genome.fa.s13.2.7.7.80.10.50.1000.5.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  5  of  199  ( 23770 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)
1571949--1572464	175	3.1	159	79	13	537	56	13	0	29	1.39
1572109--1572145	19	1.9	19	94	0	65	48	16	0	35	1.46
1572237--1572263	14	1.9	14	100	0	54	66	11	0	22	1.22
1572268--1572309	8	5.0	8	78	21	50	61	14	0	23	1.32
1572268--1572323	27	2.1	26	93	3	94	58	14	0	26	1.36
1572302--1572525	61	3.4	61	72	21	207	59	10	0	29	1.30
1572363--1572645	19	14.3	19	68	21	129	56	12	0	30	1.38
1572395--1572490	27	3.3	27	69	18	84	63	9	0	27	1.25
1572443--1572620	80	2.3	79	79	10	188	56	12	0	31	1.37
1572382--1572525	61	2.4	61	97	0	270	59	10	0	29	1.30
1572518--1572607	27	3.2	27	84	9	117	54	13	0	32	1.39
1572288--1572602	141	2.3	138	83	11	414	58	11	0	30	1.33
1572550--1572611	31	2.0	31	96	0	115	51	14	0	33	1.43
1572654--1572722	27	2.6	27	92	0	120	18	28	20	31	1.96
1573825--1573863	3	13.0	3	100	0	78	66	0	0	33	0.92
1573864--1573908	3	15.0	3	100	0	90	33	0	0	66	0.92
1573983--1574064	40	2.0	40	97	0	155	41	6	9	42	1.62
1580418--1580542	48	2.5	51	84	7	157	34	11	5	48	1.62
1582626--1582665	2	20.0	2	100	0	80	50	0	0	50	1.00
1587982--1588179	107	1.9	107	80	4	238	36	12	12	38	1.81
1593639--1593673	6	5.8	6	100	0	70	48	17	17	17	1.81
1597795--1597837	18	2.4	19	80	11	54	34	0	2	62	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1603577--1603622	19	2.4	19	82	17	60	39	0	8	52	1.33
1604343--1604440	31	3.2	31	71	16	85	55	9	8	27	1.60
1604520--1604592	34	2.1	34	100	0	146	31	15	17	35	1.91
1615282--1615568	108	2.6	109	88	4	418	33	20	17	28	1.95
1615896--1615938	12	3.7	11	84	9	50	60	0	0	39	0.97
1615949--1615982	17	2.0	17	88	0	50	50	2	8	38	1.49
1616165--1616203	16	2.4	16	87	8	53	74	2	5	17	1.12
1616381--1616498	3	39.3	3	78	13	109	63	0	5	30	1.18
1616381--1616498	51	2.4	50	84	12	147	63	0	5	30	1.18
1619114--1619147	16	2.2	15	89	5	50	29	0	14	55	1.40
1626277--1626320	2	22.0	2	95	0	79	47	0	2	50	1.13
1631594--1631620	14	1.9	14	100	0	54	33	0	0	66	0.92
1632250--1632337	43	2.0	43	91	8	144	32	2	6	57	1.37
1636180--1636204	5	5.0	5	100	0	50	0	20	60	20	1.37
1636219--1636280	27	2.3	27	97	0	115	29	22	33	14	1.94
1636424--1636483	21	2.7	22	78	17	54	60	5	1	33	1.29
1636443--1636530	24	3.9	23	81	8	94	63	0	1	35	1.02
1636462--1636527	12	5.6	12	85	7	91	62	0	1	36	1.05
1636615--1636709	27	3.7	27	78	17	112	35	1	11	51	1.45
1636619--1636762	48	3.0	48	83	7	186	33	1	13	52	1.49
1636805--1636842	19	2.0	19	89	0	58	36	5	7	50	1.54
1637052--1637128	27	2.9	28	90	3	115	19	38	24	16	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1640643--1640815	26	6.0	27	65	21	75	43	0	1	54	1.15
1640858--1640892	17	2.1	16	89	5	52	34	0	0	65	0.93
1640557--1641030	119	4.0	120	93	2	809	42	0	4	52	1.26
1640557--1641030	239	2.0	234	92	2	797	42	0	4	52	1.26
1645349--1645377	3	9.7	3	100	0	58	0	65	0	34	0.93
1647794--1647822	7	4.3	7	91	8	51	55	0	0	44	0.99
1651541--1651589	25	1.9	26	91	4	82	40	20	6	32	1.77
1651809--1651835	13	2.1	13	100	0	54	37	0	7	55	1.28
1654712--1654781	16	4.4	16	88	0	104	32	1	35	30	1.67
1654712--1654781	32	2.2	32	94	0	122	32	1	35	30	1.67
1654995--1655035	16	2.6	16	84	11	57	53	0	0	46	1.00
1654995--1655045	15	3.5	15	84	10	61	52	0	0	47	1.00
1655030--1655216	61	3.1	60	69	14	177	47	7	2	42	1.45
1655001--1655216	120	1.8	120	95	0	396	48	6	2	43	1.41
1655031--1655217	59	3.1	58	68	20	168	47	7	2	42	1.45
