genome.fa.s339.2.7.7.80.10.50.1000.8.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: Scaffold339
Parameters: 2 7 7 80 10 50 1000
Length:  1314099

Tables:   1   2   3   4   5   6   7   8   9   

This is table  8  of  9  ( 1034 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)
1100951--1101011	31	2.0	31	100	0	122	44	26	3	26	1.69
1102805--1102842	13	2.9	13	96	0	67	31	15	18	34	1.92
1104922--1104952	15	2.1	15	93	0	53	12	22	16	48	1.80
1109018--1109043	13	2.0	13	100	0	52	30	15	15	38	1.88
1109082--1109157	21	3.7	21	80	3	100	28	17	11	42	1.84
1109103--1109175	20	3.6	20	81	3	101	31	19	13	35	1.91
1109082--1109175	41	2.3	41	98	0	179	29	18	12	39	1.88
1111461--1111515	20	2.8	20	91	0	83	36	10	14	38	1.81
1111380--1111598	103	2.1	103	99	0	429	31	10	18	38	1.86
1111586--1111624	13	3.0	13	88	0	60	35	15	15	33	1.89
1111667--1111727	21	2.8	22	92	5	106	36	11	26	26	1.90
1111715--1111745	10	3.1	10	90	0	53	41	6	29	22	1.78
1111769--1111903	53	2.6	53	92	1	227	26	17	18	37	1.92
1111875--1111943	20	3.5	20	77	14	74	30	14	15	39	1.88
1111983--1112023	21	2.0	21	85	9	57	36	12	12	39	1.80
1113644--1113668	13	1.9	13	100	0	50	32	16	16	36	1.90
1115168--1115332	84	2.0	84	81	9	194	24	19	4	52	1.64
1117450--1117510	21	2.8	22	92	5	106	36	11	26	26	1.90
1117498--1117528	10	3.1	10	90	0	53	41	6	29	22	1.78
1117552--1117688	53	2.6	53	92	1	229	27	17	18	37	1.93
1117658--1117728	20	3.5	20	77	11	74	29	14	16	39	1.88
1119035--1119125	29	3.1	29	69	17	80	32	8	16	41	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1119157--1119256	29	3.4	29	72	16	82	28	7	13	52	1.66
1119148--1119257	58	1.9	58	83	7	143	28	8	13	50	1.70
1119047--1119256	116	1.8	116	79	8	248	30	9	12	47	1.73
1121010--1121055	20	2.2	20	88	3	65	41	6	17	34	1.75
1121017--1121083	20	3.2	20	85	14	84	41	5	17	34	1.74
1124124--1124246	59	2.1	59	84	3	158	24	30	15	30	1.96
1124181--1124517	78	4.3	77	76	7	265	27	26	14	32	1.95
1124181--1124523	156	2.2	156	82	7	412	27	26	14	32	1.95
1124464--1124576	50	2.2	51	86	7	151	30	27	8	32	1.87
1124383--1124653	129	2.1	129	82	6	327	27	25	14	31	1.95
1124510--1124761	79	3.2	78	79	5	258	26	24	15	33	1.95
1124510--1124816	158	1.9	158	79	6	345	26	24	14	34	1.94
1128684--1128732	20	2.5	20	87	9	66	32	18	12	36	1.88
1128794--1128866	20	3.7	20	100	0	146	35	15	19	30	1.92
1128998--1129049	21	2.5	20	90	3	77	51	17	3	26	1.62
1129687--1129712	13	2.0	13	100	0	52	38	15	15	30	1.88
1130905--1130993	19	5.1	18	71	24	75	38	11	15	34	1.83
1130928--1131006	32	2.5	32	93	0	131	36	12	16	34	1.87
1131045--1131072	13	2.2	13	100	0	56	28	14	17	39	1.89
1131025--1131090	33	2.0	33	87	0	96	28	15	13	42	1.85
1133437--1133611	50	3.4	51	82	7	221	30	27	12	30	1.92
1133591--1133641	27	1.9	26	100	0	93	29	33	15	21	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1133542--1133745	107	1.9	106	85	6	277	27	27	15	28	1.96
1133618--1133901	79	3.6	79	89	2	446	26	26	15	31	1.96
1133857--1133928	28	2.6	28	93	0	117	20	29	22	27	1.99
1133887--1134059	79	2.2	79	86	4	233	28	26	13	31	1.94
1133699--1134062	186	2.0	186	81	6	434	26	26	15	31	1.96
1135227--1135264	18	2.2	18	85	4	51	65	13	13	7	1.46
1136855--1136997	71	2.0	71	95	0	259	40	14	20	24	1.90
1136977--1137003	13	2.1	13	100	0	54	40	14	14	29	1.86
1144087--1144310	49	4.6	49	81	7	244	31	16	25	26	1.97
1144027--1144304	101	2.8	101	81	5	297	30	17	26	25	1.97
1144184--1144310	43	2.8	43	82	7	137	33	18	22	26	1.96
1144332--1144968	29	22.3	29	78	8	605	20	17	29	32	1.96
1144366--1144968	57	10.6	57	81	7	573	20	18	29	32	1.96
1144366--1144968	85	7.1	83	86	5	613	20	18	29	32	1.96
