genome.fa.s1.2.7.7.80.10.50.1000.29.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  29  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)
5073264--5073356	43	2.2	43	94	0	159	37	19	12	30	1.89
5073708--5073751	23	1.9	23	86	9	63	31	6	20	40	1.79
5081274--5081326	19	2.8	19	88	0	79	49	0	37	13	1.42
5081417--5081459	21	2.0	22	90	4	70	44	0	27	27	1.55
5082173--5082209	13	2.8	13	100	0	74	35	16	16	32	1.91
5087615--5087771	58	2.7	57	79	6	147	47	14	12	26	1.79
5090437--5090482	24	2.0	23	87	12	67	73	0	21	4	1.00
5090426--5090502	27	2.7	27	76	13	75	74	0	20	5	1.01
5105917--5105980	33	1.9	33	84	6	85	39	9	17	34	1.82
5106016--5106077	19	3.6	19	71	24	64	38	17	9	33	1.83
5106033--5106057	13	1.9	13	100	0	50	32	16	16	36	1.90
5106001--5106081	32	2.5	32	87	2	117	37	16	11	35	1.84
5106045--5106104	19	3.0	20	76	9	61	31	11	13	43	1.80
5107888--5107996	52	2.1	53	92	1	184	44	7	15	32	1.74
5110601--5110817	52	4.2	51	80	7	213	34	11	23	29	1.91
5110800--5110874	27	2.7	27	87	2	105	18	21	36	24	1.95
5110749--5110952	104	1.9	105	85	2	275	28	17	28	25	1.97
5110936--5111056	51	2.4	51	84	5	156	33	12	25	28	1.92
5110974--5111101	51	2.5	51	83	5	143	35	10	26	27	1.90
5111038--5111212	79	2.2	79	83	4	210	30	14	28	27	1.95
5111165--5111239	27	2.7	28	87	2	98	21	18	34	25	1.96
5111223--5111344	51	2.3	52	88	5	176	31	11	23	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5113690--5113731	21	2.0	21	95	0	75	28	16	9	45	1.79
5113748--5113799	13	3.5	13	73	26	50	36	17	13	32	1.89
5113756--5113818	19	3.7	18	76	24	73	36	17	12	33	1.88
5113748--5113820	32	2.3	32	97	0	137	35	17	12	34	1.88
5113787--5113848	19	3.2	19	73	13	63	27	16	14	41	1.87
5113878--5113953	21	3.7	21	81	13	95	39	18	9	32	1.82
5113889--5113948	19	3.1	19	90	4	84	41	16	8	33	1.78
5115304--5115529	90	2.5	90	86	4	296	26	26	9	36	1.87
5115304--5115674	90	4.1	90	75	8	279	27	25	9	37	1.87
5117079--5117229	28	5.5	28	75	6	85	33	28	15	23	1.95
5117050--5117171	56	2.2	55	78	7	129	32	27	15	24	1.95
5117106--5117431	28	11.7	28	74	6	124	31	26	16	24	1.96
5117002--5117281	138	2.0	138	81	1	319	32	27	16	24	1.96
5117273--5117434	56	2.9	55	77	5	164	30	28	16	24	1.96
5128593--5128692	36	2.9	35	88	8	143	55	0	1	44	1.06
5132573--5132643	28	2.6	26	80	10	72	43	0	2	53	1.15
5133301--5133331	15	2.0	16	93	6	55	48	0	0	51	1.00
5133356--5133407	15	3.3	15	72	5	50	46	1	3	48	1.31
5134237--5134261	11	2.3	11	100	0	50	72	0	0	28	0.86
5135077--5135140	5	12.4	5	75	6	56	57	0	0	42	0.98
5135082--5135141	15	3.8	16	80	10	70	55	0	0	45	0.99
5135102--5135150	15	3.3	15	77	11	55	44	0	2	53	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5135239--5135273	18	1.9	18	88	0	52	68	0	2	28	1.04
5135649--5135688	22	2.0	20	85	14	55	55	0	2	42	1.13
5146501--5146566	32	2.0	34	91	5	109	57	0	0	42	0.98
5147314--5147366	18	2.9	18	77	8	63	47	0	0	52	1.00
5147552--5147597	14	3.2	14	81	6	56	54	0	0	45	0.99
5147807--5147835	7	4.1	7	100	0	58	41	13	0	44	1.44
5148347--5148382	18	2.1	17	89	5	54	36	0	0	63	0.94
5148352--5148391	18	2.2	18	86	0	53	40	0	0	60	0.97
5148352--5148411	21	3.0	21	83	7	63	46	1	0	51	1.10
5150831--5150875	22	2.1	22	87	4	65	66	0	0	33	0.92
5150819--5150876	21	2.8	20	79	7	62	65	0	0	34	0.93
5150879--5150937	21	2.8	21	81	2	82	55	1	0	42	1.09
5151883--5151913	5	6.2	5	100	0	62	19	0	0	80	0.71
5153956--5154037	41	2.1	39	84	9	103	54	1	0	43	1.07
5154253--5154295	21	2.0	23	86	9	63	72	4	2	20	1.14
