genome.fa.s13.2.7.7.80.10.50.1000.106.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   191   192   
          193   194   195   196   197   198   199   

This is table  106  of  199  ( 23770 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)
32262170--32262215	19	2.4	19	85	7	58	47	8	19	23	1.77
32262658--32262693	17	2.1	17	89	0	54	44	19	13	22	1.86
32264380--32264432	3	17.3	3	84	11	72	66	0	3	30	1.10
32270396--32270456	27	2.3	27	97	0	113	40	4	13	40	1.65
32281525--32281572	19	2.6	19	86	3	71	37	0	14	47	1.44
32290086--32290345	135	1.9	135	87	0	376	36	12	19	31	1.89
32291442--32291509	33	2.1	32	86	5	93	39	10	23	26	1.87
32294902--32294926	12	2.1	12	100	0	50	8	8	0	84	0.79
32296477--32296562	43	2.0	43	93	2	147	38	15	5	40	1.71
32298193--32298273	42	1.9	42	82	0	99	16	33	23	27	1.95
32316800--32316835	13	2.8	13	100	0	72	13	8	5	72	1.27
32350624--32350680	16	3.6	16	95	0	87	29	0	36	33	1.58
32350915--32351049	15	8.9	15	65	24	61	50	3	2	43	1.32
32350975--32351065	44	2.1	43	81	6	103	53	3	2	40	1.29
32351134--32351169	17	2.2	16	86	13	56	47	0	5	47	1.25
32351138--32351183	17	2.5	20	86	13	71	45	2	6	45	1.41
32351190--32351384	93	2.1	92	88	4	286	47	4	4	44	1.41
32353077--32353107	15	2.1	15	100	0	62	45	0	19	35	1.51
32358470--32358514	23	2.0	23	86	0	63	57	0	6	35	1.25
32359062--32359117	29	2.0	29	82	3	69	26	0	5	67	1.11
32359142--32359178	18	2.1	18	89	0	56	32	8	0	59	1.27
32361121--32361168	10	4.4	11	82	14	55	77	0	10	12	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32362345--32362577	85	2.7	85	87	0	295	33	20	12	33	1.89
32369770--32369812	14	3.1	14	86	0	59	60	16	4	18	1.52
32376107--32376154	19	2.5	19	93	0	78	16	20	41	20	1.90
32376160--32376237	22	3.6	22	86	3	106	23	25	38	12	1.90
32386750--32386804	19	2.9	19	76	15	60	40	3	16	40	1.66
32391404--32391447	18	2.4	18	80	3	52	50	13	13	22	1.77
32394138--32394213	18	4.2	18	75	15	77	65	3	0	30	1.10
32395417--32395487	37	1.9	37	94	0	124	46	14	4	35	1.64
32401783--32401891	39	2.8	39	92	1	175	17	3	28	50	1.63
32408027--32408088	31	1.9	33	90	6	101	38	12	16	32	1.86
32408040--32408116	31	2.5	31	81	6	86	48	15	10	25	1.77
32413243--32413313	34	2.0	38	83	10	96	49	7	14	29	1.69
32416082--32416112	3	10.3	3	100	0	62	32	0	0	67	0.91
32416520--32416564	16	2.8	16	83	6	56	37	4	0	57	1.19
32417260--32417515	125	2.1	124	86	5	356	30	16	22	31	1.95
32419718--32419843	28	4.5	28	93	1	207	31	0	19	47	1.55
32421952--32421985	15	2.3	15	90	5	52	67	5	0	26	1.13
32422084--32422141	30	2.0	30	93	3	100	58	1	0	39	1.08
32422182--32422223	22	1.9	22	90	0	66	33	0	33	33	1.58
32422195--32422253	30	2.0	30	89	0	91	35	0	33	30	1.58
32422173--32422275	52	2.0	51	84	5	136	34	0	32	33	1.58
32422225--32422294	22	3.2	22	91	0	113	40	0	28	31	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32428380--32428404	9	2.8	9	100	0	50	44	24	12	20	1.85
32431310--32431344	16	2.1	17	89	10	54	77	0	11	11	1.00
32432548--32432608	8	8.2	8	75	12	51	68	0	0	31	0.89
32432530--32432629	37	2.7	36	82	13	107	65	0	1	34	1.00
32432548--32432609	21	2.9	21	85	2	70	67	0	0	32	0.91
32432548--32432608	15	4.1	15	79	8	63	68	0	0	31	0.89
32433308--32433350	21	2.1	21	87	8	63	65	0	11	23	1.25
32441639--32441835	98	2.0	98	95	0	358	27	25	10	36	1.89
32446409--32446494	45	1.9	45	92	0	145	43	11	20	24	1.85
32447867--32447894	4	7.0	4	100	0	56	50	0	0	50	1.00
32448283--32448335	27	2.0	26	96	3	97	41	22	3	32	1.72
32449675--32449699	6	4.2	6	100	0	50	0	16	0	84	0.63
32451998--32452051	26	2.1	26	100	0	108	37	37	7	18	1.79
32469884--32469917	12	2.8	12	86	0	50	5	8	11	73	1.24
32472325--32472483	35	4.5	35	72	6	115	27	25	18	28	1.98
