genome.fa.s9.2.7.7.80.10.50.1000.125.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  125  of  226  ( 27023 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)
42099571--42099596	4	6.5	4	100	0	52	73	0	0	26	0.84
42103763--42103865	44	2.3	44	81	3	118	23	23	24	29	1.99
42104111--42104442	87	3.8	87	93	0	547	25	23	21	29	1.99
42104246--42104382	43	3.2	43	62	20	104	24	23	24	27	2.00
42108660--42108727	34	2.0	34	88	0	100	30	11	26	30	1.92
42110855--42110948	44	2.1	44	92	0	152	26	15	19	38	1.92
42121629--42121685	23	2.4	23	85	2	69	21	3	47	28	1.67
42123662--42123729	26	2.6	26	92	0	118	38	20	23	17	1.93
42123936--42124078	27	5.3	28	84	5	179	20	18	18	41	1.90
42132115--42132252	28	5.0	28	80	3	136	30	23	23	23	1.99
42132134--42132252	54	2.2	55	84	3	159	32	21	21	23	1.98
42132372--42132464	26	3.6	26	82	5	107	35	16	24	23	1.95
42132403--42132465	26	2.4	26	94	0	108	38	14	20	26	1.91
42132658--42132809	27	5.6	27	89	0	223	20	18	21	39	1.93
42135324--42135360	9	4.1	9	89	0	56	45	10	10	32	1.74
42135599--42135657	29	2.1	29	87	3	84	20	47	0	32	1.50
42152253--42152375	26	5.0	26	67	19	84	18	19	20	41	1.91
42159007--42159163	26	6.3	26	67	16	100	21	20	20	38	1.94
42160937--42160990	28	1.9	28	96	0	99	24	11	1	62	1.37
42169102--42169253	27	5.7	26	82	4	133	39	21	18	21	1.93
42169102--42169469	54	6.8	53	79	6	271	38	20	18	22	1.93
42169154--42169493	27	12.6	27	82	2	310	39	20	18	22	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42169124--42169513	54	7.2	54	76	9	201	38	19	18	22	1.93
42169102--42169513	27	15.3	27	74	10	131	38	19	18	22	1.93
42169584--42169641	24	2.4	24	82	5	73	18	6	24	50	1.72
42169705--42169755	27	1.9	26	88	11	77	17	29	25	27	1.98
42169760--42169813	26	2.1	26	89	0	81	16	24	27	31	1.96
42169803--42169943	32	4.5	31	84	5	158	21	21	19	36	1.95
42171144--42171190	23	2.0	23	91	0	76	23	23	12	40	1.89
42181753--42181816	27	2.4	26	89	2	92	40	3	4	51	1.38
42189281--42189327	15	3.3	15	71	17	55	44	6	19	29	1.75
42189276--42189327	27	1.9	27	100	0	104	40	5	23	30	1.78
42216761--42216944	92	2.0	92	94	0	323	26	22	13	38	1.90
42224485--42224524	19	2.1	19	86	9	55	72	2	0	25	0.97
42225370--42225441	31	2.3	31	80	0	81	38	13	13	33	1.85
42229446--42229487	20	2.1	20	86	0	57	47	0	7	45	1.30
42236799--42236851	21	2.5	21	90	0	79	32	37	9	20	1.85
42247968--42248015	20	2.6	18	83	6	51	33	2	2	62	1.18
42248035--42248063	10	3.0	10	95	5	51	27	0	10	62	1.28
42254158--42254192	13	2.7	13	90	0	52	45	0	11	42	1.40
42255255--42255296	14	2.9	14	85	7	57	16	2	2	78	0.96
42256066--42256103	11	3.2	13	82	17	55	73	7	5	13	1.22
42268017--42268102	29	3.0	29	89	0	136	29	23	18	29	1.98
42270496--42270529	14	2.5	14	95	4	61	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42270592--42270622	10	2.9	11	90	9	55	54	0	0	45	0.99
42270591--42270625	16	2.2	16	89	0	52	54	0	0	45	0.99
42275376--42275499	43	2.8	45	78	11	132	37	15	18	28	1.91
42277595--42277634	17	2.4	17	87	4	55	25	0	2	72	0.97
42281866--42281895	13	2.4	13	94	5	53	63	6	0	30	1.20
42291713--42291747	16	2.1	17	89	5	54	42	0	11	45	1.40
42294033--42294177	49	3.0	50	80	13	176	50	2	6	41	1.39
42297184--42297225	21	2.0	21	90	9	68	61	4	9	23	1.45
42298128--42298225	35	2.8	35	95	0	169	12	12	30	44	1.78
42308680--42308818	32	4.4	31	76	9	104	38	20	19	21	1.94
42308694--42308814	64	1.9	64	81	3	145	36	21	19	22	1.95
42308695--42308820	32	3.9	32	75	6	121	37	21	19	22	1.94
42308837--42308882	14	3.4	14	70	11	51	36	26	23	13	1.91
42308821--42308889	26	2.7	26	95	0	129	33	28	24	13	1.93
42309015--42309099	24	3.5	24	87	3	100	47	20	7	25	1.75
42309124--42309333	27	7.9	27	78	4	192	21	20	21	35	1.96
