genome.fa.s3.2.7.7.80.10.50.1000.135.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  135  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)
40526459--40526510	26	1.9	27	84	7	70	5	9	9	75	1.20
40529790--40529852	26	2.4	26	97	0	117	26	28	20	23	1.99
40539906--40540157	30	8.4	30	75	8	201	36	12	26	24	1.91
40542587--40542650	30	2.2	29	81	10	76	29	28	6	35	1.82
40542594--40542650	30	1.9	30	85	3	80	29	24	7	38	1.82
40547767--40547815	20	2.5	20	83	9	64	24	4	2	69	1.17
40547871--40547920	26	2.0	25	84	4	64	64	6	4	26	1.35
40550378--40550426	22	2.2	22	78	7	55	38	0	4	57	1.18
40550380--40550419	19	2.0	20	85	4	55	30	0	5	65	1.14
40564733--40564761	5	5.8	5	100	0	58	20	79	0	0	0.74
40570813--40570890	40	1.9	40	82	15	97	47	6	3	42	1.47
40570874--40570919	20	2.3	20	85	7	58	58	8	4	28	1.47
40571043--40571092	21	2.5	21	84	9	61	58	0	8	34	1.28
40571029--40571107	9	8.6	9	75	15	63	60	0	5	34	1.18
40571211--40571246	14	2.5	15	90	4	56	30	0	0	69	0.89
40571647--40571839	10	19.4	10	68	13	69	31	2	4	61	1.28
40574920--40575047	42	3.0	42	80	6	125	44	17	22	15	1.86
40574916--40574998	21	4.0	21	69	9	62	43	19	22	14	1.87
40574939--40575010	21	3.4	21	71	7	65	45	16	22	15	1.84
40574944--40575036	21	4.4	21	72	5	62	43	19	24	12	1.86
40584121--40584152	7	4.6	7	96	0	55	28	0	9	62	1.26
40584104--40584163	14	4.4	14	83	8	63	25	0	5	70	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40584142--40584179	19	2.1	18	85	9	51	31	2	0	65	1.06
40584452--40584492	14	2.9	15	82	10	52	39	2	12	46	1.54
40586373--40586410	19	2.0	20	84	5	51	50	0	2	47	1.15
40586943--40586994	18	2.9	18	76	20	56	30	0	1	67	1.02
40592165--40592218	24	2.2	24	86	0	72	53	9	3	33	1.50
40593340--40593374	15	2.3	15	85	0	52	62	17	2	17	1.44
40594567--40594628	4	16.0	4	86	6	83	24	4	0	70	1.06
40601707--40601731	2	12.5	2	100	0	50	52	0	0	48	1.00
40607084--40607134	3	17.0	3	100	0	102	33	0	0	66	0.92
40607345--40607382	17	2.3	17	81	4	51	31	5	2	60	1.33
40607714--40608157	112	4.0	112	85	2	524	32	14	17	35	1.90
40612288--40612329	16	2.5	17	84	7	59	54	7	0	38	1.28
40618498--40618526	3	9.7	3	100	0	58	0	34	0	65	0.93
40618626--40618656	2	15.5	2	100	0	62	48	0	51	0	1.00
40631883--40631926	18	2.4	19	84	3	63	45	13	20	20	1.85
40631883--40631926	6	7.2	6	79	5	52	45	13	20	20	1.85
40631912--40632004	39	2.4	39	87	0	132	41	16	17	24	1.89
40632204--40632290	40	2.2	40	85	4	113	40	20	8	31	1.82
40634914--40634966	27	2.0	27	85	7	72	0	24	1	73	0.93
40635190--40635225	18	1.9	19	94	5	65	50	5	0	44	1.25
40636087--40636121	17	2.1	17	88	0	52	5	14	5	74	1.19
40636147--40636180	8	4.2	8	84	0	50	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40636218--40636247	5	6.0	5	100	0	60	20	0	0	80	0.72
40642420--40642506	45	1.9	45	92	0	147	43	20	13	21	1.87
40642710--40642796	40	2.2	40	85	4	113	41	20	6	31	1.79
40643548--40643582	17	2.1	17	88	0	52	5	14	5	74	1.19
40649287--40649341	18	3.1	18	91	0	92	25	7	18	49	1.73
40654850--40654904	18	3.1	18	91	0	92	23	7	20	49	1.74
40662517--40662577	32	1.9	32	90	6	97	60	0	1	37	1.07
40662530--40662620	38	2.3	40	86	7	141	64	0	3	31	1.09
40663463--40663508	2	23.5	2	86	4	58	54	0	0	45	0.99
40667566--40667595	10	3.0	10	95	0	51	50	6	0	43	1.28
40667658--40667740	2	44.0	2	76	15	70	44	4	1	49	1.31
40669498--40669574	26	3.0	25	70	21	68	19	23	20	36	1.95
40669553--40669665	26	4.5	25	72	10	79	20	23	20	35	1.96
40670305--40670337	15	2.3	15	89	5	50	39	0	24	36	1.56
40672505--40672552	24	2.0	24	92	4	80	54	4	2	39	1.32
40676976--40677000	13	1.9	13	100	0	50	16	12	24	48	1.79
