genome.fa.s64.2.7.7.80.10.50.1000.20.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: Scaffold64
Parameters: 2 7 7 80 10 50 1000
Length:  7997333

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   

This is table  20  of  45  ( 5312 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)
3729311--3729366	22	2.6	21	76	15	60	60	1	0	37	1.07
3731044--3731085	21	2.0	21	90	9	68	35	0	0	64	0.94
3734451--3734475	2	12.5	2	100	0	50	52	0	0	48	1.00
3734935--3734975	19	2.1	20	90	4	66	41	0	0	58	0.98
3738521--3738560	18	2.2	18	91	8	64	52	0	0	47	1.00
3738631--3738667	2	18.0	2	94	5	65	48	0	2	48	1.15
3739748--3739841	11	9.1	11	68	19	51	36	3	0	60	1.13
3740390--3740433	21	2.1	21	100	0	88	40	34	0	25	1.56
3740550--3740585	17	2.1	17	94	0	63	58	0	0	41	0.98
3740920--3740954	2	17.5	2	100	0	70	48	0	0	51	1.00
3741187--3741335	30	5.1	29	67	21	89	37	0	1	61	1.05
3741266--3741347	18	4.7	18	75	14	64	31	0	0	68	0.90
3741266--3741347	23	3.6	22	72	18	78	31	0	0	68	0.90
3741253--3741346	28	3.3	29	81	11	106	30	0	1	68	0.97
3743176--3743215	19	2.1	19	85	0	53	35	25	10	30	1.88
3743417--3743459	16	2.7	16	75	13	52	51	0	2	46	1.13
3743410--3743449	21	1.9	21	90	10	64	50	0	0	50	1.00
3745187--3745227	20	2.1	19	90	4	64	56	0	0	43	0.99
3746571--3746610	20	2.0	20	85	0	53	50	0	2	47	1.14
3749117--3749235	41	2.9	41	97	0	220	20	18	13	47	1.81
3749669--3749827	8	20.2	8	82	12	188	50	9	0	39	1.35
3749673--3749828	20	8.0	20	84	4	176	50	10	0	39	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3761767--3761816	24	2.1	23	85	3	64	10	84	0	6	0.79
3763794--3763828	2	17.5	2	100	0	70	51	0	0	48	1.00
3765043--3765070	2	14.0	2	100	0	56	0	50	0	50	1.00
3767104--3767143	19	2.0	20	90	4	64	55	0	2	42	1.13
3767102--3767146	21	2.1	21	88	8	65	55	0	2	42	1.12
3771191--3771251	28	2.2	27	82	8	86	45	0	0	54	1.00
3771196--3771259	29	2.2	29	88	8	94	43	0	0	56	0.99
3771355--3771397	22	2.0	21	86	4	59	48	4	0	46	1.22
3771398--3771459	21	3.1	21	80	13	60	41	0	0	58	0.98
3773722--3773758	19	1.9	19	88	0	56	51	2	2	43	1.30
3778332--3778389	27	2.2	26	87	12	82	50	0	0	50	1.00
3778317--3778393	29	2.7	28	82	6	91	50	0	0	49	1.00
3778941--3779001	22	2.8	20	72	13	59	42	0	0	57	0.98
3779144--3779296	8	19.0	8	69	19	79	35	0	3	60	1.18
3779242--3779304	13	5.0	13	77	13	60	30	3	3	63	1.25
3779288--3779326	20	2.0	20	94	0	69	30	2	0	66	1.05
3781630--3781669	20	2.0	20	85	5	53	10	15	2	72	1.21
3782602--3782670	14	5.1	13	71	13	50	53	0	4	42	1.20
3783983--3784012	2	15.5	2	93	6	53	50	0	0	50	1.00
3783984--3784009	13	2.0	13	100	0	52	53	0	0	46	1.00
3783983--3784011	15	1.9	15	100	0	58	51	0	0	48	1.00
3784756--3784818	22	2.8	22	74	13	65	60	6	0	33	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3784864--3784913	17	3.0	16	78	16	57	52	10	0	38	1.35
3787567--3787602	17	2.2	16	90	5	54	30	0	0	69	0.89
3787615--3787648	14	2.4	14	90	0	50	41	0	2	55	1.15
3787701--3787753	24	2.3	24	87	6	74	33	0	0	66	0.92
3787784--3787833	20	2.6	20	79	17	61	36	0	2	62	1.07
3787782--3787840	17	3.3	18	76	21	61	38	0	1	59	1.08
3787946--3787990	15	2.8	16	86	6	56	42	0	0	57	0.98
3788438--3788488	15	3.6	14	75	17	52	45	1	0	52	1.12
3788438--3788488	27	1.9	26	92	4	84	45	1	0	52	1.12
3789870--3789903	17	1.9	18	94	5	61	32	0	0	67	0.91
3789872--3789952	12	6.5	13	68	20	57	34	0	0	65	0.93
3790605--3790654	15	3.4	16	75	25	56	58	0	0	42	0.98
3790604--3790685	22	3.8	21	75	20	80	58	1	0	40	1.06
3794621--3794749	64	2.0	64	100	0	258	50	15	10	23	1.75
