genome.fa.s9.2.7.7.80.10.50.1000.177.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  177  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)
56645360--56645392	16	1.9	18	88	11	52	66	0	12	21	1.23
56646061--56646109	25	2.0	25	84	8	64	40	0	14	44	1.45
56646507--56646554	25	1.9	25	86	0	69	54	4	18	22	1.61
56647793--56647886	49	1.9	49	88	0	143	43	6	23	26	1.77
56652783--56652816	16	2.0	18	88	11	54	38	0	14	47	1.45
56653010--56653042	16	1.9	18	88	11	52	66	0	12	21	1.23
56654201--56654286	43	2.0	43	83	0	109	52	1	23	23	1.54
56655506--56655599	49	1.9	49	97	0	179	42	7	26	23	1.80
56656460--56656651	100	1.9	99	86	3	269	27	15	22	34	1.94
56667234--56667259	11	2.4	11	100	0	52	30	0	19	50	1.48
56671096--56671178	32	2.6	32	86	3	114	31	12	20	36	1.89
56671501--56671565	31	2.1	32	82	8	80	29	13	12	44	1.81
56675163--56675233	31	2.3	30	85	7	90	52	12	0	35	1.40
56680065--56680115	18	2.8	19	82	11	54	74	1	5	17	1.11
56680938--56680982	23	2.0	23	95	0	81	46	8	2	42	1.47
56680939--56680988	23	2.2	23	88	0	73	50	10	2	38	1.48
56682440--56682504	23	2.8	23	97	0	121	47	15	0	36	1.46
56682440--56682504	13	5.5	13	70	20	61	47	15	0	36	1.46
56683380--56683418	8	4.9	8	87	0	51	35	0	0	64	0.94
56686843--56686918	35	2.2	35	81	9	84	69	1	7	21	1.21
56688928--56688974	20	2.3	20	96	0	85	29	4	10	55	1.53
56691176--56691329	76	2.0	77	94	1	274	24	17	27	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56697345--56697803	228	2.0	228	96	0	855	31	13	26	28	1.94
56700746--56700776	9	3.4	9	90	0	53	38	22	12	25	1.90
56701708--56701862	50	3.1	50	60	20	113	32	18	14	34	1.90
56701634--56701862	102	2.2	102	100	0	458	32	19	13	33	1.91
56704944--56705020	31	2.5	31	87	4	102	27	16	7	48	1.74
56705570--56705603	18	1.9	17	94	5	59	47	2	0	50	1.16
56707659--56707723	29	2.2	29	91	0	103	27	12	15	44	1.82
56709133--56709280	24	6.2	24	76	6	113	37	37	10	15	1.81
56709143--56709233	47	1.9	47	90	0	146	35	37	9	17	1.83
56711281--56711389	46	2.4	46	92	0	173	20	20	25	33	1.96
56712800--56712876	24	3.2	24	85	3	102	31	38	10	19	1.85
56716020--56716056	15	2.4	16	90	4	58	45	16	8	29	1.76
56718406--56718452	23	2.0	23	83	8	58	42	23	19	14	1.88
56718416--56718483	24	2.8	24	84	8	77	39	23	19	17	1.92
56720810--56720857	25	2.0	24	91	4	78	43	4	2	50	1.33
56720857--56720896	22	1.9	20	85	10	53	55	0	7	37	1.29
56721743--56721786	23	1.9	23	86	9	63	52	4	15	27	1.63
56723489--56723541	28	1.9	27	85	11	72	37	0	1	60	1.08
56735970--56736023	18	2.9	19	75	10	58	22	31	1	44	1.63
56737943--56738025	24	3.5	24	83	6	89	42	6	37	14	1.70
56753398--56753954	138	4.1	137	86	4	775	39	7	6	46	1.58
56762365--56762535	32	5.4	31	83	7	177	40	19	18	22	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56762365--56762535	64	2.7	64	82	5	204	40	19	18	22	1.92
56762546--56762617	26	2.8	26	91	0	108	38	26	19	15	1.91
56762605--56762664	27	2.2	27	88	11	88	31	21	25	21	1.98
56762812--56762956	27	5.4	27	84	0	175	24	24	18	33	1.97
56768228--56768299	3	24.0	3	85	0	99	31	4	1	62	1.23
56768291--56768336	23	1.9	23	86	8	65	21	2	2	73	1.04
56769493--56769541	23	2.1	23	81	7	55	12	16	0	71	1.14
56770597--56770660	30	2.2	31	83	11	89	20	15	29	34	1.94
56770604--56770660	30	2.0	30	89	6	91	19	17	29	33	1.95
56770613--56770676	27	2.2	30	81	8	80	17	15	31	35	1.91
56780185--56780323	70	2.0	70	86	0	197	23	20	24	31	1.98
56786410--56786540	65	2.0	65	100	0	262	27	18	15	38	1.90
56788419--56788464	20	2.3	18	82	17	56	43	2	2	52	1.25
56792696--56792749	24	2.2	24	86	3	72	40	12	27	18	1.87
56796557--56796600	23	1.9	23	85	0	61	13	34	18	34	1.90
56802727--56802803	24	3.3	23	81	16	72	64	1	0	33	1.01
