Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006337.1 Corchorus capsularis cultivar CVL-1 contig06358, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 20185
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Found at i:846 original size:19 final size:18
Alignment explanation
Indices: 812--849 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
802 CTTGAAATAT
812 TTCTTCAATGATCTTCAA
1 TTCTTCAATGATCTTCAA
*
830 TTCTTCAAATTATCTTCAA
1 TTCTTC-AATGATCTTCAA
849 T
1 T
850 AAATCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.29, C:0.21, G:0.03, T:0.47
Consensus pattern (18 bp):
TTCTTCAATGATCTTCAA
Found at i:2751 original size:26 final size:27
Alignment explanation
Indices: 2722--2783 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 27
2712 GTAAAATGAT
*
2722 AAATTGTAATTAAATTCAA-AGAGTAA
1 AAATAGTAATTAAATTCAAGAGAGTAA
*
2748 AAATAGTGATTAAATTCAAGAGAGT-A
1 AAATAGTAATTAAATTCAAGAGAGTAA
2774 AAATAGTAAT
1 AAATAGTAAT
2784 CAGTAAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 27 0.84
27 5 0.16
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.29
Consensus pattern (27 bp):
AAATAGTAATTAAATTCAAGAGAGTAA
Found at i:2795 original size:22 final size:22
Alignment explanation
Indices: 2768--3013 Score: 71
Period size: 22 Copynumber: 11.0 Consensus size: 22
2758 TAAATTCAAG
2768 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
* *
2790 AGAGTAAAATGGTGAA-GAGTAA
1 AGAGTAAAATAGT-AATCAGTAA
* * *
2812 AGAGTAATA-AGTAA-AAGAAGA
1 AGAGTAAAATAGTAATCAGTA-A
***
2833 ACG-GTAAAA-AGTAAAGGGTAA
1 A-GAGTAAAATAGTAATCAGTAA
** *
2854 TCAGTAAAAAGA-TAATCAGTAA
1 AGAGT-AAAATAGTAATCAGTAA
*
2876 AGAGTAAAATAGTAA-AAGGTAA
1 AGAGTAAAATAGTAATCA-GTAA
** * *
2898 TCAGTAAAAAAGTAATGA-TAA
1 AGAGTAAAATAGTAATCAGTAA
** * *
2919 TCAGTAAAAGGTAAAATAGTAATCAGT-A
1 AGAGTAAAA--T--AGTA--AT-CAGTAA
* * *
2947 AGAGCAAAATGGTGATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
* *
2969 A-AGCAAAAATGGTAATCAGTAA
1 AGAG-TAAAATAGTAATCAGTAA
*
2991 AGAGTAAGATAGTAATCAGTAA
1 AGAGTAAAATAGTAATCAGTAA
3013 A
1 A
3014 AGGTAACCAG
Statistics
Matches: 164, Mismatches: 39, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
20 5 0.03
21 41 0.25
22 97 0.59
23 6 0.04
24 1 0.01
25 3 0.02
26 1 0.01
27 1 0.01
28 8 0.05
29 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.20
Consensus pattern (22 bp):
AGAGTAAAATAGTAATCAGTAA
Found at i:2875 original size:29 final size:28
Alignment explanation
Indices: 2842--2905 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
2832 AACGGTAAAA
*
2842 AGTAAAGGGT-AATCAGTAAAAAGATAATC
1 AGTAAAGAGTAAAT-AGT-AAAAGATAATC
*
2871 AGTAAAGAGTAAAATAGTAAAAGGTAATC
1 AGTAAAGAGT-AAATAGTAAAAGATAATC
2900 AGTAAA
1 AGTAAA
2906 AAAGTAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 25 0.81
30 3 0.10
31 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (28 bp):
AGTAAAGAGTAAATAGTAAAAGATAATC
Found at i:2912 original size:15 final size:14
Alignment explanation
