genome.fa.s3.2.7.7.80.10.50.1000.5.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  5  of  150  ( 17918 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)
1383725--1383794	29	2.7	24	68	21	59	40	18	8	32	1.81
1383851--1383917	9	7.4	9	89	0	80	40	25	8	25	1.84
1387903--1387968	13	5.1	13	81	7	80	34	21	9	34	1.85
1390297--1390351	26	2.1	26	100	0	110	23	27	27	21	1.99
1403323--1403416	48	2.0	48	97	0	179	39	4	9	46	1.56
1404386--1404476	34	2.7	34	96	0	164	40	1	16	41	1.55
1404720--1404827	49	2.2	49	91	1	171	25	14	11	48	1.77
1404888--1404977	27	3.3	27	83	6	119	22	24	32	21	1.98
1410075--1410123	3	16.3	3	100	0	98	34	0	0	65	0.93
1410472--1410523	15	3.4	15	94	5	95	57	5	0	36	1.23
1410474--1410525	16	3.3	16	94	5	97	57	5	0	36	1.23
1411261--1411301	20	2.0	20	90	0	64	26	14	46	12	1.80
1411629--1411962	125	2.7	126	87	1	492	38	17	15	29	1.91
1423185--1423214	2	15.0	2	92	0	51	46	0	0	53	1.00
1423214--1423246	2	16.5	2	100	0	66	51	0	48	0	1.00
1427181--1427222	14	2.8	15	85	7	50	66	4	4	23	1.30
1428433--1428469	2	18.5	2	100	0	74	51	0	0	48	1.00
1434462--1434491	2	15.0	2	100	0	60	50	0	0	50	1.00
1441174--1441208	6	5.8	6	86	0	52	28	2	0	68	1.04
1443161--1443214	17	3.3	17	82	14	69	53	0	7	38	1.29
1443176--1443222	17	2.5	19	71	28	55	55	0	6	38	1.26
1444000--1444030	9	3.4	9	90	0	53	25	12	22	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1444998--1445064	27	2.5	27	82	4	73	41	32	2	22	1.69
1445027--1445072	20	2.2	21	88	3	67	39	32	4	23	1.75
1445163--1445202	21	1.9	21	84	0	53	25	10	25	40	1.86
1451716--1451886	59	2.9	59	87	3	229	24	22	14	38	1.92
1453610--1453672	11	6.1	11	75	15	55	36	3	3	57	1.31
1453610--1453716	9	11.1	9	70	17	58	39	2	3	54	1.33
1453652--1453713	27	2.3	28	81	13	76	41	1	4	51	1.33
1454463--1454513	24	2.2	23	85	3	66	52	7	1	37	1.42
1454526--1454559	2	17.0	2	100	0	68	50	0	0	50	1.00
1457786--1457815	2	15.0	2	100	0	60	50	0	0	50	1.00
1461580--1461629	21	2.4	21	75	0	55	16	18	8	58	1.62
1464390--1464427	20	1.9	20	84	10	51	26	0	15	57	1.38
1465484--1465509	2	13.0	2	100	0	52	50	0	0	50	1.00
1466120--1466200	38	2.1	38	84	8	103	34	2	0	62	1.08
1466419--1466464	22	2.1	22	83	0	56	39	23	2	34	1.67
1468745--1468800	29	1.9	29	89	7	87	37	5	10	46	1.62
1468977--1469049	29	2.4	30	81	6	76	42	17	9	30	1.81
1469878--1469917	20	2.0	20	85	0	53	50	10	10	30	1.69
1476933--1476991	30	2.0	29	83	3	73	49	11	10	28	1.72
1489748--1489772	11	2.3	11	100	0	50	32	0	0	68	0.90
1490656--1490691	18	2.0	18	88	0	54	33	5	30	30	1.81
1492105--1492173	29	2.3	31	82	9	81	46	8	4	40	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1493226--1493261	6	6.0	6	93	0	54	44	0	5	50	1.25
1493230--1493266	18	2.1	18	89	0	56	45	0	8	45	1.32
1495782--1495819	20	1.9	20	89	10	60	44	0	7	47	1.32
1495824--1495897	31	2.4	31	86	0	103	31	20	24	24	1.98
1499608--1499645	3	12.7	3	100	0	76	34	0	0	65	0.93
1516302--1516413	56	2.0	56	100	0	224	39	8	21	30	1.84
1524683--1524727	18	2.6	17	77	19	56	33	2	2	62	1.20
1526472--1526527	21	2.6	22	94	5	98	26	33	10	28	1.90
1528676--1528710	14	2.5	14	90	9	54	48	14	8	28	1.73
1537550--1537746	98	2.0	98	95	2	351	36	23	10	28	1.89
1538100--1538135	2	18.5	2	94	5	65	52	0	0	47	1.00
1538530--1538568	2	19.5	2	100	0	78	51	0	0	48	1.00
1538658--1538719	3	20.7	3	100	0	124	66	0	0	33	0.92
1544375--1544431	20	2.8	20	94	5	96	40	0	1	57	1.09
1544409--1544442	14	2.5	13	85	4	50	41	0	0	58	0.98
1544497--1544551	12	4.7	12	78	13	60	50	1	0	47	1.11
