genome.fa.s4.2.7.7.80.10.50.1000.139.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  139  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)
44273044--44273136	21	4.4	21	76	2	98	4	40	16	38	1.68
44273040--44273136	42	2.3	42	75	8	108	4	40	17	38	1.69
44273163--44273294	66	2.0	66	85	2	176	15	25	17	40	1.89
44278847--44279095	9	28.8	9	70	15	116	39	1	15	42	1.57
44278847--44279144	34	8.9	34	67	18	94	40	1	15	42	1.57
44278869--44279200	165	2.1	162	94	5	595	41	1	14	42	1.56
44279165--44279210	22	2.1	22	91	0	74	43	0	10	45	1.39
44279132--44279578	65	7.5	56	77	16	423	41	1	10	46	1.46
44279187--44279554	34	11.7	34	71	19	248	41	0	10	47	1.44
44279132--44279578	90	4.9	90	86	7	625	41	1	10	46	1.46
44279441--44279486	22	2.1	22	91	0	74	41	2	10	45	1.51
44280699--44280903	108	1.9	107	83	3	268	29	24	19	26	1.98
44281270--44281299	6	5.0	6	100	0	60	33	0	0	66	0.92
44281633--44281665	17	1.9	17	93	0	57	36	36	0	27	1.57
44288901--44288992	23	3.9	23	76	15	80	20	26	22	30	1.98
44291987--44292167	61	2.9	61	81	6	186	41	16	4	38	1.68
44293251--44293375	61	2.0	61	80	6	137	36	6	16	40	1.75
44297649--44297714	13	5.5	13	71	20	63	36	1	16	45	1.57
44297645--44297714	23	3.0	23	93	0	113	37	1	17	44	1.57
44297779--44297848	16	4.4	16	96	0	113	30	0	35	34	1.58
44298058--44298112	25	2.2	25	84	9	69	52	1	0	45	1.11
44301711--44301765	28	2.0	28	92	0	92	63	5	29	1	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44306626--44306678	25	2.2	25	89	3	81	20	24	20	33	1.97
44307384--44307416	15	2.1	16	88	5	50	6	15	3	75	1.11
44308135--44308229	25	3.7	26	84	5	113	24	21	22	32	1.98
44312191--44312226	3	12.0	3	100	0	72	66	0	0	33	0.92
44313634--44313919	132	2.2	132	96	0	518	26	24	18	30	1.98
44323920--44324800	132	6.7	132	92	0	1478	27	23	18	30	1.97
44324349--44324682	44	7.6	44	66	14	159	26	24	18	29	1.98
44325923--44325968	21	2.2	20	88	3	65	26	39	10	23	1.88
44326936--44327052	13	9.0	12	73	15	54	5	7	7	79	1.05
44326929--44326975	12	4.0	12	81	10	53	0	23	0	76	0.78
44326925--44326993	25	2.7	25	76	17	61	4	18	4	72	1.18
44326988--44327052	7	9.9	7	74	12	57	6	0	10	83	0.82
44327003--44327052	8	6.5	8	80	19	54	2	0	12	86	0.67
44326987--44327052	13	5.2	12	80	12	78	6	0	10	83	0.81
44326987--44327050	17	3.7	17	74	15	60	6	0	10	82	0.82
44331813--44331837	11	2.3	11	100	0	50	40	8	0	52	1.31
44331797--44331945	40	3.7	40	89	5	212	32	3	0	63	1.11
44331823--44331878	29	1.9	28	82	13	69	30	3	0	66	1.09
44331834--44331895	9	6.4	9	74	17	54	25	1	0	72	0.94
44332323--44332349	3	9.0	3	100	0	54	66	0	0	33	0.92
44335315--44335365	17	3.1	17	76	15	54	39	3	0	56	1.18
44336208--44336267	29	2.1	29	100	0	120	31	20	6	41	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44343124--44343256	59	2.2	60	82	1	160	32	19	11	36	1.87
44344152--44344201	8	5.4	9	76	21	50	50	0	2	48	1.12
44344168--44344198	8	3.9	8	95	0	53	54	0	0	45	0.99
44362088--44362112	2	12.5	2	100	0	50	52	0	0	48	1.00
44366976--44367055	22	3.7	22	90	6	112	37	8	17	36	1.81
44367258--44367302	23	2.0	23	81	0	54	22	0	15	62	1.33
44367707--44367741	15	2.2	16	95	5	63	22	0	0	77	0.78
44367750--44367792	23	1.9	22	90	4	68	34	6	2	55	1.39
44367874--44367938	3	21.7	3	100	0	130	33	0	0	66	0.92
44371271--44371296	2	13.0	2	100	0	52	50	0	0	50	1.00
44371817--44371955	37	3.5	40	74	10	133	31	23	19	25	1.98
44381248--44381287	17	2.3	18	91	4	64	27	2	0	70	1.01
44385216--44385292	30	2.6	30	81	4	84	45	5	28	20	1.73
44385215--44385298	36	2.3	36	81	4	98	45	5	28	20	1.74
44385241--44385300	12	5.0	12	76	8	50	45	6	31	16	1.74
44385544--44385677	70	1.9	70	95	0	241	41	8	4	45	1.54
