genome.fa.s9.2.7.7.80.10.50.1000.196.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  196  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)
62265492--62265586	26	3.8	25	79	13	106	33	20	24	22	1.97
62277553--62277613	2	31.0	2	96	3	115	49	0	0	50	1.00
62292178--62292216	13	3.1	13	88	3	53	46	5	0	48	1.24
62293037--62293175	73	1.9	73	83	5	183	39	1	30	28	1.66
62296665--62296790	43	2.9	43	78	11	132	33	28	16	21	1.95
62298387--62298517	40	3.3	40	83	1	156	45	27	13	12	1.80
62303342--62303391	24	2.1	24	92	0	82	22	8	4	66	1.35
62311105--62311475	94	4.0	94	80	1	386	33	19	20	27	1.96
62311344--62311432	44	2.0	43	83	12	110	38	20	16	24	1.93
62318373--62318399	11	2.5	11	100	0	54	33	7	25	33	1.84
62326063--62326095	16	2.1	15	94	5	57	18	6	6	69	1.30
62332805--62334769	94	21.0	94	82	2	2148	33	19	20	26	1.96
62332805--62334345	44	33.0	44	66	21	395	33	19	20	26	1.97
62332805--62334769	469	4.2	470	86	2	2350	33	19	20	26	1.96
62335564--62335609	22	2.1	22	100	0	92	43	4	26	26	1.73
62339859--62339886	12	2.3	12	100	0	56	28	7	7	57	1.52
62341554--62341606	21	2.6	21	79	5	65	50	0	7	41	1.30
62342036--62342075	21	1.9	21	85	10	55	37	7	2	52	1.43
62342046--62342104	22	2.7	22	81	2	66	38	3	3	54	1.34
62343671--62343704	18	1.9	18	88	5	52	55	0	5	38	1.24
62349174--62349228	6	9.2	6	93	0	92	0	45	0	54	0.99
62350042--62350150	27	4.0	27	87	0	146	35	16	21	26	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
62356635--62356750	37	3.3	34	87	4	108	32	26	9	31	1.88
62356648--62356762	37	3.1	37	91	0	176	34	25	6	33	1.83
62356984--62357086	41	2.5	41	87	6	129	29	21	21	28	1.98
62357285--62357313	2	14.5	2	100	0	58	51	0	0	48	1.00
62366749--62366805	27	2.1	27	86	0	78	26	29	14	29	1.95
62369552--62369591	21	1.9	21	84	0	53	27	37	5	30	1.78
62372528--62372579	16	3.2	16	94	0	86	34	36	0	28	1.58
62373017--62373093	9	8.4	9	87	8	102	40	27	10	22	1.86
62373232--62373261	13	2.3	13	100	0	60	16	0	43	40	1.48
62374387--62374531	70	2.1	71	89	1	220	53	8	6	30	1.58
62376922--62376969	23	2.1	23	96	0	87	37	0	14	47	1.44
62377504--62377573	31	2.3	31	84	0	95	28	22	18	30	1.98
62388426--62388481	25	2.2	27	78	12	64	50	5	1	42	1.35
62392070--62392118	3	16.0	3	95	4	89	65	0	2	32	1.04
62392144--62392171	13	2.2	13	100	0	56	57	14	7	21	1.61
62392954--62393023	31	2.3	31	89	0	113	30	24	17	28	1.97
62393391--62393444	3	18.0	3	100	0	108	66	0	0	33	0.92
62395762--62395810	20	2.5	20	86	6	64	30	20	16	32	1.94
62397263--62397324	27	2.4	26	77	15	67	35	1	4	58	1.29
62398178--62398217	18	2.2	18	90	0	62	7	0	35	57	1.27
62400327--62400351	11	2.3	11	100	0	50	76	0	0	24	0.80
62401777--62401825	18	2.7	19	75	9	50	20	6	0	73	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
62412471--62412504	12	2.8	12	95	0	59	29	0	0	70	0.87
62412630--62412692	30	2.1	30	90	0	99	58	11	1	28	1.41
62420877--62420923	20	2.4	21	82	10	55	57	4	10	27	1.51
62461543--62461629	43	2.0	44	90	2	140	31	25	16	27	1.96
62469132--62469216	43	2.0	44	90	2	136	30	24	16	28	1.96
62470567--62470613	23	2.0	23	91	0	76	19	10	27	42	1.84
62475121--62475202	28	2.9	29	75	17	98	19	25	20	34	1.96
62478680--62478736	24	2.4	25	82	8	66	57	0	1	40	1.09
62479846--62479931	43	2.0	43	90	0	136	29	13	20	36	1.92
62490777--62490819	15	2.9	15	73	13	52	34	2	4	58	1.32
62490863--62490919	26	2.2	26	84	6	71	36	3	0	59	1.14
62490880--62490913	6	5.7	6	96	0	59	38	0	0	61	0.96
62495655--62495708	11	4.9	10	78	17	54	85	7	7	0	0.75
62495654--62495709	12	4.8	11	82	8	67	85	7	7	0	0.73
62495656--62495710	8	7.0	8	76	12	51	83	9	7	0	0.81
62495656--62495710	23	2.3	24	87	9	78	83	9	7	0	0.81
