genome.fa.s58.2.7.7.80.10.50.1000.9.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: Scaffold58
Parameters: 2 7 7 80 10 50 1000
Length:  1582273

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

This is table  9  of  10  ( 1168 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)
1346619--1346718	15	6.6	15	68	23	50	42	2	1	55	1.18
1347985--1348039	19	3.0	17	80	15	65	29	0	5	65	1.15
1348570--1348646	23	3.3	22	77	16	66	53	2	0	44	1.14
1352238--1352327	46	1.9	48	90	4	148	32	4	10	53	1.54
1352474--1352514	11	3.6	11	87	12	57	31	0	0	68	0.90
1352717--1352763	23	2.1	23	84	4	60	40	0	8	51	1.33
1353410--1353437	2	14.0	2	100	0	56	50	0	0	50	1.00
1356186--1356227	22	1.9	22	85	9	59	35	4	2	57	1.33
1356713--1356766	15	3.6	15	76	18	51	64	1	1	31	1.14
1357389--1357441	19	2.8	19	88	0	70	37	5	5	50	1.50
1359593--1359673	12	6.8	12	68	13	51	43	0	1	55	1.07
1359634--1359681	18	2.5	20	83	12	64	47	0	2	50	1.12
1362077--1362158	18	4.3	19	72	17	64	48	0	0	51	1.00
1362213--1362238	2	13.0	2	100	0	52	50	0	0	50	1.00
1362786--1362827	17	2.5	17	88	3	59	57	0	0	42	0.99
1369426--1369471	22	2.1	22	87	0	65	50	0	0	50	1.00
1369425--1369456	15	2.1	16	94	5	57	43	0	0	56	0.99
1369427--1369475	16	3.1	16	85	5	55	51	0	0	48	1.00
1370476--1370518	19	2.2	20	88	8	63	18	4	0	76	0.95
1371586--1371631	23	2.0	23	87	8	67	47	0	0	52	1.00
1371726--1371757	16	2.0	16	93	0	55	50	3	6	40	1.43
1371747--1371784	14	2.7	14	88	8	51	50	5	5	39	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1372706--1372734	14	2.1	14	100	0	58	51	0	20	27	1.47
1373367--1373426	20	2.8	21	76	16	52	56	1	0	41	1.09
1373361--1373429	28	2.3	29	85	11	88	56	1	0	42	1.08
1374907--1374977	27	2.6	27	80	8	74	8	39	5	46	1.58
1374917--1374977	18	3.4	17	80	10	68	9	39	4	45	1.59
1374912--1374978	9	7.6	9	70	20	52	8	37	7	46	1.64
1377656--1377724	32	2.1	32	82	12	79	10	10	4	75	1.17
1382823--1382847	12	2.1	12	100	0	50	16	32	28	24	1.96
1382851--1382901	12	3.9	12	78	16	57	43	5	11	39	1.66
1382857--1382913	27	2.1	27	90	0	87	40	5	19	35	1.74
1387573--1387597	12	2.1	12	100	0	50	16	32	28	24	1.96
1387601--1387651	12	3.9	12	78	16	57	43	5	11	39	1.66
1387607--1387663	27	2.1	27	90	0	87	40	5	19	35	1.74
1392347--1392378	2	16.0	2	100	0	64	50	0	0	50	1.00
1395000--1395030	15	2.1	15	93	0	53	25	0	3	70	1.02
1396452--1396493	20	2.2	20	87	12	61	35	0	2	61	1.09
1396541--1396618	26	3.0	26	79	7	88	60	3	0	35	1.15
1396551--1396618	27	2.6	25	83	6	73	61	2	0	35	1.11
1404381--1404412	8	3.9	8	92	8	55	25	0	12	62	1.30
1405574--1405604	16	1.9	16	93	0	53	54	0	0	45	0.99
1405597--1405677	14	5.8	14	72	16	60	60	0	0	39	0.97
1405595--1405651	15	3.9	15	74	19	57	54	0	0	45	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1405642--1405682	18	2.3	18	87	8	57	70	2	0	26	0.99
1405642--1405692	14	3.8	13	78	14	59	68	1	0	29	1.00
1407215--1407374	50	3.2	50	93	1	277	29	21	19	29	1.98
1411767--1411926	50	3.2	50	93	1	277	29	21	19	29	1.98
1414519--1414560	3	14.0	3	90	9	68	66	0	0	33	0.92
1417845--1417894	24	2.1	24	100	0	100	42	0	16	42	1.47
1419019--1419051	2	16.5	2	100	0	66	51	0	48	0	1.00
1420036--1420112	25	3.2	25	63	17	63	36	5	28	29	1.79
1420576--1420613	17	2.2	18	85	4	51	47	0	10	42	1.38
1420908--1420949	22	1.9	22	85	9	59	19	0	2	78	0.86
1422060--1422097	18	2.2	18	85	4	51	47	5	7	39	1.55
1425826--1425869	16	2.8	16	82	10	54	45	2	0	52	1.13
1426845--1426873	15	2.0	15	93	6	51	75	0	3	20	0.94
1427900--1427940	3	13.7	3	100	0	82	34	0	0	65	0.93
