genome.fa.s3.2.7.7.80.10.50.1000.25.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  25  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)
6543480--6543520	19	2.2	19	87	12	59	12	2	12	73	1.20
6544120--6544171	20	2.5	21	75	12	54	34	7	1	55	1.39
6544271--6544304	16	2.1	16	88	5	50	0	11	2	85	0.71
6545691--6545730	5	7.8	5	83	5	53	40	0	17	42	1.49
6546288--6546343	24	2.3	24	82	11	78	14	28	21	35	1.92
6554456--6554495	14	2.9	13	85	7	53	77	0	10	12	0.99
6554454--6554491	17	2.3	16	90	4	58	81	0	7	10	0.87
6554455--6554495	13	2.9	14	85	10	57	78	0	9	12	0.98
6554914--6554975	28	2.1	30	82	5	74	41	16	14	27	1.87
6559740--6559785	22	2.1	23	88	8	69	36	13	6	43	1.69
6574202--6574252	16	3.4	16	68	15	54	37	5	19	37	1.76
6574189--6574276	29	3.0	29	100	0	176	34	6	20	38	1.79
6576410--6576469	31	1.9	31	83	6	77	38	11	8	41	1.72
6577845--6577870	6	4.3	6	100	0	52	34	0	0	65	0.93
6590642--6590671	9	3.3	9	90	0	51	13	0	26	60	1.34
6590632--6590671	18	2.4	17	91	8	64	12	0	30	57	1.36
6590632--6590672	17	2.4	16	84	11	55	14	0	29	56	1.39
6592378--6592420	22	2.0	22	86	8	63	25	27	2	44	1.66
6592933--6592977	22	2.1	22	87	4	65	13	20	26	40	1.89
6593069--6593175	43	2.5	43	87	0	151	30	29	17	21	1.96
6593069--6593187	43	2.8	42	85	2	148	28	28	19	23	1.98
6593554--6593695	66	2.2	66	85	5	189	14	25	19	40	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6593569--6593718	66	2.3	66	83	4	178	16	25	18	39	1.91
6600688--6600772	42	2.0	42	90	0	134	43	15	11	29	1.82
6602276--6602454	66	2.7	65	82	6	202	32	16	22	29	1.95
6602355--6602454	30	3.1	30	68	25	78	33	17	21	29	1.95
6603924--6604053	39	3.4	39	95	1	235	27	9	13	50	1.71
6604108--6604173	24	2.8	24	97	0	123	28	12	10	48	1.74
6609436--6609508	18	4.1	18	75	21	64	65	1	21	10	1.31
6609556--6609603	21	2.3	21	85	7	62	62	0	25	12	1.30
6611583--6611711	39	3.3	39	97	1	242	28	9	11	50	1.69
6613561--6613772	101	2.1	101	84	1	273	34	14	22	28	1.93
6613596--6613739	33	4.3	33	70	13	96	35	13	21	29	1.92
6613595--6613819	101	2.3	99	82	4	247	34	15	23	26	1.94
6615657--6615696	17	2.4	17	86	0	53	47	0	10	42	1.37
6621965--6622100	40	3.5	40	75	9	127	31	25	18	25	1.97
6622973--6622997	9	2.8	9	100	0	50	0	44	0	56	0.99
6622993--6623024	4	7.8	4	93	6	55	0	25	0	75	0.81
6622996--6623023	13	2.2	13	100	0	56	0	21	0	78	0.75
6622996--6623080	20	4.6	17	76	20	82	1	18	7	72	1.13
6623087--6623162	7	10.7	7	80	16	68	50	2	1	46	1.24
6623097--6623193	43	2.3	41	81	14	119	47	3	1	48	1.24
6624403--6624432	15	2.0	15	93	0	51	70	13	0	16	1.18
6632717--6632744	3	9.3	3	100	0	56	67	0	32	0	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6637137--6637169	2	16.5	2	100	0	66	51	0	0	48	1.00
6640641--6640792	68	2.2	69	82	5	184	54	3	3	38	1.35
6643725--6643764	21	2.0	21	90	5	64	42	32	0	25	1.55
6647855--6648048	102	1.9	102	87	4	284	30	15	25	28	1.96
6649112--6649193	27	3.1	27	79	10	98	46	13	9	30	1.75
6649310--6649350	18	2.3	18	83	8	57	17	41	26	14	1.88
6656288--6656362	34	2.3	32	93	6	132	22	24	22	30	1.99
6656626--6656693	27	2.5	27	95	0	118	38	16	14	30	1.89
6658605--6658673	33	2.2	31	89	10	104	23	24	21	30	1.99
6658622--6658685	33	1.9	33	90	6	103	26	25	21	26	2.00
6658954--6659020	27	2.5	27	77	0	80	31	17	17	32	1.94
6665262--6665296	16	2.2	16	90	10	54	71	5	2	20	1.19
6665268--6665313	16	2.8	17	83	6	58	71	4	6	17	1.24
6665860--6666161	157	1.9	153	80	12	348	39	10	4	44	1.61
6666265--6666298	17	2.0	17	100	0	68	41	11	0	47	1.40
6666730--6666767	2	19.0	2	100	0	76	50	0	0	50	1.00
