genome.fa.s4.2.7.7.80.10.50.1000.100.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  100  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)
32121164--32121265	15	7.4	14	78	15	90	58	1	5	33	1.33
32128325--32128374	22	2.4	21	83	9	68	38	0	26	36	1.57
32130342--32130374	10	3.7	9	88	11	50	72	3	0	24	0.98
32134969--32135031	20	3.1	21	69	15	60	15	33	17	33	1.92
32134990--32135050	20	3.0	20	71	17	63	14	31	16	37	1.89
32134968--32135094	40	3.2	40	86	1	182	14	30	17	37	1.89
32135464--32135496	17	1.9	17	93	0	57	36	3	15	45	1.61
32138572--32138624	22	2.5	20	80	16	63	28	9	20	41	1.83
32138582--32138625	22	2.0	23	90	4	72	27	11	18	43	1.84
32149856--32149900	18	2.5	17	83	16	56	22	2	2	73	1.05
32150494--32150528	2	17.5	2	100	0	70	51	0	0	48	1.00
32150632--32150753	63	2.0	62	85	1	163	31	13	13	40	1.83
32151713--32151746	11	2.9	12	86	8	52	70	0	8	20	1.13
32158582--32159449	434	2.0	436	93	1	1474	28	17	18	35	1.93
32166968--32167008	19	2.2	19	90	0	64	63	7	4	24	1.40
32167967--32168005	17	2.2	18	90	4	62	20	30	0	48	1.50
32169607--32169781	76	2.3	78	83	2	210	40	4	18	37	1.69
32170142--32170353	31	6.6	31	70	12	142	28	8	19	42	1.81
32170127--32170372	33	7.5	32	72	15	184	28	8	19	43	1.79
32170127--32170353	64	3.5	64	86	3	310	28	8	19	43	1.80
32170925--32170971	23	2.0	23	100	0	94	38	4	14	42	1.66
32177404--32177566	86	1.9	86	83	2	211	28	17	19	34	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32178366--32178553	93	2.0	93	87	0	268	30	25	8	35	1.86
32182925--32182958	2	17.0	2	100	0	68	50	0	0	50	1.00
32193762--32193823	32	1.9	32	93	0	106	45	9	17	27	1.80
32201896--32201933	15	2.5	15	95	0	67	13	34	7	44	1.72
32202567--32202613	19	2.5	19	89	6	69	42	4	4	48	1.42
32204522--32204575	17	3.2	17	77	15	67	55	5	31	7	1.51
32205288--32205332	21	2.1	21	100	0	90	31	11	17	40	1.85
32207838--32207868	2	15.5	2	100	0	62	51	0	0	48	1.00
32212048--32212096	18	2.7	18	78	12	55	20	26	34	18	1.95
32212623--32212653	16	1.9	16	93	0	53	12	12	16	58	1.64
32217772--32217800	7	4.3	7	91	8	51	86	0	13	0	0.58
32217772--32217800	13	2.1	14	93	6	51	86	0	13	0	0.58
32221295--32221349	24	2.3	24	80	0	65	23	5	12	58	1.55
32221311--32221349	12	3.2	12	81	0	51	23	5	10	61	1.48
32225940--32226038	40	2.5	40	88	1	146	10	14	30	45	1.77
32227558--32227588	13	2.4	13	100	0	62	6	25	32	35	1.82
32232933--32233214	50	5.6	50	79	4	280	34	26	12	26	1.92
32233010--32233085	25	3.0	25	73	19	77	34	26	13	26	1.93
32232950--32233188	101	2.4	101	81	5	261	34	27	12	26	1.92
32233107--32233186	25	3.2	25	70	16	74	35	25	12	27	1.92
32240487--32240522	17	2.1	17	89	0	54	22	0	8	69	1.15
32240547--32240591	3	15.0	3	100	0	90	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32244475--32244528	19	2.8	19	97	0	99	14	31	16	37	1.89
32247676--32247716	12	3.6	12	81	18	52	78	9	12	0	0.98
32248738--32248820	43	1.9	43	85	4	114	25	30	22	21	1.99
32249283--32249423	51	2.8	52	75	10	143	41	5	4	47	1.49
32251781--32251936	40	3.9	40	88	0	240	28	19	24	26	1.99
32251978--32252127	40	3.8	40	85	0	192	28	20	22	29	1.98
32251794--32252212	184	2.2	189	85	5	544	29	18	22	29	1.97
32252808--32252924	7	16.4	7	72	13	69	24	0	26	47	1.57
32252808--32253009	14	14.2	14	70	12	92	22	0	30	45	1.59
32252813--32253012	7	28.1	7	69	10	66	22	1	32	44	1.59
32258802--32259028	43	5.3	43	81	6	219	20	15	28	36	1.93
32270526--32270628	35	2.9	35	79	4	118	35	33	11	18	1.87
32275556--32275617	17	3.1	21	75	20	78	56	14	6	22	1.61
32276971--32277002	13	2.3	15	89	10	50	56	0	0	43	0.99
32277073--32277130	29	2.0	29	96	0	107	22	17	24	36	1.95
32277733--32277922	7	26.7	7	68	15	59	46	29	2	22	1.63
