genome.fa.s1.2.7.7.80.10.50.1000.25.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: Scaffold1
Parameters: 2 7 7 80 10 50 1000
Length:  8764944

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   

This is table  25  of  52  ( 6211 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)
4131659--4131736	20	3.7	20	74	15	75	26	15	15	42	1.87
4131725--4131775	13	3.9	13	97	0	93	33	19	15	31	1.93
4133559--4133612	27	2.0	27	100	0	108	33	3	18	44	1.67
4134245--4134317	20	3.6	20	81	3	101	35	13	19	31	1.91
4134263--4134338	21	3.7	21	78	3	91	40	11	17	30	1.85
4134245--4134338	41	2.3	41	96	0	170	38	12	18	30	1.88
4134377--4134402	13	2.0	13	100	0	52	38	15	15	30	1.88
4137058--4137229	89	2.0	85	87	5	247	32	11	11	44	1.76
4141876--4141918	21	2.0	21	100	0	86	27	4	9	58	1.49
4142051--4142099	2	24.5	2	95	0	89	48	0	0	51	1.00
4142137--4142195	20	2.9	19	71	26	50	37	0	0	62	0.95
4142152--4142214	20	3.2	19	82	15	74	33	0	0	66	0.92
4143144--4143180	17	2.2	17	100	0	74	59	5	0	35	1.20
4146744--4146781	12	3.2	12	85	3	51	34	0	0	65	0.93
4146799--4146882	36	2.4	36	82	13	95	34	0	2	63	1.08
4146888--4146922	16	2.2	16	89	0	52	48	0	0	51	1.00
4148743--4148974	105	2.3	100	82	7	261	36	6	8	49	1.57
4149203--4149252	24	2.1	24	100	0	100	22	16	26	36	1.94
4156519--4156575	17	2.9	20	85	15	75	29	0	0	70	0.88
4157308--4157372	12	5.7	12	71	14	57	53	1	0	44	1.09
4157423--4157496	34	2.2	33	83	11	89	58	2	1	37	1.21
4160783--4161070	153	1.9	153	80	2	344	52	7	7	32	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4162035--4162116	42	2.0	42	100	0	164	47	7	19	25	1.75
4162456--4162581	43	2.9	43	80	9	123	40	15	21	22	1.91
4162477--4162581	43	2.4	44	82	9	126	39	15	23	21	1.92
4162391--4162587	44	4.5	43	73	12	152	40	14	22	22	1.91
4162691--4162877	44	4.2	45	78	6	195	41	18	21	18	1.91
4162663--4162877	88	2.4	88	80	5	220	41	19	20	18	1.91
4162816--4163071	81	3.2	80	83	4	304	42	10	24	22	1.85
4163020--4163243	35	6.4	35	79	7	177	46	9	20	22	1.80
4163020--4163243	70	3.2	71	80	6	224	46	9	20	22	1.80
4163010--4163244	105	2.2	105	83	1	283	45	9	21	22	1.81
4164169--4164208	11	3.7	11	86	3	55	2	7	15	75	1.14
4166702--4166745	4	11.0	4	100	0	88	50	0	25	25	1.50
4169233--4169289	19	3.0	20	79	7	73	33	14	17	35	1.90
4169333--4169385	13	4.5	13	73	26	64	32	13	16	37	1.88
4169317--4169385	33	2.1	33	91	5	113	30	13	18	37	1.89
4176981--4177006	13	2.0	13	100	0	52	30	15	15	38	1.88
4177714--4177757	21	2.1	21	83	8	54	25	31	4	38	1.76
4179562--4179587	13	2.0	13	100	0	52	38	15	15	30	1.88
4181623--4181653	15	2.1	15	93	0	53	12	22	16	48	1.80
4183456--4183500	21	2.1	21	88	8	65	22	17	4	55	1.60
4185716--4185741	13	2.0	13	100	0	52	30	15	15	38	1.88
4187906--4187932	13	2.1	13	100	0	54	29	14	14	40	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4187982--4188035	20	2.7	20	91	5	83	31	12	18	37	1.89
4190484--4190786	141	2.1	141	86	4	432	43	9	9	36	1.71
4190511--4190850	142	2.4	143	80	8	401	46	10	9	34	1.69
4191226--4191648	167	2.6	165	80	7	423	50	10	10	28	1.69
4194170--4194210	21	2.0	21	85	9	57	41	9	7	41	1.66
4194330--4194354	13	1.9	13	100	0	50	32	16	16	36	1.90
4194309--4194372	32	2.0	33	87	3	94	32	15	14	37	1.87
4194707--4194781	34	2.1	36	83	9	93	17	17	12	53	1.73
4199306--4199358	20	2.6	20	88	8	72	39	9	20	30	1.84
4199395--4199512	52	2.3	52	81	7	134	26	16	15	42	1.87
4204408--4204432	13	1.9	13	100	0	50	36	16	16	32	1.90
4217612--4217670	19	3.1	19	82	2	64	33	11	15	38	1.84
4218212--4218241	16	1.9	16	93	6	53	36	33	0	30	1.58
4219865--4219902	20	1.9	20	88	0	58	34	10	15	39	1.82
