genome.fa.s7.2.7.7.80.10.50.1000.129.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   199   200   201   202   203   204   

This is table  129  of  204  ( 24458 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)
39415228--39415313	45	1.9	45	90	0	136	53	2	6	37	1.41
39417123--39417156	6	5.7	6	96	0	59	55	0	26	17	1.42
39421523--39421596	26	2.8	25	77	8	76	47	4	1	47	1.29
39424451--39424601	51	3.0	51	86	0	212	22	16	29	31	1.96
39429526--39429569	21	2.1	21	83	8	54	25	9	2	63	1.35
39433915--39433979	29	2.3	27	78	5	67	61	3	1	33	1.21
39434191--39434229	17	2.3	17	86	0	51	33	2	5	58	1.33
39435349--39435378	15	2.0	15	93	0	51	30	36	20	13	1.90
39438048--39438093	6	7.5	6	83	11	58	65	0	15	19	1.28
39438234--39438298	27	2.4	27	87	2	87	40	10	15	33	1.82
39440480--39440543	12	5.5	11	74	7	56	50	17	6	26	1.69
39440475--39440554	23	3.5	23	92	0	142	48	15	7	28	1.71
39440476--39440554	11	6.9	11	71	7	59	49	15	6	29	1.69
39443305--39443330	10	2.6	10	100	0	52	69	11	7	11	1.37
39443956--39444377	27	15.6	27	83	2	461	24	15	20	39	1.91
39445378--39445420	13	3.3	14	78	18	56	27	34	0	37	1.57
39445531--39445584	25	2.2	25	89	0	81	18	46	12	22	1.83
39448692--39449466	27	28.7	27	85	2	930	25	15	19	39	1.91
39450145--39450176	10	3.2	10	95	0	55	43	0	46	9	1.35
39450632--39450685	25	2.2	25	93	0	90	16	48	12	22	1.80
39450636--39450691	25	2.4	23	85	8	69	16	48	14	21	1.81
39469273--39469297	13	1.9	13	100	0	50	28	8	24	40	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39474793--39474884	42	2.2	42	98	0	175	21	29	28	20	1.98
39477333--39477409	33	2.3	33	100	0	154	15	16	22	45	1.85
39483463--39483858	198	2.0	198	100	0	792	28	9	22	39	1.84
39498452--39498494	2	21.5	2	100	0	86	48	0	0	51	1.00
39499102--39499162	15	3.8	15	78	16	68	32	0	1	65	1.02
39499104--39499162	18	3.6	17	73	26	56	33	0	1	64	1.04
39501590--39501619	15	2.0	15	93	0	51	33	0	10	56	1.32
39502765--39502852	45	2.0	44	95	2	158	31	13	9	45	1.75
39504535--39504694	56	2.8	56	82	4	205	30	22	13	33	1.92
39507499--39507561	31	2.0	31	100	0	126	34	3	15	46	1.62
39514149--39515520	282	4.9	282	87	2	1839	33	18	22	25	1.97
39514134--39515457	561	2.4	562	87	2	1874	33	17	22	25	1.96
39518023--39518063	5	8.6	5	78	10	50	21	2	2	73	1.07
39518036--39518076	18	2.2	18	87	12	57	26	2	4	65	1.25
39522270--39522335	31	2.1	31	85	0	87	42	12	13	31	1.81
39524132--39524186	25	2.1	27	93	6	96	30	10	3	54	1.52
39531763--39532287	267	2.0	267	87	0	755	28	20	25	25	1.99
39532485--39532607	45	2.7	45	87	0	174	26	22	27	22	1.99
39532485--39532644	45	3.6	45	81	4	171	29	21	24	25	1.99
39537048--39537116	33	2.1	33	100	0	138	33	26	15	24	1.95
39537081--39537363	51	5.6	51	80	6	290	30	26	15	28	1.96
39537081--39537360	102	2.8	102	89	0	400	30	26	14	28	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39537081--39537359	153	1.8	151	82	5	355	30	26	14	28	1.95
39545602--39545640	18	2.1	19	86	13	55	33	12	17	35	1.88
39548157--39548211	25	2.2	25	100	0	110	10	7	14	67	1.41
39548554--39548603	23	2.2	23	82	7	57	60	2	10	28	1.40
39549300--39549397	19	5.3	19	70	18	55	63	1	3	32	1.17
39565282--39565356	27	2.8	26	80	8	87	45	9	14	30	1.77
39565343--39565403	29	2.2	29	79	5	72	55	13	4	26	1.57
39571003--39571034	8	3.9	8	95	4	55	87	0	12	0	0.54
39571002--39571036	18	1.9	18	94	0	61	88	0	11	0	0.51
39572120--39572144	12	2.1	12	100	0	50	24	36	24	16	1.94
39572304--39572389	9	9.4	9	86	7	111	40	26	10	22	1.86
39575868--39575929	28	2.2	29	79	2	72	53	12	6	27	1.63
39585102--39585164	27	2.3	27	86	5	83	14	20	23	41	1.89
39585620--39585700	38	2.2	38	93	2	146	43	2	19	34	1.65
39586968--39586996	6	4.8	6	100	0	58	48	0	0	51	1.00
