genome.fa.s1.2.7.7.80.10.50.1000.106.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  106  of  187  ( 22383 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)
31327794--31327959	86	1.9	86	88	2	253	36	10	17	35	1.84
31327890--31328409	143	3.7	142	84	2	657	36	10	14	39	1.80
31333386--31335377	143	14.1	141	77	6	1699	36	9	15	38	1.80
31337484--31340672	142	22.4	141	78	5	2820	36	9	14	39	1.79
31337484--31340671	286	11.2	281	76	6	2463	36	9	14	38	1.79
31337484--31340672	428	7.5	425	80	5	3053	36	9	14	39	1.79
31340982--31341023	22	1.9	22	90	0	66	42	16	19	21	1.89
31348677--31348780	22	4.9	21	72	17	81	72	0	5	22	1.06
31348733--31348794	17	3.8	17	78	22	53	74	0	6	19	1.03
31348723--31348790	15	4.5	14	75	24	50	75	0	4	20	0.98
31348728--31348794	32	2.1	32	88	5	100	74	0	5	19	1.02
31349118--31349268	64	2.4	64	84	3	189	15	35	21	27	1.94
31349089--31349287	64	3.1	62	77	7	186	12	32	24	31	1.91
31363806--31363845	4	10.0	4	100	0	80	50	0	0	50	1.00
31367750--31367788	19	2.1	19	95	0	69	28	10	41	20	1.85
31376691--31379615	142	20.5	140	78	6	2569	36	9	15	38	1.79
31376693--31388174	426	26.7	425	73	10	5548	35	9	15	38	1.80
31380861--31388176	143	51.7	138	74	10	4514	36	8	15	39	1.79
31380861--31388176	285	25.9	281	75	9	4649	36	8	15	39	1.79
31389948--31389977	15	2.0	15	100	0	60	0	60	6	33	1.23
31394672--31394718	23	2.0	25	84	16	64	61	2	2	34	1.20
31404710--31404958	50	4.9	50	78	9	238	27	20	28	22	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31405206--31405244	12	3.2	12	85	0	51	51	5	23	20	1.67
31408367--31408394	9	3.1	9	100	0	56	53	0	25	21	1.46
31421891--31422302	23	17.2	24	73	9	139	40	18	15	26	1.90
31422060--31422276	71	3.1	70	90	2	339	40	18	18	21	1.91
31422035--31422301	117	2.3	116	87	5	385	39	19	17	23	1.92
31422060--31422302	46	5.2	46	83	4	272	39	19	18	22	1.92
31423144--31423243	42	2.4	42	96	0	182	26	27	10	37	1.88
31424104--31424141	20	1.9	20	88	0	58	36	10	0	52	1.36
31426365--31426426	31	2.0	31	100	0	124	25	29	9	35	1.88
31432545--31432702	48	3.3	48	87	4	212	34	31	13	20	1.91
31434862--31434911	21	2.5	20	80	6	57	28	4	22	46	1.70
31437829--31437959	27	4.9	27	76	1	111	23	29	12	33	1.92
31437857--31437977	54	2.2	53	84	5	145	23	29	14	32	1.94
31456706--31456748	22	2.0	21	82	13	52	41	0	0	58	0.98
31458241--31458281	18	2.2	19	91	4	66	60	0	0	39	0.96
31474716--31474771	20	2.7	21	83	10	62	64	8	5	21	1.42
31475502--31475799	50	5.8	51	79	6	268	26	20	28	24	1.99
31475502--31475747	100	2.4	105	83	5	315	26	19	30	23	1.98
31481775--31481816	20	2.0	22	90	9	70	45	14	0	40	1.45
31483822--31483851	15	2.0	15	93	0	51	46	3	6	43	1.46
31485902--31485953	25	2.1	25	88	0	77	17	23	15	44	1.86
31487423--31487610	56	3.2	56	72	21	195	43	1	3	51	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31487448--31487634	61	3.1	60	70	12	184	44	0	4	50	1.25
31487396--31487634	120	2.0	120	95	0	433	43	0	4	50	1.28
31487409--31487599	61	3.2	61	73	11	212	43	1	4	50	1.28
31487423--31487635	56	3.7	56	72	20	186	44	0	4	50	1.27
31487847--31487899	16	3.3	16	91	0	79	26	30	3	39	1.74
31495785--31495847	17	3.9	17	76	17	62	49	0	0	50	1.00
31499553--31499582	15	2.0	15	93	0	51	63	3	6	26	1.35
31501356--31501406	24	2.1	24	82	7	59	52	0	39	7	1.30
31513342--31513413	26	2.8	26	84	0	99	25	23	20	30	1.99
31517178--31517207	16	1.9	16	93	6	53	50	20	0	30	1.49
31550257--31550286	14	2.1	14	93	0	51	16	43	0	40	1.48
31553904--31554019	59	2.0	59	100	0	232	38	12	22	26	1.89
31557993--31558047	24	2.3	24	70	0	56	18	5	10	65	1.42
31568916--31569243	144	2.3	144	97	0	620	41	16	21	21	1.90
31570227--31570251	8	3.1	8	100	0	50	24	12	40	24	1.88