5154235--5154295	22	2.8	22	78	14	63	70	4	1	22	1.15
5156642--5156973	173	1.9	173	98	0	637	32	17	17	33	1.93
5159774--5159804	11	2.8	11	100	0	62	38	19	0	41	1.51
5159661--5160060	139	3.0	138	90	9	698	43	12	8	35	1.73
5159661--5160058	126	3.0	127	94	5	672	43	12	8	34	1.73
5161575--5161605	15	2.1	15	93	0	53	48	3	0	48	1.17
5165456--5165486	2	15.5	2	100	0	62	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)
5166712--5166756	22	2.0	22	87	8	65	75	0	0	24	0.80
5167203--5167249	3	15.7	3	86	8	51	40	0	25	34	1.56
5167212--5167255	21	2.1	21	91	0	70	43	0	22	34	1.54
5167839--5167922	32	2.6	32	79	9	98	44	3	8	44	1.51
5169942--5169972	16	1.9	16	100	0	62	25	3	0	70	1.02
5172357--5172416	16	3.8	17	79	14	67	56	5	0	38	1.21
5172368--5172437	31	2.3	31	82	9	81	54	8	1	35	1.40
5172907--5173001	16	5.9	16	76	4	75	56	5	2	35	1.33
5172909--5172995	32	2.7	32	80	0	93	57	4	2	35	1.32
5175395--5175449	22	2.5	22	82	8	67	65	0	0	34	0.93
5175401--5175460	22	2.6	23	72	20	61	65	0	0	35	0.93
5175772--5175827	25	2.3	24	75	9	60	53	0	1	44	1.11
5177874--5177916	21	2.1	21	91	4	70	46	0	0	53	1.00
5178163--5178298	67	2.0	67	88	4	202	40	1	6	51	1.37
5181011--5181035	6	4.2	6	100	0	50	16	0	0	84	0.63
5185066--5185099	17	2.1	17	88	5	52	55	2	0	41	1.15
5185482--5185534	15	3.6	15	77	10	56	50	0	1	47	1.12
5185505--5185553	14	3.6	13	78	8	53	53	2	4	40	1.32
5185540--5185653	45	2.5	46	77	12	117	49	3	0	46	1.25
5185903--5185935	14	2.3	15	89	5	50	54	3	0	42	1.15
5186654--5186688	15	2.2	16	95	5	63	25	0	0	74	0.82
5187099--5187280	70	2.5	72	78	12	176	30	1	11	56	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5187124--5187283	74	2.2	68	77	14	153	31	0	11	56	1.40
5187453--5187484	12	2.6	13	85	14	50	15	28	31	25	1.96
5190505--5190530	13	2.0	13	100	0	52	38	15	15	30	1.88
5192745--5192789	21	2.1	21	84	8	56	53	4	20	22	1.63
5194593--5194623	15	2.1	15	93	0	53	48	16	22	12	1.80
5196701--5196739	13	3.0	13	100	0	78	30	15	15	38	1.88
5196860--5196906	21	2.3	21	79	20	55	34	19	4	42	1.70
5196862--5196904	20	2.2	19	84	16	52	32	18	4	44	1.71
5199271--5199296	13	2.0	13	100	0	52	38	15	15	30	1.88
5204282--5204344	32	2.0	32	83	0	81	39	15	14	30	1.87
5204466--5204494	14	2.1	14	100	0	58	34	6	13	44	1.71
5204466--5204498	14	2.2	15	89	10	50	33	6	12	48	1.65
5206858--5206908	16	3.3	15	78	10	66	3	13	13	68	1.34
5206857--5206901	17	2.8	17	80	10	58	4	13	15	66	1.39
5207154--5207217	8	8.0	8	80	19	80	25	1	0	73	0.92
5207152--5207207	10	5.5	10	73	26	55	26	1	0	71	0.96
5207154--5207217	23	2.7	23	86	11	85	25	1	0	73	0.92
5207152--5207217	25	2.7	25	82	17	86	25	1	0	72	0.93
5207152--5207217	33	2.0	33	94	5	116	25	1	0	72	0.93
5207309--5207521	103	2.0	104	87	5	306	38	13	17	30	1.88
5208041--5208107	33	2.0	33	88	0	98	34	11	13	40	1.81
5208061--5208085	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5208150--5208174	13	1.9	13	100	0	50	32	16	16	36	1.90
5208183--5208303	52	2.3	52	97	0	224	34	18	18	28	1.94
5215483--5215518	1	36.0	1	88	0	54	94	2	2	0	0.37
5216465--5216646	31	5.9	30	84	7	197	23	29	18	28	1.97
5216465--5216646	93	1.9	94	82	7	228	23	29	18	28	1.97
5216643--5217414	34	22.9	35	82	11	797	19	34	12	33	1.89
5216641--5217414	71	11.5	70	82	12	846	19	34	12	33	1.89
5216987--5217078	27	3.1	28	73	15	87	19	35	14	30	1.91
5217119--5217211	27	3.2	27	77	16	96	17	36	15	31	1.90
5216648--5217409	133	5.7	133	83	11	772	19	35	12	32	1.90

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