genome.fa.s4.2.7.7.80.10.50.1000.1.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: Scaffold4
Parameters: 2 7 7 80 10 50 1000
Length:  5986281

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   

This is table  1  of  31  ( 3628 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)
5539--5565	2	13.5	2	100	0	54	51	0	48	0	1.00
5774--5806	4	8.2	4	100	0	66	51	24	0	24	1.48
7878--7906	2	14.5	2	100	0	58	48	0	0	51	1.00
8014--8039	2	13.0	2	100	0	52	50	0	0	50	1.00
8934--8964	3	10.3	3	100	0	62	67	0	0	32	0.91
9673--9725	20	2.7	20	93	0	79	49	16	5	28	1.69
10800--10835	4	9.0	4	100	0	72	50	25	0	25	1.50
11189--11226	2	19.5	2	94	5	69	50	0	0	50	1.00
13393--13594	7	28.4	7	75	5	109	39	45	3	11	1.58
13500--13620	28	4.3	28	75	10	86	38	43	2	14	1.59
14026--14088	20	3.2	20	71	15	58	63	3	4	28	1.30
17427--17471	23	2.0	23	95	0	81	24	15	17	42	1.88
17845--18096	87	2.9	87	84	3	312	26	13	5	53	1.62
19390--19505	7	16.6	7	69	16	80	48	25	0	25	1.57
19496--19557	25	2.4	25	78	5	70	54	24	0	20	1.44
19559--19612	21	2.7	19	80	11	54	40	27	1	29	1.67
19610--19686	14	5.6	13	76	11	73	40	53	2	3	1.33
19596--19686	28	3.3	27	78	6	83	41	50	2	5	1.37
20174--20398	76	3.0	76	82	2	265	29	15	15	40	1.88
20228--20398	38	4.5	38	82	1	191	29	13	16	40	1.86
27288--27314	2	13.5	2	100	0	54	51	0	48	0	1.00
27523--27555	4	8.2	4	100	0	66	51	24	0	24	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29627--29655	2	14.5	2	100	0	58	48	0	0	51	1.00
29763--29790	2	14.0	2	100	0	56	50	0	0	50	1.00
30685--30715	3	10.3	3	100	0	62	67	0	0	32	0.91
32530--32579	4	12.5	4	95	0	73	50	20	0	30	1.49
32917--32956	2	20.5	2	94	5	73	50	0	0	50	1.00
40505--40594	45	2.0	45	97	0	171	37	18	8	34	1.82
44465--44497	12	2.6	13	95	4	59	33	6	0	60	1.21
45229--45261	4	8.5	4	86	6	50	72	27	0	0	0.85
46090--46169	21	3.8	21	70	9	65	53	15	5	26	1.61
47484--47536	26	2.0	26	92	0	88	41	11	11	35	1.77
55735--55762	6	4.7	6	100	0	56	32	17	0	50	1.47
55907--55953	2	23.5	2	95	0	85	0	46	2	51	1.13
60607--60661	2	27.5	2	96	0	101	49	0	1	49	1.11
61438--61470	2	16.5	2	100	0	66	48	0	0	51	1.00
61446--61575	59	2.2	58	86	8	183	48	3	7	40	1.50
62020--62047	3	9.3	3	100	0	56	67	0	0	32	0.91
62266--62294	1	29.0	1	100	0	58	0	100	0	0	0.00
63535--63575	2	20.5	2	94	0	73	48	0	2	48	1.14
67403--67438	5	7.2	5	93	0	63	16	2	38	41	1.63
67503--67537	5	7.0	5	87	12	54	20	40	0	40	1.52
72198--72296	49	2.0	49	98	0	189	36	12	21	30	1.90
76002--76313	155	2.0	154	97	0	588	26	21	19	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
76544--77758	405	3.0	405	97	0	2263	27	14	21	36	1.93
82269--82339	34	2.1	34	89	0	106	25	14	16	43	1.86
84668--84700	5	6.6	5	92	0	57	3	0	39	57	1.14
91414--91454	2	21.0	2	85	5	57	48	4	0	46	1.23
92844--92877	3	11.0	3	87	6	50	35	2	0	61	1.11
93375--93405	2	15.5	2	100	0	62	51	0	0	48	1.00
94818--94857	2	21.0	2	80	19	50	52	0	2	45	1.14
94818--94857	7	5.9	7	91	2	64	52	0	2	45	1.14
99795--99834	2	19.5	2	84	5	53	45	5	2	47	1.38
100707--100739	11	3.1	11	86	4	50	90	0	9	0	0.44
104703--104735	3	11.0	3	100	0	66	33	33	0	33	1.58
105583--105610	2	14.0	2	100	0	56	50	0	0	50	1.00
113770--113795	2	13.0	2	100	0	52	50	0	0	50	1.00
119225--119249	2	12.5	2	100	0	50	0	0	48	52	1.00
120463--120490	3	9.3	3	100	0	56	32	0	0	67	0.91