44386615--44386674	20	3.2	19	76	23	65	40	0	1	58	1.08
44386621--44386676	14	4.5	13	71	15	55	35	0	1	62	1.06
44395405--44395466	28	2.4	25	84	12	81	17	17	16	48	1.82
44396376--44396406	15	2.1	15	100	0	62	41	19	0	38	1.51
44397007--44397295	8	36.1	8	96	0	416	19	0	30	49	1.51
44397394--44397428	10	3.5	10	88	11	54	34	0	2	62	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44397970--44397995	7	3.7	7	100	0	52	76	0	11	11	1.01
44398264--44398351	43	2.0	43	84	0	113	32	14	12	39	1.84
44400380--44400406	14	1.9	14	100	0	54	51	18	7	22	1.70
44402627--44402651	2	12.5	2	100	0	50	52	0	48	0	1.00
44410959--44411085	51	2.5	51	89	1	184	24	18	26	30	1.98
44413294--44413329	15	2.5	14	86	8	54	44	8	0	47	1.33
44416964--44417119	84	1.9	84	84	10	212	30	30	17	21	1.96
44416962--44417120	43	3.8	41	78	14	157	30	30	17	21	1.96
44419838--44419905	34	2.0	34	97	0	127	33	20	22	23	1.97
44421893--44421924	15	2.1	15	94	0	55	15	6	9	68	1.36
44423520--44423589	37	1.9	35	83	11	88	40	5	2	51	1.40
44425494--44425556	3	21.7	3	88	3	85	74	0	25	0	0.82
44425494--44425556	21	3.1	21	95	4	112	74	0	25	0	0.82
44429793--44429842	20	2.5	20	83	6	57	50	18	12	20	1.78
44429700--44429977	136	2.0	136	100	0	556	41	18	10	29	1.83
44429929--44429977	20	2.5	20	83	6	55	48	18	12	20	1.79
44431230--44431263	16	2.1	16	88	5	50	8	0	14	76	1.01
44444406--44444437	16	2.0	16	100	0	64	18	31	18	31	1.95
44455762--44455801	9	4.2	10	84	12	57	17	2	0	80	0.83
44455759--44455804	18	2.7	18	86	6	60	23	2	0	73	0.94
44455762--44455801	18	2.2	19	90	4	64	17	2	0	80	0.83
44457103--44457128	13	2.0	13	100	0	52	15	7	7	69	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44459704--44459762	25	2.4	25	100	0	118	23	6	15	54	1.65
44462137--44462323	41	4.6	41	93	1	313	20	28	20	30	1.97
44462136--44462351	82	2.6	82	87	2	256	22	28	19	28	1.98
44464015--44464076	31	1.9	31	83	9	79	50	4	0	45	1.23
44474001--44474781	44	18.0	43	68	14	232	29	20	22	27	1.98
44474001--44474767	216	3.5	216	91	0	1246	29	20	22	27	1.99
44477833--44477915	44	1.9	43	82	7	105	26	21	26	25	2.00
44488772--44488805	14	2.4	14	95	0	59	26	0	8	64	1.22
44501672--44501700	7	4.3	7	95	4	51	31	0	0	68	0.89
44501939--44501974	15	2.3	16	90	4	56	77	5	13	2	1.05
44502370--44502403	17	1.9	18	88	5	52	41	0	23	35	1.55
44511195--44511401	43	4.9	43	84	1	256	31	27	15	25	1.96
44513643--44513700	29	2.0	29	96	0	107	13	25	44	15	1.83
44514532--44514569	11	3.5	11	82	13	51	21	0	0	78	0.74
44518935--44518982	5	9.2	5	86	8	69	37	0	2	60	1.09
44519693--44519757	3	21.7	3	80	0	58	38	0	3	58	1.14
44519698--44519757	27	2.2	27	93	0	102	40	0	3	56	1.16
44519717--44519763	21	2.2	22	92	3	78	40	0	2	57	1.11
44528708--44528741	17	1.9	18	88	5	52	41	0	23	35	1.55
44529043--44529115	37	2.0	36	83	2	92	43	0	23	32	1.54
44531061--44531160	42	2.4	42	94	0	173	37	15	28	20	1.92
44539450--44539506	29	1.9	30	92	3	98	70	1	1	26	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44554495--44554570	26	2.8	26	76	7	73	28	19	21	30	1.97
44557914--44557958	18	2.5	19	80	20	60	37	4	26	31	1.76
44565095--44565184	31	3.0	30	74	15	78	58	10	13	17	1.61
44566499--44566560	27	2.3	27	85	0	79	40	32	4	22	1.75
44571250--44571300	20	2.5	20	81	12	68	56	3	1	37	1.29
44571302--44571345	18	2.4	18	92	0	70	68	0	2	29	1.02
44578874--44579267	195	2.0	195	98	1	754	38	21	13	25	1.91
44579992--44580055	31	2.1	31	96	0	119	34	29	3	32	1.73
44585199--44585256	28	2.1	28	84	12	75	51	0	1	46	1.11
44589210--44589277	30	2.3	29	82	2	82	47	1	7	44	1.40

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