genome.fa.s25.2.7.7.80.10.50.1000.30.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  30  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)
5064826--5064865	18	2.2	18	90	0	62	60	0	0	40	0.97
5064975--5065020	21	2.2	21	88	3	67	39	2	2	56	1.24
5067463--5067493	13	2.3	14	94	5	55	64	0	0	35	0.94
5067574--5067622	20	2.5	20	87	9	66	51	2	0	46	1.12
5068350--5068409	17	3.5	17	80	14	70	40	0	0	60	0.97
5068336--5068453	44	2.6	45	80	9	118	38	0	1	59	1.08
5070192--5070229	18	2.2	17	86	13	51	2	15	0	81	0.80
5070864--5070890	3	9.0	3	100	0	54	33	0	0	66	0.92
5070865--5070907	13	3.2	13	87	12	52	23	2	0	74	0.93
5073607--5073651	18	2.6	17	79	6	54	57	11	11	20	1.63
5074672--5074706	14	2.4	15	90	4	54	22	0	2	74	0.95
5075364--5075418	27	2.0	28	82	10	69	50	0	1	47	1.11
5077025--5077050	2	13.0	2	100	0	52	0	50	0	50	1.00
5079894--5079926	5	6.6	5	100	0	66	39	21	0	39	1.53
5081692--5081723	17	1.9	16	93	6	55	0	9	0	90	0.45
5085322--5085383	26	2.4	26	84	7	74	38	0	11	50	1.39
5086504--5086604	51	2.0	51	88	0	148	33	12	18	34	1.89
5087968--5088015	17	2.8	18	84	6	55	45	0	0	54	0.99
5094451--5094498	15	3.3	15	77	13	55	60	2	0	37	1.09
5094444--5094482	15	2.7	14	84	4	51	56	0	0	43	0.99
5095564--5095590	2	13.5	2	100	0	54	51	0	0	48	1.00
5097694--5097739	24	1.9	24	86	0	65	45	2	8	43	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5097702--5097756	26	2.1	26	93	6	94	45	1	9	43	1.46
5097966--5098090	22	6.1	21	72	16	84	40	4	10	45	1.57
5098254--5098326	22	3.3	22	80	3	85	41	5	6	46	1.54
5099181--5099264	31	2.7	31	88	1	125	34	20	15	29	1.93
5099181--5099295	31	3.8	30	78	12	94	33	20	15	30	1.93
5099181--5099300	62	2.0	61	81	8	145	34	20	15	30	1.94
5100089--5100439	173	2.0	174	99	0	695	25	17	22	33	1.96
5100449--5100525	20	3.9	19	76	6	73	33	12	12	40	1.82
5100449--5100526	40	2.0	39	84	2	102	33	12	14	39	1.84
5105338--5105379	22	1.9	22	85	0	57	38	4	9	47	1.57
5107240--5107350	27	3.8	29	73	10	102	42	14	1	41	1.56
5107367--5107448	23	3.4	23	76	16	76	60	2	2	34	1.23
5107408--5107457	22	2.2	23	82	10	59	62	2	0	36	1.07
5109495--5109541	24	1.9	25	82	4	60	36	4	4	55	1.39
5110022--5110072	11	4.7	11	78	9	52	37	5	0	56	1.23
5110034--5110072	16	2.4	17	86	4	53	33	5	0	61	1.18
5110845--5110918	7	10.3	7	72	16	62	66	0	0	33	0.92
5110872--5110925	18	2.9	20	76	13	62	62	0	0	37	0.95
5110849--5110923	36	2.1	38	82	12	95	64	0	0	36	0.94
5110902--5110980	27	3.0	27	74	17	76	49	0	1	49	1.09
5110890--5110971	32	2.5	34	76	11	89	54	0	1	43	1.07
5111237--5111271	16	2.1	18	89	10	56	31	2	5	60	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5111602--5111643	4	10.5	4	100	0	84	50	0	0	50	1.00
5111979--5112039	27	2.3	26	75	13	70	45	0	0	54	1.00
5111982--5112054	21	3.7	20	75	12	53	46	0	0	53	1.00
5113144--5113207	2	32.0	2	90	0	101	48	0	0	51	1.00
5113440--5113477	2	19.0	2	100	0	76	50	0	0	50	1.00
5113866--5113940	27	2.8	26	82	7	105	30	5	14	49	1.66
5118423--5118495	27	2.7	27	78	0	74	26	4	20	49	1.67
5119144--5119201	27	2.1	28	81	15	68	50	3	0	46	1.18
5120682--5120757	33	2.3	33	82	8	91	48	1	3	46	1.29
5121367--5121394	13	2.2	13	100	0	56	28	14	17	39	1.89
5127849--5127899	19	2.5	20	71	6	50	25	19	19	35	1.95
5128466--5128492	14	1.9	14	100	0	54	51	7	18	22	1.70
5129337--5129366	2	15.0	2	92	0	51	53	0	0	46	1.00
5129686--5129743	25	2.3	25	93	0	98	29	5	27	37	1.78
5129698--5129750	25	2.1	25	89	0	79	32	5	28	33	1.81
