genome.fa.s12.2.7.7.80.10.50.1000.14.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  14  of  120  ( 14336 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)
4082823--4082901	16	4.9	16	72	15	56	45	0	0	54	0.99
4082852--4082887	17	2.1	17	94	0	63	41	0	0	58	0.98
4082829--4082903	32	2.4	31	78	15	82	46	0	0	53	1.00
4082857--4082910	17	3.3	17	79	7	58	51	0	0	48	1.00
4082845--4082920	32	2.4	32	80	6	82	48	0	0	51	1.00
4085176--4085200	2	12.5	2	100	0	50	48	0	0	52	1.00
4088970--4089020	23	2.2	23	85	0	66	29	7	19	43	1.79
4090735--4090908	88	2.0	89	84	5	228	37	16	20	24	1.93
4090856--4090915	31	1.9	31	86	0	84	30	18	23	28	1.98
4097648--4097681	16	2.1	16	100	0	68	41	0	17	41	1.50
4100016--4100069	3	18.7	3	90	7	85	0	29	1	68	1.00
4103838--4103870	7	4.7	7	100	0	66	42	0	45	12	1.41
4105969--4106031	27	2.3	27	97	0	117	15	22	22	39	1.92
4108151--4108262	40	2.8	40	86	8	138	35	2	0	61	1.10
4108193--4108226	17	2.0	17	88	0	50	35	0	0	64	0.94
4108181--4108238	29	2.0	29	83	6	73	36	3	0	60	1.14
4108210--4108245	11	3.3	11	88	11	56	41	2	0	55	1.14
4110385--4110439	28	2.1	25	83	12	67	43	9	0	47	1.35
4120623--4121233	305	2.0	305	100	0	1222	27	23	16	33	1.95
4121522--4121604	21	4.0	21	76	9	98	60	0	2	37	1.10
4121532--4121629	41	2.5	41	93	5	166	60	0	2	37	1.09
4121597--4121641	16	2.8	17	83	10	58	60	0	0	40	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4131246--4131297	20	2.6	20	84	0	68	46	21	5	26	1.74
4131450--4131489	21	2.0	20	85	5	53	47	5	2	45	1.38
4131615--4131670	19	2.9	19	81	2	67	33	14	8	42	1.77
4138916--4138946	14	2.2	14	94	0	53	19	6	12	61	1.53
4139448--4139526	33	2.5	32	87	6	108	24	8	8	58	1.57
4141601--4141642	13	3.4	12	87	12	59	7	0	21	71	1.09
4141601--4141643	11	3.5	11	84	15	50	6	0	20	72	1.08
4141593--4141656	25	2.5	26	80	10	69	15	0	15	68	1.21
4144442--4144487	23	2.0	23	86	0	65	45	17	8	28	1.78
4146174--4146355	69	2.6	70	80	9	201	36	16	5	41	1.72
4146598--4146866	141	1.9	142	83	5	348	32	15	13	38	1.86
4147611--4147658	21	2.3	20	83	13	62	70	2	0	27	0.98
4147615--4147660	20	2.4	19	86	13	67	69	2	0	28	1.00
4149925--4149965	18	2.1	20	86	13	59	34	0	0	65	0.93
4154898--4154968	28	2.5	29	88	2	99	29	7	7	56	1.53
4167733--4167861	60	2.1	61	80	4	136	41	14	5	38	1.69
4175453--4175500	24	2.0	24	100	0	96	29	20	12	37	1.90
4179030--4179089	11	5.2	11	75	25	61	61	1	0	36	1.06
4188040--4188091	20	2.5	20	87	3	77	34	1	5	57	1.33
4188421--4188492	2	36.0	2	100	0	144	50	0	0	50	1.00
4190987--4191027	22	1.9	21	85	5	55	9	12	4	73	1.24
4193133--4193157	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4198729--4198763	18	1.9	18	100	0	70	22	17	28	31	1.96
4200793--4200819	13	2.1	13	100	0	54	25	22	22	29	1.99
4204383--4204433	21	2.4	21	75	12	59	11	5	37	45	1.65
4204905--4204958	26	2.0	27	92	3	92	46	1	11	40	1.50
4214147--4214199	11	4.7	11	77	11	54	30	1	1	66	1.13
4216027--4216069	18	2.5	17	80	3	50	37	0	2	60	1.10
4227001--4227045	23	2.0	23	82	8	56	55	2	0	42	1.12
4226992--4227076	39	2.2	37	81	10	91	55	2	0	42	1.12
4228491--4228518	11	2.5	11	100	0	56	46	0	10	42	1.38
4231237--4231409	91	1.9	89	82	5	211	39	9	13	36	1.77
4232513--4232570	22	2.5	23	78	13	66	36	5	0	58	1.20
4238731--4238774	20	2.2	20	83	0	52	52	6	0	40	1.28
4241294--4241333	18	2.2	18	90	0	62	17	30	10	42	1.82
4242038--4242199	46	3.6	46	93	4	269	27	22	14	34	1.94
4244465--4244490	10	2.6	10	100	0	52	19	0	7	73	1.07
4244690--4244817	34	3.8	33	76	7	134	44	14	0	40	1.50
