genome.fa.s6.2.7.7.80.10.50.1000.44.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  44  of  168  ( 20060 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)
12277258--12277554	50	5.8	51	79	4	244	21	27	21	28	1.99
12280042--12280071	15	2.0	15	93	0	51	33	3	6	56	1.42
12285939--12286078	40	3.5	40	76	7	147	27	25	20	27	1.99
12287924--12287999	27	2.8	26	86	7	98	36	18	18	26	1.94
12287936--12288054	27	4.4	27	77	8	116	42	23	14	20	1.88
12289111--12289152	4	10.5	4	80	10	50	69	2	2	26	1.13
12289107--12289148	11	3.7	11	81	12	50	69	2	2	26	1.13
12289111--12289153	15	2.7	15	89	7	59	67	2	2	27	1.15
12289392--12289466	38	2.0	38	81	5	89	54	5	9	30	1.54
12289667--12289699	16	2.1	16	94	0	57	60	6	3	30	1.36
12293229--12293275	20	2.4	20	89	3	69	17	19	4	59	1.53
12293913--12293959	25	1.9	24	95	0	76	31	19	25	23	1.98
12295496--12295526	16	1.9	16	93	0	53	35	9	9	45	1.70
12295751--12295935	51	3.7	50	79	6	176	23	17	29	29	1.97
12310128--12310221	42	2.2	41	85	7	125	30	27	15	25	1.96
12313515--12313546	16	1.9	17	93	6	57	43	21	0	34	1.53
12321469--12321503	17	2.1	17	94	0	61	25	17	14	42	1.86
12323428--12323541	43	2.6	44	76	1	122	26	28	16	28	1.97
12323726--12323758	15	2.2	15	100	0	66	24	9	6	60	1.49
12324420--12324448	12	2.5	12	94	5	51	37	0	10	51	1.36
12326471--12326531	23	2.7	23	84	0	68	31	11	4	52	1.58
12341964--12342143	98	1.8	98	80	2	218	28	23	11	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12343148--12343189	22	1.9	22	90	9	68	35	4	2	57	1.33
12348120--12348157	14	2.6	15	83	4	51	31	0	18	50	1.47
12350804--12350835	15	2.1	15	94	0	55	68	9	6	15	1.36
12351606--12351657	26	2.0	26	96	0	95	50	9	15	25	1.74
12355371--12355655	59	4.8	59	76	4	286	41	11	24	21	1.86
12355343--12355594	119	2.1	119	86	2	353	41	11	24	23	1.86
12355343--12355653	119	2.6	120	80	6	321	42	11	24	21	1.86
12355370--12355655	30	9.6	30	79	5	258	41	11	24	21	1.86
12355645--12355711	30	2.2	30	84	5	82	37	11	28	22	1.90
12355371--12355711	178	1.9	178	84	2	452	40	12	24	22	1.88
12363533--12363722	45	4.2	44	79	4	166	25	15	24	34	1.95
12365749--12365939	30	6.3	31	75	6	160	37	13	24	24	1.91
12365775--12365939	60	2.8	60	80	1	179	37	13	24	24	1.91
12367668--12367915	49	4.9	50	78	7	209	22	27	21	27	1.99
12370818--12370853	17	2.1	18	89	5	56	36	13	5	44	1.68
12372708--12372747	19	2.1	19	90	0	62	35	2	5	57	1.34
12374432--12374476	22	2.0	22	83	8	56	31	0	17	51	1.46
12378217--12378255	19	2.1	19	95	0	69	25	15	17	41	1.89
12379223--12379277	15	3.4	16	76	16	60	47	1	0	50	1.11
12379221--12379277	16	3.6	15	76	9	60	45	1	0	52	1.11
12379320--12379368	20	2.7	18	77	22	57	51	4	2	42	1.32
12389125--12389158	4	8.5	4	87	12	52	26	2	0	70	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12389447--12389878	106	4.1	106	92	0	670	31	16	18	33	1.94
12397239--12397280	21	2.0	21	86	9	59	4	14	7	73	1.21
12397817--12397873	3	19.0	3	75	13	55	35	1	3	59	1.25
12397816--12397871	24	2.3	24	81	6	69	33	1	5	58	1.31
12398003--12398036	18	1.9	18	88	5	52	29	2	5	61	1.34
12405129--12405188	27	2.3	25	83	13	68	18	15	3	63	1.44
12408804--12408844	9	4.4	9	84	3	55	82	0	17	0	0.66
12410044--12410411	83	4.4	84	71	14	299	27	22	22	27	1.99
12410003--12410413	44	9.7	44	68	16	235	27	21	22	27	1.99
12410000--12410415	127	3.3	127	95	0	742	28	22	22	27	1.99
12411969--12412009	2	20.5	2	94	0	73	48	0	0	51	1.00
12412110--12412146	16	2.4	15	90	4	56	29	2	5	62	1.31
12417401--12417690	44	6.7	43	70	11	175	29	20	23	26	1.99
12417362--12417690	44	7.7	41	67	15	123	29	20	22	27	1.99
12417336--12417739	129	3.1	128	86	2	513	30	20	22	26	1.98
12417362--12417867	129	3.9	128	80	7	454	29	20	22	27	1.98
