genome.fa.s4.2.7.7.80.10.50.1000.101.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  101  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)
32388169--32388204	18	1.9	18	88	5	54	19	13	2	63	1.41
32399719--32399755	19	2.0	18	89	5	56	32	24	8	35	1.85
32401215--32401239	13	1.9	13	100	0	50	32	36	24	8	1.84
32405540--32405645	51	2.1	51	82	8	126	40	21	27	10	1.86
32406444--32406890	44	9.9	44	74	13	150	31	18	21	28	1.97
32406726--32406888	88	1.9	88	86	2	238	31	21	19	27	1.97
32406630--32406898	132	2.0	136	83	5	339	33	20	19	26	1.97
32407540--32407580	5	8.4	5	83	5	57	17	2	2	78	0.98
32422122--32422172	24	2.1	24	100	0	102	47	15	11	25	1.80
32423951--32424006	27	2.1	27	100	0	112	41	25	3	30	1.72
32427185--32427226	2	20.5	2	95	4	75	47	0	2	50	1.14
32430067--32430100	17	2.0	17	100	0	68	35	11	17	35	1.87
32432447--32432479	16	2.0	17	94	5	59	0	21	0	78	0.75
32433793--32433829	19	1.9	19	94	0	65	62	2	0	35	1.10
32436358--32436413	16	3.5	16	90	0	94	35	5	28	30	1.80
32436399--32436487	44	2.0	46	86	8	130	34	4	23	37	1.75
32436883--32436907	12	2.1	12	100	0	50	32	8	32	28	1.86
32444519--32444672	78	1.9	77	83	10	195	39	4	11	44	1.60
32444559--32444710	78	2.0	76	82	8	182	38	5	10	44	1.63
32444947--32445038	6	15.3	6	87	0	58	16	51	2	30	1.56
32444974--32445020	12	3.9	12	97	0	85	17	63	0	19	1.30
32444974--32445020	18	2.6	18	96	0	85	17	63	0	19	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32445016--32445063	18	2.7	17	78	9	51	16	31	6	45	1.72
32446836--32446934	23	4.3	23	91	6	155	31	28	21	19	1.97
32450165--32450204	21	1.9	21	84	0	53	50	10	15	25	1.74
32456176--32456334	83	1.9	83	80	5	187	24	13	28	33	1.93
32461212--32461262	15	3.6	14	80	15	61	74	1	11	11	1.15
32472345--32472471	29	4.4	29	87	0	191	25	15	22	35	1.94
32478773--32478804	7	4.6	7	100	0	64	12	46	0	40	1.42
32479699--32479771	28	2.6	27	82	4	74	27	17	26	28	1.98
32493191--32493277	37	2.4	37	80	1	104	39	29	14	16	1.88
32493888--32493969	37	2.2	37	86	0	110	39	28	15	17	1.90
32492758--32494135	688	2.0	688	96	0	2515	39	21	14	24	1.90
32496526--32496573	21	2.3	21	96	0	87	35	12	4	47	1.60
32500270--32500357	25	3.6	25	75	3	63	17	25	19	38	1.92
32500422--32500505	26	3.3	26	69	20	68	21	23	19	35	1.96
32500431--32500490	27	2.3	27	83	11	72	20	23	18	38	1.93
32500404--32500546	25	5.8	24	68	17	62	20	25	19	34	1.96
32501817--32501896	34	2.4	34	95	0	142	17	30	30	22	1.97
32504741--32504774	2	17.0	2	100	0	68	50	0	0	50	1.00
32510041--32510080	6	6.7	6	100	0	80	17	17	47	17	1.83
32531395--32531465	32	2.2	32	100	0	142	22	28	38	11	1.88
32533715--32533859	78	1.9	78	83	0	191	33	22	15	29	1.94
32536559--32536630	36	2.0	36	94	0	126	40	6	11	41	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32539200--32539242	22	2.0	22	86	9	61	60	11	9	18	1.57
32548614--32548646	2	16.5	2	100	0	66	48	0	0	51	1.00
32551561--32551600	11	3.5	11	82	3	53	57	0	2	40	1.12
32551553--32551659	41	2.7	40	83	2	142	59	0	1	38	1.08
32551622--32551660	9	4.2	9	83	6	51	56	0	0	43	0.99
32565077--32565165	44	2.0	44	93	0	151	23	28	4	43	1.73
32574891--32574932	21	2.1	21	86	8	61	26	21	35	16	1.94
32580151--32580206	28	2.0	28	96	0	103	28	14	30	26	1.95
32588507--32588717	103	2.0	105	92	5	354	51	9	5	33	1.58
32588589--32588649	23	2.7	23	84	0	68	62	1	6	29	1.30
32589355--32589426	22	3.3	22	94	0	117	30	16	27	25	1.97
32592362--32592403	19	2.2	19	83	8	50	11	7	0	80	0.88
32592369--32592393	13	1.9	13	100	0	50	4	8	0	88	0.64
32594801--32594897	49	2.0	49	87	0	140	26	24	5	43	1.75
32596179--32596222	15	2.8	17	74	19	51	22	22	0	54	1.45