32277731--32277828	28	3.5	28	74	13	76	45	31	1	21	1.58
32278260--32278432	41	4.2	41	85	4	242	30	27	20	21	1.98
32278260--32278432	82	2.1	82	90	4	269	30	27	20	21	1.98
32278434--32278522	41	2.2	40	82	7	101	31	28	20	20	1.97
32278447--32278652	41	5.0	41	80	4	220	33	27	17	22	1.96
32278248--32278604	186	1.9	186	85	5	499	31	27	19	21	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32278301--32278577	145	1.9	146	87	5	409	32	26	19	21	1.97
32278467--32278652	82	2.3	82	86	1	266	34	26	16	22	1.95
32282695--32282742	18	2.6	18	90	3	69	41	10	0	47	1.37
32284610--32284672	30	2.1	31	82	14	78	22	7	20	49	1.75
32288748--32289257	253	2.0	253	98	0	977	21	19	15	43	1.87
32292368--32292407	20	2.0	20	95	0	71	65	0	2	32	1.06
32292616--32292664	7	7.0	7	100	0	98	42	42	0	14	1.45
32293082--32293159	27	2.9	27	90	0	120	24	23	26	25	2.00
32293091--32293177	27	3.2	27	86	3	104	25	25	27	21	2.00
32298065--32298161	42	2.3	42	91	1	151	39	13	24	22	1.90
32302229--32302324	49	2.0	49	93	0	165	53	15	0	31	1.43
32302436--32302488	17	2.8	18	81	13	63	0	32	0	67	0.91
32302432--32302488	20	2.8	21	74	17	57	0	31	0	68	0.90
32302630--32302691	27	2.3	27	91	0	97	29	24	19	27	1.98
32320805--32320887	29	2.8	30	77	3	96	26	24	12	37	1.90
32320990--32321065	33	2.3	33	82	15	95	26	25	17	31	1.97
32322492--32322527	15	2.4	15	100	0	72	27	36	5	30	1.80
32327724--32327764	21	2.0	20	85	4	55	56	2	0	41	1.13
32336145--32336263	54	2.2	54	95	0	211	33	20	16	29	1.95
32342727--32342755	12	2.3	13	94	5	51	20	6	6	65	1.40
32344833--32344881	24	2.0	24	100	0	98	34	8	20	36	1.82
32355590--32355707	61	1.9	62	83	11	154	24	8	8	58	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32357729--32357764	18	2.0	18	88	0	54	58	22	5	13	1.56
32367353--32367422	17	4.1	17	72	20	56	68	4	2	24	1.21
32367381--32367422	15	2.7	16	85	14	61	69	4	0	26	1.08
32367889--32368331	143	3.1	141	85	6	572	33	17	21	27	1.96
32367889--32368331	72	6.2	73	86	3	585	33	17	21	27	1.96
32368906--32368965	7	8.7	7	78	10	52	18	1	33	46	1.59
32368885--32368965	21	3.9	21	76	14	60	20	3	28	46	1.68
32368771--32369082	157	2.0	157	91	1	509	18	2	32	46	1.64
32369028--32369095	21	3.2	21	74	0	64	20	5	26	47	1.73
32369012--32369095	7	11.9	7	80	7	53	21	5	26	46	1.74
32368998--32369324	163	2.0	163	99	0	645	28	4	19	47	1.70
32369191--32369258	21	3.2	21	74	0	64	20	5	26	47	1.73
32369175--32369258	7	11.9	7	80	7	53	21	5	26	46	1.74
32369321--32369357	2	18.5	2	94	0	65	54	0	0	45	1.00
32369580--32370359	147	5.3	143	75	10	425	26	17	22	34	1.95
32369850--32370357	147	3.4	147	77	6	465	25	16	22	35	1.95
32369826--32370425	294	2.0	295	80	2	688	25	16	21	35	1.94
32370879--32370907	14	2.1	14	100	0	58	13	6	24	55	1.63
32371341--32371506	88	1.9	88	100	0	332	31	15	10	42	1.80
32371609--32371644	6	6.5	6	87	12	51	30	0	0	69	0.89
32372300--32372691	9	46.4	9	71	17	261	46	19	0	33	1.56
32372285--32372689	25	16.4	25	76	11	239	45	19	0	33	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32372285--32372687	34	12.2	33	67	19	159	45	19	0	33	1.57
32372311--32372617	41	7.4	40	79	8	294	46	19	0	32	1.55
32372504--32372687	16	12.0	16	71	18	90	46	16	0	36	1.51
32378298--32378649	43	8.2	43	83	3	361	26	18	29	25	1.98
32378298--32378649	85	4.1	85	81	5	386	26	18	29	25	1.98
32378298--32378649	128	2.7	128	83	3	413	26	18	29	25	1.98
32378849--32378887	20	1.9	21	89	5	62	35	12	0	51	1.40
32378994--32379030	18	2.1	18	90	5	58	24	10	8	56	1.60
32383022--32383142	61	2.0	61	96	0	224	34	12	23	29	1.91
32388131--32388178	13	3.6	13	73	15	53	20	8	0	70	1.12

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