genome.fa.s12.2.7.7.80.10.50.1000.5.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: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  35429946

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   

This is table  5  of  120  ( 14336 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)
1564842--1564890	15	3.1	16	82	8	55	59	0	6	34	1.22
1568862--1568915	7	7.7	7	89	0	81	40	3	25	29	1.73
1568901--1569229	51	6.1	51	81	13	356	32	15	22	29	1.95
1569026--1569061	17	2.1	17	100	0	72	30	22	11	36	1.89
1568975--1569110	68	2.0	68	95	0	245	30	16	20	31	1.95
1568919--1569162	119	2.0	120	93	1	427	30	17	21	30	1.96
1568901--1569211	170	1.8	169	92	0	532	31	16	22	29	1.96
1576291--1576327	18	2.1	18	94	0	65	43	0	2	54	1.14
1576283--1576325	18	2.3	18	84	8	52	44	0	2	53	1.13
1590681--1590723	7	6.6	7	92	7	65	0	11	0	88	0.52
1590682--1590725	6	7.2	6	92	7	63	0	13	0	86	0.57
1590680--1590725	19	2.5	19	83	16	69	0	13	0	86	0.56
1594416--1594455	2	20.0	2	100	0	80	50	0	0	50	1.00
1599600--1599652	22	2.4	22	80	0	61	64	15	7	13	1.49
1601359--1601435	29	2.6	29	83	4	91	49	14	12	23	1.78
1604097--1604125	12	2.3	13	94	5	51	55	3	0	41	1.17
1618654--1618707	19	2.8	20	80	13	67	61	0	5	33	1.19
1618655--1618720	10	6.7	10	82	8	73	59	0	6	34	1.22
1618741--1618793	9	5.9	9	81	16	65	64	1	3	30	1.22
1618962--1619035	10	7.6	10	73	10	55	35	0	2	62	1.10
1618951--1619015	19	3.4	18	74	15	60	30	1	3	64	1.18
1618961--1619042	29	2.8	29	77	15	87	34	0	3	62	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1619197--1619408	89	2.4	88	83	6	266	34	10	17	36	1.84
1623187--1623286	49	2.0	49	98	0	191	48	9	18	25	1.77
1627598--1627724	59	2.2	59	78	14	140	41	15	17	25	1.89
1627569--1627724	56	2.7	56	77	13	147	44	14	16	24	1.85
1630156--1630233	40	2.0	40	82	5	95	33	24	2	39	1.69
1631114--1631155	20	2.0	21	86	4	59	38	0	0	61	0.96
1631301--1631332	13	2.5	13	94	0	55	59	0	0	40	0.97
1633498--1633537	2	19.5	2	94	5	71	47	0	2	50	1.14
1634583--1634784	44	4.6	44	72	7	142	25	24	21	28	1.99
1634828--1635726	132	6.8	132	90	2	1379	28	24	17	29	1.98
1634831--1635670	44	19.0	44	66	7	291	28	24	17	29	1.98
1634838--1635720	402	2.2	398	90	2	1405	28	24	17	29	1.98
1635793--1635930	44	3.2	44	67	17	133	26	21	23	28	1.99
1635727--1635937	87	2.4	87	89	0	314	24	22	23	29	1.99
1637171--1637212	7	6.0	7	79	20	52	14	16	0	69	1.20
1638141--1638188	21	2.3	21	89	10	73	66	2	16	14	1.34
1638415--1638541	63	2.0	63	100	0	254	19	28	14	37	1.91
1640176--1640201	13	2.0	13	100	0	52	46	15	7	30	1.74
1641905--1641949	2	22.5	2	100	0	90	51	0	0	48	1.00
1642085--1642140	25	2.2	26	80	6	69	48	5	7	39	1.54
1644180--1644256	29	2.6	29	83	4	91	46	15	14	23	1.82
1644342--1644397	19	2.9	18	82	15	60	57	3	0	39	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1644367--1644430	9	6.7	9	74	22	51	51	0	1	46	1.10
1644373--1644439	22	3.3	20	80	11	68	52	1	1	44	1.19
1645115--1645153	17	2.3	17	90	0	60	23	0	5	71	1.05
1649297--1649341	24	1.9	23	86	13	65	37	0	2	60	1.09
1649438--1649465	9	3.1	9	100	0	56	57	10	0	32	1.33
1649408--1649549	68	2.1	66	94	2	248	45	9	4	40	1.58
1649538--1649579	16	2.6	16	92	0	66	42	7	2	47	1.43
1649553--1649602	22	2.3	22	85	0	64	44	2	2	52	1.24
1649408--1649571	68	2.5	66	86	10	216	45	9	4	40	1.55
1649576--1649607	17	1.9	17	93	6	57	56	0	0	43	0.99
1651289--1651344	26	2.1	28	83	6	71	58	5	7	28	1.46
1652041--1652099	31	1.9	31	85	0	82	44	10	11	33	1.75
1657163--1657385	110	2.0	110	99	0	437	29	19	13	37	1.90
1660776--1660808	11	2.9	11	95	4	57	72	0	0	27	0.85
