genome.fa.s3.2.7.7.80.10.50.1000.130.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  130  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)
39168098--39168141	20	2.2	20	92	4	72	63	4	0	31	1.14
39169507--39169548	20	2.1	20	95	0	75	33	11	14	40	1.82
39171862--39172835	44	22.0	44	78	5	818	29	22	16	31	1.96
39171892--39172839	89	10.7	89	82	5	1021	29	22	16	31	1.96
39171864--39172835	266	3.7	266	86	4	1164	29	22	16	31	1.96
39171869--39172839	310	3.1	309	77	7	838	29	22	16	31	1.96
39189181--39189409	116	2.0	116	92	0	386	20	9	19	51	1.74
39198805--39198848	5	8.8	5	100	0	88	40	0	20	38	1.53
39202406--39202430	12	2.1	12	100	0	50	92	0	8	0	0.40
39208893--39208932	22	1.9	22	90	10	66	67	12	2	17	1.33
39209112--39209160	3	16.3	3	91	0	80	65	2	0	32	1.04
39212339--39212392	19	2.9	17	74	15	54	74	5	1	18	1.11
39212379--39212509	9	14.9	8	69	19	50	66	1	3	28	1.18
39212382--39212533	18	8.6	18	71	19	88	65	1	4	27	1.23
39212379--39212527	27	5.5	26	74	10	104	65	2	4	27	1.23
39213131--39213225	18	5.1	18	78	17	88	28	2	3	66	1.18
39213122--39213225	38	2.7	38	78	13	124	27	2	2	66	1.20
39213227--39213272	18	2.7	18	80	12	53	36	4	2	56	1.31
39216634--39216672	18	2.2	17	86	13	53	33	0	20	46	1.51
39216891--39217011	23	5.3	23	83	4	136	21	21	25	31	1.98
39216890--39217011	46	2.7	46	89	2	174	22	21	25	31	1.98
39218032--39218056	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39220162--39220191	4	7.5	4	100	0	60	50	0	0	50	1.00
39222362--39222423	28	2.2	28	82	5	72	50	6	0	43	1.28
39224718--39224742	2	12.5	2	100	0	50	0	52	0	48	1.00
39226153--39226177	11	2.3	11	100	0	50	48	8	24	20	1.76
39244257--39244317	30	2.0	30	100	0	122	13	16	19	50	1.77
39245779--39245822	18	2.8	17	77	22	51	6	11	4	77	1.11
39249640--39249699	31	2.0	31	90	3	95	38	10	16	35	1.82
39250624--39250661	20	1.9	20	88	0	58	57	7	0	34	1.28
39255798--39255841	23	1.9	23	95	0	79	36	38	0	25	1.56
39255813--39255843	16	1.9	16	93	0	53	35	38	0	25	1.56
39262946--39262987	22	1.9	22	90	0	66	42	7	9	40	1.65
39267511--39267575	34	1.9	34	90	0	103	52	7	7	32	1.58
39270211--39270238	2	14.0	2	100	0	56	50	0	0	50	1.00
39272300--39272333	5	7.0	5	93	6	61	20	0	0	79	0.73
39276313--39276365	21	2.5	21	81	0	70	30	33	9	26	1.88
39282567--39282616	3	16.3	3	83	4	55	42	2	0	56	1.11
39282563--39282604	22	1.9	22	90	0	66	45	2	0	52	1.13
39284127--39284230	33	2.9	38	75	16	103	20	19	22	38	1.94
39284150--39284224	33	2.3	33	90	0	114	21	17	21	40	1.92
39284219--39284265	6	7.7	6	81	13	60	17	17	17	48	1.81
39286447--39286617	64	2.6	63	78	7	173	45	12	21	20	1.84
39286424--39286617	33	6.0	31	76	10	160	45	13	21	19	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39286428--39286642	97	2.3	95	83	7	260	44	15	20	19	1.86
39302814--39302871	25	2.4	24	82	2	71	32	13	24	29	1.94
39303975--39303999	11	2.3	11	100	0	50	64	0	0	36	0.94
39305929--39305975	25	1.9	24	95	0	76	31	17	34	17	1.92
39305958--39306075	50	2.4	50	78	16	129	36	16	27	18	1.93
39306022--39306075	25	2.2	25	83	6	65	38	18	25	16	1.92
39309037--39309075	19	2.0	19	85	14	53	71	2	0	25	0.98
39309432--39309483	20	2.7	19	85	8	61	71	0	1	26	0.97
39309453--39309487	14	2.5	14	86	13	54	74	0	0	25	0.82
39314781--39314848	17	3.8	17	71	16	57	48	1	5	44	1.36
39314667--39314911	117	2.1	116	93	2	411	44	7	8	38	1.65
39314916--39315532	23	27.8	23	82	9	660	26	0	24	48	1.54
39314916--39315532	89	6.9	89	83	9	655	26	0	24	48	1.54
39315025--39315536	200	2.6	201	89	4	770	26	0	24	48	1.53
39315576--39315631	25	2.3	24	93	6	96	44	14	0	41	1.45
39316927--39316964	20	1.9	20	84	10	51	55	7	2	34	1.43
