genome.fa.s9.2.7.7.80.10.50.1000.188.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  188  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)
59718114--59718157	18	2.4	19	92	3	72	40	0	59	0	0.98
59718114--59718166	24	2.2	24	86	0	70	41	0	58	0	0.98
59718477--59718532	21	2.7	21	88	0	76	33	7	30	28	1.84
59719450--59719517	11	6.2	11	90	8	86	22	33	0	44	1.53
59719450--59719517	33	2.1	33	86	10	95	22	33	0	44	1.53
59719523--59719582	29	2.2	27	85	8	77	41	0	5	53	1.23
59720689--59720714	7	3.7	7	100	0	52	26	0	15	57	1.38
59721227--59721308	30	2.7	30	79	7	85	32	47	12	7	1.68
59721361--59721403	18	2.4	18	92	0	68	16	27	9	46	1.77
59721661--59721701	21	2.0	21	85	0	55	29	34	24	12	1.91
59725413--59725464	20	2.6	20	90	0	86	46	21	3	28	1.69
59726697--59726744	19	2.6	19	90	3	80	20	20	25	33	1.97
59728392--59728428	13	2.8	13	83	0	56	62	8	13	16	1.54
59747729--59747821	46	2.0	46	81	4	107	36	12	15	35	1.85
59748938--59749107	45	3.8	45	84	2	180	21	22	14	41	1.90
59749586--59749627	22	1.9	22	85	9	59	59	2	4	33	1.31
59750460--59750523	13	4.9	13	75	3	58	51	0	10	37	1.37
59752229--59752292	25	2.6	26	78	7	71	29	21	23	25	1.99
59763455--59763484	15	2.0	15	93	0	51	40	16	23	20	1.91
59767589--59768365	396	2.0	396	97	0	1482	31	14	16	38	1.88
59768414--59768458	23	1.9	24	90	4	74	46	6	4	42	1.50
59770096--59770171	38	2.0	38	100	0	152	18	18	7	55	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59775990--59776030	2	20.5	2	100	0	82	51	0	0	48	1.00
59782802--59782864	30	2.1	30	96	0	117	33	9	22	34	1.86
59802048--59802599	138	4.0	138	93	1	887	45	5	8	40	1.57
59802048--59802599	275	2.0	273	91	1	881	45	5	8	40	1.57
59802580--59802722	75	1.9	75	91	2	234	31	15	10	42	1.81
59804056--59804100	20	2.2	21	92	7	76	44	11	0	44	1.39
59804025--59804161	75	1.9	71	98	0	229	42	9	9	38	1.70
59807468--59807517	25	2.0	25	92	0	82	18	30	24	28	1.97
59814653--59814811	27	6.0	27	79	5	153	43	18	16	20	1.88
59814666--59814811	53	2.8	52	81	8	170	42	18	18	20	1.89
59814668--59814811	26	5.4	26	83	8	141	42	18	18	20	1.90
59814788--59814924	27	5.1	27	80	1	150	37	18	21	22	1.94
59814788--59814923	53	2.5	53	83	1	173	37	19	21	22	1.94
59814988--59815046	24	2.5	24	83	5	75	22	6	23	47	1.75
59815111--59815153	21	2.1	20	91	4	68	11	25	30	32	1.91
59815211--59815395	32	5.8	32	81	2	149	19	21	23	35	1.96
59815210--59815424	32	6.8	32	78	5	143	19	22	21	36	1.95
59818516--59818594	41	1.9	42	82	12	101	48	5	22	24	1.71
59824230--59824280	25	2.0	25	84	7	66	54	9	0	35	1.33
59829397--59829477	42	1.9	42	87	5	119	45	3	23	27	1.69
59834104--59834143	16	2.5	17	88	8	57	40	7	22	30	1.81
59834125--59834217	44	2.1	44	88	6	134	35	4	23	36	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59834329--59834445	55	2.1	54	81	7	128	49	4	0	45	1.27
59834684--59834729	23	2.0	24	100	0	78	52	13	0	34	1.40
59840321--59840441	23	5.3	23	80	4	145	20	20	26	32	1.97
59840320--59840441	46	2.7	46	89	0	181	21	20	26	31	1.98
59840555--59840607	13	4.1	13	80	0	70	30	7	28	33	1.85
59844537--59844578	18	2.3	18	80	8	50	40	2	2	54	1.26
59844502--59844558	25	2.3	25	79	8	64	31	0	1	66	1.02
59847555--59847584	14	2.1	15	93	6	53	46	0	30	23	1.52
59852258--59852315	30	1.9	30	89	0	89	36	5	25	32	1.78
59852652--59852901	50	4.9	51	79	5	213	27	21	27	24	1.99
59852652--59852902	100	2.5	101	80	5	256	27	21	27	23	1.99
59859665--59859893	50	4.5	50	78	7	194	28	23	25	22	1.99
59859665--59859912	100	2.4	102	80	7	245	27	22	26	23	1.99
59870445--59870474	14	2.1	14	93	0	51	30	0	0	70	0.88
59870742--59870779	3	12.7	3	88	0	58	34	28	0	36	1.58
59881710--59882134	210	2.0	210	96	0	787	34	22	12	30	1.91
