genome.fa.s1.2.7.7.80.10.50.1000.27.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  27  of  52  ( 6211 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)
4423594--4423657	19	3.7	18	74	25	66	26	14	15	43	1.85
4423594--4423657	32	2.0	33	93	3	112	26	14	15	43	1.85
4424156--4424542	150	2.6	150	79	11	391	50	6	6	35	1.56
4425412--4425799	150	2.6	151	78	13	406	50	6	7	35	1.56
4425618--4425669	25	2.1	24	82	10	61	51	1	5	40	1.37
4426791--4427058	60	4.5	59	77	4	173	46	17	17	17	1.84
4426751--4427061	119	2.6	117	77	7	295	46	16	17	18	1.84
4428756--4428818	7	8.1	7	77	18	54	3	1	11	84	0.81
4428762--4428822	23	2.6	24	82	14	83	4	1	8	85	0.80
4428762--4428818	24	2.4	24	88	8	82	3	1	8	85	0.77
4428766--4428823	17	3.5	17	79	6	57	6	1	6	84	0.84
4430321--4430599	135	2.0	136	90	6	443	26	11	14	47	1.78
4430992--4431045	20	2.7	20	82	0	63	37	11	12	38	1.79
4445046--4445121	9	9.1	8	78	9	73	82	11	2	2	0.87
4445045--4445107	9	6.9	9	82	8	74	84	11	3	1	0.81
4445046--4445118	27	2.6	27	84	6	92	83	10	2	2	0.85
4446337--4447044	28	24.9	28	84	4	880	29	31	17	21	1.96
4446337--4447056	114	6.3	114	87	4	956	29	31	16	22	1.96
4447975--4448052	20	3.9	20	86	6	113	33	15	11	39	1.83
4451151--4451175	13	1.9	13	100	0	50	36	16	16	32	1.90
4451131--4451197	33	2.0	33	88	0	98	32	11	14	40	1.83
4451238--4451262	13	1.9	13	100	0	50	32	16	16	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4750476--4750508	13	2.5	13	90	0	57	42	12	15	30	1.83
4756359--4756421	33	1.9	33	87	9	94	41	15	12	30	1.85
4756528--4756582	22	2.5	22	93	0	92	49	7	12	30	1.68
4759054--4759099	21	2.3	20	85	10	60	54	8	13	23	1.66
4760003--4760074	20	3.6	20	73	0	63	38	11	15	34	1.83
4760631--4761021	32	12.2	32	92	0	613	18	18	32	29	1.95
4761018--4762136	55	20.5	54	88	4	1543	28	14	33	23	1.94
4761018--4762136	27	41.0	27	88	4	1543	28	14	33	23	1.94
4761018--4762136	82	13.7	81	87	4	1543	28	14	33	23	1.94
4763147--4763179	9	3.7	9	95	0	57	0	3	6	90	0.52
4767600--4767676	21	3.7	21	89	3	111	35	12	16	35	1.88
4767712--4767779	19	3.9	19	78	21	85	35	11	14	38	1.83
4767733--4767757	13	1.9	13	100	0	50	36	16	16	32	1.90
4767714--4767776	32	2.0	32	96	0	117	34	12	15	36	1.86
4767799--4767853	20	2.8	20	82	0	74	23	14	16	45	1.84
4768826--4768888	32	1.9	33	93	6	110	30	12	12	44	1.80
4771416--4771440	13	1.9	13	100	0	50	32	16	16	36	1.90
4773484--4773514	15	2.1	15	93	0	53	12	22	16	48	1.80
4777242--4777300	32	1.9	30	83	13	75	59	10	10	20	1.58
4777560--4777611	19	2.6	20	90	6	79	26	9	15	48	1.76
4777641--4777695	20	2.7	21	85	2	76	30	18	12	38	1.88
4780207--4780282	28	2.7	30	86	8	97	25	32	17	25	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4780158--4780357	107	1.9	107	83	5	260	27	27	15	29	1.96
4780237--4780441	79	2.6	79	81	1	232	24	29	16	29	1.96
4792813--4792876	1	64.0	1	77	0	65	89	6	1	3	0.65
4792814--4792876	16	3.7	17	83	14	76	88	6	1	3	0.66
4792812--4792876	24	2.8	23	82	13	87	87	7	1	3	0.70
4793826--4795308	59	25.2	59	88	6	1938	25	28	20	25	1.99
4795177--4795266	26	3.3	26	66	14	74	27	32	18	21	1.97
4796030--4796106	21	3.7	21	89	3	111	36	12	15	35	1.86
4796142--4796209	19	3.9	19	78	21	85	35	11	14	38	1.83
4796163--4796187	13	1.9	13	100	0	50	36	16	16	32	1.90
4796144--4796206	32	2.0	32	96	0	117	34	12	15	36	1.86
4796249--4796274	13	2.0	13	100	0	52	30	15	15	38	1.88
4796229--4796295	33	2.0	33	88	0	98	25	14	16	43	1.86
4798736--4798812	28	2.8	28	87	0	100	23	33	19	23	1.97
4798690--4798886	107	1.8	108	83	3	263	27	28	14	29	1.95
4803087--4803161	20	3.8	20	80	3	80	40	12	13	34	1.81
