genome.fa.s8.2.7.7.80.10.50.1000.19.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  19  of  190  ( 22705 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)
5392957--5392987	11	2.8	11	95	0	53	48	3	29	19	1.64
5393131--5393209	40	2.0	40	89	0	122	22	31	27	17	1.97
5394739--5394826	31	2.9	30	74	11	88	67	4	2	26	1.22
5395414--5395528	9	12.0	9	73	17	81	35	0	2	61	1.10
5395417--5395510	10	9.6	10	77	9	70	35	0	3	61	1.12
5395416--5395525	58	1.9	55	91	8	177	35	0	2	61	1.10
5402295--5402453	82	2.0	80	91	2	255	40	11	22	25	1.88
5402958--5403369	217	1.9	217	95	1	747	34	12	22	31	1.91
5408812--5408864	23	2.3	23	93	0	97	32	26	20	20	1.98
5414484--5414592	36	3.0	36	93	0	182	30	19	11	38	1.88
5418660--5418711	23	2.3	23	93	0	86	32	25	21	21	1.98
5422292--5422342	15	3.1	17	71	23	54	45	1	17	35	1.60
5422905--5422939	6	5.8	6	100	0	70	34	17	31	17	1.93
5427475--5427511	15	2.5	15	90	0	56	35	10	0	54	1.36
5430574--5430637	33	1.9	33	87	6	94	50	12	6	31	1.65
5432296--5432945	114	5.7	113	89	2	980	34	21	20	24	1.97
5433355--5433417	21	3.0	21	73	19	67	22	0	38	39	1.54
5433360--5433424	21	3.1	20	72	22	53	21	0	38	40	1.54
5433357--5433485	50	2.6	50	76	7	120	23	1	33	41	1.64
5433448--5433476	15	1.9	15	100	0	58	20	3	34	41	1.69
5434316--5434694	191	2.0	190	89	0	578	18	25	13	43	1.86
5436234--5436466	27	8.8	27	81	9	239	49	15	2	32	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5436246--5436472	9	24.8	10	75	14	174	49	16	1	32	1.56
5436244--5436472	37	6.5	35	79	14	215	49	16	1	32	1.55
5442180--5442248	21	3.3	21	83	0	93	36	15	43	4	1.67
5442233--5442272	12	3.3	12	89	0	62	42	17	37	2	1.63
5442667--5442914	42	5.9	42	88	5	335	25	23	20	30	1.99
5442667--5442914	85	3.0	84	87	5	335	25	23	20	30	1.99
5446246--5446275	2	15.0	2	100	0	60	50	0	0	50	1.00
5452103--5452137	18	1.9	18	88	0	52	65	0	5	28	1.15
5453336--5453852	177	2.9	174	89	2	759	38	11	10	38	1.76
5476315--5477104	421	1.9	417	84	2	1053	31	21	14	32	1.94
5477016--5477200	92	2.0	92	95	0	334	29	22	12	34	1.92
5484019--5484081	26	2.4	26	100	0	126	47	6	17	28	1.72
5491369--5491400	12	2.7	12	100	0	64	25	50	25	0	1.50
5495382--5495423	21	2.0	22	86	9	61	9	9	11	69	1.38
5525919--5525976	24	2.4	25	76	2	64	50	0	29	20	1.49
5527195--5527280	28	3.0	28	75	11	84	60	1	4	33	1.25
5527250--5527288	19	2.1	19	85	9	53	66	0	5	28	1.12
5527237--5527292	28	2.0	28	86	10	80	62	0	3	33	1.12
5528523--5528563	20	2.2	20	86	8	59	21	4	4	68	1.28
5529106--5529181	40	1.9	40	86	0	107	22	25	30	22	1.99
5531544--5531902	103	3.5	103	90	2	551	32	28	20	18	1.96
5543983--5544293	114	2.7	113	78	5	297	27	17	23	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5544971--5545029	14	4.2	14	80	8	75	18	0	49	32	1.48
5544974--5545034	15	4.2	15	77	14	65	19	0	44	36	1.51
5544971--5545029	7	8.4	7	83	7	66	18	0	49	32	1.48
5545193--5545258	28	2.3	29	84	2	80	21	0	39	39	1.53
5545207--5545255	15	3.4	14	81	15	64	18	0	44	36	1.50
5547071--5547126	30	2.0	29	82	10	71	30	3	14	51	1.59
5548034--5548077	19	2.3	19	88	7	63	43	0	2	54	1.12
5548261--5548337	40	1.9	40	97	0	145	46	19	5	28	1.71
5548335--5548373	20	2.0	20	94	0	69	53	5	5	35	1.45
5548366--5548444	25	3.2	24	85	3	95	46	20	2	30	1.64
5548388--5548419	16	2.0	16	93	0	55	53	18	0	28	1.45
5548370--5548553	66	2.8	65	81	4	192	44	20	3	32	1.69
5548391--5548508	41	2.9	41	82	2	130	44	19	3	32	1.67
5548490--5548550	25	2.4	25	77	0	68	40	21	4	32	1.74
5554045--5554115	21	3.4	21	84	0	97	33	18	43	4	1.69
