genome.fa.s4.2.7.7.80.10.50.1000.110.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  110  of  198  ( 23681 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)
35349430--35349460	16	1.9	16	93	0	53	38	3	3	54	1.32
35351886--35351911	7	3.7	7	100	0	52	11	0	46	42	1.40
35352212--35352237	11	2.4	11	100	0	52	61	15	0	23	1.33
35352517--35352560	18	2.4	19	88	3	63	43	0	54	2	1.12
35353566--35353606	21	2.0	21	86	13	59	43	17	4	34	1.70
35354903--35354938	18	2.0	18	88	0	54	30	25	8	36	1.85
35358278--35358369	39	2.4	39	81	3	105	30	21	22	25	1.99
35359033--35359067	2	17.5	2	100	0	70	48	0	0	51	1.00
35359609--35359724	34	3.3	34	76	11	92	22	0	44	32	1.53
35359618--35359730	21	5.2	21	71	17	72	21	0	46	32	1.52
35359667--35359706	17	2.5	15	81	14	53	22	0	47	30	1.52
35359674--35359706	17	1.9	17	93	0	57	21	0	48	30	1.50
35359631--35359731	13	7.1	13	73	22	71	20	0	44	34	1.52
35359631--35359731	7	14.0	7	71	24	59	20	0	44	34	1.52
35361156--35361201	24	1.9	24	91	8	76	28	43	0	28	1.55
35361604--35361628	12	2.1	12	100	0	50	24	8	8	60	1.52
35361656--35361695	17	2.4	17	88	12	57	52	2	10	35	1.48
35362003--35362060	26	2.2	26	96	0	107	39	13	5	41	1.67
35364584--35364668	44	1.9	45	88	7	129	21	28	21	29	1.98
35364690--35365540	44	19.6	44	70	10	418	28	25	19	27	1.99
35364645--35365369	173	4.2	174	91	1	1134	28	26	19	26	1.98
35364645--35365369	347	2.1	346	90	2	1139	28	26	19	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35364645--35365496	347	2.5	348	86	2	1088	28	25	19	26	1.99
35365162--35365714	218	2.5	218	89	2	830	27	25	19	27	1.99
35364820--35365714	391	2.3	389	77	7	1015	28	25	19	27	1.99
35366967--35367017	7	7.4	7	86	4	59	9	9	1	78	1.04
35366973--35367016	20	2.2	20	87	0	61	11	9	2	77	1.08
35367895--35367943	26	1.9	25	83	4	62	12	12	6	69	1.35
35367909--35367974	6	10.7	6	80	6	51	9	9	12	69	1.36
35372779--35372829	21	2.4	21	83	0	66	35	13	43	7	1.73
35373177--35373268	43	2.1	43	84	4	114	22	17	31	28	1.97
35379953--35379977	3	8.3	3	100	0	50	32	0	0	68	0.90
35380029--35380354	43	7.6	43	84	2	388	20	19	30	30	1.97
35390699--35390741	19	2.3	18	80	4	50	46	2	4	46	1.36
35392385--35392417	15	2.1	16	88	5	50	33	0	9	57	1.30
35392468--35392791	179	1.9	175	87	8	495	34	10	13	40	1.80
35394436--35394479	19	2.4	18	81	11	54	29	2	20	47	1.62
35396874--35396943	25	2.8	25	86	0	113	24	24	24	27	2.00
35404401--35404542	25	5.6	25	87	1	158	26	23	21	28	1.99
35409358--35409406	16	3.1	16	87	0	80	34	4	36	24	1.75
35409385--35409475	45	2.0	44	89	6	139	31	5	28	34	1.80
35409620--35409661	15	2.7	16	82	14	52	52	2	0	45	1.13
35409629--35409670	15	2.9	15	82	10	52	52	0	0	47	1.00
35409735--35409781	15	3.0	16	78	12	53	53	2	0	44	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35409668--35409854	61	3.1	61	66	22	158	49	7	3	39	1.47
35409880--35409914	18	2.0	17	88	5	52	54	0	0	45	0.99
35409858--35410016	54	3.1	53	70	14	152	50	3	1	45	1.25
35409618--35409915	120	2.5	120	94	0	524	50	5	2	41	1.38
35409897--35410064	47	3.7	46	74	13	159	48	2	2	45	1.30
35409956--35410016	28	2.2	28	85	5	81	50	3	0	45	1.17
35409912--35410085	91	1.9	91	87	4	253	48	3	2	45	1.31
35414238--35414391	25	6.2	24	84	5	157	23	22	20	33	1.97
35414239--35414380	75	1.9	74	82	4	178	23	21	21	33	1.97
35418566--35418607	19	2.2	20	86	4	59	4	28	14	52	1.62
35421680--35421856	42	4.2	42	88	2	250	29	19	19	31	1.96
35424959--35425024	26	2.5	26	90	0	105	25	10	9	54	1.64
35437413--35437443	3	10.3	3	100	0	62	67	0	0	32	0.91
35438877--35438983	42	2.5	42	75	8	110	21	20	34	23	1.97
35445598--35445709	42	2.7	42	83	2	118	23	21	34	20	1.96
