genome.fa.s1.2.7.7.80.10.50.1000.109.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  109  of  187  ( 22383 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)
32473739--32473879	61	2.4	58	86	9	198	39	10	14	34	1.81
32475231--32475427	98	2.0	98	95	0	358	29	10	23	37	1.88
32476502--32476546	22	2.0	22	100	0	90	37	4	26	31	1.76
32478657--32478695	21	1.9	21	84	5	53	23	10	5	61	1.48
32482761--32482863	37	2.8	38	85	7	142	26	16	17	39	1.90
32483684--32483715	15	2.1	15	100	0	64	43	25	6	25	1.77
32488805--32488884	29	2.7	30	78	3	90	32	11	18	37	1.87
32494903--32494978	40	1.9	40	97	0	143	32	1	17	48	1.55
32496755--32496848	9	10.4	9	85	4	127	25	11	23	39	1.88
32513561--32513590	14	2.1	14	93	0	51	60	0	0	40	0.97
32517816--32518019	41	5.0	41	85	0	273	23	26	21	28	1.99
32517827--32518019	82	2.4	82	90	0	305	22	26	21	29	1.99
32517818--32518049	41	5.7	40	75	15	190	23	25	21	29	1.99
32517825--32518049	123	1.8	123	85	5	321	22	26	21	29	1.99
32517949--32518062	41	2.8	41	84	7	108	21	24	23	29	1.99
32517820--32518049	82	2.8	81	83	6	286	23	26	21	29	1.99
32520423--32520504	19	4.3	19	80	0	56	20	26	25	26	1.99
32520946--32520995	24	2.1	24	96	0	91	50	16	6	28	1.68
32532693--32532746	21	2.6	21	83	13	60	24	5	1	68	1.21
32533203--32533249	3	15.7	3	100	0	94	31	0	0	68	0.90
32533248--32533272	13	1.9	13	100	0	50	40	0	0	60	0.97
32533251--32533297	24	2.0	24	87	8	69	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32533249--32533309	20	3.2	18	73	11	52	40	3	0	55	1.16
32533289--32533470	87	2.0	95	83	12	238	48	3	3	43	1.37
32533895--32533919	13	1.9	13	100	0	50	64	4	0	32	1.12
32537313--32537364	27	1.9	27	84	7	70	67	3	7	21	1.32
32538043--32538080	13	3.0	13	96	3	69	31	0	0	68	0.90
32538320--32538368	20	2.5	19	80	6	53	67	12	10	10	1.43
32538326--32538369	20	2.2	20	87	0	61	68	11	11	9	1.40
32539198--32539234	19	1.9	19	88	0	56	40	0	5	54	1.24
32543615--32543696	18	4.6	18	92	0	128	13	41	3	41	1.62
32550608--32550652	22	2.0	22	95	0	81	42	4	33	20	1.72
32553002--32553051	25	2.0	26	88	4	75	66	12	10	12	1.46
32557338--32557375	4	9.5	4	88	0	58	26	5	0	68	1.11
32569596--32570267	50	13.5	50	69	10	435	33	25	19	21	1.97
32569545--32570371	99	8.3	99	91	1	1207	32	25	20	22	1.98
32572171--32572208	4	9.5	4	88	0	58	26	5	0	68	1.11
32573488--32573540	19	2.7	21	74	14	58	37	0	1	60	1.08
32576588--32576638	24	2.2	24	77	22	56	33	0	5	60	1.21
32576796--32576862	34	1.9	35	87	3	100	46	14	7	31	1.73
32585555--32585697	41	3.5	41	90	1	209	30	20	18	31	1.96
32585560--32585713	82	1.9	81	85	5	211	30	19	19	30	1.96
32585820--32585935	61	1.9	61	82	3	144	37	18	9	35	1.83
32586327--32586355	2	14.5	2	100	0	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32588670--32588864	75	2.6	75	86	1	257	29	16	22	31	1.96
32605948--32605997	22	2.3	22	80	13	59	40	0	0	60	0.97
32609903--32610046	76	1.9	75	79	1	162	29	9	21	39	1.85
32618480--32618709	120	1.9	120	92	0	388	25	14	18	41	1.89
32631743--32631798	24	2.3	25	84	12	80	16	33	0	50	1.45
32633050--32633074	13	1.9	13	100	0	50	24	20	16	40	1.91
32636534--32636605	35	2.1	35	94	0	126	40	12	23	23	1.89
32642654--32642687	14	2.4	14	90	0	50	41	8	0	50	1.34
32645680--32645729	18	3.0	17	85	8	59	42	0	2	56	1.11
32645640--32645943	47	6.7	43	66	19	136	45	2	3	47	1.36
32645645--32645943	91	3.3	91	96	0	535	46	3	3	47	1.35
32645959--32646252	120	2.4	120	88	2	410	41	4	6	46	1.51
32646032--32646221	61	3.1	61	67	14	176	42	2	6	48	1.42
32646082--32646116	18	2.0	17	88	5	52	45	0	0	54	0.99
32646034--32646253	120	1.8	120	97	0	413	43	2	5	48	1.39
32646215--32646256	15	2.7	16	82	14	52	45	0	2	52	1.13