56827654--56827821	41	4.1	41	81	4	160	35	31	20	13	1.91
56848557--56848619	27	2.4	27	81	5	67	22	26	1	49	1.59
56848574--56848624	25	2.0	27	84	7	70	19	29	0	50	1.48
56848598--56848649	27	2.0	25	81	7	59	23	26	0	50	1.50
56848599--56848683	43	2.0	43	90	4	136	22	25	1	50	1.56
56851136--56851166	16	1.9	16	93	0	53	12	6	6	74	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56859422--56859452	16	1.9	16	93	0	53	12	9	3	74	1.19
56863359--56864519	137	8.4	138	87	2	1654	40	8	5	45	1.59
56863359--56864519	275	4.2	276	87	1	1677	40	8	5	45	1.59
56879537--56879740	28	7.3	28	88	2	288	31	24	21	23	1.98
56879844--56879924	26	3.1	26	78	7	110	33	23	22	20	1.97
56880145--56880520	54	6.9	54	80	9	381	22	15	19	42	1.88
56880130--56880462	27	12.3	27	82	3	341	22	15	18	42	1.88
56880750--56880784	17	2.0	17	88	5	52	22	40	22	14	1.90
56889691--56889789	19	5.2	20	73	13	75	38	23	18	20	1.93
56889889--56889929	21	2.0	20	86	13	57	29	21	0	48	1.50
56890562--56890638	37	2.1	37	100	0	154	45	12	12	28	1.80
56890884--56890931	22	2.2	22	88	7	71	45	10	22	20	1.81
56892370--56892463	25	3.8	25	82	2	109	25	22	22	29	1.99
56897019--56897052	17	2.0	17	100	0	68	47	11	5	35	1.65
56907756--56907783	2	14.0	2	100	0	56	50	0	0	50	1.00
56914763--56914923	27	6.0	27	75	2	144	29	18	24	27	1.98
56919493--56919524	5	6.4	5	100	0	64	78	0	0	21	0.76
56921966--56922004	5	7.6	5	82	5	51	41	17	0	41	1.50
56925529--56925596	3	22.7	3	96	0	127	0	30	0	69	0.89
56930288--56930479	101	1.9	101	90	0	303	33	19	26	20	1.96
56934623--56934723	53	1.9	53	87	0	148	36	14	18	29	1.91
56934846--56935010	60	2.7	61	80	2	206	31	12	24	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
56934971--56935045	32	2.3	32	84	4	89	25	9	28	37	1.87
56939274--56939346	28	2.6	27	80	6	83	43	6	23	26	1.78
56940289--56940433	42	3.5	42	89	0	218	22	21	22	34	1.97
56940750--56940820	21	3.4	21	73	7	63	1	40	18	39	1.59
56943992--56944062	14	4.7	15	73	16	58	38	42	1	18	1.59
56943992--56944063	31	2.4	29	86	4	90	38	41	1	18	1.59
56944333--56944423	7	12.4	7	68	17	51	41	37	1	19	1.59
56944638--56944850	114	1.9	114	89	0	336	27	26	21	24	1.99
56944792--56944939	76	1.9	76	84	2	199	25	25	20	28	1.99
56944867--56945172	114	2.7	113	80	8	334	26	24	20	28	1.99
56952267--56952344	26	3.0	26	75	0	75	42	8	20	28	1.82
56954008--56954648	328	2.0	328	96	0	1192	36	16	9	37	1.82
56957526--56957658	50	2.7	50	80	6	153	18	28	24	27	1.98
56962964--56963052	13	6.7	13	73	10	81	43	3	20	32	1.68
56962964--56963052	40	2.2	40	95	0	160	43	3	20	32	1.68
56965381--56965474	49	1.9	49	80	8	111	41	18	17	23	1.90
56993586--56993627	14	2.8	15	78	7	50	52	0	2	45	1.13
56993709--56993786	10	7.9	10	76	12	56	33	3	2	60	1.28
56993750--56993786	19	2.0	18	89	5	56	32	0	0	67	0.91
56993756--56993798	19	2.3	19	84	8	52	32	2	0	65	1.06
56993764--56993824	27	2.2	28	82	8	72	31	3	0	65	1.09
57015788--57015943	58	2.7	59	82	4	183	39	19	16	23	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57015788--57015969	29	6.4	30	73	14	127	39	20	16	23	1.92
57015928--57015996	26	2.7	26	83	0	93	34	24	23	17	1.96
57019250--57019306	27	2.1	27	90	3	89	15	15	21	47	1.82
57024113--57024142	12	2.5	12	94	0	51	26	36	26	10	1.88
57030258--57030397	50	3.2	42	74	16	140	33	18	16	31	1.93
57036752--57036787	18	2.0	18	94	0	63	22	19	22	36	1.95
57042400--57042474	31	2.5	30	77	12	84	37	0	1	61	1.05
57042607--57042645	16	2.4	17	83	12	55	30	0	2	66	1.05
57046335--57046450	10	12.4	9	65	17	58	62	2	3	31	1.25
57046771--57046832	29	2.1	30	84	3	81	38	3	0	58	1.15

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