Indices: 2850--2913 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 14
2840 AAAGTAAAGG
2850 GTAATCAGTAAAAA
1 GTAATCAGTAAAAA
*
2864 GATAATCAGTAAAGA
1 G-TAATCAGTAAAAA
*
2879 GTAAAAT-AGTAAAAG
1 GT--AATCAGTAAAAA
2894 GTAATCAGTAAAAAA
1 GTAATCAGT-AAAAA
2909 GTAAT
1 GTAAT
2914 GATAATCAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
13 3 0.07
14 5 0.12
15 30 0.73
16 3 0.07
ACGTcount: A:0.56, C:0.05, G:0.17, T:0.22
Consensus pattern (14 bp):
GTAATCAGTAAAAA
Found at i:2947 original size:15 final size:15
Alignment explanation
Indices: 2850--2947 Score: 50
Period size: 15 Copynumber: 6.7 Consensus size: 15
2840 AAAGTAAAGG
2850 GTAATCAGTAAAA-A
1 GTAATCAGTAAAATA
2864 GATAATCAGTAAAGAGTA
1 G-TAATCAGTAAA-A-TA
* *
2882 -AAAT-AGTAAAA-G
1 GTAATCAGTAAAATA
*
2894 GTAATCAGTAAAAAA
1 GTAATCAGTAAAATA
*
2909 GTAAT--G-ATAATCA
1 GTAATCAGTAAAAT-A
*
2922 GTAA-AAGGTAAAATA
1 GTAATCA-GTAAAATA
2937 GTAATCAGTAA
1 GTAATCAGTAA
2948 GAGCAAAATG
Statistics
Matches: 63, Mismatches: 8, Indels: 25
0.66 0.08 0.26
Matches are distributed among these distances:
12 3 0.05
13 9 0.14
14 9 0.14
15 32 0.51
16 9 0.14
18 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.22
Consensus pattern (15 bp):
GTAATCAGTAAAATA
Found at i:2947 original size:65 final size:66
Alignment explanation
Indices: 2851--3015 Score: 162
Period size: 65 Copynumber: 2.5 Consensus size: 66
2841 AAGTAAAGGG
* * ** * * *
2851 TAATCAGTAAAAAG-ATAATCAGTAAAGAGTAAAATAGTAAAA-GGTAATCAGTAAAA-AAGTAA
1 TAATCAGTAAAAGGTAAAAT-AGTAATCAGTAAAAGAGCAAAATGGTAATCAGTAAAACAA-AAA
2913 TGA
64 TGA
*
2916 TAATCAGTAAAAGGTAAAATAGTAATCAGT--AAGAGCAAAATGGTGATCAGTAAAAGCAAAAAT
1 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAAGAGCAAAATGGTAATCAGTAAAA-CAAAAAT
*
2979 GG
65 GA
*
2981 TAATCAGT-AAAGAGTAAGATAGTAATCAGTAAAAG
1 TAATCAGTAAAAG-GTAAAATAGTAATCAGTAAAAG
3016 GTAACCAGTA
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
63 8 0.10
64 17 0.20
65 49 0.59
66 6 0.07
67 3 0.04
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.21
Consensus pattern (66 bp):
TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAAGAGCAAAATGGTAATCAGTAAAACAAAAATG
A
Found at i:2964 original size:21 final size:21
Alignment explanation
Indices: 2886--3110 Score: 116
Period size: 21 Copynumber: 11.0 Consensus size: 21
2876 AGAGTAAAAT
2886 AGTAAAA-GGTAATCAGTAA-
1 AGTAAAATGGTAATCAGTAAG
* * *
2905 A-AAAGTAATGATAATCAGTAAA
1 AGTAA--AATGGTAATCAGTAAG
*
2927 AGGTAAAATAGTAATCAGTAAG
1 A-GTAAAATGGTAATCAGTAAG
* * *
2949 AGCAAAATGGTGATCAGTAAA
1 AGTAAAATGGTAATCAGTAAG
*
2970 AGCAAAAATGGTAATCAGTAAAG
1 AG-TAAAATGGTAATCAGT-AAG
* * *
2993 AGTAAGATAGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAG
* *
3014 AGGTAACCA--GTAA-GAGT---
1 A-GTAA-AATGGTAATCAGTAAG
*
3031 A---AAATAGTAATCAGTAAG
1 AGTAAAATGGTAATCAGTAAG
* * *
3049 AGCAAAGTGGTAATTAGTAAG
1 AGTAAAATGGTAATCAGTAAG
*
3070 AGTAAAATAGTAATCAGTAAAG
1 AGTAAAATGGTAATCAGT-AAG
*
3092 AGTAAAA-GGTGATCAGTAA
1 AGTAAAATGGTAATCAGTAA
3111 TTCAAAGAGT
Statistics
