genome.fa.s2.2.7.7.80.10.50.1000.35.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  35  of  38  ( 4457 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)
5370642--5370696	24	2.3	25	84	9	78	60	0	0	40	0.97
5370641--5370701	23	2.7	23	85	7	72	59	0	0	40	0.98
5372083--5372111	9	3.3	9	95	4	51	10	0	6	82	0.83
5372781--5372866	23	3.7	23	82	3	102	54	15	18	11	1.70
5373199--5373247	19	2.6	19	78	15	57	65	14	14	6	1.45
5373256--5373312	22	2.5	23	80	11	64	66	12	21	0	1.23
5374454--5375125	155	4.3	154	83	4	762	24	18	20	36	1.95
5378656--5378710	24	2.2	23	79	20	58	70	0	16	12	1.16
5378916--5378968	17	3.1	17	84	13	56	73	0	18	7	1.06
5379230--5379430	81	2.5	80	84	6	230	31	19	8	40	1.81
5380599--5380818	90	2.5	89	81	3	262	29	27	16	26	1.97
5381054--5381369	48	6.6	48	80	2	323	20	21	18	39	1.92
5381074--5381351	144	1.9	144	88	0	421	21	20	19	38	1.94
5381577--5381709	42	3.1	42	81	6	144	18	27	18	36	1.94
5381861--5382590	43	17.0	42	79	5	606	15	28	17	37	1.91
5381861--5382590	129	5.7	127	80	6	702	15	28	17	37	1.91
5382722--5383016	42	7.0	42	70	7	202	21	27	17	33	1.96
5382691--5383016	84	3.9	84	78	3	332	21	27	17	32	1.96
5382693--5383120	85	5.1	85	73	9	232	22	28	16	32	1.96
5382735--5383018	127	2.2	126	79	4	295	21	26	17	33	1.96
5382742--5383052	42	7.4	43	72	10	160	21	27	17	33	1.96
5383232--5383406	82	2.1	83	80	9	189	21	23	11	43	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5384124--5384150	11	2.5	11	100	0	54	14	0	14	70	1.17
5384928--5384964	19	1.9	19	88	0	56	13	0	5	81	0.86
5385821--5386519	156	4.5	153	79	8	599	24	17	19	37	1.94
5385821--5386467	313	2.1	313	81	6	751	25	17	19	37	1.94
5388545--5388604	20	2.9	21	80	12	61	75	0	23	1	0.90
5388551--5388624	24	3.0	24	84	7	87	75	0	21	2	0.92
5388552--5388622	14	5.3	13	73	17	56	77	0	19	2	0.89
5388551--5388621	22	3.0	23	83	8	72	76	0	21	2	0.92
5389247--5389472	123	1.8	122	81	7	278	33	6	11	48	1.65
5390004--5390042	20	2.0	21	85	10	55	66	0	0	33	0.92
5389999--5390051	8	6.1	8	75	16	52	69	0	0	30	0.88
5389999--5390073	19	4.1	19	73	16	59	65	1	0	33	1.01
5390306--5390388	5	17.2	5	69	28	56	33	1	3	61	1.21
5390311--5390370	17	3.6	17	77	16	56	33	1	1	63	1.14
5390306--5390375	25	3.0	23	85	10	88	34	1	1	62	1.13
5390310--5390391	25	3.4	25	81	11	82	34	1	3	60	1.22
5393354--5393487	44	3.0	44	89	2	207	26	23	14	35	1.93
5396587--5396626	20	2.0	20	100	0	80	45	5	15	35	1.68
5397426--5397513	36	2.7	32	78	16	92	30	21	11	36	1.89
5397950--5397996	22	2.1	22	84	0	58	42	8	19	29	1.80
5397967--5398027	32	1.9	32	96	0	113	36	13	24	26	1.92
5397965--5398042	32	2.4	32	86	0	102	38	11	21	28	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5400038--5400087	21	2.5	21	87	6	68	28	16	16	40	1.89
5401833--5401859	13	2.1	13	100	0	54	37	14	14	33	1.88
5401878--5401958	13	7.1	12	71	28	70	35	17	12	34	1.87
5401879--5401958	34	2.4	34	100	0	160	35	17	12	35	1.88
5407145--5407192	19	2.5	19	79	0	60	83	10	4	2	0.87
5408494--5408708	31	6.9	30	84	8	211	25	29	15	29	1.96
5408570--5409774	34	35.8	33	86	8	1462	20	33	12	32	1.90
5409757--5409957	33	6.2	32	89	5	305	27	34	17	20	1.95
5409954--5411183	49	25.8	49	82	6	1503	24	25	18	31	1.97
5409954--5411183	92	12.9	97	92	3	1838	24	25	18	31	1.97
5411197--5411323	67	1.9	68	86	1	184	24	25	11	38	1.89
5412086--5412152	33	2.0	33	88	0	98	34	11	13	40	1.81
5412106--5412130	13	1.9	13	100	0	50	36	16	16	32	1.90
5412193--5412217	13	1.9	13	100	0	50	32	16	16	36	1.90
5412226--5412353	52	2.5	52	94	3	224	33	17	17	30	1.94
