genome.fa.s7.2.7.7.80.10.50.1000.10.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   

This is table  10  of  204  ( 24458 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)
3855535--3855574	20	2.0	20	90	0	62	27	10	12	50	1.72
3855514--3855590	14	5.0	15	71	22	54	35	7	14	42	1.74
3855922--3856044	61	2.0	61	100	0	246	39	13	26	21	1.89
3856494--3856529	13	2.8	13	82	0	54	33	8	25	33	1.86
3859589--3859622	17	1.9	18	88	5	52	41	20	11	26	1.87
3873935--3873966	2	16.0	2	100	0	64	50	0	50	0	1.00
3875961--3876012	22	2.5	20	79	14	59	36	0	3	59	1.16
3883691--3883743	24	2.3	23	78	18	56	52	1	9	35	1.45
3892973--3893004	3	10.7	3	100	0	64	68	0	31	0	0.90
3893454--3893512	26	2.2	27	82	8	68	45	1	5	47	1.34
3896584--3896614	5	6.2	5	100	0	62	61	0	0	38	0.96
3898539--3898579	5	8.0	5	97	2	73	39	0	0	60	0.96
3898687--3898722	16	2.2	16	90	0	54	41	2	0	55	1.14
3898726--3898762	16	2.2	18	85	9	51	72	5	5	16	1.21
3899472--3899509	3	12.7	3	100	0	76	34	0	0	65	0.93
3902707--3902782	23	3.3	23	96	0	143	31	26	21	21	1.98
3902869--3902897	8	3.6	8	100	0	58	34	27	13	24	1.93
3909303--3909379	23	3.3	23	94	1	136	31	27	20	20	1.98
3909466--3909494	8	3.6	8	100	0	58	34	27	13	24	1.93
3909599--3909637	18	2.2	17	86	13	53	46	20	0	33	1.51
3913725--3913782	11	5.4	11	78	15	59	37	5	0	56	1.21
3913747--3913813	9	7.0	9	77	16	55	35	1	0	62	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3913709--3913848	71	2.0	70	91	5	228	37	2	0	60	1.12
3913736--3913821	28	2.9	28	80	13	68	36	3	0	60	1.14
3916031--3916106	37	2.0	38	82	7	93	34	22	15	27	1.95
3916951--3917016	20	3.1	20	80	20	64	3	22	4	69	1.20
3919298--3919329	16	2.0	16	93	0	55	37	0	9	53	1.34
3927737--3927793	20	2.9	20	72	12	55	64	0	1	33	1.04
3928063--3928159	46	2.2	45	81	10	110	36	4	3	56	1.34
3928136--3928200	18	3.4	18	75	14	60	36	0	1	61	1.05
3930993--3931035	18	2.4	18	88	0	59	72	6	11	9	1.29
3931588--3931628	2	20.5	2	89	0	64	4	48	0	46	1.23
3936209--3936305	33	2.8	35	72	20	89	50	1	3	45	1.24
3940639--3940706	29	2.5	26	77	15	73	39	14	2	42	1.61
3943296--3943334	17	2.4	16	86	4	51	38	2	5	53	1.37
3943593--3943669	29	2.6	29	82	15	79	42	15	5	36	1.69
3944542--3944579	2	19.0	2	100	0	76	50	0	0	50	1.00
3946849--3946894	20	2.2	21	88	3	67	8	26	13	52	1.69
3975804--3975847	20	2.1	22	83	8	56	54	0	6	38	1.27
3975992--3976021	15	1.9	16	93	6	53	33	3	0	63	1.11
3975987--3976025	15	2.5	15	83	8	51	35	2	0	61	1.10
3988850--3989107	127	2.0	126	98	0	498	30	19	20	29	1.97
3991266--3991296	7	4.4	7	91	0	53	41	38	0	19	1.51
4003715--4003770	27	2.1	27	86	0	76	48	14	12	25	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4012434--4012493	2	31.5	2	83	9	81	50	3	0	46	1.18
4013440--4013494	20	2.9	19	73	7	51	56	1	10	30	1.44
4017602--4017660	13	4.0	15	74	14	52	64	1	1	32	1.13
4020528--4020590	22	2.8	22	80	4	63	60	3	0	36	1.13
4022648--4022696	22	2.2	23	88	3	73	48	2	2	46	1.25
4022645--4022702	22	2.9	21	73	16	61	46	3	3	46	1.36
4022751--4022919	35	4.6	35	67	13	106	39	5	8	46	1.60
4022691--4022930	112	2.1	112	93	1	401	40	7	7	45	1.61
4022972--4023030	15	4.1	15	75	20	72	23	0	30	45	1.53
4022998--4023080	6	13.0	6	69	20	53	20	1	40	37	1.60
4022983--4023072	27	3.1	27	83	14	126	22	0	38	38	1.54
4023098--4023163	15	4.2	15	75	17	71	25	0	28	45	1.54
4023010--4023250	100	2.4	97	86	10	330	20	0	34	43	1.58
4023226--4023260	12	2.9	12	91	0	52	11	0	40	48	1.39
4023499--4023546	21	2.3	21	85	0	60	4	27	41	27	1.74
4023761--4023795	18	1.9	19	88	11	56	25	37	20	17	1.94
