genome.fa.s25.2.7.7.80.10.50.1000.28.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   

This is table  28  of  56  ( 6609 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)
4764018--4764081	29	2.2	29	85	0	83	29	7	4	57	1.47
4766384--4766445	13	5.2	12	75	16	67	51	1	0	46	1.10
4767339--4767379	18	2.2	19	86	4	57	36	0	0	63	0.95
4768136--4768173	19	2.0	20	89	5	60	34	0	0	65	0.93
4768136--4768175	11	3.9	11	78	18	50	35	0	0	65	0.93
4768116--4768172	30	1.9	30	85	7	80	31	0	1	66	1.02
4769033--4769089	3	19.7	3	87	10	75	70	1	0	28	0.98
4769045--4769108	30	2.1	30	91	8	103	71	4	0	23	1.04
4775166--4775236	16	4.3	16	76	8	72	60	0	0	39	0.97
4775459--4775498	21	1.9	21	84	0	53	45	5	0	50	1.23
4780386--4780460	20	3.8	20	74	0	69	40	10	13	36	1.79
4780383--4780460	40	2.0	39	84	2	102	39	11	12	35	1.80
4780988--4781750	32	25.2	29	89	3	750	19	17	33	30	1.94
4782984--4783026	1	43.0	1	80	0	50	0	2	6	90	0.52
4782974--4783021	21	2.3	21	85	7	62	2	4	8	85	0.80
4782974--4783026	20	2.6	21	85	8	65	1	3	7	86	0.75
4782991--4783026	14	2.7	13	91	8	63	0	0	8	91	0.41
4794905--4794936	7	4.6	7	96	0	55	0	28	25	46	1.53
4796108--4796164	23	2.5	23	97	0	105	61	10	10	17	1.56
4797080--4797154	20	3.8	20	76	0	69	40	10	13	36	1.79
4797077--4797154	40	2.0	39	84	2	102	39	11	12	35	1.80
4798390--4798502	57	2.0	58	82	1	138	51	6	12	30	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4798910--4798977	29	2.4	29	85	7	88	45	0	13	41	1.43
4798995--4799021	2	13.5	2	100	0	54	51	0	0	48	1.00
4800373--4800434	25	2.4	26	83	2	72	24	9	3	62	1.40
4800529--4800561	12	2.7	13	90	9	52	15	30	6	48	1.69
4803921--4803949	2	15.0	2	92	7	51	48	0	0	51	1.00
4804654--4804695	14	3.0	14	86	6	50	40	0	0	59	0.97
4804716--4804768	22	2.5	21	84	6	63	52	0	5	41	1.25
4804936--4805007	29	2.6	28	84	8	85	61	1	0	37	1.05
4804938--4805004	34	1.9	35	81	3	82	61	1	0	37	1.05
4804835--4805356	285	1.9	280	95	2	938	45	5	5	43	1.51
4805220--4805292	28	2.6	29	86	6	96	64	0	0	35	0.94
4810910--4810943	15	2.3	15	89	0	50	58	5	0	35	1.22
4812245--4812269	2	12.5	2	100	0	50	52	0	48	0	1.00
4816067--4816112	20	2.4	19	85	7	65	58	0	2	39	1.10
4816069--4816119	20	2.4	21	80	12	59	58	0	1	39	1.09
4833787--4833816	7	4.3	7	100	0	60	0	0	40	60	0.97
4844089--4844129	17	2.3	18	80	12	50	48	0	0	51	1.00
4845714--4845751	20	1.9	19	89	5	58	68	0	13	18	1.21
4845714--4845751	10	3.9	10	86	3	51	68	0	13	18	1.21
4845726--4845797	34	2.2	34	80	9	87	70	1	6	20	1.18
4847233--4847266	14	2.4	14	90	5	50	88	2	2	5	0.70
4853629--4853662	16	2.1	16	89	10	52	17	8	0	73	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4854640--4854706	28	2.5	26	76	11	73	47	1	1	49	1.19
4861568--4861601	14	2.4	14	90	9	52	20	11	0	67	1.21
4868428--4868495	21	3.2	21	67	8	66	23	16	29	30	1.96
4868424--4868506	42	2.0	42	97	0	157	25	15	30	28	1.96
4868490--4868525	18	2.0	18	94	0	63	22	13	33	30	1.93
4870377--4870489	31	3.6	31	69	4	84	52	13	11	23	1.72
4871327--4871420	31	3.2	30	68	17	79	47	13	15	22	1.81
4871353--4871405	27	2.0	27	85	7	72	49	15	11	24	1.77
4871653--4871700	23	2.1	23	96	0	87	45	14	14	25	1.83
4871949--4871991	19	2.3	19	92	4	70	53	0	0	46	1.00
4874864--4874896	2	16.5	2	100	0	66	51	0	0	48	1.00
4876234--4876279	24	1.9	24	86	0	65	34	34	8	21	1.84
4876258--4877500	60	20.7	60	86	0	1176	28	41	6	24	1.78
4876328--4876428	30	3.1	36	61	31	91	29	36	6	26	1.83
4876485--4876631	30	5.0	26	76	14	69	30	42	4	22	1.72
4878414--4878442	12	2.4	12	100	0	58	68	0	0	31	0.89
