genome.fa.s341.2.7.7.80.10.50.1000.8.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: Scaffold341
Parameters: 2 7 7 80 10 50 1000
Length:  1349338

Tables:   1   2   3   4   5   6   7   8   9   

This is table  8  of  9  ( 1050 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)
1062247--1062272	3	8.7	3	100	0	52	30	0	0	69	0.89
1066606--1066656	19	2.6	20	87	3	68	37	13	13	35	1.85
1068757--1068811	15	3.7	15	76	9	58	45	1	18	34	1.60
1068756--1068823	30	2.3	30	94	0	118	48	1	17	32	1.56
1068772--1068821	15	3.3	15	82	0	64	52	2	14	32	1.53
1069993--1070047	19	2.8	20	88	2	85	30	16	14	38	1.89
1078747--1078798	20	2.7	20	87	3	79	30	17	15	36	1.91
1080493--1080586	20	4.6	19	77	12	75	31	17	14	36	1.90
1080536--1080588	20	2.7	20	88	2	81	33	15	15	35	1.88
1080492--1080586	43	2.3	43	82	7	108	32	16	14	35	1.90
1080636--1080661	13	2.0	13	100	0	52	30	15	15	38	1.88
1080616--1080682	33	2.0	33	85	5	91	34	13	17	34	1.89
1083954--1083992	17	2.3	17	100	0	78	33	5	17	43	1.72
1086462--1086552	13	6.9	13	70	26	59	26	13	15	45	1.83
1086443--1086574	33	4.0	33	86	0	192	25	14	15	44	1.84
1088366--1088507	57	2.4	60	83	5	175	47	0	23	29	1.52
1088531--1088589	21	2.8	21	97	0	109	37	1	30	30	1.68
1091822--1091867	23	1.9	25	82	8	60	32	0	8	58	1.28
1092172--1092205	3	11.3	3	93	0	59	29	2	0	67	1.05
1092357--1092387	16	1.9	16	93	0	53	35	0	0	64	0.94
1093787--1093823	18	2.1	18	100	0	74	5	16	21	56	1.59
1098506--1098544	20	2.0	20	100	0	78	41	12	20	25	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1099477--1099529	20	2.6	21	82	8	65	49	9	11	30	1.70
1099838--1099883	13	3.5	13	78	0	56	56	19	8	15	1.65
1104410--1104631	79	2.7	81	83	3	232	38	17	26	17	1.91
1104361--1104940	42	14.0	42	71	10	262	37	18	26	16	1.92
1104361--1104814	84	5.5	84	75	7	367	38	18	25	16	1.92
1104503--1104798	164	1.8	164	86	0	430	38	19	25	16	1.92
1104362--1105122	84	9.2	83	73	9	349	37	17	27	17	1.93
1104660--1104940	126	2.2	126	85	1	366	36	19	27	16	1.94
1104660--1105053	126	3.1	126	80	2	346	36	18	27	17	1.94
1104362--1105093	42	17.6	42	69	9	239	37	17	26	17	1.93
1105267--1105380	44	2.6	44	85	0	147	43	14	19	21	1.87
1106824--1106890	9	7.7	9	76	6	57	8	8	0	82	0.86
1109676--1109714	20	2.0	20	94	0	69	25	17	20	35	1.95
1117211--1117287	21	3.7	21	100	0	154	36	14	14	35	1.86
1118125--1119681	48	33.8	51	70	18	372	29	19	25	25	1.98
1118315--1119681	48	29.9	48	74	15	1128	29	19	26	25	1.98
1118224--1119673	87	16.0	87	84	7	1659	29	19	26	25	1.99
1118807--1119055	39	5.9	38	73	20	174	26	20	27	26	1.99
1118990--1119073	40	2.1	40	82	8	100	22	20	29	27	1.98
1119310--1119546	95	2.5	94	80	4	258	30	18	25	24	1.98
1118402--1119681	270	4.6	279	84	7	1243	29	19	25	25	1.98
1119673--1119732	27	2.3	26	85	5	77	35	15	26	23	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1119678--1119829	61	2.5	60	83	2	205	35	11	31	21	1.89
1119764--1120139	32	12.0	31	84	8	345	34	14	30	19	1.93
1119778--1120146	93	3.9	94	88	4	489	34	14	30	20	1.92
1119784--1120135	125	2.8	125	89	4	505	34	15	30	20	1.93
1121344--1121390	24	2.0	23	91	4	76	0	2	14	82	0.75
1121355--1121396	15	2.9	15	82	3	59	0	0	19	80	0.70
1128367--1128394	13	2.2	13	100	0	56	39	17	14	28	1.89
1128426--1128486	19	3.5	19	66	25	62	36	16	11	36	1.85
1128413--1128488	32	2.4	32	93	0	125	35	15	13	35	1.87
1131204--1131238	17	2.1	17	88	0	52	60	5	2	31	1.35
1132818--1132850	3	11.0	3	100	0	66	33	0	0	66	0.92
1133139--1133196	3	19.3	3	85	0	80	41	0	29	29	1.56
1135865--1136160	131	2.3	130	93	0	511	45	17	13	22	1.83
1137078--1137120	21	2.0	21	100	0	86	13	23	13	48	1.79
