genome.fa.s4.2.7.7.80.10.50.1000.104.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  104  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)
33363818--33363884	28	2.4	28	79	0	71	29	19	11	38	1.88
33368337--33368417	42	1.9	42	92	0	135	28	27	17	27	1.97
33381183--33381405	111	2.0	111	92	3	369	34	13	13	39	1.83
33383163--33383195	17	2.0	17	88	5	50	57	0	6	36	1.23
33388920--33388958	18	2.2	17	86	13	53	33	0	20	46	1.51
33389188--33389263	23	3.3	23	81	0	107	22	19	27	30	1.98
33395529--33395624	31	3.1	31	80	4	104	41	1	5	52	1.31
33398863--33398908	18	2.4	20	82	7	60	56	0	4	39	1.19
33400083--33400136	22	2.6	20	82	5	63	66	1	1	29	1.12
33403805--33403902	28	3.5	28	93	6	164	38	13	0	47	1.42
33403974--33404044	27	2.6	27	95	0	124	28	28	28	15	1.96
33404083--33404231	20	7.6	19	71	21	112	65	0	34	0	0.93
33404087--33404169	22	3.6	22	84	9	103	63	0	36	0	0.94
33404082--33404218	12	10.0	14	72	16	85	66	0	33	0	0.92
33404073--33404252	79	2.4	80	83	12	229	66	0	33	0	0.92
33404073--33404251	44	4.3	44	74	19	152	66	0	33	0	0.92
33410527--33410579	26	2.0	26	85	7	72	47	7	1	43	1.42
33410866--33410915	3	16.7	3	100	0	100	68	32	0	0	0.90
33410914--33410978	3	21.3	3	93	3	112	64	3	0	32	1.09
33411020--33411049	12	2.5	12	100	0	60	70	10	0	20	1.16
33411024--33411074	21	2.4	20	84	15	59	66	7	0	25	1.18
33411214--33411312	27	3.7	27	93	0	162	18	26	29	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33411386--33411486	29	3.5	29	86	8	152	50	0	10	38	1.38
33412502--33412571	36	1.9	36	82	2	86	34	7	20	38	1.80
33415659--33415975	114	2.8	113	88	1	463	24	21	27	26	1.99
33416163--33416270	38	2.8	39	79	6	114	20	0	41	37	1.59
33418952--33419040	18	4.8	18	81	14	110	44	12	0	42	1.42
33418943--33419069	39	3.1	41	82	14	147	44	11	0	44	1.39
33419803--33419878	22	3.6	21	81	15	95	47	10	1	40	1.46
33419865--33420222	9	42.2	9	68	20	132	44	15	1	39	1.53
33419821--33420018	56	3.6	56	77	13	259	45	12	0	41	1.41
33419855--33420024	34	4.9	34	78	13	202	45	12	0	41	1.41
33419861--33419994	25	5.2	24	66	20	65	45	12	0	41	1.42
33419843--33420093	106	2.3	110	91	8	397	44	13	0	42	1.44
33420010--33420042	16	2.1	16	100	0	66	45	24	0	30	1.53
33420005--33420146	25	5.6	25	72	17	98	42	16	1	39	1.57
33420005--33420217	34	6.5	33	68	16	120	43	16	1	38	1.57
33419967--33420124	84	1.9	84	85	5	221	44	14	0	40	1.50
33420100--33420217	16	7.8	16	69	19	92	45	17	1	34	1.59
33420064--33420203	25	5.7	25	76	6	133	44	16	2	37	1.60
33425688--33425759	21	3.4	21	83	5	92	38	16	43	1	1.57
33425731--33425756	12	2.2	12	100	0	52	42	15	42	0	1.47
33426192--33426443	42	6.0	42	89	4	341	24	24	20	30	1.99
33426192--33426440	127	2.0	127	86	6	353	24	24	20	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33437025--33437085	31	2.0	31	90	0	95	26	14	19	39	1.90
33438270--33438357	37	2.4	37	84	1	104	20	17	14	47	1.82
33446640--33446707	22	3.1	21	81	10	66	23	26	30	19	1.98
33450928--33450964	15	2.4	16	90	4	58	54	0	5	40	1.24
33464608--33464694	44	2.0	44	97	0	165	25	24	9	41	1.84
33466084--33466110	11	2.5	11	100	0	54	51	22	11	14	1.73
33466127--33466155	2	14.5	2	100	0	58	51	0	48	0	1.00
33471279--33471311	11	2.8	12	86	9	50	0	15	6	78	0.93
33472425--33472478	28	2.0	28	88	3	83	31	14	22	31	1.94
33472585--33472691	26	4.1	26	93	2	180	34	25	20	19	1.96
33472857--33472996	27	5.2	27	79	0	172	21	15	20	42	1.88
33472857--33472988	54	2.4	54	89	0	201	21	15	20	42	1.89
33474681--33474776	50	1.9	50	89	4	149	41	11	15	31	1.83
33476293--33476332	13	3.1	13	100	0	80	30	0	22	47	1.52
33477467--33477579	43	2.7	42	77	12	106	23	19	28	29	1.98
33478520--33478550	2	15.5	2	100	0	62	48	0	0	51	1.00