5416690--5416748	20	3.1	19	85	7	75	38	15	11	33	1.84
5416711--5416748	20	1.9	20	100	0	76	39	13	15	31	1.86
5416775--5416827	20	2.7	20	85	5	63	35	13	16	33	1.88
5423006--5423045	13	3.1	13	96	0	71	32	12	15	40	1.84
5425536--5425562	13	2.1	13	100	0	54	29	14	14	40	1.86
5425517--5425581	32	2.0	33	87	3	96	30	15	12	41	1.84
5425546--5425602	19	2.9	19	86	2	78	33	15	15	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5425631--5425684	20	2.7	20	88	5	74	31	11	18	38	1.86
5435085--5435176	46	2.0	46	93	0	157	34	15	20	29	1.93
5438504--5438557	20	2.7	20	80	5	65	38	16	11	33	1.84
5438585--5438658	20	3.8	19	84	8	87	36	16	14	32	1.89
5438647--5438698	20	2.6	20	100	0	104	23	15	26	34	1.94
5439544--5439627	29	2.9	29	85	7	107	28	27	7	36	1.83
5439821--5439905	29	2.9	30	85	7	111	29	29	4	36	1.78
5441450--5441496	23	2.0	24	84	12	62	61	19	4	14	1.49
5442366--5442450	21	4.0	21	77	7	75	20	24	1	54	1.52
5444536--5444562	13	2.1	13	100	0	54	40	14	14	29	1.86
5446714--5446789	40	1.9	40	86	0	107	21	30	11	36	1.89
5446710--5446798	40	2.2	40	79	0	106	17	29	10	42	1.82
5446928--5447108	31	5.8	31	74	5	159	27	29	23	20	1.99
5446920--5447117	62	3.2	62	88	0	279	26	30	23	19	1.98
5446927--5447153	124	1.8	124	81	3	287	28	28	23	19	1.99
5447064--5447149	31	2.8	31	76	1	93	34	33	17	13	1.89
5447867--5447940	21	3.6	21	78	7	71	41	12	16	29	1.84
5453132--5453192	20	3.0	20	72	13	61	50	24	3	21	1.63
5459034--5459089	20	2.7	21	81	10	71	39	14	10	35	1.81
5459058--5459133	21	3.6	21	77	13	75	34	13	15	36	1.87
5459122--5459188	20	3.7	19	69	22	63	34	14	13	37	1.86
5464739--5464827	44	2.0	44	84	0	115	53	1	8	35	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5465336--5465394	29	2.0	29	96	0	109	35	3	15	45	1.63
5466931--5466970	20	2.0	20	95	4	73	10	27	0	62	1.27
5467668--5467752	26	3.3	26	85	3	109	36	8	12	42	1.73
5470108--5470164	20	2.8	20	91	0	96	24	12	17	45	1.83
5470146--5470175	13	2.3	13	94	0	51	30	13	13	43	1.82
5470191--5470263	20	3.8	19	79	15	71	28	13	12	45	1.80
5470190--5470242	18	2.8	19	83	13	65	28	16	13	41	1.86
5472646--5472717	28	2.6	28	78	6	85	22	31	20	25	1.98
5472562--5472766	107	1.9	107	84	7	274	26	25	15	32	1.95
5472702--5472821	51	2.4	51	82	10	156	30	23	11	35	1.90
5472753--5472972	78	2.8	79	83	2	291	29	23	15	32	1.95
5474844--5474897	20	2.7	20	82	2	63	38	11	14	35	1.82
5474974--5475032	21	2.9	21	75	9	68	32	16	8	42	1.79
5474975--5475030	20	2.7	21	78	8	62	32	16	8	42	1.79
5478182--5478241	27	2.2	28	90	3	95	30	16	18	35	1.93
5478482--5478678	105	1.9	105	94	0	349	36	12	21	29	1.90
5480378--5480425	23	2.1	23	88	0	69	35	6	14	43	1.71
5488278--5488309	2	16.0	2	100	0	64	0	0	50	50	1.00
5488791--5488826	2	18.0	2	100	0	72	50	0	0	50	1.00
5490112--5490170	13	4.2	14	70	23	52	61	0	1	37	1.07
5491764--5491815	22	2.4	21	71	6	50	7	21	1	69	1.24
5496374--5496417	18	2.4	18	88	7	63	29	4	4	61	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5497100--5497129	3	9.7	3	92	7	51	33	0	0	66	0.92
5500897--5500925	15	1.9	15	100	0	58	20	3	0	75	0.94
5504553--5504582	2	15.0	2	92	0	51	53	0	0	46	1.00
5504948--5505049	11	9.0	11	71	14	50	56	0	0	43	0.99
5504943--5505049	22	5.0	22	70	19	82	55	0	0	43	1.06
5504967--5505020	23	2.4	22	87	9	74	64	0	0	35	0.94
5504949--5505016	18	3.9	18	73	11	61	61	0	0	38	0.96
5505038--5505071	17	2.1	15	89	10	50	55	2	0	41	1.15
5504938--5505077	62	2.3	60	78	14	151	55	0	0	43	1.10
5506190--5506216	13	2.1	13	100	0	54	37	0	0	62	0.95

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