genome.fa.s220.2.7.7.80.10.50.1000.16.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: Scaffold220
Parameters: 2 7 7 80 10 50 1000
Length:  3999181

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   

This is table  16  of  19  ( 2201 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)
3359387--3359446	17	3.6	17	80	12	56	30	0	0	70	0.88
3359498--3359536	18	2.1	18	85	4	51	48	0	5	46	1.24
3360182--3360238	16	3.7	15	75	15	62	29	8	21	40	1.83
3361786--3361826	19	2.1	19	90	4	64	58	2	2	36	1.24
3361865--3361906	20	2.1	20	86	0	57	52	0	0	47	1.00
3361969--3362016	22	2.1	23	84	3	62	50	0	0	50	1.00
3365223--3365250	1	28.0	1	100	0	56	0	100	0	0	0.00
3384497--3384548	17	3.1	16	75	5	50	65	0	0	34	0.93
3384545--3384638	18	5.5	17	72	23	74	56	1	0	42	1.06
3386069--3386140	18	4.1	17	76	15	58	47	1	1	50	1.18
3386089--3386140	17	3.0	18	80	8	63	46	1	0	51	1.12
3388206--3388247	2	21.0	2	100	0	84	50	0	0	50	1.00
3393947--3393972	13	2.0	13	100	0	52	15	30	0	53	1.42
3395957--3396005	25	2.0	25	84	8	64	61	0	0	38	0.96
3396313--3396348	19	1.9	19	94	5	65	38	0	5	55	1.23
3396945--3396976	16	2.1	15	94	5	55	68	0	0	31	0.90
3397986--3398035	19	2.6	20	79	17	61	72	2	0	26	0.96
3399136--3399183	19	2.4	20	80	13	55	50	0	0	50	1.00
3399131--3399184	21	2.5	23	77	20	62	48	0	0	51	1.00
3399114--3399187	20	3.7	20	71	25	57	50	0	0	50	1.00
3399573--3399620	19	2.6	18	81	12	53	41	0	2	56	1.11
3401283--3401380	34	2.9	34	93	1	160	26	19	22	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3409752--3409777	2	13.0	2	100	0	52	50	0	0	50	1.00
3410398--3410433	2	18.0	2	100	0	72	0	50	0	50	1.00
3414663--3414723	28	2.2	28	93	0	104	29	21	19	29	1.98
3424687--3424711	1	25.0	1	100	0	50	100	0	0	0	0.00
3428540--3428585	18	2.5	18	86	10	58	56	2	2	39	1.24
3428793--3428936	71	2.0	72	91	1	236	23	22	13	40	1.90
3429013--3429112	33	3.1	34	74	18	97	50	1	2	47	1.19
3429057--3429106	19	2.4	21	80	12	59	46	0	2	52	1.12
3429128--3429171	2	22.5	2	90	4	72	54	0	0	45	0.99
3432329--3432362	2	17.0	2	87	0	50	47	5	0	47	1.26
3432686--3432723	14	2.8	14	88	11	53	57	0	0	42	0.98
3432686--3432723	5	8.2	5	83	16	55	57	0	0	42	0.98
3432686--3432723	19	2.1	18	95	5	67	57	0	0	42	0.98
3433406--3433454	21	2.3	21	82	0	71	14	65	16	4	1.42
3437298--3437536	124	1.9	123	81	10	284	52	2	2	41	1.30
3437787--3437869	22	3.8	21	73	17	71	33	1	2	62	1.16
3437906--3437952	23	2.0	23	84	8	60	44	0	0	55	0.99
3440866--3440907	15	2.7	15	82	10	50	45	2	0	52	1.13
3447253--3447285	16	2.1	16	88	11	50	42	0	0	57	0.98
3447591--3447650	17	3.5	17	77	13	61	35	1	0	63	1.05
3448589--3448615	2	13.5	2	100	0	54	51	0	48	0	1.00
3451286--3451334	24	2.0	24	96	0	89	34	4	12	48	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3451873--3451953	27	3.0	28	71	10	69	53	0	1	45	1.08
3451860--3451922	20	3.1	20	71	15	58	47	0	0	52	1.00
3451916--3451959	20	2.1	21	83	4	54	61	0	2	36	1.09
3451917--3451972	16	3.6	16	78	2	51	57	0	3	39	1.16
3452039--3452082	10	4.3	10	82	5	52	25	2	0	72	0.96
3458755--3458786	2	16.0	2	100	0	64	50	0	0	50	1.00
3459878--3459917	15	2.5	16	84	8	55	47	0	0	52	1.00
3459878--3459920	16	2.6	17	78	10	54	48	0	0	51	1.00
3460146--3460184	20	1.9	21	89	5	62	53	0	0	46	1.00
3460994--3461059	27	2.3	29	82	12	84	60	0	0	39	0.97
3460993--3461066	17	4.8	15	70	26	57	60	0	0	39	0.97
3461004--3461069	18	3.7	18	75	16	66	60	0	0	39	0.97
3461454--3461486	17	1.9	17	93	0	57	30	0	3	66	1.06
3462112--3462151	21	1.9	21	84	0	53	17	2	10	70	1.27
