genome.fa.s6.2.7.7.80.10.50.1000.15.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  15  of  168  ( 20060 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)
4139321--4139360	3	13.3	3	100	0	80	35	0	0	65	0.93
4139896--4139942	24	2.0	24	82	0	58	70	6	4	19	1.26
4140079--4140142	29	2.1	29	83	11	76	48	17	12	21	1.80
4140155--4140210	3	18.7	3	100	0	112	32	0	0	67	0.91
4142600--4142637	20	2.0	20	94	5	69	60	0	0	39	0.97
4156379--4156467	20	4.8	19	70	14	60	56	3	1	39	1.23
4156409--4156460	26	2.0	27	84	3	70	50	1	1	46	1.23
4156438--4156477	20	2.1	19	85	4	53	65	2	0	32	1.06
4161182--4161309	51	2.5	50	78	12	145	50	2	5	41	1.38
4171449--4171797	179	1.9	180	84	2	461	41	8	10	38	1.71
4178622--4178660	8	4.8	8	96	3	69	61	0	2	35	1.10
4180237--4180298	24	2.6	24	94	0	106	27	8	38	25	1.84
4185006--4185079	36	2.1	36	92	0	121	33	13	20	32	1.91
4193128--4193166	16	2.5	16	83	4	53	23	2	2	71	1.10
4194354--4194401	22	2.3	20	85	7	60	43	2	2	52	1.24
4194454--4194499	22	2.1	22	83	0	56	13	23	21	41	1.88
4194596--4194770	42	4.2	41	88	2	251	23	21	22	33	1.98
4194596--4194770	83	2.1	84	89	1	271	23	21	22	33	1.98
4198160--4198187	9	3.1	9	100	0	56	57	0	0	42	0.99
4200645--4200687	9	4.8	9	88	8	61	34	4	23	37	1.76
4200642--4201095	18	25.2	18	79	7	305	33	1	15	49	1.54
4200642--4201095	27	16.1	27	80	12	332	33	1	15	49	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4200642--4201095	54	8.2	54	81	9	431	33	1	15	49	1.54
4200663--4201081	63	6.8	62	83	8	518	33	1	15	50	1.52
4200671--4201102	36	12.0	36	83	3	451	33	1	15	50	1.51
4204677--4204701	13	1.9	13	100	0	50	48	0	0	52	1.00
4205549--4205633	21	4.0	20	72	11	53	45	31	1	21	1.59
4205557--4205636	14	5.6	14	70	14	56	47	31	0	21	1.51
4205706--4206231	115	4.6	114	74	4	409	25	23	19	32	1.97
4221654--4222068	205	2.0	205	99	0	812	26	16	19	36	1.93
4226725--4226773	11	4.5	11	76	19	57	20	0	2	77	0.87
4227840--4227881	12	3.4	12	84	15	59	85	0	14	0	0.59
4229355--4229402	21	2.3	21	100	0	96	35	4	31	29	1.76
4229355--4229412	21	2.8	21	91	0	80	32	8	27	31	1.87
4229794--4229860	34	1.9	35	90	3	109	44	13	8	32	1.75
4230063--4230188	62	2.0	62	100	0	252	17	27	14	40	1.88
4230148--4230280	66	2.0	66	98	0	257	24	24	12	39	1.90
4230671--4230799	66	2.0	66	96	0	240	27	17	15	39	1.90
4233108--4233153	23	2.0	23	100	0	92	34	21	13	30	1.91
4235983--4236209	94	2.4	96	85	5	298	37	3	18	40	1.66
4235913--4236209	94	3.1	94	82	6	287	36	4	17	42	1.68
4236248--4236666	126	3.3	126	92	1	678	33	19	21	25	1.97
4237676--4237716	21	1.9	22	85	5	57	9	19	39	31	1.84
4238090--4238156	30	2.2	30	84	5	91	8	16	43	31	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4239409--4239442	16	2.2	16	89	5	52	73	5	2	17	1.16
4239535--4239641	34	3.2	34	82	15	159	42	4	17	34	1.70
4239559--4239658	34	3.0	33	80	15	134	48	4	16	32	1.64
4239848--4239890	3	13.7	3	90	9	68	67	2	0	30	1.03
4241511--4242361	95	9.0	95	92	2	1369	29	22	17	29	1.97
4241608--4241756	43	3.4	43	68	7	120	30	25	16	27	1.97
4241790--4242325	43	11.4	43	63	22	161	29	22	18	30	1.97
4242366--4242656	88	3.3	88	94	0	501	27	27	21	22	1.99
4242372--4242654	44	6.4	44	68	20	171	28	27	21	22	1.99
4243882--4243931	23	2.2	22	82	3	55	0	22	2	76	0.89
4248923--4248970	21	2.4	21	82	6	64	64	2	8	25	1.32
4248898--4248932	2	18.5	2	88	11	56	51	0	0	48	1.00
4250439--4250463	7	3.6	7	100	0	50	56	16	0	28	1.41
4251643--4251688	11	4.2	11	78	18	51	43	0	32	23	1.54
4251649--4251692	10	4.1	10	83	13	52	45	0	29	25	1.54
4260546--4260579	5	6.8	5	100	0	68	38	0	0	61	0.96
