genome.fa.s38.2.7.7.80.10.50.1000.8.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: Scaffold38
Parameters: 2 7 7 80 10 50 1000
Length:  2073527

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

This is table  8  of  15  ( 1750 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)
1098859--1098905	22	2.1	22	84	7	60	36	8	0	55	1.31
1103944--1103983	21	1.9	21	94	0	71	20	40	22	17	1.92
1107047--1107076	3	10.0	3	92	0	51	36	0	0	63	0.95
1107075--1107106	3	10.7	3	100	0	64	0	0	31	68	0.90
1108289--1108317	14	2.1	14	100	0	58	27	0	20	51	1.47
1108303--1108365	32	2.0	32	83	0	81	23	4	22	49	1.69
1110214--1110644	190	2.2	194	82	5	534	42	13	12	31	1.81
1111622--1111762	58	2.4	58	90	1	221	14	22	14	47	1.81
1112173--1112296	29	4.4	29	68	19	100	43	14	20	20	1.87
1112155--1112333	84	2.1	84	87	5	256	44	13	21	20	1.86
1112310--1112360	17	3.1	16	81	13	59	49	9	23	17	1.77
1113111--1113743	42	15.0	42	73	5	414	33	19	29	17	1.95
1113109--1113521	85	4.9	85	80	2	429	32	19	30	17	1.95
1113185--1113648	127	3.7	126	78	7	361	34	19	28	17	1.95
1113109--1113648	85	6.4	84	77	4	419	33	19	29	17	1.95
1113237--1113733	212	2.3	212	82	3	588	34	20	28	17	1.95
1113364--1113746	85	4.5	85	79	4	364	34	19	28	16	1.94
1115287--1115336	17	2.9	17	84	0	73	14	6	0	80	0.90
1125031--1125087	13	3.9	13	72	24	51	35	12	17	35	1.87
1125030--1125114	32	2.7	32	96	0	152	32	11	17	37	1.86
1125044--1125106	19	3.7	18	74	24	64	33	11	17	38	1.85
1125210--1125247	20	2.1	18	85	14	51	36	15	15	31	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1130055--1130476	189	2.2	187	81	7	480	43	13	11	31	1.80
1131453--1131587	58	2.3	58	90	0	216	13	25	16	44	1.84
1131728--1131793	33	2.2	30	75	19	73	21	22	4	51	1.66
1131740--1131792	16	3.2	16	68	5	52	18	24	3	52	1.62
1132082--1132121	14	2.9	14	96	0	71	42	7	25	25	1.80
1132346--1132399	22	2.4	22	87	9	74	33	1	1	62	1.16
1133377--1133455	23	3.7	23	70	16	78	67	0	29	3	1.08
1133341--1133455	41	2.8	42	86	5	146	67	0	29	2	1.04
1133354--1133459	10	10.5	10	66	17	58	68	0	28	2	1.03
1133465--1133499	17	2.1	17	89	5	54	74	0	22	2	0.95
1133547--1133589	14	3.3	13	78	12	52	46	0	0	53	1.00
1134226--1134353	63	2.0	64	87	4	188	37	3	10	49	1.53
1135812--1135854	22	2.0	21	81	4	50	46	2	0	51	1.13
1138242--1138281	17	2.2	17	86	8	53	40	2	0	57	1.12
1139551--1139594	21	2.0	22	86	4	63	43	9	9	38	1.68
1141836--1141891	17	2.9	18	84	12	60	66	0	1	32	1.03
1141846--1141941	28	3.5	27	75	20	83	62	3	2	32	1.22
1141933--1142018	17	5.2	17	72	25	78	59	2	1	37	1.18
1141975--1142005	14	2.2	14	94	0	53	64	3	0	32	1.09
1141926--1141996	19	3.9	19	67	20	53	59	4	1	35	1.26
1144837--1144877	18	2.3	19	83	12	59	56	2	0	41	1.13
1145204--1145243	21	1.9	21	85	10	55	35	5	27	32	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1145225--1145269	22	2.0	22	82	0	54	37	6	17	37	1.76
1151695--1151769	20	3.8	20	78	3	71	40	13	13	33	1.83
1151692--1151769	40	2.0	39	84	2	102	39	14	12	33	1.84
1152244--1153597	28	47.2	29	89	4	1914	21	17	32	28	1.96
1152244--1153597	57	23.6	57	89	3	1974	21	17	32	28	1.96
1154835--1154900	1	66.0	1	78	0	69	0	1	9	89	0.55
1154822--1154899	12	6.8	11	81	12	95	1	2	8	87	0.70
1154817--1154896	22	4.1	20	76	15	69	2	3	8	85	0.82
1154835--1154901	12	5.6	12	87	7	100	0	1	10	88	0.59
1162799--1162850	22	2.3	23	96	3	97	59	9	11	19	1.59
1163761--1163835	20	3.8	20	80	3	80	40	12	13	34	1.81
1163758--1163835	40	2.0	39	87	2	111	39	12	12	34	1.82
1164349--1165301	86	11.1	85	89	3	1410	21	17	32	28	1.96
1164361--1165303	29	32.9	29	91	3	1414	21	17	32	28	1.96
