genome.fa.s4.2.7.7.80.10.50.1000.23.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  23  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)
6816139--6816186	25	2.0	24	83	4	60	39	20	22	16	1.92
6816784--6816825	21	2.0	21	85	0	57	40	23	2	33	1.68
6824649--6824694	24	1.9	24	82	8	58	54	2	6	36	1.39
6830745--6830788	21	2.2	20	83	4	52	63	0	0	36	0.95
6831526--6831577	24	2.1	24	85	3	68	63	1	1	32	1.16
6831720--6831757	17	2.3	17	86	4	51	65	2	5	26	1.27
6831752--6831807	22	2.6	21	86	11	69	69	5	0	25	1.09
6831752--6831809	29	2.0	29	83	12	75	68	5	0	25	1.10
6834240--6834270	14	2.2	14	94	0	53	48	12	0	38	1.42
6838554--6838582	9	3.0	10	90	10	51	82	0	0	17	0.66
6838718--6838787	3	23.3	3	91	0	113	64	0	4	31	1.13
6841863--6842146	33	7.7	33	71	20	190	31	25	19	23	1.98
6841977--6842114	42	3.5	42	72	17	150	32	26	16	24	1.96
6841864--6842150	75	3.8	75	93	1	477	31	26	18	23	1.98
6842775--6842807	11	2.8	12	90	9	50	45	15	3	36	1.61
6845408--6845438	14	2.2	14	94	0	53	48	12	0	38	1.42
6846121--6846201	40	2.0	40	90	0	126	17	23	8	50	1.73
6847872--6847949	37	2.1	37	100	0	156	58	12	2	25	1.47
6849057--6849091	11	3.2	11	87	0	52	74	2	0	22	0.95
6854767--6854797	16	1.9	16	100	0	62	45	6	0	48	1.28
6858033--6858063	9	3.4	9	90	0	53	25	12	22	38	1.90
6858031--6858073	18	2.3	18	92	4	68	32	13	18	34	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6861287--6861341	6	8.8	6	86	6	74	45	16	20	18	1.86
6861321--6861470	45	3.3	45	87	7	223	40	19	19	20	1.91
6861788--6861846	28	2.0	31	83	9	79	44	0	5	50	1.24
6862726--6862858	45	3.0	43	82	11	157	24	18	26	30	1.97
6865806--6865847	3	14.0	3	85	9	59	28	0	0	71	0.86
6866965--6867023	22	2.5	22	78	8	64	55	3	0	40	1.16
6867587--6867639	17	3.1	17	83	5	54	47	1	0	50	1.12
6869507--6869534	2	14.0	2	100	0	56	50	0	50	0	1.00
6880177--6880206	2	14.5	2	93	6	51	50	3	0	46	1.18
6886835--6886875	20	2.0	20	95	0	73	14	29	14	41	1.86
6895823--6895882	25	2.3	26	75	18	61	36	3	13	46	1.60
6896154--6896220	26	2.6	26	90	0	107	20	29	23	25	1.99
6898991--6899022	6	5.3	6	100	0	64	84	0	0	15	0.63
6908631--6908871	50	4.7	50	83	5	277	19	29	23	26	1.98
6908632--6908871	100	2.3	104	87	6	337	20	29	23	27	1.98
6912015--6912082	25	2.6	27	86	13	97	26	27	7	38	1.83
6913426--6913568	71	2.0	72	94	1	252	26	9	20	43	1.82
6913761--6913788	14	2.0	14	100	0	56	57	0	0	42	0.99
6913821--6913905	32	2.6	33	77	5	93	44	18	10	25	1.82
6913882--6913958	14	5.0	15	71	20	52	42	15	9	32	1.78
6913898--6913937	20	2.0	20	90	0	62	50	12	10	27	1.72
6913886--6913952	34	1.9	35	90	3	109	46	13	8	31	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6913921--6913960	14	2.9	14	84	0	53	42	17	7	32	1.77
6915113--6915141	13	2.2	13	100	0	58	41	41	0	17	1.49
6915285--6915349	9	7.1	9	83	10	78	20	10	27	41	1.85
6925009--6925061	22	2.4	22	90	6	81	24	20	22	32	1.98
6927823--6927857	18	1.9	18	94	0	61	48	0	0	51	1.00
6928250--6928416	86	2.0	85	89	3	255	33	22	21	22	1.97
6928250--6928417	42	3.9	42	85	3	228	33	22	21	22	1.97
6928848--6928898	21	2.4	21	80	0	57	7	45	11	35	1.70
6933914--6934012	16	6.1	16	71	9	67	32	3	18	46	1.64
6933902--6933959	25	2.3	26	85	5	75	37	1	15	44	1.57
6933916--6933975	25	2.4	25	82	0	75	33	3	20	43	1.68
6933914--6934030	41	2.9	41	82	5	130	31	2	19	46	1.64
6933982--6934037	25	2.2	25	93	0	94	30	3	19	46	1.67
6935336--6935379	6	7.3	6	92	0	70	47	13	2	36	1.56
6936141--6936179	20	1.9	21	94	5	71	41	12	5	41	1.65
6936447--6936482	15	2.3	16	90	4	56	36	2	0	61	1.11