124001--124033	2	16.5	2	93	0	57	45	0	3	51	1.16
136016--136065	25	2.0	25	96	0	91	26	28	6	40	1.79
141751--141822	36	2.0	36	91	0	117	38	19	20	20	1.93
143948--143978	2	15.5	2	100	0	62	48	0	51	0	1.00
144296--144348	27	1.9	28	84	3	72	75	5	15	3	1.13
144861--144906	15	3.1	15	78	12	58	65	0	0	34	0.93
145197--145226	6	5.0	6	95	0	51	0	53	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
145332--145386	21	2.7	21	72	13	51	14	25	7	52	1.67
187388--187415	3	9.3	3	100	0	56	35	0	0	64	0.94
188725--188761	2	18.5	2	94	0	65	45	0	2	51	1.15
188964--188998	5	7.0	5	100	0	70	40	0	0	60	0.97
192912--192944	2	16.5	2	93	0	57	48	0	3	48	1.17
193267--193294	2	14.0	2	100	0	56	50	0	0	50	1.00
193482--193529	3	15.7	3	86	4	69	66	4	0	29	1.10
194641--194678	2	19.5	2	94	5	69	47	0	0	52	1.00
202646--202671	2	13.0	2	100	0	52	0	50	0	50	1.00
214703--214738	2	18.0	2	100	0	72	50	0	0	50	1.00
216678--216720	13	2.9	15	80	19	54	67	0	0	32	0.91
219494--219526	6	5.5	6	100	0	66	18	0	51	30	1.46
221614--221640	11	2.5	11	100	0	54	7	0	0	92	0.38
225314--225376	31	2.0	32	93	3	110	31	11	4	52	1.58
227553--227589	2	18.5	2	100	0	74	51	0	0	48	1.00
228581--228698	12	9.5	12	66	27	52	56	0	1	41	1.09
228642--228698	10	5.6	10	78	16	55	59	0	1	38	1.08
232994--233030	14	2.6	14	91	0	56	37	18	8	35	1.81
236914--236971	25	2.4	25	86	11	77	63	0	0	36	0.94
243127--243209	40	2.1	40	100	0	166	33	7	22	36	1.82
250941--250976	18	1.9	19	88	5	56	19	13	5	61	1.52
252533--252584	2	26.0	2	100	0	104	0	50	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
254272--254488	34	6.4	34	85	2	276	25	7	26	40	1.82
254272--254488	102	2.1	101	91	1	353	25	7	26	40	1.82
254793--254855	19	3.3	19	90	0	90	28	17	19	34	1.94
258921--259139	34	6.5	34	85	2	280	25	7	26	40	1.82
258921--259139	102	2.2	101	91	1	357	25	7	26	40	1.82
271241--271266	13	2.0	13	100	0	52	15	0	0	84	0.62
275924--275956	12	2.8	12	90	0	57	60	9	0	30	1.27
278110--278137	2	14.0	2	100	0	56	50	0	0	50	1.00
280134--280166	2	16.5	2	93	0	57	45	3	0	51	1.16
280925--280993	27	2.5	28	81	11	79	49	1	0	49	1.09
280925--280999	28	2.6	28	75	18	75	49	2	0	48	1.15
281070--281141	23	3.2	22	79	16	76	36	0	5	58	1.22
281866--281899	3	11.3	3	100	0	68	67	0	0	32	0.91
307374--307418	23	1.9	23	82	13	56	44	2	4	48	1.35
308331--308361	2	15.5	2	93	0	53	48	3	0	48	1.17
308521--308614	21	4.5	21	72	16	70	52	1	1	45	1.15
311208--311278	30	2.4	30	81	11	83	49	0	4	46	1.21
311568--311598	7	4.4	7	95	0	53	0	41	3	54	1.16
320965--320993	14	2.1	14	100	0	58	34	13	6	44	1.71
323132--323323	99	1.9	99	91	2	314	29	15	24	30	1.96
325473--325510	2	19.5	2	94	5	69	50	0	0	50	1.00
327069--327236	87	1.9	86	93	1	291	13	18	12	55	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
331784--331819	3	12.0	3	100	0	72	66	0	0	33	0.92
337144--337190	24	2.0	24	95	0	85	36	2	17	44	1.60
337305--337331	2	13.5	2	100	0	54	48	0	0	51	1.00
338036--338092	26	2.2	25	81	9	62	8	7	15	68	1.37
345647--345685	3	13.0	3	100	0	78	33	0	0	66	0.92
353631--353690	4	15.0	4	92	0	84	43	0	6	50	1.28
354936--354982	2	23.5	2	100	0	94	48	0	0	51	1.00
355380--355420	21	2.0	21	95	0	73	80	7	12	0	0.90
358130--358173	12	3.8	12	78	6	54	6	9	65	18	1.42
358515--358544	2	15.0	2	100	0	60	0	50	0	50	1.00

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