genome.fa.s11.2.7.7.80.10.50.1000.187.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: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

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   

This is table  187  of  210  ( 25152 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)
55211969--55212028	17	3.2	19	81	11	70	36	6	10	46	1.64
55211964--55212027	18	3.5	19	80	16	73	32	7	9	50	1.64
55212190--55212263	17	4.4	17	81	11	80	31	13	10	44	1.78
55213984--55214079	21	4.4	21	74	7	75	36	16	41	5	1.71
55214037--55214076	12	3.3	12	92	0	62	40	15	40	5	1.68
55214513--55214717	42	4.9	42	80	10	213	26	24	21	26	1.99
55214511--55214717	85	2.5	84	83	7	242	27	24	21	27	1.99
55219917--55219961	20	2.3	19	84	3	54	24	2	2	71	1.09
55230771--55230804	14	2.4	14	90	5	50	41	5	5	47	1.52
55230771--55230804	15	2.3	15	90	10	52	41	5	5	47	1.52
55238421--55238498	40	2.0	40	87	2	113	35	6	25	32	1.81
55238424--55238507	40	2.2	40	82	4	100	36	5	27	29	1.81
55238724--55238796	6	12.2	6	88	0	74	20	8	13	57	1.62
55238724--55238877	12	12.8	12	70	8	80	23	9	12	54	1.66
55238742--55238877	18	7.6	18	72	6	87	23	9	13	53	1.68
55238806--55238877	6	12.0	6	77	0	54	23	5	13	56	1.58
55239320--55239349	15	2.0	15	93	0	51	13	10	40	36	1.78
55241002--55241060	2	29.5	2	100	0	118	0	0	49	50	1.00
55242205--55242250	24	2.0	24	86	4	67	47	6	21	23	1.74
55242447--55242516	14	5.6	13	71	19	51	52	25	5	15	1.65
55242428--55242530	36	2.9	36	88	2	145	50	24	7	17	1.72
55242444--55242506	20	3.3	20	69	24	64	52	25	4	17	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55242868--55242928	26	2.3	27	83	8	72	0	29	0	70	0.88
55243500--55243545	15	2.9	16	87	6	67	43	0	0	56	0.99
55243476--55243548	16	4.5	16	74	17	62	41	1	2	54	1.23
55246065--55246133	31	2.2	31	82	5	77	44	8	11	34	1.72
55247518--55247552	17	2.1	17	94	0	61	60	14	0	25	1.35
55247817--55247865	24	2.0	25	84	7	66	55	2	0	42	1.11
55247824--55247916	40	2.3	40	80	10	102	60	2	3	34	1.25
55249928--55250494	126	4.5	125	84	2	726	29	17	22	30	1.96
55249928--55250494	251	2.3	250	87	2	780	29	17	22	30	1.96
55253665--55254850	21	55.0	21	74	10	792	24	1	29	44	1.62
55253665--55254850	43	27.5	42	74	12	756	24	1	29	44	1.62
55253956--55254059	50	2.1	50	82	10	124	28	0	25	46	1.53
55254009--55254076	35	2.0	34	82	2	82	32	0	23	44	1.54
55254436--55254559	57	2.2	57	85	1	158	23	1	26	48	1.60
55254459--55254526	36	1.9	35	85	8	93	23	0	25	51	1.48
55254548--55254585	14	2.7	14	80	11	51	23	0	36	39	1.55
55254444--55254573	57	2.3	55	77	10	127	23	1	26	47	1.60
55254513--55254616	50	2.1	50	83	7	131	22	1	30	45	1.63
55254540--55254594	28	1.9	29	85	3	76	20	3	34	41	1.69
55254563--55254850	66	4.5	65	78	7	273	23	0	32	43	1.57
55254751--55254787	14	2.8	13	84	8	56	13	0	40	45	1.43
55255424--55255466	18	2.4	18	84	0	59	46	9	27	16	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55256080--55256129	7	7.1	7	95	0	91	56	14	2	28	1.49
55257219--55257315	51	1.9	51	85	6	135	45	3	24	26	1.68
55257277--55257353	11	6.9	11	73	24	72	44	1	28	25	1.62
55257277--55257353	22	3.5	22	83	16	97	44	1	28	25	1.62
55257277--55257353	33	2.3	33	82	10	102	44	1	28	25	1.62
55258632--55258669	14	2.7	14	80	15	51	63	0	0	36	0.95
55268837--55268869	17	1.9	17	88	11	50	63	0	3	33	1.10
55276376--55276566	102	1.8	102	80	9	226	28	14	26	30	1.95
55280130--55280155	13	2.0	13	100	0	52	46	15	23	15	1.83
55287262--55287317	24	2.2	24	87	6	76	3	16	10	69	1.30
55288480--55288512	2	16.5	2	100	0	66	48	0	0	51	1.00
55293735--55293766	3	10.7	3	93	0	55	0	28	34	37	1.57
55293732--55293774	12	3.6	12	90	0	68	0	23	32	44	1.54
55305213--55305315	30	3.5	29	80	9	86	48	7	8	34	1.63