3796967--3796992	2	13.0	2	100	0	52	50	0	0	50	1.00
3798167--3798260	42	2.2	42	94	0	161	38	12	28	20	1.89
3798505--3798569	12	4.6	15	72	27	54	55	0	0	44	0.99
3798503--3798570	28	2.3	27	83	14	82	55	0	0	44	0.99
3798521--3798581	28	2.2	27	83	13	79	59	0	0	40	0.98
3803353--3803390	19	2.0	19	89	0	58	65	0	2	31	1.06
3815338--3815397	29	2.1	27	85	11	77	51	3	0	45	1.17
3819873--3819923	23	2.3	22	86	6	68	5	37	7	49	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3819886--3819935	23	2.2	23	81	0	55	8	34	10	48	1.66
3823229--3823270	20	2.0	22	86	9	61	61	9	16	11	1.55
3828370--3828433	8	8.5	8	86	13	100	50	12	0	37	1.41
3828363--3828432	14	4.9	14	86	6	104	50	12	0	37	1.41
3828363--3828433	22	3.2	22	100	0	142	49	12	0	38	1.41
3831058--3831088	16	1.9	16	93	0	53	48	3	9	38	1.52
3833635--3833672	2	19.0	2	94	0	67	47	0	2	50	1.15
3836978--3837008	2	15.5	2	100	0	62	51	0	0	48	1.00
3837021--3837045	12	2.1	12	100	0	50	32	24	16	28	1.96
3839806--3839870	33	2.0	33	93	0	112	43	29	10	16	1.82
3845816--3845916	39	2.6	39	80	4	96	47	4	7	39	1.54
3846168--3846207	20	1.9	20	85	10	53	32	5	12	50	1.62
3847820--3847848	2	14.5	2	100	0	58	51	0	0	48	1.00
3847882--3847969	45	2.0	44	82	14	110	40	0	1	57	1.06
3853257--3853285	2	14.5	2	100	0	58	0	0	48	51	1.00
3853452--3853484	2	16.5	2	100	0	66	48	0	0	51	1.00
3854389--3854434	14	3.1	15	75	15	51	43	6	4	45	1.49
3860800--3860847	18	2.6	19	80	3	53	45	0	6	47	1.27
3861555--3861600	25	1.9	24	86	8	67	58	10	2	28	1.43
3863402--3863481	40	2.0	40	80	9	92	60	0	0	40	0.97
3863623--3863670	26	1.9	25	91	8	80	27	2	4	66	1.21
3863623--3863683	25	2.4	25	86	8	79	27	1	3	67	1.16
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3863635--3863685	8	6.4	8	80	6	59	25	1	1	70	1.08
3869795--3869853	26	2.1	29	82	14	72	40	11	15	32	1.83
3872910--3872956	23	2.0	23	88	12	69	40	0	0	59	0.97
3873693--3873734	22	1.9	22	85	0	57	61	2	0	35	1.09
3874514--3874555	22	1.9	22	85	9	59	52	0	0	47	1.00
3879108--3879170	31	2.0	31	90	0	99	19	20	9	50	1.74
3879932--3880005	30	2.5	31	78	6	82	51	1	1	45	1.18
3880762--3880810	16	3.1	15	82	11	62	53	0	0	46	1.00
3880746--3880807	33	1.9	32	87	9	90	50	0	0	50	1.00
3881824--3881849	2	13.0	2	100	0	52	0	50	0	50	1.00
3884186--3884238	28	1.9	27	84	3	70	41	35	13	9	1.76
3884989--3885031	18	2.3	18	96	4	77	34	9	9	46	1.68
3888516--3888575	21	2.8	20	78	9	57	31	5	0	63	1.16
3888993--3889042	23	2.1	25	85	7	68	54	0	2	44	1.11
3888993--3889042	12	4.2	12	82	7	57	54	0	2	44	1.11
3889018--3889065	18	2.9	16	77	17	53	52	0	0	47	1.00
3889007--3889055	18	2.6	19	87	6	64	55	0	0	44	0.99
3889003--3889070	20	3.2	21	72	22	54	55	0	0	44	0.99
3890089--3890125	2	18.5	2	100	0	74	51	0	0	48	1.00
3891899--3891935	19	2.0	18	94	5	65	64	0	0	35	0.94
3891863--3891959	43	2.2	45	80	10	103	59	4	0	36	1.16
3892253--3892288	3	12.0	3	100	0	72	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)
3895234--3895259	3	8.7	3	100	0	52	69	0	0	30	0.89
3904053--3904212	68	2.4	68	81	5	173	32	28	16	23	1.96
3911180--3912556	506	2.7	504	82	4	1605	29	16	20	32	1.95
3912592--3914309	509	3.4	508	83	3	2046	28	16	21	33	1.95
3914769--3916955	494	4.3	492	80	7	2272	28	16	21	33	1.95
3915257--3916956	514	3.3	510	84	2	2131	27	16	21	34	1.95
3922134--3922166	9	3.7	9	88	12	50	21	0	0	78	0.75
3922133--3922166	17	2.0	17	94	0	59	20	0	0	79	0.73
3924597--3924654	29	2.0	30	86	3	82	32	0	1	65	1.03
3924739--3924766	1	28.0	1	100	0	56	100	0	0	0	0.00

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45