genome.fa.s1.2.7.7.80.10.50.1000.28.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: 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  28  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)
4905526--4905564	13	3.0	13	96	0	69	35	15	17	30	1.91
4905550--4905628	20	3.7	20	75	18	70	45	15	13	25	1.83
4905766--4905797	8	4.0	8	100	0	64	62	25	0	12	1.30
4907651--4907681	15	2.1	15	93	0	53	12	22	16	48	1.80
4909696--4909738	22	2.0	22	86	4	61	23	11	9	55	1.64
4911747--4911772	13	2.0	13	100	0	52	30	15	15	38	1.88
4911832--4911904	20	3.6	20	81	3	101	31	19	13	35	1.91
4911811--4911904	41	2.3	41	96	0	170	30	18	12	38	1.88
4911811--4911886	21	3.7	21	78	3	91	30	17	11	40	1.85
4912343--4912387	21	2.1	21	84	8	56	22	20	4	53	1.63
4918843--4918881	17	2.3	17	86	0	51	87	7	2	2	0.73
4918841--4918888	18	2.7	17	80	6	51	85	8	2	4	0.80
4920096--4920531	28	15.1	28	82	8	466	28	29	16	24	1.97
4920090--4920531	115	3.8	112	81	7	467	28	29	16	24	1.97
4920096--4920481	143	2.7	144	84	5	480	29	30	16	24	1.96
4921339--4921403	31	2.1	31	100	0	130	44	6	9	40	1.61
4922260--4922298	20	2.1	19	85	9	53	23	10	10	56	1.63
4925991--4926119	52	2.5	52	96	0	240	29	17	18	34	1.94
4925991--4926139	52	2.9	51	90	4	228	30	16	18	33	1.94
4926128--4926152	13	1.9	13	100	0	50	36	16	16	32	1.90
4926214--4926238	13	1.9	13	100	0	50	32	16	16	36	1.90
4926193--4926258	32	2.0	33	94	2	116	36	16	12	34	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4926896--4927090	53	3.7	52	80	4	176	35	14	24	25	1.94
4927031--4927157	67	1.9	68	88	1	193	39	12	24	23	1.89
4926991--4927211	122	1.8	120	83	5	293	36	14	23	25	1.92
4927107--4927814	49	14.7	49	78	12	688	33	16	24	25	1.96
4927161--4927814	92	6.9	92	87	5	916	33	17	24	25	1.96
4927821--4927958	33	4.2	33	87	6	210	19	16	35	28	1.94
4927819--4927958	65	2.2	64	88	6	210	19	16	35	29	1.93
4927960--4928353	33	11.8	33	76	10	361	32	13	33	19	1.91
4927965--4928384	100	4.2	100	91	1	646	32	14	33	20	1.92
4928347--4928452	30	3.5	30	88	10	153	33	16	27	22	1.95
4928552--4928597	8	5.6	8	92	5	65	26	6	23	43	1.78
4929420--4929484	11	5.7	11	81	5	67	0	6	10	83	0.82
4929415--4929483	30	2.3	31	87	9	99	0	8	8	82	0.84
4929415--4929483	16	4.5	15	82	8	86	0	8	8	82	0.84
4929738--4929772	8	4.5	8	85	7	54	0	0	11	88	0.51
4929733--4929775	13	3.1	15	80	16	56	2	0	9	88	0.60
4929743--4929775	13	2.7	12	90	9	57	0	0	9	90	0.44
4929731--4929774	10	4.1	10	81	16	52	2	0	11	86	0.66
4933050--4933108	32	1.9	30	83	13	75	59	10	10	20	1.58
4937849--4937998	52	2.9	52	89	0	228	32	16	17	34	1.92
4938059--4938083	13	1.9	13	100	0	50	32	16	16	36	1.90
4938038--4938103	32	2.0	33	91	2	107	36	15	12	36	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4948567--4948600	17	1.9	17	94	5	59	67	0	0	32	0.91
4949283--4949316	2	17.0	2	100	0	68	50	0	0	50	1.00
4950111--4950179	36	1.9	35	82	8	86	55	8	0	36	1.31
4951859--4951905	18	2.6	18	78	18	53	4	19	2	74	1.09
4953711--4953736	13	2.0	13	100	0	52	38	15	15	30	1.88
4959898--4959935	13	2.9	13	96	0	67	34	18	15	31	1.92
4960056--4960101	21	2.2	20	81	11	58	32	19	4	43	1.71
4961729--4961868	67	2.1	67	100	0	280	30	2	24	42	1.69
4962551--4962576	13	2.0	13	100	0	52	38	15	15	30	1.88
4965222--4965637	58	7.2	57	77	6	325	48	14	8	28	1.73
4965264--4965598	116	2.9	112	81	7	366	48	15	8	26	1.73
4968005--4968075	35	2.0	35	97	0	133	18	8	22	50	1.73
4970174--4970218	19	2.3	19	80	3	54	44	2	8	44	1.47
4971351--4971535	34	5.5	34	88	3	266	40	27	7	25	1.82
4971351--4971535	102	1.8	101	94	1	325	40	27	7	25	1.82