1161215--1161245	13	2.4	13	94	0	53	41	12	12	32	1.81
1161290--1161345	19	2.9	19	91	2	85	35	16	19	28	1.93
1162870--1162940	32	2.2	32	100	0	142	63	0	33	2	1.09
1164591--1164653	30	2.2	31	77	13	71	65	3	1	30	1.18
1165416--1165457	18	2.3	19	87	4	59	52	7	0	40	1.29
1168344--1168381	20	1.9	20	100	0	76	39	15	18	26	1.91
1170392--1170504	51	2.2	51	90	0	172	30	28	9	30	1.89
1170440--1171102	79	8.4	78	82	3	661	28	26	12	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1170328--1170583	130	2.0	130	83	3	327	28	25	11	33	1.91
1170440--1171079	236	2.7	236	86	1	854	28	26	12	32	1.93
1172498--1172558	31	2.0	31	93	0	104	37	9	19	32	1.85
1173110--1173172	33	1.9	32	84	12	83	33	15	19	31	1.93
1179079--1179104	13	2.0	13	100	0	52	38	15	15	30	1.88
1186246--1186563	80	4.0	79	79	5	336	27	28	11	31	1.92
1186241--1186560	160	2.0	161	82	6	391	27	29	11	31	1.92
1189674--1189723	25	2.0	25	100	0	100	48	16	8	28	1.74
1190756--1190791	18	2.0	18	88	0	54	38	0	0	61	0.96
1192044--1192169	60	2.1	60	96	0	234	50	5	7	37	1.53
1192244--1192307	31	2.2	31	83	13	82	60	3	3	32	1.28
1198271--1198359	18	4.5	18	71	22	54	46	10	0	43	1.37
1198352--1198398	12	3.8	12	83	5	58	29	0	0	70	0.88
1198793--1198859	25	2.7	25	84	6	75	59	1	1	37	1.16
1198884--1198983	6	16.7	6	74	18	68	61	0	0	39	0.96
1198885--1198983	17	5.9	17	69	23	59	61	0	0	38	0.96
1199954--1199988	17	2.1	18	89	10	56	45	0	0	54	0.99
1199970--1200011	20	2.1	21	86	8	61	47	0	0	52	1.00
1200807--1200877	36	2.0	36	83	5	90	54	0	1	43	1.08
1200842--1201187	45	7.6	44	74	18	214	53	4	1	40	1.30
1201096--1201232	43	3.1	43	79	8	143	54	4	0	40	1.25
1201198--1201392	106	1.8	106	87	5	295	57	4	1	35	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1201140--1201392	53	4.9	51	78	12	220	57	4	1	36	1.28
1201334--1201437	44	2.4	45	79	6	124	57	0	2	38	1.20
1201388--1201455	16	4.1	16	68	17	57	54	0	0	45	0.99
1201283--1201455	98	1.8	96	86	6	253	57	2	1	38	1.22
1201475--1201524	18	2.6	19	81	9	57	48	2	0	50	1.12
1201484--1201525	18	2.3	19	84	12	61	52	2	0	45	1.13
1201521--1201573	13	3.9	13	71	9	52	64	0	0	35	0.94
1201513--1201573	19	2.9	22	68	26	60	60	0	0	39	0.97
1201531--1201587	28	2.0	28	82	0	69	56	3	3	36	1.34
1206726--1206753	13	2.2	13	100	0	56	53	14	0	32	1.41
1207269--1207377	32	3.5	32	72	18	95	44	7	6	41	1.58
1207496--1207580	26	3.2	26	68	6	71	35	3	3	57	1.33
1208244--1208268	13	1.9	13	100	0	50	36	16	16	32	1.90
1208339--1208420	33	2.5	35	86	7	118	32	15	15	35	1.90
1210243--1210284	21	2.0	21	90	0	66	50	11	14	23	1.76
1214835--1214860	13	2.0	13	100	0	52	30	15	15	38	1.88
1214849--1214901	21	2.6	21	77	14	58	33	18	11	35	1.87
1215640--1216493	48	18.8	49	70	15	401	29	17	25	26	1.98
1215735--1216350	87	7.0	87	85	5	795	29	17	25	27	1.98
1215823--1216353	271	2.0	270	90	1	848	28	17	26	27	1.98
1216277--1216493	47	4.7	47	80	10	236	29	19	24	26	1.98
1215682--1216493	358	2.3	351	81	5	1011	29	17	25	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1216317--1216490	88	2.0	86	87	2	249	28	19	24	27	1.99
1216506--1216620	33	3.5	34	82	8	105	33	9	36	20	1.85
1216588--1216645	27	2.2	26	84	6	80	34	12	31	22	1.91
1216594--1216646	27	2.0	27	92	0	88	28	13	33	24	1.93
1216614--1217027	34	12.8	34	78	11	415	36	12	30	20	1.89
1216544--1216998	94	4.8	94	86	5	560	36	11	31	20	1.89
1216722--1217583	31	27.4	33	79	10	363	32	14	30	22	1.94
1216781--1216833	27	2.0	27	84	0	70	24	13	37	24	1.91
1216808--1217027	65	3.3	67	84	5	277	35	14	30	19	1.91
1217003--1217619	61	10.0	60	82	7	702	31	15	29	23	1.96

Tables:   1   2   3   4   5   6   7   8   9