genome.fa.s4.2.7.7.80.10.50.1000.90.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  90  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)
28967946--28968078	25	5.2	25	86	1	176	45	23	0	30	1.58
28972714--28972747	17	2.0	17	100	0	68	41	11	41	5	1.66
28974088--28974131	22	2.0	22	90	0	70	45	27	18	9	1.79
28974163--28974245	30	2.7	31	83	10	100	39	0	8	51	1.32
28978424--28978516	25	3.7	25	75	5	82	22	22	19	35	1.96
28979162--28979207	22	2.0	23	95	4	85	13	8	19	58	1.60
28992853--28992908	29	1.9	29	85	0	76	33	16	16	33	1.91
28994101--28994158	3	19.3	3	90	0	89	70	0	27	1	0.97
28994100--28994158	15	3.9	15	90	0	100	71	0	27	1	0.96
28994209--28994301	42	2.3	42	81	3	100	32	16	16	35	1.91
28994201--28994301	40	2.5	40	78	3	112	30	16	16	35	1.92
29000551--29000603	25	2.2	25	93	3	90	37	26	22	13	1.91
29004009--29004074	35	1.9	34	87	3	96	31	21	21	25	1.98
29004198--29004245	22	2.2	22	88	0	69	25	18	18	37	1.94
29006458--29006507	25	2.0	25	100	0	100	32	20	24	24	1.98
29013106--29013165	3	20.0	3	100	0	120	33	0	0	66	0.92
29013508--29013571	31	2.1	31	87	0	92	39	4	7	48	1.53
29021345--29021393	13	3.2	16	69	19	50	48	0	0	51	1.00
29029891--29030160	95	2.8	95	80	3	283	39	3	16	40	1.65
29030204--29030631	126	3.4	126	89	0	669	33	20	21	25	1.97
29030579--29030662	44	1.9	44	92	0	141	27	28	21	22	1.99
29031193--29031217	7	3.6	7	100	0	50	56	16	0	28	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29032162--29032225	18	3.6	18	69	23	55	60	3	0	35	1.12
29032395--29032439	21	2.1	22	95	4	83	37	0	37	24	1.56
29032395--29032439	11	4.2	11	94	5	83	37	0	37	24	1.56
29032435--29032462	12	2.3	12	100	0	56	50	0	28	21	1.49
29034667--29034731	27	2.4	27	82	2	78	44	12	12	30	1.79
29034844--29034868	2	12.5	2	100	0	50	48	0	0	52	1.00
29035827--29035868	11	3.8	11	78	9	50	28	2	2	66	1.16
29035808--29035867	21	2.9	21	87	7	79	30	3	3	63	1.27
29041723--29041920	67	3.0	66	69	14	174	40	3	5	50	1.43
29041852--29041910	17	3.6	17	75	22	63	38	1	1	57	1.19
29044415--29044739	18	18.5	17	71	16	184	45	12	11	31	1.77
29044415--29044840	36	11.7	35	74	11	281	46	11	10	31	1.73
29044615--29044651	19	1.9	19	89	10	58	37	13	10	37	1.80
29044455--29044819	17	20.2	17	72	15	202	46	11	10	30	1.75
29044454--29044739	18	16.2	17	73	13	188	45	12	11	30	1.78
29044760--29044840	21	4.1	20	79	14	96	49	8	7	34	1.62
29044451--29044840	18	21.2	20	72	17	159	46	11	10	31	1.73
29044882--29044925	18	2.5	19	82	10	58	52	11	15	20	1.74
29045257--29045295	18	2.0	20	85	9	55	76	5	0	17	0.96
29045817--29045852	4	9.2	4	93	6	65	0	25	0	75	0.81
29045816--29045848	15	2.2	15	100	0	66	0	27	0	72	0.85
29045787--29045853	19	3.6	19	80	7	75	1	25	0	73	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29045985--29046034	21	2.4	20	77	9	55	0	12	10	78	0.98
29046322--29046392	29	2.4	30	81	11	76	46	5	15	32	1.69
29046716--29047839	76	14.7	75	82	6	1185	34	20	14	30	1.93
29046968--29047140	93	1.9	93	95	0	310	28	22	13	35	1.93
29047063--29047839	74	10.4	75	88	2	1084	36	20	14	29	1.92
29047063--29047839	150	5.2	149	89	3	1114	36	20	14	29	1.92
29047064--29047839	224	3.5	224	88	3	1087	36	20	14	28	1.92
29055859--29055883	9	2.8	9	100	0	50	8	44	0	48	1.32
29059596--29059917	18	18.3	17	75	14	235	44	12	11	30	1.78
29059602--29059914	53	5.9	54	74	15	230	46	12	12	29	1.78
29059792--29059829	20	1.9	19	89	5	58	42	13	7	36	1.73
29059875--29060005	57	2.3	58	79	10	135	44	9	12	33	1.75
29059596--29059917	35	9.1	35	75	10	273	44	12	11	30	1.78
29059954--29060035	22	4.2	19	74	16	78	47	10	6	35	1.64
29059952--29060035	38	2.2	40	82	8	111	48	10	5	34	1.62
