genome.fa.s39.2.7.7.80.10.50.1000.20.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: Scaffold39
Parameters: 2 7 7 80 10 50 1000
Length:  4724573

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   

This is table  20  of  27  ( 3195 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)
3374700--3374981	83	3.4	84	80	3	277	18	30	13	37	1.90
3374912--3375088	84	2.1	84	82	6	214	17	28	15	37	1.91
3376692--3376750	32	1.9	30	83	13	75	59	10	10	20	1.58
3377029--3377054	13	2.0	13	100	0	52	30	15	15	38	1.88
3377009--3377073	33	2.0	33	87	6	96	27	13	16	41	1.87
3377482--3377564	42	2.0	43	97	2	159	45	3	14	36	1.62
3379058--3379099	9	4.8	9	82	5	59	85	14	0	0	0.59
3380419--3380739	28	11.4	29	85	5	376	33	26	17	22	1.96
3380425--3380741	57	5.6	57	84	6	346	33	27	16	22	1.96
3380419--3380739	85	3.8	83	86	5	405	33	26	17	22	1.96
3380742--3380810	31	2.3	31	84	2	86	26	26	18	28	1.98
3382087--3382140	13	4.3	12	81	6	54	74	0	24	1	0.92
3382088--3382166	24	3.4	22	80	15	61	70	1	22	5	1.14
3383791--3384003	97	2.2	97	93	0	363	30	29	10	29	1.90
3386902--3386955	20	2.7	20	91	5	83	37	18	12	31	1.89
3386983--3387040	19	3.1	18	85	11	80	32	18	13	34	1.91
3392844--3392910	33	2.0	33	88	0	98	34	11	13	40	1.81
3392864--3392888	13	1.9	13	100	0	50	36	16	16	32	1.90
3392951--3392975	13	1.9	13	100	0	50	32	16	16	36	1.90
3399924--3399984	1	61.0	1	73	0	50	86	13	0	0	0.56
3399926--3399983	13	4.6	13	83	12	77	86	13	0	0	0.58
3399924--3399984	14	4.5	13	85	6	86	86	13	0	0	0.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3399924--3399984	12	4.8	12	86	11	86	86	13	0	0	0.56
3399924--3399984	26	2.3	26	91	8	106	86	13	0	0	0.56
3399925--3399984	27	2.3	26	94	5	104	86	13	0	0	0.57
3400221--3400275	17	3.1	18	84	12	78	87	5	7	0	0.68
3400221--3400282	15	4.1	14	80	13	61	85	6	8	0	0.74
3400238--3400269	11	2.8	11	95	4	55	90	0	9	0	0.45
3400221--3400282	30	2.0	31	85	14	85	85	6	8	0	0.74
3400221--3400270	15	3.2	16	83	8	68	88	4	8	0	0.64
3401296--3401380	30	2.8	31	83	3	109	24	25	17	31	1.97
3401350--3401869	71	7.7	69	85	10	641	20	32	11	35	1.88
3401350--3401889	34	15.9	34	81	10	542	20	32	12	35	1.89
3401875--3401937	33	2.0	33	90	9	105	28	36	19	15	1.92
3401930--3402731	49	16.7	49	84	5	1048	24	26	18	30	1.98
3402417--3402740	43	7.1	43	77	13	299	24	25	18	32	1.97
3402384--3402740	92	3.9	91	94	1	606	23	25	19	31	1.98
3403657--3403723	33	2.0	33	88	0	98	34	11	13	40	1.81
3403677--3403701	13	1.9	13	100	0	50	36	16	16	32	1.90
3403764--3403788	13	1.9	13	100	0	50	32	16	16	36	1.90
3410189--3410246	19	2.9	21	82	10	68	34	12	13	39	1.82
3410896--3410944	19	2.6	19	75	18	57	40	2	4	53	1.32
3412809--3412844	18	1.9	19	94	5	65	11	16	38	33	1.84
3417351--3417391	21	2.0	21	95	0	73	12	21	31	34	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3418491--3418750	128	2.0	128	96	0	484	41	15	20	23	1.90
3420607--3420657	10	5.2	10	81	15	54	56	0	1	41	1.10
3421401--3421443	6	7.2	6	97	0	77	46	0	16	37	1.47
3422840--3422870	13	2.4	13	100	0	62	38	12	16	32	1.86
3422818--3422886	33	2.1	33	86	5	95	37	15	13	33	1.86
3424427--3424451	13	1.9	13	100	0	50	32	16	16	36	1.90
3424407--3424474	33	2.1	33	91	2	111	35	16	14	33	1.89
3430620--3430658	13	3.0	13	88	0	60	30	20	15	33	1.94
3432656--3432680	13	1.9	13	100	0	50	32	16	16	36	1.90
3432636--3432703	33	2.1	33	91	2	111	35	16	14	33	1.89
3436239--3436300	33	1.9	32	87	9	90	27	12	16	43	1.84
3436333--3436386	20	2.7	20	91	5	83	31	12	18	37	1.89
3437962--3437995	9	3.8	9	88	11	52	44	0	26	29	1.55
3439533--3439571	20	1.9	20	89	5	60	33	7	17	41	1.79