Matches: 156, Mismatches: 30, Indels: 39
0.69 0.13 0.17
Matches are distributed among these distances:
12 1 0.01
13 1 0.01
14 4 0.03
15 3 0.02
17 1 0.01
18 3 0.02
19 1 0.01
20 7 0.04
21 72 0.46
22 56 0.36
23 5 0.03
24 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.21
Consensus pattern (21 bp):
AGTAAAATGGTAATCAGTAAG
Found at i:2965 original size:43 final size:44
Alignment explanation
Indices: 2916--3019 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 44
2906 AAAGTAATGA
*
2916 TAATCAGTAAAAGGTAAAATAGTAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAATAG
* ** * * *
2959 TGATCAGTAAAAGCAAAAATGGTAATCAGTAAAGAGTAAGATAG
1 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAATAG
3003 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
3020 CCAGTAAGAG
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 26 0.52
44 24 0.48
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (44 bp):
TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAATAG
Found at i:3019 original size:22 final size:22
Alignment explanation
Indices: 2916--3019 Score: 113
Period size: 22 Copynumber: 4.8 Consensus size: 22
2906 AAAGTAATGA
2916 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
2938 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* ** *
2959 TGATCAGTAAAAGCAAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
*
2981 TAATCAGT-AAAGAGTAAGATAG
1 TAATCAGTAAAAG-GTAAAATAG
3003 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
3020 CCAGTAAGAG
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.31
22 42 0.63
23 4 0.06
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:3038 original size:35 final size:36
Alignment explanation
Indices: 2974--3090 Score: 137
Period size: 42 Copynumber: 3.1 Consensus size: 36
2964 AGTAAAAGCA
*
2974 AAAATGGTAATCAGTAAAGAGTAAGATAGTAATCAGT
1 AAAATGGTAATCAGT-AAGAGTAAAATAGTAATCAGT
*
3011 AAAA-GGTAACCAGTAAGAGTAAAATAGTAATCAGT
1 AAAATGGTAATCAGTAAGAGTAAAATAGTAATCAGT
*
3046 AAGAGCAAAGTGGTAATTAGTAAGAGTAAAATAGTAATCAGT
1 ---A--AAA-TGGTAATCAGTAAGAGTAAAATAGTAATCAGT
3088 AAA
1 AAA
3091 GAGTAAAAGG
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
35 20 0.29
36 9 0.13
37 6 0.09
38 1 0.01
39 1 0.01
40 3 0.04
42 29 0.42
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.22
Consensus pattern (36 bp):
AAAATGGTAATCAGTAAGAGTAAAATAGTAATCAGT
Found at i:3047 original size:42 final size:41
Alignment explanation
Indices: 3008--3110 Score: 143
Period size: 42 Copynumber: 2.5 Consensus size: 41
2998 GATAGTAATC
*
3008 AGTAAAAGGTAACCAGTAAGAGTAAAATAGTAATCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCAGTAAG
* * *
3049 AGCAAAGTGGTAATTAGTAAGAGTAAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAATAGTAATCAGT-AAG
*
3092 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
3111 TTCAAAGAGT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
41 5 0.10
42 39 0.75
43 8 0.15
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.21
