genome.fa.s1.2.7.7.80.10.50.1000.19.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  19  of  187  ( 22383 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)
6454977--6455035	28	2.1	28	87	0	82	38	5	3	52	1.40
6456137--6456171	18	1.9	18	88	0	52	40	14	20	25	1.90
6457891--6457924	18	1.9	18	88	5	52	35	5	2	55	1.39
6458154--6458181	2	14.0	2	100	0	56	50	0	0	50	1.00
6493183--6493256	23	3.2	23	75	11	87	40	14	18	25	1.89
6494033--6494161	43	3.0	43	76	15	131	30	26	19	24	1.98
6495517--6495575	10	5.9	10	73	13	50	59	0	3	37	1.14
6495631--6495682	20	2.6	21	75	22	58	67	0	5	26	1.13
6504500--6504536	2	18.5	2	100	0	74	51	0	0	48	1.00
6505448--6505484	3	12.3	3	100	0	74	67	0	0	32	0.91
6509799--6509944	42	3.5	42	79	7	145	43	17	21	16	1.87
6509797--6509931	21	6.4	21	71	6	87	45	17	20	16	1.85
6513738--6513856	59	2.0	59	100	0	238	41	18	6	33	1.77
6518182--6518221	21	1.9	21	89	0	62	37	10	12	40	1.77
6518243--6518362	17	6.9	17	77	11	100	45	10	10	33	1.74
6518250--6518291	20	2.2	19	95	4	75	35	9	9	45	1.69
6518182--6518342	71	2.3	69	81	8	182	47	10	9	32	1.71
6518243--6518359	34	3.4	34	79	10	112	44	11	11	33	1.75
6518397--6518464	18	3.7	18	80	5	73	50	7	14	27	1.70
6518550--6518609	31	2.0	31	86	3	86	33	6	13	46	1.69
6518597--6518635	18	2.2	18	86	9	53	48	10	15	25	1.76
6519278--6519330	19	2.8	19	91	8	90	22	22	35	18	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6519366--6519444	20	4.1	18	80	15	79	1	21	0	77	0.84
6519366--6519444	4	19.5	4	72	25	60	1	21	0	77	0.84
6519366--6519444	11	7.2	11	73	21	51	1	21	0	77	0.84
6519518--6519546	12	2.3	13	94	5	51	0	31	0	68	0.89
6519990--6520076	29	3.0	29	76	3	93	43	8	17	31	1.78
6519973--6520099	59	2.1	60	82	7	152	42	7	17	33	1.76
6519990--6520076	30	3.0	30	76	3	88	43	8	17	31	1.78
6521826--6521883	26	2.2	27	84	9	75	1	29	5	63	1.25
6523810--6523881	36	2.0	36	100	0	144	22	19	19	38	1.93
6533518--6533560	22	2.0	22	90	0	68	60	4	9	25	1.47
6538763--6538793	13	2.5	13	94	5	55	67	0	0	32	0.91
6541115--6541162	3	16.0	3	86	0	69	62	2	4	31	1.26
6541762--6541791	10	2.8	11	90	10	53	76	6	6	10	1.15
6551524--6551590	15	4.1	16	80	12	66	22	4	0	73	1.01
6551532--6551591	12	5.2	12	80	11	63	21	5	0	73	1.02
6551532--6551602	22	3.3	21	81	12	76	22	5	0	71	1.06
6551529--6551601	7	10.3	7	73	19	62	23	5	0	71	1.07
6552620--6552646	3	9.0	3	100	0	54	66	0	0	33	0.92
6554282--6554346	34	1.9	34	83	0	85	32	15	23	29	1.95
6564186--6564232	16	2.9	16	81	9	51	29	8	0	61	1.25
6566391--6566431	22	2.0	21	85	9	57	51	0	2	46	1.14
6568344--6568383	3	13.3	3	100	0	80	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6568713--6568743	16	1.9	16	93	0	53	41	16	0	41	1.48
6575720--6575843	34	3.7	33	77	7	126	43	0	12	43	1.47
6575901--6576419	125	4.2	126	88	2	724	37	17	16	29	1.91
6575901--6576419	249	2.1	250	87	2	740	37	17	16	29	1.91
6577727--6577766	15	2.7	15	96	0	71	30	17	10	42	1.82
6579976--6580012	18	2.1	18	94	0	65	40	8	27	24	1.83
6581530--6581581	25	2.1	24	82	10	61	67	3	1	26	1.18
6591958--6592077	59	2.0	59	100	0	240	27	21	11	39	1.88
6593565--6593627	21	3.2	21	65	21	64	19	14	19	47	1.82
6593545--6593628	37	2.3	37	97	0	159	19	11	19	50	1.78
6598725--6598865	68	2.1	68	100	0	282	21	13	21	43	1.87
6599279--6599434	45	3.6	45	76	16	186	51	10	21	16	1.75
6599324--6599447	37	3.2	37	72	21	126	51	10	22	15	1.73
6599278--6599447	82	2.1	82	97	1	324	50	11	21	16	1.76
6600951--6600985	18	1.9	18	94	0	61	17	8	45	28	1.77
