genome.fa.s8.2.7.7.80.10.50.1000.33.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   

This is table  33  of  190  ( 22705 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)
9481687--9481775	39	2.3	39	90	1	135	37	15	14	32	1.88
9486112--9486183	32	2.2	32	85	0	99	45	2	26	25	1.67
9486196--9486281	39	2.2	39	89	2	138	37	15	15	32	1.88
9493035--9493242	91	2.3	91	89	0	308	45	3	5	45	1.42
9493269--9493577	66	5.2	57	64	20	157	41	2	5	50	1.39
9493258--9493670	120	3.4	120	95	0	729	41	2	5	50	1.39
9493331--9493638	61	5.1	60	66	20	221	41	1	6	49	1.40
9493383--9493434	15	3.6	15	80	12	56	44	0	1	53	1.11
9493632--9493673	15	2.7	16	82	14	52	45	0	2	52	1.13
9493623--9493664	15	2.9	15	82	10	52	47	0	0	52	1.00
9493887--9493956	16	4.4	16	85	0	86	27	31	2	38	1.71
9494410--9494530	64	1.9	64	89	3	190	33	25	13	28	1.93
9495983--9496041	18	3.2	17	77	20	57	40	0	5	54	1.23
9498160--9498212	15	3.5	15	76	20	56	26	7	1	64	1.31
9499838--9499872	18	1.9	18	94	0	61	57	0	0	42	0.99
9500999--9501085	43	2.0	43	97	0	165	36	16	20	26	1.93
9501135--9501208	38	1.9	38	91	5	123	39	20	12	28	1.88
9507345--9507446	43	2.4	43	85	3	145	39	20	15	24	1.92
9509153--9509195	20	2.2	19	87	4	59	53	6	4	34	1.49
9511162--9511394	44	5.1	43	71	17	164	27	22	18	31	1.97
9511089--9511394	142	2.2	142	96	0	567	27	20	17	33	1.96
9523888--9523937	19	2.6	18	81	15	55	52	6	6	36	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9528441--9528499	31	1.9	30	86	3	82	62	8	11	16	1.52
9529587--9529626	2	20.0	2	100	0	80	50	0	0	50	1.00
9533535--9533564	11	2.7	11	100	0	60	46	0	6	46	1.29
9535141--9535167	11	2.5	11	100	0	54	22	7	18	51	1.70
9537150--9537183	16	2.0	18	88	11	54	35	2	5	55	1.39
9537562--9537665	3	34.7	3	90	0	163	34	1	0	62	1.13
9538350--9538647	110	2.7	109	88	5	424	31	13	20	34	1.91
9539307--9539451	47	3.1	47	69	16	131	44	2	4	48	1.35
9539288--9539495	91	2.3	91	93	0	344	46	3	4	46	1.39
9539410--9539470	28	2.2	28	85	5	81	45	0	3	50	1.17
9539328--9539470	44	3.2	43	69	20	121	46	2	3	48	1.31
9540812--9540853	15	2.7	16	82	14	52	45	0	2	52	1.13
9540803--9540844	15	2.9	15	82	10	52	47	0	0	52	1.00
9541061--9541098	16	2.4	16	86	0	58	28	34	2	34	1.71
9547853--9547953	45	2.2	45	87	0	139	37	15	20	25	1.93
9547869--9547955	45	1.9	45	92	0	147	35	12	21	29	1.91
9557051--9557082	7	4.4	7	96	4	55	12	0	0	87	0.54
9557278--9557320	18	2.3	19	92	4	70	69	4	2	23	1.18
9559484--9559514	15	2.0	16	93	6	55	0	51	41	6	1.27
9559768--9559812	22	2.0	23	82	4	56	40	4	13	42	1.64
9561583--9561609	6	4.5	6	100	0	54	14	0	33	51	1.43
9566486--9566514	14	2.0	15	93	6	51	24	62	0	13	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9569667--9569713	23	2.0	23	100	0	94	31	17	25	25	1.97
9570186--9570226	17	2.4	17	83	0	55	70	7	4	17	1.28
9576034--9576073	20	2.1	19	85	4	53	42	0	0	57	0.98
9584206--9584336	67	2.0	67	83	1	165	36	19	17	25	1.94
9593556--9594167	44	13.6	44	72	4	461	27	24	18	30	1.98
9593529--9594198	181	3.7	181	92	1	1035	26	24	18	29	1.98
9593528--9594197	270	2.5	268	87	2	957	26	24	18	30	1.98
9593526--9594249	44	16.1	45	69	11	198	26	24	18	29	1.98
9593528--9594198	89	7.5	89	89	2	921	26	24	18	29	1.98
9600854--9600895	19	2.3	18	88	8	66	64	2	2	30	1.19
9608560--9608600	21	2.0	21	85	0	55	31	9	4	53	1.55
9611910--9611973	29	2.2	29	94	0	110	54	14	9	21	1.67
9617671--9617779	53	1.9	53	83	10	137	22	24	22	30	1.99
9619026--9619072	24	2.0	24	83	8	60	17	31	0	51	1.46
9622253--9622294	21	2.0	21	85	0	57	54	11	7	26	1.62
9622173--9622341	82	2.1	79	87	6	241	40	13	10	35	1.79
