genome.fa.s1.2.7.7.80.10.50.1000.30.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  30  of  187  ( 22383 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)
9677874--9677919	21	2.2	20	82	14	58	34	8	2	54	1.43
9679519--9679552	12	2.8	12	83	16	52	8	0	14	76	1.01
9680171--9680217	23	2.0	23	95	0	85	61	0	0	38	0.96
9680174--9680264	32	2.9	32	87	8	134	61	0	0	38	0.96
9680186--9680287	32	3.2	31	84	8	125	56	0	0	41	1.12
9682963--9683028	35	1.9	35	87	3	98	22	12	12	53	1.71
9685120--9685163	2	22.0	2	100	0	88	50	0	0	50	1.00
9690726--9691194	237	2.0	237	91	0	767	32	27	12	26	1.93
9691380--9691447	17	4.0	17	74	12	68	48	20	4	26	1.68
9691370--9691440	34	2.1	34	84	5	90	46	19	7	26	1.75
9692649--9692718	28	2.5	28	83	4	79	37	15	21	25	1.93
9697547--9697603	2	29.0	2	96	3	107	50	0	0	49	1.00
9706421--9706453	17	1.9	17	100	0	66	24	27	6	42	1.78
9709945--9709977	17	1.9	17	93	0	57	24	24	6	45	1.75
9710916--9710952	3	12.3	3	100	0	74	32	0	0	67	0.91
9714716--9714839	49	2.5	49	81	2	151	33	10	12	43	1.76
9715222--9715316	37	2.6	36	81	6	109	43	17	16	22	1.88
9724352--9724392	21	1.9	22	90	5	66	39	12	9	39	1.76
9738164--9738191	14	2.0	14	100	0	56	42	28	7	21	1.79
9744785--9744842	24	2.4	24	100	0	116	34	17	24	24	1.96
9744919--9744996	26	3.2	26	85	7	92	35	23	25	15	1.94
9749005--9749039	18	1.9	18	100	0	70	22	0	28	48	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9749005--9749043	18	2.3	17	91	8	62	25	0	28	46	1.53
9749718--9749800	41	2.0	41	97	0	157	46	9	10	32	1.71
9752055--9752124	10	7.0	10	77	4	70	58	0	1	40	1.07
9752057--9752124	19	3.4	20	83	6	75	60	0	1	38	1.06
9754155--9754213	22	2.9	19	69	13	55	5	25	3	66	1.28
9754720--9754749	12	2.5	12	94	0	51	6	26	43	23	1.78
9754913--9754987	32	2.4	31	75	14	82	21	22	34	21	1.97
9755060--9755100	19	2.2	19	90	0	64	43	7	14	34	1.73
9756642--9756691	23	2.3	21	79	6	55	56	4	0	40	1.18
9757541--9757575	2	17.5	2	100	0	70	51	48	0	0	1.00
9762740--9762884	63	2.3	64	90	2	220	42	17	11	29	1.83
9763037--9763386	178	2.0	169	87	9	492	30	17	14	37	1.89
9768659--9768701	4	10.8	4	94	0	77	27	0	25	46	1.53
9770764--9770802	2	19.5	2	100	0	78	51	0	0	48	1.00
9776424--9776513	35	2.5	35	75	7	83	22	1	40	36	1.61
9776691--9776740	14	3.6	14	77	0	55	26	0	34	40	1.56
9777107--9777602	251	2.0	251	87	4	723	29	16	20	33	1.95
9777159--9777547	124	3.1	123	68	12	295	28	17	20	33	1.95
9780515--9780587	26	3.0	25	77	15	71	58	0	10	30	1.32
9782227--9783322	82	13.4	81	89	3	1529	21	19	26	31	1.98
9783208--9783410	82	2.4	87	80	12	217	24	22	23	30	1.99
9783248--9783641	132	3.0	132	90	1	578	25	23	20	30	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9783354--9783583	44	5.2	44	71	5	151	26	23	20	29	1.99
9783646--9784599	88	10.9	88	89	1	1376	23	22	24	29	1.99
9783715--9783937	44	5.1	44	67	11	161	23	20	24	32	1.98
9783660--9784600	175	5.4	175	91	0	1425	23	22	24	29	1.99
9783646--9784599	263	3.6	263	88	1	1369	23	22	24	29	1.99
9785041--9785236	108	1.8	108	89	2	313	46	11	16	25	1.80
9785202--9785302	45	2.3	43	80	10	112	52	8	12	25	1.68
9785584--9785623	17	2.4	17	91	4	64	0	15	2	82	0.77
9786048--9786122	9	8.1	9	74	15	64	0	8	12	80	0.92
9789699--9789758	24	2.5	24	73	15	61	60	0	10	30	1.30
9789878--9789912	2	17.5	2	100	0	70	51	0	0	48	1.00
9791284--9791322	9	4.3	9	86	0	60	46	15	0	38	1.46
9791280--9791324	18	2.5	18	92	0	72	48	13	0	37	1.42
9791346--9791379	17	1.9	18	88	5	52	38	5	0	55	1.24
9791494--9791553	9	6.7	9	82	0	75	46	15	1	36	1.55