6605934--6606046	56	2.0	56	100	0	226	42	14	15	27	1.86
6607681--6607894	71	3.0	71	86	2	288	46	20	5	28	1.71
6610702--6610740	20	2.0	20	90	10	62	87	0	7	5	0.68
6610696--6610738	13	3.4	12	83	6	50	83	2	9	4	0.87
6613935--6614025	34	2.6	34	82	1	128	37	0	17	45	1.49
6617196--6617441	125	2.0	126	87	0	359	42	17	14	26	1.87
6620470--6620520	24	2.1	24	85	7	68	68	1	0	29	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6624282--6624329	25	2.0	25	83	4	62	14	25	22	37	1.92
6628403--6628428	12	2.2	12	100	0	52	53	0	15	30	1.42
6630756--6630855	37	2.6	38	74	6	94	30	28	18	24	1.97
6631172--6631202	6	5.2	6	96	0	53	51	12	0	35	1.40
6631897--6631936	17	2.3	17	91	4	62	5	12	7	75	1.18
6631952--6631983	16	1.9	17	93	6	57	53	3	0	43	1.16
6631973--6632009	5	7.4	5	100	0	74	59	0	0	40	0.97
6639838--6639863	13	2.0	13	100	0	52	61	0	7	30	1.24
6644443--6644479	9	4.1	9	86	13	58	45	10	10	32	1.74
6644538--6644600	30	2.1	30	82	11	76	20	50	0	28	1.48
6648777--6648809	7	4.7	7	96	0	57	42	3	30	24	1.70
6648729--6648859	64	2.0	65	92	1	219	34	12	23	29	1.91
6648785--6648910	51	2.5	51	94	1	218	34	11	24	29	1.90
6653179--6653342	81	2.0	81	88	2	240	26	20	12	40	1.87
6656094--6656118	2	12.5	2	100	0	50	48	0	0	52	1.00
6658636--6658680	14	3.4	14	75	25	53	42	0	0	57	0.98
6658638--6658683	22	2.1	21	84	4	56	43	0	0	56	0.99
6661416--6661707	153	1.9	153	93	0	503	36	14	27	22	1.92
6667585--6667649	27	2.4	27	84	5	78	50	1	1	46	1.20
6667605--6667657	27	2.0	27	84	0	70	54	1	1	41	1.22
6668832--6668876	2	22.5	2	90	0	72	48	0	0	51	1.00
6668959--6669004	3	15.7	3	95	4	85	30	0	0	69	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6675308--6675577	41	6.6	41	93	0	441	28	20	29	21	1.98
6685543--6685571	2	14.5	2	100	0	58	51	0	0	48	1.00
6687982--6688076	45	2.3	43	83	10	117	46	5	6	42	1.51
6694656--6694692	15	2.5	15	95	0	65	10	32	29	27	1.90
6697056--6697096	19	2.2	18	86	4	55	41	2	9	46	1.50
6698656--6698722	29	2.4	28	87	5	98	59	1	4	34	1.26
6698656--6698734	29	2.8	28	84	5	95	58	1	6	34	1.32
6699011--6699062	19	2.8	18	75	19	54	61	1	3	32	1.25
6699020--6699063	17	2.7	16	82	13	54	61	0	4	34	1.16
6704377--6704428	15	3.6	15	80	12	56	44	0	1	53	1.11
6704326--6704544	120	1.8	120	97	0	420	43	1	6	48	1.37
6704326--6704512	61	3.1	61	70	14	197	43	1	6	48	1.39
6704506--6704547	15	2.7	16	82	14	52	45	0	2	52	1.13
6704497--6704538	15	2.9	15	82	10	52	47	0	0	52	1.00
6704688--6704782	45	2.1	44	88	1	136	33	27	6	32	1.82
6704761--6704798	16	2.4	16	90	0	58	34	34	0	31	1.58
6706915--6706992	31	2.5	31	85	4	102	57	5	8	28	1.50
6716528--6716619	47	1.9	47	80	6	105	10	18	3	67	1.34
6720979--6721016	6	6.3	6	93	0	58	15	2	68	13	1.32
6735672--6735705	15	2.1	17	89	10	54	35	0	0	64	0.94
6739677--6739701	4	6.2	4	100	0	50	48	0	0	52	1.00
6747594--6747635	17	2.4	18	80	4	50	59	0	4	35	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6748414--6748755	44	7.6	44	67	11	113	27	20	21	30	1.98
6748662--6748757	44	2.2	44	84	0	120	30	18	18	32	1.95
6748875--6749260	50	7.7	50	76	1	360	28	19	19	31	1.97
6748875--6749281	100	4.1	100	87	0	580	27	20	20	31	1.98
6749252--6749427	46	3.9	45	74	5	131	25	21	21	31	1.98
6749523--6749704	46	4.0	45	77	7	170	28	19	19	33	1.96
6749784--6749901	44	2.7	44	93	0	191	29	25	20	24	1.99
6750094--6750137	21	2.1	21	86	0	61	20	36	4	38	1.73
6750314--6750786	45	10.6	45	83	3	569	30	25	16	27	1.97
6751103--6751154	24	2.2	24	89	0	77	32	30	7	28	1.85

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