1656537--1656564	11	2.5	11	100	0	56	53	35	10	0	1.36
1661350--1661401	25	2.1	25	100	0	104	23	13	30	32	1.93
1665566--1666560	154	6.5	154	92	1	1560	25	23	22	28	1.99
1668694--1668747	20	2.5	22	82	5	67	42	1	0	55	1.10
1668903--1668944	17	2.5	17	81	11	52	57	11	7	23	1.59
1673005--1673038	18	1.9	17	88	5	50	2	20	0	76	0.92
1681727--1681771	11	4.4	10	81	15	56	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1681738--1681769	12	2.8	12	86	13	50	56	0	0	43	0.99
1684715--1684744	14	2.1	15	93	6	53	26	0	3	70	1.03
1684754--1684828	19	4.0	18	80	10	78	38	0	5	56	1.22
1684784--1684829	10	4.7	10	79	15	60	34	0	2	63	1.07
1684754--1684828	9	8.0	9	69	8	51	38	0	5	56	1.22
1686706--1686730	7	3.6	7	100	0	50	40	0	0	60	0.97
1686947--1686971	4	6.2	4	100	0	50	76	0	0	24	0.80
1687760--1687803	19	2.3	19	84	7	54	34	4	2	59	1.30
1687767--1687808	19	2.3	19	88	12	61	30	4	2	61	1.29
1688988--1689015	2	14.0	2	100	0	56	50	0	0	50	1.00
1710878--1710916	20	2.0	20	85	10	53	66	28	2	2	1.18
1710849--1710916	11	6.6	10	70	16	50	66	26	5	1	1.23
1716459--1716507	23	2.1	23	84	3	62	44	6	0	48	1.27
1718962--1719003	2	21.0	2	100	0	84	50	0	0	50	1.00
1719406--1719450	22	2.0	22	100	0	90	26	31	8	33	1.87
1739197--1739234	9	4.1	9	86	6	58	84	0	13	2	0.73
1739640--1739664	13	1.9	13	100	0	50	24	0	0	76	0.80
1742765--1743074	110	2.8	109	91	2	498	34	20	15	29	1.94
1743497--1743548	2	26.0	2	100	0	104	50	0	0	50	1.00
1745667--1745894	114	2.0	114	97	0	429	32	15	27	25	1.95
1750744--1750788	17	2.8	16	77	16	56	42	4	2	51	1.34
1755905--1755980	29	2.5	29	77	10	73	42	11	3	42	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1758722--1758763	22	2.0	21	86	9	59	42	0	4	52	1.22
1762717--1763018	37	7.7	40	78	16	230	37	14	21	27	1.92
1762755--1763018	37	6.9	37	83	9	325	37	14	20	27	1.92
1762829--1762983	82	1.9	82	94	0	274	35	14	21	27	1.93
1762717--1763018	155	1.9	156	91	0	489	37	14	21	27	1.92
1764527--1764578	24	2.2	24	85	0	68	53	9	3	32	1.51
1765092--1765117	13	2.0	13	100	0	52	46	7	15	30	1.74
1770075--1770126	21	2.3	24	77	19	74	46	3	26	23	1.69
1770082--1770124	21	2.0	21	95	0	77	48	4	30	16	1.66
1777432--1777466	6	5.8	6	96	0	52	14	22	34	28	1.93
1778156--1778181	13	2.0	13	100	0	52	23	0	0	76	0.78
1788399--1788432	2	17.0	2	100	0	68	50	0	0	50	1.00
1789048--1789087	20	2.0	20	100	0	80	25	10	10	55	1.64
1792750--1792787	19	2.0	19	89	0	58	7	18	5	68	1.34
1793553--1793596	3	14.0	3	88	4	61	31	0	4	63	1.14
1793803--1793847	16	2.9	16	83	9	58	33	6	2	57	1.37
1793867--1793932	32	2.1	31	81	15	75	34	6	1	57	1.33
1794930--1794978	9	5.4	9	79	16	57	53	0	2	44	1.12
1795040--1795074	2	17.5	2	100	0	70	51	0	0	48	1.00
1795535--1795582	17	2.9	17	72	27	50	56	0	10	33	1.34
1798305--1798481	88	2.0	88	100	0	354	36	10	21	31	1.87
1799868--1799954	44	2.0	44	86	8	124	64	2	1	32	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1799869--1799965	52	1.9	50	87	4	140	63	2	1	32	1.12
1801521--1801574	20	3.0	19	73	26	55	55	5	0	38	1.23
1802354--1802384	14	2.1	15	94	5	55	35	0	0	64	0.94
1806786--1807415	304	2.1	299	90	5	994	42	20	12	24	1.86
1813262--1813303	20	2.3	18	77	18	50	28	14	4	52	1.62
1818463--1818503	20	2.0	20	86	9	57	48	4	4	41	1.46
1833213--1833254	12	3.5	12	80	0	57	30	4	16	47	1.67
1833212--1833265	24	2.2	24	100	0	108	31	9	16	42	1.80
1833225--1833265	12	3.4	12	79	0	55	31	9	17	41	1.82
1839475--1840670	409	2.9	407	94	1	2101	39	11	15	34	1.83

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