42309125--42309317	53	3.6	53	78	2	172	20	21	23	34	1.97
42309124--42309329	80	2.6	79	78	7	227	21	20	22	35	1.96
42331350--42331404	27	2.0	27	100	0	110	41	14	14	29	1.85
42333369--42333513	73	2.0	73	89	2	220	42	13	19	25	1.87
42334861--42334887	3	9.0	3	100	0	54	0	0	66	33	0.92
42336115--42336204	27	3.4	27	95	3	164	42	10	0	47	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42336270--42336366	27	3.6	26	91	2	131	25	23	29	20	1.99
42336554--42336606	22	2.4	21	75	9	52	37	0	9	52	1.34
42336598--42336663	19	3.5	19	79	4	89	37	10	1	50	1.47
42336744--42336908	82	2.0	82	98	0	321	45	10	6	38	1.63
42336977--42337072	19	5.2	18	77	14	97	47	1	13	37	1.50
42336985--42337072	37	2.4	37	100	0	176	48	0	13	37	1.43
42336985--42337072	18	4.7	19	78	5	108	48	0	13	37	1.43
42337805--42337868	29	2.2	29	91	2	103	51	0	6	42	1.27
42338220--42338269	16	3.2	16	70	16	50	54	4	0	42	1.19
42338224--42338292	31	2.3	30	89	2	102	56	2	0	40	1.14
42338644--42338677	16	2.1	17	88	5	52	29	20	0	50	1.49
42347416--42347446	16	1.9	16	93	0	53	35	3	9	51	1.51
42359119--42359152	10	3.4	10	91	0	50	70	2	0	26	1.01
42360128--42360157	15	2.0	15	100	0	60	20	40	0	40	1.52
42361502--42361542	20	2.0	20	100	0	82	24	9	19	46	1.80
42362079--42362125	17	2.6	18	86	10	69	65	0	0	34	0.93
42362089--42362118	8	3.6	8	91	8	51	66	0	0	33	0.92
42372569--42372615	10	4.6	10	85	12	51	61	4	0	34	1.15
42376279--42376328	20	2.7	19	77	20	52	52	0	4	44	1.20
42376285--42376332	25	1.9	25	83	8	62	52	0	4	43	1.20
42376296--42376385	37	2.4	37	82	12	103	52	2	2	43	1.26
42379982--42380159	66	2.8	65	81	10	204	31	23	19	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42384977--42385015	11	3.2	12	86	10	53	61	15	0	23	1.33
42386478--42386538	30	2.0	30	84	9	79	32	45	3	18	1.65
42387439--42387463	12	2.1	12	100	0	50	32	12	8	48	1.69
42387482--42387547	13	5.5	13	71	20	63	37	0	13	48	1.43
42387479--42387547	23	3.0	23	95	0	120	39	0	13	47	1.42
42389095--42389165	36	2.0	36	94	0	124	47	12	11	28	1.76
42393348--42393418	36	2.0	36	94	0	124	47	12	11	28	1.76
42395318--42395371	22	2.3	24	75	9	58	50	9	5	35	1.58
42400488--42400529	23	1.9	22	85	9	59	66	7	4	21	1.35
42402319--42402436	44	2.7	44	86	2	157	28	21	20	29	1.98
42402443--42402632	100	1.9	100	86	2	274	27	22	19	31	1.98
42402580--42402991	167	2.5	167	86	1	558	24	25	20	29	1.99
42403020--42403192	88	2.0	88	87	0	247	26	27	20	26	1.99
42415434--42415476	23	2.0	22	86	9	61	65	4	6	23	1.37
42418622--42418701	29	2.8	29	77	7	92	56	1	11	31	1.42
42420874--42420962	21	4.6	20	70	20	57	49	2	0	48	1.13
42420968--42421009	16	2.6	16	88	0	57	54	0	0	45	0.99
42421802--42421840	19	2.0	19	90	5	60	35	2	0	61	1.10
42421806--42421848	20	2.2	19	83	4	50	34	2	4	58	1.32
42423937--42423999	4	15.2	4	74	12	56	69	3	3	23	1.17
42423958--42423999	17	2.6	16	88	3	57	76	4	0	19	0.96
42426989--42427054	8	7.4	8	73	20	51	34	1	1	62	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42426977--42427071	19	5.3	18	75	16	72	31	2	3	63	1.22
42426977--42427054	9	8.6	9	71	18	54	33	2	1	62	1.17
42426990--42427054	17	3.7	17	77	16	53	35	1	1	61	1.15
42426989--42427071	26	3.1	28	78	14	86	32	1	3	62	1.20
42427109--42427153	21	2.1	21	84	8	56	35	4	6	53	1.47
42427122--42427162	21	2.0	21	90	0	64	39	2	7	51	1.43
42427989--42428080	46	2.0	46	95	0	166	33	11	14	40	1.82
42431016--42431049	18	1.9	17	88	5	50	32	2	2	61	1.26
42431656--42431724	28	2.5	27	75	11	68	60	2	1	34	1.20
42432165--42432236	22	3.3	22	94	0	117	25	27	16	30	1.97

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   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226