genome.fa.s5.2.7.7.80.10.50.1000.10.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: Scaffold5
Parameters: 2 7 7 80 10 50 1000
Length:  1536239

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   

This is table  10  of  14  ( 1571 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)
1147764--1147821	25	2.2	28	79	17	70	48	0	1	50	1.11
1147766--1147820	27	2.1	25	83	12	67	47	0	1	50	1.11
1149995--1150045	2	25.5	2	100	0	102	49	0	0	50	1.00
1151709--1151748	20	2.0	20	90	0	62	27	2	7	62	1.35
1155419--1155443	8	3.1	8	100	0	50	76	0	0	24	0.80
1155657--1155716	22	2.7	22	78	14	61	46	0	1	51	1.10
1155774--1155895	45	2.6	44	74	20	113	50	1	0	46	1.16
1155866--1155905	21	1.9	21	84	0	53	47	0	0	52	1.00
1155867--1155918	22	2.4	21	75	6	50	50	0	0	50	1.00
1156708--1156738	14	2.1	15	94	5	55	51	3	0	45	1.17
1158823--1158910	44	2.0	45	91	4	144	45	2	14	37	1.58
1159115--1159156	20	2.1	21	86	8	61	42	2	2	52	1.27
1159138--1159162	13	1.9	13	100	0	50	44	0	0	56	0.99
1159564--1159610	5	10.0	5	84	13	55	74	0	0	25	0.82
1159567--1159608	18	2.4	18	88	4	59	73	0	0	26	0.83
1159912--1159954	19	2.2	20	91	4	70	67	0	0	32	0.91
1159916--1159957	12	3.3	12	90	9	66	66	0	0	33	0.92
1159912--1160009	26	3.7	26	75	13	85	60	0	2	37	1.09
1159996--1160045	17	2.9	17	72	24	50	56	0	0	44	0.99
1165722--1165764	17	2.5	17	84	0	59	51	2	0	46	1.13
1166481--1166513	16	1.9	18	88	11	52	66	3	15	15	1.37
1167703--1167756	16	3.5	15	76	16	56	42	24	18	14	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1167717--1167838	48	2.6	47	80	7	124	41	27	13	17	1.87
1167748--1167838	16	5.8	16	80	1	94	42	27	12	17	1.85
1167748--1167843	32	3.0	32	80	3	104	42	26	12	18	1.86
1167745--1167838	48	2.0	47	85	2	125	43	27	11	17	1.83
1168903--1169017	16	7.2	15	72	9	50	45	27	12	14	1.81
1168896--1169017	48	2.5	48	81	2	138	44	27	13	14	1.83
1168938--1169000	32	2.0	32	93	0	108	41	28	14	15	1.87
1168988--1169027	17	2.4	16	87	4	53	47	32	10	10	1.70
1172608--1172736	52	2.5	52	94	0	222	27	17	20	35	1.94
1172608--1172756	52	2.9	52	84	7	196	28	16	20	34	1.94
1172745--1172769	13	1.9	13	100	0	50	36	16	16	32	1.90
1172811--1172876	19	3.8	19	75	22	81	36	16	12	34	1.86
1172832--1172856	13	1.9	13	100	0	50	32	16	16	36	1.90
1172813--1172875	32	2.0	32	96	0	117	34	17	12	34	1.88
1173078--1173206	52	2.5	52	85	0	168	27	18	19	34	1.95
1173078--1173226	52	2.9	52	83	2	156	29	17	18	34	1.94
1174689--1174777	5	17.4	5	69	19	51	39	4	0	56	1.20
1174690--1174766	18	4.3	18	85	8	95	38	5	0	55	1.22
1174700--1174777	9	8.4	10	72	22	55	41	3	0	55	1.18
1174718--1174777	18	3.3	18	75	13	61	43	3	0	53	1.17
1174702--1174803	46	2.3	44	79	14	111	41	4	0	53	1.22
1177173--1177197	2	12.5	2	100	0	50	48	0	0	52	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1177809--1177833	10	2.5	10	100	0	50	16	0	0	84	0.63
1178819--1178863	20	2.2	20	84	7	56	42	2	0	55	1.12
1178822--1178880	11	5.1	11	76	10	55	42	1	0	55	1.09
1179653--1179691	14	2.8	14	84	0	51	43	0	0	56	0.99
1180143--1180184	17	2.3	18	81	18	52	52	2	0	45	1.13
1180100--1180171	25	2.9	25	73	19	69	50	2	0	47	1.15
1181954--1182049	29	3.1	33	72	24	93	54	0	0	45	0.99
1181991--1182040	24	2.1	24	85	14	68	54	0	0	46	1.00
1182786--1182830	11	4.3	11	78	18	51	28	2	0	68	1.01
1184518--1184556	17	2.3	17	82	8	53	28	0	0	71	0.86
1184528--1184558	14	2.1	15	94	5	55	25	0	0	74	0.82
1184518--1184562	14	2.8	17	75	25	53	28	0	0	71	0.87
1184547--1184579	13	2.6	13	90	4	50	39	0	0	60	0.97
1185910--1185973	12	5.0	13	71	16	53	46	0	1	51	1.10
