genome.fa.s99.2.7.7.80.10.50.1000.8.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: Scaffold99
Parameters: 2 7 7 80 10 50 1000
Length:  1377724

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  8  of  10  ( 1130 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)
994310--994383	21	3.6	20	83	7	78	29	18	14	36	1.91
997129--997179	27	2.0	25	81	11	59	27	31	13	27	1.94
1003948--1003973	13	2.0	13	100	0	52	38	15	15	30	1.88
1005573--1005597	12	2.1	12	100	0	50	32	0	36	32	1.58
1006189--1006233	21	2.1	22	88	8	67	55	4	17	22	1.60
1008036--1008066	15	2.1	15	93	0	53	48	16	22	12	1.80
1010137--1010162	13	2.0	13	100	0	52	30	15	15	38	1.88
1010285--1010330	21	2.2	20	81	11	58	32	19	4	43	1.71
1012725--1012750	13	2.0	13	100	0	52	38	15	15	30	1.88
1013854--1013878	11	2.3	11	100	0	50	92	0	8	0	0.40
1013854--1013895	18	2.6	16	85	11	50	83	0	14	2	0.75
1013862--1013915	20	2.5	22	77	11	58	75	1	18	3	1.03
1021832--1021960	55	2.4	57	84	6	160	25	28	14	31	1.95
1021832--1021960	28	4.7	28	75	2	120	25	28	14	31	1.95
1022356--1022405	14	3.5	14	84	10	57	80	8	2	10	0.99
1024301--1024358	29	2.0	29	86	6	82	31	15	13	39	1.86
1027175--1027264	26	3.5	26	92	0	153	44	23	16	15	1.86
1030269--1030397	52	2.5	52	98	0	249	27	18	18	34	1.95
1030406--1030430	13	1.9	13	100	0	50	36	16	16	32	1.90
1030468--1030568	32	3.1	32	88	1	148	36	13	11	37	1.82
1030524--1030548	13	1.9	13	100	0	50	32	16	16	36	1.90
1031309--1031486	49	3.6	49	79	0	203	28	20	25	25	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1031500--1031617	29	4.1	30	76	12	97	19	18	27	34	1.95
1031513--1031966	58	7.8	55	83	8	417	19	15	32	32	1.93
1031554--1031966	89	4.7	86	83	6	440	19	15	32	31	1.94
1031553--1031963	147	2.8	145	86	7	548	19	16	32	31	1.94
1033410--1033523	1	114.0	1	72	0	75	1	4	8	85	0.81
1033404--1033525	20	6.2	19	75	19	99	1	4	10	83	0.85
1047367--1047568	104	1.9	105	91	3	336	30	17	18	33	1.94
1047368--1047548	52	3.5	52	96	0	335	28	18	18	34	1.94
1047557--1047581	13	1.9	13	100	0	50	36	16	16	32	1.90
1047624--1047721	19	5.8	18	69	28	81	36	15	12	35	1.85
1047619--1047719	32	3.1	32	94	1	166	35	15	11	36	1.85
1047643--1047697	13	3.8	13	75	25	56	32	16	14	36	1.89
1052180--1052237	28	2.0	29	86	3	82	39	0	0	60	0.97
1059187--1059264	39	2.0	39	87	0	111	26	6	14	52	1.65
1059188--1059251	13	4.9	13	77	7	58	25	6	14	54	1.62
1061095--1061149	19	2.8	20	83	5	76	36	16	14	32	1.89
1061095--1061200	20	5.7	19	79	15	80	37	16	16	29	1.91
1061135--1061161	13	2.1	13	100	0	54	40	14	14	29	1.86
1061096--1061200	52	2.0	53	85	5	142	38	15	17	29	1.90
1061148--1061200	20	2.7	20	100	0	106	39	15	18	26	1.90
1061116--1061181	33	2.0	32	88	2	96	40	13	16	28	1.87
1061719--1061810	37	2.5	37	84	8	132	29	26	4	40	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1063181--1063229	20	2.5	20	100	0	98	14	30	40	14	1.85
1063660--1063688	13	2.2	13	100	0	58	41	17	13	27	1.87
1064541--1064615	20	3.8	20	78	0	87	34	13	12	40	1.81
1064541--1064618	40	2.0	39	87	2	111	34	12	12	39	1.82
1067598--1067623	13	2.0	13	100	0	52	38	15	15	30	1.88
1067580--1067643	32	2.0	33	87	3	94	40	17	14	28	1.88
1078626--1078655	13	2.3	13	100	0	60	86	6	0	6	0.70
1079646--1079894	62	4.1	62	86	8	309	24	25	20	30	1.99
1080165--1080189	13	1.9	13	100	0	50	36	16	16	32	1.90
1080145--1080208	32	2.0	33	96	3	121	34	12	18	34	1.89
1080144--1080227	19	4.7	19	80	18	108	33	11	17	36	1.87
1080270--1080294	13	1.9	13	100	0	50	32	16	16	36	1.90
1080303--1080431	52	2.5	52	97	0	240	34	17	17	29	1.94
1083532--1083856	61	5.5	61	79	10	377	26	24	17	31	1.97