9791494--9791553	27	2.2	27	90	0	93	46	15	1	36	1.55
9791501--9791555	18	3.1	18	91	0	83	49	12	0	38	1.41
9791577--9791610	17	1.9	18	88	5	52	38	5	0	55	1.24
9791280--9791780	231	2.2	231	98	0	975	46	13	0	39	1.50
9791725--9791905	9	20.3	9	85	1	240	48	16	0	34	1.51
9797561--9797626	21	3.1	21	82	8	89	33	21	42	3	1.68
9797611--9797638	12	2.3	12	100	0	56	39	17	42	0	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9798117--9798259	43	3.3	42	86	3	171	28	22	20	28	1.98
9802494--9802551	25	2.4	24	79	2	62	58	6	1	32	1.35
9805287--9805329	11	3.8	11	82	17	61	32	2	2	62	1.20
9805290--9805333	23	1.9	23	95	0	79	34	2	4	59	1.30
9807117--9807141	12	2.1	12	100	0	50	0	16	0	84	0.63
9807978--9808044	3	22.3	3	100	0	134	32	0	0	67	0.91
9808166--9808213	23	2.1	25	85	14	68	18	2	12	66	1.33
9808321--9808355	15	2.3	15	90	9	54	28	14	2	54	1.54
9809296--9809338	18	2.4	19	78	21	56	25	4	6	62	1.40
9817670--9817707	20	1.9	20	88	0	58	50	15	13	21	1.78
9822343--9822369	13	2.1	13	100	0	54	40	22	7	29	1.81
9824912--9824971	31	1.9	31	83	6	77	26	8	21	43	1.81
9825288--9825322	11	3.2	11	100	0	70	51	20	0	28	1.47
9832928--9832979	22	2.4	23	78	12	65	67	7	11	13	1.42
9833919--9833963	3	15.0	3	90	0	72	31	2	2	64	1.18
9839791--9839818	2	14.0	2	100	0	56	50	0	0	50	1.00
9848821--9848883	31	2.0	31	84	6	83	44	7	9	38	1.66
9850651--9850690	16	2.5	16	91	0	62	47	2	7	42	1.45
9850679--9850821	68	2.1	68	90	2	236	41	5	8	44	1.58
9850887--9850930	24	1.9	24	90	9	74	61	2	0	36	1.09
9852660--9852721	2	31.0	2	79	6	63	53	1	3	41	1.27
9852752--9852795	16	2.6	17	89	3	72	56	0	11	31	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9856349--9856409	33	1.9	31	83	6	77	29	13	16	40	1.86
9858741--9858791	24	2.1	24	82	17	61	45	0	0	54	0.99
9866435--9866484	26	1.9	26	91	0	82	16	36	18	30	1.92
9869267--9869324	26	2.2	26	87	0	80	44	0	18	36	1.50
9869276--9869331	26	2.2	26	96	0	103	51	0	12	35	1.40
9876382--9876418	16	2.3	16	100	0	74	37	5	35	21	1.77
9876398--9876488	46	2.0	46	93	4	159	27	4	29	38	1.76
9876398--9876505	46	2.5	44	85	11	145	29	3	30	36	1.75
9876647--9876685	17	2.5	15	84	15	60	61	0	0	38	0.96
9876652--9876685	17	2.0	17	100	0	68	58	0	0	41	0.98
9876718--9876757	20	2.0	21	85	5	55	60	5	0	35	1.19
9876609--9876804	54	3.4	54	71	17	144	54	3	1	41	1.23
9876847--9876910	32	2.0	32	81	0	74	50	1	0	48	1.10
9878250--9878354	50	2.1	50	85	1	140	50	9	8	31	1.65
9879337--9879370	12	2.8	12	90	0	59	58	17	23	0	1.38
9882967--9882995	15	1.9	15	100	0	58	75	13	0	10	1.04
9892019--9892064	24	2.0	23	86	4	65	47	4	15	32	1.65
9903468--9903513	19	2.4	19	81	3	56	23	8	0	67	1.18
9903589--9903684	3	32.0	3	82	8	115	30	3	3	63	1.25
9903936--9904040	42	2.5	42	100	0	210	19	30	32	18	1.95
9907538--9907562	10	2.5	10	100	0	50	48	0	8	44	1.32
9907546--9907727	55	3.3	55	95	2	312	43	5	12	39	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9907722--9907845	29	4.3	29	95	0	230	29	0	27	42	1.56
9907851--9908035	71	2.6	71	93	2	309	44	14	3	37	1.63
9907985--9908033	25	1.9	25	87	4	71	38	16	4	40	1.67
9910208--9910258	10	5.1	10	76	9	50	70	0	0	29	0.87
9910208--9910271	30	2.1	31	94	2	112	67	0	0	32	0.91
9910273--9910388	51	2.3	51	93	0	196	39	0	31	29	1.57
9910762--9910795	17	2.0	17	88	0	50	38	0	8	52	1.33
9910870--9910918	25	2.0	25	84	8	64	24	4	0	71	1.03
9910961--9910990	3	10.0	3	100	0	60	33	0	0	66	0.92
9911535--9911567	11	3.0	11	100	0	66	18	36	27	18	1.94

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