genome.fa.s4.2.7.7.80.10.50.1000.42.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  42  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)
12594237--12594378	50	2.8	50	82	0	176	27	22	28	21	1.99
12597208--12597337	40	3.3	39	81	4	152	26	19	32	21	1.97
12597215--12597332	20	5.9	19	71	16	69	26	19	33	20	1.96
12599693--12599786	24	3.2	31	64	27	85	40	6	11	41	1.67
12599677--12599791	58	2.0	58	100	0	230	42	6	12	38	1.69
12607626--12607658	2	16.5	2	100	0	66	0	51	0	48	1.00
12610406--12610468	31	2.0	31	100	0	126	26	9	19	44	1.81
12613123--12613165	18	2.3	18	88	11	61	20	0	27	51	1.48
12618485--12618596	42	2.7	42	81	4	120	48	18	16	16	1.82
12624511--12624571	30	2.0	30	93	0	104	29	22	14	32	1.94
12632843--12632883	22	2.0	22	85	9	59	60	2	19	17	1.46
12633561--12633593	18	1.9	18	88	11	52	45	6	0	48	1.27
12635528--12635602	31	2.5	30	85	8	91	45	0	2	52	1.15
12639645--12639686	20	2.1	20	95	0	75	16	0	7	76	1.00
12640545--12640593	19	2.5	20	80	9	57	34	4	0	61	1.15
12644738--12644810	26	2.8	26	89	4	103	30	13	9	46	1.75
12645464--12645635	89	1.9	89	91	0	281	28	17	14	39	1.89
12648142--12648173	16	2.0	16	100	0	64	43	18	0	37	1.51
12655829--12655859	10	3.0	10	95	4	53	61	0	0	38	0.96
12655877--12655948	27	2.6	26	80	12	81	68	2	1	27	1.12
12655877--12655948	22	3.8	19	76	16	71	68	2	1	27	1.12
12656566--12656608	13	3.3	13	83	0	59	34	30	9	25	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12658271--12658306	16	2.2	16	100	0	72	36	11	22	30	1.89
12661202--12661269	25	2.7	25	83	0	73	30	10	20	38	1.86
12661227--12661316	22	4.0	22	76	12	69	27	12	21	38	1.89
12663308--12663332	13	1.9	13	100	0	50	28	24	24	24	2.00
12669065--12669111	20	2.3	20	85	3	58	14	6	10	68	1.38
12670719--12670755	17	2.2	17	95	0	65	48	0	2	48	1.15
12670726--12670761	17	2.1	17	89	0	54	50	2	5	41	1.40
12679302--12679353	15	3.2	15	73	19	50	44	0	1	53	1.11
12679387--12679423	16	2.3	16	86	13	58	40	2	0	56	1.13
12679562--12679587	9	2.9	9	100	0	52	46	0	0	53	1.00
12680755--12680793	3	13.0	3	100	0	78	33	0	0	66	0.92
12682449--12682505	27	2.3	25	78	21	66	66	0	1	31	1.02
12685922--12685957	9	4.0	9	86	13	56	36	0	0	63	0.94
12688428--12688461	3	11.3	3	87	0	50	29	0	5	64	1.17
12689616--12689655	14	2.6	16	88	11	57	42	25	5	27	1.75
12690649--12690673	13	1.9	13	100	0	50	56	28	0	16	1.41
12690667--12690788	57	2.1	57	84	0	163	51	17	4	26	1.65
12690823--12691073	37	7.1	36	75	17	179	56	17	2	23	1.52
12690832--12691151	12	24.2	13	69	20	123	55	17	3	23	1.56
12690832--12691037	65	3.1	65	83	6	222	57	16	1	23	1.47
12690832--12691112	9	30.6	9	68	20	97	56	17	2	23	1.53
12691063--12691141	35	2.3	33	77	12	79	53	16	5	25	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12695036--12695072	11	3.2	12	88	7	51	64	5	0	29	1.15
12705765--12705873	20	5.2	20	71	14	76	13	22	25	37	1.92
12705764--12705868	41	2.5	42	78	4	113	14	22	24	38	1.92
12706335--12706399	28	2.3	28	81	2	67	38	10	21	29	1.87
12707647--12707701	24	2.3	24	100	0	110	43	3	5	47	1.44
12709139--12709214	39	1.9	39	82	12	93	47	14	19	18	1.83
12709307--12709433	48	2.6	48	85	4	184	16	28	9	45	1.78
12710131--12710156	11	2.4	11	100	0	52	26	0	11	61	1.30
12711624--12711675	26	2.0	26	85	7	70	44	3	1	50	1.31
12712845--12712900	20	2.5	22	83	11	62	58	3	0	37	1.15
12713261--12713368	9	12.2	9	78	9	80	47	20	0	32	1.51
12713261--12713364	43	2.4	44	90	4	165	47	20	0	32	1.50
12724565--12724613	25	1.9	25	84	12	64	40	12	12	34	1.80
12731079--12731136	28	2.1	28	100	0	116	46	6	24	22	1.76
12731860--12731884	11	2.3	11	100	0	50	28	0	8	64	1.22
12736689--12736727	20	2.0	20	85	10	53	28	12	23	35	1.91