4803084--4803161	40	2.0	39	87	2	111	39	12	12	34	1.82
4804243--4804379	46	3.0	46	90	1	213	49	5	6	37	1.53
4804765--4804852	34	2.5	35	81	3	106	39	19	13	27	1.89
4804794--4804868	35	2.1	35	83	9	91	40	18	12	29	1.87
4805753--4805795	16	2.7	16	81	0	59	32	4	9	53	1.53
4814431--4814463	16	2.1	16	88	5	50	45	3	6	45	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4816678--4816713	13	2.5	15	86	13	58	66	8	13	11	1.44
4822911--4822962	20	2.5	21	90	3	79	42	13	13	30	1.83
4826109--4826237	52	2.5	52	94	0	222	30	18	17	34	1.94
4826246--4826270	13	1.9	13	100	0	50	36	16	16	32	1.90
4826299--4826323	13	1.9	13	100	0	50	40	16	8	36	1.77
4826282--4826343	32	1.9	33	93	3	108	38	19	8	33	1.81
4830752--4830846	16	6.0	16	70	7	59	23	28	10	37	1.88
4831794--4832561	51	15.0	51	73	7	351	34	21	19	24	1.96
4831898--4832160	101	2.6	103	78	6	286	32	24	20	22	1.98
4832072--4832502	153	2.8	153	89	1	623	34	20	18	25	1.96
4832026--4832513	153	3.2	153	85	2	579	34	21	18	25	1.96
4832481--4832645	89	1.9	89	82	7	210	36	19	19	24	1.94
4832569--4832864	51	5.8	52	73	5	203	36	19	18	26	1.94
4832276--4832862	293	2.0	292	80	3	653	36	19	18	25	1.95
4833188--4833412	114	2.0	114	84	3	301	38	7	10	43	1.68
4834548--4834589	22	1.9	22	100	0	84	50	14	4	30	1.63
4839276--4839336	32	1.9	31	90	6	95	54	26	4	14	1.61
4856645--4856669	12	2.1	12	100	0	50	32	16	16	36	1.90
4856625--4856687	31	2.0	31	87	6	92	30	15	15	38	1.89
4859226--4859250	13	1.9	13	100	0	50	36	16	16	32	1.90
4861325--4861355	15	2.1	15	93	0	53	12	22	16	48	1.80
4863159--4863203	21	2.1	21	84	8	56	22	20	4	53	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4869680--4869724	18	2.4	18	85	3	54	86	6	2	4	0.76
4873133--4873281	52	2.9	51	88	4	226	30	17	18	33	1.94
4873270--4873294	13	1.9	13	100	0	50	36	16	16	32	1.90
4873337--4873401	33	2.0	33	87	0	94	40	15	13	30	1.86
4873357--4873381	13	1.9	13	100	0	50	32	16	20	32	1.94
4874212--4874495	49	5.7	52	77	11	190	32	16	25	26	1.97
4874320--4874502	42	4.0	42	74	16	152	29	17	25	27	1.97
4874275--4874454	91	1.9	93	89	3	283	31	17	24	27	1.97
4874547--4874777	30	7.7	30	74	12	181	25	16	29	29	1.96
4874721--4874782	27	2.2	28	85	2	90	17	14	35	32	1.90
4876211--4876298	1	88.0	1	75	0	77	1	2	9	87	0.68
4876211--4876295	20	4.3	19	82	5	107	1	2	9	87	0.70
4885990--4886016	10	2.7	10	100	0	54	77	22	0	0	0.76
4890131--4890259	52	2.5	52	97	0	240	29	17	17	34	1.94
4890131--4890279	52	2.9	51	90	4	228	30	17	18	33	1.94
4890268--4890292	13	1.9	13	100	0	50	36	16	16	32	1.90
4890354--4890378	13	1.9	13	100	0	50	32	16	16	36	1.90
4890333--4890398	32	2.0	33	88	2	98	39	15	12	33	1.84
4891383--4891613	49	4.9	48	84	8	287	28	19	27	25	1.98
4891374--4891613	91	2.6	93	82	11	294	28	18	27	25	1.98
4891613--4891709	33	2.9	33	96	0	176	18	18	34	28	1.95
4891634--4891980	29	11.7	29	71	15	144	24	16	30	29	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4891860--4891912	26	2.0	28	85	7	74	15	16	32	35	1.90
4895783--4895808	13	2.0	13	100	0	52	30	15	15	38	1.88
4896515--4896558	21	2.1	21	83	8	54	25	31	4	38	1.76
4898366--4898390	13	1.9	13	100	0	50	36	16	16	32	1.90
4898596--4898627	8	4.0	8	100	0	64	62	25	0	12	1.30
4900482--4900512	15	2.1	15	93	0	53	12	22	16	48	1.80
4902923--4902948	13	2.0	13	100	0	52	30	15	15	38	1.88
4903008--4903080	20	3.6	20	81	3	101	31	19	13	35	1.91
4902987--4903080	41	2.3	41	96	0	170	30	18	12	38	1.88
4902987--4903062	21	3.7	21	78	3	91	30	17	11	40	1.85

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