1186095--1186136	21	2.0	21	81	13	50	50	9	2	38	1.48
1187423--1187506	44	1.9	44	83	13	111	44	10	2	42	1.52
1190309--1190342	2	17.0	2	100	0	68	50	0	0	50	1.00
1193199--1193235	13	2.9	14	88	11	53	21	0	0	78	0.75
1193478--1193544	20	3.3	20	68	8	55	52	0	0	47	1.00
1195106--1195135	2	15.0	2	100	0	60	50	0	0	50	1.00
1197992--1198028	13	2.9	14	88	11	53	21	0	0	78	0.75
1198313--1198352	20	2.0	20	85	0	53	37	0	0	62	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1203916--1203982	31	2.3	30	82	17	79	34	1	0	64	1.03
1204150--1204177	3	9.3	3	100	0	56	32	0	0	67	0.91
1204384--1204424	18	2.2	18	86	4	55	17	12	4	65	1.42
1204498--1204548	22	2.5	22	77	22	58	50	0	0	49	1.00
1205435--1205501	35	1.9	36	87	6	102	55	0	0	44	0.99
1205428--1205504	34	2.3	34	80	12	97	54	0	0	45	0.99
1206573--1206599	5	5.4	5	100	0	54	81	0	0	18	0.69
1208157--1208228	22	3.2	22	75	12	67	43	1	1	54	1.17
1209723--1209813	43	2.1	43	93	0	155	45	4	2	48	1.34
1209855--1209893	17	2.3	17	86	8	53	53	0	2	43	1.14
1210416--1210473	27	2.2	26	87	3	80	41	1	0	56	1.09
1210427--1210459	18	1.9	18	88	11	52	39	0	0	60	0.97
1211581--1211616	2	18.0	2	94	0	63	47	2	0	50	1.15
1211807--1211853	24	2.0	24	87	8	69	55	0	4	40	1.19
1211937--1211981	2	23.0	2	95	4	83	0	51	0	48	1.00
1212405--1212438	16	2.1	17	88	5	52	44	2	0	52	1.16
1212850--1212904	26	2.1	27	89	3	85	56	0	1	41	1.10
1212926--1212980	22	2.5	21	80	11	65	56	0	3	40	1.17
1215259--1215308	19	2.6	20	78	15	52	28	2	2	68	1.12
1215275--1215319	22	2.1	21	83	4	54	31	2	0	66	1.04
1215297--1215355	30	2.0	29	93	3	100	47	0	0	52	1.00
1215458--1215511	24	2.2	24	100	0	108	33	7	0	59	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1215833--1215871	19	2.0	20	90	5	62	58	0	0	41	0.98
1218795--1218836	21	2.0	21	86	13	61	40	0	0	59	0.97
1218786--1219228	224	2.0	224	95	2	811	50	4	9	34	1.56
1219594--1219653	31	1.9	32	93	3	104	53	0	0	46	1.00
1222128--1222176	17	2.7	18	90	6	73	57	0	0	42	0.99
1222141--1222180	11	4.2	10	78	21	50	60	0	0	40	0.97
1222127--1222194	17	3.9	17	81	11	66	57	0	0	42	0.98
1222125--1222200	34	2.4	31	80	10	89	56	0	0	43	0.99
1222141--1222200	28	2.1	28	81	6	68	58	0	0	41	0.98
1222266--1222299	10	3.3	10	95	4	59	61	0	0	38	0.96
1223998--1224048	12	4.2	13	73	12	54	52	0	5	41	1.25
1224000--1224057	12	4.5	13	74	22	52	53	1	5	39	1.33
1224192--1224294	28	4.0	24	75	20	70	54	0	0	45	0.99
1224222--1224304	6	13.8	6	73	19	59	60	0	0	39	0.97
1224219--1224299	28	2.9	27	80	12	94	59	0	0	40	0.98
1224247--1224301	20	2.8	20	86	5	67	61	0	0	38	0.96
1224582--1224632	17	3.0	17	78	16	61	39	0	0	60	0.97
1224842--1224876	14	2.5	14	90	0	52	80	0	0	20	0.72
1224854--1224970	45	2.6	45	79	15	109	56	0	0	42	1.05
1224894--1224970	10	8.2	10	73	13	58	55	0	0	44	0.99
1224914--1224970	26	2.2	26	84	6	71	52	0	0	47	1.00
1225323--1225403	17	5.2	16	74	11	71	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1225319--1225403	33	2.6	31	81	7	89	56	0	0	43	0.99
1225320--1225411	17	5.6	17	67	20	61	55	1	0	43	1.07
1225498--1225534	2	19.0	2	94	5	67	48	0	0	51	1.00
1226293--1226335	22	2.0	22	86	9	61	23	2	2	72	1.08
1226291--1226335	23	2.0	23	87	12	67	24	2	2	71	1.09
1226355--1226396	21	2.1	19	86	8	57	42	0	0	57	0.99
1226873--1226900	6	4.7	6	100	0	56	46	17	17	17	1.85
1227351--1227381	16	1.9	16	93	0	53	32	0	12	54	1.38
1228837--1228875	16	2.5	15	88	8	60	41	2	5	51	1.38
1229734--1229791	22	2.7	21	73	13	55	43	0	0	56	0.99

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14