12419809--12420347	106	5.1	106	92	0	875	31	18	18	32	1.95
12421919--12421956	18	2.1	18	90	0	58	28	0	0	71	0.87
12423478--12423551	34	2.1	36	82	9	91	70	1	2	25	1.09
12423517--12423555	21	1.9	20	89	5	60	64	0	0	35	0.94
12424304--12424344	21	2.0	20	85	4	55	63	4	4	26	1.35
12446016--12446080	20	3.3	19	73	4	67	32	18	35	13	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12445921--12446217	40	7.4	40	85	1	380	31	16	30	21	1.95
12445921--12446217	160	1.9	160	87	1	443	31	16	30	21	1.95
12451189--12451258	26	2.7	26	82	6	79	24	25	25	24	2.00
12456078--12456158	40	2.0	40	83	4	101	35	17	23	23	1.95
12456101--12456279	40	4.5	40	81	6	211	31	17	28	22	1.96
12457951--12458360	43	9.8	43	82	7	450	26	33	17	23	1.96
12462823--12462894	30	2.4	29	80	11	83	47	4	2	45	1.36
12462829--12462891	20	3.1	20	77	11	74	42	4	1	50	1.32
12464410--12464523	41	2.8	41	89	0	183	31	23	21	23	1.98
12465563--12465595	12	2.6	13	85	4	50	75	0	6	18	1.00
12476403--12476507	52	2.0	52	94	0	183	46	11	17	24	1.81
12476857--12476904	23	2.1	23	88	7	71	43	20	8	27	1.80
12479979--12480265	50	5.6	50	82	6	294	26	19	29	24	1.99
12479980--12480266	149	1.9	153	83	7	379	26	19	29	24	1.99
12481741--12481791	23	2.2	23	92	0	84	41	17	9	31	1.82
12510379--12510549	54	3.2	54	89	4	256	18	21	30	29	1.96
12516836--12517083	50	4.8	50	84	3	271	27	20	29	23	1.99
12517485--12517775	43	6.8	43	84	0	332	29	31	17	21	1.96
12518746--12518799	2	27.0	2	100	0	108	50	0	0	50	1.00
12519955--12520014	24	2.5	24	86	2	86	56	10	10	23	1.62
12522627--12522668	20	2.2	19	86	4	57	66	4	4	23	1.30
12522675--12522815	41	3.4	41	81	3	149	28	25	21	24	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12522925--12523017	40	2.3	40	83	3	116	24	21	20	33	1.97
12528520--12528760	50	4.7	50	86	4	295	25	21	30	22	1.99
12528525--12528815	100	2.8	100	81	7	284	26	20	28	24	1.99
12540512--12540568	27	2.1	27	83	6	71	26	22	14	36	1.92
12546259--12546295	19	1.9	19	88	0	56	48	0	8	43	1.32
12549405--12549454	23	2.2	23	92	3	84	60	14	6	20	1.55
12556099--12556173	24	3.1	23	76	12	62	68	1	1	29	1.06
12556110--12556173	16	3.9	16	70	13	58	68	1	1	28	1.07
12556110--12556207	50	2.0	49	83	2	124	63	2	1	33	1.13
12558194--12558317	59	2.1	60	86	1	169	33	16	9	39	1.82
12560201--12560275	29	2.6	30	85	4	100	21	22	34	21	1.97
12561086--12561129	17	2.5	18	81	3	63	40	9	9	40	1.68
12571170--12571211	20	2.1	20	95	0	75	47	26	9	16	1.77
12575244--12575276	17	1.9	17	93	0	57	57	15	12	15	1.65
12577693--12577717	9	2.8	9	100	0	50	32	32	12	24	1.91
12582776--12582972	48	4.1	48	76	8	161	26	20	29	22	1.98
12582795--12582969	96	1.8	96	82	0	224	25	20	32	22	1.98
12590402--12590577	96	1.8	96	85	0	244	25	20	31	22	1.98
12590383--12590582	48	4.2	48	80	6	208	26	20	31	22	1.98
12594349--12594408	29	2.0	30	90	6	95	16	26	15	41	1.88
12594365--12594420	29	1.9	29	88	0	85	14	25	17	42	1.87
12594354--12594570	120	1.8	120	84	0	299	19	22	16	41	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12601842--12604741	735	4.0	734	86	4	4071	33	21	16	27	1.95
12602119--12604741	702	3.7	708	84	5	3398	33	22	17	27	1.96
12614822--12616505	735	2.3	735	93	0	2906	34	21	16	28	1.95
12619466--12619732	41	6.6	38	78	13	225	21	22	26	29	1.99
12619466--12619738	82	3.4	82	81	11	321	21	23	26	29	1.99
12619467--12619730	123	2.2	123	81	11	296	21	22	25	30	1.99
12620127--12620159	14	2.3	15	94	5	59	30	0	33	36	1.58
12620194--12620381	7	26.0	7	71	6	79	23	0	42	34	1.59
12620195--12620292	29	3.4	29	97	1	180	29	0	38	31	1.58
12620304--12620356	22	2.5	22	90	3	81	15	0	45	39	1.46

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