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCAGTAAG
Found at i:3185 original size:35 final size:35
Alignment explanation
Indices: 3114--3194 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
3104 TCAGTAATTC
* * *
3114 AAAGAGTAAAATGGTAGTCAGTATAAGAAAAAAAG
1 AAAGAGTAAAATGGTAATCAATAAAAGAAAAAAAG
* **
3149 -AAGAGTAAAAGTGGTAATCAATAAAAGAGAGTAAG
1 AAAGAGTAAAA-TGGTAATCAATAAAAGAAAAAAAG
3184 AAAAGAGTAAA
1 -AAAGAGTAAA
3195 TTAATAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
34 10 0.27
35 18 0.49
37 9 0.24
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.16
Consensus pattern (35 bp):
AAAGAGTAAAATGGTAATCAATAAAAGAAAAAAAG
Found at i:3237 original size:27 final size:28
Alignment explanation
Indices: 3172--3249 Score: 131
Period size: 27 Copynumber: 2.8 Consensus size: 28
3162 GTAATCAATA
3172 AAAGAGAGTAAGAAAAGAGTAAATTAAT
1 AAAGAGAGTAAGAAAAGAGTAAATTAAT
* *
3200 AAAGAGTGTAAGAAAAGAGTAAA-TAGT
1 AAAGAGAGTAAGAAAAGAGTAAATTAAT
3227 AAAGAGAGTAAGAAAAGAGTAAA
1 AAAGAGAGTAAGAAAAGAGTAAA
3250 AATGATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 25 0.53
28 22 0.47
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.15
Consensus pattern (28 bp):
AAAGAGAGTAAGAAAAGAGTAAATTAAT
Found at i:3292 original size:24 final size:23
Alignment explanation
Indices: 3239--3292 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
3229 AGAGAGTAAG
*
3239 AAAAGAGTAAAAATGATAAAAGT
1 AAAAAAGTAAAAATGATAAAAGT
* * *
3262 AGTAAAAGTAAAAATGGTAATCAGT
1 A-AAAAAGTAAAAATGATAA-AAGT
3287 AAAAAA
1 AAAAAA
3293 AGGATAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.79
25 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.17, T:0.19
Consensus pattern (23 bp):
AAAAAAGTAAAAATGATAAAAGT
Found at i:3324 original size:17 final size:17
Alignment explanation
Indices: 3271--3326 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
3261 TAGTAAAAGT
*
3271 AAAAATGGTAATCAGTA
1 AAAAATGGTAATTAGTA
*
3288 AAAAAAGGATAATTAGTA
1 AAAAATGG-TAATTAGTA
* *
3306 AAAAATGGTAGTTAATA
1 AAAAATGGTAATTAGTA
3323 AAAA
1 AAAA
3327 TGAGAGAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.59, C:0.02, G:0.16, T:0.23
Consensus pattern (17 bp):
AAAAATGGTAATTAGTA
Found at i:15465 original size:18 final size:18
Alignment explanation
Indices: 15451--15486 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
15441 ATCAGCATAT
15451 GACATTACATTAGCATTC
1 GACATTACATTAGCATTC
* *
15469 GACATTGCATTATCATTC
1 GACATTACATTAGCATTC
15487 TAACCCGCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (18 bp):
GACATTACATTAGCATTC
Found at i:18116 original size:82 final size:82
Alignment explanation
Indices: 17979--18151 Score: 206
Period size: 82 Copynumber: 2.1 Consensus size: 82
17969 CATTTAATTT
*
17979 GGTCCCTGTTTTAGATCAATTAGGTCCAAAAGTTAATAACTTTACTCTTTTAAATACATAAACCC
1 GGTCCCTGTTTTAGATCAATTAGGTCCAAAAGTTAATAACTTTACTCATTTAAATACATAAACCC
18044 TGTTCCATTTTCAATAA
66 TGTTCCATTTTCAATAA
* * * * ** **
18061 GGTCCCTGTTTTAGGTCAATTCGG-CTCGACAGTTAACTAA-TTTGGTCATTTAAATACATAATT