4245650--4245679	6	5.2	6	96	4	53	0	0	13	86	0.57
4248120--4248179	31	1.9	31	96	0	111	48	26	1	23	1.60
4249177--4249221	22	2.0	22	100	0	90	40	17	22	20	1.92
4260767--4260803	2	18.5	2	100	0	74	51	0	0	48	1.00
4261604--4261803	41	4.9	41	85	2	249	25	25	17	32	1.96
4265096--4265137	13	3.4	13	75	24	54	42	0	9	47	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4265712--4265751	19	2.0	21	85	9	57	37	0	10	52	1.35
4265690--4265768	38	2.1	39	80	7	90	36	0	8	54	1.32
4266482--4266657	94	1.9	94	100	0	352	40	7	14	37	1.75
4267325--4267371	19	2.5	19	79	10	51	59	4	6	29	1.41
4269161--4269219	12	5.2	11	74	13	57	55	0	3	40	1.16
4269144--4269254	52	2.1	50	79	11	123	61	0	1	36	1.07
4269203--4269237	18	1.9	18	94	0	61	37	0	0	62	0.95
4269638--4269675	16	2.3	17	83	16	53	26	0	7	65	1.19
4269640--4269675	18	2.1	18	90	10	58	25	0	8	66	1.19
4270991--4271121	69	1.9	69	90	0	208	31	20	20	27	1.98
4272867--4272917	26	2.0	26	85	11	70	49	3	0	47	1.20
4274158--4274315	51	3.2	49	83	12	218	28	23	14	33	1.94
4274155--4274298	44	3.1	44	81	15	191	29	22	15	32	1.95
4276260--4276333	3	24.3	3	97	2	139	32	1	0	66	1.00
4279261--4279327	31	2.2	31	78	5	75	34	7	0	58	1.26
4279392--4279421	6	5.0	6	100	0	60	50	16	0	33	1.46
4283876--4283955	1	80.0	1	69	0	52	85	2	10	2	0.80
4283878--4283955	17	4.9	16	80	16	83	84	2	10	2	0.81
4283876--4283954	10	7.8	10	79	8	72	84	2	10	2	0.80
4283876--4283954	29	2.7	30	80	9	92	84	2	10	2	0.80
4288629--4288740	54	2.1	54	100	0	224	26	33	14	25	1.94
4289476--4289507	16	2.0	17	88	11	50	59	0	34	6	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4291685--4291738	22	2.5	22	81	6	65	66	1	1	29	1.12
4292424--4292543	35	3.3	35	86	8	177	28	40	8	22	1.83
4292431--4292543	39	3.0	38	89	5	169	28	38	8	23	1.85
4297408--4297466	19	3.1	19	68	4	55	49	13	5	32	1.64
4299601--4299726	43	2.9	43	82	13	152	30	29	18	21	1.97
4301671--4301964	23	12.7	23	82	1	345	42	19	11	26	1.86
4304798--4304924	34	3.8	33	83	5	166	44	16	0	39	1.48
4304891--4304945	28	2.0	28	89	7	85	40	18	0	41	1.50
4309102--4309150	18	2.7	19	84	9	66	16	4	6	73	1.19
4315778--4315813	9	4.0	9	85	0	54	16	0	2	80	0.83
4316310--4316358	4	12.2	4	87	12	66	46	28	0	24	1.53
4316307--4316358	16	2.8	19	88	11	74	46	28	0	25	1.53
4317019--4317084	32	2.1	32	97	0	123	34	13	12	39	1.82
4317753--4317785	15	2.2	15	94	0	57	27	33	9	30	1.88
4321615--4321688	28	2.6	27	79	12	78	32	5	4	58	1.40
4321694--4321755	19	3.2	19	77	13	63	30	8	1	59	1.36
4344670--4344702	16	2.1	16	100	0	66	57	12	6	24	1.57
4347023--4347199	97	1.8	98	92	1	302	47	6	16	29	1.71
4357900--4357930	15	2.1	15	93	0	53	38	0	6	54	1.26
4367118--4367304	90	2.1	90	96	0	347	31	8	12	48	1.69
4367694--4367737	15	2.7	18	80	20	60	0	11	52	36	1.38
4372457--4372496	17	2.3	18	95	4	73	37	32	5	25	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4388623--4388817	97	2.0	97	88	4	286	38	15	15	30	1.88
4390554--4390610	26	2.2	26	84	6	71	52	3	1	42	1.28
4401661--4401834	65	2.6	65	74	11	149	20	16	18	44	1.86
4406008--4406058	22	2.3	22	93	0	84	60	13	5	19	1.53
4410226--4410259	16	2.1	16	100	0	68	35	5	23	35	1.79
4413692--4413736	22	2.1	21	84	8	56	26	8	8	55	1.60
4415894--4415936	16	2.5	18	77	7	54	41	2	0	55	1.12
4416340--4416404	32	2.0	32	93	0	112	53	0	0	46	1.00
4416416--4416465	23	2.3	23	82	6	59	30	2	4	64	1.23
4423644--4423670	7	3.9	7	100	0	54	59	11	14	14	1.62

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