62496215--62496260	7	6.6	7	79	16	51	76	0	10	13	1.03
62496214--62496260	14	3.2	15	82	11	62	76	0	10	12	1.02
62496229--62496265	14	2.6	15	87	8	51	67	0	18	13	1.23
62497535--62498017	88	5.5	88	88	4	708	28	22	25	22	1.99
62497535--62498017	176	2.8	176	92	2	794	28	22	25	22	1.99
62499885--62499927	15	2.9	15	73	13	52	34	2	4	58	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
62499975--62500030	12	4.7	12	84	0	67	37	1	0	60	1.07
62499990--62500029	6	6.7	6	97	0	71	37	0	0	62	0.95
62501998--62502028	9	3.4	9	90	0	53	77	0	22	0	0.77
62504872--62504980	41	2.7	41	92	0	182	23	28	20	27	1.99
62504872--62505017	41	3.6	41	83	9	174	23	28	20	27	1.99
62504872--62505029	82	1.9	82	83	10	207	24	27	19	28	1.99
62510469--62510728	101	2.6	101	80	3	276	26	23	16	33	1.95
62519348--62519376	12	2.3	13	94	5	51	24	0	0	75	0.80
62521331--62521368	17	2.2	17	86	9	51	44	7	0	47	1.32
62521493--62521535	22	2.0	22	81	9	52	55	2	2	39	1.25
62523220--62523262	5	8.0	5	80	14	50	25	0	0	74	0.82
62526789--62526813	4	6.2	4	100	0	50	72	0	0	28	0.86
62526995--62527173	91	2.0	90	84	3	234	31	13	22	32	1.92
62527693--62527724	14	2.3	14	94	0	55	31	0	3	65	1.08
62531816--62531856	2	20.5	2	100	0	82	0	48	0	51	1.00
62537467--62537514	23	2.0	25	88	8	73	41	6	4	47	1.48
62537755--62537828	29	2.7	29	78	18	77	63	0	0	36	0.95
62537747--62537816	27	2.5	26	76	15	70	57	0	0	42	0.99
62539957--62539986	15	2.0	15	93	0	51	70	0	0	30	0.88
62540116--62540169	17	3.2	16	81	7	54	55	12	11	20	1.67
62541181--62541338	33	4.8	32	72	8	127	30	15	25	29	1.96
62541114--62541353	101	2.4	101	93	0	399	32	15	24	28	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
62546621--62546655	18	1.9	18	88	11	54	42	0	2	54	1.15
62546952--62547020	26	2.6	26	88	2	93	18	11	28	40	1.86
62549339--62549398	28	2.1	28	87	0	84	16	1	23	58	1.47
62563235--62563673	44	10.0	43	63	15	119	32	18	23	26	1.97
62563195--62563675	132	3.6	133	90	3	774	31	19	23	25	1.98
62563195--62563675	265	1.8	265	92	2	815	31	19	23	25	1.98
62564367--62564392	13	2.0	13	100	0	52	38	7	30	23	1.83
62582557--62582681	64	2.0	64	93	0	214	25	14	30	29	1.95
62590514--62590582	16	4.2	16	96	3	129	24	0	37	37	1.56
62590514--62590582	33	2.1	32	97	2	129	24	0	37	37	1.56
62590563--62590653	45	2.0	45	85	2	121	27	6	28	37	1.82
62590798--62590852	15	3.4	16	80	16	53	54	1	0	43	1.10
62590804--62590852	16	2.9	18	80	20	61	55	0	0	44	0.99
62590900--62591112	67	3.1	67	65	16	168	46	3	3	47	1.35
62590705--62591032	156	2.1	156	96	0	602	43	3	6	47	1.44
62590974--62591008	18	2.0	17	88	5	52	54	0	0	45	0.99
62590891--62591156	137	1.9	138	90	0	426	44	3	4	47	1.38
62590912--62591190	137	2.0	135	82	6	330	45	5	3	45	1.42
62610986--62611015	13	2.3	13	94	0	51	10	6	0	83	0.81
62611815--62611849	4	8.5	4	87	6	52	20	2	0	77	0.90
62615965--62616010	24	1.9	24	86	0	65	45	17	26	10	1.81
62624268--62624865	217	2.8	217	89	1	903	29	20	22	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
62624224--62624873	44	14.9	44	70	14	336	29	20	22	27	1.98
62624146--62624655	261	2.0	261	84	5	683	29	20	22	27	1.99
62624706--62624882	89	2.0	89	84	8	236	31	19	23	25	1.98
62625541--62625570	13	2.3	13	94	0	51	10	6	0	83	0.81
62626327--62626379	19	2.9	19	80	5	65	20	1	1	75	0.99
62629887--62629938	22	2.4	22	83	0	68	38	1	0	59	1.08
62641126--62641171	16	2.8	17	74	9	51	54	0	4	41	1.20
62649507--62649533	3	9.0	3	100	0	54	33	0	0	66	0.92
62655589--62655616	6	4.7	6	100	0	56	46	0	0	53	1.00
62661289--62661349	27	2.2	29	83	11	76	39	18	16	26	1.91

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