genome.fa.s9.2.7.7.80.10.50.1000.117.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  117  of  226  ( 27023 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)
39919964--39920080	41	2.9	41	83	5	121	29	25	19	25	1.99
39920935--39920965	9	3.4	9	95	0	53	61	25	0	12	1.32
39920928--39920975	18	2.7	18	80	6	53	60	22	0	16	1.36
39921670--39921694	13	1.9	13	100	0	50	68	24	0	8	1.16
39922797--39922821	2	12.5	2	100	0	50	48	0	0	52	1.00
39929167--39929208	21	2.0	21	100	0	84	28	4	28	38	1.77
39929314--39929590	88	3.2	88	88	3	432	35	15	15	33	1.89
39938697--39938860	78	2.1	78	93	0	274	23	25	3	48	1.65
39946390--39947375	497	2.0	487	86	5	1376	29	22	15	31	1.95
39948722--39948756	16	2.1	17	89	5	54	17	8	8	65	1.44
39953436--39953486	24	2.1	25	82	10	61	50	1	0	47	1.12
39954747--39954787	3	13.7	3	84	0	55	34	0	31	34	1.58
39954747--39954786	12	3.3	12	92	0	62	35	0	30	35	1.58
39959098--39959142	19	2.6	17	80	16	56	35	0	0	64	0.94
39960901--39960936	9	3.9	9	88	3	54	33	11	13	41	1.80
39961596--39961640	13	3.5	13	84	0	63	22	8	31	37	1.85
39962180--39962234	21	2.6	21	88	0	83	23	9	38	29	1.85
39968598--39968772	72	2.4	73	83	6	230	53	13	6	26	1.64
39969191--39969238	18	2.7	18	96	0	87	39	12	12	35	1.81
39973320--39973442	25	5.2	25	78	11	141	48	23	24	3	1.65
39973310--39973392	19	4.1	19	75	17	76	50	21	25	2	1.61
39973310--39973417	44	2.5	44	90	0	171	50	23	24	1	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39973392--39973465	19	3.6	19	70	20	60	50	20	24	5	1.69
39973320--39973459	69	2.0	69	88	0	208	49	22	24	3	1.66
39984109--39984134	7	3.7	7	100	0	52	84	0	0	15	0.62
39987742--39987901	43	3.8	42	78	8	162	29	26	15	28	1.96
39995674--39995748	29	2.6	29	85	4	98	37	21	18	22	1.94
39995670--39995777	29	3.7	29	79	4	85	38	21	14	25	1.91
39995756--39995874	29	4.1	29	81	0	130	42	16	10	29	1.82
39995744--39995855	58	1.9	58	81	3	136	44	16	10	27	1.81
39995756--39995874	58	2.1	58	83	0	148	42	16	10	29	1.82
39995970--39996019	25	2.0	25	88	0	73	42	16	12	30	1.84
40008555--40008588	17	2.0	17	100	0	68	17	29	5	47	1.71
40014605--40014826	51	4.4	50	78	3	194	26	17	26	30	1.97
40022246--40022465	51	4.3	51	79	4	230	25	17	26	30	1.97
40025789--40025833	23	2.0	23	95	0	81	35	8	15	40	1.79
40025954--40026094	70	2.0	70	97	0	264	39	3	18	39	1.68
40027718--40027763	3	15.3	3	90	0	74	32	4	0	63	1.14
40030498--40030528	14	2.1	15	94	5	55	29	0	0	70	0.87
40031083--40031142	30	2.0	31	86	3	86	21	35	0	43	1.53
40031900--40031925	5	5.2	5	100	0	52	19	19	19	42	1.90
40036441--40036481	19	2.2	19	95	0	73	34	31	0	34	1.58
40037016--40037083	21	3.3	21	77	4	68	38	22	29	10	1.87
40037033--40037145	42	2.7	42	83	5	138	42	17	23	15	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40037073--40037140	21	3.2	20	73	8	64	44	17	19	19	1.88
40039287--40039340	20	2.7	20	91	0	90	35	29	3	31	1.75
40039287--40039345	10	5.9	10	69	15	50	37	30	3	28	1.74
40043707--40043751	23	2.0	23	100	0	90	42	26	17	13	1.86
40043649--40043740	46	2.0	46	84	0	121	32	17	26	23	1.97
40045549--40045622	36	2.1	36	84	5	96	43	17	16	22	1.88
40055637--40055722	21	4.1	21	66	18	54	61	0	0	38	0.96
40055655--40055735	41	2.0	40	81	13	94	55	0	2	41	1.13
40060422--40061024	207	2.9	207	79	2	658	30	16	23	28	1.96
40068415--40068464	26	1.9	26	84	8	66	32	4	6	58	1.41
40069229--40069299	29	2.5	28	77	20	69	46	5	2	45	1.41
40071420--40071523	49	2.1	49	90	0	163	29	7	10	51	1.64
40072909--40072951	21	2.0	21	82	8	52	34	2	6	55	1.39
40073052--40073221	38	4.9	35	68	22	99	42	1	6	49	1.36
40073002--40073563	102	5.4	102	76	15	579	42	1	5	49	1.37
40073206--40073239	16	2.1	16	100	0	68	35	0	0	64	0.94