59885493--59885637	50	2.9	50	84	0	173	25	21	29	23	1.99
59905684--59905753	31	2.3	31	95	2	124	40	22	10	27	1.86
59906541--59906569	15	1.9	15	100	0	58	31	13	27	27	1.94
59912498--59912594	49	2.0	49	89	0	149	44	8	16	30	1.77
59915486--59915526	2	20.5	2	100	0	82	48	0	0	51	1.00
59919008--59919050	22	2.0	22	86	9	61	55	0	6	37	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59919014--59919062	10	4.5	11	74	20	50	63	0	2	34	1.06
59919273--59919307	12	2.8	13	86	8	54	54	0	0	45	0.99
59919574--59919614	22	1.9	21	90	5	64	58	0	2	39	1.11
59922492--59922548	30	1.9	30	89	7	89	40	3	10	45	1.56
59923289--59923330	22	1.9	22	85	9	59	76	7	14	2	1.10
59925511--59925556	22	2.1	22	95	0	83	26	30	21	21	1.99
59928210--59928248	16	2.4	16	86	4	51	30	10	15	43	1.80
59936915--59937106	32	6.0	32	83	2	233	38	20	20	20	1.94
59937278--59937383	24	4.4	24	85	0	113	45	23	7	23	1.78
59937290--59937386	48	2.0	48	84	7	126	45	22	7	24	1.78
59937407--59937547	27	5.2	27	73	6	115	25	19	16	39	1.92
59938574--59938660	41	2.1	41	89	0	129	58	3	21	16	1.52
59938912--59938977	24	2.8	24	76	4	62	15	46	6	31	1.70
59940429--59940479	24	2.1	24	92	7	86	21	27	0	50	1.48
59940420--59940479	24	2.8	20	73	26	68	21	30	0	48	1.51
59945427--59945511	33	2.6	33	88	1	127	25	8	52	12	1.67
59948632--59948665	3	11.3	3	87	12	52	29	2	0	67	1.05
59948620--59948658	15	2.6	15	95	0	69	25	5	0	69	1.09
59959331--59959373	21	2.0	21	100	0	86	32	4	23	39	1.75
59959577--59959746	41	4.1	41	86	1	189	22	26	15	34	1.95
59974271--59974316	23	2.0	23	83	8	58	32	8	15	43	1.77
59976222--59976278	23	2.5	23	97	0	105	35	19	0	45	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
59981196--59981459	40	6.6	40	84	2	298	21	29	15	33	1.95
59981138--59981406	120	2.2	119	83	3	335	22	29	15	32	1.95
59988370--59988431	26	2.4	26	89	5	90	33	14	12	38	1.84
60004220--60004292	30	2.5	30	88	6	105	42	6	2	47	1.44
60009232--60009564	171	1.9	171	90	0	531	27	15	26	30	1.96
60029641--60029680	21	1.9	22	90	10	66	55	2	10	32	1.47
60030321--60030382	30	2.1	30	87	6	90	48	11	8	32	1.68
60041015--60041164	38	3.9	38	80	0	174	38	28	17	15	1.90
60041016--60041164	76	2.0	76	84	0	199	38	28	16	15	1.90
60054918--60055082	40	4.1	40	87	2	224	29	19	23	27	1.98
60066134--60066408	7	38.6	7	67	12	60	22	1	31	45	1.59
60066159--60066351	86	2.2	85	95	1	341	23	1	30	44	1.60
60066134--60066408	14	19.3	14	67	14	89	22	1	31	45	1.59
60066306--60066438	7	18.7	7	71	9	63	19	0	37	42	1.57
60071666--60071764	43	2.3	43	92	0	162	23	14	25	37	1.92
60073604--60073780	50	3.5	49	74	15	130	35	21	20	22	1.96
60073637--60073734	25	4.0	25	77	1	99	35	19	21	23	1.96
60074378--60074416	5	7.6	5	82	5	51	41	17	0	41	1.50
60081538--60081658	25	4.9	25	82	3	115	35	16	27	20	1.94
60081595--60081658	24	2.7	24	97	2	121	40	15	25	18	1.90
60081745--60081812	26	2.7	25	84	4	91	33	23	26	16	1.95
60101436--60101650	107	2.0	107	100	0	430	40	12	26	21	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
60104949--60104998	27	1.9	25	84	8	64	44	4	28	24	1.72
60108985--60109065	28	3.0	26	75	8	81	64	2	0	33	1.07
60108976--60109068	8	13.0	7	71	18	50	63	2	0	34	1.07
60108965--60109093	62	2.1	61	81	8	145	64	2	2	31	1.19
60109576--60109627	19	2.7	19	81	16	63	32	1	1	63	1.16
60109579--60109627	10	5.1	10	79	13	50	34	2	2	61	1.19
60109576--60109626	9	5.4	9	82	15	59	31	1	1	64	1.15
60109512--60109634	29	4.5	27	71	16	78	31	4	2	60	1.30
60113919--60114088	29	5.8	29	82	6	191	36	12	28	21	1.91
60113914--60114088	59	3.0	59	85	8	225	36	13	29	21	1.92

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