genome.fa.s11.2.7.7.80.10.50.1000.22.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: Scaffold11
Parameters: 2 7 7 80 10 50 1000
Length:  5230303

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   

This is table  22  of  29  ( 3461 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)
3423366--3423450	7	10.6	8	68	22	54	35	1	2	61	1.17
3423368--3423422	23	2.5	23	80	14	62	32	1	1	63	1.15
3423698--3423727	5	6.0	5	100	0	60	40	0	0	60	0.97
3423729--3423783	23	2.4	23	76	8	60	47	0	0	52	1.00
3424539--3424574	2	18.0	2	100	0	72	50	0	0	50	1.00
3424627--3424691	21	3.0	22	80	15	64	46	0	15	38	1.46
3424637--3424711	21	3.5	21	77	13	57	44	0	17	38	1.49
3426133--3426193	27	2.3	27	97	0	113	36	1	0	62	1.05
3426146--3426193	16	3.3	16	70	27	52	37	2	0	60	1.09
3426473--3426557	42	2.1	40	86	8	111	41	2	1	55	1.20
3427120--3427171	22	2.4	21	81	12	61	53	1	1	42	1.23
3427289--3427386	30	3.2	31	82	10	128	55	1	1	42	1.13
3428568--3428609	2	21.0	2	100	0	84	50	0	0	50	1.00
3429454--3429490	2	18.5	2	88	0	56	51	0	48	0	1.00
3430795--3430841	14	3.4	14	88	5	60	53	0	0	46	1.00
3430976--3431016	2	21.0	2	85	5	57	43	0	4	51	1.23
3432051--3432079	2	15.0	2	92	7	51	51	0	0	48	1.00
3433349--3433390	22	2.0	21	90	4	66	16	7	11	64	1.48
3439516--3439560	21	2.2	20	84	11	56	55	0	0	44	0.99
3447495--3447530	18	2.0	18	88	0	54	36	2	0	61	1.11
3447797--3447840	19	2.3	19	84	7	54	38	2	4	54	1.33
3448910--3449009	30	3.3	30	81	4	112	42	3	1	54	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3448892--3449009	29	4.0	29	78	10	114	39	2	1	55	1.23
3448950--3449013	19	3.4	19	74	18	55	40	1	0	57	1.08
3448965--3449018	18	2.9	19	73	15	58	44	0	0	55	0.99
3449584--3449641	22	2.6	21	83	8	62	58	0	1	39	1.08
3451160--3451189	15	2.1	14	93	6	51	56	0	0	43	0.99
3451160--3451189	7	4.1	7	91	8	51	56	0	0	43	0.99
3456613--3456671	31	2.0	29	83	12	75	44	0	1	54	1.10
3456616--3456671	27	2.0	28	83	13	71	44	0	1	53	1.11
3456683--3456749	29	2.3	29	84	5	82	38	4	1	55	1.29
3457292--3457349	22	2.6	21	83	8	62	58	0	1	39	1.08
3463865--3463939	34	2.3	32	79	6	87	46	1	1	50	1.18
3467706--3467756	18	2.8	19	71	11	54	37	1	1	58	1.20
3467909--3467952	20	2.1	21	84	12	56	56	2	0	40	1.11
3469039--3469095	22	2.6	23	79	20	68	36	0	0	63	0.95
3469490--3469548	13	4.9	12	76	14	59	62	0	0	37	0.95
3469486--3469559	26	3.0	26	78	11	75	60	0	0	39	0.97
3469490--3469558	11	6.5	11	73	20	58	62	0	0	37	0.96
3470807--3470840	11	3.0	11	91	4	50	50	0	2	47	1.16
3479361--3479408	23	2.1	22	84	3	60	33	2	2	62	1.18
3479460--3479521	26	2.3	27	88	2	90	51	1	1	45	1.20
3479587--3479627	10	4.0	10	93	3	64	70	0	0	29	0.87
3479586--3479619	14	2.4	14	90	9	52	73	0	0	26	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3480003--3480071	23	2.8	24	74	12	61	37	1	0	60	1.06
3480045--3480094	19	2.5	19	87	6	64	44	0	0	56	0.99
3480193--3480224	2	16.0	2	100	0	64	50	0	0	50	1.00
3480449--3480477	14	2.1	14	100	0	58	48	0	0	51	1.00
3481374--3481410	14	2.8	14	84	8	51	62	0	0	37	0.96
3481413--3481438	7	3.7	7	100	0	52	46	0	0	53	1.00
3486339--3486383	23	2.1	21	88	12	65	60	20	13	6	1.55
3497945--3497971	13	2.1	13	100	0	54	62	0	0	37	0.95
3498029--3498073	16	3.1	15	79	14	51	44	0	0	55	0.99
3498088--3498190	26	3.9	26	71	13	77	61	1	0	36	1.07
3498144--3498209	28	2.3	27	84	10	78	65	0	0	34	0.93
3499154--3499214	29	2.1	30	84	9	81	47	0	0	52	1.00
3499185--3499230	25	1.9	23	86	8	65	47	0	0	52	1.00
3499162--3499226	29	2.2	28	79	12	69	52	0	0	47	1.00