32472334--32472466	70	1.9	70	84	0	176	30	22	15	30	1.95
32472324--32472483	70	2.3	70	75	0	167	27	25	18	28	1.98
32478095--32478161	28	2.3	29	90	7	102	0	28	1	70	0.96
32478095--32478162	7	9.6	7	72	25	54	0	27	1	70	0.96
32478095--32478165	14	5.0	14	80	14	83	0	28	1	70	0.96
32494548--32494588	19	2.2	19	100	0	82	39	0	21	39	1.54
32504352--32504400	21	2.3	21	92	0	89	42	24	8	24	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32508658--32508852	89	2.2	87	79	6	205	31	5	21	41	1.76
32510808--32510832	12	2.1	12	100	0	50	68	0	32	0	0.90
32511035--32511138	32	3.5	28	89	6	102	25	2	19	51	1.60
32511048--32511146	32	3.1	32	94	0	171	28	3	17	51	1.60
32512378--32512414	16	2.4	16	91	8	60	45	0	0	54	1.00
32512495--32512540	19	2.3	20	88	7	76	54	17	4	23	1.61
32512528--32512554	14	1.9	14	100	0	54	44	22	0	33	1.53
32515250--32515302	25	2.1	25	83	13	65	41	0	1	56	1.10
32520599--32520668	23	3.0	23	77	8	79	38	12	14	34	1.84
32542277--32542550	46	6.3	46	74	12	213	29	20	21	28	1.98
32542370--32542473	41	2.6	40	79	11	124	25	16	25	32	1.96
32542370--32542469	39	2.5	39	79	12	114	26	17	23	34	1.96
32542273--32542633	170	2.1	173	90	3	559	29	20	21	27	1.98
32544111--32544144	3	11.3	3	100	0	68	32	0	0	67	0.91
32550078--32550135	24	2.5	24	82	15	70	43	1	3	51	1.28
32550236--32550289	7	7.9	7	80	19	53	44	0	0	55	0.99
32552023--32552059	17	2.2	17	90	0	56	5	21	0	72	1.04
32552694--32552733	21	1.9	21	84	0	53	35	7	2	55	1.42
32552715--32552954	3	80.0	3	74	4	189	33	5	1	60	1.28
32553066--32553113	17	2.8	17	75	12	53	16	6	2	75	1.11
32558314--32558351	19	2.0	19	100	0	76	42	21	10	26	1.85
32565234--32565652	44	9.5	44	71	12	207	30	18	24	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32565234--32565644	178	2.3	176	80	7	456	30	18	24	27	1.98
32565270--32565644	89	4.2	88	74	9	280	29	18	24	27	1.98
32567060--32567099	21	1.9	21	84	0	53	35	7	2	55	1.42
32567081--32567291	3	71.0	3	72	7	144	32	6	1	59	1.31
32574141--32574239	31	3.1	31	75	8	92	28	2	15	54	1.52
32574141--32574208	34	2.0	33	82	2	82	27	2	11	57	1.49
32574174--32574255	31	2.6	31	80	3	85	25	3	18	52	1.61
32578855--32578906	23	2.3	23	89	0	77	32	19	25	23	1.97
32582101--32582161	31	1.9	32	86	3	88	42	16	9	31	1.81
32583691--32583744	26	2.1	26	92	0	90	24	9	7	59	1.54
32597782--32597980	36	5.4	36	68	10	123	26	20	14	39	1.90
32597739--32597979	75	3.2	75	83	1	295	26	20	13	39	1.89
32597965--32598032	27	2.5	27	97	0	127	23	17	17	41	1.90
32598095--32598219	36	3.4	35	74	10	115	24	18	14	42	1.88
32598053--32598629	75	7.7	76	81	5	487	24	20	14	40	1.90
32598049--32598479	39	11.5	38	68	13	149	24	20	14	40	1.90
32598056--32598635	150	3.9	149	81	2	565	24	21	14	40	1.90
32598245--32598592	39	9.4	36	67	10	153	24	20	14	40	1.89
32598080--32598556	224	2.1	225	82	2	575	24	20	13	40	1.89
32598354--32598639	39	7.6	39	69	7	149	24	20	13	41	1.88
32598673--32598792	23	5.2	23	68	11	68	34	20	10	35	1.87
32598683--32598792	47	2.4	47	83	11	138	31	20	11	36	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32601873--32602066	90	2.1	92	77	7	200	37	19	19	23	1.94
32602272--32602311	13	3.1	13	77	0	53	32	5	27	35	1.79
32604222--32604266	18	2.4	18	85	10	56	66	4	0	28	1.11
32607120--32607249	69	1.9	69	83	0	170	33	15	23	26	1.95
32609574--32609807	43	5.5	43	80	2	220	40	21	14	23	1.90
32611851--32611914	25	2.6	25	94	0	110	51	26	21	0	1.48
32619786--32619813	2	14.0	2	100	0	56	50	0	0	50	1.00
32624336--32624376	19	2.2	19	100	0	82	9	48	0	41	1.36
32631868--32631899	7	4.6	7	100	0	64	62	12	0	25	1.30
32632825--32632863	9	4.3	9	83	0	51	23	38	0	38	1.55

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   191   192   
          193   194   195   196   197   198   199