genome.fa.s4.2.7.7.80.10.50.1000.108.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  108  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)
34597519--34597783	29	9.3	29	81	3	229	36	22	16	24	1.94
34598632--34598705	24	3.2	24	62	14	64	36	13	2	47	1.57
34598615--34598709	46	2.1	46	97	0	181	37	12	3	46	1.58
34599880--34599908	14	2.1	14	100	0	58	37	27	0	34	1.57
34603057--34603300	28	8.8	28	80	1	199	27	23	14	34	1.93
34603066--34603268	111	1.8	111	89	2	318	27	23	14	34	1.93
34603084--34603300	56	3.9	56	80	4	242	28	23	14	34	1.94
34603073--34603320	111	2.2	111	82	2	284	27	24	14	33	1.94
34603804--34603866	31	2.0	31	84	0	81	25	12	20	41	1.88
34605605--34605714	45	2.6	41	77	9	107	31	5	29	33	1.80
34605798--34605835	18	2.0	21	85	15	55	42	5	5	47	1.48
34607574--34607637	31	2.1	31	100	0	128	39	39	3	18	1.67
34609261--34609348	42	2.1	42	97	0	167	37	21	17	23	1.94
34609669--34609721	21	2.5	21	100	0	106	35	5	15	43	1.70
34611834--34612066	51	4.6	51	93	0	376	33	15	23	27	1.95
34620216--34620276	33	1.9	33	86	6	90	42	6	3	47	1.45
34626261--34626290	2	15.5	2	93	6	53	50	0	0	50	1.00
34626496--34626549	26	2.2	25	83	6	65	16	22	0	61	1.35
34627550--34627589	21	1.9	21	94	0	71	35	10	22	32	1.87
34636302--34636359	20	2.9	19	75	12	55	55	6	5	32	1.49
34641280--34641311	16	2.0	16	93	0	55	25	3	0	71	1.00
34641674--34641720	24	1.9	25	82	4	60	55	6	0	38	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34644597--34644626	13	2.3	13	100	0	60	16	0	43	40	1.48
34646941--34646973	15	2.1	16	88	5	50	69	3	0	27	1.03
34647746--34647795	17	2.9	17	82	5	57	74	0	8	18	1.06
34648634--34648966	44	7.6	45	76	5	263	28	23	18	29	1.98
34648634--34648966	88	3.8	88	79	2	341	28	23	18	29	1.98
34648996--34650242	50	24.9	50	71	4	769	25	20	21	32	1.98
34649109--34650250	100	11.4	100	86	1	1520	25	21	20	32	1.98
34656942--34657006	3	21.7	3	73	6	51	61	7	3	27	1.38
34656979--34657011	15	2.1	16	88	5	50	69	3	0	27	1.03
34665944--34666037	46	2.0	46	97	0	179	40	10	11	37	1.77
34668399--34668485	35	2.5	34	92	5	140	54	10	3	32	1.51
34669448--34669511	28	2.3	28	84	7	85	54	3	1	40	1.25
34683348--34683467	63	1.9	63	87	0	177	25	25	19	29	1.98
34685718--34685752	18	2.0	18	88	5	54	34	2	5	57	1.37
34688167--34688197	2	16.0	2	93	6	55	51	0	0	48	1.00
34690419--34690455	18	2.1	18	100	0	74	43	29	21	5	1.75
34696249--34696274	13	2.0	13	100	0	52	38	0	7	53	1.30
34698248--34698436	91	2.1	91	87	2	272	44	3	4	48	1.38
34698577--34698628	15	3.6	15	80	12	56	44	0	1	53	1.11
34698452--34698744	120	2.5	117	91	6	459	42	2	4	50	1.36
34698701--34698742	15	2.7	16	82	14	52	45	0	2	52	1.13
34698692--34698733	15	2.9	15	82	10	52	47	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34698845--34698879	18	2.0	17	88	5	52	45	0	0	54	0.99
34698676--34698992	157	2.0	157	96	0	589	47	5	3	44	1.42
34698677--34698915	75	3.1	75	64	18	191	46	3	3	46	1.35
34699068--34699121	16	3.4	16	92	0	81	29	35	1	33	1.69
34699525--34699601	19	3.7	19	67	16	55	28	1	3	66	1.17
34701579--34701762	4	46.0	4	97	0	350	25	1	24	49	1.57
34701754--34702968	327	3.7	327	95	0	2139	32	12	26	27	1.93
34703149--34703207	25	2.4	25	91	0	91	23	25	20	30	1.98
34704522--34704631	25	4.4	24	82	5	112	23	21	20	33	1.97
34704522--34704660	50	2.8	50	80	2	127	25	19	22	33	1.97
34704522--34704660	75	1.9	75	81	0	170	25	19	22	33	1.97
34706310--34706557	45	5.5	45	72	8	148	23	16	14	44	1.86
34706342--34706554	89	2.4	90	78	3	207	24	16	15	43	1.86
34719086--34719152	3	22.3	3	90	0	107	64	2	1	31	1.18
34719726--34720153	213	2.0	214	95	1	770	25	30	15	28	1.96
34721088--34721458	132	2.8	132	90	2	575	27	23	18	29	1.98
