genome.fa.s9.2.7.7.80.10.50.1000.14.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  14  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)
6549624--6549696	9	8.0	9	72	17	53	60	0	1	38	1.06
6549601--6549733	41	3.3	40	89	6	207	60	0	2	36	1.15
6549588--6549721	11	13.1	11	71	21	80	56	0	2	40	1.17
6555859--6555886	14	2.0	14	100	0	56	35	7	21	35	1.81
6562389--6562488	41	2.5	40	82	6	116	33	25	16	26	1.96
6563367--6563423	4	14.0	4	82	14	64	1	19	1	77	0.95
6563368--6563421	19	2.9	18	83	8	65	1	18	1	77	0.95
6578410--6578452	20	2.1	21	86	4	61	48	11	0	39	1.40
6583915--6583948	18	1.9	18	88	5	52	32	14	11	41	1.82
6607152--6607191	21	1.9	21	85	10	55	32	0	0	67	0.91
6611119--6611182	32	2.1	32	82	11	80	48	10	0	40	1.38
6615999--6616224	96	2.3	96	83	5	260	42	3	14	39	1.61
6616265--6616565	126	2.4	126	89	0	449	32	18	21	26	1.97
6617982--6618180	107	1.9	107	94	2	355	30	18	18	33	1.94
6623444--6623675	46	5.0	46	88	2	340	37	9	24	28	1.87
6625501--6625548	21	2.3	21	78	7	53	6	18	39	35	1.76
6627676--6627721	11	4.1	11	85	2	56	47	0	26	26	1.52
6627673--6627732	22	2.7	21	82	12	68	48	0	26	25	1.52
6627682--6627730	12	4.2	12	82	17	59	46	0	28	24	1.53
6631777--6631816	2	20.5	2	94	5	73	50	0	0	50	1.00
6663677--6663705	3	9.7	3	100	0	58	34	0	0	65	0.93
6674585--6674767	37	5.0	37	95	1	316	24	21	16	37	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6674731--6675045	46	6.6	46	84	8	387	28	21	14	34	1.93
6674731--6675039	98	3.1	98	84	9	396	28	22	14	35	1.93
6674730--6675045	144	2.2	144	95	0	560	28	22	14	34	1.93
6688317--6688369	5	10.8	5	97	2	99	41	0	0	58	0.98
6688420--6688463	17	2.6	18	78	10	56	65	2	25	6	1.28
6688455--6688482	14	2.0	14	100	0	56	85	0	14	0	0.59
6689138--6689184	24	2.0	23	84	12	60	36	0	14	48	1.44
6689167--6689214	15	3.1	15	78	18	53	37	0	12	50	1.41
6689326--6689465	40	3.5	40	76	6	142	27	17	23	30	1.97
6701517--6701549	16	2.0	17	94	5	59	48	0	0	51	1.00
6711087--6711133	21	2.3	20	79	10	60	42	0	0	57	0.98
6711113--6711162	25	2.0	25	88	0	73	46	0	0	54	1.00
6711110--6711160	14	3.9	14	75	15	54	45	0	0	54	0.99
6718462--6718520	27	2.2	27	81	6	66	57	16	10	15	1.64
6729388--6729477	42	2.2	40	84	4	108	65	13	1	20	1.32
6730781--6730818	18	2.2	17	86	9	51	21	7	2	68	1.28
6733487--6733549	22	2.9	22	82	0	72	34	17	30	17	1.93
6733533--6733587	25	2.2	25	90	0	83	36	21	25	16	1.94
6734546--6734594	2	26.0	2	84	12	68	53	0	0	46	1.00
6767016--6767045	15	2.0	15	100	0	60	53	0	0	46	1.00
6773192--6773270	27	2.9	27	96	0	140	16	20	39	24	1.92
6773370--6773618	27	9.4	27	65	24	129	53	12	0	33	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6773394--6773600	19	9.0	22	67	26	112	54	12	0	32	1.45
6773391--6773563	19	8.9	19	72	18	119	53	12	1	32	1.46
6773371--6773600	115	2.0	116	93	0	390	53	12	0	33	1.45
6773394--6773618	47	4.9	46	79	14	225	53	12	0	32	1.44
6773311--6773608	96	3.1	94	77	15	256	53	13	1	32	1.47
6773391--6773606	66	3.2	65	83	10	247	53	12	0	32	1.45
6773490--6773618	27	5.2	27	73	24	131	54	12	0	33	1.38
6773490--6773591	28	3.9	27	83	13	133	53	11	0	34	1.37
6777976--6778018	19	2.3	19	80	4	52	39	2	0	58	1.11
6789596--6789636	21	2.0	20	90	9	66	39	4	0	56	1.21
6803014--6803038	12	2.1	12	100	0	50	48	0	20	32	1.50
6805339--6805372	4	8.5	4	100	0	68	23	0	0	76	0.79
6808364--6808396	2	16.0	2	93	6	57	48	0	48	3	1.17
6813196--6813237	21	1.9	23	85	9	61	57	14	2	26	1.50
6813798--6813841	17	2.4	18	79	20	56	36	0	4	59	1.18
