genome.fa.s43.2.7.7.80.10.50.1000.12.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: Scaffold43
Parameters: 2 7 7 80 10 50 1000
Length:  2559314

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

This is table  12  of  19  ( 2200 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)
1389011--1389061	23	2.2	23	86	6	68	56	1	0	41	1.10
1389452--1389487	3	12.0	3	93	0	63	36	30	0	33	1.58
1390354--1390409	24	2.4	23	77	8	60	55	0	1	42	1.10
1390377--1390438	32	1.9	31	87	6	88	51	0	0	48	1.00
1390395--1390455	20	2.8	22	78	7	72	54	0	0	45	1.00
1390395--1390455	22	2.7	23	73	12	65	54	0	0	45	1.00
1390917--1390983	21	3.2	21	74	14	59	52	0	1	46	1.09
1390946--1391013	28	2.4	28	82	7	75	55	1	1	41	1.18
1391799--1391828	2	15.0	2	100	0	60	50	0	0	50	1.00
1392666--1392690	2	12.5	2	100	0	50	52	0	0	48	1.00
1394018--1394143	18	6.5	19	70	16	71	54	0	0	45	0.99
1394112--1394154	6	7.0	6	80	15	52	53	0	0	46	1.00
1394689--1394754	14	4.6	14	77	3	60	40	0	0	59	0.98
1394692--1394730	15	2.6	15	88	8	53	35	0	0	64	0.94
1394730--1394814	36	2.4	34	80	9	91	48	1	0	50	1.08
1394913--1394951	7	5.4	7	96	3	69	58	0	0	41	0.98
1395520--1395567	16	2.9	17	81	6	53	41	0	2	56	1.11
1396606--1396648	22	2.0	22	82	17	54	44	0	2	53	1.13
1397513--1397552	19	2.2	18	86	8	55	47	0	0	52	1.00
1397956--1397999	22	2.0	22	81	0	52	50	0	0	50	1.00
1401213--1401255	19	2.2	20	83	4	52	37	0	11	51	1.39
1404797--1404865	18	3.8	18	77	9	77	46	0	2	50	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1406734--1406825	22	4.2	22	71	15	75	61	0	1	36	1.03
1406800--1406838	8	4.8	8	87	6	51	69	0	0	30	0.89
1406728--1406831	39	2.7	37	77	14	102	63	0	0	35	1.01
1406733--1406838	25	4.3	25	71	17	87	63	0	0	35	1.01
1406772--1406836	17	3.8	17	75	15	55	66	0	0	33	0.92
1406721--1406846	17	7.0	18	68	22	52	63	0	0	34	1.06
1407221--1407252	16	1.9	17	93	6	57	43	0	3	53	1.16
1407221--1407258	17	2.2	17	86	9	51	44	0	2	52	1.14
1407263--1407301	20	2.0	20	90	10	62	51	0	0	48	1.00
1407272--1407326	20	2.8	20	83	8	67	60	0	0	40	0.97
1408144--1408188	6	7.5	6	94	0	54	53	6	0	40	1.27
1408138--1408191	12	4.5	12	88	0	72	51	7	0	40	1.30
1408138--1408191	10	5.4	10	88	0	63	51	7	0	40	1.30
1408531--1408618	18	4.7	18	71	16	72	45	0	0	54	0.99
1408554--1408646	39	2.3	41	78	16	113	41	0	0	58	0.98
1408620--1408668	11	4.3	11	85	15	64	32	0	0	67	0.91
1408607--1408653	16	3.1	16	80	17	55	34	0	0	65	0.93
1409037--1409074	15	2.6	15	87	4	51	65	0	0	34	0.93
1411742--1411812	29	2.5	28	80	14	83	36	1	1	60	1.14
1413232--1413266	16	2.1	18	89	10	56	62	8	0	28	1.24
1413340--1413457	11	10.7	11	65	20	50	56	0	0	42	1.05
1413327--1413421	17	5.5	17	72	18	72	55	0	1	43	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1413325--1413424	33	2.9	32	77	15	94	55	0	1	44	1.06
1413375--1413454	27	2.8	28	80	16	85	57	0	0	42	0.98
1413356--1413457	22	4.4	22	72	19	82	56	0	0	43	0.99
1413717--1413743	4	6.8	4	100	0	54	77	0	0	22	0.76
1413814--1413873	28	2.1	30	81	9	72	48	0	0	51	1.00
1414070--1414128	20	3.2	19	79	11	61	49	1	0	49	1.11
1415934--1416002	23	3.0	23	83	8	70	44	7	1	46	1.40
1416716--1416813	28	3.4	27	74	18	74	56	1	1	41	1.13
1416756--1416817	32	2.0	31	90	3	97	54	1	0	43	1.09
1417607--1417639	14	2.4	14	90	10	50	63	0	0	36	0.95
1417952--1417997	22	2.0	23	87	4	67	32	2	2	63	1.19
1418112--1418156	23	2.0	23	86	0	63	62	2	2	33	1.20
1418328--1418371	2	22.5	2	95	4	81	50	0	0	50	1.00
1421345--1421383	13	3.1	13	88	3	62	76	0	0	23	0.78