1083503--1083856	122	3.0	121	84	7	442	27	24	17	30	1.97
1083702--1083801	50	2.0	50	90	3	157	25	23	22	30	1.99
1084808--1085021	107	2.0	107	97	0	401	16	23	11	48	1.79
1090133--1090257	52	2.4	52	95	0	223	28	17	18	36	1.94
1090133--1090277	52	2.8	51	89	4	211	29	17	18	34	1.94
1090266--1090290	13	1.9	13	100	0	50	36	16	16	32	1.90
1090333--1090430	19	5.8	18	71	28	90	36	17	12	33	1.87
1090352--1090408	13	3.9	13	76	24	60	33	17	14	35	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1090331--1090428	32	3.0	32	96	1	178	35	17	12	34	1.87
1092602--1092711	42	2.6	43	83	8	138	13	41	0	43	1.50
1094329--1094719	61	6.4	61	85	0	498	24	25	19	30	1.98
1094329--1094719	183	2.1	182	87	0	548	24	25	19	30	1.98
1095586--1095625	21	1.9	21	85	10	55	20	35	10	35	1.86
1097141--1097816	78	8.7	79	78	8	575	28	22	12	36	1.91
1097151--1097817	79	8.6	77	76	11	444	28	22	12	35	1.91
1097149--1097817	157	4.3	157	77	11	635	28	22	13	35	1.91
1099847--1099878	12	2.7	12	95	0	55	18	6	0	75	1.01
1105168--1105335	51	3.3	51	83	0	228	29	12	29	28	1.93
1105217--1105653	130	3.4	127	79	8	427	33	11	26	28	1.91
1108046--1108194	50	3.0	50	87	2	201	39	14	20	24	1.91
1108693--1109176	180	2.7	183	84	5	635	29	17	25	26	1.97
1108674--1109184	61	8.5	61	81	3	570	29	17	26	26	1.98
1110143--1110206	9	7.0	9	82	8	67	0	9	6	84	0.78
1117863--1118094	97	2.4	97	93	0	401	28	14	31	25	1.95
1120273--1120349	20	3.8	20	86	6	111	40	12	15	31	1.85
1121221--1121889	28	22.9	28	82	5	568	24	18	28	28	1.98
1121215--1121895	113	5.8	114	80	8	669	24	17	28	28	1.98
1122856--1122913	13	4.9	13	72	23	65	29	17	15	37	1.90
1122868--1122933	20	3.7	20	73	26	83	27	18	15	39	1.90
1122856--1122934	33	2.4	33	100	0	158	27	17	15	39	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1122922--1123050	52	2.5	52	98	0	249	35	17	17	28	1.93
1130193--1130240	24	2.0	24	84	15	64	79	4	16	0	0.89
1130200--1130239	21	1.9	21	94	0	71	80	2	17	0	0.83
1130180--1130235	29	2.0	27	86	10	76	80	5	14	0	0.88
1131191--1131317	34	3.7	35	82	11	131	21	31	14	33	1.93
1131189--1131285	34	2.8	35	84	4	133	20	29	13	36	1.91
1131252--1131332	32	2.5	32	95	0	144	22	34	13	29	1.92
1131324--1131426	32	3.2	32	87	5	156	31	33	17	17	1.93
1131314--1131419	33	3.2	33	87	5	160	27	34	16	21	1.94
1131414--1132063	92	7.1	92	91	4	885	24	25	18	32	1.97
1131419--1132107	233	2.9	233	88	5	961	24	24	17	32	1.97
1132017--1132163	52	2.7	55	81	3	183	25	23	15	36	1.94
1132783--1132838	20	2.9	19	86	5	85	44	16	12	26	1.83
1132783--1132838	19	2.8	20	84	10	80	44	16	12	26	1.83
1141597--1141622	13	2.0	13	100	0	52	38	15	15	30	1.88
1141578--1141642	33	2.0	33	87	6	96	41	16	13	27	1.87
1142148--1142298	52	3.1	48	87	7	148	35	17	16	30	1.93
1142170--1142298	52	2.5	52	97	0	240	36	17	17	28	1.93
1146553--1146630	9	7.9	10	70	12	54	6	2	7	83	0.89
1146547--1146594	25	2.0	24	83	4	60	4	10	8	77	1.12
1146578--1146630	1	53.0	1	76	0	52	5	0	5	88	0.62
1146580--1146630	18	2.8	18	90	0	75	5	0	5	88	0.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1146580--1146630	26	2.0	26	96	0	93	5	0	5	88	0.64
1152318--1152343	13	2.0	13	100	0	52	38	15	15	30	1.88
1154547--1154591	21	2.1	21	84	8	56	53	4	20	22	1.63
1156394--1156424	15	2.1	15	93	0	53	48	16	22	12	1.80
1158503--1158528	13	2.0	13	100	0	52	30	15	15	38	1.88
1166216--1166262	23	2.1	22	84	4	58	68	8	14	8	1.39
1168170--1168379	96	2.2	97	95	0	377	29	14	30	26	1.95
1170572--1170626	20	2.8	20	85	0	74	40	14	10	34	1.81
1172162--1172189	13	2.2	13	100	0	56	28	14	17	39	1.89
1179127--1179185	11	5.5	11	79	4	66	84	15	0	0	0.62

Tables:   1   2   3   4   5   6   7   8   9   10