genome.fa.s7.2.7.7.80.10.50.1000.4.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: 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  4  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)
1426193--1426232	3	13.3	3	89	0	53	35	40	0	25	1.56
1430814--1430923	57	1.9	56	80	8	125	41	2	0	54	1.21
1440197--1440265	32	2.1	33	97	2	131	33	8	13	44	1.74
1444543--1444608	16	4.5	16	76	19	56	48	0	1	50	1.10
1454948--1454995	24	2.0	24	84	15	64	31	0	16	52	1.45
1458733--1458772	2	20.0	2	100	0	80	50	0	0	50	1.00
1461093--1461125	2	16.5	2	100	0	66	48	0	0	51	1.00
1463041--1463099	26	2.4	23	81	13	57	23	5	5	66	1.32
1467270--1467751	167	2.9	167	97	0	919	27	25	24	23	2.00
1470871--1470915	22	2.1	21	84	8	56	64	4	4	26	1.32
1471435--1471513	19	4.2	19	72	15	67	43	2	2	51	1.28
1472662--1472727	31	2.1	31	85	0	87	60	7	1	30	1.33
1476920--1477222	150	2.0	150	98	0	579	31	12	29	27	1.92
1483338--1483362	10	2.5	10	100	0	50	8	0	0	92	0.40
1483334--1483369	18	2.0	18	88	0	54	16	0	0	83	0.65
1486697--1486737	21	2.0	20	85	9	55	14	21	21	41	1.89
1494660--1494984	162	2.0	162	96	1	607	32	24	16	26	1.96
1495876--1495915	16	2.5	17	80	19	50	35	5	0	60	1.19
1506885--1506936	18	2.8	18	80	11	52	59	5	1	32	1.32
1507043--1507095	2	26.5	2	100	0	106	49	0	0	50	1.00
1509036--1509069	18	1.9	18	88	5	52	41	0	8	50	1.34
1509751--1509804	22	2.5	23	85	8	69	7	18	9	64	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1514992--1515057	33	2.0	33	93	0	114	27	10	34	27	1.90
1519806--1519847	22	1.9	22	85	0	57	26	7	4	61	1.42
1527855--1527880	11	2.4	11	100	0	52	84	0	0	15	0.62
1527851--1527927	10	7.8	10	68	17	54	67	2	2	27	1.17
1527851--1527921	29	2.5	28	76	19	74	67	1	2	28	1.13
1539261--1539294	17	2.1	17	88	5	52	26	2	2	67	1.19
1549896--1550019	62	2.0	61	84	7	162	20	16	17	44	1.87
1553704--1553771	33	2.1	33	91	0	109	29	23	16	30	1.96
1555702--1555947	123	2.0	122	99	0	483	29	14	20	35	1.93
1558607--1558657	15	3.4	15	94	0	93	29	37	27	5	1.80
1562000--1562037	3	12.7	3	94	0	67	65	31	2	0	1.06
1568902--1568958	24	2.5	24	77	5	64	43	0	0	56	0.99
1568911--1568949	15	2.4	16	87	8	53	35	0	0	64	0.94
1569112--1569193	21	4.0	22	69	18	68	57	0	1	41	1.06
1569112--1569153	11	3.9	11	87	6	68	54	0	0	45	0.99
1569116--1569240	39	3.2	39	86	3	171	61	0	2	36	1.09
1569111--1569194	11	8.1	11	78	12	54	55	0	1	42	1.07
1570397--1570433	19	1.9	19	100	0	74	32	10	0	56	1.34
1576706--1577045	125	2.7	124	86	3	452	31	15	20	33	1.93
1577308--1577410	21	4.8	20	73	14	80	22	3	25	48	1.67
1577306--1577413	23	4.9	23	74	12	109	25	4	24	46	1.71
1577306--1577410	44	2.4	44	91	0	183	23	3	24	47	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1577415--1577575	25	6.6	25	77	13	174	42	15	0	41	1.47
1578008--1578047	18	2.2	18	86	0	53	40	5	30	25	1.77
1578865--1578902	20	1.9	20	84	10	51	55	7	2	34	1.43
1579836--1579956	51	2.4	51	87	2	172	42	0	26	30	1.61
1579936--1579981	11	4.1	11	91	2	74	50	0	32	17	1.47
1592561--1592586	2	13.0	2	100	0	52	50	0	0	50	1.00
1593694--1593740	24	1.9	25	91	4	78	25	6	19	48	1.72
1594119--1594145	14	1.9	14	100	0	54	55	14	0	29	1.40
1597019--1597086	32	2.1	32	83	5	84	30	4	4	60	1.36
1613056--1613607	284	1.9	284	90	1	883	37	21	13	27	1.90
1618006--1618046	14	2.9	15	78	14	59	58	2	0	39	1.11
1621449--1621476	14	2.0	14	100	0	56	14	14	21	50	1.78
1629450--1629544	4	23.8	4	100	0	190	50	25	0	24	1.49
1637920--1637963	20	2.2	20	87	4	61	54	2	4	38	1.33
1640290--1640347	31	1.9	30	92	3	98	53	5	13	27	1.61
