genome.fa.s10.2.7.7.80.10.50.1000.4.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: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62175169

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   

This is table  4  of  202  ( 24201 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)
1160095--1160165	22	3.2	22	65	21	58	57	12	5	23	1.56
1168990--1169045	2	28.0	2	96	0	103	48	0	51	0	1.00
1174944--1174981	18	2.2	18	90	9	62	71	2	5	21	1.19
1180981--1181024	18	2.4	19	81	14	56	70	0	15	13	1.17
1187337--1187369	3	11.0	3	93	0	57	30	3	33	33	1.73
1190204--1190241	18	2.1	19	90	9	62	26	10	5	57	1.53
1194540--1194580	2	20.5	2	100	0	82	51	0	0	48	1.00
1194692--1194725	3	11.3	3	93	0	59	67	2	0	29	1.05
1194915--1194956	21	2.0	21	90	0	66	33	19	14	33	1.91
1197837--1197912	32	2.4	32	86	2	100	26	19	9	44	1.80
1204217--1204340	58	2.1	58	100	0	248	37	6	16	39	1.75
1219297--1219346	20	2.5	20	80	3	64	28	2	2	68	1.12
1226830--1226862	8	4.1	8	100	0	66	24	0	0	75	0.80
1232305--1232348	22	2.0	21	82	4	52	31	2	18	47	1.61
1232399--1232434	17	2.1	18	89	5	56	52	0	0	47	1.00
1232515--1232560	22	2.1	22	95	0	83	41	6	0	52	1.27
1235425--1235486	28	2.2	28	100	0	124	30	16	6	46	1.72
1236545--1236574	15	2.0	15	93	0	51	50	0	0	50	1.00
1246037--1246075	3	13.0	3	100	0	78	33	0	0	66	0.92
1249425--1249581	84	1.9	84	89	4	246	31	7	15	45	1.74
1253458--1253489	2	16.0	2	100	0	64	50	0	0	50	1.00
1255738--1255782	16	2.8	16	82	0	54	60	17	0	22	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1256432--1256461	8	3.8	8	95	0	51	46	0	0	53	1.00
1263043--1263090	2	24.0	2	100	0	96	50	0	0	50	1.00
1273763--1273831	31	2.2	31	82	10	79	34	15	11	37	1.84
1277046--1277075	14	2.1	15	93	6	53	53	0	0	46	1.00
1277045--1277078	14	2.5	13	86	13	50	50	0	0	50	1.00
1277263--1277301	19	2.2	19	86	9	55	58	2	0	38	1.12
1289462--1289547	9	9.4	9	85	7	93	41	24	10	23	1.85
1289794--1289946	22	7.0	22	90	0	225	32	14	26	26	1.94
1290084--1290112	4	7.2	4	100	0	58	27	24	24	24	2.00
1294658--1294682	2	12.5	2	100	0	50	48	0	0	52	1.00
1295908--1295938	2	15.5	2	100	0	62	48	0	0	51	1.00
1298818--1298891	25	3.1	25	67	11	73	47	18	9	24	1.78
1298792--1298891	47	2.1	47	96	0	182	46	21	10	23	1.81
1298796--1298870	22	3.3	22	69	10	69	45	25	10	18	1.82
1301558--1301646	39	2.2	41	88	5	130	53	7	0	38	1.30
1302797--1302895	52	1.9	52	80	0	117	36	31	11	21	1.88
1306278--1306303	3	8.7	3	100	0	52	69	0	30	0	0.89
1307496--1307563	29	2.3	30	77	10	77	38	8	10	42	1.70
1312471--1312526	29	2.0	28	86	10	80	50	3	0	46	1.19
1318318--1318355	17	2.4	17	82	8	53	42	7	2	47	1.46
1320442--1320483	19	2.1	21	82	8	52	47	2	2	47	1.28
1320871--1320903	6	5.3	6	92	7	57	81	0	0	18	0.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1332326--1332384	31	1.9	31	86	3	84	40	5	13	40	1.67
1332905--1332929	6	4.2	6	100	0	50	52	16	0	32	1.44
1333084--1333270	66	2.8	66	95	1	331	37	16	24	21	1.93
1335856--1335913	29	2.0	28	83	12	73	46	10	5	37	1.60
1335896--1335946	23	2.3	22	75	3	57	56	1	1	39	1.22
1337207--1337260	27	2.0	27	88	0	81	40	5	11	42	1.64
1337769--1337794	2	13.0	2	100	0	52	50	0	0	50	1.00
1340480--1340518	2	19.5	2	100	0	78	51	0	0	48	1.00
1340585--1340612	4	7.0	4	100	0	56	50	0	25	25	1.50
1346565--1346627	27	2.3	27	81	10	83	42	7	6	42	1.59
1352322--1352406	42	2.0	42	88	2	125	20	14	15	50	1.77
1354928--1354971	13	3.3	13	82	17	63	34	2	20	43	1.64
1354927--1354972	14	3.4	14	77	17	60	32	2	19	45	1.62
1359713--1360044	177	1.9	177	87	1	486	34	19	18	27	1.96
