genome.fa.s39.2.7.7.80.10.50.1000.7.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: scaffold165.1
Parameters: 2 7 7 80 10 50 1000
Length:  1724686

Tables:   1   2   3   4   5   6   7   8   

This is table  7  of  8  ( 876 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)
1387075--1387132	4	15.2	4	77	22	63	74	0	25	0	0.82
1387076--1387131	18	3.1	17	87	12	76	76	0	23	0	0.78
1387999--1388117	41	3.0	40	76	9	145	26	15	23	34	1.95
1388002--1388104	37	2.7	38	81	6	118	25	16	25	33	1.96
1393107--1393153	11	4.3	11	81	5	51	29	0	2	68	1.02
1394898--1394931	16	2.1	16	88	0	50	52	5	5	35	1.50
1396996--1397140	74	1.9	74	86	9	206	13	19	3	64	1.42
1404054--1404113	30	2.0	30	96	0	111	21	20	36	21	1.95
1405128--1405154	2	13.5	2	100	0	54	51	0	48	0	1.00
1406907--1406967	31	1.9	32	96	3	115	54	6	8	31	1.56
1406915--1406995	31	2.6	31	84	3	92	55	4	9	29	1.54
1408552--1408586	14	2.6	14	90	4	54	62	2	0	34	1.10
1410602--1410631	15	1.9	16	93	6	53	43	23	6	26	1.78
1414340--1414409	31	2.2	32	85	9	92	37	12	22	27	1.91
1414351--1414422	31	2.4	31	85	2	92	36	13	19	30	1.91
1418052--1418285	116	2.0	116	99	0	459	54	5	11	28	1.59
1418818--1418974	80	2.0	80	98	0	305	24	21	28	25	1.99
1419272--1419648	189	2.0	189	97	1	720	41	14	10	33	1.80
1420232--1420543	130	2.4	130	87	5	425	30	24	16	29	1.96
1420248--1420719	44	10.8	44	70	11	258	29	23	16	30	1.96
1420213--1420766	175	3.2	174	76	7	575	29	23	18	29	1.97
1432122--1432299	89	2.0	89	97	0	338	32	14	20	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1433528--1433555	14	2.0	14	100	0	56	50	14	21	14	1.78
1433728--1433868	71	2.0	70	97	1	264	53	11	4	29	1.57
1434893--1435204	130	2.4	130	87	5	425	30	24	16	29	1.96
1434909--1435380	44	10.8	44	70	11	258	29	23	16	30	1.96
1434874--1435427	175	3.2	174	76	7	575	29	23	18	29	1.97
1450500--1450534	12	2.8	12	91	4	52	60	0	8	31	1.27
1452867--1452925	21	2.8	20	80	14	57	55	3	0	40	1.16
1452908--1452933	11	2.4	11	100	0	52	61	0	0	38	0.96
1452917--1452992	17	4.7	17	69	12	61	63	0	1	35	1.03
1456378--1456498	61	2.0	61	88	0	179	33	20	12	33	1.90
1466613--1466659	5	9.0	5	80	17	51	14	6	0	78	0.93
1473589--1473647	32	2.0	31	83	12	79	33	1	23	40	1.65
1473977--1474024	26	2.0	25	84	15	66	39	12	4	43	1.62
1479944--1479997	25	2.2	25	86	0	72	22	25	18	33	1.97
1480919--1480988	30	2.3	30	80	0	86	22	27	32	17	1.96
1482388--1482461	25	2.9	26	81	4	78	18	22	21	36	1.95
1482423--1482483	25	2.5	25	83	2	70	18	26	24	31	1.97
1482473--1482525	24	2.2	23	83	9	70	16	16	20	45	1.86
1488715--1488786	26	2.8	25	72	4	72	15	23	25	36	1.94
1488713--1488840	25	5.2	24	70	11	71	17	23	24	34	1.96
1490457--1490612	78	2.0	78	87	2	224	31	15	14	39	1.87
1491043--1491100	28	2.1	27	84	12	73	50	1	5	43	1.35
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1495081--1495154	29	2.4	30	82	10	89	25	14	10	48	1.77
1495579--1495797	59	3.8	59	73	13	195	44	10	19	25	1.83
1495555--1495686	31	4.4	31	77	9	128	43	9	19	27	1.83
1495591--1495731	60	2.4	59	84	5	187	45	9	19	25	1.80
1501643--1501693	24	2.1	24	89	7	77	7	11	21	58	1.58
1502624--1502653	15	1.9	16	93	6	53	23	0	6	70	1.11
1502798--1502841	21	2.1	21	91	8	72	13	11	29	45	1.79
1502976--1503238	43	6.1	42	92	2	411	30	27	20	21	1.98
1502984--1503234	128	2.0	128	93	1	432	30	26	20	22	1.98
1503531--1503585	21	2.6	21	88	0	74	5	45	18	30	1.72
1503632--1503672	21	2.0	21	95	0	73	7	43	14	34	1.73
1503552--1503734	87	2.1	87	86	8	248	11	33	18	37	1.86
1503638--1503683	21	2.2	21	88	0	65	4	41	17	36	1.69
1509678--1509712	14	2.5	14	90	0	52	40	2	5	51	1.40
