genome.fa.s1.2.7.7.80.10.50.1000.1.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: chr1
Parameters: 2 7 7 80 10 50 1000
Length:  37323695

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   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   

This is table  1  of  93  ( 11113 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)
6433--6583	7	21.9	7	91	2	234	40	45	0	14	1.45
10549--10649	51	2.0	51	86	0	139	40	27	14	16	1.88
11279--11303	7	3.6	7	100	0	50	32	32	12	24	1.91
11644--11932	7	42.4	7	74	12	120	40	43	5	11	1.62
11664--11790	33	3.8	33	87	5	166	44	43	2	10	1.51
11742--11906	20	8.1	21	67	14	78	35	45	7	11	1.68
11868--11920	27	2.0	27	88	7	81	41	47	3	7	1.50
11658--11932	20	13.5	20	69	15	66	40	43	5	11	1.62
11658--11932	41	6.8	40	73	10	112	40	43	5	11	1.62
31472--31580	34	3.2	34	62	23	84	27	14	11	46	1.78
31461--31596	68	2.0	68	100	0	272	25	16	11	47	1.80
38049--38279	115	2.0	116	89	0	356	27	20	17	34	1.95
41717--41770	20	2.7	21	76	23	62	57	1	0	40	1.09
45771--45795	2	12.5	2	100	0	50	52	0	0	48	1.00
47008--47070	27	2.3	27	86	5	74	47	25	15	11	1.79
47018--47071	27	2.0	27	96	0	99	40	27	18	12	1.87
52151--52248	38	2.6	38	95	0	169	21	30	19	28	1.97
52531--52660	48	2.7	48	89	0	197	26	11	23	38	1.89
59597--59644	24	2.0	24	87	0	69	35	12	47	4	1.60
64501--64548	2	24.0	2	100	0	96	50	0	0	50	1.00
77525--77592	5	13.2	5	76	6	64	70	0	4	25	1.05
77679--77703	11	2.3	11	100	0	50	84	0	0	16	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
77770--77808	19	2.0	19	85	14	53	56	0	0	43	0.99
77765--77823	26	2.2	28	84	6	86	54	0	0	45	0.99
77923--77958	17	2.1	17	89	0	54	55	2	2	38	1.29
78789--78895	45	2.4	45	93	0	178	26	20	18	34	1.96
86306--86338	2	17.0	2	93	6	59	0	51	0	48	1.00
101676--101702	13	2.1	13	100	0	54	70	7	0	22	1.12
101883--101915	16	1.9	18	88	11	52	54	3	0	42	1.15
102161--102222	31	2.0	31	93	0	106	41	25	16	16	1.88
103103--103148	23	2.0	23	95	0	83	34	8	15	41	1.78
108279--108304	4	6.5	4	100	0	52	76	0	23	0	0.78
110502--110526	4	6.2	4	100	0	50	0	24	52	24	1.48
135285--135375	46	2.0	46	97	0	173	39	37	7	15	1.76
136317--136359	7	6.3	7	94	2	61	30	0	37	32	1.58
158167--158194	2	14.0	2	100	0	56	50	0	0	50	1.00
158195--158219	13	1.9	13	100	0	50	36	0	32	32	1.58
158314--158340	3	9.0	3	100	0	54	33	0	33	33	1.58
158469--158496	2	14.0	2	100	0	56	50	0	50	0	1.00
161138--161192	25	2.2	24	81	12	67	63	0	36	0	0.95
161146--161355	61	3.5	59	70	21	175	56	5	38	0	1.22
161109--161371	121	2.1	123	89	4	404	57	5	37	0	1.22
161264--161304	21	2.0	21	85	9	57	65	0	34	0	0.93
161259--161314	25	2.3	25	81	12	71	64	0	35	0	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
161272--161313	21	2.0	21	81	9	50	69	0	30	0	0.89
161334--161384	17	3.0	17	78	18	61	74	0	25	0	0.82
164554--164602	2	24.5	2	95	0	89	46	0	2	51	1.12
166356--166383	2	14.0	2	100	0	56	50	0	0	50	1.00
179583--179776	98	2.0	98	93	0	334	44	18	16	20	1.87
187420--187458	13	2.9	14	80	7	53	38	0	0	61	0.96
188274--188323	20	2.4	21	81	18	61	48	2	2	48	1.24
188285--188323	20	2.0	20	90	9	64	46	0	2	51	1.14
188361--188445	23	3.5	22	70	23	73	60	2	1	35	1.18
188392--188463	16	4.4	16	68	16	58	61	1	2	33	1.19
188364--188462	50	2.0	48	96	3	180	59	2	2	35	1.20
189719--189756	15	2.5	15	83	8	51	44	10	0	44	1.38
195222--195272	8	6.8	8	80	13	54	70	0	0	29	0.87
217153--217184	5	6.4	5	96	0	55	15	81	0	3	0.82
221152--221497	69	5.0	69	86	1	417	30	19	24	25	1.98
