genome.fa.s1.2.7.7.80.10.50.1000.22.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  22  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)
3432274--3432383	50	2.2	49	93	1	184	26	17	17	39	1.91
3432272--3432405	49	2.7	50	88	1	198	28	16	17	38	1.91
3434670--3434779	50	2.2	50	87	6	152	27	22	9	40	1.84
3434736--3435073	79	4.3	79	77	7	289	25	24	14	35	1.93
3449618--3449650	13	2.5	13	100	0	66	33	18	15	33	1.92
3451980--3452593	61	10.0	61	85	3	806	25	27	19	28	1.99
3453281--3453334	20	2.7	20	91	0	90	27	14	14	42	1.85
3453230--3453381	69	2.2	70	83	4	191	28	17	13	40	1.87
3455310--3455482	79	2.2	78	82	3	195	30	15	26	28	1.96
3455437--3455510	28	2.6	29	82	6	107	25	21	29	22	1.99
3455466--3455829	79	4.6	79	89	2	534	29	16	28	25	1.97
3455704--3455902	106	1.9	107	83	7	262	29	15	27	27	1.96
3455840--3456070	51	4.5	51	83	5	306	34	10	24	30	1.90
3455839--3456070	102	2.3	102	88	4	344	34	10	24	30	1.90
3458433--3458457	13	1.9	13	100	0	50	32	20	16	32	1.94
3458498--3458522	13	1.9	13	100	0	50	32	20	24	24	1.98
3459225--3459397	42	4.1	41	74	10	109	44	12	23	19	1.85
3459249--3459398	42	3.5	42	76	7	167	41	12	24	21	1.88
3459367--3460087	61	12.5	56	80	8	720	26	20	26	26	1.99
3459367--3460395	228	4.5	222	81	10	1026	27	19	27	25	1.99
3459375--3460089	173	4.1	170	83	6	830	26	20	26	26	1.99
3460095--3460404	62	5.2	61	82	11	376	29	18	27	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3459956--3460246	156	1.9	149	86	7	415	24	20	29	25	1.99
3460105--3460402	118	2.5	118	89	2	449	28	19	26	25	1.99
3460717--3460741	13	1.9	13	100	0	50	36	16	16	32	1.90
3460697--3460760	32	2.0	33	93	3	112	34	10	18	35	1.86
3460696--3460778	19	4.6	19	78	18	97	32	10	18	38	1.85
3460835--3460983	52	2.9	50	89	6	217	33	16	17	32	1.93
3462591--3462619	10	2.7	11	94	5	51	24	24	0	51	1.48
3463111--3463164	27	2.1	26	86	10	76	25	38	14	20	1.91
3465119--3465570	240	1.9	240	99	0	895	25	23	11	39	1.88
3468148--3468181	12	2.8	13	91	8	54	76	5	11	5	1.14
3469395--3469517	30	3.9	30	73	15	113	21	29	17	32	1.96
3469495--3469538	23	1.9	23	90	0	70	29	29	22	18	1.97
3469518--3469957	100	4.5	99	81	10	551	20	33	13	32	1.91
3469615--3469988	128	2.9	131	81	6	431	21	33	12	33	1.90
3469634--3469935	65	4.7	66	86	6	431	20	34	12	32	1.91
3469804--3469988	36	5.4	34	75	14	105	21	34	10	33	1.88
3469832--3469980	33	4.5	34	73	15	87	19	32	10	37	1.86
3469978--3470138	32	5.0	33	90	4	265	28	36	18	16	1.92
3470186--3471023	43	18.1	43	80	12	821	24	25	18	31	1.97
3470329--3471069	92	8.0	92	95	0	1266	24	25	18	31	1.98
3470133--3471069	184	5.0	184	92	2	1397	24	25	18	31	1.97
3470678--3470745	21	3.2	20	66	25	50	27	26	16	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3471967--3472050	19	4.7	19	74	18	90	34	10	17	36	1.85
3472106--3472254	52	2.9	50	88	6	217	34	17	16	31	1.93
3475398--3475668	121	2.2	120	87	3	393	30	19	25	24	1.98
3481806--3482166	79	4.6	79	89	0	533	31	16	26	26	1.96
3482039--3482239	106	1.9	107	85	7	284	29	16	27	26	1.97
3482177--3482292	51	2.3	51	83	5	146	31	12	24	31	1.93
3482275--3482348	28	2.6	28	80	0	94	29	20	27	22	1.98
3482307--3482666	79	4.6	79	90	0	524	31	15	26	26	1.96
3481732--3482789	500	2.1	501	95	0	1913	32	14	25	27	1.95
3482677--3482909	51	4.6	51	83	2	288	33	11	24	31	1.90
3482673--3482909	102	2.3	102	86	1	332	33	11	24	30	1.91
3486812--3486943	50	2.6	50	86	1	174	26	24	12	36	1.91
3487035--3487211	79	2.2	78	82	1	183	25	23	16	34	1.95
3490015--3490171	48	3.3	47	79	12	158	37	17	10	34	1.84
3490929--3490985	21	2.7	21	97	0	105	33	10	19	36	1.86
