genome.fa.s105.2.7.7.80.10.50.1000.9.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: Scaffold105
Parameters: 2 7 7 80 10 50 1000
Length:  2918491

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

This is table  9  of  16  ( 1849 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)
1354006--1354040	12	2.8	13	86	8	54	71	0	2	25	1.00
1361156--1361184	2	14.5	2	100	0	58	48	0	0	51	1.00
1361696--1361759	24	2.5	25	78	16	78	35	0	4	59	1.18
1365206--1365243	3	13.0	3	83	5	51	63	2	0	34	1.09
1370712--1370754	2	21.5	2	100	0	86	48	0	0	51	1.00
1376129--1376158	15	2.0	15	93	0	51	36	0	33	30	1.58
1376665--1376711	23	2.0	24	87	4	69	51	0	0	48	1.00
1376803--1376845	22	2.0	22	86	4	61	37	6	0	55	1.27
1377140--1377180	20	2.0	20	95	0	73	26	24	2	46	1.65
1378317--1378375	24	2.6	23	76	12	59	37	0	1	61	1.07
1378318--1378363	22	2.1	22	84	11	60	39	0	0	60	0.97
1378508--1378553	24	2.0	23	82	4	56	32	6	2	58	1.36
1380030--1380066	16	2.4	16	91	8	60	16	0	0	83	0.64
1383810--1383837	2	14.0	2	100	0	56	50	0	0	50	1.00
1386930--1386984	29	1.9	28	81	3	65	29	10	10	49	1.72
1392466--1392518	25	2.1	25	82	0	61	39	0	1	58	1.09
1392871--1392905	2	17.5	2	100	0	70	48	0	0	51	1.00
1393522--1393569	24	2.0	25	84	12	64	68	4	0	27	1.07
1394486--1394524	19	2.1	19	90	0	60	69	0	0	30	0.89
1394537--1394596	18	3.3	18	76	23	56	50	1	0	48	1.11
1395228--1395256	14	2.1	14	100	0	58	37	6	0	55	1.27
1396679--1396731	15	3.5	15	78	17	56	49	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1398666--1398699	3	11.3	3	87	0	50	29	2	2	64	1.22
1402695--1402735	18	2.3	18	91	0	64	46	2	4	46	1.37
1402840--1402874	3	11.7	3	93	0	61	34	2	0	62	1.10
1402828--1402874	12	3.9	12	91	0	58	31	6	2	59	1.34
1404472--1404498	2	13.5	2	100	0	54	48	0	0	51	1.00
1404613--1404719	31	3.5	30	76	19	107	42	0	0	56	1.05
1404964--1405000	16	2.3	16	90	0	56	45	0	0	54	1.00
1407986--1408011	2	13.0	2	100	0	52	50	0	0	50	1.00
1414276--1414302	4	6.8	4	100	0	54	22	0	0	77	0.76
1414485--1414513	2	14.5	2	100	0	58	48	0	0	51	1.00
1417219--1417279	10	5.5	11	75	13	54	36	0	1	62	1.05
1417222--1417282	21	2.9	21	78	7	61	39	0	1	59	1.08
1417303--1417348	21	2.2	21	84	3	58	36	2	2	58	1.22
1417323--1417383	22	2.6	23	82	17	65	40	0	0	59	0.98
1418315--1418367	21	2.5	20	73	11	52	50	0	0	49	1.00
1418739--1418764	4	6.5	4	100	0	52	26	0	0	73	0.84
1419353--1419399	19	2.3	20	78	14	51	29	0	4	65	1.11
1419363--1419408	19	2.3	19	82	17	58	30	0	4	65	1.12
1419728--1419772	2	22.0	2	86	4	63	46	4	2	46	1.35
1420481--1420513	2	16.5	2	100	0	66	51	0	0	48	1.00
1420874--1420910	18	2.0	19	89	5	58	56	0	2	40	1.13
1420869--1420914	19	2.3	20	82	14	60	54	0	2	43	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1421595--1421628	18	1.9	18	88	5	52	52	5	2	38	1.41
1421948--1421991	3	14.3	3	85	4	61	38	0	2	59	1.10
1422099--1422158	29	2.1	29	84	6	77	51	0	0	48	1.00
1426913--1426953	13	3.1	14	75	10	50	41	0	0	58	0.98
1426926--1426984	16	3.6	17	70	25	56	50	0	0	49	1.00
1427744--1427819	25	2.8	28	72	20	72	34	5	6	53	1.49
1428209--1428241	6	5.5	6	100	0	66	51	15	0	33	1.43
1428450--1428496	14	3.4	14	77	11	51	48	0	2	48	1.13
1428450--1428520	28	2.8	25	76	19	76	47	0	1	50	1.09
1428462--1428519	25	2.3	27	75	19	63	50	0	1	48	1.11
1431168--1431237	30	2.3	32	80	9	83	41	1	4	52	1.30
1432126--1432205	25	3.4	26	67	24	68	57	0	0	42	0.98
1432119--1432192	37	2.1	35	82	10	87	59	0	0	40	0.97
1432126--1432201	26	2.9	28	80	16	76	59	0	0	40	0.98
