genome.fa.s8.2.7.7.80.10.50.1000.25.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  25  of  190  ( 22705 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)
7073196--7073256	11	5.3	11	79	11	68	78	0	21	0	0.75
7073187--7073256	23	3.0	23	85	2	86	77	0	22	0	0.78
7073196--7073255	16	3.6	16	68	18	50	78	0	21	0	0.75
7073544--7073588	21	2.2	20	92	4	72	77	0	22	0	0.76
7074035--7074506	18	25.8	17	69	19	169	32	13	10	43	1.79
7074029--7074220	35	5.4	34	74	13	145	38	10	9	42	1.72
7074249--7074431	35	5.2	35	77	12	164	27	17	11	43	1.83
7074268--7074488	53	4.1	53	78	12	195	25	15	11	46	1.80
7078603--7078638	4	9.0	4	100	0	72	25	0	25	50	1.50
7080546--7080648	20	5.8	18	67	20	56	59	3	1	34	1.27
7080546--7080581	19	1.9	19	88	5	56	61	5	0	33	1.19
7082000--7082053	23	2.3	23	96	0	99	38	0	12	48	1.42
7082009--7082051	13	3.5	13	75	18	56	37	0	13	48	1.43
7082873--7082911	17	2.3	17	86	0	51	35	5	2	56	1.35
7088112--7088155	23	1.9	23	100	0	88	34	18	27	20	1.96
7089662--7089736	23	3.3	23	90	0	114	37	1	12	49	1.48
7106095--7106120	2	13.0	2	100	0	52	50	0	0	50	1.00
7106866--7106912	21	2.2	22	81	11	62	38	0	0	61	0.96
7107032--7107062	13	2.4	13	94	0	53	25	12	12	48	1.77
7108026--7108067	20	2.2	19	87	8	59	30	0	45	23	1.53
7108049--7108164	54	2.2	52	83	4	142	42	0	32	24	1.61
7107992--7108132	74	1.9	73	84	7	187	42	0	34	22	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7108049--7108185	54	2.6	51	78	12	141	43	0	31	24	1.59
7111203--7111252	25	2.0	26	88	4	75	38	8	16	38	1.78
7120026--7120055	14	2.1	15	93	6	53	20	6	20	53	1.67
7120191--7120258	25	2.7	25	81	0	82	44	1	14	39	1.55
7120854--7120891	2	19.0	2	100	0	76	50	0	0	50	1.00
7121867--7121937	27	2.6	29	77	8	85	26	16	26	29	1.97
7126941--7126997	22	2.6	23	80	8	73	40	19	26	14	1.89
7126941--7127021	22	3.5	22	75	8	65	39	19	25	14	1.90
7126989--7127044	25	2.2	25	87	0	76	37	21	25	16	1.93
7127989--7128031	5	8.6	5	89	0	50	48	6	0	44	1.29
7127988--7128036	15	3.3	15	74	2	55	46	6	0	46	1.27
7129076--7129115	19	2.1	19	86	9	55	55	2	0	42	1.13
7132018--7132064	15	3.1	15	76	11	51	38	4	0	57	1.18
7138029--7138067	14	2.7	15	84	8	53	20	10	15	53	1.70
7141359--7141422	13	4.9	13	90	0	92	26	10	23	39	1.88
7141359--7141422	26	2.5	26	94	0	110	26	10	23	39	1.88
7141997--7142040	22	2.0	22	86	4	63	40	4	11	43	1.61
7147307--7147338	6	5.3	6	100	0	64	15	15	18	50	1.79
7148533--7148641	54	2.0	54	100	0	218	47	16	6	29	1.71
7154554--7154604	4	12.8	4	79	8	59	23	5	27	43	1.77
7154556--7154602	12	3.9	12	88	0	76	23	6	27	42	1.78
7155813--7155935	62	2.0	62	100	0	246	15	24	22	37	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7158926--7159088	36	4.5	36	73	10	134	37	12	23	26	1.91
7159031--7159120	36	2.4	36	87	9	119	36	7	23	32	1.83
7162202--7162229	11	2.5	11	100	0	56	35	17	17	28	1.93
7166736--7166805	28	2.5	29	90	6	110	42	8	1	47	1.43
7166850--7166956	27	4.0	27	96	0	169	26	28	29	14	1.95
7169651--7169688	18	2.1	18	90	0	58	15	44	5	34	1.69
7169654--7169695	18	2.3	18	83	0	57	21	47	2	28	1.63
7170426--7170499	3	24.7	3	100	0	148	66	0	0	33	0.92
7170785--7170864	27	3.0	27	94	0	133	13	30	27	28	1.94
7170891--7170928	12	3.2	12	88	7	51	0	2	7	89	0.57
7170926--7170996	27	2.7	26	91	6	115	46	1	8	43	1.42
7173134--7173161	2	14.0	2	100	0	56	50	0	0	50	1.00
7184146--7184190	22	2.0	22	100	0	90	62	4	8	24	1.43
7184432--7184475	21	2.0	22	83	12	56	43	9	11	36	1.72
7186149--7186283	68	1.9	68	82	7	162	40	3	7	48	1.49