1510102--1510160	27	2.1	28	90	6	102	52	3	3	40	1.35
1512087--1512131	23	2.0	23	82	8	56	40	31	6	22	1.80
1512876--1512920	23	2.0	23	82	8	56	40	31	6	22	1.80
1513823--1513902	41	2.0	41	82	5	99	27	30	22	20	1.98
1513822--1513918	41	2.4	41	78	3	97	28	27	21	21	1.99
1514029--1514374	112	3.1	113	91	1	541	26	22	23	27	2.00
1514361--1514500	40	3.5	39	75	7	106	20	17	22	40	1.92
1515138--1515179	22	2.0	22	86	9	61	38	7	4	50	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1521611--1521674	29	2.1	29	82	5	74	51	12	10	25	1.72
1527420--1527478	31	1.9	31	89	6	93	42	6	6	44	1.57
1528800--1528851	24	2.2	24	89	0	77	55	9	1	32	1.43
1530769--1530820	24	2.2	24	89	0	77	55	9	1	32	1.43
1533425--1533494	31	2.3	31	92	0	113	40	7	14	38	1.73
1537116--1537360	42	5.8	42	90	2	377	32	21	22	23	1.98
1537127--1537360	126	1.9	126	94	1	416	31	21	22	24	1.98
1537116--1537447	84	4.0	83	82	4	369	30	21	21	27	1.98
1537127--1537447	126	2.5	126	86	2	394	29	20	21	28	1.98
1537773--1537843	21	3.4	21	80	0	79	2	45	18	33	1.64
1543294--1543484	18	11.0	18	65	31	73	33	0	20	46	1.51
1543294--1543484	7	22.0	9	64	32	73	33	0	20	46	1.51
1543339--1543693	26	14.1	26	88	7	502	32	0	20	47	1.55
1543553--1543674	18	6.4	18	67	26	74	35	1	18	44	1.60
1543729--1543953	73	3.1	73	98	1	423	41	6	1	50	1.37
1543815--1543936	41	3.2	41	64	21	118	41	5	1	50	1.36
1543730--1543950	74	3.0	74	98	0	426	41	6	1	50	1.37
1544100--1544170	13	5.5	13	86	0	106	50	2	7	39	1.44
1544099--1544170	26	2.8	26	100	0	144	50	2	6	40	1.44
1544175--1544473	17	16.6	17	70	23	161	42	1	11	43	1.51
1544142--1544482	57	6.5	57	75	20	375	44	2	10	42	1.51
1544192--1544302	44	2.7	40	86	10	177	44	1	10	43	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1544159--1544461	101	3.0	100	94	4	533	44	1	10	42	1.50
1544293--1544399	40	2.7	40	94	2	189	43	1	11	42	1.51
1544142--1544450	97	3.1	97	93	4	521	44	2	10	42	1.51
1545816--1545855	11	3.7	11	93	3	64	27	27	10	35	1.89
1547281--1547310	14	2.1	14	100	0	60	53	6	13	26	1.64
1547498--1547613	36	3.2	36	69	20	116	46	18	6	29	1.72
1547446--1547646	71	2.8	71	96	1	368	50	18	4	25	1.67
1547953--1547999	22	2.1	22	96	0	85	40	23	8	27	1.83
1549156--1549226	14	5.0	14	69	16	56	40	35	1	22	1.63
1549463--1549668	113	1.8	115	84	2	290	28	23	18	29	1.98
1549479--1550111	208	2.9	209	84	7	741	27	21	18	32	1.97
1549676--1550342	113	5.9	112	78	7	605	26	22	18	32	1.97
1549676--1550228	227	2.4	227	87	2	680	26	21	18	32	1.97
1551824--1551895	27	2.7	27	80	0	90	23	33	33	9	1.88
1551940--1551982	20	2.2	20	91	0	68	65	0	34	0	0.93
1551948--1551991	10	4.4	10	80	11	54	70	0	29	0	0.88
1551961--1552079	48	2.6	43	71	17	105	58	1	38	0	1.14
1552310--1552359	16	3.2	16	70	13	50	66	4	8	22	1.35
1552362--1553413	160	6.6	157	90	4	1619	52	9	9	28	1.64
1552362--1553413	158	6.6	158	89	4	1598	52	9	9	28	1.64
1555730--1555771	8	5.4	8	85	5	59	50	26	0	23	1.50
1559041--1559082	17	2.6	17	82	17	54	0	26	0	73	0.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1559043--1559086	11	4.3	11	73	26	51	0	27	0	72	0.85
1563652--1563706	23	2.3	23	84	9	67	65	5	10	18	1.42
1571560--1571696	51	2.7	51	77	0	166	40	6	13	39	1.71
1573392--1573534	42	3.5	40	88	5	196	36	2	0	60	1.11
1574150--1574213	19	3.4	19	73	18	62	35	4	0	59	1.18
1574136--1574221	36	2.4	36	77	11	88	40	3	0	55	1.17
1578270--1578324	22	2.5	22	90	0	74	10	23	12	52	1.71
1587828--1587893	9	7.2	9	85	10	80	39	27	10	22	1.87
1587828--1587893	20	3.6	18	80	11	80	39	27	10	22	1.87
1587854--1587901	20	2.4	20	96	0	87	41	29	8	20	1.81

Tables:   1   2   3   4   5   6   7   8