genome.fa.s3.2.7.7.80.10.50.1000.34.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  34  of  150  ( 17918 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)
9042089--9042134	22	2.0	24	84	12	62	43	2	2	52	1.25
9042165--9042318	77	2.0	77	97	0	290	50	5	5	38	1.51
9043300--9043364	20	3.0	20	70	12	58	41	3	1	53	1.25
9043345--9043378	18	1.9	18	88	5	52	41	2	0	55	1.15
9054785--9054829	17	2.6	17	86	6	56	40	6	4	48	1.49
9054935--9055004	29	2.5	29	83	4	81	45	4	5	44	1.47
9054967--9055095	64	2.0	63	82	5	154	40	3	9	46	1.54
9063137--9063190	3	17.0	3	77	11	54	29	1	7	61	1.34
9063322--9063355	18	1.9	18	88	5	52	29	8	5	55	1.54
9064430--9064490	31	1.9	33	83	6	81	34	3	3	59	1.30
9072617--9072652	16	2.2	16	90	0	54	50	5	5	38	1.49
9077138--9077168	5	6.2	5	92	0	53	41	16	19	22	1.89
9078200--9078236	9	4.1	9	92	0	65	29	10	13	45	1.77
9090020--9090061	4	11.0	4	85	10	61	73	2	0	23	0.94
9090375--9090452	41	1.9	41	86	5	113	58	2	6	32	1.37
9090545--9090575	2	15.5	2	100	0	62	51	0	0	48	1.00
9092035--9092198	44	3.8	45	76	9	137	29	23	18	28	1.98
9092251--9092758	44	11.6	45	73	5	396	30	24	14	30	1.94
9092305--9092753	132	3.4	132	85	3	527	30	24	14	29	1.95
9092659--9092736	37	2.1	38	85	2	104	30	25	16	26	1.97
9093589--9093637	26	1.9	26	88	12	75	61	8	14	16	1.56
9112869--9112950	25	3.2	26	77	16	73	18	23	21	36	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9113000--9113069	25	2.8	25	73	6	61	24	21	18	35	1.95
9115427--9115469	20	2.2	20	86	0	59	39	2	2	55	1.25
9120593--9120635	14	3.1	14	81	12	54	62	6	0	30	1.21
9124445--9124528	29	2.8	30	78	10	100	28	15	22	33	1.95
9133799--9133841	19	2.2	20	87	4	61	18	4	4	72	1.20
9149732--9149764	12	2.8	12	86	13	50	72	0	9	18	1.10
9150089--9150157	5	13.8	5	100	0	138	39	0	0	60	0.97
9150177--9150229	6	8.8	6	100	0	106	0	0	15	84	0.61
9164753--9164809	20	2.8	21	76	7	55	45	8	1	43	1.45
9170445--9170513	36	1.9	36	90	0	111	21	5	31	40	1.77
9182325--9182359	17	2.1	17	94	0	61	57	0	0	42	0.99
9185152--9185519	102	3.6	102	91	0	601	18	21	29	30	1.97
9188718--9188764	24	1.9	25	86	4	69	21	6	25	46	1.74
9196212--9196262	23	2.2	23	85	0	66	31	5	17	45	1.72
9197470--9197644	50	3.4	50	92	4	269	24	30	18	26	1.98
9200696--9200741	23	2.0	23	91	0	74	32	6	19	41	1.77
9202918--9202950	14	2.4	14	95	5	59	24	24	9	42	1.83
9203233--9203270	17	2.2	17	86	9	51	34	13	2	50	1.55
9211978--9212075	29	3.5	29	78	10	89	39	25	14	20	1.90
9215045--9215135	47	1.9	48	82	8	116	14	13	14	58	1.64
9227464--9227500	17	2.2	17	90	0	56	21	2	0	75	0.92
9233120--9233250	28	4.9	26	78	3	109	28	16	23	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9233172--9233382	28	7.6	28	81	1	235	25	14	25	35	1.94
9233114--9233387	84	3.3	84	83	4	319	27	14	23	35	1.93
9236737--9236834	23	4.2	23	77	2	79	19	19	22	38	1.93
9241224--9241280	19	2.7	22	84	10	66	36	8	15	38	1.79
9242865--9242898	18	1.9	18	94	5	61	58	8	2	29	1.43
9243961--9244029	31	2.3	31	82	7	79	46	21	10	21	1.81
9245825--9245850	2	13.0	2	100	0	52	50	0	0	50	1.00
9245934--9245982	22	2.2	22	83	16	66	48	0	2	48	1.12
9254376--9254415	16	2.5	16	91	0	62	50	2	22	25	1.62
9254391--9254487	44	2.2	44	81	10	117	35	4	23	37	1.74
9254626--9254857	120	1.9	120	93	1	403	51	4	1	43	1.29
9256186--9256247	29	2.2	28	82	2	70	24	11	14	50	1.75
9256479--9256504	12	2.2	12	100	0	52	30	30	0	38	1.58
9256477--9256598	51	2.4	51	93	4	201	28	29	0	41	1.56
9256613--9256657	21	2.2	21	84	7	58	37	2	0	60	1.09