3491041--3491108	19	3.9	19	78	21	85	35	11	14	38	1.83
3491062--3491086	13	1.9	13	100	0	50	36	16	16	32	1.90
3491043--3491105	32	2.0	32	96	0	117	34	12	15	36	1.86
3491148--3491173	13	2.0	13	100	0	52	30	15	15	38	1.88
3491128--3491194	33	2.0	33	88	0	98	26	14	14	43	1.85
3493630--3493700	27	2.6	27	86	2	88	23	32	21	22	1.98
3493685--3493854	52	3.3	50	78	6	178	31	24	11	32	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3493521--3493928	211	1.9	211	85	3	561	29	26	12	31	1.93
3505945--3506009	12	5.4	12	85	12	80	84	10	4	0	0.75
3505945--3506013	24	2.9	24	91	4	104	84	11	4	0	0.77
3505959--3506019	17	3.4	17	81	16	70	86	9	3	0	0.67
3505959--3506019	1	61.0	1	75	0	50	86	9	3	0	0.67
3506999--3507638	55	11.4	54	85	8	791	27	28	20	22	1.99
3508389--3508442	18	2.9	18	97	2	99	35	11	14	38	1.82
3508462--3508524	33	1.9	33	83	0	81	25	12	19	42	1.86
3510993--3511165	52	3.4	51	80	2	202	31	24	11	31	1.91
3510860--3511193	183	1.8	183	88	2	519	30	25	11	31	1.92
3511148--3511229	28	2.9	28	83	7	96	24	32	17	25	1.96
3515508--3515566	29	2.0	29	100	0	118	33	20	13	32	1.91
3518818--3518937	50	2.4	50	84	4	152	28	26	12	32	1.93
3518946--3519064	51	2.3	51	82	2	141	29	22	11	36	1.90
3518822--3519141	124	2.5	124	81	4	372	27	25	12	34	1.92
3518997--3519265	79	3.4	79	82	3	281	26	27	12	33	1.93
3521896--3521968	20	3.6	20	81	3	101	35	13	19	31	1.91
3521896--3521990	41	2.3	42	96	1	174	40	12	17	29	1.87
3522029--3522054	13	2.0	13	100	0	52	38	15	15	30	1.88
3524872--3525127	123	2.1	123	84	0	334	29	5	20	44	1.75
3525434--3525468	15	2.2	16	90	5	54	20	11	22	45	1.82
3526788--3526841	20	2.7	20	86	11	67	38	18	12	29	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3526869--3526920	20	2.7	19	85	11	70	34	15	13	36	1.87
3527428--3527469	22	1.9	22	85	0	57	52	0	0	47	1.00
3527592--3527636	20	2.2	20	88	7	65	53	0	0	46	1.00
3527691--3527800	34	3.3	34	80	12	106	55	0	0	43	1.06
3527735--3527798	15	4.3	15	76	9	69	59	0	0	40	0.97
3530816--3530884	29	2.3	30	92	2	113	33	4	1	60	1.25
3531478--3531541	21	3.0	21	83	2	74	35	14	6	43	1.70
3531944--3531991	14	3.4	14	70	0	51	33	6	0	60	1.22
3531943--3532009	28	2.4	28	94	2	116	34	4	0	61	1.16
3534131--3534170	3	13.7	3	86	5	55	62	0	2	35	1.09
3534138--3534175	14	2.9	14	88	7	53	63	0	0	36	0.95
3534704--3534730	2	13.5	2	100	0	54	51	0	0	48	1.00
3542575--3542609	13	2.6	14	91	8	56	68	0	0	31	0.90
3542575--3542633	22	2.7	22	82	10	59	71	1	0	27	0.96
3542591--3542642	26	2.0	25	85	10	70	75	3	0	21	0.97
3542977--3543038	21	3.0	21	80	4	54	61	0	4	33	1.17
3543240--3543299	29	2.1	28	87	6	86	51	0	5	43	1.23
3544025--3544097	32	2.3	32	79	15	80	46	16	9	27	1.78
3545588--3545652	17	3.8	16	74	11	58	35	0	1	63	1.04
3545600--3545659	16	3.6	16	74	14	50	36	0	1	61	1.06
3545594--3545665	35	2.1	35	82	10	85	40	0	1	58	1.07
3545683--3545745	28	2.2	29	81	16	78	33	0	1	65	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3545706--3545762	11	5.0	11	79	12	62	35	0	1	63	1.05
3548217--3548300	22	3.8	22	74	12	82	40	1	0	58	1.06
3548250--3548318	24	2.9	23	82	10	77	33	1	1	63	1.12
3548410--3548811	125	3.3	121	74	13	358	52	1	2	43	1.24
3548664--3548690	14	1.9	14	100	0	54	74	0	0	25	0.83
3548475--3548842	125	3.0	125	80	8	427	51	1	3	43	1.27
3549767--3549831	20	3.6	20	73	26	81	29	15	15	40	1.88
3549787--3549844	13	4.9	13	70	23	56	32	15	15	36	1.89
3549765--3549863	33	3.0	33	94	4	166	31	15	15	38	1.88
3549829--3549885	19	3.0	20	84	7	82	33	15	17	33	1.92

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