genome.fa.s19.2.7.7.80.10.50.1000.9.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: Scaffold19
Parameters: 2 7 7 80 10 50 1000
Length:  2266706

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

This is table  9  of  15  ( 1733 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)
1149112--1149137	13	2.0	13	100	0	52	38	15	15	30	1.88
1149162--1149214	19	2.8	19	85	0	61	37	11	11	39	1.77
1151953--1151978	13	2.0	13	100	0	52	30	15	15	38	1.88
1151933--1151996	32	2.0	33	90	3	103	28	14	15	42	1.86
1152698--1152741	21	2.1	21	83	8	54	25	31	2	40	1.68
1154539--1154577	13	3.0	13	96	0	69	35	15	17	30	1.91
1156646--1156676	15	2.1	15	93	0	53	12	22	16	48	1.80
1160752--1160777	13	2.0	13	100	0	52	30	15	15	38	1.88
1163619--1163657	19	2.1	19	100	0	78	25	23	10	41	1.86
1164631--1164693	8	6.9	8	77	22	54	77	4	0	17	0.93
1164631--1164691	9	6.4	9	73	15	52	78	4	0	16	0.91
1169528--1169586	29	2.0	29	100	0	118	40	16	10	32	1.82
1171633--1171671	19	2.2	17	90	9	60	33	0	0	66	0.92
1171747--1171814	16	3.7	18	81	16	77	25	5	1	67	1.21
1171747--1171814	10	7.3	9	71	15	50	25	5	1	67	1.21
1171746--1171814	36	1.9	36	85	11	97	26	5	1	66	1.22
1171753--1171823	16	3.9	20	82	15	68	23	5	2	67	1.25
1173432--1173488	25	2.2	26	78	9	64	3	22	5	68	1.25
1176150--1176179	6	5.0	6	100	0	60	16	0	83	0	0.65
1177156--1177385	43	5.3	42	68	22	161	43	3	7	44	1.50
1177081--1177427	88	4.0	88	90	3	517	43	4	7	44	1.52
1177141--1177356	45	4.9	44	68	23	134	43	4	6	44	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1178719--1178765	11	4.4	11	78	5	51	63	2	2	31	1.18
1179126--1179160	16	2.1	17	89	5	54	57	0	0	42	0.99
1179122--1179188	17	3.8	18	74	14	68	58	0	0	41	0.98
1179981--1180033	21	2.5	22	72	22	58	49	1	1	47	1.23
1180786--1180847	33	1.9	32	86	3	88	22	6	0	70	1.09
1180781--1180855	33	2.3	32	81	2	87	20	6	0	73	1.05
1181193--1181223	15	2.1	15	100	0	62	35	0	12	51	1.40
1181267--1181324	16	3.6	16	71	0	53	25	6	18	48	1.73
1182843--1182935	40	2.3	40	85	3	116	35	3	10	50	1.53
1182847--1182921	21	3.6	22	68	15	70	30	2	12	54	1.51
1183506--1183531	13	2.0	13	100	0	52	38	15	15	30	1.88
1183487--1183550	33	2.0	33	90	3	103	40	17	14	28	1.88
1189717--1189753	12	2.9	13	92	4	58	32	16	16	35	1.91
1191296--1191338	22	2.0	20	86	8	59	18	9	13	58	1.62
1192221--1192246	13	2.0	13	100	0	52	38	15	15	30	1.88
1192202--1192266	33	2.0	33	87	6	96	41	16	13	27	1.87
1194447--1194499	18	2.7	19	74	11	54	49	1	0	49	1.12
1195137--1195177	2	20.5	2	100	0	82	48	0	0	51	1.00
1195922--1195959	20	1.9	19	89	5	58	34	7	18	39	1.80
1195921--1196059	51	2.7	54	84	6	189	31	14	13	40	1.85
1209963--1210040	11	6.9	11	72	16	70	83	8	3	3	0.89
1209968--1210038	37	1.9	36	83	11	90	83	8	4	4	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1209965--1210040	14	5.3	14	76	7	73	84	7	3	3	0.87
1211119--1211464	28	12.1	28	82	4	361	28	28	18	23	1.98
1212362--1212415	20	2.7	20	88	5	74	33	12	16	37	1.87
1212362--1212503	40	3.7	39	69	16	127	29	15	15	39	1.88
1212434--1212510	20	3.8	20	78	0	82	28	16	16	37	1.91
1212352--1212490	72	1.9	72	94	0	242	28	15	15	40	1.88
1215988--1216017	2	15.0	2	92	0	51	53	0	0	46	1.00
1216879--1216916	20	1.9	20	88	0	58	55	0	0	44	0.99
1220506--1220580	20	3.8	20	87	0	114	41	12	13	33	1.81
1221462--1222511	28	37.4	28	88	0	1321	22	19	31	27	1.97
1223726--1223805	12	6.5	12	74	21	51	2	2	11	83	0.83
1223718--1223787	21	3.2	22	79	16	67	2	4	10	82	0.90
1223752--1223807	7	7.1	8	88	11	73	0	0	14	85	0.59
1223753--1223794	7	5.9	7	94	5	75	0	0	11	88	0.53
