genome.fa.s6.2.7.7.80.10.50.1000.5.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  5  of  168  ( 20060 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)
1350085--1350111	12	2.2	12	100	0	54	77	0	0	22	0.76
1355609--1355740	25	5.3	25	80	5	151	18	27	19	34	1.96
1355611--1355739	49	2.6	50	86	4	172	18	27	19	34	1.95
1359549--1359593	17	2.7	16	83	10	63	24	4	0	71	1.05
1359584--1359618	15	2.2	17	90	10	56	34	2	0	62	1.10
1359632--1359671	18	2.2	17	86	8	53	20	0	7	72	1.08
1359678--1359717	12	3.5	12	83	13	57	37	0	10	52	1.35
1360028--1360066	13	3.2	12	86	13	53	15	2	7	74	1.15
1360382--1360577	98	2.0	98	96	0	365	29	9	23	37	1.86
1361143--1361283	25	5.7	25	77	9	110	20	26	19	32	1.97
1363431--1363694	136	1.9	136	92	0	438	39	9	18	32	1.83
1364348--1364397	25	2.0	25	92	7	84	44	0	4	52	1.20
1365286--1365414	43	3.0	43	76	13	129	24	18	27	30	1.98
1366452--1366489	2	19.0	2	94	0	67	47	0	2	50	1.15
1367451--1367486	2	18.0	2	100	0	72	50	0	0	50	1.00
1377681--1377735	26	2.1	26	100	0	110	36	12	21	29	1.91
1377894--1377962	11	5.9	12	75	11	63	42	5	0	52	1.25
1377909--1377961	24	2.2	25	86	10	74	45	3	0	50	1.19
1379147--1379215	35	1.9	36	97	2	131	52	18	2	26	1.60
1379183--1379252	27	2.5	28	81	6	81	52	21	2	22	1.60
1383321--1383388	25	2.6	27	86	13	97	38	7	27	26	1.83
1386462--1386537	36	2.1	35	82	2	98	31	27	23	17	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1387774--1387930	41	3.8	41	90	0	233	33	28	19	18	1.96
1389121--1389219	42	2.4	42	87	0	135	28	26	9	36	1.87
1392263--1392305	2	21.5	2	100	0	86	48	0	0	51	1.00
1395627--1395802	40	4.4	39	81	4	199	25	18	22	33	1.97
1395639--1395802	80	2.0	80	89	2	249	24	19	21	34	1.97
1408159--1408198	21	1.9	21	90	10	64	22	2	25	50	1.62
1414301--1414330	9	3.3	9	90	0	51	23	13	23	40	1.90
1414625--1414684	30	2.0	31	83	3	77	18	41	0	40	1.50
1417313--1417350	20	1.9	20	88	0	58	57	2	7	31	1.41
1417520--1417546	4	6.8	4	100	0	54	25	25	0	48	1.52
1418043--1418079	2	18.5	2	100	0	74	48	0	0	51	1.00
1421186--1421247	30	2.1	30	87	3	90	25	11	11	51	1.71
1426654--1426770	58	2.0	58	100	0	234	32	18	18	29	1.95
1442405--1442449	22	2.0	22	100	0	90	8	8	55	26	1.60
1443228--1443288	10	6.3	10	77	7	54	37	8	0	54	1.31
1447995--1448039	9	4.8	10	81	8	51	80	0	17	2	0.82
1447996--1448042	17	2.8	16	87	9	58	80	0	17	2	0.80
1449260--1449471	44	4.8	45	77	5	207	29	24	22	23	1.99
1449260--1449485	89	2.5	90	84	2	305	30	23	23	23	1.99
1449472--1449830	132	2.7	132	90	0	565	31	17	24	27	1.97
1449628--1450003	176	2.1	176	94	0	653	29	18	25	26	1.98
1449487--1450005	132	3.9	129	79	10	405	30	18	24	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1449678--1449959	88	3.2	88	70	11	279	30	19	24	25	1.98
1449804--1450089	132	2.2	132	93	0	482	31	19	23	25	1.98
1449496--1450089	308	1.9	308	93	0	1017	31	18	23	26	1.98
1453807--1453905	27	3.7	27	90	5	155	35	11	24	29	1.90
1453813--1453989	27	6.5	27	80	6	144	33	12	25	27	1.93
1454019--1454091	27	2.7	26	83	8	76	35	5	23	35	1.78
1454020--1454108	27	3.3	27	80	3	72	32	8	24	33	1.87
1456822--1456955	40	3.5	40	71	10	134	36	22	18	22	1.95
1456738--1456990	76	3.4	76	79	4	275	32	24	20	22	1.98
1466787--1466832	15	3.1	15	93	0	83	54	21	10	13	1.69
1475288--1475346	24	2.5	24	86	5	84	32	20	30	16	1.95
1475381--1475439	26	2.3	26	85	5	75	38	18	25	16	1.92
1476445--1476477	14	2.2	16	89	10	52	18	12	0	69	1.18
1478647--1478872	47	4.6	47	86	9	294	23	30	19	25	1.98
1479144--1479280	41	3.4	41	77	10	147	32	27	16	23	1.95
