genome.fa.s52.2.7.7.80.10.50.1000.7.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: Scaffold52
Parameters: 2 7 7 80 10 50 1000
Length:  1774672

Tables:   1   2   3   4   5   6   7   8   9   

This is table  7  of  9  ( 1067 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)
1222896--1222940	2	22.5	2	86	8	65	46	0	4	48	1.22
1223137--1223184	18	2.6	17	75	12	51	54	0	2	43	1.12
1224477--1224521	6	7.5	6	87	0	54	48	6	2	42	1.41
1224477--1224521	4	11.2	4	85	0	54	48	6	2	42	1.41
1224740--1224773	12	2.8	12	86	0	50	58	0	0	41	0.98
1224739--1224802	26	2.5	26	78	14	69	56	1	0	42	1.09
1224769--1224827	21	3.0	20	72	18	52	52	1	0	45	1.10
1224735--1224832	26	3.9	26	67	23	66	54	1	0	44	1.07
1224782--1224840	23	2.7	23	79	10	61	55	0	0	44	0.99
1225450--1225479	2	15.0	2	100	0	60	50	0	0	50	1.00
1226242--1226266	2	12.5	2	100	0	50	48	0	0	52	1.00
1226738--1226772	2	18.0	2	94	5	63	48	0	0	51	1.00
1230441--1230489	20	2.6	18	75	12	53	55	0	0	44	0.99
1230988--1231019	3	10.7	3	93	0	55	28	0	0	71	0.86
1232857--1232916	30	2.0	30	96	0	111	28	15	33	23	1.94
1233074--1233112	19	2.1	19	100	0	78	33	15	5	46	1.68
1243878--1243911	2	17.0	2	93	0	59	50	2	0	47	1.16
1244550--1244611	29	2.2	27	76	18	63	35	0	3	61	1.12
1244906--1244968	28	2.3	28	78	15	69	36	9	1	52	1.44
1245023--1245060	3	12.7	3	89	10	60	36	0	0	63	0.95
1247079--1247111	2	16.5	2	100	0	66	51	0	0	48	1.00
1247753--1247820	26	2.6	26	76	2	73	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1247761--1247822	22	2.6	25	75	21	69	48	0	0	51	1.00
1252001--1252052	24	2.2	24	100	0	104	46	7	3	42	1.51
1252158--1252204	22	2.1	22	84	0	58	31	12	2	53	1.51
1252584--1252624	14	2.9	14	85	10	57	53	0	0	46	1.00
1259529--1259592	33	1.9	34	81	15	80	54	0	0	45	0.99
1259905--1259985	35	2.2	36	82	8	94	60	2	1	35	1.18
1262927--1262984	30	2.0	29	86	10	82	50	3	1	44	1.29
1263423--1263485	24	2.7	23	78	7	65	42	3	3	50	1.34
1263443--1263485	22	2.0	20	82	8	50	39	2	2	55	1.25
1268295--1268344	19	2.5	20	80	6	57	36	2	2	60	1.20
1271321--1271452	65	2.0	65	98	0	255	33	22	18	25	1.97
1271442--1271475	17	2.0	17	88	0	50	26	8	26	38	1.85
1275372--1275432	5	12.4	5	75	16	56	34	1	1	62	1.15
1276979--1278081	86	13.1	86	75	8	651	49	11	5	33	1.61
1277714--1277952	78	2.9	79	78	12	250	49	11	5	33	1.61
1277792--1277995	87	2.4	83	85	7	250	50	12	4	31	1.61
1277921--1278064	77	1.9	73	80	10	166	53	11	4	29	1.58
1278145--1278403	86	3.0	83	76	9	261	49	9	5	35	1.58
1278181--1278403	86	2.7	83	78	5	268	49	10	4	35	1.57
1278390--1278427	17	2.2	17	95	0	67	63	2	5	28	1.30
1278423--1278581	81	2.0	81	83	0	201	52	8	3	35	1.47
1279854--1279896	22	2.0	22	86	4	61	48	11	32	6	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1280957--1281002	22	2.0	24	88	12	71	63	2	2	32	1.19
1281505--1281540	18	2.1	19	85	15	51	36	5	0	58	1.22
1281499--1281647	79	1.9	79	87	2	219	33	12	6	46	1.68
1281705--1281735	16	2.0	15	93	6	53	58	0	0	41	0.98
1281701--1281794	20	4.7	20	69	19	61	55	1	1	42	1.14
1281725--1281807	40	2.0	41	84	6	107	50	1	1	46	1.16
1286849--1286878	9	3.4	9	90	9	53	80	0	0	20	0.72
1287527--1287558	16	2.0	16	93	0	55	65	0	0	34	0.93
1287528--1287577	23	2.1	25	85	7	68	62	2	0	36	1.07
1287689--1287762	25	2.9	26	81	18	86	60	0	0	39	0.97
1287681--1287762	16	4.9	17	85	5	107	59	0	0	40	0.97
1288338--1288386	25	2.0	25	84	8	64	55	0	0	44	0.99
1291127--1291167	16	2.5	17	80	11	50	56	0	0	43	0.99
1291632--1291683	20	2.6	19	76	8	50	48	1	0	50	1.12