39587393--39587444	25	2.1	24	86	10	70	26	3	5	63	1.34
39597158--39597219	30	2.1	30	87	0	88	33	8	9	48	1.65
39603302--39603328	14	1.9	14	100	0	54	37	22	25	14	1.93
39607087--39607181	49	2.0	48	83	8	122	53	10	7	28	1.62
39610140--39610181	12	3.7	11	79	14	50	9	11	0	78	0.96
39610118--39610181	10	6.1	10	73	10	56	6	12	1	79	0.98
39619275--39619312	19	2.0	19	85	10	51	21	39	2	36	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39625626--39625667	21	2.0	21	85	0	57	16	38	21	23	1.93
39642650--39642951	27	11.3	27	81	7	291	19	16	21	43	1.88
39642650--39642950	81	3.8	80	83	8	328	19	15	21	43	1.88
39645250--39645308	29	1.9	31	86	10	86	40	11	15	32	1.83
39645711--39645962	54	4.7	53	84	5	283	20	17	19	43	1.88
39645710--39645962	27	9.4	27	79	7	237	20	17	19	43	1.89
39647550--39647742	50	3.8	50	85	3	253	22	28	22	26	1.99
39647550--39647742	100	1.9	101	87	1	280	22	28	22	26	1.99
39651499--39651534	18	2.0	18	100	0	72	27	11	11	50	1.72
39652038--39652261	121	1.9	121	88	3	344	28	15	14	41	1.87
39657926--39657956	16	1.9	16	100	0	62	32	12	3	51	1.56
39660837--39660986	73	2.1	73	94	2	266	24	14	32	30	1.94
39669401--39669636	50	4.7	50	87	0	301	26	21	30	22	1.99
39691621--39691650	15	2.0	15	93	0	51	70	13	3	13	1.30
39691985--39692019	13	2.7	13	90	0	52	80	0	8	11	0.92
39700473--39700506	16	2.2	15	89	5	50	44	0	0	55	0.99
39702149--39702183	12	2.9	12	95	0	61	71	2	25	0	1.00
39703753--39704082	165	2.0	165	97	0	624	26	14	29	28	1.95
39712450--39712537	44	2.0	46	84	8	119	40	23	2	32	1.67
39712524--39712554	16	1.9	16	93	0	53	29	25	3	41	1.71
39719382--39719406	12	2.1	12	100	0	50	56	0	0	44	0.99
39724272--39724350	23	3.3	23	85	5	113	56	0	3	39	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39724274--39724351	25	3.2	24	89	7	122	56	0	3	39	1.18
39726208--39726248	18	2.2	20	82	8	50	26	0	4	68	1.10
39730341--39730389	20	2.5	20	82	0	62	16	20	4	59	1.53
39732803--39732837	18	1.9	18	88	0	52	42	11	17	28	1.83
39738348--39738378	16	1.9	16	100	0	62	38	3	0	58	1.15
39744576--39744971	27	14.7	27	83	6	443	40	17	15	26	1.90
39745120--39745201	27	3.0	25	79	12	83	20	25	21	31	1.98
39747235--39747284	25	2.0	25	88	3	75	34	20	26	20	1.96
39750483--39750541	27	2.2	27	84	3	75	23	16	23	35	1.95
39750496--39750695	27	7.4	26	78	7	195	19	17	23	40	1.91
39750507--39750695	81	2.3	80	82	5	218	19	16	24	39	1.91
39753632--39753692	31	2.0	30	81	9	70	47	13	9	29	1.74
39754058--39754141	27	3.1	27	80	13	75	23	17	21	36	1.94
39754091--39754233	27	5.3	27	87	0	187	17	14	23	44	1.85
39762097--39762151	25	2.2	25	96	0	101	29	14	18	38	1.90
39762673--39762719	24	1.9	24	86	4	67	36	0	38	25	1.56
39763496--39763643	52	2.8	52	96	0	269	22	15	33	28	1.94
39763587--39763617	14	2.2	14	94	0	53	19	9	45	25	1.81
39763935--39764105	80	2.1	81	89	1	254	42	19	17	20	1.89
39763935--39764117	27	6.8	27	81	5	210	40	20	16	21	1.91
39769420--39769532	57	2.0	57	98	0	217	53	19	3	23	1.60
39773605--39773662	26	2.2	26	93	0	98	37	15	22	24	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39773616--39773702	26	3.5	25	81	9	81	39	17	19	24	1.92
39773656--39773702	23	2.0	23	88	8	69	42	19	17	21	1.89
39773856--39774023	27	6.3	27	84	2	115	20	16	22	41	1.90
39773869--39774034	54	3.1	54	87	0	235	19	16	20	43	1.88
39777206--39777277	31	2.3	32	92	2	119	48	13	20	16	1.80
39798169--39798377	46	4.5	46	79	3	190	27	18	22	31	1.97
39801782--39801814	16	2.1	16	100	0	66	33	36	24	6	1.80
39808826--39808877	22	2.3	22	83	9	61	61	3	1	32	1.25
39809542--39809588	18	2.8	17	78	12	60	55	0	4	40	1.19
39809546--39809582	16	2.3	16	90	9	58	59	0	2	37	1.12

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   199   200   201   202   203   204