1544481--1544608	36	3.6	36	72	16	115	55	3	0	41	1.15
1544475--1544607	11	11.1	12	69	22	66	55	3	0	40	1.18
1544485--1544608	35	3.5	36	74	16	118	56	3	0	40	1.15
1544673--1544783	18	5.6	19	70	18	59	59	0	0	39	1.04
1544737--1544784	22	2.1	24	88	7	73	60	0	0	39	0.97
1544706--1544784	38	2.1	39	81	11	92	63	1	0	35	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1558173--1558235	28	2.2	29	86	8	85	73	1	7	17	1.16
1560563--1560587	8	3.1	8	100	0	50	48	0	0	52	1.00
1566456--1566497	21	2.0	21	86	13	59	64	0	0	35	0.94
1568052--1568089	20	1.9	20	88	0	58	73	15	0	10	1.09
1575427--1575465	15	2.6	16	84	12	55	53	2	0	43	1.14
1575518--1575565	3	16.0	3	100	0	96	33	0	0	66	0.92
1588840--1588881	18	2.3	18	83	0	57	50	7	14	28	1.69
1589878--1589920	23	1.9	22	95	0	68	53	0	23	23	1.46
1589990--1590047	5	11.4	5	81	17	66	39	0	0	60	0.97
1589985--1590047	15	3.7	17	80	16	76	38	0	1	60	1.07
1589990--1590048	31	2.0	29	87	12	84	40	0	0	59	0.97
1593141--1593427	130	2.2	130	84	3	380	36	13	19	31	1.90
1593385--1593451	24	2.7	24	90	6	98	38	14	13	32	1.86
1593294--1593581	154	1.9	154	88	2	445	37	12	18	31	1.88
1593143--1593851	284	2.6	282	83	5	868	37	12	18	31	1.89
1593412--1593879	130	3.6	130	87	0	636	37	12	18	31	1.88
1600603--1600654	26	2.0	27	81	11	63	34	7	21	36	1.82
1605654--1605695	22	1.9	23	85	9	61	50	2	0	47	1.14
1605746--1605807	29	2.1	31	85	11	85	35	3	1	59	1.23
1605754--1605811	15	4.0	14	78	8	62	37	1	1	58	1.18
1607939--1608218	141	2.0	141	90	4	442	50	8	21	19	1.75
1609721--1609763	14	3.0	14	75	3	50	65	0	2	32	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1612338--1612435	28	3.5	28	97	2	180	38	13	0	47	1.42
1612785--1612834	3	16.7	3	100	0	100	0	0	32	68	0.90
1613072--1613102	12	2.6	12	94	0	53	19	0	19	61	1.35
1618736--1618770	11	3.2	11	83	0	52	28	0	14	57	1.38
1619365--1619402	19	2.0	19	85	10	51	60	7	0	31	1.25
1619423--1619510	44	2.0	44	82	10	108	1	35	0	63	1.02
1619481--1619544	26	2.5	26	85	12	96	0	31	0	68	0.90
1619705--1619799	27	3.5	27	87	8	140	50	0	8	41	1.33
1619784--1619823	11	3.9	11	78	18	50	32	0	2	65	1.06
1630253--1630384	45	3.0	44	82	2	140	33	28	16	21	1.95
1635920--1636012	46	2.0	46	100	0	186	47	26	2	23	1.63
1640854--1640933	31	2.7	28	73	16	72	43	8	8	38	1.67
1645686--1645710	12	2.1	12	100	0	50	16	24	24	36	1.94
1646160--1646214	18	3.1	18	76	10	58	49	0	0	50	1.00
1655424--1655482	31	1.9	31	85	0	82	42	6	11	38	1.68
1658281--1658311	16	1.9	16	93	0	53	38	29	0	32	1.57
1666851--1667144	9	33.3	9	74	13	263	31	1	21	45	1.61
1666866--1666932	26	2.6	26	97	0	125	32	2	20	43	1.67
1666848--1666923	17	4.8	17	71	28	78	31	3	22	42	1.72
1667202--1667240	9	4.3	9	90	0	60	30	0	23	46	1.53
1667106--1667298	96	2.0	96	98	0	377	34	2	17	45	1.62
1667395--1667428	12	2.8	13	86	13	54	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1670248--1670336	39	2.3	40	82	3	119	39	40	2	17	1.63
1670613--1670703	7	12.4	7	68	17	51	40	39	1	18	1.58
1670616--1670661	17	2.9	15	87	12	58	34	45	0	19	1.51
1670918--1671374	114	4.0	110	79	10	449	28	24	21	26	1.99
1670918--1671374	227	2.0	227	81	6	543	28	24	21	26	1.99
1677470--1677518	20	2.5	20	82	0	71	22	4	20	53	1.63
1680235--1680293	31	1.9	31	89	0	91	44	6	11	37	1.68
1688084--1688562	44	10.6	44	72	9	266	31	18	20	29	1.96
1688084--1688389	139	2.2	140	87	2	463	31	17	20	29	1.96
1688232--1688555	89	3.6	89	72	9	280	32	18	20	28	1.97

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