9622995--9623033	18	2.2	18	90	0	60	30	2	7	58	1.39
9628866--9628896	9	3.4	9	90	0	53	25	12	22	38	1.90
9636831--9636870	19	2.0	20	95	4	73	30	10	25	35	1.88
9637976--9638122	24	6.0	25	78	10	101	23	17	26	32	1.96
9638017--9638171	24	6.4	24	74	11	127	23	15	25	34	1.94
9638037--9638187	49	3.1	49	81	2	187	23	14	27	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9638904--9638945	9	4.7	9	79	8	50	45	23	9	21	1.81
9638945--9639016	37	1.9	37	88	0	108	45	13	2	37	1.59
9639143--9639259	39	3.0	39	96	1	209	18	2	28	50	1.60
9639240--9639264	13	1.9	13	100	0	50	12	0	48	40	1.40
9640279--9640312	12	2.7	13	95	4	61	44	0	0	55	0.99
9640895--9640919	12	2.1	12	100	0	50	60	0	8	32	1.26
9644237--9644369	22	6.0	22	75	6	108	39	19	21	19	1.92
9644237--9644367	44	3.0	43	75	3	127	40	19	21	19	1.92
9647904--9647972	33	2.1	34	91	2	113	33	14	7	44	1.73
9648115--9648144	14	2.2	13	94	5	51	46	0	6	46	1.29
9649768--9649816	18	2.7	18	81	6	55	48	6	0	44	1.27
9654012--9654048	2	18.5	2	100	0	74	0	0	48	51	1.00
9654775--9655001	41	5.5	41	92	1	357	26	21	29	22	1.99
9657132--9657160	12	2.4	12	100	0	58	31	27	24	17	1.97
9660766--9660802	2	18.5	2	100	0	74	0	0	48	51	1.00
9661529--9661796	41	6.5	41	92	0	421	26	22	28	22	1.99
9661529--9661796	123	2.2	123	94	0	464	26	22	28	22	1.99
9664541--9664585	19	2.4	18	82	10	56	26	4	0	68	1.08
9664611--9664659	18	2.7	18	82	14	57	22	10	2	65	1.34
9667028--9667112	18	4.7	18	75	18	61	57	1	2	38	1.19
9667525--9667562	20	2.0	20	90	10	62	31	0	10	57	1.32
9682574--9682613	2	20.0	2	100	0	80	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9683889--9683985	49	2.0	49	83	2	124	21	14	21	42	1.88
9690533--9690558	11	2.4	11	100	0	52	69	15	0	15	1.20
9700821--9700902	24	3.4	24	75	14	78	28	23	17	31	1.96
9704153--9704218	32	2.1	32	86	10	93	63	1	0	34	1.04
9711499--9711562	32	2.0	32	100	0	128	21	37	6	34	1.79
9713736--9713775	16	2.5	16	91	0	62	47	2	7	42	1.45
9713989--9714022	16	2.1	16	100	0	68	70	11	0	17	1.16
9715223--9715268	24	1.9	24	86	0	65	15	43	2	39	1.59
9715291--9715320	14	2.1	14	93	0	51	10	43	10	36	1.72
9715747--9715804	27	2.1	27	90	6	91	36	29	6	27	1.83
9717145--9717187	17	2.7	15	83	13	59	23	11	9	55	1.64
9718098--9718128	15	2.1	15	93	0	53	35	35	3	25	1.72
9718249--9718325	20	3.8	20	75	13	77	58	2	3	35	1.30
9718412--9718451	20	2.0	20	90	0	62	50	12	10	27	1.72
9718435--9718472	14	2.7	14	87	0	58	39	18	7	34	1.80
9718631--9718670	6	6.7	6	100	0	80	15	0	0	85	0.61
9724081--9724143	31	2.0	31	100	0	126	38	6	30	25	1.81
9726369--9726393	10	2.5	10	100	0	50	60	0	20	20	1.37
9728461--9728502	13	3.5	13	75	18	54	38	0	11	50	1.40
9728454--9728502	23	2.2	22	96	3	89	38	0	10	51	1.36
9731215--9731253	19	2.1	19	85	0	51	56	0	2	41	1.13
9731202--9731263	27	2.3	25	79	20	63	56	0	1	41	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9733017--9733087	30	2.4	30	95	0	124	19	30	29	19	1.97
9734244--9734356	25	4.5	25	77	8	95	31	20	21	26	1.98
9736652--9736757	18	6.1	18	67	23	66	33	0	0	65	1.06
9736674--9736778	40	2.6	40	86	3	158	34	1	0	62	1.12
9736714--9736777	29	2.1	30	86	11	87	34	3	1	60	1.22
9736752--9736791	21	1.9	21	84	0	53	35	5	0	60	1.19
9739744--9739811	34	2.0	34	97	0	127	26	4	32	36	1.76
9742613--9742682	31	2.3	31	76	0	77	47	8	1	42	1.43
9748265--9748397	40	3.3	39	84	5	160	33	23	22	21	1.98
9748282--9748416	40	3.4	38	82	8	139	37	24	20	17	1.94

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   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190