genome.fa.s9.2.7.7.80.10.50.1000.174.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  174  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)
55694317--55694528	85	2.5	85	96	0	390	33	24	18	23	1.96
55694317--55694528	43	5.0	43	82	10	267	33	24	18	23	1.96
55694540--55694728	51	3.7	50	81	5	220	32	27	16	23	1.96
55694538--55694722	101	1.8	102	88	5	286	32	27	17	23	1.96
55694533--55694722	102	1.9	102	86	5	260	32	26	16	23	1.96
55697279--55697405	49	2.6	48	81	4	150	31	25	14	28	1.95
55699501--55699712	85	2.5	85	95	0	372	34	24	17	23	1.96
55699501--55699712	43	5.0	43	80	10	249	34	24	17	23	1.96
55699724--55699912	51	3.7	50	81	5	220	32	27	16	23	1.96
55699722--55699906	101	1.8	102	88	5	286	32	27	17	23	1.96
55699716--55699906	102	1.9	102	86	5	262	32	26	17	23	1.96
55704055--55704089	15	2.4	15	90	4	54	48	0	8	42	1.33
55706394--55706438	19	2.4	19	82	14	58	17	20	0	62	1.33
55725328--55725387	26	2.3	26	82	0	66	30	20	30	20	1.97
55740158--55740193	16	2.2	17	90	5	56	25	38	16	19	1.92
55740928--55741041	58	1.9	59	87	5	169	49	8	2	39	1.48
55746282--55746546	131	2.0	131	95	0	476	36	24	12	25	1.91
55748700--55748770	15	4.5	15	70	16	54	22	2	15	59	1.49
55748658--55748735	9	8.4	9	71	10	59	20	2	14	62	1.42
55750594--55750618	10	2.5	10	100	0	50	16	0	0	84	0.63
55754924--55755233	43	7.2	43	78	3	302	30	30	15	23	1.96
55754924--55755233	86	3.6	86	84	0	361	30	30	15	23	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55754926--55755233	129	2.4	128	80	2	339	30	30	15	23	1.95
55755261--55755314	22	2.3	23	81	9	65	44	0	7	48	1.31
55756964--55757021	24	2.4	24	91	0	98	29	15	15	39	1.88
55757538--55757595	29	2.0	29	96	0	107	25	13	15	44	1.83
55760212--55760243	13	2.3	15	89	10	50	56	0	0	43	0.99
55760918--55760961	7	6.3	7	84	10	63	45	38	0	15	1.47
55760918--55761110	14	13.4	14	68	11	68	45	32	1	21	1.59
55761417--55761689	41	6.8	41	86	5	353	30	28	20	20	1.98
55761420--55761689	81	3.3	80	87	6	352	30	28	20	20	1.97
55761744--55761819	40	1.9	40	83	2	100	25	22	19	32	1.97
55764733--55764797	19	3.4	19	69	12	60	55	10	3	30	1.50
55764720--55764799	39	2.1	39	92	0	133	52	10	6	31	1.59
55766361--55767230	436	2.0	435	95	0	1551	26	23	14	35	1.94
55771089--55771125	3	12.3	3	100	0	74	32	0	0	67	0.91
55775945--55776472	87	6.1	87	89	0	745	24	23	22	29	1.99
55777714--55777739	13	2.0	13	100	0	52	15	15	0	69	1.20
55778122--55778194	27	2.6	27	84	6	83	8	9	9	72	1.28
55778102--55778180	30	2.6	30	73	18	81	10	12	6	70	1.32
55778138--55778200	33	1.9	33	87	6	92	6	9	7	76	1.16
55778117--55778215	33	2.9	34	73	5	85	10	7	11	71	1.30
55783104--55783150	18	2.6	18	96	0	85	63	17	0	19	1.30
55785690--55785723	18	1.9	17	88	5	50	38	0	2	58	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55785694--55785767	24	3.2	24	64	14	66	40	4	2	52	1.34
55789184--55789305	63	1.9	64	94	1	219	34	18	5	41	1.74
55795754--55795986	40	5.8	39	78	4	200	21	27	14	37	1.92
55795751--55795999	80	3.1	80	80	4	288	21	27	14	36	1.92
55795754--55795985	120	1.9	120	85	5	317	21	27	14	37	1.92
55801898--55801952	21	2.6	21	97	0	101	18	30	32	18	1.95
55808335--55808392	25	2.4	24	80	11	73	63	1	1	32	1.14
55809933--55809984	16	3.2	16	88	0	77	40	3	30	25	1.73
55809970--55810058	44	2.0	46	91	4	146	28	5	29	37	1.80
55809970--55810071	39	2.4	44	82	12	124	29	4	30	35	1.79
55810218--55810270	18	3.0	17	91	5	79	56	1	1	39	1.21
55820052--55820101	26	2.0	24	84	7	64	56	2	6	36	1.36
55820072--55820121	14	3.4	14	76	15	55	60	8	2	30	1.37
55820072--55820131	31	2.0	30	90	3	93	60	8	1	30	1.36
55822075--55822173	39	2.5	39	86	0	135	43	21	5	30	1.74
