genome.fa.s6.2.7.7.80.10.50.1000.42.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  42  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)
11515110--11515399	125	2.3	125	90	1	447	26	20	19	33	1.96
11515436--11515774	97	3.6	94	82	6	378	39	19	2	39	1.64
11515760--11515824	33	1.9	35	90	6	107	49	40	0	10	1.38
11518454--11518500	22	2.1	22	100	0	94	36	8	10	44	1.70
11519727--11519787	18	3.4	18	73	8	61	45	8	34	11	1.70
11526844--11526912	25	2.8	25	86	0	93	28	20	24	26	1.99
11532074--11532098	7	3.6	7	100	0	50	36	0	0	64	0.94
11532095--11532143	25	1.9	26	87	4	73	36	4	4	55	1.38
11532187--11532227	16	2.8	15	89	10	59	41	4	0	53	1.22
11532500--11532951	109	4.2	109	93	0	757	30	17	17	34	1.93
11539543--11539567	2	12.5	2	100	0	50	52	0	0	48	1.00
11540166--11540346	64	2.9	63	87	8	246	41	17	7	33	1.78
11540375--11540488	61	1.9	60	83	8	151	43	14	2	39	1.59
11541415--11541471	28	2.0	28	90	6	89	38	5	0	56	1.22
11541663--11541691	14	2.0	15	93	6	51	51	20	0	27	1.47
11547695--11547933	44	5.5	43	70	14	152	31	21	22	24	1.98
11547871--11547975	44	2.5	44	84	9	130	29	18	26	25	1.98
11547672--11547931	129	2.0	130	87	3	371	32	23	21	23	1.98
11549622--11549676	27	2.0	27	86	6	76	38	10	1	49	1.49
11549858--11549894	15	2.5	15	87	12	51	40	2	0	56	1.13
11549942--11549973	2	16.0	2	93	0	55	50	3	0	46	1.17
11550183--11550521	109	3.1	109	93	1	565	33	17	16	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11550898--11550922	11	2.3	11	100	0	50	28	16	8	48	1.74
11556545--11556570	3	8.7	3	100	0	52	65	0	0	34	0.93
11557345--11557384	20	2.0	20	85	9	55	10	17	0	72	1.11
11557345--11557384	21	2.0	20	90	5	62	10	17	0	72	1.11
11563738--11563796	29	2.0	29	100	0	118	40	13	11	33	1.81
11569092--11569133	20	2.1	20	82	8	50	64	2	11	21	1.38
11579807--11580222	94	4.5	95	74	19	292	33	21	7	37	1.82
11579998--11580163	83	2.0	83	85	2	226	31	21	6	40	1.79
11580083--11580265	94	1.9	94	84	3	242	37	19	4	39	1.71
11580087--11580291	94	2.2	94	81	3	225	35	20	3	40	1.71
11584795--11584828	10	3.3	10	92	8	59	32	17	2	47	1.63
11592734--11592793	25	2.4	26	78	10	63	41	18	21	18	1.90
11593746--11594230	50	9.6	50	84	4	562	22	29	20	27	1.98
11597374--11597407	17	2.1	17	88	5	52	55	0	0	44	0.99
11597378--11597427	22	2.3	23	86	6	68	48	0	0	52	1.00
11597369--11597407	17	2.4	16	82	4	51	51	0	2	46	1.14
11600221--11600349	43	3.0	43	76	6	134	31	26	17	24	1.97
11605890--11606068	40	4.5	39	79	9	177	27	17	23	31	1.97
11605885--11606080	80	2.5	81	78	8	224	28	18	23	30	1.98
11608858--11608906	21	2.3	21	92	0	80	26	22	36	14	1.92
11609596--11609650	20	2.8	20	100	0	110	41	14	5	38	1.69
11613234--11613320	43	2.0	43	95	0	156	34	16	14	34	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11618376--11618424	17	3.1	17	82	14	68	55	0	2	42	1.11
11628396--11628452	18	3.4	17	75	20	57	28	1	3	66	1.18
11628418--11628461	18	2.4	18	88	3	61	31	0	2	65	1.05
11637598--11637742	25	5.8	25	75	10	109	16	28	22	32	1.96
11637598--11637754	74	2.1	76	81	7	187	16	29	22	31	1.96
11641151--11641180	15	1.9	16	93	6	53	53	0	20	26	1.46
11642287--11642341	21	2.7	20	80	11	58	38	9	20	32	1.84
11642353--11642388	17	2.1	17	89	0	54	27	5	0	66	1.13
11645167--11645204	2	19.0	2	84	10	51	47	2	2	47	1.30
11651708--11651839	10	13.7	9	67	17	61	61	3	1	34	1.21
11651690--11651839	20	7.7	19	69	13	74	62	3	2	32	1.23
11651690--11651839	19	7.7	19	68	18	69	62	3	2	32	1.23
11651874--11651938	19	3.3	20	78	6	71	61	0	7	30	1.24
11652144--11652200	28	2.0	28	86	6	80	36	1	1	59	1.18
11652172--11652218	19	2.4	19	85	3	58	31	2	2	63	1.18
11652136--11652232	9	10.6	9	70	16	65	29	3	2	64	1.20