6667777--6667811	13	2.7	13	90	0	52	5	0	11	82	0.82
6667805--6667835	10	3.1	10	90	0	53	0	12	0	87	0.55
6670057--6670114	19	2.8	20	75	19	57	51	5	1	41	1.34
6670106--6670142	19	1.9	19	88	0	56	54	0	0	45	1.00
6670130--6670170	11	3.8	11	84	9	50	73	0	2	24	0.96
6679871--6679974	22	4.4	23	81	11	106	40	19	24	16	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6680122--6680208	2	45.0	2	80	19	105	48	3	0	48	1.18
6680143--6680208	31	2.1	31	100	0	132	48	3	0	48	1.17
6680109--6680179	21	3.4	21	98	0	133	46	4	1	47	1.30
6680973--6681011	19	2.1	19	85	9	53	10	17	0	71	1.12
6681067--6681113	23	2.0	23	83	0	58	42	12	4	40	1.63
6682985--6683072	25	3.4	26	79	13	83	57	4	6	30	1.45
6686007--6686053	24	2.0	23	84	12	60	51	8	2	38	1.45
6686018--6686430	144	2.8	145	81	9	404	40	12	5	41	1.65
6686195--6686503	148	2.1	144	81	5	311	42	12	5	40	1.65
6688723--6688756	18	1.9	18	94	5	61	17	29	41	11	1.85
6689475--6689522	24	2.0	24	100	0	96	12	8	25	54	1.65
6693380--6693468	24	3.7	24	79	10	110	44	5	25	23	1.75
6693358--6693467	48	2.3	48	85	4	150	43	5	27	23	1.75
6693612--6693679	21	3.2	21	71	8	66	17	23	16	42	1.88
6693581--6693677	42	2.3	42	83	0	122	16	22	18	42	1.89
6693597--6693705	42	2.6	42	82	2	121	16	24	15	43	1.87
6700527--6700923	30	13.2	30	86	1	519	43	18	7	30	1.78
6700506--6700934	121	3.5	121	85	5	537	43	18	7	30	1.78
6700506--6700923	151	2.7	151	89	3	608	43	18	7	30	1.78
6707922--6708621	30	23.2	30	87	1	927	43	18	8	29	1.80
6707929--6708621	121	5.7	121	88	1	926	43	18	8	29	1.80
6707901--6708621	91	7.9	91	90	1	1000	42	18	8	29	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6712920--6713053	58	2.2	60	82	8	150	43	2	6	47	1.42
6714873--6714945	29	2.5	29	82	12	80	26	23	19	31	1.98
6715064--6715213	53	2.8	54	88	5	225	28	26	13	32	1.94
6717835--6718213	22	17.2	21	82	7	416	41	17	11	29	1.85
6717835--6718216	44	8.7	44	89	0	530	41	17	11	29	1.85
6717898--6717997	11	9.0	12	67	16	72	43	17	10	30	1.81
6718396--6718431	2	18.0	2	100	0	72	50	0	0	50	1.00
6719952--6720006	27	2.0	27	96	0	101	34	21	7	36	1.81
6723679--6723741	26	2.4	26	89	0	90	38	11	14	36	1.81
6726592--6726708	22	5.3	22	88	0	162	27	25	14	32	1.95
6728827--6728870	13	3.3	14	87	6	56	20	20	11	47	1.80
6739569--6739987	110	3.8	107	89	4	556	34	18	16	31	1.93
6739961--6740002	18	2.3	18	87	0	57	33	7	4	54	1.49
6740111--6740162	24	2.0	27	85	10	74	63	11	5	19	1.47
6742204--6742258	27	2.0	27	100	0	110	36	18	10	34	1.86
6742582--6742634	16	3.4	15	75	14	54	64	3	7	24	1.37
6745425--6745537	25	4.5	25	83	4	120	18	25	21	34	1.96
6745416--6745560	50	2.9	50	80	3	159	16	26	22	35	1.95
6745514--6745599	25	3.5	24	81	9	77	17	25	23	33	1.96
6745541--6745611	25	2.8	26	85	10	87	19	28	22	29	1.98
6746550--6746634	41	2.1	41	90	0	134	18	24	30	25	1.98
6749462--6749515	3	18.0	3	100	0	108	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6750341--6750386	13	3.5	13	81	0	56	30	8	21	39	1.84
6752309--6752984	343	2.0	343	97	0	1280	30	16	12	39	1.86
6754005--6754400	162	2.5	162	85	4	500	47	13	11	27	1.77
6754050--6754400	81	4.3	82	84	1	454	47	13	11	27	1.77
6754529--6754652	51	2.5	48	83	7	151	53	8	1	37	1.40
6754529--6754660	50	2.7	49	80	8	144	52	8	1	37	1.41
6767868--6767976	40	2.7	41	78	13	134	15	17	28	38	1.90
6769949--6769984	18	2.0	18	100	0	72	11	16	22	50	1.77
6774740--6774835	31	3.1	31	95	3	174	31	9	13	45	1.75
6776652--6776694	18	2.4	18	92	3	70	55	0	20	23	1.43

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