genome.fa.s4.2.7.7.80.10.50.1000.153.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  153  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)
48472405--48472461	24	2.4	24	82	5	62	36	7	10	45	1.66
48476616--48476667	24	2.2	24	85	0	68	34	3	11	50	1.57
48485875--48486129	27	9.5	27	78	9	254	43	20	15	20	1.88
48485933--48486129	53	3.7	52	84	11	240	43	20	16	19	1.88
48485875--48486127	80	3.1	80	84	5	314	43	20	15	20	1.87
48486334--48486414	26	3.1	26	82	5	92	24	22	19	33	1.97
48486517--48486604	28	3.1	28	93	0	158	22	23	22	30	1.99
48488313--48488353	19	2.2	19	86	4	57	46	9	17	26	1.79
48491844--48491879	18	1.9	19	88	5	56	38	0	27	33	1.57
48494315--48494340	10	2.6	10	100	0	52	69	11	0	19	1.18
48495063--48495096	6	5.8	6	86	6	52	0	14	0	85	0.60
48495062--48495100	20	2.0	20	90	10	62	0	15	0	84	0.62
48495062--48495099	11	3.4	11	85	7	58	0	13	0	86	0.56
48497516--48497547	16	2.0	16	100	0	64	31	0	43	25	1.55
48497864--48497921	30	2.0	30	83	10	75	48	6	6	37	1.57
48506381--48506410	7	4.3	7	100	0	60	56	0	0	43	0.99
48506473--48506511	12	3.4	12	82	13	55	74	0	25	0	0.82
48508594--48508655	30	2.1	30	93	0	106	32	29	24	14	1.94
48511942--48512077	42	3.3	42	82	4	150	25	16	19	38	1.93
48513299--48513357	22	2.5	22	84	13	66	66	3	1	28	1.18
48513375--48513415	21	2.0	21	85	0	55	56	4	7	31	1.48
48513966--48514099	19	6.5	21	79	14	84	41	14	6	37	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48513966--48514023	22	2.6	22	84	7	73	43	17	3	36	1.66
48513979--48514099	21	5.9	19	85	7	125	39	14	7	38	1.75
48514013--48514096	21	4.1	21	89	6	136	39	13	8	39	1.74
48513995--48514096	40	2.6	40	82	11	140	38	14	7	39	1.75
48514476--48515118	44	14.6	43	78	7	621	29	25	15	29	1.96
48514476--48515120	132	4.9	132	90	1	961	29	25	15	29	1.96
48516424--48516469	9	5.1	9	94	0	83	45	13	10	30	1.77
48516682--48516738	30	1.9	30	85	0	78	19	35	0	45	1.50
48517496--48517526	15	2.1	15	100	0	62	25	19	12	41	1.87
48517605--48517669	27	2.4	26	80	7	67	10	13	3	72	1.23
48520693--48520750	23	2.5	23	86	8	73	65	3	3	27	1.25
48520770--48520810	21	2.0	21	85	0	55	56	4	7	31	1.48
48521360--48521417	22	2.6	22	81	7	64	43	17	1	37	1.59
48521373--48521472	21	4.8	19	78	14	83	40	15	5	40	1.68
48521407--48521471	21	3.1	21	90	0	103	40	12	6	41	1.67
48524022--48524075	27	2.0	27	92	0	90	18	18	18	44	1.87
48527356--48527832	50	9.7	50	80	8	516	21	31	20	26	1.97
48527314--48527841	97	5.4	98	80	8	531	22	31	19	26	1.98
48527356--48527841	147	3.3	147	89	1	758	21	32	19	26	1.97
48527405--48527832	197	2.2	195	84	6	551	20	31	20	27	1.97
48540080--48540236	56	2.8	56	94	0	260	45	15	8	30	1.77
48555535--48555601	26	2.6	27	81	9	86	16	22	23	37	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48555519--48555677	25	6.4	25	71	15	109	17	25	23	33	1.96
48555524--48555663	48	2.8	51	78	11	137	17	25	21	35	1.95
48555571--48555710	72	1.9	73	82	7	178	17	25	22	33	1.96
48555544--48555724	72	2.5	71	75	8	175	18	25	21	34	1.96
48562021--48562092	32	2.2	32	97	2	135	26	26	9	37	1.87
48563920--48564022	54	1.9	54	88	7	156	18	29	21	31	1.97
48565868--48565942	32	2.3	32	82	8	91	44	20	2	33	1.65
48566042--48566100	16	3.7	16	71	10	50	38	16	8	35	1.80
48566687--48566742	28	2.0	28	92	0	94	58	1	16	23	1.47
48573637--48573664	3	9.3	3	100	0	56	35	0	0	64	0.94
48574866--48575007	69	2.1	69	94	2	250	38	5	16	38	1.73
48575715--48575764	24	2.1	24	92	0	82	14	34	14	38	1.85
48575751--48575809	24	2.6	22	77	12	66	22	33	11	32	1.90
48575829--48575871	9	4.8	9	91	0	68	32	32	23	11	1.90
48576114--48576175	30	2.0	32	84	9	83	17	20	41	19	1.90
