genome.fa.s4.2.7.7.80.10.50.1000.14.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  14  of  198  ( 23681 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)
4428238--4428283	21	2.2	21	84	7	58	63	0	0	36	0.95
4440580--4440667	26	3.3	26	91	1	140	39	13	12	34	1.83
4440621--4440679	26	2.3	26	82	5	66	35	16	11	35	1.86
4447965--4448022	28	2.1	27	81	9	64	48	0	1	50	1.11
4448164--4448193	15	1.9	16	93	6	53	26	0	0	73	0.84
4449373--4449409	16	2.2	18	85	9	51	29	2	0	67	1.04
4449435--4449479	18	2.3	21	81	11	60	35	0	4	60	1.17
4449595--4449648	23	2.3	23	100	0	108	24	14	16	44	1.85
4456698--4456924	126	1.8	125	84	6	316	33	16	16	33	1.92
4458875--4458944	34	2.1	34	100	0	140	30	25	18	25	1.98
4459059--4459335	44	6.4	44	74	11	241	26	19	23	30	1.98
4459054--4459209	85	1.8	85	84	0	213	26	20	23	29	1.99
4459059--4459341	129	2.2	129	89	0	422	26	19	23	30	1.98
4460485--4460556	27	2.7	27	93	4	85	2	27	2	66	1.19
4463703--4463749	19	2.5	20	86	6	62	42	10	21	25	1.85
4476143--4476224	3	28.0	3	92	4	141	65	1	0	32	1.00
4483773--4483840	2	33.5	2	91	2	109	50	0	2	47	1.16
4486349--4486409	23	2.6	23	84	7	70	49	0	1	49	1.10
4486361--4486409	23	2.1	23	88	7	73	51	0	2	46	1.12
4486640--4486689	20	2.4	21	80	3	66	24	16	20	40	1.91
4491517--4491558	22	1.9	22	100	0	84	38	14	26	21	1.91
4494223--4494263	2	20.0	2	95	5	73	48	2	0	48	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4496225--4496295	27	2.6	26	80	8	79	2	21	4	71	1.15
4500381--4500414	16	2.1	16	88	0	50	35	20	2	41	1.68
4506104--4506146	8	5.2	8	80	5	50	30	2	0	67	1.03
4507512--4507543	2	16.0	2	100	0	64	50	0	0	50	1.00
4517862--4517923	26	2.3	26	80	2	79	43	9	12	33	1.76
4521281--4521355	33	2.2	34	90	2	116	41	14	6	37	1.72
4523130--4523168	18	2.2	18	86	9	53	5	17	5	71	1.23
4525115--4525161	24	1.9	25	95	4	87	46	12	19	21	1.82
4528234--4528304	35	2.0	35	100	0	142	49	19	2	28	1.62
4532466--4532529	29	2.2	30	77	8	69	26	3	7	62	1.38
4542639--4542678	19	2.0	19	85	9	53	70	5	0	25	1.08
4546612--4546796	46	4.0	46	86	1	246	29	23	9	37	1.87
4548021--4548053	17	1.9	17	100	0	66	57	18	0	24	1.40
4548489--4548591	37	2.8	37	88	4	154	31	24	15	29	1.96
4548570--4548869	148	2.0	148	90	2	478	31	26	12	30	1.92
4548910--4548955	2	23.0	2	100	0	92	50	0	0	50	1.00
4549203--4549243	19	2.1	20	86	4	57	31	9	2	56	1.45
4549653--4549682	14	2.1	14	93	0	51	0	16	0	83	0.65
4551932--4551980	22	2.2	23	85	3	64	32	28	14	24	1.94
4557636--4557700	30	2.1	31	85	2	87	50	4	3	41	1.38
4561010--4561036	2	13.5	2	100	0	54	51	0	0	48	1.00
4563221--4563281	31	1.9	33	90	6	99	31	1	4	62	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4564087--4564133	12	3.8	12	78	13	51	27	0	4	68	1.08
4566097--4566180	34	2.4	35	78	7	100	28	27	25	19	1.98
4566257--4566376	40	3.1	40	75	11	142	35	21	20	22	1.96
4566257--4566400	75	1.9	75	88	2	218	33	22	21	22	1.97
4566455--4566527	37	2.0	37	97	0	137	36	23	0	39	1.55
4566466--4566522	17	3.2	17	70	29	55	35	21	0	43	1.52
4573095--4573331	91	2.6	90	82	4	271	27	12	15	45	1.81
4573598--4573650	18	2.9	18	86	8	72	13	32	0	54	1.39
4573596--4573652	9	6.3	9	79	0	60	17	31	0	50	1.46
4575955--4576195	88	2.7	87	79	10	227	27	11	11	49	1.73
4576268--4576295	5	5.6	5	100	0	56	17	0	0	82	0.68
4576278--4576650	90	4.2	90	80	7	372	24	8	16	50	1.73
4575721--4576650	177	5.2	178	71	13	455	26	10	14	48	1.76
4588219--4588243	2	12.5	2	100	0	50	48	0	0	52	1.00
4590560--4590647	44	2.0	44	100	0	176	38	6	15	38	1.75