4262105--4262139	16	2.2	16	100	0	70	34	20	5	40	1.76
4269309--4269335	12	2.2	12	100	0	54	70	7	0	22	1.12
4270339--4270380	21	2.0	20	86	4	57	26	21	4	47	1.70
4271940--4271967	7	4.0	7	100	0	56	85	0	0	14	0.59
4278001--4278075	38	2.0	37	82	17	93	40	1	6	52	1.36
4284346--4284395	25	2.0	25	100	0	100	32	12	16	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4285388--4285428	11	3.7	11	86	0	55	7	39	12	41	1.70
4286819--4287000	7	26.0	7	80	0	139	40	1	30	28	1.64
4286819--4286993	56	3.1	56	87	0	233	40	1	30	28	1.64
4297171--4297195	1	25.0	1	100	0	50	100	0	0	0	0.00
4297369--4297411	21	2.0	21	86	8	61	39	2	4	53	1.34
4297726--4297755	15	2.1	14	93	6	51	73	3	0	23	0.98
4299746--4299787	22	1.9	22	100	0	84	33	4	7	54	1.49
4303018--4303065	22	2.2	22	82	14	55	50	18	0	31	1.48
4305965--4306027	3	21.0	3	76	0	54	58	4	7	28	1.47
4306535--4306568	12	2.8	12	83	16	52	79	0	14	5	0.91
4307577--4308524	50	19.1	50	74	4	707	26	19	20	32	1.97
4307590--4308518	100	9.3	100	87	1	1141	26	19	20	32	1.97
4308690--4309120	88	4.9	88	81	2	497	27	24	19	29	1.98
4310369--4310419	22	2.3	21	83	12	59	11	15	1	70	1.25
4311326--4311375	14	3.5	14	81	5	55	18	2	8	72	1.19
4315096--4315193	3	32.7	3	78	0	61	55	4	10	30	1.52
4319952--4320021	30	2.3	30	85	4	97	15	41	34	8	1.78
4326959--4326996	19	2.0	19	100	0	76	21	0	21	57	1.40
4339101--4339158	24	2.4	24	88	5	82	34	12	22	31	1.91
4339474--4340002	43	12.5	42	72	12	231	30	21	22	24	1.99
4339603--4339923	40	7.8	40	76	9	313	29	22	23	24	1.99
4339604--4340028	210	2.0	207	90	2	672	30	22	22	25	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4339468--4339919	167	2.7	167	81	11	580	30	21	23	24	1.99
4339474--4340028	127	4.4	125	77	10	468	30	21	22	24	1.99
4339604--4340028	40	10.2	40	72	12	300	30	22	22	25	1.99
4343788--4343830	21	2.0	21	86	0	59	32	11	30	25	1.91
4345436--4345918	184	2.6	184	87	1	646	42	20	8	28	1.81
4350287--4350320	12	2.8	12	90	4	50	70	0	2	26	1.01
4359350--4359724	186	2.0	186	94	0	651	28	17	13	40	1.88
4363541--4363592	21	2.4	22	76	20	56	36	13	3	46	1.62
4369508--4369609	22	4.5	22	70	7	71	49	33	1	15	1.56
4369508--4369659	45	3.4	46	83	3	157	46	34	2	16	1.61
4369513--4369659	23	6.5	23	74	3	138	46	35	2	16	1.59
4370910--4370985	38	2.0	38	94	0	134	38	22	9	30	1.85
4371148--4371459	29	10.7	29	73	9	154	37	11	26	24	1.89
4371237--4371471	87	2.7	87	83	0	290	35	12	27	24	1.91
4371266--4371471	29	7.1	29	76	3	171	35	12	27	24	1.92
4384149--4384208	27	2.2	26	79	5	57	43	18	18	20	1.88
4384203--4384455	27	9.4	27	83	4	287	45	19	16	18	1.86
4384205--4384441	81	2.9	79	84	5	323	46	18	17	17	1.84
4391555--4391604	20	2.5	20	87	6	66	54	0	26	20	1.45
4397231--4397286	28	2.0	28	89	0	85	48	19	5	26	1.70
4397426--4397536	58	1.9	58	90	3	179	24	26	11	37	1.89
4397434--4397538	29	3.6	29	84	2	140	22	26	11	39	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4397426--4397565	29	4.8	29	81	0	136	25	25	11	37	1.89
4397428--4397569	58	2.4	58	82	4	178	25	25	11	38	1.89
4404178--4404262	29	2.9	29	82	0	107	25	24	12	36	1.92
4405639--4405679	18	2.4	18	80	11	52	7	4	4	82	0.93
4406899--4406962	30	2.1	30	94	0	110	32	34	17	15	1.91
4408039--4408080	18	2.4	18	92	4	68	42	2	9	45	1.49
4409237--4409516	143	2.0	143	91	1	454	24	12	22	40	1.89
4411307--4411347	17	2.4	17	91	0	64	34	12	29	24	1.91
4412316--4412368	20	2.7	20	82	5	63	28	18	5	47	1.72
4427747--4428013	27	9.9	27	88	0	374	25	16	19	38	1.91

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