48578677--48578792	56	2.1	56	88	3	171	44	10	20	24	1.82
48579093--48579138	22	2.1	22	100	0	92	17	17	4	60	1.51
48585607--48585695	42	2.1	41	81	8	99	42	15	23	17	1.88
48587540--48587577	5	8.0	5	91	8	62	42	0	0	57	0.98
48588551--48588612	22	2.8	23	78	11	67	17	27	17	37	1.93
48589613--48589672	30	2.0	30	100	0	120	30	6	30	33	1.83
48592990--48593045	22	2.5	23	85	8	80	14	25	19	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48599398--48599535	50	2.8	49	82	4	159	27	14	27	30	1.95
48602278--48602358	21	3.9	21	68	12	67	40	13	28	17	1.87
48609134--48609215	36	2.3	36	89	0	119	30	7	18	43	1.77
48609271--48609473	95	2.1	95	89	0	307	31	16	14	37	1.89
48609436--48609897	64	7.1	63	65	16	197	32	13	12	41	1.83
48609369--48610008	131	4.9	130	87	1	742	31	14	12	40	1.84
48609500--48609709	67	3.2	67	66	11	198	29	11	14	44	1.81
48609199--48609604	226	1.8	223	86	0	515	32	14	14	39	1.86
48623995--48624049	26	2.1	26	83	6	67	58	3	0	38	1.16
48624610--48624649	17	2.3	17	86	4	53	25	2	0	72	0.97
48626265--48626299	7	4.9	7	93	6	61	14	0	40	45	1.45
48626267--48626298	15	2.1	15	100	0	64	12	0	37	50	1.41
48626489--48626902	202	2.0	202	93	0	702	30	14	20	34	1.92
48628129--48628199	37	2.0	35	83	10	90	39	2	2	54	1.29
48629596--48629658	13	4.8	13	76	7	65	28	4	28	38	1.77
48634664--48634695	6	5.5	6	96	3	57	0	12	53	34	1.39
48634784--48634818	16	2.2	16	89	0	52	37	2	60	0	1.12
48640129--48640170	17	2.5	17	80	11	50	38	7	4	50	1.51
48653192--48653451	51	5.3	51	85	7	340	30	24	13	31	1.94
48653244--48653458	95	2.3	95	94	1	369	29	24	15	30	1.95
48653301--48653393	44	2.3	39	81	15	109	30	23	16	30	1.96
48654389--48654478	44	2.0	44	97	0	171	28	23	7	40	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48656851--48656890	19	2.1	19	95	0	71	42	17	22	17	1.89
48667414--48667440	2	13.5	2	100	0	54	48	0	0	51	1.00
48670307--48670339	11	2.8	12	81	9	50	54	15	15	15	1.71
48675148--48675277	41	3.2	41	86	1	163	36	20	20	23	1.95
48675479--48675530	23	2.2	24	89	3	79	13	28	7	50	1.69
48676949--48676980	16	2.0	16	100	0	64	31	6	12	50	1.65
48678604--48678683	35	2.4	32	82	13	108	48	8	6	36	1.59
48678616--48678682	35	1.9	35	93	0	116	46	10	5	37	1.63
48678703--48678813	43	2.5	44	75	15	113	49	15	0	34	1.51
48703688--48703749	31	2.0	31	90	6	99	24	4	17	53	1.63
48708833--48708893	26	2.4	26	76	18	65	60	0	1	37	1.07
48710419--48710452	11	3.1	11	91	8	52	50	26	8	14	1.72
48716607--48716688	41	2.0	41	97	0	155	28	7	23	41	1.81
48719026--48719127	33	3.1	33	85	2	134	44	29	7	18	1.78
48719026--48719106	32	2.5	32	89	2	117	40	30	8	19	1.82
48724966--48725031	5	13.2	5	74	17	57	57	3	0	39	1.14
48728932--48728962	15	2.1	15	93	0	53	32	0	6	61	1.21
48729319--48729376	11	4.7	11	73	22	53	34	3	0	62	1.12
48729326--48729391	28	2.4	27	80	10	71	33	4	0	62	1.16
48737698--48737742	11	4.0	11	91	2	72	17	33	0	48	1.48
48737724--48737844	51	2.4	51	90	2	181	30	24	0	43	1.60
48738959--48738990	7	4.6	7	96	0	55	25	0	12	62	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48738962--48738996	14	2.5	13	86	13	52	25	0	14	60	1.35
48747054--48747118	32	2.1	32	97	2	123	47	12	9	30	1.72
48748259--48748288	5	6.0	5	92	0	51	76	0	3	20	0.92
48750527--48750576	8	5.7	9	77	13	50	28	2	2	68	1.12
48750512--48750609	27	3.7	25	72	12	70	36	1	3	59	1.20
48756571--48756617	24	2.0	24	82	0	58	29	4	2	63	1.25
48764070--48764099	3	10.0	3	100	0	60	33	33	0	33	1.58
48765848--48765879	3	10.7	3	93	0	55	0	37	0	62	0.95
48768528--48768589	18	3.7	17	75	18	67	51	1	1	45	1.20
48768541--48768588	14	3.1	14	73	21	51	50	2	2	45	1.25

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