	19	75	15	62	57	3	1	36	1.26
10297978--10298006	7	4.1	7	100	0	58	82	0	0	17	0.66

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120