1479165--1479282	40	2.9	41	83	2	148	31	29	16	22	1.96
1484996--1485178	47	3.7	49	83	13	223	24	31	20	24	1.98
1484996--1485178	101	1.8	101	89	5	289	24	31	20	24	1.98
1485446--1485582	41	3.4	41	78	10	156	33	27	16	23	1.95
1485467--1485584	40	2.9	41	84	2	157	32	28	16	22	1.95
1491429--1491484	27	2.1	26	83	9	69	39	1	0	58	1.08
1492424--1492450	2	13.5	2	100	0	54	51	0	48	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1497288--1497375	25	3.1	30	79	15	114	26	23	6	43	1.79
1499072--1499116	12	4.0	12	77	16	60	33	46	0	20	1.51
1500043--1500075	17	2.1	16	88	11	50	24	0	18	57	1.40
1503302--1503352	3	17.3	3	80	11	61	27	1	0	70	0.98
1503304--1503367	6	10.3	6	82	12	58	23	3	0	73	0.97
1504543--1504575	17	2.1	16	88	11	50	24	0	18	57	1.40
1507499--1507707	43	4.9	43	91	1	312	26	29	17	25	1.98
1508054--1508103	21	2.4	21	80	6	66	2	42	18	38	1.61
1513554--1513822	9	31.4	9	71	20	181	31	1	20	46	1.58
1513547--1513796	16	16.2	16	74	18	169	31	1	20	47	1.58
1513559--1513596	12	3.2	12	96	0	67	34	2	15	47	1.60
1513583--1513779	25	7.9	25	75	12	156	30	1	20	47	1.57
1513553--1513830	66	4.4	64	74	14	222	31	1	20	46	1.58
1513653--1513775	57	2.1	58	83	8	153	32	1	18	47	1.59
1513653--1513794	57	2.4	56	81	11	135	33	1	19	46	1.58
1513803--1513842	20	2.1	19	90	4	62	32	0	12	55	1.38
1513868--1513908	16	2.5	16	84	4	55	34	0	9	56	1.32
1513845--1513913	12	5.4	12	72	16	50	37	0	10	52	1.36
1513976--1514018	15	2.9	15	85	0	50	60	0	4	34	1.17
1514833--1514870	13	2.9	13	77	14	51	44	31	5	18	1.72
1516487--1516577	47	1.9	47	82	4	112	32	8	12	46	1.72
1516620--1516763	14	10.2	14	64	10	51	43	32	2	21	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1517029--1517112	39	2.2	39	93	0	141	50	22	2	25	1.61
1517364--1517607	114	2.1	114	81	5	278	27	19	20	32	1.96
1531480--1531699	108	2.0	108	98	0	422	30	13	17	38	1.88
1537250--1537326	38	2.0	38	90	5	120	38	15	2	42	1.61
1555978--1556029	25	2.1	24	89	3	77	59	1	1	36	1.19
1555997--1556047	15	3.1	15	75	20	57	62	0	1	35	1.06
1556769--1556801	17	1.9	17	93	0	57	27	24	15	33	1.95
1558724--1558761	19	2.0	20	84	5	51	44	28	7	18	1.78
1562274--1562325	24	2.2	24	85	0	68	53	9	3	32	1.51
1565268--1565315	17	2.8	17	90	9	71	33	35	16	14	1.89
1574011--1574051	21	2.0	20	85	4	55	36	2	21	39	1.67
1575298--1575322	3	8.3	3	100	0	50	0	36	0	64	0.94
1575324--1575351	3	9.3	3	100	0	56	32	0	35	32	1.58
1575828--1575880	3	17.7	3	84	7	72	67	1	28	1	1.11
1600654--1600704	22	2.3	22	86	0	66	25	25	25	23	2.00
1603297--1603348	25	2.0	27	85	7	72	46	1	0	51	1.12
1611114--1611156	20	2.1	21	84	16	56	67	0	9	23	1.19
1611164--1611256	34	2.6	38	76	11	95	51	1	9	37	1.42
1611164--1611257	36	2.6	35	75	14	93	51	1	9	38	1.42
1611242--1611297	10	5.7	10	82	4	60	50	0	8	41	1.34
1611150--1611280	2	66.5	2	71	13	58	50	0	8	40	1.38
1611241--1611297	8	6.8	8	80	11	60	49	0	8	42	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1611668--1611709	3	14.0	3	100	0	84	66	0	0	33	0.92
1612766--1612791	11	2.4	11	100	0	52	0	7	34	57	1.27
1612861--1613123	60	4.3	60	81	4	258	28	25	16	30	1.97
1612942--1613116	61	2.8	62	85	0	235	27	25	16	30	1.96
1612945--1613116	62	2.8	61	84	0	227	27	25	16	30	1.96
1613085--1613151	29	2.3	29	92	0	107	26	26	20	25	1.99
1613029--1613212	90	2.0	91	88	1	271	28	25	17	28	1.98
1613113--1613282	61	2.8	60	90	2	268	27	25	17	28	1.98
1613085--1613272	29	6.3	28	68	15	92	28	26	18	27	1.98
1615630--1615704	9	8.2	9	81	8	89	41	28	9	21	1.84

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