genome.fa.s9.2.7.7.80.10.50.1000.95.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  95  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)
32769475--32769929	44	10.9	39	76	16	352	29	25	15	30	1.96
32769644--32769702	31	1.9	31	89	0	91	23	27	11	37	1.90
32769600--32769746	75	2.0	75	93	0	249	28	26	13	31	1.94
32769561--32769795	119	2.0	114	92	4	389	28	27	14	30	1.95
32769675--32769923	133	1.9	133	87	1	365	29	24	15	30	1.96
32769715--32769951	89	2.7	89	93	0	413	29	24	16	29	1.97
32777335--32777368	17	2.0	17	94	0	59	38	29	20	11	1.88
32784895--32784941	19	2.4	20	85	7	78	27	10	12	48	1.74
32785017--32785059	18	2.4	18	88	0	59	48	4	0	46	1.22
32790432--32790515	32	2.6	31	83	5	96	28	2	17	51	1.58
32791607--32791681	24	3.2	24	69	27	70	28	6	22	42	1.78
32791597--32791692	46	2.1	46	92	0	156	28	7	21	42	1.79
32792880--32792936	28	2.1	27	83	3	69	38	5	7	49	1.53
32799747--32799802	30	2.0	26	83	13	67	30	1	1	66	1.12
32799773--32799804	16	2.0	16	93	0	55	34	0	0	65	0.93
32799786--32799825	20	2.0	21	85	14	57	50	2	0	47	1.14
32802718--32802757	19	2.0	20	85	4	55	45	7	12	35	1.70
32805569--32805621	18	2.9	18	80	2	61	41	45	1	11	1.51
32805725--32805773	9	5.4	9	78	9	55	26	8	20	44	1.79
32813025--32813140	62	1.9	61	85	5	164	50	5	4	40	1.44
32813119--32813167	20	2.7	18	77	22	57	51	4	2	42	1.32
32815306--32815420	51	2.3	51	84	3	151	47	6	18	27	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32817692--32817728	2	18.5	2	100	0	74	48	0	0	51	1.00
32822385--32822429	17	2.8	17	80	12	51	66	4	0	28	1.11
32822921--32822948	2	14.0	2	100	0	56	50	0	0	50	1.00
32823140--32823177	10	3.9	10	89	3	51	31	5	0	63	1.17
32823866--32823946	31	2.7	30	85	9	103	55	8	11	24	1.63
32824231--32824288	25	2.3	25	90	0	89	34	31	18	15	1.93
32824917--32824987	33	2.2	33	86	0	97	30	9	15	43	1.79
32827089--32827227	22	6.3	22	89	0	197	33	14	25	26	1.94
32828509--32828657	56	2.7	56	89	0	217	31	6	16	46	1.71
32831083--32831145	31	2.0	31	96	0	117	46	9	7	36	1.66
32843791--32843840	2	25.0	2	100	0	100	50	0	0	50	1.00
32843908--32843938	2	15.5	2	100	0	62	51	0	0	48	1.00
32850727--32850767	20	2.0	20	95	0	73	29	12	24	34	1.91
32852838--32852871	14	2.3	15	90	5	52	20	0	2	76	0.92
32853100--32853204	55	1.9	55	88	0	156	24	16	20	38	1.93
32853165--32853474	44	6.8	44	76	10	221	26	20	20	32	1.97
32853148--32853519	138	2.7	137	76	3	379	26	19	20	33	1.97
32853148--32853509	94	3.9	93	67	17	230	25	20	19	33	1.96
32859994--32860028	17	2.1	16	89	5	52	71	0	8	20	1.11
32871541--32871581	13	3.2	13	86	3	57	7	19	2	70	1.22
32873179--32873211	15	2.1	16	88	5	50	33	0	0	66	0.92
32874521--32874569	22	2.2	21	82	7	53	48	4	0	46	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32877298--32877350	2	26.0	2	92	3	88	49	3	0	47	1.19
32878565--32878605	21	2.0	20	85	4	55	46	0	7	46	1.30
32880123--32880233	29	3.8	29	76	1	96	22	16	22	38	1.92
32880123--32880233	58	1.9	59	83	1	143	22	16	22	38	1.92
32883879--32884025	41	3.6	41	85	1	125	31	21	19	27	1.97
32883916--32884051	41	3.3	41	93	0	227	30	20	18	30	1.96
32884666--32884690	2	12.5	2	100	0	50	52	0	0	48	1.00
32886421--32886457	2	18.5	2	100	0	74	51	0	0	48	1.00
32886877--32886977	41	2.5	41	90	3	152	34	23	17	23	1.96
32887093--32887266	64	2.7	63	87	5	228	42	17	7	32	1.77
32887301--32887333	2	16.5	2	100	0	66	51	0	0	48	1.00
32888365--32888421	28	2.0	28	86	6	80	36	5	0	57	1.21
32889627--32889671	19	2.4	18	78	7	54	24	26	2	46	1.64
32899719--32899764	19	2.5	18	79	6	56	26	26	0	47	1.52
32904752--32904782	15	2.1	15	93	0	53	16	6	9	67	1.39
32906408--32906445	20	1.9	20	100	0	76	42	2	10	44	1.52
