genome.fa.s9.2.7.7.80.10.50.1000.122.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  122  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)
41320388--41320425	20	1.9	20	84	10	51	55	7	2	34	1.43
41321455--41321527	11	6.5	11	75	24	73	43	2	27	26	1.68
41321455--41321527	22	3.3	23	88	9	107	43	2	27	26	1.68
41321457--41321524	33	2.1	33	83	10	86	44	2	27	25	1.68
41334135--41334395	42	6.0	42	78	12	251	31	20	22	26	1.98
41334135--41334397	85	3.0	84	77	13	255	31	20	22	26	1.98
41334138--41334391	136	1.9	136	85	6	354	30	20	22	25	1.98
41334839--41334907	21	3.3	21	80	11	79	2	42	18	36	1.66
41337058--41337296	25	8.9	25	71	20	128	38	0	18	42	1.56
41337058--41337410	9	39.3	9	67	17	173	35	1	18	44	1.60
41337058--41337358	25	11.2	25	69	21	125	37	0	17	43	1.56
41337127--41337178	19	2.8	19	85	2	70	32	1	19	46	1.61
41337111--41337346	16	14.8	16	72	16	118	36	0	17	45	1.55
41340569--41340620	14	3.7	15	72	27	51	50	25	3	21	1.65
41340560--41340620	21	2.9	21	71	9	61	47	29	3	19	1.65
41340738--41340787	20	2.5	21	87	6	77	48	36	0	16	1.46
41341032--41341092	7	8.4	7	80	7	68	36	45	1	16	1.57
41341449--41341592	75	1.9	77	85	5	204	29	25	25	19	1.98
41341692--41341871	72	2.5	71	81	3	193	27	23	22	26	1.99
41347889--41347996	53	2.0	53	100	0	216	47	9	26	16	1.77
41349277--41349319	14	3.3	13	81	9	52	41	0	2	55	1.12
41349524--41349586	19	3.2	19	71	13	56	69	1	28	0	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41360190--41360337	44	3.4	44	88	0	206	28	20	22	28	1.99
41360190--41360523	88	3.8	87	82	4	269	29	21	23	25	1.99
41360307--41360523	88	2.5	88	90	0	328	29	21	23	25	1.99
41360313--41360523	44	4.8	44	81	3	264	30	22	22	24	1.99
41360456--41361092	216	2.9	216	85	3	836	29	20	22	26	1.99
41360900--41361109	84	2.4	86	76	10	221	29	21	22	26	1.99
41369595--41369726	44	3.0	45	79	8	137	22	19	13	43	1.86
41369609--41369726	45	2.7	43	79	11	123	23	19	12	44	1.85
41369933--41370136	109	1.9	109	98	0	399	42	19	1	35	1.63
41378129--41378166	13	2.9	13	80	11	51	57	5	0	36	1.21
41382239--41383197	482	2.0	484	94	0	1690	30	23	14	31	1.95
41387252--41387289	16	2.4	16	95	0	67	28	15	10	44	1.80
41388405--41388503	29	3.2	29	64	33	71	45	6	15	33	1.70
41388408--41388510	33	3.2	33	65	25	92	43	4	16	34	1.69
41388397--41388524	64	2.0	64	98	0	247	44	5	17	32	1.71
41389573--41389801	35	6.5	35	79	2	235	20	12	28	38	1.88
41389577--41389780	105	1.9	105	83	0	264	20	12	27	38	1.89
41397265--41397520	35	7.3	35	83	0	287	19	12	27	39	1.88
41403056--41403225	30	5.7	30	77	7	125	23	26	14	35	1.94
41403071--41403249	60	3.0	58	71	12	146	22	25	13	37	1.91
41403277--41403342	28	2.3	29	78	5	71	24	22	13	39	1.90
41403294--41403366	28	2.6	28	91	0	119	23	19	20	36	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41406281--41406342	25	2.5	25	81	0	79	24	19	22	33	1.97
41407716--41407740	10	2.5	10	100	0	50	12	24	28	36	1.91
41407770--41407803	16	2.1	16	100	0	68	44	11	11	32	1.77
41411569--41411763	3	66.0	3	71	9	64	27	9	2	60	1.40
41411610--41411698	43	2.1	42	85	6	117	25	12	1	60	1.39
41411723--41411763	20	2.0	20	90	0	64	29	7	2	60	1.36
41416231--41416287	24	2.4	23	83	16	73	77	5	17	0	0.95
41417235--41417669	134	3.2	134	90	1	658	27	16	25	29	1.97
41417646--41417995	134	2.6	134	85	2	445	28	15	26	30	1.96
41417422--41417893	224	2.1	224	88	0	703	27	15	25	30	1.96
41417816--41417982	89	1.9	89	81	5	203	28	15	26	29	1.96
41417295--41417995	358	2.0	358	89	1	1075	27	16	25	30	1.96
41417296--41417995	45	15.6	45	73	8	552	27	16	25	30	1.96
41418081--41418220	44	3.2	44	81	4	165	26	21	23	28	1.99
41418347--41418763	129	3.2	129	85	1	503	31	22	20	25	1.98
41418347--41418811	44	10.7	42	71	8	274	31	21	20	26	1.98
