genome.fa.s500.2.7.7.80.10.50.1000.7.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: Scaffold500
Parameters: 2 7 7 80 10 50 1000
Length:  2046043

Tables:   1   2   3   4   5   6   7   8   9   10   

This is table  7  of  10  ( 1137 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)
1090703--1090825	20	6.1	20	71	19	85	55	0	0	44	0.99
1105692--1105717	13	2.0	13	100	0	52	15	7	15	61	1.55
1108520--1108559	19	2.1	19	100	0	80	50	5	20	25	1.68
1110019--1110064	13	3.1	15	81	18	60	36	4	0	58	1.18
1112672--1112701	2	15.0	2	92	0	51	46	0	0	53	1.00
1113670--1113696	3	9.0	3	100	0	54	33	33	33	0	1.58
1118379--1118420	16	2.5	18	88	11	63	76	4	19	0	0.96
1118381--1118428	26	1.9	25	87	8	71	79	4	16	0	0.89
1118379--1118428	17	3.0	17	80	11	59	78	4	18	0	0.91
1120970--1121003	16	2.1	16	89	10	52	73	0	0	26	0.83
1124778--1124841	26	2.4	26	78	17	69	54	3	0	42	1.16
1126237--1126263	2	13.5	2	100	0	54	51	0	0	48	1.00
1127578--1127623	14	3.1	15	84	9	67	58	0	0	41	0.98
1128181--1128232	25	2.0	26	85	11	70	57	1	1	38	1.21
1129764--1129801	13	3.0	13	84	3	51	28	0	2	68	1.03
1129765--1129795	16	1.9	16	93	0	53	25	0	3	70	1.02
1131943--1132007	34	1.9	34	84	12	89	40	0	4	55	1.21
1134430--1134454	12	2.1	12	100	0	50	60	40	0	0	0.97
1134432--1134458	14	1.9	14	100	0	54	59	40	0	0	0.98
1140163--1140203	18	2.5	17	81	14	50	26	7	7	58	1.51
1141600--1141655	24	2.4	23	84	3	67	44	1	0	53	1.11
1141685--1141768	32	2.5	33	88	5	116	38	2	1	58	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1142210--1142253	17	2.7	15	80	19	52	36	0	2	61	1.09
1146317--1146343	2	13.5	2	100	0	54	0	48	0	51	1.00
1147039--1147108	37	1.9	35	86	11	97	42	2	0	54	1.15
1150758--1150807	3	16.7	3	95	0	91	34	0	2	64	1.05
1151816--1151866	5	10.6	5	83	8	54	78	17	1	1	0.94
1152020--1152056	13	2.8	13	91	4	56	64	0	35	0	0.94
1152614--1152641	6	4.7	6	100	0	56	32	0	0	67	0.91
1156576--1156615	20	2.0	21	85	5	55	70	7	7	15	1.33
1161720--1161754	4	8.8	4	100	0	70	74	0	0	25	0.82
1162497--1162557	22	2.7	23	70	19	56	29	6	1	62	1.30
1165179--1165222	16	2.6	16	85	7	52	9	11	2	77	1.08
1165175--1165217	18	2.4	18	81	11	54	9	11	2	76	1.10
1171138--1171168	2	15.5	2	100	0	62	48	0	0	51	1.00
1172453--1172502	24	2.1	24	85	10	68	34	0	2	64	1.05
1172461--1172501	9	4.9	9	77	17	52	34	0	0	65	0.93
1178629--1178898	134	2.0	134	92	0	450	30	20	22	27	1.98
1183927--1183968	20	2.1	20	95	0	75	23	7	14	54	1.64
1186899--1186936	18	2.1	18	100	0	76	36	10	13	39	1.79
1197013--1197058	2	23.0	2	100	0	92	50	0	0	50	1.00
1199095--1199223	66	2.0	65	84	1	168	33	8	5	52	1.55
1199204--1199251	26	1.9	26	87	8	73	41	10	2	45	1.50
1204704--1204736	16	2.1	16	100	0	66	30	21	12	36	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1206771--1206848	37	2.1	37	90	4	122	61	0	0	38	0.96
1212192--1212218	12	2.2	12	100	0	54	0	11	22	66	1.22
1212341--1212542	100	2.0	100	100	0	404	22	13	16	46	1.83
1212814--1212847	2	17.0	2	100	0	68	50	0	0	50	1.00
1216062--1216104	14	3.0	14	80	16	52	55	0	2	41	1.12
1223948--1224023	14	5.9	14	71	14	56	64	1	0	34	1.02
1223980--1224023	12	3.4	13	84	9	54	65	2	0	31	1.05
1223987--1224031	17	2.6	18	83	13	58	66	2	0	31	1.04
1234787--1234888	31	3.4	31	79	9	95	59	0	0	38	1.10
1239710--1239762	21	2.5	21	84	6	63	45	0	3	50	1.19
1239746--1239789	17	2.8	15	80	12	52	38	0	2	59	1.10
1252978--1253025	21	2.4	21	80	16	57	50	0	0	50	1.00
1256648--1256674	3	9.0	3	100	0	54	33	0	0	66	0.92
1257181--1257212	2	16.0	2	100	0	64	50	0	0	50	1.00