32908123--32908192	16	4.4	16	94	0	104	31	0	34	34	1.58
32908171--32908280	45	2.6	41	78	9	116	35	4	28	31	1.77
32908426--32908460	18	2.0	17	88	5	52	54	0	0	45	0.99
32908313--32908629	157	2.0	157	97	0	598	44	3	5	47	1.41
32908583--32908617	18	2.0	17	88	5	52	54	0	0	45	0.99
32908363--32908678	157	2.0	155	85	5	413	46	4	4	45	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32911477--32911512	16	2.2	16	100	0	72	25	0	36	38	1.56
32911493--32911583	45	2.0	45	85	2	121	27	6	28	37	1.82
32918620--32918654	19	1.9	17	88	11	52	25	11	0	62	1.28
32918708--32918758	2	25.0	2	84	4	66	45	3	0	50	1.20
32919962--32920019	17	3.2	17	77	15	55	65	1	3	29	1.19
32923615--32923710	42	2.3	42	92	0	165	30	6	12	51	1.64
32941936--32942014	29	2.7	29	84	4	86	25	13	13	46	1.81
32952431--32952488	27	2.1	27	96	0	107	20	27	20	31	1.98
32961564--32961604	20	2.0	20	100	0	82	51	9	9	29	1.67
32970976--32971021	23	2.0	23	100	0	92	39	17	13	30	1.87
32975054--32975099	3	15.3	3	100	0	92	65	0	0	34	0.93
32975098--32975134	3	12.3	3	100	0	74	35	0	0	64	0.94
32991182--32991237	24	2.3	24	81	3	67	32	19	19	28	1.97
32991924--32991967	20	2.2	20	84	8	54	61	2	15	20	1.45
32992414--32992443	16	1.9	16	93	6	53	30	0	20	50	1.49
33005699--33005735	17	2.1	19	85	10	51	54	18	0	27	1.44
33009634--33009808	37	4.7	37	84	0	206	31	16	16	36	1.91
33010142--33010197	22	2.5	23	82	5	69	42	16	5	35	1.70
33011996--33012204	103	2.0	103	87	1	303	54	15	1	28	1.50
33013485--33013648	80	2.0	80	92	0	274	31	15	25	27	1.96
33013818--33014023	97	2.0	101	80	9	226	34	19	13	31	1.91
33019997--33020028	11	2.9	11	95	0	55	28	31	0	40	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33019991--33020035	22	2.0	22	83	8	56	26	31	2	40	1.68
33023413--33023444	11	2.9	11	95	0	55	28	31	0	40	1.57
33023407--33023451	22	2.0	22	83	8	56	26	31	2	40	1.68
33025454--33025511	28	2.1	27	83	3	71	25	5	5	63	1.36
33031033--33031068	13	2.8	13	91	4	56	69	2	13	13	1.30
33032333--33032987	218	3.0	218	94	0	1130	27	18	26	27	1.98
33032688--33033241	174	3.2	173	81	7	676	27	19	25	27	1.99
33032348--33033240	85	10.3	85	68	10	299	27	18	25	27	1.98
33032340--33033197	44	19.8	44	71	9	350	28	18	25	27	1.98
33034065--33034169	28	3.6	28	78	11	97	57	5	2	34	1.37
33034316--33034359	17	2.6	17	85	3	63	47	0	11	40	1.39
33034270--33034414	60	2.4	61	81	6	170	51	1	8	37	1.42
33034288--33034393	33	3.4	33	69	21	84	51	1	11	34	1.49
33034381--33034421	2	21.0	2	95	5	75	51	0	0	48	1.00
33034496--33034597	3	33.3	3	75	14	84	64	3	0	30	1.18
33034565--33034601	7	5.4	7	96	3	67	70	0	0	29	0.88
33034898--33034947	19	2.6	19	96	0	91	36	14	14	36	1.86
33043222--33043312	25	3.6	25	75	0	92	30	19	20	28	1.97
33044478--33044507	12	2.5	12	94	0	51	26	36	26	10	1.88
33048734--33048839	51	2.1	51	100	0	212	48	23	5	22	1.72
33060199--33060248	21	2.4	22	83	9	61	26	0	6	68	1.13
33060367--33060427	29	2.1	30	87	9	90	39	1	3	55	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
33060345--33060419	37	1.9	39	81	7	91	36	4	2	57	1.32
33062772--33062802	10	3.1	10	95	0	53	45	0	0	54	0.99
33075710--33075757	24	2.0	24	87	0	69	22	6	50	20	1.71
33081517--33081620	51	2.0	51	87	3	147	34	21	11	32	1.89
33082565--33082634	29	2.4	29	83	6	90	30	21	12	35	1.91
33083734--33083771	20	1.9	20	94	0	67	39	7	0	52	1.31
33083746--33083777	15	2.1	16	94	5	57	37	6	0	56	1.25
33086690--33086774	25	3.5	24	83	6	91	25	24	21	28	1.99
33099102--33099187	44	2.0	44	90	0	136	29	5	36	29	1.81
33100400--33100461	27	2.3	27	77	0	70	33	17	12	35	1.88

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