4220210--4220306	19	5.8	18	70	27	79	36	13	17	32	1.89
4220211--4220318	32	3.4	32	93	0	180	35	14	17	32	1.91
4220230--4220319	13	6.0	13	69	26	54	36	15	16	31	1.90
4220357--4220417	13	5.2	13	72	22	62	29	14	18	37	1.90
4220403--4220506	30	3.5	30	97	0	190	30	15	18	35	1.92
4222813--4222937	51	2.4	53	84	9	168	33	24	11	30	1.90
4222995--4223071	27	2.8	28	82	9	97	24	33	19	22	1.97
4223028--4223182	80	1.9	79	84	10	208	27	27	14	30	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4226351--4226393	21	2.1	20	83	12	52	53	6	13	25	1.65
4226351--4226393	20	2.1	21	83	12	54	53	6	13	25	1.65
4232780--4232806	13	2.1	13	100	0	54	29	14	14	40	1.86
4238214--4238251	15	2.5	16	83	12	53	31	13	5	50	1.63
4240207--4240246	20	2.0	21	95	5	73	30	12	15	42	1.83
4240232--4240256	13	1.9	13	100	0	50	36	16	16	32	1.90
4246440--4246464	13	1.9	13	100	0	50	40	16	12	32	1.84
4246658--4246892	117	2.0	117	88	0	353	33	14	12	39	1.83
4248055--4248111	19	2.9	20	84	10	82	42	19	12	26	1.86
4248137--4248207	20	3.7	20	80	12	69	40	18	12	28	1.87
4248798--4248841	19	2.3	19	84	0	52	36	4	18	40	1.71
4250545--4250618	21	3.6	20	68	13	51	47	0	18	33	1.49
4256770--4256794	13	1.9	13	100	0	50	32	16	16	36	1.90
4256751--4256815	33	2.0	32	90	3	103	40	12	15	32	1.84
4258984--4259383	153	2.6	152	82	7	411	49	9	8	33	1.65
4259043--4259393	153	2.3	151	83	5	413	49	9	8	33	1.66
4261409--4261453	20	2.2	20	88	0	63	51	8	0	40	1.33
4263400--4263474	19	3.9	19	77	10	80	34	13	10	41	1.79
4264331--4264421	44	2.1	44	100	0	182	21	17	13	47	1.82
4264331--4264400	24	3.1	24	69	23	78	21	17	14	47	1.82
4264345--4264420	20	3.6	20	74	19	82	21	18	11	48	1.79
4271441--4271484	15	2.9	15	79	0	52	43	40	0	15	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4275241--4275297	19	2.9	19	86	2	78	33	15	17	33	1.92
4276938--4276970	3	11.0	3	93	0	57	36	0	30	33	1.58
4280623--4280662	21	2.0	21	85	5	55	32	17	0	50	1.47
4285149--4285234	10	8.1	10	77	13	66	81	13	1	3	0.88
4285144--4285232	38	2.3	38	85	9	119	79	15	1	3	0.92
4285471--4285522	14	3.5	15	85	15	72	86	9	3	0	0.69
4285472--4285524	12	4.6	12	81	6	65	88	7	3	0	0.61
4285471--4285524	22	2.4	22	87	3	81	87	9	3	0	0.67
4285471--4285524	17	3.3	16	85	10	65	87	9	3	0	0.67
4285472--4285524	1	53.0	1	76	0	52	88	7	3	0	0.61
4286485--4286590	33	3.3	33	69	7	110	22	27	16	33	1.95
4286461--4286622	63	2.6	63	91	3	256	21	30	14	32	1.94
4286504--4286603	30	3.2	30	69	8	92	25	29	15	31	1.95
4286461--4286749	63	4.6	62	79	9	232	22	29	14	33	1.94
4286597--4286685	30	2.8	33	83	6	103	23	26	16	32	1.96
4286660--4286987	34	9.8	35	82	11	341	19	31	12	35	1.89
4286661--4286987	68	4.9	68	86	6	411	19	31	12	36	1.89
4286661--4286987	102	3.3	102	87	4	427	19	31	12	36	1.89
4286817--4287040	69	3.3	68	79	10	172	21	30	11	35	1.89
4286998--4287294	32	9.3	31	88	5	391	29	34	17	17	1.93
4286997--4287294	97	3.1	94	88	5	445	29	34	17	17	1.94
4286997--4287294	129	2.3	128	93	2	508	29	34	17	17	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4287333--4288432	92	12.0	88	88	4	1185	25	25	18	31	1.97
4287446--4287513	21	3.2	21	63	19	50	25	26	16	32	1.96
4287630--4287697	21	3.2	21	62	25	52	25	29	17	27	1.97
4287646--4287716	24	3.2	24	61	19	62	23	28	19	28	1.99
4287651--4287719	22	3.2	22	62	25	56	23	28	17	30	1.97
4287275--4288489	276	4.4	270	85	7	1341	24	25	18	31	1.97
4288340--4288489	52	2.9	52	85	0	210	22	24	18	34	1.96
4289334--4289358	13	1.9	13	100	0	50	36	16	16	32	1.90
4289291--4289382	32	3.1	31	81	18	117	34	10	17	36	1.85
4289420--4289444	13	1.9	13	100	0	50	32	16	16	36	1.90

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