genome.fa.s9.2.7.7.80.10.50.1000.101.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  101  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)
34739224--34739302	39	2.0	39	100	0	158	18	17	22	40	1.91
34743749--34743839	20	4.6	19	69	18	53	37	18	27	16	1.92
34745518--34745636	42	2.8	42	79	1	130	20	26	33	19	1.96
34753269--34753404	20	6.8	20	76	1	139	41	21	25	12	1.88
34753277--34753391	59	1.9	60	89	1	178	41	21	23	13	1.88
34753441--34753597	77	2.0	77	98	0	305	29	21	8	39	1.84
34759827--34759875	19	2.6	19	81	9	57	53	12	8	26	1.66
34765753--34765777	6	4.2	6	100	0	50	16	16	16	52	1.76
34769466--34769511	16	3.1	15	82	17	60	50	0	23	26	1.50
34770404--34770428	6	4.2	6	100	0	50	16	16	16	52	1.76
34780784--34780817	15	2.3	15	94	0	59	44	0	14	41	1.45
34781439--34781638	105	1.9	105	83	7	264	29	15	9	46	1.76
34786423--34786498	22	3.5	22	92	0	116	32	13	26	27	1.93
34804014--34804080	21	3.1	21	82	2	89	37	29	22	10	1.88
34804894--34804935	7	5.9	7	83	8	50	73	0	2	23	0.94
34804895--34804935	16	2.5	17	82	17	52	73	0	2	24	0.96
34809024--34809083	4	14.5	4	76	13	59	73	1	0	25	0.93
34809024--34809093	34	2.1	34	100	0	140	70	2	0	27	1.02
34810594--34810618	2	12.5	2	100	0	50	52	0	0	48	1.00
34817249--34817406	50	3.1	51	80	11	182	42	11	14	31	1.81
34821482--34821506	6	4.2	6	100	0	50	84	0	0	16	0.63
34821871--34821907	17	2.2	17	90	9	58	75	0	5	18	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34832311--34832398	29	3.1	29	72	9	72	35	20	19	25	1.96
34836742--34836788	24	2.0	24	95	0	85	46	17	4	31	1.67
34839055--34839123	25	2.8	25	81	0	84	24	18	26	30	1.98
34854487--34854540	26	2.1	26	100	0	108	18	14	3	62	1.46
34854914--34854976	29	2.2	29	97	0	117	47	6	4	41	1.50
34877108--34877152	10	4.3	10	81	10	54	31	0	13	55	1.38
34881189--34881256	22	3.1	22	97	0	127	35	13	25	26	1.92
34885301--34885347	16	3.1	15	82	11	53	46	6	0	46	1.28
34889496--34889539	21	2.1	21	83	8	54	18	6	15	59	1.58
34890310--34890347	15	2.5	15	100	0	76	18	18	7	55	1.66
34892685--34892722	11	3.5	11	85	3	51	36	0	0	63	0.95
34895941--34896236	42	7.1	42	88	2	436	20	20	22	36	1.95
34895938--34896236	125	2.4	125	89	1	467	20	20	22	36	1.96
34895938--34896236	83	3.6	82	89	2	463	20	20	22	36	1.96
34896554--34896624	21	3.4	20	82	7	79	4	43	18	33	1.69
34903034--34903084	27	1.9	26	88	4	75	47	11	0	41	1.40
34903777--34903945	41	4.1	41	74	10	141	32	27	21	17	1.96
34904043--34904121	40	2.0	40	89	0	122	21	22	25	30	1.99
34904043--34904154	40	2.8	40	84	4	118	20	24	24	31	1.98
34904740--34904775	18	2.0	18	89	10	56	38	0	0	61	0.96
34906747--34907022	113	2.4	112	75	10	261	39	10	10	39	1.75
34912943--34913033	45	2.0	45	100	0	182	45	15	13	26	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34923978--34924269	50	5.7	50	81	5	259	22	28	20	28	1.99
34929091--34929259	25	6.8	25	74	9	123	20	28	19	31	1.97
34929074--34929276	50	4.1	49	77	8	153	20	28	20	31	1.97
34929097--34929262	74	2.2	74	81	7	176	21	28	19	30	1.97
34929091--34929276	99	1.9	99	83	4	241	20	29	19	30	1.97
34931310--34931664	179	2.0	179	95	0	638	35	16	5	42	1.72
34932532--34932611	42	1.9	41	82	2	97	25	26	2	46	1.65
34947908--34947955	21	2.3	21	79	13	55	31	20	29	18	1.97
34949132--34949225	40	2.2	42	88	7	138	63	0	2	34	1.06
34949188--34949254	11	6.5	11	73	20	56	70	0	1	28	0.96
34949186--34949236	22	2.3	22	90	10	77	66	0	1	31	1.03
34949166--34949263	51	1.9	51	93	0	169	62	0	2	35	1.07
34949138--34949236	12	8.0	12	69	14	51	66	0	2	31	1.03
34949182--34949254	10	7.3	10	73	21	64	69	0	1	28	0.96
34949309--34949340	5	6.2	5	92	7	55	0	43	56	0	0.99
34949793--34949820	9	3.1	9	100	0	56	32	10	10	46	1.73