1361163--1361218	19	2.8	20	82	10	71	30	25	7	37	1.82
1361184--1361225	20	2.1	20	90	0	66	30	28	4	35	1.78
1361912--1362021	57	1.9	56	90	1	175	29	15	4	50	1.63
1361932--1362021	26	3.1	29	72	20	98	28	17	4	48	1.66
1366131--1366197	33	2.0	33	100	0	134	50	25	2	20	1.62
1367142--1367186	16	2.7	16	86	6	54	57	6	26	8	1.54
1369427--1369460	16	2.0	18	88	11	54	67	0	0	32	0.91
1374872--1374917	22	2.1	22	87	0	65	19	15	13	52	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1400120--1400149	12	2.5	12	94	0	51	33	0	3	63	1.11
1405843--1405886	19	2.2	21	92	8	74	22	15	9	52	1.71
1411691--1411771	34	2.4	34	95	2	146	35	4	0	59	1.19
1411691--1411781	34	2.7	34	91	1	112	37	4	0	58	1.18
1412935--1413029	23	4.1	23	88	0	136	22	28	4	45	1.71
1416041--1416084	19	2.2	21	92	8	74	22	15	9	52	1.71
1417573--1417606	15	2.3	15	85	14	52	35	0	0	64	0.94
1417575--1417606	14	2.2	15	94	5	57	34	0	0	65	0.93
1428843--1428898	26	2.2	26	90	6	87	16	17	21	44	1.86
1428851--1428971	25	4.9	25	67	12	63	19	23	22	35	1.96
1431316--1431360	23	2.0	23	90	0	72	73	0	8	17	1.08
1441508--1441532	2	12.5	2	100	0	50	52	0	0	48	1.00
1442073--1442106	2	17.0	2	100	0	68	50	0	0	50	1.00
1444118--1444153	2	18.5	2	94	5	65	0	50	0	50	1.00
1444213--1444242	2	15.0	2	100	0	60	50	0	0	50	1.00
1444752--1444790	2	19.5	2	100	0	78	51	0	0	48	1.00
1446586--1446671	45	1.9	45	90	0	136	50	1	6	41	1.37
1446610--1446674	24	3.0	20	74	24	60	47	0	6	46	1.27
1446613--1446681	20	3.2	20	72	27	61	50	0	5	43	1.26
1450582--1450633	24	2.2	24	89	0	77	36	3	9	50	1.54
1452239--1452288	26	1.9	26	87	0	73	52	18	14	16	1.76
1457667--1457720	26	2.3	24	84	15	69	59	3	0	37	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1459196--1459228	15	2.3	15	89	5	50	75	0	6	18	1.00
1464960--1465003	2	22.0	2	100	0	88	50	0	0	50	1.00
1465390--1465450	2	30.5	2	100	0	122	49	0	0	50	1.00
1466588--1466634	19	2.3	21	82	7	62	40	40	6	12	1.69
1466635--1466697	20	3.0	21	79	4	74	25	9	26	38	1.87
1466635--1466697	21	3.0	21	81	4	74	25	9	26	38	1.87
1466639--1466711	21	3.5	20	76	12	67	23	8	28	39	1.83
1467728--1467765	16	2.3	17	82	17	53	55	23	2	18	1.55
1468451--1468502	4	14.0	4	77	18	51	23	1	0	75	0.91
1468451--1468501	13	4.2	12	78	19	52	21	1	0	76	0.88
1468460--1468497	10	3.5	11	86	13	53	21	2	0	76	0.91
1484411--1484463	26	2.0	26	81	0	61	49	1	5	43	1.37
1485057--1485086	10	3.0	10	100	0	60	50	10	0	40	1.36
1485353--1485393	2	20.5	2	100	0	82	51	0	0	48	1.00
1487354--1487398	16	2.8	16	78	21	58	31	8	17	42	1.80
1502637--1502666	4	7.5	4	100	0	60	50	23	0	26	1.50
1503713--1503738	3	8.7	3	100	0	52	69	0	0	30	0.89
1504527--1504563	17	2.2	18	85	14	60	64	0	0	35	0.94
1516094--1516126	15	2.2	15	100	0	66	24	15	24	36	1.93
1530439--1530482	19	2.2	20	84	11	56	40	2	0	56	1.11
1531630--1532235	198	3.1	197	87	4	864	29	16	17	36	1.92
1536486--1536544	29	2.0	29	83	0	73	35	5	20	38	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1537142--1537179	16	2.4	17	86	8	53	60	13	0	26	1.33
1538988--1539184	98	2.0	98	95	0	358	36	23	10	29	1.89
1540506--1540563	22	2.6	22	84	7	73	43	17	3	36	1.66
1540553--1540614	21	3.1	21	84	11	94	35	14	11	38	1.82
1542279--1542320	16	2.7	15	85	7	66	73	4	0	21	1.01
1542529--1542567	19	2.2	19	86	9	55	61	0	0	38	0.96
1543898--1543936	19	2.2	17	86	9	51	56	5	10	28	1.54
1545833--1546396	180	3.1	177	82	8	599	29	11	17	40	1.85
1549563--1549599	13	2.7	14	87	8	58	32	5	18	43	1.73
1556664--1556753	25	3.6	25	69	11	76	37	14	26	21	1.92

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