40682936--40682968	2	16.5	2	100	0	66	48	0	0	51	1.00
40716098--40716166	10	6.5	10	73	18	50	63	2	1	31	1.18
40716491--40716775	147	1.9	147	80	7	326	40	8	11	39	1.73
40722094--40722122	15	1.9	15	100	0	58	51	0	0	48	1.00
40727302--40727341	3	13.3	3	100	0	80	32	0	0	67	0.91
40734213--40734299	39	2.2	40	85	8	124	19	25	27	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40745883--40745915	15	2.1	16	88	5	50	42	0	3	54	1.15
40749242--40749302	32	1.9	32	83	12	81	44	3	1	50	1.28
40750004--40750036	15	2.3	15	89	5	50	21	15	9	54	1.68
40750462--40750502	18	2.3	18	95	0	73	46	0	0	53	1.00
40751732--40751792	32	1.9	32	100	0	122	50	19	3	26	1.63
40751732--40751805	32	2.5	30	87	10	100	51	20	2	25	1.60
40755306--40755338	15	2.2	15	100	0	66	60	0	6	33	1.21
40757858--40757910	17	3.4	17	70	20	60	54	20	9	15	1.68
40757853--40757911	30	2.0	30	93	0	100	54	20	10	15	1.70
40758720--40758782	32	2.0	32	93	6	110	60	0	1	38	1.07
40758736--40758940	40	5.1	40	92	4	324	63	0	3	32	1.13
40758734--40758940	79	2.6	78	84	11	285	62	0	3	33	1.13
40758720--40758891	11	16.9	11	66	22	65	60	0	3	36	1.14
40765439--40765516	31	2.5	31	79	4	86	37	16	8	37	1.80
40766401--40766442	2	21.5	2	90	4	68	54	0	45	0	0.99
40766395--40766442	10	5.1	10	82	12	57	58	0	41	0	0.98
40782879--40782943	30	2.2	30	83	10	80	52	10	3	33	1.52
40792169--40792214	22	2.0	23	88	12	69	36	0	0	63	0.95
40795972--40796076	34	3.1	34	78	6	115	29	12	16	41	1.84
40797914--40797974	29	2.0	31	81	12	74	44	13	8	34	1.73
40807606--40807704	36	2.8	35	90	9	157	37	15	19	28	1.92
40809539--40809604	34	1.9	34	87	0	96	51	4	12	31	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40812297--40812376	41	2.0	40	87	2	115	50	15	8	26	1.72
40814655--40814689	15	2.3	15	100	0	70	40	5	20	34	1.76
40820404--40820472	36	1.9	36	93	0	120	26	18	15	39	1.91
40824085--40824195	55	2.0	55	96	0	204	35	20	9	34	1.86
40828069--40828136	22	3.1	22	76	0	73	60	11	11	16	1.59
40832476--40832509	13	2.6	13	90	0	50	20	0	0	79	0.73
40834964--40835028	32	2.0	32	100	0	130	43	12	20	24	1.86
40836441--40836487	24	2.0	24	86	0	67	59	0	2	38	1.09
40836434--40836497	33	1.9	33	81	12	78	59	0	1	39	1.07
40837750--40837889	59	2.3	60	85	2	192	43	4	10	42	1.57
40837760--40837904	59	2.5	59	83	2	157	43	4	10	41	1.60
40843876--40843915	19	2.1	19	100	0	80	27	20	10	42	1.83
40845148--40845180	6	5.5	6	100	0	66	51	15	0	33	1.43
40847617--40847650	17	1.9	18	88	5	52	44	2	0	52	1.16
40853783--40853816	11	3.1	11	91	0	50	38	0	0	61	0.96
40854716--40854748	14	2.4	14	90	5	50	42	0	0	57	0.98
40854948--40854985	19	2.0	19	89	0	58	39	28	2	28	1.70
40855522--40855579	29	1.9	31	89	6	93	36	0	44	18	1.50
40860773--40860840	3	22.7	3	96	0	127	30	0	1	67	0.99
40880090--40880359	94	2.9	95	77	9	252	31	18	20	29	1.96
40880104--40880588	44	10.7	44	73	14	274	31	18	22	28	1.97
40882307--40882379	3	24.3	3	100	0	146	32	0	0	67	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40891071--40891104	17	2.0	17	94	0	59	23	2	0	73	0.97
40899796--40899862	22	3.0	22	97	0	125	26	23	13	35	1.92
40901834--40901902	30	2.4	30	79	13	90	46	4	0	49	1.21
40901948--40902013	27	2.4	27	89	0	96	30	28	25	15	1.96
40902251--40902282	3	10.7	3	100	0	64	0	0	31	68	0.90
40903755--40903928	86	2.0	86	97	0	330	26	14	29	29	1.95
40914049--40914203	43	3.6	43	75	12	131	25	18	27	28	1.98
40914049--40914172	43	2.8	44	81	7	137	25	16	27	30	1.97
40916089--40916132	6	7.3	6	81	0	52	18	61	2	18	1.45
40916099--40916130	12	2.7	12	100	0	64	15	59	0	25	1.36

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