3445172--3445217	20	2.3	20	88	7	67	30	10	19	39	1.86
3447352--3447403	20	2.9	16	72	22	50	34	9	13	42	1.77
3449756--3449974	78	2.8	78	77	7	219	26	26	10	35	1.90
3449756--3450257	80	6.3	79	74	9	256	26	26	11	34	1.91
3449914--3450257	81	4.3	80	75	8	234	27	27	11	33	1.91
3450190--3450306	53	2.3	50	82	4	126	29	24	9	36	1.87
3450246--3450434	80	2.4	76	80	9	193	29	24	7	38	1.83
3450403--3450516	51	2.2	52	81	6	133	27	28	7	36	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3450549--3450660	58	2.0	58	85	7	158	28	31	6	33	1.82
3450320--3450735	137	3.1	130	75	7	395	27	27	8	36	1.86
3450749--3450903	80	1.9	81	80	3	179	29	22	8	39	1.83
3455146--3455521	52	7.4	52	77	10	169	31	15	26	26	1.96
3455201--3455520	52	6.3	49	82	4	246	30	15	27	25	1.96
3455146--3455520	101	3.7	100	79	7	362	31	15	26	26	1.95
3455144--3455520	202	1.9	202	81	3	463	31	15	26	26	1.95
3455310--3455582	153	1.8	144	79	9	307	30	17	25	26	1.97
3455140--3455582	202	2.2	196	77	7	462	32	15	25	26	1.96
3455604--3455935	29	11.6	29	82	7	365	21	17	30	31	1.96
3455586--3455935	115	3.0	114	85	6	431	22	17	29	30	1.97
3455604--3455929	144	2.3	142	84	5	408	20	17	29	31	1.96
3456280--3456364	37	2.3	37	95	0	152	43	15	14	27	1.85
3457397--3457459	6	11.0	6	78	10	69	0	4	11	84	0.77
3457398--3457456	11	5.4	11	86	11	77	0	5	10	84	0.76
3457398--3457456	17	3.6	16	84	11	75	0	5	10	84	0.76
3459590--3459641	19	2.7	20	84	6	70	40	17	13	28	1.87
3464245--3464275	15	2.1	15	93	0	53	48	16	22	12	1.80
3466359--3466396	13	2.9	13	96	0	67	34	18	15	31	1.92
3466508--3466553	21	2.2	20	81	11	58	32	19	4	43	1.71
3468962--3468987	13	2.0	13	100	0	52	38	15	15	30	1.88
3482032--3482057	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)
3484006--3484420	207	2.0	207	100	0	830	37	15	21	25	1.93
3486866--3486921	4	14.2	4	74	10	53	71	0	1	26	0.96
3486975--3487136	14	11.4	14	70	11	105	24	18	12	44	1.84
3487106--3487154	23	2.1	23	88	0	71	26	20	10	42	1.84
3486977--3487136	43	3.7	43	86	0	239	25	18	11	44	1.84
3487868--3487927	15	3.6	15	69	30	50	50	28	16	5	1.66
3487833--3487932	36	2.9	36	89	4	152	49	26	20	5	1.69
3487930--3487971	23	1.9	21	85	9	57	61	21	9	7	1.50
3487931--3487987	23	2.5	21	78	10	51	61	26	5	7	1.43
3491690--3491764	20	3.8	20	78	0	87	34	13	12	40	1.81
3491690--3491767	40	2.0	39	87	2	111	34	12	12	39	1.82
3492657--3492711	22	2.5	22	100	0	110	18	10	9	61	1.54
3492657--3492718	22	2.9	21	90	4	63	20	11	9	58	1.61
3499540--3499593	18	3.0	18	72	0	54	68	3	1	25	1.16
3501494--3501559	19	3.8	18	75	24	79	33	12	16	37	1.86
3501515--3501539	13	1.9	13	100	0	50	36	16	16	32	1.90
3501496--3501558	32	2.0	32	96	0	117	34	12	17	34	1.88
3503787--3504172	52	7.4	52	71	11	182	30	25	11	31	1.92
3503787--3503909	53	2.4	51	83	5	158	31	23	11	33	1.90
3503893--3503967	27	2.7	28	89	2	107	24	34	20	21	1.96
3503951--3504173	52	4.3	51	78	7	200	30	26	11	31	1.91
3504156--3504232	28	2.8	28	86	7	95	25	35	16	22	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3503787--3504283	264	1.9	262	88	1	753	29	27	12	30	1.93
3505475--3505633	30	5.5	28	72	8	124	33	27	14	24	1.94
3505658--3505728	29	2.5	29	86	2	90	35	25	14	25	1.93
3505678--3505817	29	4.6	29	80	12	131	30	28	16	24	1.96
3505692--3505830	32	4.5	32	80	11	146	30	27	19	23	1.98
3505857--3506164	163	1.9	161	82	5	379	26	23	14	35	1.93
3506980--3507118	52	2.7	52	86	7	178	31	12	13	42	1.81
3512561--3512586	13	2.0	13	100	0	52	38	7	15	38	1.76
3512540--3512606	33	2.0	33	82	5	82	34	13	11	40	1.81
3512635--3512690	19	2.9	19	83	2	76	37	12	17	32	1.88

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