34721390--34721635	44	5.6	44	67	14	148	28	24	17	30	1.97
34721290--34721577	88	3.3	88	67	16	234	27	25	17	30	1.97
34721434--34721717	132	2.2	132	88	0	444	26	24	17	30	1.97
34721289--34721635	176	2.0	176	91	1	561	27	24	17	29	1.97
34721127--34721711	308	1.9	308	89	0	902	27	24	17	30	1.97
34721825--34722530	87	8.2	87	91	0	1141	23	23	22	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34721855--34721992	42	3.2	43	65	17	113	26	25	22	25	2.00
34724176--34724285	47	2.4	46	82	7	118	10	10	7	72	1.27
34724195--34724270	34	2.3	32	84	6	98	11	9	7	71	1.32
34732288--34732329	21	2.0	22	85	4	59	61	16	0	21	1.34
34738257--34738306	19	2.7	19	79	11	59	70	0	24	6	1.10
34738401--34738446	23	2.0	23	100	0	92	52	13	17	17	1.75
34741613--34741659	15	3.1	15	81	9	51	42	0	2	55	1.12
34763487--34763635	74	2.0	74	97	0	280	41	23	9	25	1.84
34764100--34764151	27	1.9	27	88	0	77	15	19	38	26	1.91
34765054--34765115	31	2.0	31	90	0	97	19	17	25	37	1.94
34769022--34769085	24	2.6	25	70	2	67	14	23	18	43	1.86
34769132--34769176	24	1.9	23	86	4	63	22	22	20	35	1.96
34769131--34769182	24	2.2	23	79	3	59	19	23	19	38	1.93
34769141--34769244	24	4.2	24	75	8	86	21	25	18	34	1.96
34769165--34769256	25	3.7	25	76	4	80	21	26	19	32	1.97
34778592--34778634	23	1.9	23	85	4	61	62	4	2	30	1.28
34796530--34796663	50	2.7	50	83	3	171	25	19	25	29	1.98
34798429--34798460	16	2.0	16	93	0	55	25	15	0	59	1.36
34798688--34798878	51	3.8	51	75	11	185	31	27	16	24	1.97
34798686--34798870	101	1.8	102	87	3	275	31	26	17	24	1.97
34803690--34803750	20	3.3	18	76	13	61	49	4	3	42	1.40
34808358--34808414	27	2.0	29	83	12	75	35	26	5	33	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34810816--34811112	63	4.7	63	85	1	353	31	28	19	21	1.97
34811679--34811730	18	2.9	18	77	5	61	78	0	17	3	0.89
34811679--34811731	7	7.4	7	79	12	54	79	0	16	3	0.88
34815498--34815550	26	2.0	26	96	0	97	18	22	32	26	1.97
34815524--34815761	85	2.8	83	83	7	282	23	18	25	33	1.97
34815527--34815752	42	5.4	42	74	12	180	22	17	25	34	1.96
34831293--34831368	40	1.9	40	83	0	98	25	10	31	32	1.89
34831348--34831576	104	2.2	104	84	3	307	31	17	23	28	1.96
34835301--34835499	48	4.1	47	98	0	344	36	8	6	49	1.57
34835318--34835506	23	8.0	23	78	13	195	34	8	6	50	1.60
34835301--34835499	96	2.1	96	100	0	398	36	8	6	49	1.57
34836693--34836768	23	3.3	23	94	0	134	46	26	6	21	1.75
34836754--34836799	22	2.1	21	84	11	58	58	17	4	19	1.55
34837964--34837999	17	2.1	17	94	0	63	69	11	8	11	1.37
34839565--34839625	28	2.2	29	80	14	74	29	11	9	49	1.71
34841559--34841608	11	4.6	11	76	14	50	76	0	22	2	0.89
34841559--34841608	16	3.1	16	80	8	57	76	0	22	2	0.89
34841562--34841607	22	2.1	22	88	8	67	76	0	21	2	0.90
34846929--34846970	21	2.0	21	85	0	57	42	16	0	40	1.48
34850185--34850224	21	1.9	21	94	0	71	35	15	25	25	1.94
34862305--34862365	25	2.6	23	80	17	63	44	0	32	22	1.54
34863711--34863749	2	19.5	2	94	0	69	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34868590--34868661	23	3.2	23	86	9	112	26	13	11	48	1.76
34874784--34874868	27	3.2	26	73	9	73	37	30	7	24	1.82
34874790--34874940	54	2.8	54	80	7	182	31	29	13	26	1.94
34874794--34874941	27	5.5	27	75	3	136	30	29	13	26	1.94
34884324--34884489	35	4.5	35	73	15	118	28	24	16	29	1.97
34886661--34886756	30	3.2	29	75	12	70	26	22	7	43	1.79
34897138--34897175	20	1.9	20	89	10	60	57	0	0	42	0.98
34897159--34897191	15	2.1	16	88	11	50	66	0	0	33	0.92
34897152--34897203	26	2.0	25	85	3	68	69	0	1	28	0.99
34909837--34909886	19	2.6	19	81	6	66	38	28	4	30	1.75

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