35459423--35459481	31	1.9	30	86	10	84	62	10	13	13	1.54
35459940--35459982	20	2.1	21	86	4	61	55	4	0	39	1.20
35460596--35460640	22	2.0	22	95	0	81	53	17	13	15	1.73
35478684--35478727	15	2.8	16	80	13	56	40	9	29	20	1.83
35486823--35486856	17	2.0	17	88	11	52	61	0	0	38	0.96
35486821--35486866	14	2.9	16	75	15	51	58	0	0	41	0.98
35486840--35486882	21	2.0	22	86	4	61	62	0	0	37	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35487952--35488022	31	2.2	32	87	5	99	35	5	4	54	1.43
35490118--35490161	23	1.9	23	90	9	72	36	4	6	52	1.49
35492697--35492830	38	3.4	39	64	18	96	35	8	4	50	1.54
35492668--35492830	81	2.0	81	98	0	317	36	8	4	50	1.55
35503478--35503774	50	5.8	50	78	5	231	28	20	28	23	1.99
35503478--35503725	50	4.8	50	80	6	239	27	19	29	23	1.98
35505524--35505587	24	2.7	22	81	15	67	71	0	25	3	1.00
35505544--35505584	15	2.8	15	85	3	57	70	0	26	2	0.99
35505533--35505596	10	6.5	10	75	12	53	71	0	25	3	1.00
35507586--35507687	40	2.5	40	92	3	161	35	22	1	40	1.65
35507585--35507674	13	6.8	13	71	18	69	35	22	2	40	1.66
35509783--35509816	17	2.0	17	94	0	59	17	8	38	35	1.81
35509932--35510073	71	2.0	71	97	0	266	26	5	22	45	1.74
35512228--35512259	13	2.5	13	100	0	64	59	0	0	40	0.97
35521075--35521208	40	3.5	39	77	10	141	24	23	19	32	1.97
35521108--35521242	40	3.7	36	77	8	119	22	21	20	34	1.96
35521075--35521242	75	2.2	76	86	1	221	24	22	19	33	1.97
35521109--35521275	36	4.6	36	78	7	131	22	20	19	36	1.95
35525107--35525146	14	2.9	15	82	14	50	25	15	25	35	1.94
35536824--35536877	27	2.0	27	100	0	108	40	7	3	48	1.49
35539750--35539835	28	3.1	28	76	6	84	31	20	16	31	1.95
35540923--35541026	53	2.0	53	84	0	136	37	15	22	25	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35541204--35541267	28	2.3	28	83	5	76	35	14	21	28	1.92
35542058--35542095	18	2.1	19	85	14	53	47	0	23	28	1.52
35542721--35542830	35	3.2	34	71	5	87	27	23	20	29	1.99
35544857--35544898	14	3.1	14	86	6	59	52	2	0	45	1.13
35544877--35544922	19	2.4	20	82	7	60	47	2	0	50	1.13
35545788--35545813	3	8.7	3	100	0	52	0	30	0	69	0.89
35557332--35557372	7	5.9	7	100	0	82	0	12	0	87	0.53
35561091--35561230	68	2.1	68	95	0	253	24	7	22	45	1.78
35562575--35562682	51	2.1	51	91	3	173	42	10	15	31	1.80
35565692--35565780	27	3.3	27	81	9	110	43	17	20	17	1.88
35565955--35566057	26	4.0	26	93	0	161	15	22	23	38	1.92
35566163--35566224	28	2.2	28	94	0	106	22	24	24	29	1.99
35566178--35566259	28	2.9	28	83	0	92	20	30	26	21	1.98
35570683--35570794	34	3.4	33	81	9	138	39	0	11	49	1.39
35570854--35571492	125	5.1	125	87	6	879	35	17	18	28	1.93
35574398--35574446	25	1.9	25	84	12	64	57	4	2	36	1.30
35574394--35574450	24	2.3	23	78	18	62	52	3	1	42	1.28
35576646--35576710	30	2.2	30	88	0	94	35	3	30	30	1.73
35577180--35577208	6	4.8	6	100	0	58	31	0	0	68	0.89
35577519--35577570	22	2.4	22	83	6	61	55	11	7	25	1.61
35577553--35577590	17	2.2	17	86	9	51	63	7	7	21	1.47
35580422--35580502	19	4.3	19	71	6	65	35	30	17	16	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
35580422--35580534	38	2.9	38	78	3	102	32	28	20	18	1.96
35581652--35581788	25	5.4	25	75	7	134	34	19	12	33	1.89
35581631--35581802	50	3.4	49	81	7	168	34	21	13	29	1.92
35581717--35581797	25	3.2	25	72	16	78	33	23	11	32	1.90
35589623--35589725	27	3.7	29	76	8	88	29	18	19	33	1.96
35589816--35589917	29	3.4	29	69	7	87	28	28	13	29	1.94
35589780--35589978	61	3.3	59	84	2	227	29	25	14	30	1.94
35590109--35590252	53	2.7	53	80	6	148	28	25	13	33	1.93
35619163--35619291	44	3.0	43	73	13	129	24	18	26	31	1.98
35623367--35623395	13	2.1	14	93	6	51	68	13	6	10	1.37

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