39324303--39324358	24	2.3	24	100	0	112	51	3	0	44	1.18
39325513--39326057	298	1.8	290	81	8	661	27	13	16	42	1.85
39335902--39335989	45	2.0	45	90	4	142	40	4	5	48	1.47
39343648--39343692	23	2.0	23	81	0	54	60	6	4	28	1.42
39347044--39347086	20	2.0	22	86	8	63	30	0	6	62	1.21
39347347--39347410	32	2.0	32	81	6	76	29	3	4	62	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39350249--39350289	5	7.6	5	84	15	55	41	53	0	4	1.22
39350237--39350279	18	2.4	18	88	0	59	41	44	2	11	1.53
39350397--39350463	9	7.4	9	91	0	98	25	8	23	41	1.83
39351079--39351158	26	3.1	26	71	8	74	22	22	18	36	1.95
39351174--39351219	24	1.9	24	91	8	76	19	19	19	41	1.91
39351507--39351537	15	2.0	16	93	6	55	41	12	0	45	1.42
39353207--39353238	16	2.0	16	93	0	55	25	15	0	59	1.36
39353462--39353542	26	3.2	26	66	22	71	34	28	14	22	1.94
39353466--39353656	51	3.8	51	80	8	237	30	27	17	24	1.97
39353464--39353648	101	1.8	102	90	3	302	30	27	18	23	1.98
39358404--39358474	36	2.0	36	91	0	115	30	9	18	40	1.83
39358702--39358794	48	1.9	48	86	0	132	21	16	19	43	1.88
39363542--39363612	36	2.0	36	94	0	124	30	8	18	42	1.80
39363837--39363932	48	2.0	48	89	0	147	20	17	20	40	1.91
39373458--39373485	2	14.0	2	100	0	56	50	0	0	50	1.00
39376726--39376776	3	17.3	3	77	18	54	68	0	31	0	0.90
39376726--39376775	20	2.5	20	87	9	66	68	0	32	0	0.90
39376725--39376776	14	3.8	14	87	7	72	67	0	32	0	0.91
39376939--39377272	22	15.0	21	71	21	159	31	1	12	54	1.45
39376939--39377108	19	8.3	20	71	18	100	31	0	11	56	1.40
39377073--39377299	27	9.1	25	77	17	233	32	1	12	53	1.47
39377073--39377352	49	5.7	49	85	3	370	31	1	13	53	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39377213--39377325	8	13.4	8	65	17	50	33	0	15	50	1.45
39377343--39377461	60	2.0	60	83	6	152	31	0	13	54	1.45
39377495--39377576	38	2.2	38	97	0	155	54	3	2	39	1.31
39377613--39377654	16	2.7	15	85	7	57	38	2	2	57	1.25
39381135--39381164	11	2.7	11	94	0	51	40	10	23	26	1.86
39381549--39381593	22	2.1	21	87	4	63	2	31	2	64	1.18
39381678--39381749	27	2.7	27	93	0	126	19	38	26	15	1.91
39389178--39389311	19	6.7	21	78	10	77	40	14	6	38	1.72
39389178--39389235	22	2.6	22	81	7	64	41	17	5	36	1.72
39389214--39389324	19	5.8	19	89	0	177	37	13	9	39	1.76
39389214--39389317	38	2.7	38	98	0	199	38	12	8	40	1.74
39389720--39389933	44	4.9	44	67	6	110	28	24	18	28	1.98
39389650--39390016	132	2.8	132	92	2	605	28	23	19	28	1.98
39394022--39394067	24	1.9	24	86	0	65	10	26	17	45	1.81
39396990--39397124	19	6.7	21	77	11	79	41	13	5	40	1.66
39396990--39397048	22	2.7	22	84	7	75	42	16	3	37	1.66
39397004--39397137	19	6.8	19	84	3	151	40	13	6	39	1.71
39397029--39397137	57	1.9	57	90	0	173	40	11	7	40	1.70
39397027--39397130	38	2.7	38	92	0	172	40	11	6	41	1.68
39400715--39400769	28	2.0	28	85	3	76	63	1	0	34	1.05
39401187--39401238	24	2.2	24	89	0	77	53	7	1	36	1.41
39403941--39403983	21	2.0	21	86	8	61	37	2	4	55	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39403984--39404041	31	1.9	29	82	6	71	39	3	5	51	1.41
39404011--39404127	62	1.9	62	84	5	159	41	3	5	49	1.41
39407333--39407408	37	2.1	37	100	0	152	38	21	11	28	1.89
39407482--39407624	41	3.5	42	82	6	152	27	25	19	27	1.99
39407794--39407824	2	15.5	2	100	0	62	51	0	0	48	1.00
39414788--39415123	167	2.0	167	97	0	636	38	18	11	31	1.87
39415100--39415242	41	3.5	42	82	6	152	27	25	19	27	1.99
39415412--39415442	2	15.5	2	100	0	62	51	0	0	48	1.00
39415963--39416115	22	7.0	22	90	0	225	32	14	26	26	1.94
39417581--39417641	28	2.1	30	81	6	72	21	40	26	11	1.87

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