3499190--3499238	21	2.1	25	82	14	61	55	0	0	44	0.99
3499227--3499292	32	2.0	34	82	8	82	59	1	0	39	1.07
3502625--3502896	136	2.0	136	98	0	526	26	15	17	39	1.90
3507830--3507873	2	22.0	2	90	0	70	50	0	4	45	1.22
3508818--3508868	8	6.2	8	75	20	52	39	0	0	60	0.97
3508810--3508872	33	1.9	32	93	3	108	41	0	0	58	0.98
3508854--3508943	32	2.9	31	80	9	87	41	1	2	55	1.19
3508820--3508956	30	4.6	30	68	23	85	39	0	1	58	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3508905--3508957	21	2.4	21	81	6	61	37	0	0	62	0.96
3508903--3508962	18	3.4	18	76	2	50	36	0	0	63	0.95
3508905--3508958	23	2.3	23	84	6	65	37	0	0	62	0.95
3509097--3509126	5	6.0	5	92	0	51	23	0	0	76	0.78
3509498--3509522	3	8.3	3	100	0	50	32	0	0	68	0.90
3513018--3513049	2	16.0	2	100	0	64	50	0	50	0	1.00
3514922--3514956	2	17.5	2	100	0	70	0	48	0	51	1.00
3519362--3519387	2	13.0	2	100	0	52	50	0	50	0	1.00
3520345--3520374	14	2.1	14	100	0	60	23	20	33	23	1.97
3525465--3525538	37	1.9	39	83	5	98	58	0	1	40	1.07
3525574--3525628	12	4.7	12	77	18	62	32	0	1	65	1.03
3525645--3525675	2	15.5	2	100	0	62	51	0	0	48	1.00
3529343--3529384	2	21.0	2	100	0	84	50	0	0	50	1.00
3530109--3530133	2	12.5	2	100	0	50	48	0	0	52	1.00
3531104--3531170	24	2.9	24	82	12	79	46	0	0	53	1.00
3531106--3531144	20	1.9	21	89	5	62	41	0	0	58	0.98
3532081--3532146	33	2.0	33	100	0	132	39	15	21	24	1.91
3537364--3537394	2	15.5	2	100	0	62	51	0	48	0	1.00
3538215--3538268	21	2.7	20	75	13	58	48	0	0	51	1.00
3538196--3538278	43	2.0	42	81	11	100	45	1	0	53	1.08
3542623--3542686	20	3.2	20	80	4	65	39	4	3	53	1.38
3548068--3548122	30	1.9	27	85	10	74	47	7	0	45	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3548073--3548115	21	2.1	21	82	4	52	48	6	0	44	1.29
3560666--3560702	2	18.5	2	100	0	74	48	0	0	51	1.00
3564289--3564315	2	13.5	2	100	0	54	48	0	0	51	1.00
3565202--3565256	29	1.9	28	85	10	76	43	1	7	47	1.41
3565277--3565307	16	1.9	16	93	0	53	70	0	0	29	0.87
3565810--3565839	2	15.0	2	100	0	60	50	0	0	50	1.00
3566062--3566089	2	14.0	2	100	0	56	50	50	0	0	1.00
3571044--3571081	2	19.5	2	94	5	69	50	0	0	50	1.00
3575502--3575527	2	13.0	2	100	0	52	50	0	0	50	1.00
3578163--3578198	2	18.0	2	100	0	72	50	0	0	50	1.00
3590239--3590265	2	13.5	2	100	0	54	51	0	0	48	1.00
3591024--3591076	18	2.9	18	80	5	54	66	0	0	33	0.92
3592425--3592458	13	2.5	13	90	4	50	58	0	0	41	0.98
3606027--3606075	2	24.5	2	100	0	98	48	0	0	51	1.00
3606902--3606942	14	2.9	14	85	3	55	31	7	0	60	1.24
3611747--3611776	2	15.0	2	100	0	60	50	0	50	0	1.00
3629530--3629558	2	14.5	2	100	0	58	48	0	0	51	1.00
3633438--3633481	23	2.0	23	86	8	65	47	0	2	50	1.13
3637280--3637316	19	1.9	19	94	0	65	35	13	16	35	1.88
3640477--3640529	24	2.3	23	90	6	81	62	0	0	37	0.96
3645553--3645583	15	2.1	15	93	0	53	25	16	38	19	1.92
3649445--3649477	2	16.5	2	93	0	57	0	45	3	51	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3657405--3657431	2	13.5	2	100	0	54	0	0	48	51	1.00
3657775--3657816	2	21.0	2	95	0	75	50	2	0	47	1.14
3659329--3659356	2	14.0	2	100	0	56	50	0	0	50	1.00
3659527--3659555	3	9.7	3	100	0	58	65	0	0	34	0.93
3662541--3662842	155	1.9	155	96	0	559	28	19	17	34	1.95
3670696--3670948	117	2.2	117	93	0	425	16	37	11	33	1.86
3670696--3670986	117	2.5	116	85	6	293	18	36	10	33	1.86
3677128--3677170	2	21.5	2	95	0	77	48	2	0	48	1.14
3688578--3688624	18	2.5	19	80	13	62	61	0	2	36	1.08
3689753--3689804	24	2.3	23	83	9	70	67	0	19	13	1.23

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