genome.fa.s4.2.7.7.80.10.50.1000.9.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: CP032248.1 Gossypioides kirkii chromosome KI_06
Parameters: 2 7 7 80 10 50 1000
Length:  60359545

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   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   

This is table  9  of  193  ( 23090 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)
3217640--3218109	60	8.1	59	73	11	301	42	14	17	25	1.87
3217724--3218172	229	2.0	228	81	4	528	42	14	17	25	1.87
3222966--3223006	4	10.0	4	91	2	64	73	0	24	2	0.96
3228833--3228902	30	2.3	30	87	2	95	35	12	25	25	1.92
3233821--3233885	24	2.8	25	72	11	57	56	1	0	41	1.08
3233900--3233931	7	4.6	7	100	0	64	62	12	0	25	1.30
3236794--3236818	2	12.5	2	100	0	50	48	0	0	52	1.00
3240881--3240925	23	2.0	23	95	0	81	48	8	11	31	1.69
3246676--3246718	19	2.3	19	84	4	61	30	0	11	58	1.34
3250445--3250489	22	2.1	22	83	4	56	37	20	6	35	1.79
3268074--3268098	4	6.2	4	100	0	50	28	72	0	0	0.86
3269059--3269105	15	3.1	15	79	8	51	51	0	12	36	1.40
3274607--3274639	15	2.1	16	94	5	59	63	6	6	24	1.40
3275204--3275452	130	1.9	132	85	8	353	23	13	12	50	1.75
3275257--3275526	130	2.1	125	81	11	298	25	10	12	50	1.73
3281349--3281382	16	2.1	16	100	0	68	41	17	11	29	1.85
3285332--3285361	15	1.9	16	93	6	53	26	0	0	73	0.84
3287860--3287884	4	6.2	4	100	0	50	52	24	0	24	1.48
3289079--3289103	7	3.6	7	100	0	50	48	12	0	40	1.40
3308365--3308425	31	1.9	32	83	9	81	32	9	0	57	1.32
3308358--3308425	30	2.2	29	84	7	82	33	8	1	55	1.40
3309955--3310040	42	2.0	42	97	0	163	27	8	6	56	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3313253--3313301	20	2.4	21	89	3	73	32	14	10	42	1.79
3323448--3323495	24	2.0	24	84	8	62	77	6	2	14	1.06
3330836--3330891	19	3.0	18	94	2	94	21	12	16	50	1.78
3330867--3330926	29	2.1	29	83	0	75	20	6	18	55	1.65
3333020--3333085	24	2.7	24	76	2	69	19	4	7	68	1.32
3333122--3333178	11	5.1	11	73	12	53	15	8	21	54	1.68
3335054--3335091	3	12.7	3	100	0	76	0	31	0	68	0.90
3342500--3342542	21	2.0	22	86	9	61	46	0	2	51	1.13
3342525--3342575	16	3.4	16	69	20	56	54	0	0	45	0.99
3342503--3342575	28	2.5	30	91	4	114	52	0	1	46	1.09
3343353--3343394	22	2.0	22	85	4	59	50	0	0	50	1.00
3346969--3347046	29	2.6	30	81	6	77	47	6	6	39	1.55
3350143--3350991	424	2.0	424	100	0	1698	32	11	22	33	1.90
3353410--3353474	29	2.2	30	83	2	78	47	1	3	47	1.27
3353913--3353968	23	2.4	23	96	0	103	50	5	7	37	1.53
3360712--3360743	12	2.7	12	100	0	64	6	9	25	59	1.52
3363430--3363659	109	2.1	109	92	2	383	19	7	23	50	1.72
3364458--3364526	21	3.3	21	78	13	79	31	20	14	33	1.92
3368598--3368642	14	3.1	14	81	6	54	66	0	2	31	1.04
3368595--3368642	15	3.3	14	80	16	53	66	0	2	31	1.03
3370820--3370854	18	1.9	18	88	0	52	31	14	14	40	1.86
3376690--3376790	48	2.1	48	100	0	202	51	11	9	26	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3387796--3387901	31	3.5	29	75	10	86	43	6	11	38	1.67
3389166--3389206	21	2.0	21	85	0	55	24	24	12	39	1.89
3391420--3391705	58	4.9	58	79	8	294	35	29	1	33	1.68
3391457--3391706	29	8.6	28	70	23	135	34	30	1	34	1.68
3414570--3414912	181	1.9	181	90	0	542	35	11	14	38	1.81
3422648--3422681	14	2.4	14	90	0	50	64	2	32	0	1.08
3425476--3425507	17	1.9	17	93	6	57	62	6	0	31	1.20
3427575--3427614	20	2.0	20	90	0	62	35	20	2	42	1.65
3435931--3436179	120	2.1	120	99	0	489	28	12	28	30	1.92
3438898--3438973	40	1.9	40	97	0	143	23	25	22	28	1.99
3445269--3445295	2	13.5	2	100	0	54	48	0	51	0	1.00
3445942--3445997	23	2.5	23	79	2	69	33	5	0	60	1.19
3445942--3445996	11	4.9	11	75	4	56	32	5	0	61	1.19
3446044--3446105	32	1.9	32	87	9	90	33	0	3	62	1.11