1293670--1293704	3	11.7	3	93	0	61	71	0	0	28	0.86
1293831--1293866	2	18.0	2	100	0	72	50	0	0	50	1.00
1294309--1294346	19	2.0	20	89	5	60	39	2	0	57	1.12
1294550--1294607	26	2.2	27	84	9	75	27	6	0	65	1.18
1294692--1294739	21	2.2	22	81	7	62	47	2	0	50	1.12
1295260--1295285	2	13.0	2	100	0	52	50	0	0	50	1.00
1295586--1295633	21	2.3	20	79	6	51	45	6	0	47	1.27
1295852--1295961	5	20.6	5	68	18	53	43	0	3	52	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1295913--1295969	30	1.9	30	89	7	89	50	0	0	49	1.00
1296002--1296034	16	2.1	16	88	5	50	30	0	0	69	0.88
1297212--1297252	3	13.7	3	100	0	82	34	0	0	65	0.93
1297362--1297393	3	10.7	3	93	0	55	28	0	3	68	1.04
1297750--1297783	9	3.8	9	88	0	50	26	0	0	73	0.83
1304083--1304143	27	2.3	25	78	15	68	47	0	0	52	1.00
1311866--1311910	18	2.5	18	85	0	63	40	40	0	20	1.52
1313741--1313795	24	2.2	24	87	3	74	38	1	3	56	1.28
1314218--1314262	3	15.0	3	90	0	72	0	31	2	66	1.04
1315095--1315178	42	2.0	42	97	0	159	25	4	10	59	1.50
1318783--1318814	16	2.0	16	100	0	64	31	12	6	50	1.65
1322503--1322527	2	12.5	2	100	0	50	48	0	0	52	1.00
1329281--1329317	2	18.5	2	94	0	65	51	2	0	45	1.15
1331374--1331451	29	2.7	29	88	6	122	53	0	0	46	1.00
1331680--1331708	2	14.5	2	100	0	58	51	0	0	48	1.00
1331838--1331883	24	2.0	23	83	12	58	52	0	0	47	1.00
1331875--1331925	9	4.9	10	78	21	52	60	0	0	39	0.97
1331875--1331925	5	9.8	5	78	21	52	60	0	0	39	0.97
1331881--1331925	9	5.0	9	82	17	58	60	0	0	40	0.97
1331877--1331933	17	3.5	16	79	15	64	57	0	0	42	0.98
1333617--1333679	3	21.0	3	93	6	110	31	1	0	66	1.01
1337628--1337716	25	3.8	25	70	18	77	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1337635--1337710	40	1.9	40	86	10	111	65	0	0	34	0.93
1337631--1337710	20	4.3	18	76	20	67	65	0	0	35	0.93
1337647--1337711	20	3.2	20	78	10	69	63	0	0	36	0.95
1337633--1337715	10	8.4	10	74	15	57	65	0	0	34	0.93
1423359--1423402	20	2.2	20	84	12	54	45	4	0	50	1.22
1423956--1423995	2	20.0	2	85	10	55	47	2	0	50	1.14
1424356--1424423	32	2.3	28	75	22	75	63	0	1	35	1.04
1424365--1424434	32	2.2	33	87	7	99	58	0	1	40	1.07
1424613--1424655	20	2.0	20	86	8	59	69	0	0	30	0.88
1424650--1424693	22	2.0	22	82	4	54	63	0	0	36	0.95
1424616--1424738	28	3.9	31	77	12	117	60	0	0	39	0.96
1424631--1424731	32	2.9	35	80	12	95	60	0	0	39	0.97
1426994--1427072	28	2.7	28	74	18	72	54	2	1	41	1.22
1427017--1427072	22	2.6	21	81	10	60	55	1	0	42	1.10
1426994--1427091	16	6.5	15	71	18	62	55	3	1	40	1.22
1427505--1427566	18	3.3	18	72	20	56	41	0	1	56	1.09
1435150--1435189	18	2.2	18	86	0	53	50	0	0	50	1.00
1435941--1436031	40	2.3	38	79	9	94	51	3	0	45	1.17
1436449--1436504	18	2.7	21	77	20	64	58	5	0	35	1.21
1436584--1436635	26	2.0	26	88	7	79	38	0	0	61	0.96
1436595--1436649	20	2.7	20	85	2	74	41	0	1	56	1.10
1436783--1436844	31	2.1	29	80	19	74	54	1	0	43	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1441021--1441049	2	14.5	2	100	0	58	51	0	0	48	1.00
1442251--1442282	2	16.0	2	100	0	64	50	0	50	0	1.00
1442462--1442510	17	2.8	18	75	9	57	53	0	0	46	1.00
1445142--1445201	20	3.0	22	79	13	67	56	0	0	43	0.99
1445141--1445202	22	3.0	20	75	11	63	58	0	0	41	0.98
1446853--1446924	32	2.2	33	82	9	85	34	5	5	54	1.47
1447141--1447207	33	2.0	33	88	0	98	40	13	11	34	1.81
1448466--1448515	25	2.0	26	84	11	68	72	2	2	24	1.06
1448463--1448554	10	8.4	10	71	18	51	69	3	2	25	1.15
1448483--1448532	19	2.6	18	84	12	64	72	4	0	24	1.02

Tables:   1   2   3   4   5   6   7   8   9