genome.fa.s4.2.7.7.80.10.50.1000.107.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  107  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)
34248399--34248444	2	23.5	2	95	4	85	52	0	0	47	1.00
34254192--34254228	2	18.5	2	100	0	74	48	0	0	51	1.00
34254946--34254984	14	2.8	14	84	0	51	61	2	0	35	1.10
34255139--34255191	19	2.7	19	82	2	61	67	11	0	20	1.21
34257491--34257532	20	2.2	19	91	4	66	38	9	11	40	1.75
34258121--34258295	87	2.0	87	98	0	341	39	25	6	29	1.80
34262905--34263183	140	2.0	141	98	0	542	32	11	21	34	1.89
34265955--34265993	18	2.2	17	86	13	53	33	0	20	46	1.51
34266219--34266294	23	3.3	23	88	0	125	23	21	25	30	1.99
34279500--34279543	22	2.0	22	82	13	54	61	2	4	31	1.28
34279917--34279962	22	2.0	23	95	4	85	21	10	4	63	1.44
34280349--34280506	31	5.4	30	66	19	100	44	12	18	24	1.84
34280347--34280506	58	2.8	57	91	1	248	44	11	18	25	1.84
34280380--34280476	27	3.4	27	67	25	83	43	11	19	25	1.84
34280347--34280485	27	4.9	27	66	13	73	45	11	19	23	1.83
34280751--34280800	21	2.4	21	80	12	59	46	2	0	52	1.12
34289270--34289307	20	1.9	20	94	0	67	47	10	0	42	1.38
34289263--34289297	12	2.9	12	91	0	52	48	11	2	37	1.54
34299239--34299292	22	2.5	22	78	0	63	61	18	12	7	1.54
34304041--34304083	16	2.4	17	85	14	52	39	4	11	44	1.62
34312618--34312666	6	8.2	6	100	0	98	16	48	18	16	1.81
34315856--34316030	82	2.1	81	80	3	181	40	19	6	33	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34322576--34322692	38	3.1	38	97	0	216	25	6	17	50	1.70
34324048--34324153	43	2.5	42	82	13	128	18	18	27	34	1.95
34324876--34324917	2	21.5	2	95	4	77	52	0	0	47	1.00
34337910--34337970	31	2.0	31	100	0	122	36	14	13	36	1.85
34342333--34342438	41	2.6	41	90	0	176	26	19	23	30	1.98
34342334--34342481	41	3.6	41	83	1	136	27	20	23	28	1.99
34351374--34351436	29	2.3	27	83	5	72	63	9	1	25	1.34
34353667--34353740	6	13.2	6	74	14	61	77	0	20	2	0.90
34353667--34353728	16	3.9	16	86	0	88	79	0	19	1	0.82
34353667--34353728	32	1.9	32	93	0	106	79	0	19	1	0.82
34354082--34354176	45	2.1	47	82	7	115	44	6	3	46	1.44
34354716--34354774	27	2.2	27	85	8	77	76	5	1	16	1.05
34358097--34358167	36	2.0	36	91	0	115	42	14	18	25	1.87
34361340--34361380	20	2.0	20	95	0	73	36	29	12	21	1.90
34361808--34361851	3	14.7	3	95	0	79	63	0	2	34	1.07
34361850--34361893	3	14.7	3	90	0	70	34	4	0	61	1.16
34387960--34388019	27	2.3	26	80	5	66	30	6	3	60	1.39
34389542--34389572	15	2.1	15	93	0	53	51	12	0	35	1.40
34390864--34390905	11	3.7	11	81	6	57	2	9	2	85	0.77
34390860--34390905	23	2.1	23	88	11	71	2	10	2	84	0.79
34397060--34397805	44	17.0	44	79	5	704	31	25	14	29	1.94
34397058--34397810	132	5.7	132	86	2	1075	30	25	14	29	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34397071--34397805	264	2.8	264	93	0	1231	30	25	14	29	1.95
34398676--34398724	26	1.9	26	84	12	66	61	8	12	18	1.55
34413542--34413575	16	2.1	17	94	5	61	70	0	5	23	1.09
34413620--34413678	16	3.6	16	86	4	73	45	0	3	50	1.18
34417105--34417129	2	12.5	2	100	0	50	48	0	0	52	1.00
34418603--34419095	100	4.9	100	86	2	618	26	18	21	33	1.96
34418730--34419067	50	6.8	50	67	4	191	25	19	21	33	1.97
34419076--34419179	44	2.3	45	85	3	129	22	22	26	28	1.99
34419235--34419338	45	2.3	45	81	1	120	28	29	15	25	1.96
34419101--34419743	217	3.0	218	88	0	964	28	25	18	27	1.98
34419580--34419872	129	2.3	129	89	1	444	30	22	18	28	1.97
34419363--34420042	347	2.0	346	87	2	981	29	24	17	27	1.98
34419194--34420039	44	19.5	44	68	11	339	30	25	17	27	1.97
34420031--34420433	129	3.1	129	92	0	662	25	22	19	32	1.98
34420431--34420521	44	2.1	44	93	4	157	20	24	20	34	1.97