1166495--1166547	1	53.0	1	80	0	61	0	1	7	90	0.52
1166485--1166548	12	5.6	11	82	12	76	1	3	9	85	0.76
1166502--1166547	13	3.7	13	82	11	69	0	0	8	91	0.43
1176275--1176301	4	6.8	4	100	0	54	77	0	0	22	0.76
1180563--1180637	20	3.8	20	80	3	80	40	12	13	34	1.81
1180560--1180637	40	2.0	39	87	2	111	39	12	12	34	1.82
1181239--1181278	19	2.1	19	85	0	53	12	10	7	70	1.35
1186126--1186177	21	2.5	21	69	12	52	32	17	21	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1186224--1186281	13	3.9	13	73	26	53	32	13	13	39	1.85
1186204--1186303	33	3.0	33	94	0	164	32	12	14	42	1.82
1186237--1186305	20	3.8	19	73	26	78	28	11	11	47	1.75
1186346--1186370	13	1.9	13	100	0	50	32	16	16	36	1.90
1191102--1191130	12	2.4	12	100	0	58	37	0	24	37	1.56
1194524--1194557	11	3.0	11	91	4	50	85	11	2	0	0.71
1194525--1194558	16	2.1	16	94	0	59	88	8	2	0	0.62
1194526--1194586	20	3.0	20	82	4	59	80	9	4	4	1.01
1195808--1196247	29	15.1	29	86	3	555	28	29	17	25	1.97
1195806--1196242	86	5.0	87	85	4	576	28	29	17	24	1.97
1195808--1196225	115	3.6	115	86	3	545	28	29	16	24	1.97
1196801--1196875	20	3.8	20	80	0	96	33	13	12	41	1.81
1196801--1196878	40	2.0	39	89	2	120	33	12	12	41	1.82
1197783--1197828	20	2.4	20	82	7	60	23	17	8	50	1.74
1198015--1198094	39	2.1	39	100	0	160	25	7	25	42	1.80
1200483--1200658	80	2.2	81	84	6	252	37	6	20	35	1.79
1200954--1201017	19	3.4	19	82	0	83	31	18	17	32	1.94
1208409--1208436	13	2.2	13	100	0	56	39	17	14	28	1.89
1208391--1208456	33	2.0	33	88	5	98	39	13	15	31	1.86
1209083--1209157	20	3.8	20	78	0	87	34	13	12	40	1.81
1209083--1209160	40	2.0	39	87	2	111	34	12	12	39	1.82
1210068--1210124	23	2.5	23	100	0	114	17	10	8	63	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1210076--1210131	23	2.6	21	86	8	51	19	8	8	62	1.51
1223190--1223225	14	2.5	15	90	4	56	86	8	2	2	0.77
1223191--1223225	15	2.3	15	90	0	52	88	5	2	2	0.68
1224447--1224544	28	3.4	28	88	5	135	31	32	15	20	1.93
1224526--1224621	31	3.1	32	91	7	162	30	37	18	13	1.90
1224635--1225768	32	36.3	31	87	9	1495	31	36	18	13	1.90
1224741--1224784	20	2.2	20	100	0	88	29	38	22	9	1.85
1224850--1224932	39	2.1	41	91	8	136	34	38	15	10	1.83
1224761--1225768	159	6.3	159	92	5	1629	31	36	18	13	1.90
1226304--1226376	20	3.8	20	74	7	78	34	13	12	39	1.82
1226304--1226379	38	2.0	38	84	7	100	34	13	13	39	1.83
1230383--1230431	3	16.0	3	95	4	89	65	0	0	34	0.93
1231823--1231854	2	16.0	2	100	0	64	50	0	0	50	1.00
1234455--1234504	24	2.1	25	85	14	70	48	6	4	42	1.46
1235567--1235609	17	2.6	16	82	7	59	51	0	0	48	1.00
1238587--1238622	18	2.0	18	88	0	54	41	2	2	52	1.30
1239016--1239065	2	25.0	2	100	0	100	50	0	0	50	1.00
1239852--1239885	14	2.5	14	90	4	52	38	0	0	61	0.96
1239854--1239919	35	1.9	33	85	11	89	42	0	1	56	1.08
1239852--1239923	17	4.8	15	72	18	53	40	0	1	58	1.07
1240318--1240375	29	2.0	29	80	9	66	55	0	0	44	0.99
1240344--1240382	18	2.2	18	86	9	53	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1240733--1240767	2	17.5	2	100	0	70	51	0	0	48	1.00
1241202--1241229	2	14.0	2	100	0	56	50	0	0	50	1.00
1241772--1241822	3	17.0	3	100	0	102	66	0	0	33	0.92
1242311--1242394	24	3.5	23	70	23	57	64	0	2	33	1.07
1242361--1242423	32	2.0	31	87	3	90	60	0	0	39	0.97
1242375--1242418	20	2.2	20	84	8	54	63	0	0	36	0.95
1242364--1242419	15	3.3	18	71	19	57	62	0	0	37	0.95
1242386--1242437	26	2.0	28	85	11	74	59	0	0	40	0.97
1242317--1242452	57	2.4	55	74	12	132	62	0	1	36	1.04
1245227--1245281	25	2.3	23	87	6	74	61	5	1	30	1.29

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