genome.fa.s1.2.7.7.80.10.50.1000.34.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  34  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)
10812637--10812702	20	3.6	18	79	8	80	22	9	28	39	1.85
10812637--10812701	17	3.6	17	81	6	67	23	9	29	38	1.85
10818282--10818358	6	12.5	6	75	15	59	16	1	6	75	1.08
10818667--10818700	17	2.0	17	100	0	68	17	5	23	52	1.66
10822568--10822618	20	2.5	20	93	0	84	17	35	15	31	1.92
10822541--10822660	61	2.0	61	81	5	143	15	25	19	39	1.91
10823664--10823714	15	3.4	15	75	20	61	23	29	33	13	1.93
10823658--10823725	30	2.3	30	92	0	118	17	27	35	19	1.94
10834217--10834257	13	2.8	15	75	17	50	58	2	0	39	1.11
10834241--10834309	26	2.6	28	77	11	72	59	5	1	33	1.30
10834925--10834983	31	1.9	31	82	6	75	28	3	3	64	1.26
10836251--10836276	5	5.2	5	100	0	52	19	61	19	0	1.35
10837541--10837606	31	2.1	31	85	0	87	39	10	9	40	1.71
10843888--10843919	2	16.5	2	93	6	57	50	0	0	50	1.00
10846478--10846521	21	2.1	21	100	0	88	29	13	38	18	1.89
10849811--10849837	1	27.0	1	100	0	54	100	0	0	0	0.00
10857982--10858026	20	2.3	19	84	3	54	73	2	22	2	1.05
10864962--10865006	20	2.3	19	88	3	63	75	2	20	2	1.01
10865909--10866021	37	2.9	40	75	9	115	25	17	24	31	1.97
10869887--10869962	23	3.3	23	92	0	134	30	26	21	22	1.99
10877287--10877339	23	2.3	23	93	0	97	32	26	20	20	1.98
10881639--10881673	17	2.1	17	89	10	54	57	5	0	37	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10900230--10900354	28	4.4	28	85	2	160	30	11	26	32	1.91
10900230--10900354	57	2.2	56	84	4	162	30	11	26	32	1.91
10913674--10913740	24	2.8	24	86	4	91	28	16	4	50	1.64
10915715--10915758	18	2.4	18	84	3	52	61	2	2	34	1.21
10918581--10918654	11	6.7	11	73	23	59	70	2	22	4	1.17
10926558--10926594	16	2.3	16	86	13	58	40	0	0	59	0.97
10928803--10928876	35	2.2	35	82	4	89	33	1	1	63	1.11
10929519--10929560	21	2.0	22	90	4	68	38	26	4	30	1.77
10932547--10932605	25	2.3	27	80	16	72	45	5	22	27	1.73
10935054--10935208	42	3.7	42	86	10	201	28	27	16	27	1.97
10941722--10941824	21	4.9	21	71	13	59	49	3	1	44	1.31
10941748--10941863	62	1.9	61	85	5	164	50	4	2	42	1.35
10941748--10941946	62	3.2	59	73	18	161	51	5	3	40	1.39
10944016--10944068	27	2.0	27	92	7	90	37	22	16	22	1.94
10944832--10944888	29	2.0	29	92	0	96	28	10	12	49	1.73
10945937--10945995	30	2.0	30	89	0	91	30	22	3	44	1.69
10951953--10952109	43	3.7	42	80	9	174	33	25	19	22	1.97
10953907--10953931	11	2.3	11	100	0	50	28	0	0	72	0.86
10956839--10957191	186	1.9	186	88	2	539	30	17	18	34	1.94
10957025--10957291	126	2.1	126	85	1	356	31	16	17	35	1.92
10959894--10959956	22	3.2	22	64	36	61	41	3	14	41	1.61
10959892--10959963	37	1.9	37	97	0	135	40	4	15	40	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10961427--10961494	27	2.5	28	73	7	68	25	2	17	54	1.57
10962870--10962914	14	3.1	14	80	3	54	40	20	8	31	1.83
10962832--10962897	34	1.9	35	90	3	107	43	15	10	30	1.80
10962927--10963032	33	3.3	32	84	10	137	50	11	0	37	1.45
10963927--10963970	18	2.3	20	88	7	65	63	0	2	34	1.07
10968854--10968922	26	2.7	25	77	6	75	71	4	20	4	1.21
10968854--10968945	10	8.8	10	72	12	51	71	3	21	3	1.14
10968905--10968945	16	2.6	15	85	11	55	78	0	21	0	0.76
10968907--10968941	12	2.8	13	82	8	54	77	0	22	0	0.78
10969645--10969669	11	2.3	11	100	0	50	36	0	8	56	1.29
10971093--10971179	44	2.0	45	90	2	140	37	9	31	21	1.85
10971696--10971760	28	2.3	28	92	7	105	0	10	12	76	1.01
10971696--10971749	28	1.9	28	100	0	108	0	12	12	74	1.08
10972309--10972404	31	3.1	31	95	3	174	45	13	9	31	1.75
10973755--10973815	29	2.1	29	100	0	122	39	9	9	40	1.72