1661006--1661031	13	2.0	13	100	0	52	53	15	7	23	1.67
1665216--1665240	7	3.6	7	100	0	50	36	0	16	48	1.46
1676864--1676896	18	1.9	18	88	11	52	33	0	12	54	1.37
1680064--1680095	16	2.0	17	88	11	50	59	0	3	37	1.13
1681218--1681275	27	2.2	26	84	9	73	67	1	3	27	1.17
1681214--1681279	9	7.2	9	73	10	53	65	1	3	30	1.17
1681793--1681852	22	2.7	22	79	5	59	51	3	1	43	1.28
1681818--1681888	11	6.9	11	76	20	82	54	0	1	43	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1681834--1681933	28	3.6	28	86	8	132	63	0	2	35	1.06
1681844--1681877	17	2.0	17	100	0	68	58	0	0	41	0.98
1682918--1682944	13	2.1	13	100	0	54	48	7	14	29	1.71
1683769--1683831	31	2.0	31	100	0	126	28	0	19	52	1.46
1686342--1686397	18	2.9	19	92	7	96	35	0	0	64	0.94
1686695--1686727	17	2.1	17	88	11	52	63	0	0	36	0.95
1690209--1690410	97	2.1	97	100	0	404	33	15	28	21	1.95
1692691--1692735	14	3.1	14	82	14	56	37	2	0	60	1.09
1695629--1695674	20	2.3	20	92	0	74	65	0	0	34	0.93
1713947--1714041	29	3.2	30	86	5	140	36	22	2	38	1.66
1714395--1714426	3	10.7	3	100	0	64	68	0	31	0	0.90
1714543--1714577	13	2.6	13	86	4	52	82	8	8	0	0.83
1714601--1714640	19	2.1	19	90	9	64	27	42	30	0	1.56
1714708--1714788	10	8.5	10	80	13	91	83	0	16	0	0.64
1714713--1714781	7	9.9	7	79	14	72	84	0	15	0	0.63
1714731--1714784	1	54.0	1	77	0	54	88	0	11	0	0.50
1714708--1714788	17	4.9	16	73	23	62	83	0	16	0	0.64
1714711--1714788	29	2.7	29	88	5	106	84	0	15	0	0.62
1714711--1714788	37	2.1	38	86	11	108	84	0	15	0	0.62
1714710--1714788	28	2.8	26	85	11	95	84	0	15	0	0.61
1715100--1715139	21	1.9	22	90	10	66	32	17	10	40	1.83
1715170--1715360	37	5.2	37	73	16	123	30	13	10	45	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1715370--1715411	20	2.0	20	86	4	57	30	11	9	47	1.72
1715108--1715514	18	21.9	18	67	15	154	29	12	11	46	1.77
1719015--1719047	11	3.0	11	100	0	66	9	9	18	63	1.49
1719014--1719063	22	2.3	22	82	0	64	8	8	20	64	1.46
1725856--1725905	19	2.6	20	84	15	70	30	0	8	62	1.24
1725830--1725904	18	4.2	18	73	11	66	37	0	6	56	1.26
1734917--1734945	2	14.5	2	100	0	58	48	0	0	51	1.00
1739764--1739816	6	8.8	6	100	0	106	67	0	15	16	1.23
1741045--1741178	67	2.0	67	98	0	259	23	23	8	44	1.81
1746631--1746668	18	2.1	18	90	5	58	63	2	18	15	1.43
1748108--1748181	37	2.0	37	83	0	94	36	10	18	33	1.86
1760778--1760815	20	1.9	19	89	5	58	55	23	0	21	1.44
1760856--1760930	14	5.2	14	75	18	57	49	25	2	22	1.63
1761331--1761371	21	2.0	21	85	9	57	41	26	0	31	1.56
1761622--1761670	16	3.1	16	93	0	89	34	6	36	22	1.79
1761650--1761739	45	2.0	44	89	6	137	32	5	28	33	1.80
1761884--1761925	15	2.7	16	82	14	52	52	2	0	45	1.13
1761893--1761934	15	2.9	15	82	10	52	52	0	0	47	1.00
1761919--1762106	61	3.1	61	70	14	199	49	6	1	42	1.36
1761887--1762179	120	2.4	121	94	1	509	50	5	2	42	1.36
1761887--1762183	59	5.0	59	67	17	184	50	5	2	42	1.35
1762003--1762054	15	3.6	15	80	12	56	53	1	0	44	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1762226--1762296	27	2.8	27	81	8	69	50	5	0	43	1.25
1762458--1762502	22	2.0	22	100	0	90	42	13	0	44	1.43
1765207--1765265	20	2.9	19	82	9	64	45	28	1	23	1.63
1765398--1765471	21	3.5	21	76	10	62	51	31	0	17	1.46
1765906--1766028	35	3.5	34	76	13	117	44	33	0	21	1.58
1765946--1766038	20	4.5	20	76	6	78	46	33	0	20	1.51
1766140--1766184	23	1.9	22	82	13	54	57	8	6	26	1.54
1767223--1767265	22	2.0	22	82	13	54	37	0	11	51	1.39
1767543--1767621	30	2.5	31	81	10	97	17	6	21	54	1.65
1770062--1770113	21	2.5	21	83	0	68	36	40	11	11	1.78

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