40073104--40073341	118	2.0	118	95	0	431	42	1	5	51	1.34
40072923--40073563	220	3.0	219	91	5	999	42	1	6	49	1.38
40073731--40073768	16	2.4	16	95	0	67	26	34	2	36	1.71
40073930--40073972	21	2.0	21	86	0	59	37	4	25	32	1.77
40074405--40074547	26	5.6	26	83	7	152	14	27	22	35	1.93
40080677--40080781	52	2.0	52	94	0	183	44	18	21	15	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40081663--40081808	74	2.0	74	95	0	265	37	5	17	39	1.73
40082124--40082185	25	2.5	25	78	0	61	24	17	19	38	1.93
40087344--40087368	13	1.9	13	100	0	50	40	48	0	12	1.40
40087349--40087465	39	3.0	39	96	1	209	50	28	2	18	1.60
40087602--40087660	17	3.3	17	68	13	55	35	3	10	50	1.53
40087676--40087743	9	7.6	9	90	6	111	32	10	13	44	1.77
40087668--40087743	18	4.2	18	93	0	116	31	10	15	42	1.81
40089581--40089617	17	2.2	17	90	4	58	18	2	10	67	1.32
40091493--40091551	10	5.9	10	80	11	59	74	0	5	20	1.00
40098508--40098537	14	2.1	14	93	0	51	0	16	0	83	0.65
40101717--40101850	58	2.3	58	83	6	173	41	1	3	52	1.28
40108487--40108538	21	2.5	21	96	0	95	55	13	1	28	1.49
40111608--40112102	138	3.6	137	79	3	465	19	21	23	36	1.95
40111602--40112102	69	7.3	69	78	3	348	19	21	23	35	1.95
40119245--40119301	12	4.5	12	74	20	53	49	1	1	47	1.22
40119450--40119486	13	3.0	13	84	7	51	43	8	2	45	1.47
40119684--40119725	15	2.7	16	85	10	52	47	4	9	38	1.57
40119641--40120005	199	1.8	202	86	2	529	38	7	7	46	1.61
40120290--40120327	20	2.0	18	90	10	58	36	0	7	55	1.29
40122744--40122770	2	13.5	2	100	0	54	51	0	0	48	1.00
40136998--40137226	43	5.3	44	81	5	157	30	30	17	21	1.96
40137021--40137205	86	2.2	85	81	5	203	27	30	18	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40141455--40141495	21	2.0	20	90	4	64	39	39	0	21	1.54
40141739--40141900	7	22.9	7	67	12	62	46	34	0	18	1.54
40141739--40141900	14	11.4	14	72	12	107	46	34	0	18	1.54
40141738--40141900	29	5.8	29	70	15	85	46	34	0	19	1.55
40142073--40142325	41	6.1	41	86	2	308	29	30	18	20	1.97
40142073--40142325	84	3.0	82	85	2	301	29	30	18	20	1.97
40142073--40142325	125	2.0	124	84	2	328	29	30	18	20	1.97
40142360--40142488	40	3.3	39	85	5	154	19	25	24	31	1.98
40143166--40143198	12	2.6	13	90	4	50	24	0	0	75	0.80
40146713--40146737	6	4.2	6	100	0	50	84	16	0	0	0.63
40147138--40147221	42	2.0	44	85	4	118	42	1	8	47	1.41
40146979--40147375	142	2.7	145	84	9	480	43	4	10	42	1.58
40147868--40147921	20	2.7	20	77	8	56	22	3	1	72	1.10
40148586--40148620	13	2.6	14	81	9	54	71	2	0	25	1.00
40148816--40148865	25	1.9	27	84	8	68	52	16	12	20	1.75
40161960--40162006	20	2.3	21	81	7	60	12	23	21	42	1.87
40161972--40162018	20	2.2	20	85	7	58	12	27	19	40	1.88
40169614--40169654	20	2.0	20	100	0	82	41	4	34	19	1.73
40172760--40173083	162	2.0	162	97	0	612	32	17	17	32	1.94
40177955--40178072	43	2.8	43	80	1	139	29	26	19	24	1.98
40179108--40179134	14	1.9	14	100	0	54	44	22	3	29	1.70
40180742--40180920	50	3.6	49	78	8	159	27	20	27	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40181136--40181168	12	2.8	12	95	0	57	51	9	24	15	1.72
40181142--40181180	20	2.0	20	90	10	62	56	5	23	15	1.59
40186125--40186162	20	1.9	20	100	0	76	44	13	21	21	1.85
40188618--40188661	22	2.0	22	90	0	70	9	18	27	45	1.79
40188756--40188938	43	4.3	43	90	0	294	29	32	17	20	1.95
40193813--40193858	21	2.2	21	84	0	56	36	47	0	15	1.45
40193800--40193845	7	6.6	7	92	0	65	32	50	0	17	1.47
40193712--40193995	151	1.8	152	81	9	335	41	32	1	25	1.63
40194005--40194037	14	2.3	15	94	5	59	36	33	0	30	1.58
40194453--40194664	41	5.2	41	91	1	336	28	24	23	24	2.00

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   199   200   201   202   203   204   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226