genome.fa.s2.2.7.7.80.10.50.1000.22.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: Scaffold2
Parameters: 2 7 7 80 10 50 1000
Length:  5794061

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   

This is table  22  of  38  ( 4457 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)
3371840--3371922	32	2.6	32	90	1	132	32	14	15	37	1.88
3371872--3371896	13	1.9	13	100	0	50	32	16	16	36	1.90
3371884--3371943	19	3.1	19	75	13	59	30	13	13	43	1.82
3372343--3372508	51	3.3	50	74	5	145	30	24	13	31	1.93
3372495--3372568	28	2.6	28	89	0	103	24	32	18	24	1.97
3372660--3372881	51	4.3	52	74	7	195	29	22	13	34	1.92
3372444--3372725	110	2.6	106	77	9	316	29	25	14	30	1.95
3372661--3372881	103	2.2	102	84	4	275	29	22	13	34	1.92
3376523--3377073	61	9.0	61	85	3	689	24	29	19	26	1.99
3376523--3377074	305	1.8	304	88	2	847	24	29	19	26	1.99
3377076--3377411	131	2.5	134	79	9	335	20	26	13	39	1.89
3377093--3377410	43	7.1	45	76	12	237	20	27	12	40	1.88
3378184--3378290	20	5.7	19	73	22	93	27	16	14	41	1.88
3378183--3378288	53	2.0	52	83	10	135	28	16	15	39	1.89
3378204--3378268	33	2.0	33	93	0	112	26	18	16	38	1.92
3380198--3380232	18	1.9	18	94	0	61	80	0	0	20	0.72
3380182--3380232	24	2.1	24	85	3	66	74	1	0	23	0.92
3380411--3380472	17	3.6	17	80	2	79	17	24	11	46	1.81
3388061--3388507	85	5.3	85	75	6	268	19	25	17	38	1.93
3388343--3388501	79	2.0	80	81	3	187	21	25	16	37	1.93
3388459--3388552	43	2.2	43	84	0	116	20	25	13	40	1.89
3388524--3388577	25	2.2	25	82	0	63	14	33	14	37	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3388554--3389513	42	22.8	42	72	6	542	18	29	17	34	1.94
3388548--3389343	85	9.4	84	78	4	620	17	29	17	34	1.94
3388610--3389514	85	10.7	83	75	8	334	18	28	17	35	1.94
3388737--3389512	127	6.1	126	74	9	350	18	28	17	35	1.94
3390593--3390771	82	2.2	81	87	2	252	49	12	21	16	1.79
3391226--3391279	12	4.5	12	72	9	56	62	25	9	1	1.35
3392077--3392101	13	1.9	13	100	0	50	32	16	16	36	1.90
3392141--3392216	21	3.7	21	80	3	100	28	17	11	42	1.84
3392162--3392234	20	3.6	20	81	3	101	31	19	13	35	1.91
3392141--3392234	41	2.3	41	98	0	179	29	18	12	39	1.88
3394687--3394722	13	2.8	13	95	0	63	33	16	16	33	1.92
3394711--3394787	20	3.6	20	77	16	73	42	15	15	25	1.86
3398621--3398665	21	2.1	21	84	8	56	22	20	4	53	1.63
3400882--3400907	13	2.0	13	100	0	52	30	15	15	38	1.88
3400946--3401021	21	3.7	21	80	3	100	28	17	11	42	1.84
3400967--3401039	20	3.6	20	81	3	101	31	19	13	35	1.91
3400946--3401039	41	2.3	41	98	0	179	29	18	12	39	1.88
3406374--3406414	11	3.6	11	96	3	73	80	0	19	0	0.71
3406738--3406768	16	1.9	16	100	0	62	70	0	6	22	1.09
3406782--3406838	21	2.7	21	97	0	105	33	10	19	36	1.86
3406894--3406961	19	3.9	19	78	21	85	35	11	14	38	1.83
3406915--3406939	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3406896--3406958	32	2.0	32	96	0	117	34	12	15	36	1.86
3407001--3407026	13	2.0	13	100	0	52	30	15	15	38	1.88
3406981--3407044	33	1.9	33	87	0	92	25	15	17	42	1.88
3409507--3409676	51	3.3	50	79	8	180	29	25	12	32	1.92
3409660--3409741	28	2.9	28	82	7	96	24	31	17	26	1.97
3411173--3411199	13	2.1	13	100	0	54	29	14	14	40	1.86
3411154--3411217	32	2.0	32	87	9	94	29	17	14	39	1.88
3411184--3411238	19	2.8	19	88	2	83	32	23	9	34	1.86
3415629--3415834	80	2.6	79	85	1	277	29	27	12	31	1.92
3415769--3415888	52	2.3	51	85	4	161	28	29	12	30	1.93
3415691--3416045	132	2.7	131	85	6	470	29	27	11	31	1.91
3415920--3416016	51	1.9	51	95	0	176	31	23	8	36	1.85
3416146--3416329	79	2.3	79	82	1	235	28	22	14	34	1.93
3422102--3422151	19	2.6	19	93	0	82	36	18	14	32	1.90
3422211--3422266	21	2.7	21	91	0	94	37	16	8	37	1.80