33480359--33480432	32	2.3	33	79	11	82	39	8	9	43	1.67
33483677--33483715	19	2.1	19	100	0	78	43	5	15	35	1.69
33494685--33494735	25	2.0	25	100	0	102	41	11	35	11	1.78
33502957--33502989	11	2.9	12	86	13	52	66	0	0	33	0.92
33507697--33507749	3	17.7	3	88	0	52	58	3	7	30	1.43
33511191--33511281	43	2.1	44	82	10	107	37	30	13	18	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33513005--33513095	41	2.2	41	90	0	146	30	14	10	43	1.80
33516387--33516423	20	1.9	20	88	5	58	51	0	0	48	1.00
33516912--33516949	19	2.1	18	90	9	60	60	2	0	36	1.11
33517751--33517794	18	2.5	17	82	10	52	38	2	2	56	1.24
33518163--33518200	19	2.1	18	90	5	58	26	0	7	65	1.19
33518889--33518920	16	1.9	17	93	6	57	46	0	0	53	1.00
33518942--33518971	15	1.9	16	93	6	53	50	6	6	36	1.55
33522180--33522227	25	2.0	25	87	4	71	16	25	20	37	1.93
33526318--33526759	109	4.1	109	94	0	762	31	16	17	34	1.92
33527676--33527711	16	2.2	16	95	0	63	22	16	19	41	1.90
33535028--33535071	21	2.1	21	100	0	88	38	18	13	29	1.89
33537391--33537587	108	1.8	108	82	4	254	25	16	11	45	1.81
33538039--33538385	40	8.2	43	71	11	254	31	23	20	24	1.98
33538039--33538383	126	2.7	126	96	0	629	31	24	20	24	1.98
33540662--33541093	109	4.0	107	87	5	642	32	16	17	33	1.92
33540662--33541093	212	2.0	212	91	2	704	32	16	17	33	1.92
33545672--33545706	11	3.1	12	88	12	56	34	0	0	65	0.93
33548415--33548460	15	2.9	17	78	12	53	47	0	19	32	1.50
33561838--33561884	24	2.0	23	84	12	60	44	8	21	25	1.80
33568455--33568514	24	2.5	24	83	0	75	16	38	5	40	1.71
33571587--33571629	22	2.0	22	100	0	86	37	13	25	23	1.92
33576728--33576804	38	2.0	38	100	0	154	49	10	12	27	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33582070--33582135	32	2.1	32	100	0	132	40	9	21	28	1.83
33587333--33587396	25	2.6	25	80	14	87	25	23	20	31	1.98
33592739--33592852	41	2.8	41	90	1	174	24	28	21	25	1.99
33593297--33593364	25	2.6	26	88	4	102	41	8	0	50	1.34
33593432--33593525	27	3.5	27	83	2	118	27	27	27	17	1.97
33593606--33593642	11	3.5	11	88	7	58	70	0	29	0	0.88
33593670--33593708	19	2.0	21	85	10	55	23	0	10	66	1.22
33593754--33593788	3	11.3	3	87	6	52	31	0	5	62	1.18
33593787--33593866	3	26.7	3	100	0	160	0	0	32	67	0.91
33594056--33594108	26	2.0	26	96	0	97	43	0	7	49	1.31
33594114--33594144	12	2.6	12	94	0	53	19	0	19	61	1.35
33594054--33594153	26	4.0	25	65	16	73	34	0	12	54	1.38
33603462--33603536	29	2.6	28	85	8	98	44	0	10	45	1.38
33604261--33604307	16	3.0	17	76	20	57	36	2	2	59	1.21
33612828--33612899	32	2.2	33	82	7	85	29	2	15	52	1.56
33614670--33614727	28	2.1	28	81	12	66	55	5	0	39	1.22
33614669--33614730	29	2.2	27	78	16	63	56	4	0	38	1.21
33615987--33616035	24	2.0	25	84	8	64	18	2	8	71	1.21
33616298--33616945	100	6.5	100	87	2	798	24	18	23	33	1.97
33616340--33616923	50	11.7	50	69	3	368	23	17	23	34	1.96
33618224--33618273	7	7.0	7	76	19	50	16	12	0	72	1.13
33618226--33618274	15	3.3	15	81	18	59	14	10	0	75	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33618225--33618274	21	2.3	22	82	6	66	16	10	0	74	1.08
33618234--33618278	13	3.4	13	82	14	56	13	11	0	75	1.05
33618224--33618278	27	2.0	27	86	6	76	14	12	0	72	1.12
33621201--33621593	109	3.6	109	85	1	520	24	16	27	31	1.96
33623041--33623117	20	3.7	20	82	6	91	27	29	32	10	1.90
33642604--33642665	24	2.6	24	77	10	72	25	20	30	22	1.98
33642720--33642922	24	8.5	24	88	2	266	22	22	39	15	1.92
33649634--33649846	91	2.3	92	80	6	229	17	21	19	41	1.90
33649691--33649848	46	3.5	46	85	2	203	15	20	18	44	1.86
33649691--33649891	45	4.4	45	81	3	170	17	20	18	42	1.89

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