1 GGTCCCTGTTTTAGATCAATTAGGTC-CAAAAGTTAA-TAACTTTACTCATTTAAATACATAAAC
*
18124 TCTGTTCCATTTTCAATAA
64 CCTGTTCCATTTTCAATAA
* *
18143 AGCCCCTGT
1 GGTCCCTGT
18152 ATCGATTTGA
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 1 0.01
82 73 0.95
83 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (82 bp):
GGTCCCTGTTTTAGATCAATTAGGTCCAAAAGTTAATAACTTTACTCATTTAAATACATAAACCC
TGTTCCATTTTCAATAA
Found at i:19219 original size:37 final size:38
Alignment explanation
Indices: 19176--19316 Score: 130
Period size: 37 Copynumber: 3.7 Consensus size: 38
19166 GAAAAGAAAT
19176 TAATCAGTAAATTGA-TAATTAAGAGTCAAGATAATAG
1 TAATCAGTAAATTGAGTAATTAAGAGTCAAGATAATAG
* * * * *
19213 TGATCAGTAAAGTCAGTAATCAAGAGTCAAGGTAAAAATAG
1 TAATCAGTAAATTGAGTAATTAAGAGTCAA-G--ATAATAG
* * *
19254 TAATCAGTAAATTGA-TAATGAAAAGTCAA-AGTGAT-G
1 TAATCAGTAAATTGAGTAATTAAGAGTCAAGA-TAATAG
19290 ATAATCAGTAAATT-AGTAATTAAGAGT
1 -TAATCAGTAAATTGAGTAATTAAGAGT
19317 GAGTGATTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 14
0.75 0.13 0.13
Matches are distributed among these distances:
36 3 0.04
37 36 0.43
38 13 0.16
39 1 0.01
40 12 0.14
41 18 0.22
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (38 bp):
TAATCAGTAAATTGAGTAATTAAGAGTCAAGATAATAG
Found at i:19717 original size:26 final size:26
Alignment explanation
Indices: 19688--19738 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
19678 ATAAATGGTA
19688 ATTAAATTCAA-AGAGTAAAAATAGTG
1 ATTAAATTCAAGAGAGT-AAAATAGTG
19714 ATTAAATTCAAGAGAGTAAAATAGT
1 ATTAAATTCAAGAGAGTAAAATAGT
19739 AATCAGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTG
Found at i:19753 original size:22 final size:22
Alignment explanation
Indices: 19726--19776 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
19716 TAAATTCAAG
19726 AGAGTAAAATAGT-AATCAGTAA
1 AGAGTAAAATAGTGAA-CAGTAA
* *
19748 AGAGTAAAATGGTGAAGAGTAA
1 AGAGTAAAATAGTGAACAGTAA
19770 AGAGTAA
1 AGAGTAA
19777 TAAGTAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 24 0.92
23 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.20
Consensus pattern (22 bp):
AGAGTAAAATAGTGAACAGTAA
Found at i:19855 original size:22 final size:21
Alignment explanation
Indices: 19726--19870 Score: 57
Period size: 22 Copynumber: 6.7 Consensus size: 21
19716 TAAATTCAAG
*
19726 AGAGTAAAATAGTAATCA-GTAA
1 AGAGTAAAA-AGTAA-AAGGTAA
* *
19748 AGAGTAAAATGGT-GAAGAGTAA
1 AGAGTAAAA-AGTAAAAG-GTAA
*
19770 AGAGTAATAAGTAAAAGAAG-AA
1 AGAGTAAAAAGTAAAAG--GTAA
* *
19792 CG-GTAAAAAGTAAAGGGTAA
1 AGAGTAAAAAGTAAAAGGTAA
** **
19812 TCAGTAAAAAGATACTCA-GTAA
1 AGAGTAAAAAG-TA-AAAGGTAA
19834 AGAGTAAAATAGTAAAAGGTAA
1 AGAGTAAAA-AGTAAAAGGTAA
**
19856 TCAGTAAAAAAGTAA
1 AGAGT-AAAAAGTAA
19871 TGATAATCAG
Statistics
Matches: 92, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 23 0.25
22 57 0.62
23 8 0.09
ACGTcount: A:0.55, C:0.04, G:0.22, T:0.19
Consensus pattern (21 bp):
AGAGTAAAAAGTAAAAGGTAA
Found at i:19865 original size:15 final size:15
Alignment explanation