3427076--3427307	79	2.9	78	87	1	313	28	23	14	34	1.93
3427245--3427361	50	2.3	50	86	5	164	33	25	9	31	1.88
3427166--3427437	129	2.1	129	83	1	339	30	25	12	32	1.92
3427089--3427517	207	2.1	209	85	4	591	28	24	13	33	1.93
3427294--3427562	79	3.4	78	78	7	276	29	23	12	34	1.91
3427295--3427585	157	1.9	155	81	5	352	28	22	13	35	1.92
3440808--3441203	61	6.4	61	81	7	460	27	25	17	29	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3440808--3441203	121	3.2	120	82	3	443	27	25	17	29	1.97
3441224--3441313	40	2.2	40	84	2	126	18	25	15	40	1.90
3441234--3441369	41	3.3	40	76	14	116	24	23	15	36	1.93
3444208--3444648	79	5.6	78	79	2	400	28	23	13	34	1.93
3444207--3444646	237	1.9	237	84	2	598	28	23	13	34	1.93
3449658--3449693	13	2.8	13	95	0	63	36	19	13	30	1.91
3449637--3449779	31	4.4	31	75	17	130	36	12	21	29	1.90
3449811--3449947	53	2.6	53	94	1	238	27	16	18	37	1.92
3449917--3449987	20	3.5	20	77	11	74	29	14	16	39	1.88
3456250--3456304	19	2.8	19	83	2	65	30	21	10	36	1.88
3456369--3456459	20	4.6	20	94	0	155	42	10	14	31	1.80
3462456--3462481	13	2.0	13	100	0	52	30	15	15	38	1.88
3465027--3465065	13	3.0	13	96	0	69	35	15	17	30	1.91
3465051--3465129	20	3.7	20	78	15	77	44	15	15	25	1.85
3467145--3467175	15	2.1	15	93	0	53	12	22	16	48	1.80
3468952--3468996	21	2.1	21	84	8	56	22	20	4	53	1.63
3471216--3471241	13	2.0	13	100	0	52	30	15	15	38	1.88
3474088--3474112	13	1.9	13	100	0	50	36	16	8	40	1.77
3478302--3478328	13	2.1	13	100	0	54	29	14	14	40	1.86
3481552--3481616	11	6.5	10	82	7	71	78	0	16	4	0.91
3481878--3481945	19	3.9	19	78	21	85	35	11	14	38	1.83
3481899--3481923	13	1.9	13	100	0	50	36	16	16	32	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3481880--3481942	32	2.0	32	96	0	117	34	12	15	36	1.86
3484500--3484669	51	3.3	50	79	8	180	29	25	12	32	1.92
3484653--3484734	28	2.9	28	82	7	96	24	31	17	26	1.97
3486166--3486192	13	2.1	13	100	0	54	29	14	14	40	1.86
3486147--3486210	32	2.0	32	87	9	94	29	17	14	39	1.88
3486177--3486231	19	2.8	19	88	2	83	32	23	9	34	1.86
3490622--3490826	79	2.6	79	86	1	277	29	27	12	31	1.92
3490761--3490880	51	2.4	51	87	2	170	29	28	12	30	1.93
3490684--3491035	130	2.7	130	87	4	489	29	27	11	31	1.91
3490891--3491012	51	2.4	51	86	1	174	29	25	11	33	1.91
3491136--3491319	79	2.3	79	82	1	235	28	22	14	34	1.93
3497095--3497144	19	2.6	19	87	0	73	34	18	16	32	1.92
3497204--3497259	21	2.7	21	91	0	94	37	16	8	37	1.80
3502071--3502303	79	2.9	77	85	2	277	28	23	13	34	1.93
3502240--3502357	51	2.3	50	85	7	157	33	25	9	32	1.88
3502290--3502559	80	3.4	78	77	9	269	29	23	12	34	1.91
3502160--3502433	129	2.1	130	83	0	352	30	24	12	32	1.92
3502084--3502514	208	2.1	210	84	5	570	29	24	12	33	1.92
3515730--3516124	61	6.4	60	81	7	436	27	25	17	29	1.97
3516145--3516234	40	2.2	40	84	2	126	18	25	15	40	1.90
3516155--3516290	41	3.3	40	76	14	116	24	23	15	36	1.93
3519130--3519570	79	5.6	78	79	2	400	28	23	13	34	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3519129--3519568	237	1.9	237	84	2	598	28	23	13	34	1.93
3520516--3520541	13	2.0	13	100	0	52	23	15	23	38	1.92
3524581--3524616	13	2.8	13	95	0	63	36	19	13	30	1.91
3524610--3524758	33	4.8	33	76	17	158	36	11	22	29	1.89
3524660--3524715	24	2.3	24	100	0	112	33	12	21	32	1.91
3524701--3524759	31	1.9	31	92	0	100	37	11	25	25	1.90
3524791--3524927	53	2.6	53	94	1	238	27	16	18	37	1.92
3524897--3524967	20	3.5	20	77	11	74	29	14	16	39	1.88
3531230--3531284	19	2.8	19	83	2	65	30	21	10	36	1.88
3531349--3531439	20	4.6	20	94	0	155	42	10	14	31	1.80

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