genome.fa.s439.2.7.7.80.10.50.1000.4.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: Scaffold439
Parameters: 2 7 7 80 10 50 1000
Length:  1094049

Tables:   1   2   3   4   5   6   7   

This is table  4  of  7  ( 799 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)
496223--496370	79	1.9	79	84	2	199	53	5	1	39	1.32
496472--496516	16	2.9	15	87	9	63	55	2	0	42	1.12
500683--500722	19	2.1	19	86	9	55	37	0	2	60	1.11
500769--500812	17	2.5	17	85	3	52	61	2	0	36	1.09
501441--501557	11	10.5	11	71	19	75	39	0	0	60	0.97
501495--501557	17	3.5	17	74	21	56	34	0	0	65	0.93
501934--501987	23	2.3	24	81	9	67	48	3	0	48	1.19
502106--502156	3	16.7	3	91	4	84	62	0	1	35	1.06
502312--502382	28	2.6	27	80	10	74	40	4	0	54	1.20
502870--502913	10	4.4	10	79	0	52	65	0	0	34	0.93
502869--502917	25	1.9	26	87	4	73	63	0	0	36	0.95
502867--502917	26	2.0	26	84	7	68	62	0	0	37	0.95
502856--502913	30	1.9	30	86	6	82	62	0	0	37	0.96
502864--502931	35	1.9	35	82	14	86	61	0	1	36	1.05
505291--505400	20	5.4	20	79	3	87	34	10	12	42	1.76
505291--505378	40	2.2	41	89	2	133	34	10	13	42	1.78
510618--510660	11	4.0	11	77	17	54	34	2	0	62	1.08
511254--511283	14	2.1	14	100	0	60	30	13	26	30	1.94
511303--511355	7	7.1	7	76	19	54	20	0	0	79	0.74
511305--511353	15	3.4	14	76	17	55	18	0	0	81	0.69
511315--511381	20	3.2	20	70	15	55	29	0	0	70	0.88
511335--511397	27	2.5	25	80	12	74	33	0	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
511304--511382	42	2.0	38	85	9	104	27	0	0	72	0.85
511345--511390	19	2.3	21	75	21	53	36	0	0	63	0.95
511840--511872	15	2.2	15	89	10	50	6	21	0	72	1.05
517579--517763	11	16.4	11	67	22	57	37	0	1	61	1.04
517579--517752	33	5.5	32	69	17	96	38	0	1	60	1.04
517654--517691	14	2.7	15	88	8	53	44	0	0	55	0.99
517618--517708	46	2.0	46	82	8	114	42	0	1	56	1.06
517680--517771	38	2.4	38	80	12	100	33	0	1	65	1.00
517666--517769	17	5.9	18	78	16	78	34	0	0	64	1.00
517666--517759	49	1.9	47	81	16	111	32	0	1	65	0.99
517691--517763	22	3.3	22	76	7	76	30	0	1	68	0.98
526269--526338	14	5.4	14	74	20	64	55	0	0	44	0.99
526342--526434	40	2.5	35	76	11	96	58	2	1	38	1.17
527144--527179	16	2.2	16	90	0	54	30	2	0	66	1.06
529240--529275	3	12.0	3	100	0	72	66	0	0	33	0.92
529596--529624	3	9.7	3	100	0	58	65	0	0	34	0.93
531995--532037	20	2.2	20	95	4	79	25	20	13	39	1.90
534499--534667	51	3.3	51	85	0	230	32	21	10	35	1.87
535842--536279	111	4.0	109	84	5	508	31	18	17	32	1.94
535862--536277	218	1.9	219	84	2	557	31	18	18	32	1.94
536343--536394	17	3.1	16	78	10	59	67	5	1	25	1.23
537975--538101	28	4.5	28	77	7	114	25	13	25	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
537993--538106	56	2.0	56	81	0	129	24	14	27	34	1.94
537975--538186	84	2.5	84	82	3	232	23	13	28	34	1.93
538145--538229	26	3.3	26	88	0	116	22	16	25	35	1.95
551322--551725	109	3.7	110	81	5	476	34	17	14	33	1.90
551797--551840	17	2.7	16	78	3	52	65	4	0	29	1.12
553040--553070	16	1.9	16	93	0	53	16	0	3	80	0.83
553031--553078	24	2.0	24	84	8	62	18	0	4	77	0.93
553086--553126	15	2.7	16	81	11	50	51	2	0	46	1.14
553186--553234	12	4.2	12	74	25	52	32	0	0	67	0.91
553186--553228	15	2.9	15	80	16	54	34	0	0	65	0.93
553188--553234	19	2.8	17	82	17	62	31	0	0	68	0.90
554390--554418	15	2.0	15	93	6	51	27	3	0	68	1.05
554852--554882	15	2.1	15	93	0	53	41	6	9	41	1.63
554927--554962	16	2.2	16	90	0	54	25	11	16	47	1.79