Indices: 19807--19871 Score: 55
Period size: 15 Copynumber: 4.4 Consensus size: 15
19797 AAAAGTAAAG
19807 GGTAATCAGTAAAAA
1 GGTAATCAGTAAAAA
* * *
19822 GATACTCAGTAAAGA
1 GGTAATCAGTAAAAA
19837 -GTAAAAT-AGT-AAAA
1 GGT--AATCAGTAAAAA
19851 GGTAATCAGTAAAAA
1 GGTAATCAGTAAAAA
*
19866 AGTAAT
1 GGTAAT
19872 GATAATCAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
13 3 0.08
14 7 0.18
15 26 0.68
16 2 0.05
ACGTcount: A:0.54, C:0.06, G:0.18, T:0.22
Consensus pattern (15 bp):
GGTAATCAGTAAAAA
Found at i:19898 original size:65 final size:66
Alignment explanation
Indices: 19836--19973 Score: 169
Period size: 65 Copynumber: 2.1 Consensus size: 66
19826 CTCAGTAAAG
* * *
19836 AGTAAAATAGTAAAA-GGTAATCAGTAAAA-AAGTAATGATAATCAGTAAA-AGGTAAAATAGTA
1 AGTAAAAGAGCAAAATGGTAATCAGTAAAACAA-AAATGATAATCAGTAAAGA-GTAAAATAGTA
19898 ATC
64 ATC
* *
19901 AGT--AAGAGCAAAATGGTGATCAGTAAAAGCAAAAATGGTAATCAGTAAAGAGTAAAATAGTAA
1 AGTAAAAGAGCAAAATGGTAATCAGTAAAA-CAAAAATGATAATCAGTAAAGAGTAAAATAGTAA
19964 TC
65 TC
19966 AGTAAAAG
1 AGTAAAAG
19974 GTAACCAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
63 8 0.13
64 13 0.21
65 35 0.56
66 3 0.05
67 3 0.05
ACGTcount: A:0.54, C:0.06, G:0.20, T:0.21
Consensus pattern (66 bp):
AGTAAAAGAGCAAAATGGTAATCAGTAAAACAAAAATGATAATCAGTAAAGAGTAAAATAGTAAT
C
Found at i:19902 original size:22 final size:22
Alignment explanation
Indices: 19874--19977 Score: 122
Period size: 22 Copynumber: 4.8 Consensus size: 22
19864 AAAGTAATGA
19874 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
19896 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* ** *
19917 TGATCAGTAAAAGCAAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
19939 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
19961 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
19978 CCAGTAAGAG
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.31
22 43 0.63
23 4 0.06
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:19922 original size:21 final size:21
Alignment explanation
Indices: 19844--20068 Score: 125
Period size: 21 Copynumber: 11.0 Consensus size: 21
19834 AGAGTAAAAT
19844 AGTAAAA-GGTAATCAGTAA-
1 AGTAAAATGGTAATCAGTAAG
* * *
19863 A-AAAGTAATGATAATCAGTAAA
1 AGTAA--AATGGTAATCAGTAAG
*
19885 AGGTAAAATAGTAATCAGTAAG
1 A-GTAAAATGGTAATCAGTAAG
* * *
19907 AGCAAAATGGTGATCAGTAAA
1 AGTAAAATGGTAATCAGTAAG
*
19928 AGCAAAAATGGTAATCAGTAAAG
1 AG-TAAAATGGTAATCAGT-AAG
* *
19951 AGTAAAATAGTAATCAGTAAA
1 AGTAAAATGGTAATCAGTAAG
* *
19972 AGGTAACCA--GTAA-GAGT---
1 A-GTAA-AATGGTAATCAGTAAG
*
19989 A---AAATAGTAATCAGTAAG
1 AGTAAAATGGTAATCAGTAAG
* * *
20007 AGCAAAGTGGTAATTAGTAAG
1 AGTAAAATGGTAATCAGTAAG
*
20028 AGTAAAATAGTAATCAGTAAAG
1 AGTAAAATGGTAATCAGT-AAG
*
20050 AGTAAAA-GGTGATCAGTAA
1 AGTAAAATGGTAATCAGTAA
20069 TTCAAAGAGT
Statistics
Matches: 157, Mismatches: 29, Indels: 39
0.70 0.13 0.17
Matches are distributed among these distances:
12 1 0.01
13 1 0.01
14 4 0.03
15 3 0.02
17 1 0.01
18 3 0.02
19 1 0.01
20 7 0.04
21 72 0.46
