genome.fa.s7.2.7.7.80.10.50.1000.27.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  27  of  204  ( 24458 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)
9866563--9866618	21	2.7	21	82	0	67	26	8	35	28	1.87
9871368--9871425	9	6.4	9	86	7	82	43	18	10	27	1.83
9872955--9872984	2	15.0	2	92	0	51	53	0	0	46	1.00
9873906--9873943	18	2.2	18	90	4	60	76	5	7	10	1.15
9876400--9876461	22	2.8	22	92	0	97	35	14	25	24	1.93
9877515--9878778	423	3.0	419	92	1	2140	35	16	18	29	1.93
9884800--9884890	7	12.9	7	69	11	51	18	1	34	46	1.57
9884849--9884890	20	2.0	21	90	4	68	16	2	33	47	1.60
9884907--9884939	16	2.1	16	88	11	50	42	0	0	57	0.98
9885161--9885218	28	2.1	28	83	6	73	43	0	3	53	1.17
9885171--9885224	27	2.0	27	85	7	74	37	1	3	57	1.27
9885171--9885224	28	2.0	27	88	3	81	37	1	3	57	1.27
9889216--9889373	43	3.7	43	87	0	208	22	15	27	34	1.95
9889507--9889619	43	2.6	43	81	0	136	22	16	25	35	1.95
9889668--9889693	5	5.2	5	100	0	52	42	19	19	19	1.90
9890763--9890799	9	4.1	9	92	0	65	29	10	13	45	1.77
9890853--9890883	9	3.4	9	90	0	53	38	22	12	25	1.90
9891073--9891165	2	46.5	2	100	0	186	50	0	49	0	1.00
9894684--9894711	6	4.7	6	100	0	56	85	0	0	14	0.59
9896092--9896214	28	4.5	28	84	2	151	34	11	26	28	1.91
9896095--9896214	55	2.2	54	83	5	143	34	10	25	29	1.90
9900355--9900392	11	3.2	12	82	17	53	60	0	2	36	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9900376--9900408	15	2.1	17	88	11	52	60	0	0	39	0.97
9924515--9924677	81	2.0	81	96	0	299	34	15	15	33	1.90
9950323--9950350	6	4.7	6	100	0	56	67	0	0	32	0.91
9951550--9951593	18	2.4	18	80	3	52	29	2	6	61	1.34
9955306--9955339	17	1.9	17	88	5	50	47	0	17	35	1.48
9955387--9955449	3	21.0	3	100	0	126	33	0	0	66	0.92
9956099--9956178	21	3.7	22	66	19	60	18	18	23	38	1.93
9956096--9956158	23	2.9	21	70	9	54	19	20	23	36	1.95
9956567--9956617	25	2.0	25	96	0	93	37	5	19	37	1.76
9970909--9970939	9	3.4	9	90	0	53	25	12	22	38	1.90
9973683--9973744	24	2.6	24	82	7	72	33	14	27	24	1.94
9973820--9973893	26	2.9	25	82	6	94	37	22	22	16	1.93
9979521--9979551	14	2.2	14	94	0	53	25	6	6	61	1.45
9979582--9979646	30	2.2	30	94	0	112	23	3	13	60	1.48
9985288--9985340	28	2.0	26	88	7	79	20	13	7	58	1.59
9985795--9985831	20	1.9	18	89	10	56	48	0	10	40	1.38
9989490--9989551	25	2.5	25	94	0	106	27	9	20	41	1.84
9989695--9989735	20	2.2	19	91	8	66	31	0	19	48	1.49
9991725--9991799	18	3.8	18	77	17	69	40	1	4	54	1.27
9991732--9991776	7	6.7	7	76	19	51	40	0	2	57	1.11
9991727--9991789	23	2.7	23	82	7	65	39	0	4	55	1.21
9991655--9991813	84	1.9	82	87	12	234	42	1	5	50	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10014513--10014561	25	1.9	26	91	4	82	40	10	16	32	1.82
10018767--10018855	32	2.8	31	93	5	142	37	2	0	60	1.09
10018817--10018856	21	1.9	21	94	0	71	35	2	0	62	1.09
10030751--10030801	15	3.1	16	78	21	61	29	1	9	58	1.41
10041476--10041600	42	3.0	42	98	0	241	27	26	24	21	1.99
10053580--10053615	17	2.0	18	89	10	56	0	27	0	72	0.85
10053669--10053734	20	3.2	20	85	8	71	21	4	4	69	1.24
10053768--10053817	19	2.6	20	84	6	59	36	8	4	52	1.50
10054507--10054542	18	2.1	17	94	5	63	50	0	0	50	1.00
10056046--10056126	3	26.7	3	76	7	74	64	2	3	29	1.24
10056338--10056371	17	1.9	18	88	5	52	70	8	2	17	1.25
10057601--10057651	23	2.2	23	82	6	59	19	3	13	62	1.46
10069698--10069728	14	2.1	15	94	5	55	29	6	0	64	1.18
10069703--10069735	14	2.4	14	90	5	50	27	6	0	66	1.15
10075876--10075905	15	1.9	16	93	6	53	70	3	0	26	1.03
10075863--10075908	15	2.8	16	81	18	51	63	2	2	32	1.19