5554462--5554643	43	4.3	43	88	2	242	25	20	28	25	1.99
5556212--5556255	22	2.0	23	81	4	54	40	9	9	40	1.68
5556536--5556835	156	1.9	156	86	5	428	32	20	12	35	1.89
5557009--5557070	27	2.2	28	85	2	90	37	22	0	40	1.54
5557009--5557078	27	2.5	28	81	6	81	37	22	1	38	1.64
5558743--5558824	38	2.1	38	84	6	103	75	3	0	20	0.95
5558733--5558831	30	3.2	29	75	13	83	68	3	1	27	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5558746--5558829	14	6.2	14	71	25	56	73	3	0	22	0.98
5558746--5558829	23	3.8	22	75	9	64	73	3	0	22	0.98
5561489--5561547	30	1.9	31	83	10	77	44	5	6	44	1.52
5564980--5565025	22	2.0	24	87	8	69	26	0	8	65	1.21
5577237--5577372	40	3.4	39	81	4	148	32	13	28	25	1.94
5578275--5578314	15	2.8	14	85	7	53	25	2	2	70	1.13
5601713--5601743	6	5.2	6	100	0	62	19	16	32	32	1.94
5603615--5603692	26	3.1	24	79	15	79	51	2	2	43	1.29
5606402--5606737	51	6.6	51	82	5	344	29	15	24	30	1.95
5606398--5606737	102	3.4	100	86	4	418	29	15	24	30	1.96
5610567--5610614	16	3.0	16	82	8	53	43	25	0	31	1.55
5620878--5621074	98	2.0	98	93	0	340	38	23	9	29	1.86
5621741--5621788	25	1.9	25	86	0	69	56	4	6	33	1.44
5622398--5622455	22	2.6	22	81	7	64	44	17	1	36	1.59
5622434--5622487	19	2.8	19	91	0	90	35	16	11	37	1.84
5629646--5629729	42	2.0	42	100	0	168	23	28	19	28	1.98
5632167--5632198	16	2.0	16	93	0	55	31	0	9	59	1.29
5632621--5632665	22	2.0	22	95	0	81	24	13	24	37	1.91
5636156--5636191	18	2.0	18	100	0	72	27	16	27	27	1.97
5636319--5636371	25	2.1	25	96	0	97	18	16	24	39	1.91
5637247--5637288	19	2.2	19	95	0	75	26	30	26	16	1.97
5640227--5640258	16	2.0	16	93	0	55	34	0	6	59	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5640686--5640728	12	3.4	12	80	20	52	9	9	0	81	0.88
5641206--5641293	43	2.0	43	100	0	176	25	12	20	42	1.87
5642991--5643019	15	1.9	15	100	0	58	13	20	17	48	1.81
5646884--5646946	3	21.0	3	100	0	126	66	0	0	33	0.92
5649147--5649176	9	3.3	9	90	0	51	43	0	3	53	1.17
5650534--5650720	43	4.3	43	89	1	259	29	28	17	24	1.97
5654789--5655182	105	3.7	103	75	11	395	26	12	10	50	1.73
5654751--5655165	215	1.9	210	89	6	647	26	13	11	48	1.77
5655217--5655295	40	2.0	40	87	0	113	21	21	17	39	1.93
5655352--5655389	15	2.7	15	84	15	55	23	0	5	71	1.07
5656041--5656081	13	2.9	14	82	13	57	36	36	0	26	1.57
5656268--5656352	15	5.8	15	71	15	52	35	42	0	22	1.54
5656601--5656852	114	2.2	114	92	3	420	25	27	22	23	2.00
5662310--5662578	43	6.4	41	81	8	274	30	20	23	25	1.99
5663010--5663061	12	4.3	12	87	0	77	7	38	11	42	1.70
5663010--5663061	24	2.2	24	92	0	86	7	38	11	42	1.70
5663046--5663135	21	4.3	21	86	0	90	2	40	20	37	1.65
5663046--5663135	42	2.1	42	83	0	108	2	40	20	37	1.65
5665695--5665788	44	2.1	44	82	3	109	36	9	32	21	1.86
5667323--5668049	115	6.3	112	71	8	443	28	22	19	29	1.98
5667588--5668033	114	3.9	114	74	9	361	26	25	19	28	1.98
5667466--5668036	229	2.5	229	88	4	850	27	23	19	29	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5667985--5668146	75	2.2	75	81	0	189	27	22	16	33	1.95
5669130--5669367	49	4.8	49	82	8	275	53	13	8	23	1.67
5684405--5684441	9	4.1	9	92	0	65	29	10	13	45	1.77
5709890--5709945	27	2.0	28	86	10	80	71	0	23	5	1.06
5709890--5709955	25	2.5	25	80	11	71	72	0	21	6	1.05
5711073--5711102	12	2.6	12	94	5	53	43	13	6	36	1.70
5724799--5724839	22	1.9	21	85	5	55	68	4	14	12	1.36
5725787--5725831	22	2.2	21	88	11	67	17	11	0	71	1.14
5727989--5728123	69	2.0	69	90	0	216	17	15	20	47	1.83
5730899--5731124	123	1.8	123	90	0	362	35	12	26	24	1.92

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