1428814--1428906	47	2.0	46	80	16	102	38	0	0	61	0.96
1428846--1428906	22	2.6	23	78	17	63	34	0	0	65	0.93
1430950--1431011	21	3.0	20	76	6	61	46	1	3	48	1.28
1430974--1431010	11	3.5	11	82	14	51	45	0	0	54	1.00
1430978--1431021	19	2.3	19	88	4	61	45	0	0	54	0.99
1430977--1431006	15	1.9	16	93	6	53	43	0	0	56	0.99
1431153--1431201	18	2.6	19	83	6	55	51	0	2	46	1.12
1433919--1433949	2	15.5	2	100	0	62	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1435512--1435544	12	2.6	13	85	4	50	78	0	21	0	0.75
1437132--1437165	17	2.0	17	88	11	52	29	0	0	70	0.87
1437961--1437998	14	2.8	14	80	4	51	50	0	2	47	1.15
1439855--1439911	29	1.9	30	92	7	98	45	0	1	52	1.11
1439855--1439941	29	2.9	29	84	8	95	43	4	3	48	1.40
1446214--1446238	11	2.3	11	100	0	50	52	8	0	40	1.31
1447537--1447566	3	10.0	3	100	0	60	33	0	0	66	0.92
1447649--1447708	4	15.5	4	82	6	79	76	0	23	0	0.78
1447651--1447718	22	3.0	22	84	4	82	76	0	22	1	0.87
1447738--1447762	6	4.2	6	100	0	50	16	0	16	68	1.22
1448986--1449021	16	2.3	16	90	4	56	38	0	0	61	0.96
1452086--1452142	10	5.8	10	81	4	53	38	3	3	54	1.35
1452086--1452126	19	2.1	19	86	4	55	41	2	2	53	1.27
1452432--1452482	9	5.3	10	75	17	54	56	0	0	43	0.99
1452960--1453031	29	2.5	28	82	13	85	56	0	2	40	1.13
1453043--1453072	3	10.0	3	92	0	51	30	0	0	70	0.88
1455000--1455064	16	4.1	16	75	15	62	55	0	0	44	0.99
1455460--1455486	14	1.9	14	100	0	54	62	0	0	37	0.95
1455778--1455815	18	2.1	18	90	0	58	42	0	0	57	0.98
1459474--1459548	20	3.8	19	78	7	87	41	12	13	33	1.81
1462065--1462106	16	2.6	16	78	14	50	30	4	14	50	1.63
1462050--1462124	32	2.3	32	81	0	87	29	5	13	52	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1463145--1463169	12	2.1	12	100	0	50	16	32	28	24	1.96
1463175--1463227	27	2.0	27	92	0	88	45	5	11	37	1.64
1466000--1466040	18	2.3	18	100	0	82	41	14	29	14	1.86
1469022--1469075	22	2.5	22	82	11	69	46	1	0	51	1.11
1469022--1469078	16	3.2	17	78	12	53	43	1	0	54	1.10
1470715--1470755	21	2.0	21	85	9	57	46	0	0	53	1.00
1471075--1471117	2	21.5	2	100	0	86	48	0	0	51	1.00
1473232--1473521	149	1.9	150	85	5	399	38	14	12	34	1.84
1474006--1474049	17	2.6	17	79	13	54	54	6	0	38	1.27
1474164--1474210	23	2.0	23	100	0	94	38	17	12	31	1.87
1475165--1475215	27	2.0	26	84	7	68	58	11	1	27	1.44
1476754--1476800	17	2.8	16	84	12	51	34	0	6	59	1.23
1476819--1476901	15	6.2	14	71	23	54	44	0	1	54	1.08
1476787--1476884	41	2.4	42	79	6	110	40	0	2	57	1.10
1476788--1476882	14	6.5	15	70	13	58	40	0	2	57	1.10
1476801--1476862	29	2.1	31	82	11	76	40	0	1	58	1.08
1476992--1477280	50	5.8	50	85	2	375	29	18	18	33	1.95
1476992--1477299	100	3.1	100	86	0	429	29	18	19	32	1.95
1483694--1483748	17	3.3	16	80	7	65	1	18	0	80	0.81
1483696--1483749	24	2.5	22	83	16	76	1	18	0	79	0.82
1483713--1483750	20	1.9	20	94	0	67	5	21	0	73	1.02
1485226--1485685	50	9.2	50	83	1	546	29	16	18	35	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1487775--1487937	84	1.9	84	88	0	245	42	12	4	39	1.65
1488704--1488743	21	1.9	21	90	10	64	60	2	0	37	1.11
1490640--1490687	21	2.3	21	89	3	71	41	0	0	58	0.98
1492372--1492419	23	2.1	23	100	0	96	37	8	33	20	1.83
1497993--1498200	80	2.6	79	83	2	238	29	16	29	24	1.97
1498152--1498223	28	2.6	28	86	0	90	25	19	33	22	1.97
1498212--1498550	52	6.4	52	68	17	162	31	13	25	29	1.93
1498355--1498436	27	3.0	28	80	10	89	26	21	28	23	1.99
1498145--1498550	212	1.9	212	87	3	602	31	14	26	27	1.95
1498427--1498545	51	2.3	53	85	7	154	33	11	22	31	1.90

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