genome.fa.s60.2.7.7.80.10.50.1000.9.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: Scaffold60
Parameters: 2 7 7 80 10 50 1000
Length:  3815296

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   

This is table  9  of  21  ( 2419 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)
1183937--1183976	7	6.3	7	78	21	52	40	0	0	60	0.97
1183937--1183976	11	3.1	14	76	23	52	40	0	0	60	0.97
1183956--1184038	32	2.7	29	73	12	85	43	2	1	53	1.21
1183929--1183995	20	3.4	19	80	15	57	40	1	1	56	1.17
1184025--1184085	24	2.7	24	76	19	67	32	1	0	65	1.02
1184269--1184323	15	3.8	13	80	17	56	60	0	1	38	1.08
1185532--1185633	18	5.2	20	68	22	72	39	1	0	57	1.16
1185911--1185961	23	2.3	23	90	10	79	29	1	0	68	1.00
1186044--1186068	13	1.9	13	100	0	50	36	8	0	56	1.29
1187551--1187598	20	2.3	21	89	3	80	43	0	0	56	0.99
1187532--1187598	20	3.2	22	81	14	79	38	0	1	59	1.06
1188160--1188199	21	1.9	21	90	10	64	65	0	0	35	0.93
1189191--1189230	20	2.0	21	90	5	64	30	0	0	70	0.88
1189219--1189275	15	3.8	14	78	15	60	49	0	0	50	1.00
1189511--1189555	3	15.0	3	95	0	81	31	0	2	66	1.04
1194129--1194177	20	2.5	20	80	9	55	40	0	0	59	0.98
1194143--1194211	22	3.1	22	76	15	63	44	1	0	53	1.09
1194168--1194211	23	2.0	23	86	13	65	47	2	0	50	1.13
1194383--1194423	13	3.2	13	82	6	57	48	0	2	48	1.14
1194510--1194549	14	2.9	14	88	0	62	42	2	12	42	1.56
1194595--1194619	9	2.8	9	100	0	50	68	0	8	24	1.16
1196903--1196928	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1197296--1197336	11	3.6	12	83	9	50	48	0	0	51	1.00
1198343--1198387	3	15.0	3	100	0	90	66	0	0	33	0.92
1198941--1199047	14	7.3	15	72	16	64	47	0	0	51	1.07
1203147--1203223	4	19.8	4	88	5	104	50	18	0	31	1.47
1203151--1203245	20	4.8	20	89	5	131	50	14	0	34	1.43
1203145--1203245	12	8.6	12	83	4	107	50	14	0	34	1.44
1203167--1203243	4	19.2	4	91	0	73	50	11	0	37	1.39
1204147--1204173	2	13.5	2	100	0	54	51	0	0	48	1.00
1204511--1204537	13	2.1	13	100	0	54	44	0	0	55	0.99
1204503--1204561	18	3.3	18	79	13	59	44	0	0	55	0.99
1204500--1204577	32	2.6	30	76	15	72	43	0	0	56	0.99
1204499--1204638	60	2.4	58	74	14	133	45	0	0	53	1.05
1207957--1208003	23	2.0	23	100	0	94	46	0	29	23	1.52
1208964--1209008	23	2.0	23	82	8	56	37	0	2	60	1.09
1209197--1209228	2	16.0	2	100	0	64	50	0	0	50	1.00
1214987--1215027	2	20.5	2	94	0	73	53	0	46	0	1.00
1215201--1215230	15	1.9	16	93	6	53	90	0	10	0	0.47
1216121--1216151	16	1.9	16	93	0	53	51	0	0	48	1.00
1216136--1216230	33	3.1	29	75	20	79	43	0	1	55	1.06
1216715--1216768	26	2.2	26	86	6	76	48	0	0	51	1.00
1220879--1220903	13	1.9	13	100	0	50	24	0	0	76	0.80
1230819--1230915	36	2.7	36	77	0	104	17	19	35	27	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1232074--1232105	16	2.0	16	100	0	64	25	18	12	43	1.85
1240275--1240310	2	18.0	2	88	0	54	44	0	5	50	1.25
1240440--1240489	19	2.4	21	75	21	52	38	2	6	54	1.37
1250523--1250565	20	2.2	20	83	4	52	20	18	2	58	1.50
1255234--1255317	11	7.5	11	68	22	50	63	0	0	36	0.95
1256249--1256282	6	5.7	6	96	0	50	50	0	8	41	1.34
1260922--1261027	10	10.3	11	69	16	59	33	3	3	58	1.34
1260932--1260967	12	3.2	12	85	14	51	30	0	0	69	0.89
1260922--1261114	31	6.2	30	66	15	99	35	4	3	56	1.36
1260983--1261031	21	2.4	21	83	10	57	32	4	8	55	1.48
1261018--1261096	41	2.0	39	87	9	115	37	5	2	54	1.36
1261010--1261097	21	4.4	20	77	18	94	36	5	2	55	1.36
1261022--1261109	41	2.1	41	81	8	99	36	4	3	55	1.37
1261167--1261207	21	2.0	20	85	4	55	39	2	4	53	1.35