5131050--5131265	34	6.4	34	81	3	222	28	7	23	41	1.81
5131050--5131265	102	2.1	102	87	4	303	28	7	23	41	1.81
5136624--5136842	34	6.5	33	80	9	244	42	26	6	25	1.79
5136624--5136847	102	2.2	101	87	2	331	41	25	6	25	1.79
5139852--5139888	14	2.4	17	86	13	53	59	2	0	37	1.12
5140161--5140217	23	2.4	23	85	8	71	66	7	8	17	1.41
5140173--5140219	23	2.0	24	95	4	87	59	8	8	23	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5140943--5140989	18	2.6	18	80	12	60	42	2	0	55	1.12
5142431--5142479	16	3.1	16	75	18	50	55	2	0	42	1.11
5142767--5142813	2	24.0	2	95	4	87	51	0	0	48	1.00
5143251--5143280	9	3.2	9	90	9	51	33	0	0	66	0.92
5143253--5143296	10	4.4	10	83	11	54	31	0	0	68	0.90
5143251--5143286	11	3.5	11	78	21	51	33	0	0	66	0.92
5143251--5143289	19	2.1	19	90	4	62	35	0	0	64	0.94
5143281--5143326	19	2.3	20	78	14	51	34	0	0	65	0.93
5143290--5143350	29	2.1	29	84	6	79	36	0	3	60	1.13
5146293--5146372	20	3.7	22	76	19	71	61	0	0	38	0.96
5146294--5146385	20	4.4	20	71	20	64	58	0	0	41	0.98
5146307--5146380	25	3.0	25	76	19	75	60	0	0	39	0.97
5146374--5146415	18	2.3	18	80	15	50	50	0	0	50	1.00
5146322--5146404	20	4.6	20	70	22	58	59	0	0	40	0.98
5146354--5146408	17	3.4	17	75	25	55	58	0	0	41	0.98
5146295--5146411	25	4.2	26	69	22	71	58	0	0	41	0.98
5146955--5147014	23	2.6	24	79	12	63	45	0	1	53	1.10
5146962--5147024	24	2.6	24	82	10	74	44	0	0	55	0.99
5150116--5150158	2	21.5	2	95	0	77	48	2	0	48	1.14
5150727--5150770	21	2.1	21	86	0	61	54	2	0	43	1.12
5152623--5152655	17	1.9	17	88	11	50	69	0	0	30	0.88
5152744--5152770	2	13.5	2	100	0	54	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5153088--5153114	3	9.0	3	100	0	54	66	0	0	33	0.92
5153459--5153500	22	2.0	22	90	9	70	52	0	0	47	1.00
5153459--5153515	22	2.8	21	79	15	66	57	0	0	42	0.98
5154676--5154718	16	2.6	17	82	10	54	53	0	0	46	1.00
5154671--5154763	40	2.2	45	83	11	124	50	0	0	49	1.00
5155005--5155066	31	2.0	31	84	6	81	51	3	11	33	1.54
5155729--5155778	17	3.0	16	75	25	50	66	2	0	32	1.03
5155850--5155879	8	3.8	8	100	0	60	10	0	0	90	0.47
5155877--5155919	4	11.2	4	80	9	54	0	20	0	79	0.74
5155877--5155904	11	2.5	11	100	0	56	0	25	0	75	0.81
5155874--5155916	7	5.9	7	78	10	50	0	18	0	81	0.69
5155857--5155917	11	5.4	11	77	14	52	3	13	0	83	0.76
5156999--5157039	17	2.5	17	92	7	68	46	0	0	53	1.00
5156999--5157050	17	3.1	17	86	8	54	51	0	0	48	1.00
5157102--5157152	18	2.8	17	88	8	66	62	3	3	29	1.31
5157318--5157356	18	2.1	19	85	4	53	48	0	0	51	1.00
5157326--5157365	20	2.1	19	85	4	53	55	0	0	45	0.99
5158751--5158805	21	2.7	20	75	13	58	49	0	7	43	1.30
5163458--5163550	16	5.8	17	68	22	58	39	3	1	55	1.23
5170170--5170247	22	3.5	22	66	7	59	53	3	10	32	1.52
5170342--5170393	22	2.3	23	83	3	61	51	5	5	36	1.50
5170385--5170434	21	2.5	19	81	12	64	56	4	2	38	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5172440--5172493	25	2.3	26	87	9	64	61	0	0	38	0.96
5173310--5173335	2	13.0	2	100	0	52	50	0	0	50	1.00
5173953--5174008	29	1.9	29	88	0	85	58	8	3	28	1.45
5174399--5174453	25	2.2	25	96	0	101	29	16	5	49	1.68
5174794--5174889	47	2.0	48	84	9	126	47	1	3	47	1.24
5174790--5174896	24	4.4	24	70	14	69	48	0	2	47	1.22
5175633--5175700	29	2.3	29	82	9	77	66	1	2	29	1.15
5175653--5175700	14	3.4	13	78	16	51	68	0	2	29	1.01
5181183--5181224	20	2.2	19	83	12	50	59	0	0	40	0.97
5195658--5195702	17	2.7	16	86	10	63	40	0	2	57	1.11

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