12752024--12752110	35	2.4	36	84	7	115	41	31	14	12	1.84
12766808--12767101	51	5.8	51	77	7	301	28	15	26	29	1.96
12766808--12767089	102	2.8	102	92	0	440	29	15	26	29	1.96
12766815--12767134	102	3.1	102	87	1	311	30	14	26	29	1.95
12769093--12769137	15	3.1	14	81	9	54	71	4	22	2	1.15
12769310--12769354	18	2.5	19	75	13	51	22	40	0	37	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12775560--12775592	17	2.1	16	88	11	50	57	15	6	21	1.59
12777642--12777680	18	2.2	18	86	9	53	25	15	0	58	1.37
12781008--12781062	20	2.8	20	88	2	76	40	0	7	52	1.29
12781870--12781921	16	3.2	16	72	0	50	57	3	23	15	1.54
12782054--12782092	20	2.0	20	94	0	69	46	7	17	28	1.76
12784863--12784902	18	2.2	19	82	13	57	57	0	7	35	1.27
12785063--12785113	3	17.7	3	76	8	52	62	0	1	35	1.06
12786594--12786857	128	2.1	127	81	2	296	26	20	22	30	1.98
12786866--12787025	50	3.2	50	70	7	144	25	23	21	29	1.99
12786895--12787074	50	3.6	49	71	5	146	23	24	23	28	2.00
12787277--12787440	88	1.9	88	88	0	247	27	28	17	26	1.98
12787292--12787428	45	3.1	45	68	8	118	28	29	16	25	1.97
12792187--12792244	26	2.3	26	85	5	75	62	3	17	17	1.47
12792206--12792269	27	2.4	27	81	5	67	60	9	12	17	1.57
12799507--12799574	26	2.6	26	83	2	73	50	2	10	36	1.52
12802910--12802956	11	4.2	11	81	13	51	23	0	6	70	1.10
12802880--12803028	65	2.3	64	80	7	167	26	1	13	59	1.43
12806984--12807045	32	1.9	32	96	0	115	40	12	1	45	1.52
12815254--12815295	21	2.0	21	85	0	57	21	0	40	38	1.53
12815515--12815555	14	2.9	14	82	13	57	26	2	36	34	1.70
12817980--12818108	67	1.9	67	80	9	147	45	7	3	43	1.48
12818190--12818229	19	2.1	19	90	0	62	42	2	0	55	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12818196--12818250	19	2.9	19	84	7	60	40	5	0	54	1.23
12818217--12818250	17	1.9	17	88	5	50	38	5	0	55	1.24
12818372--12818898	9	60.2	9	79	7	577	48	19	0	31	1.52
12818317--12818905	27	22.7	27	83	6	579	49	19	0	31	1.53
12818441--12818906	219	2.1	219	92	0	774	48	20	0	30	1.50
12824370--12824441	21	3.4	21	92	0	117	37	18	41	2	1.65
12824857--12824953	42	2.3	42	80	8	108	26	16	23	32	1.96
12824882--12825116	42	5.5	41	78	8	213	28	19	20	32	1.96
12824881--12825106	85	2.7	83	78	13	226	28	19	20	31	1.97
12824874--12825116	127	1.9	129	83	5	323	28	19	20	32	1.97
12825232--12825377	72	2.0	72	95	0	265	34	19	21	25	1.96
12829128--12829172	5	9.8	5	85	9	53	20	0	0	80	0.72
12829128--12829172	13	3.3	15	76	20	53	20	0	0	80	0.72
12833653--12833797	7	21.7	6	89	5	87	73	12	0	13	1.15
12833669--12833799	7	18.7	7	92	5	205	72	12	0	13	1.17
12833804--12833836	12	2.5	14	90	9	52	72	0	27	0	0.85
12834673--12834698	12	2.2	12	100	0	52	69	0	15	15	1.20
12834667--12834719	20	2.8	18	89	10	88	77	0	11	11	1.00
12834669--12834710	8	5.8	8	78	21	56	76	0	11	11	1.03
12835899--12836579	88	7.8	88	92	2	1034	28	23	24	24	2.00
12836738--12837129	44	9.0	43	71	11	264	30	19	21	27	1.98
12836597--12836878	142	2.0	141	86	4	390	33	20	19	25	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12836754--12837078	175	1.9	175	94	0	569	30	20	20	28	1.98
12836611--12837242	304	2.0	307	87	5	900	31	19	20	28	1.97
12836925--12837223	129	2.3	129	92	0	499	30	18	22	29	1.97
12838889--12838933	5	9.8	5	85	9	53	20	0	0	80	0.72
12838889--12838933	13	3.3	15	76	20	53	20	0	0	80	0.72
12845330--12845364	17	2.1	17	88	0	52	2	40	37	20	1.67
12857453--12857506	29	1.9	28	92	7	92	27	16	27	27	1.97
12857514--12857555	18	2.4	17	88	11	59	33	4	42	19	1.72
12858453--12858494	15	2.7	16	82	14	52	52	2	0	45	1.13
12858462--12858503	15	2.9	15	82	10	52	52	0	0	47	1.00

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