4590853--4590903	10	5.0	10	78	2	57	11	23	0	64	1.26
4591585--4591609	7	3.6	7	100	0	50	76	0	12	12	1.04
4598154--4598203	22	2.3	22	86	6	66	20	12	10	58	1.62
4601479--4601536	31	1.9	30	82	10	73	60	0	1	37	1.07
4603298--4603350	15	3.4	15	79	12	54	67	0	1	30	1.01
4603312--4603348	17	2.2	17	95	0	65	70	0	2	27	1.01
4605728--4605828	31	3.4	31	68	13	102	21	19	14	43	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4606229--4606392	60	2.7	60	78	6	170	51	12	14	22	1.75
4615642--4615968	164	2.0	164	88	3	489	32	12	19	35	1.90
4621851--4621883	14	2.4	14	90	5	50	57	0	3	39	1.14
4622690--4622731	20	2.2	20	91	4	68	14	4	2	78	1.01
4623290--4623334	3	15.3	3	95	4	83	31	0	0	68	0.89
4623404--4623491	2	46.0	2	74	17	62	44	4	2	48	1.35
4625100--4625130	16	1.9	16	93	0	53	29	19	16	35	1.93
4625509--4625534	13	2.0	13	100	0	52	30	7	15	46	1.74
4625568--4625607	19	2.0	20	85	4	55	25	20	7	47	1.75
4627470--4627509	19	2.1	19	90	0	62	12	12	7	67	1.41
4628466--4628507	7	6.0	7	81	18	52	69	0	16	14	1.20
4628466--4628507	21	2.0	21	86	9	59	69	0	16	14	1.20
4629951--4630412	44	10.5	43	69	17	227	29	19	23	27	1.98
4629769--4630512	132	5.6	132	89	2	1102	29	18	23	27	1.98
4629770--4630512	264	2.8	264	92	0	1245	29	18	23	27	1.98
4631635--4631664	12	2.4	12	94	5	51	86	13	0	0	0.57
4636840--4637001	42	3.9	41	79	6	164	32	26	17	23	1.97
4661076--4661108	15	2.1	17	88	11	52	75	15	6	3	1.11
4661224--4661258	17	2.1	17	88	0	52	45	0	8	45	1.34
4661228--4661270	17	2.5	16	82	14	50	44	2	9	44	1.49
4667052--4667176	55	2.3	55	87	0	178	49	17	8	24	1.73
4667408--4667477	35	2.0	35	94	0	122	12	38	7	41	1.71
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4670662--4670763	41	2.5	41	87	6	136	27	23	20	28	1.99
4672430--4672455	13	2.0	13	100	0	52	61	23	0	15	1.33
4674996--4675072	26	3.1	25	90	7	97	45	22	7	24	1.78
4679680--4679741	29	2.1	29	100	0	124	35	19	19	25	1.95
4680236--4680305	3	23.3	3	100	0	140	67	0	0	32	0.91
4681172--4681214	21	2.0	21	86	8	61	74	0	11	13	1.07
4681860--4682483	143	4.4	143	87	0	872	26	20	20	31	1.98
4682112--4682471	44	7.7	44	66	15	139	25	21	22	30	1.99
4687929--4687973	9	5.4	9	77	20	53	77	0	0	22	0.76
4690009--4690917	469	1.9	467	87	2	1333	32	26	11	30	1.91
4692511--4692545	11	2.9	12	87	12	54	22	0	8	68	1.16
4697834--4697871	17	2.2	17	95	0	67	39	7	7	44	1.63
4698970--4698999	15	2.0	15	93	0	51	36	6	6	50	1.55
4699521--4699575	21	2.7	21	75	13	60	29	1	3	65	1.20
4699528--4699574	11	4.3	11	81	10	51	23	2	4	70	1.16
4716258--4716302	19	2.3	21	77	14	51	48	2	13	35	1.54
4719852--4719890	19	2.0	19	85	5	51	41	10	10	38	1.73
4724172--4724212	16	2.6	16	80	0	55	60	0	2	36	1.10
4732349--4732375	6	4.5	6	100	0	54	29	0	0	70	0.88
4738466--4738497	2	16.0	2	100	0	64	50	0	0	50	1.00
4738972--4739322	41	8.6	41	88	0	495	28	19	28	23	1.98
4739606--4739633	2	14.0	2	100	0	56	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)
4745147--4745173	2	13.5	2	100	0	54	51	0	0	48	1.00
4747668--4747705	20	1.9	20	94	0	67	52	0	0	47	1.00
4747727--4747774	22	2.3	22	85	7	64	52	0	4	43	1.20
4748243--4748299	10	5.7	10	74	15	55	29	5	3	61	1.35
4748245--4748285	19	2.2	18	91	4	64	34	4	0	60	1.18
4748243--4748300	21	2.9	21	80	12	68	29	5	3	62	1.33
4748245--4748300	20	2.8	20	86	5	69	30	5	3	60	1.36
4748295--4748333	17	2.4	16	87	8	53	30	2	0	66	1.05
4755854--4755902	2	25.0	2	83	4	64	44	4	0	51	1.20
4757537--4757640	44	2.3	44	96	1	190	30	3	25	39	1.74

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