32646206--32646247	15	2.9	15	82	10	52	47	0	0	52	1.00
32646468--32646518	16	3.2	16	88	0	75	23	27	5	43	1.77
32655149--32655199	2	25.5	2	95	0	93	0	47	0	52	1.00
32661763--32661793	16	1.9	16	93	0	53	45	22	22	9	1.81
32665356--32665385	15	2.0	15	100	0	60	26	26	20	26	1.99
32666096--32666152	25	2.3	25	90	0	87	21	19	22	36	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32667458--32667500	21	2.0	21	95	0	77	13	30	18	37	1.90
32668516--32668579	2	33.5	2	90	9	107	51	0	0	48	1.00
32672536--32672564	8	3.6	8	100	0	58	24	13	27	34	1.93
32672651--32672726	23	3.3	23	94	0	134	22	21	25	31	1.98
32676225--32676276	16	3.0	16	75	13	50	50	0	25	25	1.50
32676634--32676670	9	4.1	9	85	0	56	32	10	10	45	1.74
32680024--32680087	21	3.0	21	90	0	101	15	29	17	37	1.91
32681316--32681724	50	8.2	50	82	4	423	20	16	26	35	1.94
32684045--32684233	40	4.7	38	81	8	207	34	18	3	43	1.66
32684045--32684242	80	2.5	79	89	0	297	35	18	3	42	1.65
32684045--32684176	13	9.9	13	70	14	90	34	20	3	41	1.68
32688786--32688824	21	2.0	20	90	10	62	20	7	15	56	1.63
32689397--32689442	20	2.3	20	85	10	60	43	17	13	26	1.85
32690566--32690615	25	2.0	25	85	14	68	38	22	0	40	1.54
32691053--32691086	2	17.0	2	100	0	68	50	0	0	50	1.00
32691809--32691858	16	3.1	16	79	0	55	16	10	6	68	1.38
32696981--32697022	22	1.9	22	100	0	84	26	14	14	45	1.83
32719970--32720001	5	6.4	5	100	0	64	0	0	18	81	0.70
32726772--32726907	68	2.0	68	97	0	254	41	13	21	22	1.88
32728678--32728710	17	2.0	17	88	5	50	15	0	21	63	1.30
32731161--32731239	39	2.0	39	97	0	149	45	15	11	27	1.80
32731160--32731226	17	3.6	17	72	18	62	46	13	11	28	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32732738--32732784	20	2.3	20	78	7	51	29	29	14	25	1.95
32734299--32734327	14	2.1	14	93	6	51	75	6	3	13	1.13
32734320--32734371	14	3.8	13	78	14	52	78	1	15	3	0.98
32734327--32734379	16	3.4	15	75	14	54	73	1	18	5	1.12
32735440--32735486	15	3.1	15	84	9	60	70	0	17	12	1.17
32735516--32735555	12	3.3	12	82	0	53	60	2	22	15	1.47
32737428--32737474	20	2.3	20	85	7	60	27	29	17	25	1.97
32740685--32740763	39	2.0	39	90	0	122	45	12	11	30	1.77
32745532--32745557	13	2.0	13	100	0	52	30	30	23	15	1.95
32748292--32748423	43	3.1	42	88	6	203	20	29	21	28	1.98
32748932--32748993	25	2.4	26	89	2	90	40	1	14	43	1.55
32748932--32749003	17	4.2	17	72	13	58	40	1	13	44	1.53
32749096--32749155	17	3.5	17	75	8	59	36	1	16	45	1.58
32749099--32749182	34	2.3	36	86	8	109	34	1	16	47	1.55
32749123--32749279	46	3.3	46	70	15	145	33	1	17	47	1.56
32749099--32749155	9	6.8	8	76	7	51	33	1	17	47	1.58
32749129--32749184	17	3.1	17	74	18	58	37	0	14	48	1.44
32752613--32753488	147	6.1	146	88	7	1326	24	15	14	44	1.85
32752768--32753481	281	2.5	283	87	7	1027	24	16	15	43	1.86
32753585--32753618	14	2.4	14	90	9	52	32	44	0	23	1.54
32753645--32753691	15	3.3	15	79	8	53	38	31	2	27	1.69
32753934--32754117	73	2.5	73	98	0	350	23	28	22	25	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32754013--32754336	114	2.9	112	87	3	456	25	26	23	23	2.00
32754673--32754711	20	2.0	20	90	9	64	66	0	0	33	0.92
32754894--32754965	9	7.8	9	74	11	65	34	2	38	23	1.70
32755495--32755555	20	3.1	19	83	9	61	68	4	1	24	1.18
32756283--32756311	2	14.5	2	100	0	58	51	0	0	48	1.00
32766133--32766191	27	2.2	27	84	0	82	35	11	22	30	1.90
32766140--32766213	27	2.7	26	85	4	85	29	12	24	33	1.91
32766330--32766380	26	2.0	26	84	7	68	37	5	23	33	1.79
32777862--32778159	29	10.4	29	77	2	253	36	21	16	25	1.93
32777922--32778137	88	2.5	86	82	3	270	38	21	14	25	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   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187