genome.fa.s9.2.7.7.80.10.50.1000.20.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  20  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)
9115141--9115306	84	2.0	83	95	1	296	41	19	13	25	1.88
9115222--9115358	23	5.9	23	78	3	148	39	18	15	26	1.91
9115222--9115356	70	1.9	70	93	0	234	39	18	15	26	1.91
9116118--9116216	41	2.5	40	85	3	126	25	24	11	39	1.88
9118567--9118615	25	2.0	25	100	0	98	12	28	16	42	1.84
9128979--9129003	12	2.1	12	100	0	50	24	28	16	32	1.96
9132817--9132915	23	4.3	23	93	0	162	20	21	27	31	1.98
9137747--9137855	39	2.8	39	97	1	202	51	28	2	17	1.59
9137983--9138057	37	2.0	37	84	5	98	36	6	16	41	1.74
9138056--9138089	9	3.8	9	88	0	50	23	8	29	38	1.85
9139260--9139317	22	2.5	23	83	5	64	50	1	3	44	1.29
9139285--9139448	68	2.4	67	89	7	244	43	4	8	43	1.54
9139390--9139417	9	3.1	9	100	0	56	32	0	10	57	1.33
9139514--9139557	24	1.9	24	90	9	74	61	2	0	36	1.09
9141095--9141292	83	2.3	85	93	3	328	26	13	18	41	1.87
9141682--9141717	17	2.1	17	89	5	54	19	2	11	66	1.35
9142401--9142434	14	2.5	14	90	4	52	0	14	0	85	0.60
9144907--9144973	15	4.6	15	76	14	77	41	0	1	56	1.08
9144924--9144977	10	5.7	10	77	18	53	46	0	1	51	1.11
9144904--9144973	17	4.2	16	75	20	63	41	0	1	57	1.08
9146394--9146433	2	20.0	2	100	0	80	50	0	0	50	1.00
9148480--9148515	16	2.2	16	90	0	54	30	16	5	47	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9156675--9156750	27	2.8	27	91	0	116	42	25	6	26	1.79
9156675--9156750	9	8.4	9	83	0	80	42	25	6	26	1.79
9157123--9157148	2	13.0	2	100	0	52	50	0	0	50	1.00
9157864--9157919	29	1.9	29	92	7	96	25	0	12	62	1.30
9164352--9164398	22	2.3	20	82	13	60	65	0	2	31	1.04
9164354--9164400	21	2.2	22	88	3	69	70	0	2	27	0.99
9170792--9170862	24	2.9	24	95	2	124	16	21	25	36	1.94
9179594--9179644	25	2.0	25	84	0	66	37	15	27	19	1.92
9192045--9192069	10	2.5	10	100	0	50	60	0	0	40	0.97
9207756--9207849	47	2.0	47	100	0	188	31	17	21	29	1.96
9239392--9239449	3	19.3	3	100	0	116	67	0	0	32	0.91
9248183--9248208	9	2.9	9	100	0	52	23	11	19	46	1.82
9249002--9249059	25	2.3	25	82	5	64	13	24	20	41	1.89
9249127--9249200	26	2.8	26	91	0	112	20	18	22	37	1.94
9249117--9249283	26	6.6	25	71	15	80	19	23	21	35	1.95
9256987--9257020	15	2.2	16	89	5	52	67	2	0	29	1.05
9272148--9272211	31	2.1	30	85	2	83	40	0	4	54	1.21
9273782--9273820	17	2.3	17	86	0	51	15	2	10	71	1.23
9276385--9276412	3	9.3	3	100	0	56	32	0	0	67	0.91
9277798--9277845	15	2.9	16	77	22	55	62	0	0	37	0.95
9278597--9278648	21	2.4	22	84	12	63	71	15	5	7	1.29
9278601--9278648	24	2.0	24	88	4	71	70	16	6	6	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9280065--9280102	13	2.7	14	88	8	51	63	5	2	28	1.30
9285767--9285905	46	3.0	46	91	0	224	34	8	26	30	1.86
9286270--9286392	33	3.7	33	79	4	131	27	23	16	32	1.96
9286252--9286393	66	2.2	66	94	0	248	26	22	16	33	1.96
9286374--9286413	20	2.0	20	100	0	80	25	30	15	30	1.95
9309616--9309675	31	1.9	31	93	0	102	45	16	6	31	1.74
9311914--9311982	22	3.0	22	75	19	77	34	17	26	21	1.95
9311932--9311993	25	2.5	25	94	0	106	37	16	24	22	1.94
9319775--9319834	30	2.0	30	83	0	75	36	3	11	48	1.56
9319895--9319941	25	2.0	23	84	16	60	44	2	4	48	1.34
9322739--9323018	124	2.3	124	82	3	339	29	13	22	33	1.93
9324979--9325034	28	2.0	29	92	3	96	60	1	0	37	1.07
9325076--9325117	22	1.9	22	90	0	66	33	0	33	33	1.58
9325067--9325169	52	2.0	51	83	9	129	34	0	32	33	1.58
9325119--9325210	22	4.2	23	82	8	111	42	0	27	30	1.56
