genome.fa.s6.2.7.7.80.10.50.1000.31.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:  35726063

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   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   

This is table  31  of  109  ( 13028 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)
10052263--10052361	46	2.2	44	87	7	137	42	30	5	22	1.75
10053522--10053556	18	1.9	18	88	11	54	68	0	5	25	1.11
10054439--10054488	19	2.6	21	78	18	63	46	0	2	52	1.12
10061350--10061392	21	2.0	21	81	0	50	39	18	2	39	1.64
10069354--10069551	50	3.8	50	79	4	198	23	29	20	26	1.99
10072033--10072148	61	1.9	58	87	5	169	50	1	5	42	1.34
10072161--10072218	17	3.6	16	76	19	59	56	1	3	37	1.26
10072680--10072760	31	2.6	31	96	0	144	32	11	13	43	1.79
10072702--10072821	31	4.0	30	82	5	127	34	10	15	40	1.82
10074614--10074725	56	2.0	56	98	0	215	18	21	31	28	1.97
10085547--10085618	26	2.8	26	81	8	65	30	13	11	44	1.79
10087263--10087295	11	2.8	12	86	13	50	27	21	0	51	1.48
10093502--10093552	24	2.2	24	77	22	56	33	0	5	60	1.21
10093723--10093762	20	2.0	20	100	0	80	45	15	10	30	1.78
10093713--10093777	34	1.9	33	87	9	96	41	15	9	33	1.79
10093746--10093783	14	2.7	14	91	0	58	36	18	7	36	1.80
10098584--10098630	23	2.0	23	100	0	94	53	4	8	34	1.51
10098947--10098983	7	5.3	7	96	0	65	29	0	10	59	1.31
10103644--10103713	21	3.5	19	77	11	61	44	8	10	37	1.69
10103644--10103713	19	3.5	20	78	5	70	44	8	10	37	1.69
10106058--10106253	97	2.0	98	93	1	340	27	9	25	37	1.87
10108770--10108816	23	2.0	23	92	8	78	59	0	2	38	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10108841--10108867	6	4.5	6	100	0	54	55	29	14	0	1.40
10113315--10113340	5	5.2	5	100	0	52	23	19	19	38	1.93
10119426--10119476	20	2.5	20	87	6	68	3	23	5	66	1.30
10119446--10119480	5	7.0	5	86	0	52	2	20	2	74	1.08
10119442--10119480	20	2.0	20	100	0	78	5	20	5	69	1.28
10123059--10123184	60	2.1	60	100	0	252	46	0	38	15	1.46
10130666--10130750	44	1.9	45	92	2	145	51	7	8	32	1.59
10138284--10138354	36	2.0	36	97	0	133	22	19	19	38	1.94
10153915--10154264	44	8.1	43	70	14	177	28	22	20	29	1.98
10159402--10159463	31	2.0	31	100	0	124	29	19	6	45	1.75
10161918--10162293	193	1.9	193	95	0	680	23	23	15	38	1.93
10166285--10166321	18	2.1	18	100	0	74	35	0	16	48	1.46
10166435--10166522	46	1.9	46	81	4	106	59	9	3	28	1.44
10166902--10166941	16	2.5	17	76	15	50	62	10	5	22	1.46
10169420--10169472	25	2.2	25	83	6	65	26	0	1	71	0.96
10172654--10172706	11	4.6	11	76	15	54	28	5	5	60	1.42
10173225--10173250	13	2.0	13	100	0	52	38	30	7	23	1.83
10176358--10176484	3	41.7	3	69	14	73	24	5	2	67	1.24
10176549--10176582	13	2.7	12	90	9	50	23	5	0	70	1.09
10176544--10176586	16	2.6	17	79	20	56	27	4	0	67	1.10
10181565--10181589	12	2.1	12	100	0	50	48	8	16	28	1.74
10181913--10181955	22	2.0	22	95	0	77	16	23	16	44	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10181914--10181968	22	2.5	22	87	0	74	18	23	16	41	1.89
10185253--10185295	19	2.3	19	80	8	52	39	9	16	34	1.80
10194779--10194853	31	2.5	31	88	2	116	24	16	18	41	1.90
10198525--10198561	17	2.2	16	90	4	56	72	5	21	0	1.04
10199484--10199535	3	17.3	3	100	0	104	32	0	0	67	0.91
10204148--10204216	24	2.9	23	85	10	86	84	0	14	1	0.70
10204148--10204214	34	2.0	34	87	0	98	83	0	14	1	0.72
10204149--10204217	6	12.0	6	75	14	65	82	0	15	1	0.74
10204148--10204216	15	4.3	15	80	10	75	84	0	14	1	0.70
10204484--10204682	97	2.0	98	84	3	258	26	16	9	47	1.77
10205356--10205391	16	2.3	16	95	4	65	38	22	5	33	1.77
10205602--10206357	46	16.5	46	89	1	1086	28	16	25	29	1.97
10207124--10207165	20	2.1	20	90	0	66	19	42	21	16	1.89
10207199--10207237	8	4.8	8	87	6	60	74	7	17	0	1.05
10208169--10208220	3	17.3	3	91	0	86	30	1	0	67	1.02
