genome.fa.s7.2.7.7.80.10.50.1000.9.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  9  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)
3500258--3500301	23	1.9	23	90	0	70	18	22	20	38	1.93
3501574--3501608	13	2.7	13	81	0	52	11	20	34	34	1.88
3503200--3503615	46	9.6	46	83	12	472	28	22	14	34	1.94
3503289--3503615	82	3.9	82	78	8	338	28	22	13	35	1.92
3503243--3503615	126	2.9	126	88	4	552	28	22	13	34	1.93
3507916--3507987	29	2.5	28	81	4	81	62	1	0	36	1.04
3511143--3511335	48	4.0	48	80	5	196	8	21	21	48	1.77
3511143--3511335	96	2.0	95	82	6	228	8	21	21	48	1.77
3513057--3513095	20	2.0	20	85	10	53	20	5	38	35	1.75
3515434--3515493	28	2.1	28	90	0	93	33	16	10	40	1.82
3527074--3527206	25	5.6	25	83	7	127	38	16	23	21	1.93
3527353--3527389	2	19.0	2	84	15	51	48	2	0	48	1.15
3528166--3528215	16	2.9	16	88	8	64	56	0	0	44	0.99
3528175--3528215	8	5.0	8	88	5	64	58	0	0	41	0.98
3528180--3528250	28	2.4	29	76	19	76	53	1	1	43	1.18
3529337--3529366	14	2.1	14	93	0	51	50	6	0	43	1.28
3529227--3529365	62	2.2	62	90	0	224	37	6	7	48	1.56
3529368--3529393	12	2.2	12	100	0	52	15	7	15	61	1.55
3530631--3530682	27	1.9	27	84	7	70	69	9	3	17	1.31
3533998--3534022	5	5.0	5	100	0	50	0	60	20	20	1.37
3534183--3534249	31	2.2	30	83	2	80	10	32	37	19	1.86
3540373--3540436	21	3.1	21	78	12	62	26	3	3	67	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3540415--3540455	19	2.2	19	86	4	57	36	0	2	60	1.10
3541066--3541127	28	2.3	28	94	5	110	41	6	0	51	1.27
3541368--3541428	18	3.5	18	82	10	74	44	11	0	44	1.40
3541382--3541431	15	3.1	15	85	8	64	44	14	0	42	1.44
3542177--3542238	26	2.4	26	94	0	106	50	0	8	41	1.32
3545746--3545798	7	7.9	7	85	8	74	54	3	0	41	1.18
3557609--3557640	13	2.5	13	100	0	64	21	12	9	56	1.64
3561241--3561313	25	2.9	25	89	4	103	42	2	0	54	1.14
3561291--3561328	11	3.5	11	85	0	58	47	0	0	52	1.00
3564072--3564189	60	2.0	60	96	0	218	29	7	21	41	1.80
3564844--3564884	2	20.5	2	100	0	82	48	0	0	51	1.00
3569407--3569450	20	2.3	20	84	7	56	40	4	0	54	1.21
3576091--3576121	16	1.9	16	93	0	53	48	9	6	35	1.62
3579205--3579230	4	6.5	4	100	0	52	53	0	0	46	1.00
3587053--3587090	18	2.1	18	90	0	58	57	5	0	36	1.21
3590745--3590786	23	1.9	21	85	9	57	61	0	4	33	1.17
3592101--3592144	10	4.7	10	81	18	51	38	0	0	61	0.96
3595891--3596057	59	2.8	58	76	9	142	50	14	11	22	1.75
3595924--3596089	89	1.9	88	82	13	209	51	14	10	22	1.73
3598428--3598479	24	2.2	24	82	0	59	51	9	3	34	1.53
3600128--3600157	13	2.3	13	94	0	51	40	40	0	20	1.52
3601314--3601468	81	1.9	80	81	9	188	34	8	12	45	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3618171--3618218	17	2.8	17	83	3	51	62	6	0	31	1.20
3622868--3622913	19	2.4	19	82	7	58	63	0	36	0	0.95
3623049--3623096	19	2.5	19	75	0	51	37	6	4	52	1.46
3625895--3625933	16	2.4	16	100	0	78	58	5	0	35	1.20
3626116--3626150	10	3.4	11	88	11	56	37	0	0	62	0.95
3626574--3626629	17	3.5	16	72	16	53	57	3	0	39	1.16
3631556--3631598	12	3.4	12	81	9	50	27	0	6	65	1.18
3635660--3635718	31	1.9	31	82	0	73	49	10	8	32	1.67
3640762--3640844	20	4.4	20	67	20	61	46	4	9	38	1.58
3654556--3654597	21	2.0	21	90	0	66	30	11	50	7	1.66
3654562--3654602	21	2.0	21	95	0	73	26	12	56	4	1.56
3671604--3671657	13	4.2	13	77	17	58	70	0	29	0	0.88
3671749--3671867	60	2.0	60	94	0	211	33	0	12	53	1.39
3672172--3672283	55	2.1	54	87	1	161	34	14	8	41	1.77
3672258--3672309	20	2.5	22	70	20	56	40	0	1	57	1.10
3680273--3680309	17	2.1	19	85	10	51	56	0	0	43	0.99