7192151--7192185	17	2.0	18	88	5	54	65	22	0	11	1.24
7196167--7196229	23	2.7	22	79	16	74	17	7	22	52	1.70
7196179--7196336	34	4.5	35	65	18	94	21	6	24	47	1.75
7196248--7196336	23	4.0	22	73	17	78	17	7	22	51	1.71
7196135--7196364	107	2.1	107	98	0	442	24	6	24	44	1.78
7200342--7200493	47	3.3	47	71	18	165	44	2	3	48	1.35
7200327--7200611	91	3.3	90	86	10	396	46	3	3	46	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7200357--7200510	44	3.4	44	70	15	143	44	3	3	48	1.35
7200327--7200645	44	7.3	44	65	23	122	46	3	3	47	1.35
7200450--7200603	78	2.0	78	93	0	263	47	3	2	46	1.32
7200747--7201165	59	7.0	57	66	20	200	44	2	5	47	1.40
7200987--7201021	18	2.0	17	88	5	52	45	0	0	54	0.99
7201107--7201141	18	2.0	17	88	5	52	45	0	0	54	0.99
7200627--7201161	120	4.5	119	95	0	883	43	2	4	48	1.39
7210920--7210955	12	3.0	12	91	0	63	50	13	16	19	1.79
7220021--7220062	18	2.3	18	84	8	50	28	2	2	66	1.16
7220578--7220753	93	1.9	92	85	1	244	37	17	9	35	1.83
7220769--7220841	36	2.1	34	84	5	92	60	0	2	36	1.11
7221258--7221450	86	2.2	88	88	4	295	30	9	21	37	1.86
7233329--7233377	25	1.9	26	91	4	82	30	2	16	51	1.56
7240223--7240330	40	2.7	40	87	4	148	34	21	18	25	1.96
7241200--7241275	4	18.2	4	74	15	50	0	22	3	73	0.99
7241287--7241333	19	2.5	19	82	0	58	27	2	2	68	1.13
7252101--7252131	4	8.0	4	92	7	55	48	0	0	51	1.00
7255107--7255167	30	2.1	30	84	3	79	44	3	18	34	1.66
7255504--7255753	50	4.9	50	85	5	297	26	20	30	22	1.98
7260346--7260416	3	23.7	3	94	0	124	32	0	1	66	1.01
7263009--7263054	24	1.9	24	86	0	65	45	17	26	10	1.81
7265658--7265699	14	2.9	14	85	3	57	80	0	19	0	0.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7265659--7265698	20	2.0	20	95	0	71	82	0	17	0	0.67
7266955--7267452	132	3.8	132	90	1	766	29	18	23	28	1.98
7277190--7277259	36	2.0	36	91	2	115	14	11	31	42	1.81
7277167--7277259	35	2.6	36	84	5	127	13	9	32	44	1.77
7277935--7277988	19	2.8	19	97	0	99	37	9	16	37	1.81
7277948--7278011	19	3.0	22	86	8	80	37	6	17	39	1.75
7277977--7278021	23	2.0	23	86	4	65	33	4	15	46	1.66
7278310--7278355	21	2.2	21	84	7	58	28	8	0	63	1.24
7278603--7278651	24	2.0	24	88	8	71	30	8	4	57	1.47
7279316--7279510	98	2.0	98	94	0	345	28	9	24	37	1.87
7281047--7281093	19	2.5	20	86	6	71	38	0	2	59	1.09
7281041--7281117	24	3.2	24	67	10	59	35	0	1	63	1.03
7281090--7281131	20	2.2	20	86	4	59	38	0	0	61	0.96
7285185--7285212	3	9.3	3	100	0	56	0	35	0	64	0.94
7289603--7289634	7	4.7	7	96	3	57	53	0	0	46	1.00
7290182--7290244	19	3.3	19	84	6	74	57	1	0	41	1.08
7290187--7290240	28	1.9	28	85	14	76	53	1	0	44	1.11
7290187--7290243	9	6.1	9	76	15	53	56	1	0	42	1.10
7290295--7290339	17	2.6	17	82	6	56	53	0	2	44	1.13
7290632--7290671	21	1.9	21	90	10	64	55	7	12	25	1.63
7291096--7291162	3	22.3	3	100	0	134	0	32	0	67	0.91
7293594--7293734	42	3.1	45	69	19	130	35	25	9	29	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7294981--7295007	5	5.4	5	100	0	54	0	0	81	18	0.69
7309677--7309719	20	2.2	20	83	4	52	41	11	9	37	1.74
7312541--7312581	3	13.7	3	89	0	64	26	0	4	68	1.10
7317780--7317823	17	2.6	17	96	0	79	40	18	0	40	1.50
7318417--7318473	30	1.9	30	85	0	78	14	31	33	21	1.92
7324005--7324270	135	2.0	135	90	0	424	34	13	26	25	1.93
7324290--7324401	18	6.4	18	84	7	133	60	1	35	1	1.17
7324290--7324379	3	30.0	3	93	0	153	63	0	36	0	0.95
7325920--7325957	19	2.0	19	100	0	76	36	21	15	26	1.93
7327196--7327248	9	5.6	10	82	6	58	26	0	1	71	0.96

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