4023801--4023843	18	2.4	18	88	0	59	44	9	27	18	1.80
4025606--4025705	51	2.0	51	86	4	139	44	2	28	26	1.65
4025665--4025716	11	4.7	12	73	21	51	42	1	30	25	1.66
4025667--4025716	22	2.3	22	89	6	75	42	2	32	24	1.66
4028517--4028678	88	1.8	89	85	4	229	27	15	12	45	1.82
4045747--4045903	79	2.0	76	85	3	206	28	22	17	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4047850--4047923	2	37.0	2	100	0	148	50	0	0	50	1.00
4048612--4048656	2	22.5	2	86	0	63	51	0	0	48	1.00
4048619--4048656	14	2.7	14	100	0	76	55	0	0	44	0.99
4052133--4052203	28	2.6	28	93	4	119	46	9	0	43	1.37
4052858--4052916	19	3.2	19	82	4	84	37	13	0	49	1.43
4053111--4053179	19	3.7	19	78	3	86	50	1	10	37	1.45
4053580--4053634	28	2.0	27	96	3	101	38	0	7	54	1.28
4053585--4053654	28	2.5	28	86	2	88	41	0	10	48	1.36
4053846--4053922	29	2.6	30	83	6	95	53	3	2	40	1.33
4064844--4064875	15	2.3	15	89	10	50	40	18	0	40	1.51
4065363--4065405	6	6.8	6	81	7	50	44	16	20	18	1.87
4065390--4065580	39	4.4	41	82	13	183	41	20	17	19	1.90
4065430--4065456	6	4.5	6	100	0	54	48	14	18	18	1.82
4065374--4065540	51	3.4	50	82	12	211	41	19	18	19	1.90
4065383--4065613	45	5.1	45	81	13	251	40	20	19	19	1.92
4070576--4070622	23	2.1	22	84	4	58	42	6	2	48	1.40
4074838--4074947	21	5.2	21	68	0	67	16	23	17	42	1.88
4074843--4074947	42	2.5	42	88	0	147	17	24	17	40	1.90
4074843--4074968	42	3.0	41	83	2	135	18	23	15	42	1.89
4077233--4077289	28	2.0	30	86	10	84	31	12	1	54	1.48
4078273--4078335	8	7.8	8	73	16	58	61	1	0	36	1.05
4078279--4078335	5	10.6	5	78	14	60	61	1	0	36	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4079943--4080249	43	7.2	41	85	8	362	26	26	21	25	1.99
4079943--4080249	86	3.6	85	88	3	402	26	26	21	25	1.99
4079943--4080249	129	2.4	128	86	5	406	26	26	21	25	1.99
4080412--4080441	14	2.1	14	93	0	51	50	13	6	30	1.67
4085016--4085056	21	2.0	21	90	0	64	29	46	0	24	1.53
4085356--4085407	15	3.4	16	82	12	65	46	40	0	13	1.43
4085366--4085435	30	2.4	31	83	11	85	44	38	0	17	1.49
4085368--4085449	14	5.6	14	71	15	51	43	37	0	18	1.50
4085837--4086149	41	7.7	41	87	1	414	32	28	21	18	1.97
4086137--4086252	40	3.0	37	74	16	101	23	21	19	35	1.96
4086007--4086251	82	3.0	80	79	8	212	26	24	20	28	1.99
4086079--4086229	40	3.8	40	75	14	123	25	23	20	31	1.98
4100443--4100488	24	1.9	24	81	0	56	39	17	2	41	1.62
4110216--4110251	16	2.2	16	90	0	54	41	0	11	47	1.39
4112603--4112633	9	3.4	9	90	0	53	25	12	22	38	1.90
4112686--4112722	9	4.1	9	92	0	65	45	13	10	29	1.77
4114884--4114942	30	2.0	29	93	3	100	45	16	8	28	1.77
4115077--4115289	103	2.1	103	88	0	309	25	8	5	60	1.46
4118608--4118664	4	14.0	4	75	10	53	70	1	5	22	1.17
4119930--4119964	18	1.9	18	94	0	61	11	5	20	62	1.48
4129142--4129211	32	2.2	30	82	12	79	41	12	7	38	1.71
4131686--4132162	245	2.0	241	87	2	686	36	14	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4133412--4133486	26	2.9	26	78	9	75	41	1	2	54	1.23
4133414--4133452	15	2.4	16	87	8	53	35	0	0	64	0.94
4140582--4140612	14	2.2	14	100	0	62	29	29	0	41	1.56
4140845--4140944	25	4.3	23	77	8	71	41	21	22	16	1.90
4140888--4140989	25	4.1	25	87	0	114	39	19	21	19	1.93
4144875--4144932	27	2.2	26	79	14	66	0	31	5	63	1.16
4144972--4145012	3	14.0	3	94	5	75	65	0	0	34	0.93
4147538--4147584	21	2.2	21	85	11	60	51	0	2	46	1.13
4148207--4148244	20	1.9	20	84	10	51	42	0	0	57	0.98
4164742--4164798	24	2.4	24	82	14	73	43	0	1	54	1.10

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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204