1421348--1421390	22	2.0	22	90	0	68	74	0	2	23	0.93
1421347--1421391	16	2.9	15	83	6	54	75	0	2	22	0.91
1425389--1425426	20	1.9	20	88	0	58	42	0	0	57	0.98
1426035--1426090	25	2.2	25	84	9	69	41	1	0	57	1.09
1426046--1426100	23	2.4	24	85	11	71	41	0	0	58	0.98
1426367--1426405	19	2.0	19	90	5	60	53	0	2	43	1.14
1426794--1426830	17	2.2	17	95	0	65	48	0	0	51	1.00
1427293--1427356	29	2.3	27	83	5	74	56	0	1	42	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1427319--1427369	26	1.9	27	84	4	68	54	3	0	41	1.19
1427319--1427359	13	3.1	13	82	3	55	60	0	0	39	0.96
1429242--1429312	28	2.5	28	79	16	83	38	0	4	57	1.18
1429242--1429313	30	2.5	29	79	16	78	38	0	4	56	1.18
1436185--1436229	23	2.0	22	82	4	54	17	8	0	73	1.08
1436705--1436734	3	10.0	3	100	0	60	33	0	0	66	0.92
1446156--1446206	24	2.1	25	85	3	68	64	0	3	31	1.11
1448340--1448405	23	2.8	23	75	13	55	43	6	1	48	1.36
1448453--1448501	18	2.7	18	81	9	64	77	10	0	12	0.99
1450421--1450451	13	2.4	13	88	0	53	45	0	0	54	0.99
1450940--1451022	29	2.9	29	78	7	89	55	0	1	43	1.07
1453805--1453848	18	2.5	17	89	7	70	45	0	0	54	0.99
1455106--1455168	34	1.9	32	84	12	83	50	0	0	49	1.00
1457469--1457504	17	2.1	17	89	0	54	44	0	0	55	0.99
1457924--1457970	13	3.5	13	85	11	51	63	2	2	31	1.18
1458133--1458185	19	2.8	19	75	16	56	43	1	0	54	1.11
1458159--1458315	74	2.1	75	87	1	226	47	4	5	42	1.45
1458459--1458500	17	2.4	18	84	8	59	52	0	0	47	1.00
1458454--1458511	16	3.6	16	73	15	57	50	0	0	50	1.00
1459155--1459201	23	2.0	24	91	4	78	57	2	0	40	1.11
1460018--1460046	14	2.1	14	93	6	51	51	0	0	48	1.00
1460333--1460372	2	20.0	2	100	0	80	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)
1461170--1461222	27	2.1	24	86	10	70	37	0	1	60	1.08
1461707--1461768	32	1.9	32	83	6	81	58	0	0	41	0.98
1463587--1463668	16	5.2	16	69	8	51	52	8	6	32	1.57
1467353--1467380	2	14.0	2	100	0	56	50	0	0	50	1.00
1470185--1470226	21	2.0	22	90	4	68	61	0	0	38	0.96
1472447--1472479	13	2.5	13	95	5	57	84	0	0	15	0.61
1472447--1472479	7	4.9	7	92	7	59	84	0	0	15	0.61
1476092--1476147	6	10.0	6	75	21	59	64	0	0	35	0.94
1476092--1476147	17	3.4	17	78	14	71	64	0	0	35	0.94
1476092--1476160	24	3.0	24	81	14	83	60	0	1	37	1.06
1477263--1477329	22	2.8	24	72	17	68	47	0	0	52	1.00
1477528--1477634	37	2.7	39	75	16	98	57	3	0	39	1.17
1477547--1477657	37	3.0	37	74	11	109	56	5	0	37	1.22
1477664--1477702	17	2.2	19	86	9	55	69	12	0	17	1.19
1479092--1479159	29	2.3	29	78	12	68	58	0	0	41	0.98
1479119--1479159	18	2.2	19	86	4	57	63	0	0	36	0.95
1480637--1480668	17	1.9	16	93	6	55	56	0	0	43	0.99
1481805--1481868	17	3.8	16	78	12	58	28	1	3	67	1.15
1481951--1481989	20	1.9	21	84	5	53	38	5	2	53	1.37
1484944--1484971	13	2.2	13	100	0	56	42	0	0	57	0.99
1487290--1487426	68	2.0	68	95	0	247	38	6	7	47	1.57
1487443--1487548	16	6.7	16	76	2	106	13	16	28	41	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1487552--1487587	16	2.2	16	90	0	54	22	13	22	41	1.89
1487789--1487828	15	2.7	14	92	7	62	30	0	0	70	0.88
1487789--1487828	7	5.4	7	91	8	62	30	0	0	70	0.88
1490645--1490693	16	3.0	16	81	3	53	48	0	2	48	1.12
1491707--1491741	15	2.2	17	90	10	56	54	0	0	45	0.99
1491717--1491758	20	2.2	19	83	12	50	59	0	0	40	0.97
1491727--1491781	16	3.5	16	80	14	62	58	0	0	41	0.98
1491736--1491770	15	2.3	15	90	5	52	60	0	0	40	0.97
1492670--1492701	12	2.6	12	95	5	55	43	0	0	56	0.99
1494193--1494221	15	2.0	15	93	6	51	79	0	20	0	0.74

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