3452513--3452571	24	2.5	24	81	10	59	37	5	0	57	1.21
3452532--3452690	58	2.7	57	86	10	196	46	1	0	51	1.13
3452609--3452690	32	2.9	26	69	19	74	48	0	1	50	1.08
3452785--3452878	44	2.1	44	86	7	127	37	26	5	30	1.79
3455815--3455855	3	13.7	3	100	0	82	65	0	0	34	0.93
3463955--3464003	17	2.8	18	82	14	59	46	0	0	53	1.00
3463962--3464007	16	2.9	16	81	15	60	45	0	0	54	0.99
3465029--3465078	22	2.2	23	82	10	59	48	32	2	18	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3465291--3465326	16	2.2	16	90	0	54	47	0	0	52	1.00
3477256--3477286	15	2.1	15	93	0	53	48	12	0	38	1.42
3485462--3485511	20	2.6	20	87	6	68	52	0	8	40	1.31
3486534--3486858	30	10.9	30	83	6	358	38	22	2	35	1.69
3486534--3486858	61	5.4	60	83	6	367	38	22	2	35	1.69
3486534--3486842	148	2.1	149	85	4	419	39	22	2	34	1.70
3497401--3497462	32	1.9	32	93	0	106	40	20	9	29	1.84
3499112--3499149	12	3.0	13	84	7	51	44	2	2	50	1.30
3499291--3499332	21	2.0	21	81	9	50	69	4	2	23	1.20
3509542--3509782	23	10.6	23	73	14	160	42	21	23	12	1.86
3509635--3509803	48	3.6	46	82	10	200	40	22	24	12	1.88
3509646--3509803	71	2.2	71	93	2	273	39	22	24	13	1.90
3509635--3509803	23	7.2	23	82	11	200	40	22	24	12	1.88
3513091--3513129	17	2.3	17	90	0	60	46	25	12	15	1.81
3516380--3517435	528	2.0	527	92	1	1740	35	20	18	24	1.95
3523089--3523163	17	4.2	17	79	14	80	41	1	6	50	1.37
3523117--3523165	11	4.4	11	79	5	62	46	0	4	48	1.20
3523110--3523167	23	2.6	23	83	8	66	43	0	5	51	1.24
3523096--3523163	6	11.3	6	78	12	68	41	1	5	51	1.35
3523948--3523998	24	2.1	24	100	0	102	7	33	37	21	1.82
3523948--3524013	24	2.8	24	90	2	80	10	33	33	22	1.89
3524972--3525138	30	5.7	29	82	10	162	34	26	1	37	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3524972--3525138	89	1.9	89	81	12	209	34	26	1	37	1.65
3525205--3525267	29	2.2	29	88	2	92	28	28	12	30	1.93
3530049--3530088	17	2.4	17	91	0	62	47	25	12	15	1.80
3533066--3533092	4	6.8	4	100	0	54	22	0	0	77	0.76
3533108--3533138	13	2.4	13	94	0	53	77	0	0	22	0.77
3533187--3533227	6	7.0	6	91	8	59	19	0	0	80	0.71
3533187--3533227	11	3.5	12	83	16	59	19	0	0	80	0.71
3533179--3533219	12	3.7	11	87	9	57	17	2	0	80	0.82
3541394--3541432	21	1.9	20	84	5	51	25	5	10	58	1.51
3550427--3550481	28	2.0	28	92	0	92	36	5	12	45	1.66
3555998--3556166	58	3.0	56	80	6	180	43	2	1	52	1.24
3556247--3556341	43	2.1	43	84	9	118	41	27	2	29	1.68
3556385--3556426	19	2.2	20	82	4	50	38	4	2	54	1.34
3562179--3562230	21	2.5	21	80	0	59	50	0	46	3	1.20
3562203--3562239	15	2.5	15	90	0	56	48	0	51	0	1.00
3562191--3562236	21	2.2	21	84	0	56	50	0	47	2	1.13
3563103--3563131	8	3.6	8	100	0	58	89	0	0	10	0.48
3566825--3566851	9	3.0	9	100	0	54	77	0	0	22	0.76
3571148--3571241	26	3.5	26	75	5	80	60	9	5	24	1.48
3571082--3571245	54	2.9	53	75	9	141	55	10	7	26	1.61
3571173--3571250	28	2.9	26	77	12	77	61	11	1	25	1.37
3573554--3573602	15	3.1	16	81	16	50	20	8	0	71	1.11
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3574356--3574412	29	1.9	30	85	3	80	45	3	5	45	1.43
3574678--3574707	3	10.0	3	92	0	51	33	36	0	30	1.58
3583685--3583727	16	2.6	16	85	10	52	58	0	9	32	1.30
3584205--3584266	30	2.1	30	93	0	106	33	14	3	48	1.60
3587573--3587813	115	2.1	116	93	1	412	36	26	14	22	1.93
3592336--3592384	15	3.3	16	72	16	52	32	0	4	63	1.13
3596845--3596906	32	1.9	32	96	0	115	32	9	19	38	1.84
3614419--3614452	17	2.0	17	100	0	68	29	23	11	35	1.90
3622003--3622484	156	3.0	158	89	5	709	43	17	15	23	1.87
3627432--3627467	18	1.9	19	88	5	56	30	0	2	66	1.06

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   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193