1258346--1258384	2	19.5	2	89	0	60	48	0	5	46	1.24
1265369--1265430	14	4.5	14	87	4	81	67	0	0	32	0.91
1265367--1265425	25	2.3	25	85	8	75	67	0	0	32	0.91
1266788--1266841	26	2.1	26	96	0	99	40	24	11	24	1.87
1267011--1267167	75	2.1	75	80	4	174	42	8	8	40	1.66
1267374--1267422	16	2.9	18	76	14	59	32	0	0	67	0.91
1267372--1267422	18	3.1	16	77	22	52	33	0	0	66	0.92
1267371--1267431	23	2.6	23	80	17	72	36	0	0	63	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1273658--1273740	27	3.3	24	82	12	96	34	1	1	62	1.11
1273674--1273733	27	2.2	27	96	0	111	35	1	0	63	1.05
1273674--1273741	27	2.5	26	86	9	100	33	1	0	64	1.02
1273750--1273793	15	2.8	16	86	10	56	56	0	2	40	1.11
1274944--1275024	32	2.5	33	87	6	119	44	1	0	54	1.08
1275017--1275066	19	2.4	20	80	16	57	36	0	0	64	0.94
1275031--1275067	19	1.9	19	94	0	65	29	0	0	70	0.88
1282950--1282993	2	22.0	2	85	0	61	52	2	0	45	1.13
1283949--1284014	32	2.1	32	97	0	123	31	6	6	56	1.48
1292021--1292080	28	2.2	28	78	3	68	58	5	1	35	1.30
1292116--1292212	50	2.0	48	82	10	115	60	14	1	23	1.40
1292364--1292475	13	8.5	14	66	22	57	42	0	0	55	1.12
1292366--1292510	30	5.2	29	71	13	99	40	0	1	57	1.12
1292442--1292495	17	3.2	16	81	7	54	42	0	1	55	1.10
1296227--1296275	2	24.5	2	91	0	80	44	0	0	55	0.99
1307207--1307358	76	2.0	77	98	1	297	46	15	1	36	1.55
1307389--1307434	23	2.0	24	86	4	67	32	6	0	60	1.22
1307843--1307886	2	22.0	2	95	0	79	47	0	0	52	1.00
1314376--1314412	3	12.3	3	100	0	74	67	0	0	32	0.91
1317215--1317252	18	2.1	19	95	5	69	5	5	23	65	1.34
1317520--1317544	1	25.0	1	100	0	50	0	100	0	0	0.00
1325730--1325764	18	1.9	18	88	0	52	31	2	0	65	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1335569--1335633	34	1.9	33	96	3	121	0	15	12	72	1.13
1343287--1343328	2	21.0	2	100	0	84	50	0	0	50	1.00
1345682--1345727	11	4.3	10	86	10	56	63	0	0	36	0.95
1345682--1345727	13	3.4	14	77	19	53	63	0	0	36	0.95
1345732--1345775	15	2.9	15	81	15	54	43	2	0	54	1.12
1348709--1348737	2	14.5	2	100	0	58	0	0	48	51	1.00
1349206--1349237	2	16.0	2	100	0	64	50	0	0	50	1.00
1349862--1349906	19	2.4	19	88	0	63	40	4	2	53	1.33
1350265--1350295	16	1.9	16	93	0	53	58	0	0	41	0.98
1354936--1354969	12	2.8	12	86	0	50	2	58	14	23	1.50
1361466--1361531	26	2.5	26	85	11	91	50	0	0	50	1.00
1361482--1361525	13	3.5	13	78	9	56	52	0	0	47	1.00
1361558--1361602	19	2.4	18	79	17	56	35	0	2	62	1.08
1361860--1361896	18	2.1	18	100	0	74	27	27	21	24	1.99
1362862--1362912	25	2.0	25	92	7	86	37	3	3	54	1.37
1362875--1362927	12	4.4	12	77	15	56	39	1	5	52	1.36
1362868--1362920	11	4.6	11	78	15	54	33	1	5	58	1.32
1371815--1372026	107	2.0	106	94	0	370	34	18	19	26	1.95
1373209--1373246	3	13.0	3	94	5	69	0	34	0	65	0.93
1373980--1374012	14	2.4	14	89	0	57	84	0	0	15	0.61
1376314--1376359	4	11.5	4	100	0	92	50	0	26	23	1.50
1376599--1376627	2	14.5	2	100	0	58	0	51	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1376720--1376747	3	9.3	3	100	0	56	32	0	0	67	0.91
1378059--1378100	18	2.3	18	87	4	57	54	0	0	45	0.99
1378068--1378112	17	2.6	18	89	6	67	51	0	0	48	1.00
1378079--1378141	29	2.1	30	85	8	85	49	0	0	50	1.00
1378078--1378119	17	2.6	16	81	7	57	52	0	0	47	1.00
1378461--1378501	16	2.6	17	78	21	54	53	0	0	46	1.00
1378771--1378803	14	2.3	15	89	5	50	0	6	6	87	0.65
1380618--1380684	31	2.2	31	84	10	84	64	0	1	34	1.03
1380598--1380684	36	2.7	32	79	12	88	65	2	1	31	1.12
1381930--1381987	27	2.2	25	80	14	64	65	1	1	31	1.13

Tables:   1   2   3   4   5   6   7   8   9   10