10080428--10080510	43	1.9	43	100	0	166	24	19	22	33	1.97
10081781--10081826	20	2.4	19	77	19	51	56	2	6	34	1.37
10082409--10082438	2	15.0	2	100	0	60	50	0	0	50	1.00
10093869--10093898	6	5.0	6	100	0	60	33	0	0	66	0.92
10094947--10094987	19	2.3	18	87	8	57	46	2	2	48	1.28
10098142--10098191	24	2.1	24	84	0	64	42	20	26	12	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10098199--10098233	3	11.7	3	100	0	70	34	0	34	31	1.58
10098313--10098348	3	12.0	3	100	0	72	33	0	33	33	1.58
10098574--10098644	3	23.7	3	91	0	79	35	8	32	23	1.85
10098915--10098957	3	14.3	3	100	0	86	67	0	32	0	0.91
10099464--10099597	65	2.1	65	100	0	268	33	8	11	45	1.72
10100812--10100846	16	2.2	16	89	0	52	68	5	0	25	1.11
10101315--10101369	28	2.0	28	92	0	92	1	29	5	63	1.27
10101343--10101414	38	1.9	37	82	2	90	6	26	8	58	1.53
10104573--10104607	15	2.2	16	90	5	54	48	0	0	51	1.00
10104710--10104744	18	2.0	17	88	5	52	45	0	0	54	0.99
10104890--10104999	45	2.6	43	81	8	129	31	30	5	32	1.80
10104980--10105029	16	3.1	16	94	0	82	34	36	0	30	1.58
10108019--10108055	20	1.9	19	89	10	58	45	16	21	16	1.84
10108262--10108286	13	1.9	13	100	0	50	40	48	0	12	1.40
10108389--10108490	9	11.4	9	79	2	98	27	11	22	38	1.89
10108389--10108480	35	2.6	36	92	3	159	27	11	23	36	1.90
10111173--10111268	46	2.1	46	100	0	192	44	12	19	22	1.84
10115491--10115537	21	2.2	21	77	7	51	6	14	4	74	1.17
10117315--10117349	17	2.0	18	88	5	54	31	11	2	54	1.51
10117460--10117495	16	2.3	16	90	4	56	22	2	0	75	0.94
10117980--10118051	36	2.1	36	86	5	103	62	1	2	33	1.18
10123405--10123491	24	3.4	26	85	9	83	42	2	3	51	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10123427--10123483	24	2.4	24	100	0	114	42	3	3	50	1.36
10125032--10125066	16	2.2	16	90	10	54	28	5	2	62	1.32
10133248--10133311	30	2.1	32	91	5	105	31	10	7	50	1.66
10147599--10147635	17	2.1	19	85	10	51	45	0	10	43	1.39
10150974--10151025	6	8.3	6	80	16	52	75	0	3	21	0.97
10150979--10151033	25	2.2	25	84	12	69	70	0	7	21	1.11
10158182--10158248	34	1.9	35	87	3	100	44	14	8	31	1.76
10160363--10160392	14	2.1	14	93	0	51	63	0	13	23	1.29
10165980--10166018	19	2.1	19	100	0	78	25	25	5	43	1.75
10172892--10172917	2	13.0	2	100	0	52	50	0	0	50	1.00
10173014--10173045	15	2.0	17	88	11	50	34	0	9	56	1.32
10181621--10181671	23	2.2	23	96	0	93	37	0	13	49	1.43
10181630--10181671	13	3.5	13	75	18	54	38	0	11	50	1.40
10184188--10184253	26	2.6	25	81	11	71	37	24	21	16	1.93
10188204--10188248	20	2.2	20	88	7	65	28	0	4	66	1.11
10188261--10188301	19	2.2	19	86	0	55	21	0	4	73	1.02
10189410--10189459	3	17.0	3	91	4	84	64	0	36	0	0.94
10199496--10199526	2	15.5	2	100	0	62	0	51	0	48	1.00
10214103--10214145	18	2.4	18	88	7	61	53	0	0	46	1.00
10232246--10232306	31	2.0	30	81	12	72	55	6	4	32	1.47
10232241--10232312	32	2.3	31	80	7	74	54	6	4	34	1.47
10233068--10233112	23	1.9	24	86	4	65	51	2	2	44	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10247541--10247584	12	3.7	12	84	0	61	40	22	34	2	1.67
10247541--10247582	18	2.3	18	83	0	66	42	21	33	2	1.66
10249981--10250005	12	2.1	12	100	0	50	24	36	24	16	1.94
10253755--10254171	89	4.7	89	76	12	342	29	10	12	47	1.75
10253770--10254150	176	2.1	177	79	9	411	29	10	13	46	1.77
10253769--10254378	89	7.0	88	73	12	305	28	11	14	46	1.78
10255494--10255534	21	2.0	21	85	9	57	41	2	0	56	1.13
10259065--10259217	75	2.0	75	94	0	270	36	16	18	27	1.93
10268013--10268064	24	2.2	24	82	6	61	50	3	3	42	1.39
10282785--10282823	18	2.2	17	86	13	53	33	0	20	46	1.51

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