11652365--11652715	90	3.9	90	82	5	374	34	9	20	35	1.85
11653115--11653157	23	1.9	23	85	4	61	30	4	2	62	1.28
11663430--11663522	45	2.1	44	87	2	132	27	19	7	45	1.77
11673737--11673830	45	2.1	45	91	0	152	31	24	18	25	1.97
11673827--11674022	51	3.9	50	76	4	205	30	28	17	23	1.97
11673833--11674018	101	1.8	100	88	3	257	31	27	17	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11689376--11689437	31	2.0	31	100	0	124	41	16	9	32	1.80
11702667--11702697	15	2.1	15	100	0	62	19	0	51	29	1.47
11704400--11704496	33	2.9	33	82	1	131	38	9	29	22	1.85
11709444--11709481	19	2.0	19	100	0	76	52	21	10	15	1.72
11709444--11709481	9	4.0	10	90	10	62	52	21	10	15	1.72
11716875--11716924	23	2.1	23	92	3	82	64	16	0	20	1.30
11718585--11718632	7	6.9	7	100	0	96	43	14	0	41	1.45
11726177--11726218	22	2.0	21	90	4	66	26	7	0	66	1.17
11727134--11727193	29	2.0	32	83	9	81	48	6	26	18	1.72
11732108--11732165	30	2.0	30	83	6	75	24	6	17	51	1.69
11732217--11732262	23	2.0	23	87	8	67	52	2	0	45	1.13
11732211--11732264	27	1.9	28	88	7	83	50	1	0	48	1.11
11737370--11737433	27	2.4	27	82	10	87	54	21	1	21	1.53
11741491--11741559	32	2.2	32	86	0	93	37	20	15	26	1.93
11742038--11742103	26	2.5	26	85	4	89	34	19	21	24	1.96
11745779--11745900	36	3.2	35	68	24	86	34	17	14	33	1.90
11749576--11749619	20	2.2	20	84	8	54	34	22	6	36	1.81
11752532--11752564	12	2.8	12	95	0	57	9	9	48	33	1.66
11757156--11757207	26	1.9	27	84	7	70	28	26	7	36	1.84
11762744--11762807	25	2.4	25	84	10	74	29	1	3	65	1.17
11766223--11766419	98	2.0	98	97	0	376	36	24	10	28	1.88
11767434--11767478	22	2.0	22	86	4	63	66	15	0	17	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11768534--11768849	44	7.2	44	63	16	134	24	25	19	29	1.99
11768448--11769205	132	5.8	132	92	1	1224	23	25	20	29	1.99
11780557--11780753	98	2.0	98	93	0	340	37	24	9	28	1.86
11791570--11791729	75	2.1	75	84	3	214	30	23	23	23	1.99
11795726--11795776	18	2.7	20	75	25	56	70	7	3	17	1.27
11797491--11797533	7	6.1	7	83	0	59	27	0	27	44	1.55
11801293--11801449	83	1.9	82	82	8	194	36	24	20	18	1.95
11806970--11807031	32	1.9	32	96	0	115	37	14	19	29	1.91
11812226--11812301	26	2.9	27	94	4	136	17	22	31	28	1.96
11812354--11812456	27	3.8	27	98	0	197	18	24	30	27	1.98
11812379--11812600	96	2.3	99	88	5	335	20	20	29	29	1.98
11812223--11812527	123	2.4	125	92	3	499	20	20	29	29	1.98
11812506--11812637	33	3.7	33	73	15	120	20	19	28	31	1.97
11814375--11814414	19	2.1	19	86	9	55	57	0	7	35	1.27
11820808--11820870	25	2.5	26	86	2	92	66	1	1	30	1.10
11821244--11821283	20	1.9	22	90	10	66	40	0	0	60	0.97
11825373--11825586	109	2.0	105	84	5	277	28	19	9	42	1.82
11825416--11825611	109	1.8	107	81	6	243	29	17	10	42	1.82
11825490--11825705	78	2.8	77	92	2	342	27	14	11	46	1.79
11825645--11826062	113	3.6	115	86	6	530	30	16	9	43	1.80
11827043--11827079	2	18.5	2	100	0	74	51	0	0	48	1.00
11827434--11827462	2	14.5	2	100	0	58	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11828601--11828630	14	2.1	15	93	6	53	73	6	0	20	1.05
11829680--11829714	3	11.3	3	87	6	52	31	2	2	62	1.24
11838870--11839509	44	14.7	44	68	13	315	30	20	22	26	1.98
11838911--11839154	129	1.9	130	79	9	282	29	20	22	27	1.99
11839262--11839515	129	2.0	128	87	3	368	31	21	20	26	1.98
11838912--11839470	173	3.2	172	88	2	787	29	20	23	26	1.99
11840988--11841022	18	1.9	18	88	11	54	28	8	5	57	1.52
11844678--11844744	26	2.6	26	90	0	116	20	25	26	26	1.99
11853056--11853179	49	2.5	50	77	1	133	20	26	25	28	1.99
11860415--11860581	50	3.2	50	78	6	129	23	26	22	28	1.99

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