10979782--10979820	17	2.2	18	86	4	53	28	7	17	46	1.76
10983854--10983922	33	2.1	33	97	0	129	34	13	5	46	1.67
10995582--10995650	28	2.4	29	80	4	77	30	2	11	55	1.50
10996231--10996272	20	2.0	21	86	4	59	9	9	16	64	1.49
10996928--10996993	31	2.1	31	91	0	105	39	4	7	48	1.52
10999216--10999270	2	27.5	2	96	0	101	0	1	49	49	1.11
11014867--11014899	17	2.1	17	88	11	52	27	0	0	72	0.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11015413--11015464	21	2.5	21	78	12	61	23	1	34	40	1.66
11015674--11015715	22	1.9	22	95	0	75	45	14	9	30	1.77
11022801--11022840	20	2.0	20	85	4	55	15	2	5	77	1.04
11023317--11023378	23	2.7	23	87	2	90	51	0	0	48	1.00
11023352--11023393	16	2.6	16	92	0	66	50	0	4	45	1.23
11023404--11023549	59	2.5	59	95	2	258	40	4	8	46	1.55
11023466--11023490	9	2.8	9	100	0	50	36	0	8	56	1.29
11023457--11023582	68	1.9	68	90	5	202	41	6	7	44	1.59
11023525--11023552	9	3.1	9	100	0	56	32	0	10	57	1.33
11031855--11031912	13	4.2	13	74	20	55	22	5	0	72	1.04
11031860--11031919	22	2.9	21	85	11	72	21	6	0	71	1.08
11031854--11031911	12	5.2	11	79	20	59	20	5	0	74	1.01
11031855--11031918	7	9.3	7	75	20	55	21	6	0	71	1.07
11032818--11032857	14	2.9	14	84	0	53	87	2	10	0	0.63
11032818--11032857	20	2.0	21	90	5	64	87	2	10	0	0.63
11038389--11038440	26	2.0	26	100	0	104	19	23	19	38	1.93
11040534--11040588	27	2.0	28	82	3	67	25	10	12	50	1.73
11060931--11060973	2	21.5	2	100	0	86	0	48	0	51	1.00
11061848--11061912	31	2.1	31	86	11	89	43	9	15	32	1.78
11064856--11064907	16	3.2	16	94	0	95	26	0	34	38	1.57
11066497--11066526	13	2.3	13	100	0	60	60	13	6	20	1.55
11068657--11068697	8	5.0	8	82	5	55	60	0	14	24	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11069096--11069134	4	9.5	4	88	5	60	76	0	0	23	0.78
11069208--11069241	2	17.0	2	100	0	68	50	0	0	50	1.00
11069264--11069305	3	15.0	3	80	14	54	64	2	0	33	1.07
11069264--11069305	10	3.8	11	84	9	50	64	2	0	33	1.07
11069257--11069321	30	2.3	28	82	10	78	66	1	3	29	1.16
11069990--11070014	6	4.2	6	100	0	50	84	0	0	16	0.63
11070804--11070986	44	4.2	44	69	14	110	28	20	21	30	1.98
11070741--11071008	129	2.1	129	89	0	401	27	22	19	30	1.98
11070824--11071006	44	4.2	43	73	10	149	26	23	20	28	1.99
11071619--11071900	129	2.2	129	92	1	458	31	21	18	29	1.97
11071696--11072247	175	3.2	175	87	4	787	29	22	18	29	1.97
11071523--11072077	304	1.8	304	94	0	977	29	22	19	29	1.98
11072034--11072364	129	2.6	128	80	4	301	28	21	18	32	1.97
11071523--11072325	304	2.6	304	84	5	898	29	22	18	29	1.97
11072139--11072325	44	4.3	45	72	8	138	30	20	17	32	1.95
11072331--11072570	88	2.7	88	81	5	281	24	24	22	28	1.99
11072430--11073070	87	7.4	87	86	4	805	25	23	21	29	1.99
11072430--11073072	172	3.7	173	87	5	879	25	23	21	29	1.99
11074169--11074215	21	2.2	21	88	0	67	25	38	10	25	1.88
11074300--11074347	17	2.6	19	83	6	64	12	10	0	77	1.00
11074307--11074348	9	4.6	9	80	16	50	11	9	0	78	0.96
11074310--11074347	19	1.9	21	89	10	62	13	10	0	76	1.02
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11075170--11075246	20	3.9	21	86	9	92	11	1	9	77	1.04
11075168--11075244	27	3.0	26	76	12	70	12	1	9	76	1.07
11075196--11075246	9	5.4	9	88	9	75	9	0	7	82	0.85
11075177--11075246	29	2.4	29	83	13	90	11	0	8	80	0.92
11075177--11075239	21	3.0	21	88	9	94	11	0	9	79	0.94
11075196--11075257	29	2.2	29	85	2	81	12	0	8	79	0.94
11077860--11077902	19	2.3	17	78	21	50	41	13	23	20	1.88
11079818--11079858	8	5.0	8	82	5	55	60	0	14	24	1.34
11080391--11080438	3	17.0	3	83	12	66	64	2	0	33	1.05
11080391--11080438	16	2.9	17	81	12	64	64	2	0	33	1.05

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