31572885--31572950	25	2.6	25	90	4	89	25	27	21	25	1.99
31586084--31586122	16	2.5	15	83	8	51	43	0	2	53	1.14
31586869--31586905	18	2.2	18	85	9	51	37	16	8	37	1.78
31587542--31587612	36	2.0	36	88	0	106	23	22	16	36	1.94
31589465--31589518	25	2.1	26	83	10	67	27	3	3	64	1.27
31591835--31592013	27	6.6	27	87	2	234	41	20	17	20	1.90
31591819--31592013	82	2.4	82	85	2	241	43	20	16	19	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31609261--31609299	17	2.3	17	86	8	53	76	2	10	10	1.10
31610527--31610656	49	2.7	49	81	2	154	30	18	29	22	1.97
31613946--31614001	24	2.3	24	96	0	103	32	17	17	32	1.94
31614138--31614209	20	3.7	19	85	9	92	55	6	0	37	1.27
31614222--31614276	20	2.8	19	78	8	65	70	3	1	23	1.12
31614222--31614301	39	2.0	39	83	11	101	63	3	2	30	1.25
31614479--31614539	5	12.2	5	92	0	77	21	31	19	27	1.97
31614479--31614565	15	5.7	15	75	15	81	21	29	17	31	1.96
31615068--31615153	30	2.9	30	91	0	136	50	11	18	19	1.77
31616077--31616101	13	1.9	13	100	0	50	24	8	20	48	1.76
31631474--31631541	15	4.5	15	85	3	82	35	16	8	39	1.79
31631474--31631541	30	2.2	31	89	2	102	35	16	8	39	1.79
31635925--31635988	26	2.5	26	84	0	83	21	26	23	28	1.99
31641946--31642016	38	1.9	36	88	5	106	50	9	1	38	1.44
31652126--31652882	379	2.0	379	93	0	1289	37	17	11	33	1.86
31657515--31657543	12	2.3	13	94	5	51	65	6	6	20	1.40
31659725--31659753	14	2.1	14	100	0	58	41	24	6	27	1.80
31665392--31665432	3	13.7	3	100	0	82	31	0	0	68	0.90
31665676--31665721	21	2.2	21	88	0	65	10	10	10	67	1.43
31666451--31666488	15	2.5	15	91	0	58	18	0	0	81	0.69
31674127--31674278	38	4.0	37	81	5	169	29	19	23	27	1.98
31674115--31674309	76	2.6	75	83	4	234	29	20	23	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31674808--31674860	21	2.5	20	82	14	63	50	1	0	47	1.12
31681086--31681248	68	2.4	68	83	4	186	39	19	19	21	1.93
31681140--31681290	68	2.2	68	81	4	171	41	20	19	19	1.91
31699794--31699842	24	2.0	24	100	0	98	57	14	4	24	1.55
31701899--31701979	39	2.1	39	100	0	162	41	11	9	37	1.74
31702289--31702323	18	2.0	17	88	5	52	54	0	0	45	0.99
31702246--31702497	82	3.2	82	64	14	218	47	3	3	46	1.34
31702170--31702492	157	2.0	160	93	3	562	43	3	5	47	1.41
31702426--31702467	15	2.7	16	82	14	52	52	2	0	45	1.13
31702435--31702476	15	2.9	15	82	10	52	52	0	0	47	1.00
31702424--31702721	120	2.5	121	91	5	480	48	5	3	42	1.40
31702545--31702587	15	2.8	16	79	10	54	53	2	0	44	1.13
31702461--31702651	61	3.2	61	69	16	198	47	6	3	42	1.44
31713560--31713804	122	2.0	122	95	0	445	38	19	10	31	1.86
31717437--31717471	18	1.9	18	88	0	52	20	28	8	42	1.81
31717735--31717778	21	2.1	21	87	8	63	36	34	22	6	1.81
31718008--31718069	22	2.8	22	92	4	99	48	27	0	24	1.51
31721888--31721935	22	2.1	23	85	11	64	29	0	2	68	1.01
31722408--31722448	21	2.0	21	86	9	59	21	0	9	68	1.18
31722421--31722973	114	5.1	108	82	8	624	24	1	14	59	1.42
31722419--31722968	208	2.5	219	83	9	709	24	1	14	59	1.42
31724167--31724207	20	2.1	19	86	9	55	21	0	7	70	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
31728341--31728586	108	2.3	105	84	6	293	57	15	1	25	1.47
31728530--31728577	25	1.9	25	83	8	62	60	10	2	27	1.41
31728662--31728688	14	1.9	14	100	0	54	92	7	0	0	0.38
31736553--31736595	17	2.4	18	84	11	61	16	20	41	20	1.90
31736946--31737358	27	15.4	27	78	2	339	38	19	19	23	1.93
31736946--31737358	54	7.7	54	80	4	386	38	19	19	23	1.93
31737338--31737414	26	3.0	25	79	5	75	23	16	23	36	1.94
31737377--31737473	24	4.0	24	90	0	149	23	6	20	49	1.71
31737377--31737485	24	4.5	24	88	0	137	23	6	21	48	1.73
31737554--31737611	27	2.1	27	84	12	75	20	25	20	32	1.97

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