41418393--41418811	88	4.8	88	76	8	358	32	20	20	26	1.97
41420771--41420817	20	2.3	21	82	14	62	29	8	2	59	1.39
41420597--41420802	3	67.7	3	74	8	78	28	8	2	59	1.42
41423028--41423066	20	2.1	18	90	9	60	71	2	0	25	0.98
41423040--41423064	13	1.9	13	100	0	50	80	0	0	20	0.72
41423858--41423891	16	2.2	16	94	5	61	79	0	5	14	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41433354--41433411	24	2.4	24	91	0	89	29	24	12	34	1.91
41434351--41434387	11	3.5	11	79	20	51	2	21	0	75	0.92
41434345--41434392	13	3.6	14	78	18	57	4	22	0	72	1.01
41442200--41442226	2	13.5	2	100	0	54	0	48	0	51	1.00
41442845--41442883	20	2.0	20	94	0	69	48	0	2	48	1.15
41442983--41443020	20	1.9	20	100	0	76	44	15	7	31	1.75
41445324--41445353	15	1.9	16	93	6	53	73	0	16	10	1.09
41449038--41449188	74	2.0	74	92	0	248	25	21	26	26	2.00
41458009--41458249	50	4.7	50	76	4	198	27	21	26	24	1.99
41458460--41458497	16	2.4	16	86	0	58	60	2	23	13	1.45
41459902--41460100	47	4.2	47	75	11	158	27	14	25	32	1.95
41463015--41463044	16	1.9	16	93	6	53	50	20	0	30	1.49
41465300--41465366	32	2.1	31	83	2	80	50	2	4	41	1.37
41482638--41482725	42	2.1	42	100	0	176	25	19	6	48	1.73
41492224--41492271	12	4.4	11	78	17	55	27	0	2	70	0.98
41493375--41493409	17	2.0	18	88	5	54	17	45	17	20	1.85
41493815--41493879	6	10.5	6	81	6	67	13	1	6	78	1.01
41493802--41493861	15	4.0	14	75	14	57	13	1	6	78	1.02
41493821--41493879	25	2.4	24	81	13	66	15	0	6	77	0.96
41493802--41493870	31	2.1	33	82	12	81	14	1	7	76	1.06
41497919--41497951	2	17.0	2	93	6	59	51	0	0	48	1.00
41518473--41518515	6	7.2	6	97	0	59	9	0	55	34	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41522026--41522091	33	2.0	33	90	0	105	30	15	25	28	1.96
41528920--41528966	25	1.9	25	82	4	60	44	2	0	53	1.12
41529028--41529098	23	3.1	23	91	0	106	36	1	14	47	1.52
41529052--41529092	13	3.4	13	80	19	61	34	0	17	48	1.47
41532754--41532790	18	2.0	20	89	10	60	29	8	32	29	1.86
41532957--41533020	31	2.1	31	90	0	101	35	9	17	37	1.82
41538071--41538286	91	2.4	92	87	2	310	28	17	21	32	1.96
41541528--41541572	19	2.3	20	84	3	56	62	2	6	28	1.33
41542188--41542579	194	2.0	194	98	0	766	42	17	10	30	1.82
41545187--41545243	20	2.8	20	89	5	89	22	29	19	28	1.98
41554836--41554867	14	2.4	14	94	5	57	28	40	9	21	1.84
41560649--41560890	50	4.7	50	81	4	218	23	28	21	26	1.99
41561514--41561597	38	2.2	38	95	2	150	47	20	7	25	1.75
41567645--41567706	6	10.7	6	80	11	51	70	9	4	14	1.29
41567651--41567757	28	4.0	28	69	20	86	71	8	8	11	1.30
41567677--41567701	7	3.6	7	100	0	50	76	12	0	12	1.04
41567671--41567784	50	2.2	53	81	10	137	72	6	11	9	1.26
41568688--41568756	7	10.0	7	86	9	97	69	0	14	15	1.19
41568698--41568753	20	2.8	20	97	0	103	69	0	16	14	1.19
41568688--41568756	13	5.0	14	85	8	97	69	0	14	15	1.19
41570126--41570832	44	15.9	44	71	14	355	30	18	22	28	1.98
41570126--41570772	87	7.4	90	72	11	297	30	18	22	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41570040--41570780	219	3.4	219	92	1	1236	30	19	22	28	1.97
41570126--41570690	131	4.3	130	72	10	303	29	19	23	27	1.98
41570636--41571062	142	3.0	142	89	4	605	33	18	20	28	1.96
41570418--41570914	186	2.8	176	74	13	492	32	18	20	28	1.96
41570940--41571313	44	8.6	44	72	6	228	32	21	20	25	1.98
41571028--41571247	88	2.5	88	88	2	284	34	21	19	25	1.97
41570940--41571184	129	1.9	129	91	0	400	32	21	20	25	1.98
41571067--41571272	88	2.3	88	91	0	331	34	20	20	24	1.96
41573437--41573744	108	2.8	110	89	3	475	29	14	20	35	1.92
41574756--41574837	33	2.5	33	82	7	87	28	26	15	29	1.96

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   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