32596164--32596249	43	2.0	43	86	0	118	22	24	2	51	1.60
32597473--32597508	3	12.0	3	100	0	72	33	0	0	66	0.92
32602055--32602140	43	2.0	43	83	0	109	24	22	1	52	1.54
32602810--32602853	19	2.4	18	80	3	52	34	13	0	52	1.41
32603264--32603298	15	2.2	16	90	5	54	0	20	2	77	0.90
32604264--32604313	25	1.9	27	84	8	68	66	0	2	32	1.03
32604932--32604959	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)
32611989--32612014	3	8.7	3	100	0	52	0	0	65	34	0.93
32614981--32615037	28	2.0	28	96	0	105	29	28	8	33	1.87
32618606--32618843	29	8.2	29	83	3	266	26	14	22	36	1.92
32626191--32626220	11	2.9	10	90	9	51	16	0	43	40	1.48
32626844--32626875	15	2.1	16	94	5	57	71	0	6	21	1.07
32628019--32628054	6	6.0	6	100	0	72	83	0	16	0	0.65
32632333--32632795	29	16.0	29	77	4	323	26	15	19	38	1.92
32636444--32636651	28	7.4	28	79	8	226	24	16	22	36	1.94
32636444--32636651	57	3.7	57	87	5	289	24	16	22	36	1.94
32636444--32636651	112	1.9	111	87	3	294	24	16	22	36	1.94
32636656--32636851	61	3.2	61	85	2	277	33	12	24	29	1.92
32636688--32636839	28	4.9	32	69	20	126	30	11	26	31	1.91
32636690--32636855	33	5.3	33	66	22	124	31	11	25	31	1.91
32644533--32644582	6	8.5	6	82	12	59	76	0	4	20	0.95
32644526--32644581	18	3.2	16	85	12	67	76	0	7	16	0.99
32650651--32650694	19	2.2	21	92	8	74	68	2	0	29	1.02
32650662--32650701	13	3.2	13	86	13	57	70	0	0	30	0.88
32657330--32657358	10	2.9	10	100	0	58	51	10	10	27	1.68
32657804--32657847	18	2.4	18	92	0	70	47	15	2	34	1.58
32658425--32658463	15	2.6	15	87	0	51	51	0	23	25	1.49
32663111--32663310	68	3.1	64	73	16	196	42	4	5	48	1.45
32663184--32663299	61	1.9	58	83	8	144	43	3	4	49	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32664362--32664387	12	2.2	12	100	0	52	69	7	0	23	1.14
32675939--32676051	55	2.0	56	93	1	192	47	13	8	30	1.73
32676351--32676430	35	2.4	34	76	4	90	8	31	10	50	1.66
32677615--32677690	23	3.5	22	76	16	70	18	7	23	50	1.73
32682791--32682999	92	2.3	91	86	5	278	45	3	3	46	1.39
32682927--32682974	26	1.9	25	84	16	64	45	0	2	52	1.12
32683053--32683260	66	3.3	64	68	22	181	41	3	6	48	1.46
32683015--32683307	120	2.4	120	93	3	493	42	3	4	49	1.39
32683145--32683191	15	3.3	15	82	11	55	44	0	2	53	1.12
32683269--32683310	15	2.7	16	82	14	52	45	0	2	52	1.13
32683260--32683301	15	2.9	15	82	10	52	47	0	0	52	1.00
32683244--32683560	157	2.0	157	96	0	589	47	5	3	44	1.41
32683413--32683447	18	2.0	17	88	5	52	45	0	0	54	0.99
32683245--32683483	75	3.1	75	65	18	200	46	3	3	47	1.35
32683594--32683703	45	2.6	44	81	8	131	31	29	5	33	1.80
32683682--32683735	16	3.4	16	94	0	90	31	35	0	33	1.58
32685875--32686021	43	3.4	44	75	10	126	42	18	17	21	1.90
32689085--32689111	13	2.1	13	100	0	54	48	0	14	37	1.45
32690821--32690918	49	2.0	49	91	0	160	30	14	10	44	1.78
32697473--32697692	51	4.2	51	81	8	262	33	14	23	28	1.94
32697567--32697691	58	2.2	58	94	0	214	32	15	26	26	1.95
32697843--32697879	9	4.1	9	89	0	56	48	13	10	27	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32698092--32698151	30	2.0	31	86	3	86	20	40	0	40	1.52
32698796--32698821	5	5.2	5	100	0	52	23	19	19	38	1.93
32698911--32698936	5	5.2	5	100	0	52	19	19	19	42	1.90
32698952--32698977	7	3.7	7	100	0	52	42	11	30	15	1.82
32699703--32699761	29	2.0	29	86	0	82	20	11	37	30	1.89
32700430--32700511	42	2.0	42	100	0	164	41	14	9	34	1.79
32707182--32707229	25	1.9	25	82	0	60	22	25	4	47	1.69
32707488--32707586	29	3.3	29	64	8	81	26	26	15	32	1.95
32707480--32707657	61	2.9	61	91	0	275	26	24	15	33	1.95
32707455--32707686	61	3.8	61	86	4	254	26	25	13	34	1.93

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