554933--554968	16	2.2	16	90	0	54	22	13	22	41	1.89
555795--555857	16	3.9	16	81	8	83	30	14	12	42	1.82
555857--555887	16	1.9	16	93	0	53	22	0	22	54	1.44
566298--566360	31	2.1	30	84	3	81	52	0	0	47	1.00
566570--566621	18	3.0	17	78	10	61	40	0	0	59	0.97
566583--566651	9	7.0	10	74	15	56	46	0	0	53	1.00
566566--566650	36	2.4	37	79	16	106	42	0	0	57	0.98
566570--566684	36	3.4	34	77	18	105	42	1	0	55	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
566627--566682	24	2.3	23	77	14	60	44	3	0	51	1.18
566718--566760	17	2.4	18	92	7	70	34	0	2	62	1.08
568116--568165	10	5.0	10	80	11	50	26	0	0	74	0.83
568116--568148	11	2.9	11	95	4	57	21	0	0	78	0.75
568131--568166	17	2.1	17	94	0	63	33	0	0	66	0.92
568112--568163	12	4.5	12	83	7	54	26	0	0	73	0.84
574185--574220	18	2.0	18	89	10	56	77	0	8	13	0.98
576587--576660	12	6.3	12	72	19	50	48	0	1	50	1.09
577293--577322	2	15.0	2	100	0	60	0	50	0	50	1.00
577322--577351	2	15.0	2	100	0	60	50	0	0	50	1.00
580103--580138	16	2.2	16	95	0	63	52	0	2	44	1.15
583401--583494	32	3.0	31	78	3	91	50	7	3	39	1.47
589598--589677	29	2.9	29	78	10	87	52	1	0	46	1.08
591124--591180	29	2.0	29	82	6	71	38	3	3	54	1.35
591189--591237	20	2.5	18	81	15	53	59	0	4	36	1.17
591188--591235	22	2.3	20	78	7	51	60	0	4	35	1.16
591420--591483	29	2.1	29	80	5	74	57	3	1	37	1.24
592232--592273	19	2.3	18	87	4	57	45	2	0	52	1.13
593839--593892	23	2.3	24	77	6	65	42	0	0	57	0.98
593989--594048	27	2.2	28	80	11	72	61	1	0	36	1.06
596673--596808	41	3.4	40	76	9	125	45	14	13	25	1.82
596690--596832	41	3.5	40	76	10	112	46	14	14	24	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
598317--598527	115	1.8	116	80	3	255	31	9	10	47	1.71
599384--599445	31	2.0	31	81	12	74	59	0	0	40	0.97
600078--600129	27	1.9	27	88	7	79	51	0	0	48	1.00
600050--600203	25	6.2	25	70	16	90	58	0	0	40	1.08
600051--600142	20	4.6	20	68	15	57	52	0	1	46	1.07
600146--600203	8	6.8	9	79	16	70	67	1	0	31	1.01
600105--600195	30	2.9	30	77	12	76	60	1	1	37	1.11
600080--600200	16	7.5	16	72	14	88	60	0	0	38	1.08
600051--600199	8	18.4	8	68	23	64	57	0	0	40	1.08
600455--600491	20	1.9	20	94	5	67	45	8	0	45	1.32
601414--601456	19	2.2	20	80	19	56	58	0	0	41	0.98
602495--602527	2	16.5	2	93	0	57	51	0	45	3	1.16
605440--605516	28	2.8	27	84	7	93	24	31	18	25	1.97
605468--605803	79	4.3	78	85	2	361	26	26	14	32	1.95
605468--605806	158	2.1	158	83	2	412	26	25	14	32	1.95
608132--608176	2	22.5	2	100	0	90	48	0	0	51	1.00
608535--608577	19	2.3	18	84	11	52	23	4	9	62	1.44
609685--609793	56	1.9	57	87	7	159	40	8	3	47	1.51
610019--610094	14	5.4	14	78	13	52	42	0	0	57	0.98
610033--610094	14	4.4	14	82	8	72	41	0	0	58	0.98
610130--610164	2	18.0	2	94	5	63	48	0	0	51	1.00
611530--611570	20	2.1	19	86	4	55	51	4	2	41	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
612830--612882	2	26.5	2	100	0	106	49	0	0	50	1.00
613158--613186	6	5.0	6	91	8	51	31	0	0	68	0.89
613997--614072	29	2.6	29	79	8	73	46	1	0	52	1.08
614382--614510	10	12.9	11	69	21	63	58	0	2	39	1.11
614425--614561	5	27.2	5	65	17	61	57	0	0	41	1.04
614403--614497	28	3.4	27	76	11	86	61	0	2	36	1.08
614433--614463	11	2.8	11	95	0	53	67	0	0	32	0.91
614444--614556	37	2.7	41	76	22	110	56	0	0	43	0.99
614424--614552	27	4.6	29	75	11	101	57	0	0	41	1.04
614444--614561	23	5.3	23	68	17	72	56	0	0	43	0.99

Tables:   1   2   3   4   5   6   7