29059977--29060037	17	3.4	17	70	16	50	49	9	6	34	1.62
29060099--29060148	17	2.8	18	77	14	59	46	10	14	30	1.77
29060478--29060516	18	2.0	20	85	9	55	76	5	0	17	0.96
29061019--29061086	4	17.5	4	76	11	70	0	23	1	75	0.89
29061020--29061080	31	1.9	32	87	9	90	0	24	1	73	0.92
29061027--29061086	23	2.6	24	84	5	79	0	25	1	73	0.93
29061023--29061080	15	3.9	15	79	20	68	0	24	1	74	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29066452--29066599	35	4.2	34	82	4	154	18	12	29	39	1.88
29067101--29067143	22	2.0	22	100	0	86	23	25	13	37	1.92
29070482--29070549	22	3.3	21	69	21	63	27	4	22	45	1.71
29070473--29070652	39	4.6	39	92	0	261	30	4	21	43	1.72
29074100--29074128	14	2.1	14	100	0	58	17	20	34	27	1.95
29076181--29076244	33	1.9	34	84	9	87	48	3	3	45	1.34
29077694--29077728	11	3.2	11	88	11	54	68	2	0	28	1.04
29077695--29077732	11	3.3	12	82	10	53	65	2	0	31	1.06
29081058--29081099	21	2.0	22	85	4	59	57	0	2	40	1.12
29081588--29081626	20	2.0	20	84	0	51	53	0	10	35	1.35
29081965--29082097	61	2.2	58	82	6	169	51	3	1	43	1.29
29083153--29083183	15	2.1	15	100	0	62	29	25	0	45	1.54
29087170--29087621	38	11.9	38	84	1	530	15	16	24	43	1.86
29087174--29087621	188	2.4	190	85	3	607	15	16	24	43	1.86
29091081--29091282	40	5.0	40	76	4	190	24	25	15	34	1.95
29094872--29094910	3	13.0	3	100	0	78	33	0	0	66	0.92
29094930--29094968	18	2.2	18	85	0	51	56	5	0	38	1.22
29096990--29097032	12	3.8	11	79	14	52	60	0	39	0	0.97
29097780--29097822	22	2.0	22	90	0	68	32	9	0	58	1.30
29098776--29098810	3	11.7	3	87	0	52	62	2	2	31	1.24
29099630--29099685	22	2.5	23	82	2	69	51	1	1	44	1.22
29099661--29099700	16	2.5	16	91	0	62	47	2	7	42	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29099711--29099880	59	2.9	59	97	0	313	40	4	9	45	1.57
29099947--29099991	24	1.9	23	90	4	72	60	2	2	35	1.22
29101911--29101953	7	6.1	7	100	0	86	27	0	13	58	1.37
29101910--29101959	21	2.4	21	84	15	77	30	0	14	56	1.39
29102604--29102643	18	2.2	18	95	0	71	22	30	5	42	1.75
29103224--29103296	21	3.4	21	84	1	101	39	35	1	23	1.63
29103269--29103363	29	3.3	29	89	4	140	48	34	1	15	1.53
29103290--29103379	22	3.8	22	79	18	83	51	33	1	14	1.50
29103348--29103400	15	3.6	15	78	14	56	50	26	0	22	1.49
29103297--29103396	51	2.0	51	83	0	128	51	31	1	17	1.52
29103348--29103404	14	3.9	14	75	6	51	47	29	0	22	1.52
29106100--29106128	15	1.9	15	100	0	58	48	3	0	48	1.18
29107342--29107499	77	2.0	78	98	1	309	32	3	20	44	1.67
29108773--29108846	20	3.7	20	92	0	121	12	31	32	24	1.92
29112091--29112134	23	1.9	23	85	0	61	29	20	22	27	1.99
29112550--29112632	22	3.9	20	70	10	58	25	1	27	45	1.61
29112551--29112690	14	9.8	14	68	13	61	22	0	30	46	1.57
29112627--29112687	21	2.9	22	80	4	81	18	0	36	45	1.49
29112600--29112733	7	18.7	7	72	13	58	22	0	34	43	1.54
29112993--29113217	7	31.9	7	69	16	56	24	0	29	45	1.59
29112981--29113130	14	10.8	13	73	13	81	22	0	30	47	1.56
29112993--29113124	21	6.4	19	70	20	70	22	0	28	48	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29113008--29113110	48	2.1	48	82	12	122	22	0	28	48	1.57
29113149--29113217	14	4.9	14	73	3	66	24	1	27	46	1.61
29113145--29113211	29	2.4	28	82	7	73	25	1	26	46	1.62
29114437--29114480	3	14.7	3	100	0	88	31	0	0	68	0.90
29120178--29120375	98	2.0	98	95	4	357	25	9	16	48	1.75
29125491--29125675	43	4.3	42	80	6	158	24	11	26	37	1.89
29125492--29125675	86	2.1	86	84	4	228	24	11	26	37	1.89
29125551--29125689	43	3.2	43	77	3	154	25	14	24	35	1.93
29126633--29126703	30	2.3	32	80	9	85	49	9	11	29	1.71
29127010--29127054	22	1.9	24	86	13	67	48	4	4	42	1.43

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