genome.fa.s25.2.7.7.80.10.50.1000.35.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: Scaffold25
Parameters: 2 7 7 80 10 50 1000
Length:  9553305

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   

This is table  35  of  56  ( 6609 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)
6057376--6057415	16	2.5	16	87	0	53	52	0	0	47	1.00
6057388--6057427	16	2.5	16	100	0	80	47	0	0	52	1.00
6057408--6057442	13	2.6	13	90	4	52	42	0	0	57	0.99
6057786--6057826	15	2.7	15	96	0	73	43	0	2	53	1.13
6057785--6057843	15	3.9	15	82	6	57	45	0	1	52	1.10
6057781--6057842	31	2.0	31	84	12	83	45	0	3	51	1.17
6057849--6057926	32	2.5	31	79	6	75	21	10	21	46	1.81
6058995--6059055	16	3.8	16	80	0	68	18	14	24	42	1.88
6058996--6059134	32	4.3	32	80	3	129	20	15	23	41	1.90
6059018--6059151	64	2.1	64	83	8	166	20	15	22	41	1.90
6059002--6059173	16	10.8	16	70	14	97	19	15	23	40	1.90
6058995--6059134	48	2.9	47	76	8	131	20	15	23	40	1.90
6066904--6066934	2	15.5	2	93	0	53	48	0	3	48	1.17
6068647--6068683	19	1.9	19	89	10	58	35	0	0	64	0.94
6068691--6068731	19	2.2	19	86	8	57	48	0	2	48	1.14
6068675--6068761	45	1.9	45	88	0	129	49	0	2	48	1.13
6068955--6069001	16	3.0	15	81	9	58	59	0	0	40	0.97
6069422--6069499	23	3.5	21	75	17	61	33	0	2	64	1.08
6069442--6069499	24	2.5	23	84	13	75	34	0	0	65	0.93
6081179--6081206	2	14.0	2	100	0	56	50	0	50	0	1.00
6082911--6082945	16	2.1	17	89	5	54	51	0	0	48	1.00
6083782--6083824	20	2.0	22	91	8	72	23	0	4	72	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6083853--6083890	17	2.2	18	90	4	60	57	5	0	36	1.21
6083906--6083952	22	2.2	20	81	7	58	51	0	0	48	1.00
6083910--6083965	26	2.1	27	90	3	87	48	0	1	50	1.11
6084010--6084054	10	4.4	10	81	15	56	57	0	0	42	0.98
6084057--6084110	26	2.1	25	82	6	63	33	0	0	66	0.92
6085232--6085264	2	16.5	2	100	0	66	0	0	48	51	1.00
6088588--6088678	30	3.0	30	100	0	182	50	19	6	23	1.71
6092401--6092430	1	30.0	1	100	0	60	100	0	0	0	0.00
6093360--6093796	211	2.1	210	98	1	693	50	2	5	40	1.41
6094181--6094212	11	2.8	12	90	9	50	43	0	0	56	0.99
6094446--6094488	22	2.0	22	81	9	52	41	4	9	44	1.57
6094649--6094706	19	3.0	20	76	19	59	36	1	1	60	1.17
6095350--6095415	14	4.2	16	70	24	52	59	0	0	40	0.98
6095340--6095399	26	2.3	26	83	11	70	56	0	1	41	1.09
6095347--6095414	6	10.3	7	74	17	56	57	0	0	42	0.98
6096020--6096091	11	6.5	11	77	17	69	40	1	0	58	1.07
6096020--6096091	5	14.0	5	76	16	67	40	1	0	58	1.07
6096570--6096595	11	2.4	11	100	0	52	53	11	7	26	1.63
6097096--6097185	24	3.8	23	75	19	71	2	24	1	72	1.03
6098664--6098706	18	2.4	17	77	11	50	30	0	6	62	1.21
6099347--6099371	13	1.9	13	100	0	50	48	0	0	52	1.00
6102999--6103309	157	2.0	157	94	0	541	38	4	10	46	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6109547--6109582	2	18.0	2	100	0	72	50	0	0	50	1.00
6110174--6110220	18	2.6	18	86	6	60	53	2	2	42	1.25
6110582--6110615	15	2.2	16	89	5	52	47	0	8	44	1.34
6115755--6116145	199	2.0	199	100	0	782	43	8	14	34	1.75
6116949--6116978	15	2.0	15	93	0	51	66	10	10	13	1.44
6117863--6117888	13	2.0	13	100	0	52	38	15	15	30	1.88
6117845--6117907	32	2.0	32	90	6	101	41	15	14	28	1.87
6118346--6118412	37	1.9	35	88	11	102	32	11	25	29	1.92
6119031--6119074	20	2.1	21	87	4	63	54	20	6	18	1.66
6124977--6125052	20	3.7	20	77	16	66	31	14	13	40	1.84
6131097--6131346	34	7.4	34	69	14	140	22	25	11	40	1.87
6131077--6131374	68	4.4	67	79	6	280	23	26	10	39	1.87
6131104--6131363	136	1.9	136	83	6	339	22	25	10	41	1.86
6131348--6131401	27	2.0	27	81	0	63	27	29	11	31	1.91