55823395--55823446	21	2.4	22	78	15	54	44	11	13	30	1.79
55827981--55828010	12	2.5	12	94	0	51	23	40	26	10	1.86
55829065--55829122	29	2.0	29	100	0	116	41	10	6	41	1.66
55830992--55831591	298	2.0	298	99	0	1191	36	7	13	42	1.73
55840089--55840254	48	3.5	48	91	0	278	24	29	19	27	1.98
55845873--55845908	3	12.0	3	100	0	72	66	0	0	33	0.92
55846389--55846522	41	3.3	41	89	2	207	19	20	26	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55846533--55846624	41	2.2	41	80	0	112	19	17	25	38	1.93
55846421--55846624	104	2.0	103	83	4	259	19	17	24	38	1.92
55847002--55847029	14	2.0	14	100	0	56	28	0	35	35	1.58
55847358--55847421	14	4.4	15	76	4	51	18	1	43	35	1.60
55847353--55847407	22	2.5	22	79	2	58	21	1	40	36	1.64
55847376--55847409	14	2.4	14	90	9	52	23	2	44	29	1.68
55847017--55847832	305	2.6	301	84	8	939	28	2	26	43	1.67
55847866--55847896	2	15.5	2	93	0	53	48	3	0	48	1.17
55848146--55848184	19	2.1	18	85	4	51	76	2	2	17	1.01
55848179--55848277	47	2.1	48	86	1	137	43	9	1	46	1.42
55849906--55849930	13	1.9	13	100	0	50	32	8	16	44	1.76
55849961--55849987	14	1.9	14	100	0	54	29	11	7	51	1.64
55850501--55850585	23	3.7	24	77	17	99	43	5	3	47	1.44
55850501--55850595	23	4.2	22	78	15	88	43	5	3	48	1.41
55850499--55850593	46	2.1	43	88	9	138	42	5	4	48	1.45
55850723--55850747	12	2.1	12	100	0	50	52	16	0	32	1.44
55850770--55851007	9	28.3	9	68	19	140	45	21	2	29	1.66
55850770--55850908	63	2.4	56	77	21	160	46	20	4	28	1.69
55850788--55850965	63	2.8	63	85	6	225	47	20	3	28	1.66
55850789--55850965	34	5.4	33	78	9	175	46	20	3	28	1.67
55850799--55851006	25	8.4	25	71	17	100	45	22	2	29	1.67
55850770--55850987	25	8.3	25	73	15	92	45	21	3	29	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55850975--55851134	66	2.5	62	80	9	171	46	18	0	33	1.54
55851758--55851792	18	2.0	17	88	5	52	54	0	0	45	0.99
55851645--55851963	159	2.0	157	94	1	557	44	3	4	47	1.39
55852016--55852058	15	2.8	16	82	10	63	55	0	0	44	0.99
55851897--55852432	120	4.5	120	95	1	916	49	5	2	42	1.39
55852136--55852187	15	3.6	15	80	12	56	53	1	0	44	1.11
55852256--55852307	15	3.6	15	80	12	56	53	1	0	44	1.11
55852564--55852737	92	1.9	92	85	7	246	47	4	4	44	1.42
55873539--55873914	142	2.7	142	90	0	583	31	18	22	27	1.97
55874478--55874515	20	1.9	20	88	0	58	71	2	18	7	1.23
55876655--55876708	27	2.0	27	100	0	108	33	7	14	44	1.73
55880169--55880205	17	2.2	17	90	0	56	45	24	5	24	1.74
55880926--55880982	26	2.1	27	87	9	82	26	7	7	59	1.49
55891809--55891856	19	2.5	20	80	12	66	70	4	8	16	1.27
55904282--55904355	27	2.7	28	83	8	82	27	20	29	22	1.98
55915360--55915404	21	2.1	23	88	12	69	26	8	13	51	1.70
55920948--55920998	20	2.5	20	100	0	102	9	15	41	33	1.80
55922437--55922483	24	2.0	24	95	0	85	36	19	21	23	1.95
55926917--55926955	18	2.2	17	86	13	53	33	0	20	46	1.51
55927184--55927276	23	4.0	23	95	0	168	20	21	27	30	1.98
55927184--55927276	46	2.0	46	100	0	186	20	21	27	30	1.98
55935400--55935523	66	1.9	66	93	3	214	41	4	25	29	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55937383--55937411	14	2.0	15	93	6	51	68	0	0	31	0.89
55940668--55940753	13	6.6	13	72	7	59	18	2	5	73	1.15
55940753--55940794	19	2.1	21	82	8	52	9	14	7	69	1.37
55943896--55943939	22	2.0	22	100	0	88	36	9	31	22	1.86
55948184--55948244	30	2.0	30	96	0	113	29	19	14	36	1.92
55949276--55949306	16	1.9	16	93	0	53	41	9	0	48	1.36
55961509--55961551	19	2.5	16	85	14	59	60	0	2	37	1.10
55962167--55962228	24	2.7	22	80	11	70	48	30	1	19	1.58
55962358--55962401	2	22.0	2	95	0	79	0	52	0	47	1.00
55963126--55963264	2	69.5	2	100	0	278	0	49	0	50	1.00

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