genome.fa.s9.2.7.7.80.10.50.1000.154.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  154  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)
50103072--50103102	12	2.6	12	89	0	53	25	16	0	58	1.38
50106148--50106191	4	11.0	4	90	0	52	22	6	2	68	1.25
50111029--50111372	86	4.0	86	100	0	688	32	12	12	41	1.81
50115712--50115745	9	3.9	9	84	7	52	44	0	2	52	1.16
50122223--50122253	6	5.2	6	100	0	62	32	0	0	67	0.91
50125412--50125490	29	2.8	28	82	5	95	59	2	6	31	1.36
50128025--50128520	88	5.6	89	79	4	468	24	23	22	29	1.99
50128025--50128522	177	2.8	177	79	3	455	24	23	22	29	1.99
50128027--50128520	265	1.9	265	86	0	711	24	24	22	29	1.99
50130774--50130833	25	2.4	25	83	8	70	58	5	16	20	1.56
50134492--50134570	29	2.8	28	82	5	95	59	2	6	31	1.36
50134959--50135007	16	3.0	16	73	5	53	53	0	6	40	1.26
50134955--50135024	30	2.3	31	80	11	83	50	2	8	38	1.48
50138983--50139036	28	1.9	28	85	7	74	3	18	5	72	1.20
50139781--50139809	7	4.1	7	100	0	58	31	0	13	55	1.39
50141474--50141527	20	2.7	20	73	2	63	61	0	11	27	1.30
50141785--50141838	28	1.9	28	85	7	74	3	18	5	72	1.20
50155775--50155819	10	4.6	10	83	2	56	37	6	2	53	1.40
50155771--50155819	20	2.5	19	80	3	62	38	6	2	53	1.38
50164043--50164099	28	2.0	30	86	6	82	26	21	5	47	1.71
50169447--50169514	35	1.9	35	82	11	86	8	22	14	54	1.67
50169487--50169527	19	2.1	20	86	4	57	7	14	19	58	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50171126--50171171	20	2.3	20	92	0	74	10	32	13	43	1.78
50173799--50173841	17	2.6	16	82	13	52	46	4	25	23	1.71
50179640--50179714	38	2.0	38	97	0	141	42	9	13	34	1.76
50182135--50182174	4	10.0	4	94	0	62	25	5	0	70	1.08
50186263--50186293	15	2.1	15	93	0	53	64	6	0	29	1.18
50187287--50187335	22	2.4	19	80	16	53	10	22	53	14	1.71
50188307--50188376	16	4.4	16	88	0	104	32	1	35	30	1.67
50188307--50188376	32	2.2	32	94	0	122	32	1	35	30	1.67
50188355--50188464	45	2.6	43	80	9	129	34	5	28	31	1.80
50188590--50188631	15	2.7	16	82	14	52	52	2	0	45	1.13
50188599--50188640	15	2.9	15	82	10	52	52	0	0	47	1.00
50190586--50190612	11	2.5	11	100	0	54	51	18	7	22	1.70
50192285--50192407	32	3.5	32	76	23	131	50	1	17	30	1.55
50192269--50192407	75	1.9	75	96	3	262	47	2	16	33	1.61
50192701--50192725	13	1.9	13	100	0	50	20	16	8	56	1.65
50195396--50195438	18	2.3	19	88	4	61	39	0	0	60	0.97
50213238--50213297	21	2.9	21	73	9	59	40	15	21	23	1.91
50214529--50214887	44	8.2	45	72	11	194	27	20	25	27	1.99
50214343--50214852	214	2.4	214	90	0	806	28	19	24	27	1.99
50214343--50214867	44	12.2	44	69	15	172	28	19	24	27	1.99
50217861--50217920	30	2.0	30	100	0	120	26	13	20	40	1.89
50219266--50219310	16	2.9	15	83	9	56	55	2	4	37	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50227103--50227137	18	1.9	18	88	0	52	62	5	22	8	1.45
50228443--50228565	61	2.0	61	100	0	246	34	9	16	39	1.81
50239406--50239467	29	2.2	27	78	16	63	53	4	1	40	1.32
50241157--50242774	597	2.7	593	89	2	2398	34	15	15	33	1.90
50243673--50243723	19	2.8	18	77	11	50	27	5	1	64	1.27
50243691--50243760	10	7.3	10	74	7	56	37	5	0	57	1.23
50245676--50245757	40	2.0	41	85	4	112	23	28	25	23	2.00
50250314--50250361	23	2.1	23	88	0	69	45	6	14	33	1.70
50253009--50253071	3	21.3	3	87	9	94	31	1	1	65	1.12
50254282--50254342	19	3.2	19	77	15	63	65	0	9	24	1.23
50254360--50254392	17	1.9	17	93	0	57	54	0	18	27	1.44
50256539--50256577	19	2.1	19	90	0	60	38	7	2	51	1.44
50257605--50257632	11	2.5	11	100	0	56	21	0	17	60	1.36
50259056--50259101	20	2.3	21	75	14	53	65	0	8	26	1.21
50264193--50264219	2	13.5	2	100	0	54	48	0	0	51	1.00
50265516--50265606	46	2.0	46	85	6	123	40	15	12	31	1.84