34421783--34421824	7	6.1	7	84	15	61	14	14	0	71	1.15
34422653--34422728	6	12.8	6	83	8	75	13	7	10	68	1.39
34422645--34422729	41	2.0	42	86	2	118	11	10	9	68	1.40
34422660--34422733	35	2.1	35	85	2	96	10	6	12	70	1.34
34426022--34426173	71	2.1	71	100	0	304	31	15	26	26	1.95
34427630--34427666	2	18.5	2	94	0	65	51	0	0	48	1.00
34433208--34433250	22	2.0	21	86	4	59	48	0	2	48	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34433572--34433605	14	2.3	14	90	10	50	41	0	2	55	1.15
34437788--34437902	61	1.9	59	89	3	176	40	3	4	51	1.39
34437794--34437951	61	2.6	60	84	7	162	39	3	6	50	1.46
34441833--34441957	61	2.1	60	93	1	214	41	5	23	29	1.77
34444974--34445044	30	2.3	31	80	2	90	42	0	19	38	1.52
34448430--34448475	11	4.4	11	74	20	53	43	2	0	54	1.12
34448422--34448509	20	4.8	18	72	20	67	43	3	1	52	1.25
34456658--34456707	18	2.8	18	81	9	66	46	0	14	40	1.44
34464362--34464437	21	3.6	21	78	3	73	31	3	21	43	1.71
34464661--34464702	20	2.1	20	82	8	50	35	21	16	26	1.94
34465550--34465699	39	3.9	38	78	8	169	45	20	4	30	1.69
34465550--34465701	78	2.0	77	88	3	225	45	20	3	30	1.69
34473381--34473923	88	6.2	87	85	3	694	23	25	24	26	2.00
34473381--34473923	264	2.1	264	89	0	825	23	25	24	26	2.00
34475176--34475207	15	2.1	16	94	5	57	0	18	0	81	0.70
34475189--34475235	24	2.0	24	83	8	60	12	17	0	70	1.17
34486222--34486287	21	3.2	20	82	8	78	31	1	19	46	1.59
34486230--34486301	21	3.4	21	79	7	74	29	2	19	48	1.63
34488137--34488161	13	1.9	13	100	0	50	40	8	0	52	1.31
34489166--34489207	19	2.3	18	76	15	50	45	2	7	45	1.44
34493582--34493784	43	4.7	43	82	3	230	30	25	18	25	1.98
34495457--34495669	7	29.9	7	74	9	117	44	33	0	21	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34495458--34495674	14	15.2	14	75	8	143	45	32	0	22	1.56
34495502--34495570	29	2.4	28	85	7	86	43	40	0	15	1.47
34495558--34495606	15	3.4	15	76	18	50	46	30	0	22	1.52
34496085--34496175	40	2.3	40	86	0	128	26	24	21	27	1.99
34496109--34496386	106	2.6	106	87	2	396	28	20	19	32	1.96
34496318--34496416	40	2.5	40	94	0	171	28	21	22	28	1.99
34503925--34503979	3	18.3	3	96	0	101	30	1	34	32	1.69
34513403--34513450	18	2.7	18	81	15	55	41	14	0	43	1.45
34514386--34514420	17	2.0	18	88	5	54	11	45	28	14	1.79
34522167--34522262	28	3.4	28	94	0	156	33	25	10	31	1.89
34524657--34524686	14	2.1	14	93	0	51	16	6	6	70	1.31
34526013--34526055	19	2.3	19	83	0	50	53	2	6	37	1.41
34526491--34526601	37	3.1	36	82	11	115	43	0	2	53	1.21
34526491--34526601	12	9.8	11	72	19	79	43	0	2	53	1.21
34530310--34530375	29	2.3	28	86	2	87	33	7	15	43	1.74
34542585--34542651	20	3.0	22	77	18	68	58	4	0	37	1.19
34547618--34547651	15	2.3	15	90	5	52	17	14	29	38	1.90
34547946--34548574	44	14.3	44	65	10	212	24	24	21	29	1.99
34547994--34548624	132	4.8	132	96	0	1127	24	25	20	29	1.99
34560050--34560240	98	1.9	98	92	0	319	36	25	10	27	1.89
34562074--34562107	15	2.3	15	90	5	52	17	14	29	38	1.90
34562359--34562479	44	2.8	44	79	2	127	28	20	16	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34562227--34562567	131	2.6	130	80	4	400	25	23	19	31	1.98
34562428--34562712	154	1.9	154	88	0	435	25	21	19	32	1.97
34562323--34562860	285	1.9	285	87	2	785	25	22	19	31	1.98
34562582--34562857	131	2.1	131	93	2	473	24	23	21	31	1.98
34584984--34585083	35	2.9	35	90	0	155	20	12	28	40	1.87
34584980--34585102	35	3.5	34	84	4	147	18	13	30	38	1.89
34595821--34595868	16	3.1	16	76	14	55	56	2	6	35	1.36
34595824--34595872	20	2.5	20	80	6	55	55	2	4	38	1.31
34596204--34596250	22	2.2	22	84	3	60	8	19	19	53	1.70
34596239--34596280	22	1.9	22	85	9	59	21	14	7	57	1.61

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