4975601--4975663	19	3.3	19	90	0	90	34	19	17	28	1.94
4975969--4976151	34	5.4	34	88	3	262	39	27	7	25	1.82
4975969--4976151	102	1.8	101	93	1	321	39	27	7	25	1.82
4978110--4978134	2	12.5	2	100	0	50	0	48	0	52	1.00
4978502--4978723	59	3.7	59	74	5	201	27	14	22	35	1.93
4987178--4987292	61	1.9	61	88	0	176	41	11	20	26	1.86
4987412--4987493	43	1.9	43	87	0	119	30	14	26	28	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4987446--4987619	61	2.9	61	79	6	201	33	13	27	24	1.93
4987670--4987787	32	3.7	30	81	9	137	15	17	34	32	1.91
4987661--4987788	63	2.0	65	85	8	174	18	16	35	29	1.93
4987966--4988058	28	3.4	28	89	1	134	27	21	24	25	1.99
4989426--4989481	8	7.2	8	78	10	55	1	0	12	85	0.67
4989422--4989482	9	6.3	10	81	12	74	1	0	13	85	0.68
4989426--4989482	18	3.1	18	87	5	87	1	0	12	85	0.66
4989426--4989484	29	2.0	29	90	6	93	1	0	11	86	0.65
5003767--5003890	61	2.0	61	88	0	185	37	12	25	25	1.90
5003897--5004055	43	3.5	43	78	14	165	34	19	21	24	1.96
5003831--5004072	95	2.5	95	82	2	279	34	16	23	25	1.96
5003927--5004025	52	1.9	52	95	0	180	36	18	22	23	1.95
5004021--5004176	61	2.6	61	75	0	150	35	16	26	21	1.94
5004245--5004363	32	3.8	31	80	11	138	16	15	33	34	1.90
5004236--5004369	63	2.1	64	87	5	191	20	14	35	30	1.92
5004542--5004641	28	3.6	28	85	4	132	23	22	29	26	1.99
5016890--5016929	21	1.9	22	85	10	57	40	0	7	52	1.30
5018294--5018356	33	1.9	32	87	12	92	33	12	19	34	1.89
5026973--5026999	13	2.1	13	100	0	54	29	14	14	40	1.86
5027049--5027102	20	2.7	19	88	11	74	31	14	18	35	1.91
5030400--5030528	52	2.5	52	97	0	240	28	18	17	34	1.94
5030604--5030733	19	7.8	18	70	29	110	36	16	12	33	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5030599--5030731	32	4.1	32	98	0	239	36	17	12	34	1.87
5030623--5030711	13	5.9	13	72	27	70	34	16	13	34	1.88
5032076--5032217	38	3.8	38	75	10	123	31	16	15	36	1.90
5032159--5032370	116	1.8	116	87	2	318	30	11	18	39	1.87
5037925--5038045	38	3.2	38	78	10	106	25	14	19	41	1.88
5037950--5038047	38	2.5	40	80	8	114	29	13	17	39	1.87
5049129--5049216	10	9.1	9	82	11	95	85	11	2	1	0.75
5049124--5049250	17	7.7	17	72	12	88	82	12	3	1	0.85
5049123--5049211	30	2.9	30	83	6	117	85	11	2	1	0.74
5049124--5049211	1	88.0	1	74	0	68	86	10	2	1	0.72
5050496--5050657	28	5.8	28	89	2	245	29	27	18	24	1.98
5050496--5050657	84	1.9	84	92	0	270	29	27	18	24	1.98
5051608--5051866	79	3.3	79	82	2	342	30	16	28	24	1.96
5051819--5051889	28	2.6	28	84	8	92	22	19	36	21	1.95
5051877--5052272	52	7.6	51	71	10	280	31	10	27	30	1.91
5051768--5052261	262	1.9	261	93	0	844	30	12	28	28	1.93
5054665--5054706	21	2.0	21	100	0	84	28	19	9	42	1.82
5054731--5054793	19	3.7	18	76	24	73	36	17	12	33	1.88
5054724--5054795	32	2.2	32	97	0	135	36	16	12	34	1.87
5054750--5054774	13	1.9	13	100	0	50	32	16	16	36	1.90
5054762--5054822	19	3.1	19	73	13	61	27	16	13	42	1.85
5055105--5055690	28	20.9	28	80	5	601	32	31	15	20	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5055820--5055951	49	2.8	48	80	7	146	21	25	18	35	1.95
5056611--5056665	20	2.8	20	77	0	65	36	10	10	41	1.75
5056600--5056763	71	2.4	69	88	6	235	28	17	10	43	1.82
5056651--5056763	31	3.5	31	67	15	93	26	20	11	41	1.86
5065533--5065584	13	4.0	13	75	9	52	48	1	0	50	1.12
5065523--5065567	13	3.6	13	77	16	51	53	2	0	44	1.13
5065834--5065861	8	3.5	8	100	0	56	75	0	25	0	0.81
5068983--5069080	46	2.1	46	85	7	128	51	4	3	41	1.36
5069041--5069117	38	2.1	37	79	13	90	58	3	3	33	1.35
5073089--5073155	20	3.4	20	87	6	93	29	14	14	40	1.87

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