6936646--6936700	7	7.9	7	80	8	58	43	40	1	14	1.56
6937410--6937736	112	2.9	110	70	13	252	25	19	24	30	1.98
6938814--6938894	34	2.4	34	76	15	89	51	6	13	28	1.65
6940326--6940372	24	2.0	24	83	8	60	29	0	4	65	1.11
6943892--6943967	31	2.4	32	80	2	91	53	5	6	34	1.49
6951572--6951627	22	2.5	23	94	2	96	48	7	8	35	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6951588--6951637	22	2.2	22	89	3	73	60	6	6	28	1.44
6952328--6952383	28	2.0	28	82	0	67	42	12	0	44	1.42
6952800--6952887	45	2.0	45	88	4	133	40	19	17	22	1.91
6958836--6958893	15	3.8	15	86	4	80	41	1	32	24	1.65
6958836--6958889	5	10.6	5	78	4	54	38	1	35	24	1.66
6959341--6959383	15	2.9	15	92	0	68	27	32	0	39	1.57
6984057--6984618	281	2.0	280	94	0	989	33	16	16	34	1.90
6984337--6987595	755	4.3	750	89	2	4881	34	15	13	35	1.88
6988043--6988069	10	2.7	10	100	0	54	18	0	18	62	1.32
6988890--6988922	7	5.0	7	89	10	52	24	0	0	75	0.80
6988903--6988944	19	2.2	19	86	0	57	21	4	0	73	1.01
6988890--6988945	25	2.2	24	84	9	76	21	3	0	75	0.96
6992399--6992542	27	5.3	27	78	7	116	40	22	17	20	1.91
6992395--6992720	54	6.0	55	77	7	145	36	20	20	22	1.95
6992400--6992597	81	2.4	83	81	8	214	38	22	18	21	1.93
6992510--6992738	27	8.5	27	84	0	271	32	20	22	24	1.98
6992540--6992738	81	2.5	81	90	0	317	32	19	22	25	1.98
6992960--6992984	11	2.3	11	100	0	50	40	8	0	52	1.31
6992943--6993104	51	3.7	41	72	22	125	33	3	0	63	1.10
6992970--6993081	51	2.1	54	93	6	194	33	2	0	63	1.09
6992960--6993098	51	2.7	50	84	9	174	33	2	0	64	1.09
6993390--6993471	24	3.5	24	81	5	78	19	4	25	50	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6993587--6993644	26	2.2	26	78	0	62	20	17	24	37	1.93
6993643--6993898	32	8.0	31	78	5	226	19	20	22	37	1.95
6993661--6993891	96	2.4	96	83	2	286	20	20	23	35	1.96
6996998--6997067	5	13.0	5	84	11	61	14	1	4	80	0.94
6996999--6997067	6	11.5	6	82	15	65	13	1	4	81	0.91
7017000--7017032	16	2.1	16	100	0	66	24	12	12	51	1.73
7025048--7025171	40	3.1	40	88	0	185	16	16	25	41	1.88
7025056--7025186	40	3.4	38	81	6	104	16	14	26	42	1.86
7028016--7028565	274	2.0	274	94	0	974	32	24	11	32	1.91
7032425--7032459	18	1.9	18	88	0	52	71	8	8	11	1.31
7032988--7033232	122	2.0	122	100	0	490	44	13	13	28	1.82
7033728--7033775	18	2.7	18	83	6	53	14	8	6	70	1.31
7053181--7053226	24	1.9	24	82	8	58	47	4	8	39	1.54
7053334--7053384	21	2.4	21	93	0	84	37	31	0	31	1.58
7053655--7053722	34	2.0	34	100	0	136	41	26	0	32	1.56
7060568--7060592	2	12.5	2	100	0	50	52	0	0	48	1.00
7062186--7062211	2	13.0	2	100	0	52	50	0	0	50	1.00
7064690--7064742	23	2.3	22	81	15	63	52	0	0	47	1.00
7067217--7067244	13	2.2	13	100	0	56	32	28	14	25	1.94
7067838--7068009	30	5.7	30	88	2	220	43	16	8	31	1.78
7067839--7068004	90	1.8	90	88	0	251	43	16	9	31	1.79
7078722--7078810	37	2.4	37	92	0	151	42	14	7	34	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7078853--7078928	33	2.3	33	97	0	143	43	15	5	35	1.70
7081994--7082187	92	2.1	92	87	3	275	45	4	4	45	1.43
7082130--7082177	26	1.9	25	84	16	64	45	0	2	52	1.12
7082256--7082466	66	3.4	63	67	23	176	40	3	6	49	1.45
7082218--7082510	120	2.4	120	90	5	468	41	2	5	50	1.40
7082463--7082504	15	2.9	15	82	10	52	47	0	0	52	1.00
7082447--7082762	156	2.0	157	93	1	546	47	5	3	43	1.44
7083880--7083915	2	18.5	2	94	5	65	50	0	0	50	1.00
7084541--7084574	2	17.5	2	93	6	61	52	0	0	47	1.00
7084540--7084579	10	4.3	9	90	9	55	55	0	0	45	0.99

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