50265498--50265606	45	2.4	45	78	4	121	41	17	11	29	1.85
50266995--50267080	34	2.5	34	98	0	163	22	18	30	29	1.97
50268469--50268512	4	11.0	4	90	0	52	22	6	2	68	1.25
50278508--50278541	9	3.9	9	84	7	52	44	0	2	52	1.16
50282426--50282496	20	3.6	19	76	10	72	38	8	0	53	1.31
50282426--50282498	30	2.4	29	82	6	92	38	8	0	53	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50282426--50282497	10	7.3	10	82	1	65	37	8	0	54	1.31
50282721--50282749	15	1.9	15	100	0	58	44	6	20	27	1.77
50293023--50293069	19	2.5	19	80	16	53	70	0	4	25	1.05
50298101--50298659	280	2.0	276	98	1	1073	33	10	8	48	1.67
50299748--50299851	45	2.3	45	80	5	129	39	17	13	29	1.88
50313464--50313490	9	3.0	9	100	0	54	33	11	11	44	1.75
50316102--50316209	30	3.5	30	75	14	119	24	4	8	62	1.42
50316140--50316186	12	3.8	12	86	10	67	23	0	6	70	1.10
50316143--50316209	26	2.4	29	90	9	104	22	2	7	67	1.30
50316091--50316213	64	1.9	65	93	1	212	25	4	8	62	1.41
50318961--50319054	40	2.5	37	81	11	109	54	8	3	34	1.47
50318961--50319054	37	2.6	34	78	17	84	54	8	3	34	1.47
50319149--50319184	16	2.2	16	90	9	56	55	8	2	33	1.44
50319350--50319414	24	2.7	24	68	0	58	3	24	1	70	1.10
50319440--50319492	3	18.3	3	75	21	51	1	33	0	64	1.05
50321025--50321187	68	2.4	69	81	1	175	29	25	17	26	1.98
50325597--50325653	20	2.9	20	81	2	71	36	0	5	57	1.21
50325646--50325686	22	1.9	22	90	5	66	36	4	0	58	1.20
50334457--50334482	8	3.2	8	100	0	52	57	0	0	42	0.98
50334870--50334915	25	1.9	23	86	8	65	32	2	2	63	1.19
50335970--50337353	597	2.3	597	92	0	2277	34	15	16	33	1.91
50344282--50344485	68	3.0	68	98	0	390	37	19	14	28	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50346615--50346663	22	2.2	23	79	17	59	16	6	28	48	1.69
50346743--50346782	18	2.2	18	86	13	55	12	17	7	62	1.52
50354444--50354576	51	2.7	48	81	3	158	42	20	24	13	1.88
50356141--50356590	181	2.5	174	83	3	524	31	16	21	30	1.95
50355781--50356452	96	7.3	96	69	14	296	32	16	20	30	1.95
50356463--50356535	37	2.0	37	88	0	110	24	19	27	28	1.98
50356500--50357535	143	7.2	143	88	0	1478	30	19	22	27	1.98
50359129--50359197	3	23.0	3	96	0	129	31	0	0	68	0.90
50368573--50368607	12	2.9	12	91	0	52	20	2	31	45	1.65
50371702--50371927	43	5.3	43	90	0	317	20	19	34	26	1.96
50372021--50372063	22	2.0	22	90	0	68	41	25	20	11	1.86
50372073--50372182	43	2.6	43	91	0	175	31	30	16	20	1.95
50377234--50377289	13	4.3	13	75	8	60	64	0	0	35	0.94
50377447--50377496	15	3.1	17	80	16	52	46	8	2	44	1.44
50379986--50380045	15	4.1	15	82	8	70	35	40	8	16	1.79
50380968--50381012	5	9.4	5	80	9	58	20	2	0	77	0.87
50380975--50381018	15	3.0	15	83	12	56	22	2	0	75	0.92
50381301--50381339	12	3.2	12	81	0	51	38	2	0	58	1.12
50381300--50381352	24	2.2	25	80	10	65	35	7	0	56	1.28
50383308--50383380	10	7.3	10	80	4	58	56	0	6	36	1.26
50383309--50383380	20	3.6	20	75	3	74	55	0	6	37	1.27
50385663--50385697	18	1.9	18	94	0	61	25	22	22	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
50387948--50388000	15	3.6	15	85	14	74	39	35	0	24	1.56
50387951--50388002	14	3.6	14	82	17	61	36	40	0	23	1.55
50387951--50388015	7	9.0	7	72	12	51	38	38	0	23	1.55
50387941--50388015	29	2.6	29	82	2	96	37	38	1	22	1.63
50387980--50388031	22	2.4	21	90	3	77	36	44	0	19	1.51
50387951--50388010	15	4.1	15	82	4	68	36	41	0	21	1.54
50388243--50388293	23	2.2	24	92	3	86	33	47	1	17	1.59
50388309--50388356	14	3.4	14	80	5	51	45	35	0	18	1.50
50388628--50388778	41	3.8	41	88	5	227	32	26	21	19	1.97
50388628--50388778	79	1.9	80	87	4	223	32	26	21	19	1.97

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