3686230--3686317	44	2.0	44	82	6	106	39	2	14	43	1.58
3686230--3686289	22	2.7	21	73	21	50	43	1	11	43	1.51
3692553--3692580	6	4.7	6	100	0	56	17	0	0	82	0.68
3696280--3696325	11	4.2	11	82	0	65	19	0	10	69	1.17
3696272--3696319	22	2.3	20	82	10	62	16	0	14	68	1.21
3696307--3696336	14	2.1	14	93	0	51	23	3	6	66	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3697935--3697959	13	1.9	13	100	0	50	64	8	8	20	1.46
3699348--3699427	40	2.0	40	100	0	160	45	12	10	32	1.75
3705623--3705664	19	2.2	19	95	0	75	26	16	9	47	1.77
3720035--3720083	24	2.1	22	85	7	62	24	12	24	38	1.90
3723039--3723079	14	2.6	16	77	14	50	34	34	26	4	1.78
3727054--3727137	41	2.0	41	93	0	141	27	7	11	53	1.63
3728931--3728985	2	28.5	2	85	14	80	47	0	1	50	1.11
3729195--3729246	22	2.4	22	80	6	61	53	17	1	26	1.54
3732212--3732305	47	2.0	47	95	0	170	40	17	9	32	1.81
3733928--3734002	31	2.5	31	91	6	118	25	5	1	68	1.19
3733989--3734028	20	2.0	20	85	0	53	30	0	7	62	1.23
3736413--3736470	29	2.0	29	93	0	98	53	15	12	18	1.72
3746692--3746717	7	3.7	7	100	0	52	15	15	42	26	1.87
3749392--3749418	2	13.5	2	100	0	54	48	0	0	51	1.00
3755895--3755932	19	2.0	20	84	5	51	55	2	5	36	1.37
3757879--3757909	14	2.2	14	94	0	53	48	0	0	51	1.00
3772250--3772816	165	3.5	164	84	4	700	29	12	8	48	1.71
3778504--3778798	2	146.5	2	83	2	214	40	3	10	46	1.53
3778792--3778937	23	6.3	23	85	4	186	46	19	8	25	1.78
3778931--3778973	2	21.5	2	100	0	86	51	0	0	48	1.00
3783745--3784112	51	7.4	51	91	4	615	29	22	15	33	1.94
3784543--3784607	31	2.1	31	97	0	121	29	18	12	40	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3788631--3788668	19	2.0	19	94	0	67	36	39	7	15	1.77
3794701--3794729	7	4.1	7	100	0	58	41	13	0	44	1.44
3796682--3796742	31	2.0	31	87	6	88	49	0	4	45	1.23
3804947--3805185	43	5.4	42	76	15	205	29	21	23	25	1.99
3805032--3805138	54	2.0	53	96	1	196	26	21	25	27	1.99
3804989--3805177	96	2.0	96	84	8	251	29	20	24	25	1.99
3809169--3809224	16	3.5	16	80	7	69	23	7	3	66	1.33
3813044--3813086	9	5.0	8	81	10	50	2	23	0	74	0.93
3813044--3813086	13	3.3	14	87	6	56	2	23	0	74	0.93
3813044--3813086	4	10.0	4	80	14	50	2	23	0	74	0.93
3816784--3816811	2	14.0	2	100	0	56	50	0	0	50	1.00
3829090--3829262	89	1.9	89	85	2	240	31	17	24	26	1.97
3829097--3829253	45	3.5	45	68	13	126	32	18	24	24	1.97
3829111--3829286	89	2.0	89	85	0	235	31	19	23	25	1.98
3829503--3829594	47	2.0	47	97	0	175	38	13	20	28	1.90
3832820--3832857	10	4.1	9	84	15	51	76	0	2	21	0.91
3834516--3834553	3	12.7	3	94	0	67	31	2	0	65	1.06
3837542--3837602	19	3.2	19	76	15	63	60	0	3	36	1.13
3837819--3837875	20	2.9	20	74	12	55	28	7	7	57	1.51
3837860--3837953	29	3.3	27	76	19	93	32	8	2	56	1.41
3837912--3837982	19	3.8	18	76	10	72	30	5	2	60	1.34
3837903--3837991	38	2.3	39	78	9	101	29	8	2	59	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3838100--3838273	90	2.0	89	82	4	217	33	9	18	37	1.84
3844116--3844218	39	2.6	39	95	4	181	64	0	2	33	1.09
3844174--3844226	16	3.4	16	75	17	58	62	0	3	33	1.13
3844104--3844238	39	3.5	36	77	16	119	65	0	2	31	1.07
3844104--3844243	40	3.6	37	80	14	131	65	0	2	32	1.08
3853444--3853498	29	1.9	28	82	17	69	58	3	0	38	1.16
3853552--3853605	21	2.5	22	75	16	60	44	3	3	48	1.38
3854001--3854043	23	1.9	23	85	4	61	58	0	2	39	1.11
3854290--3854322	16	2.0	17	88	5	50	48	0	0	51	1.00
3854614--3854654	15	2.7	16	81	7	50	48	4	4	41	1.46

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