6814245--6814279	3	11.7	3	100	0	70	65	0	0	34	0.93
6815595--6815642	11	4.2	11	76	10	51	64	0	0	35	0.94
6815589--6815651	32	1.9	32	87	9	92	61	0	0	38	0.96
6815656--6815681	11	2.4	11	100	0	52	61	0	0	38	0.96
6815602--6815772	39	4.4	39	88	3	229	63	0	1	34	1.05
6842988--6843038	24	2.1	24	96	0	93	37	15	25	21	1.93
6843088--6843143	26	2.2	26	87	6	78	37	16	26	19	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6850277--6850334	21	2.8	21	79	10	73	17	20	13	48	1.81
6851575--6851700	66	1.9	66	96	0	234	26	35	19	19	1.95
6855677--6855848	72	2.4	72	86	4	260	25	6	14	54	1.64
6866175--6866209	6	5.8	6	96	0	52	22	0	45	31	1.53
6877926--6877984	31	1.9	31	92	0	100	22	18	3	55	1.57
6878077--6878143	22	3.0	22	76	8	57	41	17	22	17	1.90
6881604--6881638	13	2.6	14	81	9	54	0	25	2	71	1.00
6883864--6883903	16	2.4	17	83	8	55	30	0	0	70	0.88
6883887--6883946	32	1.9	32	89	3	95	35	5	6	53	1.49
6899352--6899393	17	2.5	16	88	7	57	16	11	0	71	1.14
6899903--6899953	25	2.1	25	85	3	68	49	1	3	45	1.32
6901835--6901866	16	1.9	17	93	6	57	31	31	18	18	1.95
6912647--6912684	17	2.2	17	95	0	67	78	0	7	13	0.94
6921517--6921546	16	1.9	15	93	6	51	0	10	0	90	0.47
6922485--6922530	22	2.1	22	88	8	67	65	2	4	28	1.23
6926686--6926876	23	8.3	23	98	0	364	18	21	29	30	1.97
6956626--6956669	19	2.2	20	80	11	56	68	4	4	22	1.27
6957606--6957672	9	7.4	9	91	0	98	23	11	25	38	1.89
6960655--6960730	37	2.1	37	92	5	127	27	13	22	36	1.91
6967189--6967213	12	2.1	12	100	0	50	24	36	24	16	1.94
6967376--6967446	9	7.9	9	87	0	97	35	26	9	28	1.88
6967376--6967450	27	2.8	27	91	0	123	34	25	9	30	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6968586--6968619	15	2.4	14	90	5	50	67	5	20	5	1.33
6971406--6971650	81	3.1	81	80	4	230	31	47	7	13	1.71
6971423--6971948	39	13.3	39	72	12	281	33	47	6	12	1.67
6971381--6971499	60	2.0	60	85	3	159	31	47	8	13	1.73
6971484--6971534	21	2.3	22	80	13	59	29	47	7	15	1.74
6971586--6971764	57	3.1	56	76	13	175	31	49	7	11	1.67
6971583--6971767	60	3.1	59	81	8	225	31	49	7	11	1.65
6971607--6971769	57	2.8	58	85	4	222	33	49	7	10	1.65
6971682--6971926	60	4.1	60	80	2	255	33	49	5	11	1.62
6971506--6971947	99	4.5	99	77	7	375	33	48	6	12	1.66
6971800--6972064	99	2.7	99	80	2	291	32	46	7	13	1.71
6971960--6972097	39	3.5	39	80	2	143	31	44	6	17	1.74
6986187--6986239	13	4.1	13	76	9	54	35	30	5	28	1.80
6997226--6997266	21	2.0	21	85	0	55	9	0	39	51	1.35
6997346--6997783	125	3.5	125	93	0	743	30	17	23	28	1.97
7000425--7000482	30	1.9	30	89	0	89	41	3	24	31	1.71
7000694--7000725	13	2.5	13	94	0	55	31	0	12	56	1.37
7000820--7001061	50	4.7	51	84	5	283	27	24	28	20	1.99
7000820--7001069	100	2.4	103	86	6	337	26	24	28	21	1.99
7003633--7003662	6	5.0	6	91	0	51	20	0	46	33	1.51
7003653--7003727	21	3.5	21	87	8	107	24	0	30	45	1.53
7003769--7003883	22	5.0	22	74	13	106	27	0	27	43	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
7003777--7003890	50	2.3	50	98	0	219	27	0	28	43	1.55
7003777--7003940	50	3.1	51	88	9	210	26	0	29	44	1.54
7003887--7003936	21	2.3	21	86	13	75	24	0	30	46	1.53
7004179--7004223	21	2.1	21	84	8	56	4	31	35	28	1.77
7005315--7005352	20	1.9	20	84	10	51	55	7	2	34	1.43
7006250--7006276	14	1.9	14	100	0	54	44	0	0	55	0.99
7006286--7006385	51	2.0	51	88	4	148	47	2	25	26	1.63
7007036--7007163	65	2.0	66	87	1	186	53	6	7	33	1.53
7007164--7007196	16	2.0	17	88	5	50	54	3	6	36	1.41
7007290--7007364	8	10.4	8	71	26	53	28	0	6	65	1.18

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