genome.fa.s7.2.7.7.80.10.50.1000.142.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  142  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)
42848055--42848099	3	15.0	3	100	0	90	66	0	0	33	0.92
42849048--42849144	21	4.7	21	89	5	153	41	11	10	37	1.75
42863923--42863975	25	2.1	25	100	0	106	45	16	7	30	1.75
42864971--42865018	23	2.2	22	85	14	64	70	0	29	0	0.87
42864977--42865025	23	2.1	23	85	7	64	73	0	24	2	0.94
42874291--42874330	20	2.0	20	90	0	62	7	32	22	37	1.82
42886376--42886418	22	2.0	22	86	9	61	25	6	16	51	1.69
42896130--42896210	41	2.0	41	95	0	144	48	2	27	22	1.63
42905383--42905503	38	3.0	38	83	13	161	32	19	23	23	1.98
42905370--42905530	44	3.8	44	84	9	226	30	21	22	26	1.99
42905151--42905722	301	1.9	301	90	0	912	32	19	20	27	1.97
42905421--42905924	219	2.3	219	83	4	726	32	19	20	27	1.97
42907964--42907998	19	1.9	19	88	11	56	45	0	5	48	1.26
42910923--42910971	20	2.5	20	83	3	55	63	6	2	28	1.30
42912427--42912699	128	2.1	128	89	2	415	23	24	20	32	1.98
42912686--42913385	88	8.0	88	88	0	990	24	26	22	26	2.00
42912799--42913281	44	11.0	44	67	14	228	24	27	22	25	2.00
42915535--42915582	7	6.6	7	88	7	69	4	10	0	85	0.73
42918708--42919654	500	1.9	500	100	0	1894	35	20	17	26	1.94
42920673--42920768	39	2.4	40	81	10	108	38	21	20	18	1.93
42920799--42920993	41	4.7	41	88	0	264	23	19	26	30	1.98
42920799--42920993	82	2.4	82	88	2	293	23	19	26	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42921125--42921196	35	2.1	35	100	0	144	59	2	5	31	1.35
42921352--42921400	14	3.5	14	88	0	71	24	0	26	48	1.51
42921614--42921672	7	8.4	7	86	0	82	18	1	49	30	1.58
42922432--42922476	22	2.0	22	91	0	72	26	8	13	51	1.70
42924711--42924746	18	2.0	18	94	0	63	16	25	11	47	1.79
42926612--42926818	43	4.9	42	77	6	168	24	17	29	27	1.98
42926600--42926818	86	2.6	84	82	7	230	25	17	29	27	1.97
42927042--42927090	20	2.5	20	83	3	55	63	6	2	28	1.30
42929685--42929731	20	2.3	20	96	0	85	25	10	8	55	1.62
42932506--42932585	37	2.2	37	84	10	110	33	0	6	60	1.22
42932596--42932655	25	2.3	26	80	2	68	31	3	3	61	1.28
42933950--42934027	29	2.7	29	85	2	93	32	11	17	38	1.86
42933967--42934037	29	2.4	29	90	0	106	33	9	18	38	1.84
42946050--42946094	6	7.5	6	97	0	72	17	60	17	4	1.53
42959418--42959552	40	3.4	40	87	2	193	34	19	24	21	1.96
42959592--42959742	41	3.7	41	91	1	232	22	20	29	27	1.99
42961363--42961405	21	2.0	21	86	9	59	41	39	2	16	1.61
42964607--42964890	43	6.7	43	82	2	295	24	17	32	26	1.97
42964607--42964890	129	2.2	128	81	2	329	24	17	32	26	1.97
42964961--42965004	22	2.0	21	86	4	61	43	25	18	13	1.86
42967154--42967218	34	1.9	34	84	6	87	35	20	21	23	1.96
42967391--42967506	55	2.1	55	95	1	205	17	6	18	57	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42967638--42967675	18	2.1	18	85	9	51	47	7	13	31	1.71
42970882--42970916	3	11.7	3	93	0	61	62	0	2	34	1.10
42972612--42972723	44	2.5	43	84	5	127	29	22	20	27	1.98
42973721--42973777	30	1.9	30	85	3	80	42	1	24	31	1.65
42973990--42974020	13	2.4	13	94	0	53	32	0	12	54	1.38
42974115--42974224	50	2.2	50	100	0	220	26	22	31	19	1.97
42978130--42978164	16	2.2	16	89	0	52	45	17	17	20	1.85
42979073--42979731	109	6.1	109	94	0	1090	34	17	16	31	1.93
42990537--42990766	102	2.3	102	89	1	354	30	14	24	30	1.95
42990533--42990770	51	4.7	51	79	2	255	30	14	24	30	1.95
42990748--42990791	14	3.1	14	96	0	79	29	15	25	29	1.96
42995069--42995096	5	5.6	5	100	0	56	39	0	21	39	1.54
42997175--42997315	41	3.4	41	91	0	228	33	24	16	25	1.96
42997175--42997332	82	1.9	81	89	1	244	34	24	17	23	1.95
42997175--42997334	41	3.9	42	86	4	211	35	24	16	23	1.95