1432187--1432219	16	2.0	17	94	5	59	57	0	0	42	0.98
1432666--1432702	3	12.3	3	100	0	74	32	0	0	67	0.91
1433183--1433322	69	2.0	69	100	0	280	31	14	19	35	1.91
1441933--1441993	24	2.7	23	72	22	58	49	0	1	49	1.10
1449425--1449470	22	2.1	22	84	8	58	50	0	0	50	1.00
1449812--1449860	17	2.9	17	85	8	73	42	0	0	57	0.99
1450107--1450139	2	16.5	2	93	0	57	0	48	0	51	1.00
1450496--1450546	17	3.1	16	77	8	57	66	0	0	33	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1450489--1450540	17	3.0	17	75	10	52	65	0	0	34	0.93
1450508--1450548	21	1.9	22	90	5	66	58	0	0	41	0.98
1450651--1450703	19	2.7	19	85	8	63	56	0	3	39	1.17
1450687--1450741	15	3.6	15	76	11	58	56	0	0	43	0.99
1450671--1450749	31	2.5	32	82	13	94	59	0	0	40	0.97
1453003--1453129	51	2.5	51	82	5	134	40	16	4	37	1.70
1453730--1453776	3	15.7	3	100	0	94	31	0	0	68	0.90
1455948--1456000	27	1.9	28	92	3	90	39	1	3	54	1.29
1470422--1470496	40	1.9	38	83	5	96	48	0	0	52	1.00
1470425--1470500	17	3.6	22	70	25	65	50	0	0	50	1.00
1470803--1470864	26	2.3	27	81	13	67	50	1	0	48	1.10
1470861--1470916	9	5.7	10	78	19	64	28	0	1	69	0.98
1471207--1471274	20	3.2	21	74	19	61	51	1	0	47	1.09
1474720--1474749	15	2.0	15	93	0	51	50	6	30	13	1.67
1475254--1475305	28	2.0	28	85	11	74	61	3	1	32	1.25
1476597--1476638	22	1.9	22	90	0	66	50	0	0	50	1.00
1477269--1477304	18	2.0	18	88	0	54	50	2	0	47	1.15
1478676--1478719	17	2.3	20	85	14	58	43	0	0	56	0.99
1478711--1478771	18	3.3	18	72	14	52	45	0	3	50	1.17
1479337--1479396	30	2.0	30	83	6	77	50	1	3	45	1.28
1479353--1479413	30	2.0	30	84	6	79	52	1	3	42	1.27
1480159--1480193	14	2.6	13	86	8	52	57	0	0	42	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1480398--1480432	3	11.3	3	93	6	61	62	0	0	37	0.95
1480841--1480874	2	17.0	2	100	0	68	50	0	0	50	1.00
1483067--1483091	13	1.9	13	100	0	50	88	0	12	0	0.53
1495211--1495247	2	18.5	2	100	0	74	51	0	0	48	1.00
1496423--1496447	2	12.5	2	100	0	50	48	0	0	52	1.00
1502318--1502352	2	17.5	2	100	0	70	51	0	0	48	1.00
1506262--1506302	21	2.0	20	82	17	50	0	19	0	80	0.71
1511195--1511224	4	7.5	4	100	0	60	23	0	0	76	0.78
1511893--1511919	2	13.5	2	100	0	54	51	0	0	48	1.00
1512066--1512090	2	12.5	2	100	0	50	52	0	48	0	1.00
1513406--1513448	21	2.0	21	86	8	61	39	2	4	53	1.34
1515063--1515144	14	6.6	12	74	22	55	47	1	0	51	1.08
1515077--1515213	15	9.9	15	72	16	82	50	0	0	48	1.05
1515084--1515151	14	4.9	14	85	8	70	51	0	0	48	1.00
1516664--1516693	13	2.3	13	94	0	51	36	3	0	60	1.14
1517424--1517517	32	3.1	31	76	14	81	56	0	0	43	0.99
1517445--1517534	24	3.7	24	71	4	72	55	1	0	43	1.07
1517769--1517798	2	15.0	2	100	0	60	50	0	50	0	1.00
1520635--1520674	19	2.1	19	86	9	55	57	0	0	42	0.98
1523698--1523778	42	2.0	40	81	13	94	48	3	2	45	1.33
1523855--1523916	21	3.0	21	87	0	88	54	3	1	40	1.26
1523882--1523951	21	3.5	20	77	14	63	54	5	0	40	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1523909--1524031	21	5.9	21	77	12	87	53	9	0	35	1.40
1523924--1524031	21	5.1	21	78	10	105	53	9	0	36	1.39
1523861--1524006	52	2.7	51	83	9	161	52	7	1	38	1.38
1525725--1525771	23	2.0	23	83	0	58	46	10	0	42	1.38
1526328--1526371	14	3.0	14	86	6	61	54	0	0	45	0.99
1528942--1528973	3	10.7	3	100	0	64	68	0	0	31	0.90
1536355--1536423	27	2.6	26	68	22	61	23	10	23	43	1.84
1541481--1541541	18	3.0	20	72	23	56	47	0	1	50	1.10
1541481--1541539	21	2.8	21	75	12	59	49	0	1	49	1.11
1541472--1541541	18	3.7	18	71	22	54	48	0	1	50	1.09

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