6131404--6131491	31	2.8	32	81	11	110	27	23	21	27	1.99
6131487--6131557	32	2.2	32	80	5	90	30	33	18	16	1.93
6131564--6132074	52	9.9	52	81	4	570	25	23	14	36	1.93
6133067--6133104	20	1.9	20	84	10	51	31	5	7	55	1.51
6138614--6138688	27	2.8	27	85	0	105	26	26	12	34	1.91
6141315--6141349	18	2.0	18	88	5	54	2	0	8	88	0.61
6142842--6142892	20	2.4	21	83	9	59	72	3	1	21	1.11
6143835--6143879	10	4.5	10	83	8	56	22	2	13	62	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6152087--6152136	14	3.6	14	74	17	50	42	2	2	54	1.23
6152688--6152727	18	2.2	18	86	0	53	32	2	7	57	1.40
6152917--6152974	24	2.4	24	77	8	64	65	1	6	25	1.27
6153632--6153709	32	2.4	33	85	8	97	47	5	5	42	1.47
6153632--6153709	34	2.4	32	85	8	95	47	5	5	42	1.47
6155270--6155374	30	3.6	30	81	3	115	55	4	4	35	1.42
6156523--6156548	2	13.0	2	100	0	52	50	0	0	50	1.00
6157231--6157299	18	3.8	18	70	14	52	43	4	1	50	1.30
6158672--6158713	21	2.0	21	100	0	84	38	9	14	38	1.78
6159954--6160006	24	2.2	25	83	6	65	54	0	1	43	1.11
6161107--6161158	11	4.9	11	81	6	54	51	0	0	48	1.00
6161108--6161153	16	2.9	16	83	0	65	54	0	0	45	0.99
6161128--6161195	30	2.4	28	78	16	68	51	0	0	48	1.00
6161196--6161290	35	2.7	36	75	4	97	48	0	0	51	1.00
6161216--6161254	20	2.0	20	85	5	53	48	0	0	51	1.00
6161194--6161260	23	2.7	25	73	19	61	50	0	0	49	1.00
6161434--6161462	12	2.3	13	94	5	51	17	0	0	82	0.66
6161558--6161597	20	1.9	22	90	10	66	52	0	0	47	1.00
6161720--6161756	18	2.1	18	90	10	58	43	0	0	56	0.99
6162204--6162301	23	4.2	24	71	11	69	37	1	2	59	1.16
6163737--6163763	2	13.5	2	100	0	54	0	48	0	51	1.00
6171000--6171025	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6170980--6171044	33	2.0	33	87	6	96	27	13	16	41	1.87
6172043--6172216	93	1.9	93	81	0	213	44	4	5	45	1.48
6172998--6173048	23	2.2	24	82	3	59	50	3	1	43	1.31
6173791--6173978	95	2.0	95	91	0	304	36	10	12	40	1.77
6180427--6180468	22	1.9	22	100	0	84	30	19	16	33	1.94
6182287--6182325	15	2.6	15	84	15	62	46	12	5	35	1.65
6182507--6182537	13	2.4	13	100	0	62	19	6	0	74	1.03
6182537--6182566	15	2.0	15	93	0	51	66	0	3	30	1.07
6182616--6182662	23	2.0	23	100	0	94	44	8	4	42	1.54
6183152--6183212	18	3.3	18	78	17	63	72	1	1	24	1.03
6187053--6187092	13	2.7	15	82	17	57	80	0	20	0	0.72
6187056--6187089	15	2.5	13	90	9	50	82	0	17	0	0.67
6190051--6190138	43	2.0	43	100	0	176	21	18	32	27	1.96
6190377--6190403	13	2.1	13	100	0	54	37	14	14	33	1.88
6190389--6190442	19	2.7	20	83	8	74	33	14	12	38	1.85
6190479--6190517	21	1.9	20	94	5	69	35	12	15	35	1.86
6191242--6191696	48	9.8	47	76	13	365	29	19	25	25	1.98
6191391--6191555	39	4.0	39	74	13	159	25	21	26	26	1.99
6191343--6191596	87	2.9	87	94	0	463	27	20	26	25	1.99
6191516--6191690	51	3.7	48	83	9	191	30	18	24	25	1.98
6192113--6192180	33	2.1	33	94	2	120	33	20	13	32	1.91
6192133--6192158	13	2.0	13	100	0	52	30	15	15	38	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6194819--6194886	34	2.0	34	100	0	136	32	11	32	23	1.91
6198327--6198364	13	2.9	13	96	0	67	31	15	18	34	1.92
6200209--6200331	61	2.0	61	98	0	237	33	4	28	33	1.79
6201004--6201055	20	2.7	20	93	3	88	36	23	11	28	1.90
6201797--6202227	49	9.2	48	76	13	364	30	18	25	25	1.98
6201962--6202171	39	4.9	40	75	16	163	27	21	26	24	1.99
6202001--6202227	48	4.9	48	79	10	256	30	19	24	25	1.98
6201862--6202227	136	2.7	136	90	1	561	29	19	25	25	1.98
6202226--6202305	34	2.4	34	83	8	101	27	16	41	15	1.88
6202358--6202413	27	2.1	26	90	3	85	33	14	30	21	1.93

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