1137386--1137474	18	4.8	18	72	23	62	22	2	3	71	1.11
1141679--1141711	17	1.9	17	100	0	66	36	12	18	33	1.88
1143647--1143688	21	2.0	21	100	0	84	28	0	33	38	1.58
1144427--1144451	13	1.9	13	100	0	50	32	16	16	36	1.90
1144406--1144470	32	2.0	33	87	3	96	29	15	15	40	1.88
1146727--1146758	7	4.6	7	100	0	64	15	31	28	25	1.96
1150682--1150739	20	2.8	19	85	12	71	39	13	20	25	1.90
1150787--1150842	20	2.7	21	80	5	69	32	17	10	39	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1150787--1150860	21	3.6	21	76	7	71	31	16	13	39	1.87
1152558--1152601	3	14.7	3	100	0	88	65	0	0	34	0.93
1155456--1155621	83	2.0	83	100	0	332	31	15	21	31	1.95
1159499--1159523	5	5.0	5	100	0	50	80	0	0	20	0.72
1163451--1163501	17	3.1	17	82	2	59	41	9	7	41	1.67
1168355--1168408	14	3.9	13	79	11	63	35	0	3	61	1.14
1168397--1168544	28	5.1	28	68	18	88	40	0	4	55	1.19
1168422--1168455	16	2.1	17	88	5	52	44	0	0	55	0.99
1169191--1169229	9	4.3	9	93	0	60	56	0	0	43	0.99
1169184--1169223	13	3.0	13	88	3	53	52	0	0	47	1.00
1169185--1169229	18	2.6	18	85	3	65	55	0	0	44	0.99
1169655--1169698	14	3.2	14	81	15	56	65	0	0	34	0.93
1169654--1169703	21	2.5	20	84	12	68	64	0	0	36	0.94
1169801--1169849	21	2.3	22	79	10	57	46	2	0	51	1.12
1171036--1171060	2	12.5	2	100	0	50	52	0	0	48	1.00
1171847--1171879	9	3.7	9	84	15	50	66	0	0	33	0.92
1171848--1171883	18	2.0	18	100	0	72	61	0	0	38	0.96
1173168--1173208	16	2.5	17	80	15	50	31	0	2	65	1.05
1173276--1173354	32	2.5	32	87	4	106	49	2	1	46	1.23
1176529--1176655	59	2.2	59	82	5	150	28	9	15	46	1.77
1180743--1180854	51	2.2	51	91	0	179	31	12	25	30	1.93
1180839--1180913	28	2.7	29	84	13	95	28	21	29	21	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1180870--1181117	77	3.2	77	85	5	295	33	16	23	26	1.95
1182502--1182527	13	2.0	13	100	0	52	30	23	15	30	1.95
1182556--1182654	21	4.6	22	88	10	134	37	11	22	29	1.88
1182556--1182654	41	2.3	42	84	11	130	37	11	22	29	1.88
1182642--1182672	10	3.1	10	95	0	53	41	3	29	25	1.71
1182696--1182832	53	2.6	53	91	1	229	27	16	18	37	1.92
1182802--1182872	20	3.5	20	77	11	74	29	12	16	40	1.86
1182912--1182952	21	2.0	21	85	9	57	39	9	12	39	1.76
1183486--1183510	13	1.9	13	100	0	50	36	16	16	32	1.90
1183603--1183783	52	3.5	52	95	0	326	35	18	18	28	1.94
1188630--1188657	13	2.2	13	100	0	56	39	17	14	28	1.89
1188644--1188685	21	2.0	21	90	0	66	28	19	9	42	1.82
1188702--1188774	32	2.3	32	90	0	119	35	15	12	36	1.84
1189442--1189658	119	1.8	117	79	9	253	40	11	25	22	1.87
1189629--1190031	55	7.1	54	81	9	428	26	19	26	28	1.99
1204193--1204255	27	2.4	27	97	2	119	60	15	11	12	1.59
1204427--1204524	50	1.9	51	85	2	135	51	15	5	28	1.65
1212490--1212521	8	3.9	8	95	4	55	87	0	3	9	0.64
1212520--1212556	13	2.8	13	95	4	65	72	0	16	10	1.10
1214846--1214896	3	16.7	3	86	11	68	27	0	1	70	0.98
1217784--1217849	19	3.8	19	77	22	81	33	10	15	40	1.81
1217786--1217846	32	1.9	32	96	0	113	34	9	16	39	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1217805--1217904	52	1.9	53	85	6	141	29	13	16	42	1.85
1217857--1217882	13	2.0	13	100	0	52	30	15	15	38	1.88
1217835--1217903	33	2.1	33	88	0	102	26	14	15	43	1.85
1220339--1220415	27	2.8	27	88	5	102	25	33	16	23	1.96
1226670--1227431	55	13.3	55	85	8	949	27	29	20	23	1.99
1226664--1227431	116	6.7	116	92	2	1177	26	29	20	23	1.99
1228194--1228218	13	1.9	13	100	0	50	36	16	16	32	1.90
1230784--1231064	78	3.6	77	82	3	276	24	29	14	30	1.95
1236854--1236930	28	2.7	30	84	7	90	22	19	33	24	1.97
1236913--1237133	52	4.3	53	76	9	181	33	11	25	28	1.91

Tables:   1   2   3   4   5   6   7   8   9