34956817--34956864	17	3.1	16	82	11	55	62	0	0	37	0.95
34958071--34958104	15	2.3	15	89	0	50	23	2	2	70	1.15
34958110--34958168	23	2.6	23	81	5	66	32	13	15	38	1.86
34960086--34960120	10	3.2	11	88	12	54	17	37	0	45	1.48
34960101--34960224	51	2.4	54	89	6	193	29	25	0	44	1.60
34962535--34962755	29	8.9	23	73	20	130	44	25	0	29	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34962546--34962588	23	2.0	20	90	9	59	46	20	2	30	1.63
34962538--34962725	45	3.6	53	76	20	214	45	25	0	28	1.58
34962539--34962655	29	4.2	29	89	7	165	44	26	0	28	1.60
34962634--34962700	23	3.0	22	75	14	75	44	25	0	29	1.54
34962664--34962730	30	2.2	30	91	0	107	43	28	0	28	1.55
34962591--34962755	75	2.2	74	93	1	276	44	26	0	29	1.55
34963340--34963793	236	1.9	238	95	0	822	24	26	18	29	1.98
34965215--34965240	12	2.2	12	100	0	52	11	30	34	23	1.90
34966097--34966415	121	2.6	122	84	7	403	33	21	13	31	1.92
34972059--34972089	6	5.3	6	92	7	55	16	0	48	35	1.46
34972059--34972088	11	2.6	11	94	5	51	16	0	50	33	1.46
34972163--34972430	96	2.9	88	74	14	245	40	3	16	40	1.64
34972239--34972430	96	2.0	97	86	3	271	40	3	18	38	1.66
34972470--34972758	126	2.3	125	87	3	427	34	18	20	27	1.95
34975854--34975912	28	2.0	29	83	9	75	47	6	6	38	1.57
34978174--34978207	13	2.6	13	86	13	52	67	0	0	32	0.91
34978251--34978315	11	5.9	11	85	0	94	43	0	32	24	1.55
34978248--34978340	22	4.2	22	84	2	116	47	1	29	22	1.58
34978839--34978884	9	5.1	9	83	0	56	52	15	4	28	1.61
34978839--34978885	18	2.6	18	93	0	85	51	17	4	27	1.64
34980553--34980623	13	5.5	13	81	0	88	30	30	4	33	1.77
34980553--34980631	26	3.0	26	96	0	140	34	29	5	31	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
34988435--34988477	21	2.0	22	82	13	54	41	9	18	30	1.82
34992518--34992879	27	13.4	27	85	1	465	40	21	18	19	1.91
34996136--34996182	23	2.1	21	85	14	60	27	6	4	61	1.39
34998456--34998498	21	2.0	22	82	13	54	41	9	18	30	1.82
35000673--35000982	33	8.7	33	68	21	132	21	19	26	32	1.97
35000696--35000981	74	3.8	75	87	1	412	21	18	26	32	1.97
35006940--35007016	20	3.7	20	80	16	102	40	24	3	31	1.73
35006928--35007016	43	2.1	43	100	0	178	40	23	4	31	1.75
35006928--35006997	23	3.2	23	76	19	94	40	22	4	32	1.74
35007359--35007384	12	2.2	12	100	0	52	7	23	38	30	1.83
35008408--35008527	37	3.2	37	72	4	125	36	31	15	16	1.90
35011351--35011395	19	2.3	20	88	3	65	31	20	2	46	1.62
35016325--35016358	16	2.1	16	88	0	50	32	14	0	52	1.42
35017056--35017345	50	5.7	50	83	3	278	21	28	22	27	1.99
35017690--35017746	30	1.9	30	82	7	71	26	26	5	42	1.76
35020274--35020387	54	2.1	54	82	8	142	15	30	24	28	1.96
35020594--35020685	18	4.9	19	75	11	91	25	22	1	51	1.55
35028701--35028743	21	2.0	21	86	0	59	6	39	0	53	1.28
35036501--35036540	16	2.4	16	87	8	53	75	2	5	17	1.10
35041535--35041559	12	2.1	12	100	0	50	24	40	28	8	1.83
35042963--35043109	75	2.0	75	89	2	224	45	9	11	33	1.73
35043143--35043277	45	3.2	42	71	21	122	49	5	3	41	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35043157--35043296	40	3.5	40	71	14	133	47	5	5	42	1.49
35043146--35043304	81	2.0	82	89	1	248	47	6	4	41	1.48
35046225--35046295	24	3.0	24	70	15	65	47	1	42	8	1.42
35050950--35051233	51	5.6	50	79	7	315	28	26	15	28	1.96
35050944--35051233	102	2.9	102	89	0	429	28	26	15	28	1.96
35050940--35051229	153	1.9	151	83	6	379	28	26	15	28	1.96
35069884--35070061	92	1.9	92	97	0	338	41	11	7	39	1.70
35070596--35070660	32	2.0	32	100	0	130	46	15	9	29	1.77
35072129--35072257	66	2.0	66	82	3	161	29	21	20	28	1.98
35073714--35073758	18	2.5	18	81	0	63	24	28	4	42	1.74

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