3467797--3467847	23	2.3	22	93	3	84	37	9	21	31	1.86
3470619--3470666	14	3.6	14	76	17	50	56	2	0	41	1.11
3470625--3470736	33	3.5	32	73	19	99	53	1	0	43	1.17
3470636--3470728	27	3.5	26	74	14	73	50	2	1	46	1.20
3470675--3470725	20	2.5	20	84	12	61	50	0	1	47	1.12
3471528--3471649	32	3.9	31	79	4	129	50	4	2	43	1.34
3471676--3471719	14	3.1	14	80	6	52	20	20	9	50	1.75
3473833--3473867	18	2.0	17	88	5	52	51	5	2	40	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3479286--3479332	22	2.4	21	80	19	57	68	0	0	31	0.90
3479301--3479335	18	1.9	18	94	0	61	68	0	0	31	0.90
3484782--3484840	26	2.3	26	100	0	118	32	18	23	25	1.97
3485189--3485227	2	20.0	2	94	5	71	48	0	0	51	1.00
3486676--3486702	6	4.5	6	100	0	54	0	14	0	85	0.61
3490858--3490895	18	2.1	19	85	9	53	23	0	7	68	1.16
3490866--3490913	22	2.0	25	88	11	75	25	0	6	68	1.12
3491646--3491685	2	20.0	2	100	0	80	50	0	0	50	1.00
3493283--3493324	17	2.5	17	85	11	59	40	0	4	54	1.21
3493635--3493659	2	12.5	2	100	0	50	52	0	0	48	1.00
3494320--3494345	2	13.0	2	100	0	52	50	0	0	50	1.00
3495232--3495277	4	11.5	4	95	0	83	28	0	21	50	1.49
3500441--3500466	2	13.0	2	100	0	52	50	0	0	50	1.00
3503266--3503390	40	3.3	40	68	17	120	53	4	1	40	1.32
3503246--3503393	74	2.0	74	97	0	278	50	7	2	39	1.45
3503340--3503397	20	2.9	19	74	5	53	58	1	0	39	1.08
3508613--3508642	3	10.0	3	100	0	60	0	0	33	66	0.92
3509139--3509201	24	2.7	23	79	13	65	53	3	1	41	1.26
3509172--3509232	31	1.9	32	87	9	90	59	1	0	39	1.08
3509481--3509541	20	3.1	20	79	6	63	60	1	0	37	1.07
3510865--3510922	29	2.0	30	86	3	82	39	5	0	55	1.22
3515835--3515871	2	18.5	2	94	0	65	0	2	48	48	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3524426--3524452	14	1.9	14	100	0	54	44	0	0	55	0.99
3525287--3525339	2	27.0	2	77	11	56	43	0	7	49	1.31
3526073--3526131	22	2.7	22	82	15	77	38	0	0	61	0.96
3526067--3526130	28	2.3	27	89	7	94	39	0	0	60	0.97
3528311--3528338	2	14.0	2	100	0	56	50	0	0	50	1.00
3528669--3528702	18	1.9	18	88	5	52	38	0	2	58	1.13
3528760--3528803	23	2.0	23	86	8	65	47	0	2	50	1.13
3530034--3530069	16	2.2	17	95	5	65	52	0	0	47	1.00
3531654--3531704	17	2.8	18	79	11	59	64	1	0	33	1.05
3531695--3531749	26	2.0	28	86	6	78	54	1	0	43	1.10
3533327--3533376	19	2.5	20	77	3	57	52	2	0	46	1.12
3534000--3534029	13	2.2	14	94	5	53	40	0	6	53	1.27
3534231--3534265	16	2.2	16	89	0	52	57	0	2	40	1.14
3540421--3540449	2	14.5	2	100	0	58	0	48	0	51	1.00
3540957--3541044	11	8.5	11	67	13	53	45	0	2	52	1.13
3540997--3541057	29	2.0	31	90	9	99	54	0	0	45	1.00
3541299--3541333	17	2.1	17	89	5	54	60	0	0	40	0.97
3541691--3541739	13	3.7	13	80	2	53	65	0	0	34	0.93
3541698--3541736	20	2.0	20	85	10	53	64	0	0	35	0.94
3542124--3542148	13	1.9	13	100	0	50	12	0	0	88	0.53
3547612--3547653	14	2.9	14	82	10	50	57	2	2	38	1.25
3548341--3548411	20	3.8	19	70	21	60	69	1	1	28	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3548980--3549009	14	2.1	14	93	0	51	16	0	30	53	1.44
3551489--3551515	2	13.5	2	100	0	54	51	0	0	48	1.00
3552458--3552488	2	15.5	2	100	0	62	48	0	0	51	1.00
3555680--3555718	14	2.8	13	85	11	51	25	5	0	69	1.09
3556899--3556992	48	2.0	48	100	0	188	52	11	14	21	1.74
3557938--3558027	30	3.1	29	77	7	76	47	2	2	47	1.26
3558016--3558065	18	2.8	18	72	24	52	56	2	0	42	1.11
3558026--3558054	14	2.0	15	93	6	51	55	3	0	41	1.17
3558841--3558881	5	8.4	5	79	15	50	63	0	0	36	0.95
3558840--3558932	27	3.7	26	80	9	86	59	2	0	38	1.10

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19