221948--221996	25	2.0	25	83	0	62	81	4	12	2	0.91
230186--230231	23	2.1	22	84	11	60	41	2	0	56	1.11
238511--238545	12	2.9	12	91	0	52	25	2	54	17	1.57
238508--238548	18	2.3	18	87	8	57	29	2	53	14	1.54
265357--265395	16	2.4	16	82	0	51	20	33	0	46	1.51
266097--266148	24	2.2	24	100	0	104	38	15	19	26	1.91
283880--283936	29	2.0	29	89	0	87	52	14	3	29	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
287797--287821	3	8.3	3	100	0	50	0	32	0	68	0.90
292822--292853	17	1.9	16	93	6	55	0	15	0	84	0.63
300729--300766	2	19.0	2	100	0	76	50	0	0	50	1.00
322190--322224	2	18.0	2	88	5	54	51	2	0	45	1.16
323593--323633	16	2.6	16	92	0	64	26	7	17	48	1.73
325400--325437	15	2.5	15	86	0	58	2	21	23	52	1.59
333400--333434	2	17.5	2	87	0	52	0	45	5	48	1.26
339178--339241	26	2.5	26	86	0	92	26	12	10	50	1.73
354519--354557	20	2.0	20	84	0	51	46	20	12	20	1.83
361312--361342	2	15.5	2	93	0	53	51	0	45	3	1.17
362625--362710	17	4.9	17	69	8	57	47	1	0	51	1.08
362666--362716	17	2.7	19	74	20	54	50	0	1	47	1.12
362788--362826	10	3.8	10	86	3	51	46	0	0	53	1.00
381906--381944	14	2.8	14	80	11	53	30	12	20	35	1.90
387557--387638	6	13.7	6	86	0	119	47	1	30	20	1.58
389590--389615	12	2.2	12	100	0	52	50	7	23	19	1.73
390087--390139	25	2.1	25	85	0	70	33	15	15	35	1.88
390502--390537	2	18.0	2	94	0	63	47	0	2	50	1.15
395879--396047	55	3.1	54	80	3	178	14	14	30	41	1.85
396086--396165	23	3.5	23	85	0	106	25	20	30	25	1.99
398643--398700	31	2.0	28	83	10	71	53	5	12	29	1.59
398643--398700	14	3.9	15	76	14	59	53	5	12	29	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
400171--400355	31	6.0	31	74	9	83	40	20	18	20	1.92
400171--400473	62	4.9	62	73	10	228	40	19	18	21	1.91
400204--400478	93	3.0	93	87	1	381	40	18	19	21	1.91
400210--400473	31	8.5	31	73	12	170	40	18	19	21	1.92
400838--401134	156	1.9	156	86	1	425	27	18	18	34	1.95
400828--401181	156	2.3	156	82	2	424	30	18	16	33	1.94
402808--402959	31	4.9	31	83	6	166	38	21	15	25	1.92
403438--403556	53	2.3	52	89	1	175	26	29	20	24	1.99
403547--403628	24	3.5	23	69	15	69	18	30	23	28	1.97
403468--403629	47	3.2	53	79	8	133	24	30	19	25	1.98
403544--403941	47	8.5	47	83	1	449	21	33	17	27	1.96
403544--403937	187	2.1	188	85	0	538	21	33	17	27	1.96
403548--403941	94	4.2	94	85	0	502	21	32	17	27	1.96
410789--410888	50	2.0	50	98	0	191	45	12	23	20	1.84
420243--420287	12	3.8	12	84	0	63	0	15	0	84	0.62
420215--420278	27	2.2	29	86	13	89	1	18	0	79	0.81
420245--420290	22	2.1	21	88	11	67	0	17	0	82	0.67
420241--420289	24	2.0	24	96	0	89	0	18	0	81	0.69
421687--421726	21	1.9	21	89	0	62	42	10	7	40	1.67
422275--422317	21	2.0	21	86	13	61	53	0	6	39	1.28
422354--422419	22	2.7	24	78	15	73	51	0	0	48	1.00
422356--422417	8	7.6	8	72	16	56	53	0	0	46	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
456715--456765	23	2.3	23	79	3	59	15	27	3	52	1.60
457143--457218	29	2.8	28	78	9	77	46	15	2	35	1.60
457173--457255	26	3.3	25	75	8	78	37	15	9	37	1.81
457196--457263	24	2.6	27	73	15	72	30	13	13	42	1.82
457345--457471	24	5.3	24	78	5	105	27	16	16	39	1.90
457265--457406	69	2.1	69	80	0	158	28	19	16	35	1.94
457369--457619	75	3.4	75	85	6	329	33	14	13	38	1.86
457588--457706	24	5.1	24	72	11	95	21	18	20	39	1.92
457573--457739	68	2.4	69	86	1	228	26	18	18	35	1.94
457661--457713	24	2.2	24	82	0	61	20	15	18	45	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   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93