22 57 0.36
23 5 0.03
24 2 0.01
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.21
Consensus pattern (21 bp):
AGTAAAATGGTAATCAGTAAG
Found at i:19923 original size:43 final size:44
Alignment explanation
Indices: 19874--19977 Score: 147
Period size: 43 Copynumber: 2.4 Consensus size: 44
19864 AAAGTAATGA
*
19874 TAATCAGTAAAAGGTAAAATAGTAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAATAG
* ** * *
19917 TGATCAGTAAAAGCAAAAATGGTAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAATAG
19961 TAATCAGTAAAAGGTAA
1 TAATCAGTAAAAGGTAA
19978 CCAGTAAGAG
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
43 26 0.51
44 25 0.49
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (44 bp):
TAATCAGTAAAAGGTAAAATAGTAATCAGTAAAGAGCAAAATAG
Found at i:20005 original size:42 final size:41
Alignment explanation
Indices: 19844--20068 Score: 180
Period size: 42 Copynumber: 5.5 Consensus size: 41
19834 AGAGTAAAAT
* *
19844 AGTAAAAGGTAATCAGTAA-A--AAAGTAATGATAATCAGTAAA
1 AGTAAAAGGTAATCAGTAAGAGTAAAAT-A-G-TAATCAGTAAG
* * * * *
19885 AGGTAAAATAGTAATCAGTAAGAGCAAAATGGTGATCAGTAAA
1 A-GTAAAA-GGTAATCAGTAAGAGTAAAATAGTAATCAGTAAG
*
19928 AGCAAAAATGGTAATCAGTAAAGAGTAAAATAGTAATC------
1 AG-TAAAA-GGTAATCAGT-AAGAGTAAAATAGTAATCAGTAAG
*
19966 AGTAAAAGGTAACCAGTAAGAGTAAAATAGTAATCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCAGTAAG
* * *
20007 AGCAAAGTGGTAATTAGTAAGAGTAAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAATAGTAATCAGT-AAG
*
20050 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
20069 TTCAAAGAGT
Statistics
Matches: 150, Mismatches: 19, Indels: 29
0.76 0.10 0.15
Matches are distributed among these distances:
35 18 0.12
36 9 0.06
37 4 0.03
38 2 0.01
41 6 0.04
42 46 0.31
43 44 0.29
44 17 0.11
46 4 0.03
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.21
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATCAGTAAG
Found at i:20143 original size:35 final size:35
Alignment explanation
Indices: 20072--20152 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 35
20062 TCAGTAATTC
* * *
20072 AAAGAGTAAAATGGTAGTCAGTATAAGAAAAAAAG
1 AAAGAGTAAAATGGTAATCAATAAAAGAAAAAAAG
* **
20107 -AAGAGTAAAAGTGGTAATCAATAAAAGAGAGTAAG
1 AAAGAGTAAAA-TGGTAATCAATAAAAGAAAAAAAG
20142 AAAAGAGTAAA
1 -AAAGAGTAAA
20153 TTAATAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
34 10 0.27
35 18 0.49
37 9 0.24
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.16
Consensus pattern (35 bp):
AAAGAGTAAAATGGTAATCAATAAAAGAAAAAAAG
Found at i:20145 original size:29 final size:28
Alignment explanation
Indices: 20122--20181 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
20112 TAAAAGTGGT
20122 AATCAATAAAAGAGAGTAAGAAAAGAGTA
1 AATCAAT-AAAGAGAGTAAGAAAAGAGTA
* *
20151 AATTAATAAAGAGTGTAAGAAAAGAGTA
1 AATCAATAAAGAGAGTAAGAAAAGAGTA
20179 AAT
1 AAT
20182 AGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.60, C:0.02, G:0.20, T:0.18
Consensus pattern (28 bp):
AATCAATAAAGAGAGTAAGAAAAGAGTA
Done.