1646068--1646095	14	2.0	14	100	0	56	35	0	14	50	1.43
1652479--1652525	24	2.0	24	87	8	69	38	2	4	55	1.31
1657982--1658012	2	15.5	2	100	0	62	51	0	0	48	1.00
1659413--1659454	22	1.9	22	90	0	66	59	4	11	23	1.51
1659694--1659743	10	5.2	10	83	9	59	52	4	0	44	1.20
1659686--1659743	12	4.7	12	81	8	62	51	3	1	43	1.28
1659685--1659734	2	25.0	2	91	0	82	50	2	2	46	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1664597--1664659	31	2.0	31	96	0	117	55	4	6	33	1.46
1664954--1665016	30	2.1	30	93	0	108	55	15	3	25	1.55
1666045--1666079	17	2.0	17	88	5	52	31	2	0	65	1.07
1666498--1666540	18	2.4	18	96	0	77	53	9	37	0	1.33
1673229--1673287	29	2.0	30	90	3	93	28	3	11	55	1.52
1673649--1673680	2	16.0	2	100	0	64	50	0	0	50	1.00
1676690--1676742	25	2.1	25	89	6	81	66	9	0	24	1.21
1677525--1677796	112	2.5	109	84	3	357	40	13	14	31	1.85
1677866--1677954	29	3.2	29	63	18	71	58	0	15	25	1.38
1677789--1677997	54	3.9	54	89	5	307	54	0	18	26	1.48
1677971--1678009	21	1.9	21	89	5	62	53	2	12	30	1.52
1680009--1680047	18	2.2	17	86	4	51	69	0	0	30	0.89
1680873--1680933	31	2.0	31	86	0	86	32	18	11	37	1.86
1681542--1681567	4	6.5	4	100	0	52	46	0	0	53	1.00
1681789--1681883	31	3.2	30	71	14	90	45	8	18	27	1.78
1681780--1681925	57	2.6	57	83	3	188	52	8	15	24	1.70
1699829--1699899	31	2.3	31	85	4	90	29	2	16	50	1.60
1700854--1700883	15	1.9	16	93	6	53	70	0	0	30	0.88
1706783--1706826	2	23.0	2	86	9	65	50	2	0	47	1.13
1706891--1706928	19	2.0	20	89	5	60	60	2	5	31	1.33
1708778--1708959	44	4.2	44	74	6	147	28	24	17	29	1.97
1708752--1708915	87	1.9	87	89	0	256	26	21	21	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1708722--1708929	87	2.4	87	80	1	247	26	22	20	30	1.98
1709071--1709308	45	5.4	45	64	9	130	23	26	22	26	2.00
1709038--1709173	43	3.1	41	65	15	94	24	27	23	24	2.00
1708988--1709420	88	4.9	88	86	3	532	24	25	23	26	2.00
1714974--1715034	31	2.0	29	90	6	95	50	3	1	44	1.28
1727820--1727871	19	2.7	19	75	16	54	40	9	0	50	1.35
1731409--1731486	37	2.1	37	100	0	156	44	24	7	23	1.79
1731521--1731554	2	17.0	2	87	0	50	44	0	5	50	1.26
1731894--1731967	31	2.4	31	88	4	105	25	12	10	51	1.71
1753204--1753228	12	2.1	12	100	0	50	36	8	0	56	1.29
1754590--1754620	7	4.4	7	91	0	53	48	16	0	35	1.46
1766717--1766778	21	3.0	20	77	9	63	59	1	0	38	1.07
1774725--1774758	16	2.3	14	90	10	50	70	0	5	23	1.09
1774725--1774758	15	2.2	16	89	5	52	70	0	5	23	1.09
1775670--1775757	43	2.1	43	93	2	151	32	18	11	37	1.86
1776769--1776801	12	2.8	12	90	0	57	72	12	15	0	1.12
1780509--1780596	9	9.8	9	76	14	83	64	3	30	1	1.17
1780583--1780630	18	2.7	18	75	12	53	52	12	35	0	1.40
1780777--1780816	20	2.0	20	100	0	80	45	15	5	35	1.68
1800425--1800461	19	1.9	19	88	0	56	29	0	0	70	0.88
1800780--1800811	7	4.6	7	92	0	55	50	0	50	0	1.00
1802215--1802251	6	6.2	6	96	0	65	35	32	18	13	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1812598--1812646	24	2.1	23	84	3	62	57	2	4	36	1.30
1818158--1818186	2	14.5	2	100	0	58	51	0	0	48	1.00
1821249--1821810	186	3.0	188	93	1	952	35	15	15	33	1.89
1838647--1838880	116	2.0	116	96	0	432	35	17	12	33	1.88
1842145--1842228	26	3.3	26	66	21	68	46	7	3	42	1.48
1842157--1842231	25	3.0	23	69	16	60	46	8	4	41	1.52
1842243--1842270	12	2.3	12	100	0	56	39	14	10	35	1.81
1846335--1846385	25	2.0	25	84	0	66	58	7	11	21	1.58
1850518--1850552	17	2.0	18	88	5	54	45	0	0	54	0.99
1850518--1850555	18	2.1	18	85	9	51	47	0	0	52	1.00

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