1261287--1261378	21	4.5	21	77	11	86	36	1	13	48	1.49
1261386--1261442	10	5.6	10	75	6	53	40	1	1	56	1.20
1261283--1261415	21	6.6	21	71	10	80	37	1	9	51	1.44
1261425--1261499	21	3.6	21	78	7	98	37	1	6	54	1.35
1261535--1261596	21	2.9	21	74	11	54	35	6	4	53	1.48
1265155--1265193	2	19.5	2	100	0	78	51	0	0	48	1.00
1265193--1265224	2	16.0	2	100	0	64	50	0	50	0	1.00
1265610--1265643	2	17.0	2	100	0	68	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1268356--1268397	19	2.2	19	95	0	75	28	11	30	28	1.92
1272524--1272586	28	2.2	29	86	8	85	50	1	0	47	1.10
1273793--1273840	18	2.6	19	80	12	55	37	2	2	58	1.22
1277433--1277533	19	5.6	18	68	28	63	45	0	0	54	0.99
1277446--1277533	5	17.2	5	70	17	56	44	0	0	55	0.99
1277430--1277533	37	2.9	33	75	21	95	46	0	0	53	1.00
1277809--1278103	149	2.0	149	99	0	581	40	10	10	37	1.75
1278113--1278286	50	3.5	49	83	3	204	31	16	14	37	1.90
1278111--1278309	50	4.0	50	83	0	200	32	15	16	36	1.90
1282680--1282935	50	5.1	50	83	0	305	31	16	17	34	1.92
1283083--1283111	14	2.0	15	93	6	51	20	0	0	79	0.74
1284452--1284493	22	1.9	22	85	0	57	45	0	4	50	1.23
1285005--1285085	7	10.7	7	71	23	58	34	0	0	65	0.93
1285019--1285066	25	1.9	25	84	16	64	41	0	0	58	0.98
1284998--1285085	17	5.8	15	74	20	76	36	0	0	63	0.95
1285007--1285094	8	11.6	7	74	19	54	34	0	0	65	0.93
1285091--1285138	10	5.1	10	72	23	50	60	0	0	39	0.97
1284989--1285109	53	2.2	58	82	13	155	38	0	0	60	1.03
1285111--1285178	21	3.3	21	75	18	63	63	1	0	35	1.04
1285342--1285367	2	13.0	2	100	0	52	0	50	0	50	1.00
1285851--1285885	15	2.3	15	95	0	61	14	2	2	80	0.95
1285943--1286031	18	4.5	20	68	19	62	53	1	0	44	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1285967--1286024	15	3.8	14	75	20	53	51	1	0	46	1.11
1285997--1286034	20	1.9	20	94	0	67	55	2	0	42	1.14
1285998--1286041	20	2.2	20	87	0	61	59	2	0	38	1.10
1287192--1287230	2	20.5	2	89	10	64	51	0	0	48	1.00
1287894--1287935	22	2.0	21	85	4	57	38	0	0	61	0.96
1294644--1294669	2	13.0	2	100	0	52	50	0	0	50	1.00
1295749--1295792	20	2.1	21	87	4	63	70	0	0	29	0.88
1295743--1295812	21	3.0	22	76	18	63	64	0	0	35	0.94
1297251--1297278	3	9.3	3	100	0	56	67	0	0	32	0.91
1298225--1298266	22	2.0	21	85	4	57	52	4	0	42	1.22
1300359--1300442	9	9.1	9	71	15	57	52	1	0	46	1.08
1300564--1300588	12	2.1	12	100	0	50	44	24	8	24	1.80
1303305--1303343	17	2.3	17	86	0	51	56	0	0	43	0.99
1307681--1307709	14	2.1	14	100	0	58	34	6	0	58	1.25
1308109--1308163	23	2.4	22	84	6	74	56	0	0	43	0.99
1308103--1308177	33	2.3	34	75	13	86	50	0	0	49	1.00
1308109--1308165	22	2.6	22	86	8	73	57	0	0	42	0.98
1309349--1309394	24	2.0	22	87	8	65	26	0	0	73	0.83
1309328--1309404	29	2.5	31	77	14	88	35	0	0	64	0.93
1312300--1312334	2	17.5	2	100	0	70	51	0	0	48	1.00
1318315--1318353	3	12.3	3	89	10	60	64	0	0	35	0.94
1318317--1318470	7	23.9	7	78	13	129	55	1	1	42	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1318338--1318468	4	35.0	4	69	22	72	52	1	1	44	1.19
1331396--1331475	5	16.8	5	68	19	55	57	0	2	40	1.12
1331432--1331486	18	3.1	18	75	17	60	60	0	1	38	1.08
1331404--1331467	26	2.3	30	87	12	93	59	0	1	39	1.07
1331404--1331475	27	2.5	31	79	20	95	58	0	2	38	1.13
1331859--1331901	19	2.2	19	88	12	61	51	0	0	48	1.00
1331906--1331943	18	2.2	17	90	4	58	68	2	0	28	1.03
1334247--1334302	23	2.4	22	80	16	60	46	0	1	51	1.11
1334918--1334965	2	24.0	2	84	16	64	50	0	4	45	1.21
1336679--1336710	2	16.0	2	100	0	64	50	0	0	50	1.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21