9325119--9325210	44	2.1	44	85	4	123	42	0	27	30	1.56
9325911--9326023	38	2.9	39	87	6	169	38	2	21	38	1.67
9330241--9330280	20	2.0	20	90	0	62	32	17	10	40	1.83
9330448--9330556	37	2.8	40	75	9	116	35	22	15	26	1.94
9330716--9330762	24	2.0	24	84	16	62	51	17	0	31	1.46
9331422--9331485	17	3.8	17	74	12	51	1	21	3	73	1.06
9331506--9331606	35	2.8	36	79	10	109	44	5	0	49	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9331548--9331604	28	2.0	28	90	6	89	45	1	0	52	1.11
9331553--9331591	20	2.0	19	85	5	51	48	2	0	48	1.15
9334334--9334414	25	3.2	25	94	0	135	16	24	22	37	1.93
9334334--9334424	25	3.8	24	89	4	87	16	25	21	36	1.94
9335417--9335517	51	2.0	51	92	0	166	34	26	8	29	1.87
9335688--9335762	33	2.3	33	83	4	89	22	49	2	25	1.63
9336351--9336561	117	1.8	117	92	0	359	42	23	10	23	1.85
9336748--9336792	16	2.8	16	93	3	72	31	0	28	40	1.57
9337402--9337453	18	2.8	18	83	13	70	36	0	3	59	1.16
9343003--9343125	50	2.5	49	82	5	131	27	20	30	21	1.98
9343396--9343434	20	2.0	20	89	0	60	53	2	25	17	1.56
9354877--9354902	7	3.7	7	100	0	52	0	15	0	84	0.62
9365809--9365923	23	4.8	23	81	10	68	30	1	24	43	1.64
9365773--9366196	28	15.4	28	87	6	582	30	1	22	45	1.60
9365871--9365925	23	2.4	21	100	0	74	27	0	25	47	1.52
9365796--9366196	113	3.7	112	90	4	581	30	0	22	45	1.59
9365773--9366196	141	3.1	140	90	5	634	30	1	22	45	1.60
9376996--9377020	8	3.1	8	100	0	50	76	0	0	24	0.80
9395095--9395121	3	9.0	3	100	0	54	66	0	0	33	0.92
9416825--9416914	46	2.0	46	97	0	171	37	17	13	31	1.89
9417209--9417273	30	2.1	31	83	8	80	41	6	7	44	1.58
9417466--9417499	10	3.4	10	91	0	50	17	5	2	73	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9425164--9425189	2	13.0	2	100	0	52	50	0	0	50	1.00
9425255--9425303	23	2.3	22	86	10	66	57	6	6	30	1.48
9425248--9425296	23	2.1	23	100	0	98	59	8	4	28	1.45
9433481--9433525	23	1.9	24	90	4	74	57	6	6	28	1.50
9434153--9434247	27	3.5	27	86	2	120	9	31	32	26	1.88
9434268--9434313	20	2.2	20	84	3	56	10	8	8	71	1.30
9439598--9439814	45	5.2	39	81	14	125	18	20	22	39	1.93
9439625--9439863	45	5.3	45	91	1	372	18	20	21	39	1.92
9439629--9439863	89	2.6	90	89	1	364	18	20	21	39	1.92
9445552--9445694	45	3.2	45	86	1	189	39	20	20	18	1.93
9448145--9448182	18	2.1	18	90	9	60	21	0	5	73	1.02
9453428--9453484	24	2.4	24	75	0	60	28	54	3	14	1.56
9453458--9453508	18	2.8	18	85	5	68	29	54	3	11	1.54
9465140--9465169	12	2.6	11	94	5	51	33	0	0	66	0.92
9469764--9469790	2	13.5	2	100	0	54	51	0	0	48	1.00
9472679--9472781	51	2.0	52	98	1	199	29	7	5	57	1.50
9472687--9472793	51	2.1	51	87	6	155	31	8	6	53	1.57
9476411--9476670	127	2.0	127	99	0	511	31	26	7	33	1.85
9482668--9482743	31	2.4	32	82	6	102	56	2	10	30	1.47
9482961--9482985	5	5.0	5	100	0	50	40	40	0	20	1.52
9483902--9483941	21	1.9	21	85	10	55	52	12	10	25	1.70
9485089--9485128	19	2.1	19	86	9	55	35	0	5	60	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9492761--9492790	3	10.0	3	100	0	60	66	0	0	33	0.92
9507743--9507794	24	2.2	24	82	6	61	44	28	21	5	1.75
9511909--9511947	20	2.0	20	85	5	53	38	0	0	61	0.96
9513967--9513995	3	9.7	3	100	0	58	34	0	31	34	1.58
9516481--9516539	31	1.9	31	82	6	75	55	3	5	35	1.38
9516674--9516708	17	2.0	18	88	5	54	28	0	0	71	0.86
9526895--9526922	2	14.0	2	100	0	56	50	0	0	50	1.00
9527108--9527213	37	2.8	37	81	5	122	24	17	26	31	1.97
9532404--9532446	20	2.2	19	83	8	50	53	0	13	32	1.41
9534369--9534413	21	2.1	21	83	0	54	68	0	6	24	1.13

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