1227559--1227614	20	2.8	20	83	5	78	30	17	12	39	1.87
1230017--1230238	51	4.4	51	80	4	164	28	24	13	33	1.93
1230017--1230238	102	2.2	102	81	4	261	28	24	13	33	1.93
1238394--1238418	13	1.9	13	100	0	50	36	16	16	32	1.90
1238375--1238445	32	2.2	32	92	0	115	32	14	16	36	1.89
1240627--1240695	27	2.6	27	97	0	129	24	46	15	13	1.82
1244083--1244120	18	2.1	18	90	0	58	36	5	15	42	1.70
1245294--1245358	20	3.2	21	84	6	89	40	12	15	32	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1249309--1249408	38	2.6	38	80	4	112	36	15	6	43	1.71
1249378--1249462	38	2.5	31	72	22	89	38	16	5	38	1.73
1249488--1249512	2	12.5	2	100	0	50	52	0	0	48	1.00
1250357--1250417	32	2.0	32	87	6	90	59	0	0	40	0.98
1250359--1250441	21	3.7	21	73	19	60	61	0	1	37	1.04
1251017--1251060	9	4.9	9	83	10	54	52	0	0	47	1.00
1251275--1251351	30	2.5	30	81	10	93	44	9	0	46	1.35
1251353--1251391	17	2.4	16	83	8	51	48	0	0	51	1.00
1254334--1254372	20	2.0	20	94	0	69	35	0	0	64	0.94
1254311--1254364	26	2.1	25	86	3	72	37	0	3	59	1.15
1258428--1258459	16	1.9	17	93	6	57	50	9	6	34	1.60
1260056--1260081	6	4.3	6	100	0	52	30	34	0	34	1.58
1260079--1260128	12	4.2	12	84	0	73	28	28	2	42	1.67
1261225--1261262	16	2.4	16	95	0	67	50	13	13	23	1.76
1262964--1262988	13	1.9	13	100	0	50	32	16	16	36	1.90
1262976--1263028	20	2.6	21	82	8	65	37	16	16	28	1.91
1263089--1263113	13	1.9	13	100	0	50	32	16	20	32	1.94
1263070--1263134	34	2.0	32	88	11	96	36	16	16	29	1.92
1269699--1269743	20	2.1	22	84	15	60	17	46	31	4	1.68
1271117--1271180	20	3.0	21	88	6	103	35	0	26	37	1.57
1271842--1271887	15	2.6	19	74	25	64	39	15	17	28	1.90
1271853--1271900	15	3.3	15	88	8	73	41	14	16	27	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1277445--1277517	20	3.7	19	72	7	65	41	12	10	35	1.78
1277445--1277525	40	2.0	41	90	2	128	38	13	9	38	1.78
1277545--1277618	20	3.6	20	81	3	67	32	14	12	40	1.83
1288365--1288407	16	2.7	16	85	0	68	34	9	9	46	1.68
1294535--1294833	71	4.1	69	70	17	237	59	4	17	18	1.53
1294674--1294773	22	4.3	22	70	18	78	65	4	14	17	1.42
1294413--1294751	52	6.7	49	89	7	520	61	4	16	17	1.49
1294764--1294851	28	3.4	28	69	18	98	57	3	17	21	1.53
1294742--1294895	50	3.1	50	96	0	274	59	3	17	18	1.52
1294792--1294873	22	3.5	22	69	18	74	63	3	14	18	1.45
1294625--1294873	121	2.1	119	93	5	432	61	4	16	18	1.48
1299763--1300253	52	9.7	51	89	8	590	60	3	16	18	1.50
1299768--1300275	99	5.0	99	89	7	697	60	3	17	18	1.51
1299763--1300275	50	10.2	50	89	6	779	60	3	17	18	1.51
1305636--1305684	19	2.4	19	80	13	53	30	20	4	44	1.70
1311711--1311751	20	2.2	17	87	12	55	46	4	12	36	1.63
1313883--1315864	42	47.1	42	74	8	1380	15	30	17	36	1.90
1316356--1316415	28	2.2	28	82	8	70	76	5	5	13	1.11
1316424--1316503	25	3.2	25	63	19	67	57	3	18	20	1.55
1316395--1316805	50	8.2	50	88	5	600	61	3	16	18	1.49
1316701--1316783	22	3.5	22	67	17	67	65	3	13	18	1.41
1316754--1316806	19	2.7	20	82	11	56	66	3	15	15	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1319515--1319568	20	2.7	20	91	8	83	38	11	18	31	1.86
1319625--1319679	20	2.8	20	77	0	56	38	10	10	40	1.76
1319536--1319770	111	2.1	111	94	0	407	38	12	14	34	1.84
1319787--1319824	20	1.9	19	94	5	67	26	10	7	55	1.61
1320152--1320187	13	2.8	13	95	0	63	22	50	8	19	1.74
1324613--1324646	15	2.2	16	89	5	52	52	0	2	44	1.16
1327107--1327161	2	27.5	2	96	0	101	49	1	0	49	1.11
1328063--1328108	22	2.1	22	83	0	56	30	0	4	65	1.12
1329188--1329213	2	13.0	2	100	0	52	50	0	0	50	1.00
1329927--1329968	21	2.0	21	81	9	50	61	2	33	2	1.21

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