55308057--55308109	23	2.3	23	87	3	72	66	15	5	13	1.43
55311367--55311399	15	2.1	16	88	5	50	66	0	0	33	0.92
55311781--55311824	19	2.3	19	84	7	54	31	2	0	65	1.05
55311792--55311837	23	2.1	23	88	8	69	26	4	2	67	1.21
55311778--55311821	18	2.4	18	78	10	54	29	2	0	68	1.02
55311778--55311829	19	2.9	17	76	15	52	30	1	0	67	1.02
55312936--55312975	21	1.9	21	100	0	80	70	15	5	10	1.32
55332425--55332459	17	2.1	17	94	0	61	22	14	20	42	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55333135--55333191	26	2.2	26	87	0	78	47	3	5	43	1.43
55333409--55333447	21	2.0	20	90	10	62	56	0	2	41	1.13
55336376--55336417	20	2.1	20	86	0	57	47	0	7	45	1.30
55341741--55341774	17	2.0	17	100	0	68	29	17	35	17	1.93
55347732--55347909	71	2.5	71	78	7	191	27	22	23	26	1.99
55349498--55349657	77	2.1	77	97	0	302	28	13	16	41	1.86
55354389--55354418	16	1.9	16	93	6	53	66	6	6	20	1.38
55356827--55357042	111	1.9	111	91	0	351	20	36	14	28	1.92
55357276--55357403	30	4.3	30	88	0	175	17	51	7	22	1.71
55357303--55357418	60	1.9	60	87	0	169	20	52	6	19	1.69
55365538--55365572	6	5.8	6	89	0	52	0	60	0	40	0.97
55370935--55370976	17	2.5	17	96	0	75	50	0	2	47	1.14
55373096--55373122	14	1.9	14	100	0	54	59	0	0	40	0.98
55375751--55375816	31	2.1	31	91	5	107	42	7	12	37	1.71
55375757--55375823	31	2.2	31	86	5	91	46	7	11	34	1.69
55377303--55377351	25	2.0	25	84	8	64	51	4	4	40	1.40
55385819--55385843	13	1.9	13	100	0	50	48	0	0	52	1.00
55389698--55389933	67	3.6	66	86	2	314	25	10	7	55	1.60
55396468--55396519	19	2.9	18	72	13	54	61	3	0	34	1.14
55401045--55401090	23	2.0	23	91	0	74	28	32	10	28	1.91
55401346--55401391	23	2.0	23	91	0	74	28	32	10	28	1.91
55406108--55406160	21	2.4	22	78	18	56	56	0	24	18	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55409631--55409721	17	5.4	17	66	23	57	43	3	3	49	1.35
55409673--55409730	31	1.9	29	82	6	71	39	3	5	51	1.41
55417584--55417620	9	4.1	9	85	0	56	48	13	8	29	1.71
55418622--55418647	5	5.2	5	100	0	52	19	19	19	42	1.90
55419894--55420096	90	2.2	90	81	6	241	37	17	20	25	1.93
55429815--55429856	15	2.7	16	82	14	52	52	2	0	45	1.13
55429824--55429865	15	2.9	15	82	10	52	52	0	0	47	1.00
55429850--55430037	61	3.1	61	70	14	199	48	6	1	42	1.39
55429818--55430078	120	2.2	121	95	1	472	50	5	2	41	1.39
55429934--55429985	15	3.6	15	80	12	56	53	1	0	44	1.11
55433673--55433698	6	4.3	6	100	0	52	50	0	0	50	1.00
55433783--55433821	17	2.4	17	91	4	62	48	5	12	33	1.63
55433801--55433863	20	3.1	20	64	28	51	44	4	11	39	1.61
55434201--55434225	12	2.1	12	100	0	50	40	20	0	40	1.52
55438961--55439025	34	1.9	34	84	6	87	27	16	24	30	1.97
55440993--55441017	13	1.9	13	100	0	50	48	0	8	44	1.32
55446653--55446805	79	1.9	79	97	0	288	24	16	16	42	1.88
55447108--55447144	18	2.1	18	90	5	58	29	5	0	64	1.15
55452383--55452425	16	2.8	16	86	6	63	58	2	0	39	1.11
55453276--55453530	53	4.8	54	78	13	235	43	10	15	30	1.80
55453295--55453521	35	6.5	35	81	7	214	44	10	15	29	1.80
55453276--55453521	18	13.9	17	76	13	205	44	10	15	29	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55453667--55453704	20	2.0	20	89	5	60	42	7	7	42	1.63
55454018--55454079	27	2.3	26	83	8	79	3	14	0	82	0.80
55454018--55454079	14	4.4	15	70	13	51	3	14	0	82	0.80
55454334--55454383	5	9.2	5	79	16	55	2	18	62	18	1.43
55454334--55454383	11	4.6	10	79	16	55	2	18	62	18	1.43
55454618--55454670	22	2.3	23	83	6	72	3	9	18	67	1.33
55455164--55455264	30	3.4	30	72	16	84	42	3	16	36	1.67
55455130--55455264	59	2.3	57	75	3	135	42	5	18	33	1.75
55455675--55456400	76	9.6	77	88	4	946	34	20	17	27	1.95
55455675--55456394	225	3.2	224	85	6	943	34	20	17	28	1.95

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