42997483--42997606	65	1.9	65	88	6	189	43	16	7	33	1.75
43000536--43000587	3	17.3	3	95	0	95	32	0	1	65	1.04
43003093--43003122	15	2.0	15	93	0	51	23	20	6	50	1.71
43005608--43005659	7	7.6	7	76	20	56	69	1	15	13	1.28
43007151--43007509	50	7.2	50	73	3	274	33	23	19	23	1.97
43007140--43007509	100	3.7	100	88	0	526	33	23	19	22	1.97
43008991--43009038	3	16.0	3	100	0	96	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43028215--43028307	46	2.0	46	93	0	159	20	24	13	40	1.89
43028810--43028879	24	3.0	22	74	12	59	40	12	10	37	1.77
43030730--43030835	55	1.9	55	98	0	203	44	21	11	22	1.84
43031284--43031346	31	2.0	31	87	6	92	36	20	17	25	1.94
43034342--43034403	30	2.1	30	100	0	124	32	19	22	25	1.97
43036631--43036730	51	1.9	52	93	2	175	29	1	16	54	1.49
43037479--43037507	14	2.0	15	93	6	51	31	6	6	55	1.53
43042842--43043148	46	6.6	46	79	15	344	34	15	21	28	1.94
43042842--43043148	98	3.3	95	78	18	338	34	15	21	28	1.94
43042955--43043043	38	2.3	38	96	0	160	32	17	21	28	1.96
43042993--43043148	52	3.1	52	78	15	191	35	14	21	27	1.93
43042878--43043296	136	3.3	135	83	13	525	36	15	20	27	1.93
43043112--43043294	37	5.0	37	95	1	316	38	16	19	25	1.92
43048019--43048067	25	1.9	25	83	4	62	30	14	8	46	1.73
43050403--43050428	11	2.4	11	100	0	52	61	0	0	38	0.96
43065833--43065860	13	2.2	13	100	0	56	92	7	0	0	0.37
43066192--43066255	20	3.3	19	73	18	60	68	0	3	28	1.04
43066231--43066258	12	2.3	12	100	0	56	78	0	7	14	0.95
43066231--43066266	11	3.2	11	92	4	54	75	0	5	19	1.00
43066340--43066364	13	1.9	13	100	0	50	64	0	0	36	0.94
43066538--43066603	21	3.1	21	77	10	55	28	3	4	63	1.29
43066872--43066931	30	2.0	30	100	0	120	50	10	16	23	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43069816--43069881	29	2.3	29	84	5	89	36	1	1	60	1.15
43070017--43070336	90	3.5	92	79	7	300	38	9	15	37	1.79
43076429--43076465	16	2.3	16	95	0	65	35	0	13	51	1.41
43091344--43091390	21	2.2	21	88	0	67	19	36	27	17	1.93
43094945--43094975	15	2.1	15	100	0	62	16	0	38	45	1.47
43097364--43097391	5	5.6	5	100	0	56	42	0	0	57	0.99
43098959--43098998	21	1.9	21	89	0	62	75	5	0	20	0.99
43099193--43099244	19	2.8	19	75	13	54	42	17	3	36	1.67
43101636--43101682	18	2.7	18	86	3	60	70	0	0	29	0.88
43101636--43101675	19	2.2	18	86	4	53	67	0	0	32	0.91
43103906--43103938	6	5.5	6	96	0	57	36	0	63	0	0.95
43103906--43103944	18	2.2	18	85	0	51	41	0	58	0	0.98
43113049--43113100	27	2.0	26	85	11	70	44	5	9	40	1.61
43125450--43125598	73	2.0	73	98	0	289	19	20	10	49	1.77
43125943--43126003	30	2.0	30	96	0	113	50	6	21	21	1.70
43132679--43132855	44	4.0	44	88	0	228	28	24	18	28	1.98
43132916--43133057	44	3.3	43	67	7	133	17	27	29	25	1.97
43132932--43133075	44	3.3	44	66	7	121	20	22	31	25	1.98
43132866--43133519	88	7.4	88	86	1	819	21	24	26	27	1.99
43133135--43133274	45	3.2	45	68	11	135	23	23	22	30	1.99
43132889--43133526	351	1.8	352	87	1	967	21	24	26	27	1.99
43153878--43153913	18	1.9	18	88	5	54	22	16	11	50	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43159882--43159922	2	20.5	2	100	0	82	51	0	0	48	1.00
43160280--43160337	19	2.8	21	82	17	68	51	3	0	44	1.18
43169106--43169172	29	2.3	30	82	7	84	44	17	7	29	1.76
43177161--43177201	21	1.9	22	85	5	57	26	0	29	43	1.55
43183023--43183075	21	2.6	22	80	14	69	67	0	15	16	1.23
43185078--43185120	17	2.6	16	85	3	59	55	2	0	41	1.12
43186831--43186858	2	14.0	2	100	0	56	0	50	0	50	1.00
43197924--43197976	22	2.5	20	74	17	54	71	9	3	15	1.26
43198203--43198255	23	2.3	24	80	9	65	62	11	5	20	1.49
43198228--43198262	16	2.2	16	89	0	52	57	17	5	20	1.60

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