4878540--4878586	24	1.9	24	86	4	67	74	6	2	17	1.12
4878930--4878981	12	4.3	12	74	16	54	36	0	0	63	0.95
4878924--4878977	23	2.5	22	82	14	67	33	0	0	66	0.92
4878925--4878982	18	3.2	20	68	22	56	34	0	0	65	0.93
4879320--4879353	2	17.0	2	100	0	68	50	0	0	50	1.00
4880376--4880419	12	3.6	12	80	17	54	70	9	4	15	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4883006--4883154	78	1.9	78	90	0	235	26	19	28	25	1.99
4883085--4883251	52	3.2	52	80	0	217	26	17	31	25	1.97
4883010--4883172	78	2.1	78	83	0	200	26	18	29	25	1.98
4882983--4883391	182	2.2	182	85	0	550	27	17	29	26	1.97
4883137--4883428	130	2.2	130	82	1	334	26	16	31	24	1.96
4883270--4883398	52	2.5	52	87	0	177	27	17	31	24	1.97
4883371--4883424	26	2.1	26	85	0	72	22	18	40	18	1.91
4883195--4883477	130	2.2	130	81	1	334	27	16	31	24	1.96
4883365--4883707	78	4.2	79	71	10	237	26	15	34	22	1.94
4883453--4883593	29	4.9	29	83	3	149	25	11	43	19	1.85
4886547--4886597	16	3.4	16	76	15	63	60	0	1	37	1.08
4886535--4886597	29	2.2	29	91	0	99	55	0	6	38	1.25
4886746--4886796	23	2.2	23	79	6	59	43	0	0	56	0.99
4890114--4890710	79	7.6	79	82	5	674	27	23	11	36	1.90
4890114--4890723	236	2.6	233	83	6	746	27	23	11	37	1.90
4890114--4890711	315	1.9	314	83	5	787	27	23	11	36	1.90
4894703--4894842	35	4.0	35	97	0	262	43	5	30	20	1.75
4894784--4894887	49	2.1	49	100	0	208	37	6	35	20	1.79
4894819--4894856	14	2.7	14	100	0	76	28	7	42	21	1.81
4896228--4896894	79	8.4	79	88	3	900	28	24	13	33	1.93
4896228--4896894	317	2.1	316	89	2	1036	28	24	13	33	1.93
4896826--4896946	52	2.3	52	91	1	190	29	26	13	30	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4896748--4897072	131	2.5	132	85	4	343	27	24	13	34	1.93
4899140--4899164	4	6.2	4	100	0	50	24	0	0	76	0.80
4910465--4910613	61	2.4	61	88	4	228	24	28	20	26	1.99
4910631--4910879	55	4.4	56	86	7	333	28	28	20	22	1.98
4910894--4911101	61	3.4	61	80	7	251	25	27	18	28	1.98
4911232--4911335	42	2.5	41	80	10	113	17	27	10	44	1.82
4911824--4911980	21	8.5	21	69	26	131	43	5	30	19	1.74
4911799--4911910	56	2.0	56	100	0	224	46	5	28	19	1.72
4911845--4911990	35	4.2	35	98	0	283	41	6	32	19	1.77
4913392--4914217	79	10.4	79	90	1	1217	27	25	14	33	1.94
4919469--4919505	17	2.1	18	85	14	51	70	8	13	8	1.34
4921221--4921249	15	1.9	15	100	0	58	58	0	0	41	0.98
4921231--4921270	20	1.9	22	90	10	66	67	0	0	32	0.91
4922705--4922754	16	3.1	16	100	0	100	24	26	6	44	1.76
4928318--4928358	16	2.8	15	89	10	59	43	0	0	56	0.99
4928427--4928511	11	7.7	11	74	19	70	32	1	0	65	1.00
4928437--4928499	18	3.2	19	78	14	65	31	1	0	66	1.01
4928423--4928512	29	2.8	31	75	16	85	33	1	0	65	1.00
4928435--4928501	19	3.4	19	78	8	80	32	1	0	65	1.02
4929143--4929613	89	5.3	89	82	3	515	40	15	14	29	1.87
4929143--4929613	178	2.7	178	86	3	594	40	15	14	29	1.87
4934301--4934343	22	2.0	22	90	9	70	39	0	0	60	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4935911--4935974	33	1.9	33	90	0	101	28	6	45	20	1.75
4935935--4936068	45	3.0	45	88	2	198	31	4	44	20	1.71
4936109--4936251	45	3.1	45	72	9	126	27	2	47	22	1.62
4936235--4936278	21	2.1	21	86	0	61	15	2	61	20	1.45
4936301--4936407	54	2.0	51	82	8	126	23	4	49	22	1.68
4936349--4936463	48	2.4	48	79	2	124	23	4	49	22	1.67
4936480--4936698	48	4.6	48	81	2	224	25	4	46	23	1.70
4936450--4936539	42	2.1	43	85	6	130	20	5	51	23	1.68
4936533--4936620	27	3.5	26	67	17	69	27	4	44	23	1.73
4936471--4936698	96	2.4	96	82	2	253	25	3	47	22	1.69

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