10210213--10210237	13	1.9	13	100	0	50	36	8	24	32	1.84
10216932--10216981	25	2.0	25	84	7	66	38	8	8	46	1.63
10219741--10219837	30	3.2	30	91	0	158	14	30	28	25	1.95
10220311--10220349	17	2.4	17	86	4	53	53	2	23	20	1.57
10223079--10223138	31	2.0	30	90	3	93	10	31	5	53	1.56
10226261--10226551	26	11.3	26	68	10	123	27	22	15	34	1.94
10226262--10226558	52	5.8	52	74	4	242	27	22	14	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10226592--10226679	22	4.0	23	69	15	69	20	35	19	25	1.96
10231786--10231814	1	29.0	1	100	0	58	100	0	0	0	0.00
10232829--10232873	22	2.0	22	87	8	65	37	6	11	44	1.66
10233187--10233327	71	2.0	71	87	2	203	34	17	18	30	1.94
10237027--10237080	18	2.8	18	83	13	56	64	1	0	33	1.04
10237052--10237108	10	6.0	9	76	17	53	66	1	0	31	1.02
10241486--10241579	39	2.4	38	87	1	125	36	3	8	52	1.48
10247979--10248009	16	1.9	16	93	0	53	38	9	3	48	1.52
10253596--10253652	24	2.4	24	78	0	69	36	14	21	28	1.92
10253952--10254108	50	3.2	50	71	1	154	27	22	22	27	1.99
10253952--10254154	99	2.0	100	92	0	336	29	20	21	28	1.98
10253975--10254154	50	3.6	50	73	1	182	30	19	20	29	1.97
10253952--10254216	100	2.7	99	86	0	350	27	19	23	29	1.98
10254230--10255265	130	8.0	130	92	0	1689	31	22	20	25	1.98
10254243--10255186	44	21.8	45	72	11	557	31	22	20	25	1.98
10256625--10256654	14	2.1	14	93	0	51	43	16	0	40	1.48
10256694--10256753	22	2.8	22	80	7	70	40	8	1	50	1.43
10265024--10265142	46	2.6	46	89	0	166	30	21	19	29	1.97
10264890--10265291	221	1.8	221	90	0	651	31	18	20	29	1.96
10265310--10265460	50	3.0	50	71	7	126	28	23	25	23	1.99
10277638--10277808	27	6.3	27	83	2	193	45	16	14	23	1.85
10277638--10277808	81	2.1	82	85	4	231	45	16	14	23	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10282400--10282433	17	2.0	17	100	0	68	23	17	35	23	1.95
10285011--10285078	27	2.5	27	83	4	75	42	11	16	29	1.83
10285076--10285227	27	5.6	27	84	1	189	44	19	17	19	1.87
10285033--10285117	43	2.0	43	85	0	116	45	12	18	22	1.83
10285006--10285148	70	2.0	70	82	2	171	44	14	17	23	1.85
10285076--10285227	81	1.9	81	86	5	218	44	19	17	19	1.87
10297690--10297755	6	10.0	6	77	18	51	77	6	3	13	1.08
10297690--10297763	27	2.7	26	83	8	85	77	5	4	13	1.10
10297690--10297743	15	3.9	14	76	16	58	77	5	1	14	1.03
10297708--10297748	21	2.0	21	90	0	64	78	4	2	14	1.03
10299525--10299597	4	19.8	4	83	13	79	73	0	1	24	0.90
10299534--10299576	3	13.7	3	83	9	50	72	0	2	25	0.97
10299525--10299597	23	3.1	24	82	11	89	73	0	1	24	0.90
10304225--10304312	30	2.9	30	79	0	104	13	27	36	22	1.92
10306852--10306895	14	3.1	15	80	12	56	45	6	2	45	1.42
10306848--10306909	28	2.2	28	77	5	72	38	8	1	51	1.41
10310022--10310059	20	1.9	20	94	0	67	23	28	23	23	1.99
10310342--10310381	13	2.9	13	88	7	53	7	12	20	60	1.56
10315603--10315655	26	2.0	26	85	7	72	30	9	13	47	1.74
10321135--10321189	20	2.7	20	91	2	83	12	29	23	34	1.92
10321081--10321198	21	5.7	20	74	6	67	14	27	26	31	1.95
10322972--10322996	10	2.5	10	100	0	50	68	0	0	32	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10323204--10323231	12	2.3	12	100	0	56	0	7	0	92	0.37
10327007--10327036	9	3.4	9	90	9	53	0	10	0	90	0.47
10327007--10327039	8	4.1	8	92	7	50	0	9	0	90	0.44
10330483--10330526	23	1.9	23	85	0	61	38	0	6	54	1.27
10333094--10333131	20	2.0	20	89	5	60	55	15	10	18	1.68
10335442--10335496	20	2.8	20	82	0	65	32	7	10	49	1.65
10338090--10338122	4	8.2	4	100	0	66	0	24	0	75	0.80
10352661--10353165	97	5.0	99	79	13	564	26	16	9	48	1.75
10352661--10353168	205	2.5	205	95	1	905	26	16	9	48	1.76
10354061--10354794	46	16.0	46	90	0	1049	26	15	27	30	1.96

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   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109