9257743--9257774	7	4.6	7	100	0	64	28	0	12	59	1.34
9258864--9259049	26	7.7	25	64	20	92	38	2	14	44	1.59
9258862--9259046	71	2.6	71	94	0	325	37	2	14	45	1.59
9259042--9259075	18	1.9	18	94	5	52	52	17	0	29	1.45
9259052--9259500	29	15.3	29	92	4	715	43	26	0	29	1.60
9259052--9259500	59	7.6	58	90	5	715	43	26	0	29	1.60
9259052--9259500	88	5.1	88	91	4	726	43	26	0	29	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9259495--9259675	55	3.3	55	100	0	362	38	12	4	44	1.63
9259659--9259683	10	2.5	10	100	0	50	44	8	0	48	1.32
9262888--9263112	123	1.8	123	97	0	423	31	22	16	30	1.96
9264603--9264632	16	1.9	15	93	6	51	13	10	16	60	1.59
9269081--9269175	33	2.8	33	74	14	97	51	0	0	48	1.00
9269117--9269163	20	2.2	22	88	7	71	55	0	0	44	0.99
9273467--9273496	15	1.9	16	93	6	53	40	6	10	43	1.64
9274857--9275036	88	2.0	89	91	1	290	35	11	20	33	1.88
9275980--9276047	20	3.4	20	80	8	75	36	5	16	41	1.72
9276020--9276057	20	1.9	20	88	0	58	34	2	13	50	1.55
9276553--9276588	17	2.2	16	90	5	54	27	0	2	69	1.02
9276976--9277009	11	3.1	11	82	0	50	20	32	2	44	1.67
9276976--9277025	22	2.3	22	89	6	75	24	32	2	42	1.66
9277104--9277128	9	2.8	9	100	0	50	24	0	0	76	0.80
9279526--9279659	15	8.2	15	67	22	74	44	32	0	21	1.58
9279474--9279769	101	3.2	86	77	16	272	45	34	1	18	1.57
9279523--9279745	101	2.2	101	94	0	383	44	34	1	20	1.60
9282073--9282121	24	2.0	24	100	0	98	46	12	12	28	1.77
9286981--9287079	6	15.5	6	72	19	67	39	39	0	21	1.53
9286959--9287153	27	7.1	27	75	19	131	42	33	0	24	1.55
9287014--9287101	45	2.0	45	93	4	151	38	38	0	22	1.55
9286959--9287073	33	3.5	33	96	1	205	40	37	0	22	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9287059--9287195	27	4.7	33	64	27	78	43	33	0	22	1.59
9286981--9287134	72	2.1	74	87	7	222	40	36	0	22	1.54
9286981--9287134	78	2.1	75	89	7	233	40	36	0	22	1.54
9287065--9287187	54	2.3	53	83	10	144	44	31	0	22	1.59
9287172--9287203	6	5.3	6	100	0	64	37	46	0	15	1.46
9287152--9287203	18	2.9	18	85	0	59	44	38	1	15	1.58
9287218--9287378	35	4.4	35	64	18	94	46	8	4	39	1.56
9287201--9287439	112	2.1	111	91	0	379	44	7	7	40	1.60
9287434--9287475	16	2.6	16	96	0	75	45	4	2	47	1.36
9287449--9287499	22	2.3	23	89	3	77	45	1	1	50	1.24
9288535--9288651	18	7.0	18	67	19	56	30	11	1	56	1.44
9289459--9289501	19	2.3	19	92	8	70	46	11	16	25	1.80
9293325--9293543	56	3.9	56	86	6	329	47	5	10	36	1.62
9293316--9293542	110	2.0	113	94	3	397	47	5	11	36	1.62
9293541--9293800	29	8.8	29	90	5	387	24	0	30	45	1.54
9293616--9293674	18	3.3	18	63	13	50	23	0	32	44	1.54
9293541--9293800	122	2.2	116	91	4	414	24	0	30	45	1.54
9293785--9293810	5	5.2	5	100	0	52	19	0	42	38	1.51
9293876--9293924	25	1.9	26	91	4	82	38	14	4	42	1.64
9294685--9294716	7	4.6	7	92	0	55	59	9	0	31	1.29
9295798--9295862	31	2.1	31	94	0	112	66	0	0	33	0.92
9299928--9299965	20	1.9	20	94	0	67	21	15	23	39	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9313289--9313343	26	2.2	25	87	6	76	49	3	0	47	1.19
9313843--9313872	6	5.0	6	100	0	60	33	50	0	16	1.46
9318897--9318944	17	2.8	18	78	9	55	52	2	0	45	1.12
9319457--9319503	21	2.2	22	84	3	60	34	0	2	63	1.06
9320483--9320516	17	2.1	17	94	5	61	44	0	0	55	0.99
9324373--9324412	20	2.0	21	85	5	55	75	2	17	5	1.10
9326332--9326418	45	1.9	45	90	0	138	34	21	16	27	1.95
9335863--9335917	20	2.8	20	85	0	74	41	10	10	36	1.75
9341588--9341617	16	1.9	16	93	6	53	50	20	0	30	1.49
9352813--9352952	43	3.3	43	80	6	158	28	22	17	31	1.97

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