Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_198 ID=scaffold_198-JGI_221_v2.0
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: 11942
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.25
Warning! 2487 characters in sequence are not A, C, G, or T
Found at i:816 original size:38 final size:38
Alignment explanation
Indices: 765--850 Score: 163
Period size: 38 Copynumber: 2.3 Consensus size: 38
755 AGATAATCCT
765 GTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCA
1 GTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCA
*
803 GTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCT
1 GTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCA
841 GTCATTTATC
1 GTCATTTATC
851 ATTACAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.47
Consensus pattern (38 bp):
GTCATTTATCCGGTTTGTTTGAATAATTTCAACTTCCA
Found at i:1245 original size:33 final size:33
Alignment explanation
Indices: 1208--1270 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1198 GAACTTTAAG
**
1208 TTGGTTATATTTTTTTTGTATAGTTTAATTTTT
1 TTGGTTATATTTTAGTTGTATAGTTTAATTTTT
1241 TTGGTTATATTTTAGTTGTATAGTTTAATT
1 TTGGTTATATTTTAGTTGTATAGTTTAATT
1271 ATTATTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.65
Consensus pattern (33 bp):
TTGGTTATATTTTAGTTGTATAGTTTAATTTTT
Found at i:2907 original size:34 final size:33
Alignment explanation
Indices: 2864--3107 Score: 163
Period size: 34 Copynumber: 7.4 Consensus size: 33
2854 AACTTACAAC
** *
2864 TTACATAACTTACTTTTTTTTAATTATTCATAAA
1 TTACATAACTTACTTTAATTAAATTA-TCATAAA
* **
2898 TTACATAACTTACATTAATGCAA-TA-CATAAA
1 TTACATAACTTACTTTAATTAAATTATCATAAA
*
2929 TTACATAACTTA-TTTAATTAATATTATACATAAC
1 TTACATAACTTACTTTAATTAA-ATTAT-CATAAA
2963 TTACATAACTTACATAACTTACATTAATATTATACATAAA
1 TTACATAACTTAC-T---TTA-ATTAA-ATTAT-CATAAA
*
3003 TTACATAACTTA-ATTAA-T--A-TA-CATAAA
1 TTACATAACTTACTTTAATTAAATTATCATAAA
* *
3030 TTACATAACTTACATTAA-T--GTTATACATAAA
1 TTACATAACTTACTTTAATTAAATTAT-CATAAA
* * *
3061 TTACATAACTTA-GTTAATTCATATTATACATAAC
1 TTACATAACTTACTTTAATT-AAATTAT-CATAAA
3095 TTACATAACTTAC
1 TTACATAACTTAC
3108 AACTTACATA
Statistics
Matches: 176, Mismatches: 15, Indels: 37
0.77 0.07 0.16
Matches are distributed among these distances:
27 18 0.10
28 6 0.03
29 4 0.02
30 11 0.06
31 38 0.22
32 2 0.01
33 3 0.02
34 58 0.33
35 3 0.02
36 1 0.01
39 3 0.02
40 29 0.16
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.41
Consensus pattern (33 bp):
TTACATAACTTACTTTAATTAAATTATCATAAA
Found at i:2910 original size:9 final size:9
Alignment explanation
Indices: 2892--3313 Score: 196
Period size: 9 Copynumber: 48.0 Consensus size: 9
2882 TTTAATTATT
*
2892 CATAAATTA
1 CATAACTTA
2901 CATAACTTA
1 CATAACTTA
*
2910 CATTAATGCAATA
1 CA-TAA--C-TTA
*
2923 CATAAATTA
1 CATAACTTA
2932 CATAACTTA
1 CATAACTTA
**
2941 TTTAA-TTA
1 CATAACTTA
*
2949 -AT-ATTATA
1 CATAACT-TA
2957 CATAACTTA
1 CATAACTTA
2966 CATAACTTA
1 CATAACTTA
2975 CATAACTTA
1 CATAACTTA
*
2984 CATTAATATTATA
1 CA-T-A-ACT-TA
*
2997 CATAAATTA
1 CATAACTTA
3006 CATAACTTA
1 CATAACTTA
3015 -ATTAA-TATA
1 CA-TAACT-TA
*
3024 CATAAATTA
1 CATAACTTA
3033 CATAACTTA
1 CATAACTTA
*
3042 CATTAATGTTATA
1 CA-TAA--CT-TA
*
3055 CATAAATTA
1 CATAACTTA
3064 CATAACTTA
1 CATAACTTA
**
3073 GTTAA-TT-
1 CATAACTTA
*
3080 CAT-ATTATA
1 CATAACT-TA
3089 CATAACTTA
1 CATAACTTA
3098 CATAACTTA
1 CATAACTTA
3107 C--AACTTA
1 CATAACTTA
3114 CATAACTTA
1 CATAACTTA
***
3123 CATGTTTTTA
1 CAT-AACTTA
*
3133 -ATTA-TT-
1 CATAACTTA
*
3139 CATAAATTA
1 CATAACTTA
3148 CATAACTTA
1 CATAACTTA
* * *
3157 CTTAATTTT
1 CATAACTTA
3166 CATAA--TA
1 CATAACTTA
*
3173 AATAACTTA
1 CATAACTTA
3182 CATAACTTA
1 CATAACTTA
3191 CATAACTTA
1 CATAACTTA
3200 CATAA--TA
1 CATAACTTA
3207 CATAACTTA
1 CATAACTTA
* *
3216 TATGACTTA
1 CATAACTTA
3225 CATAACTTA
1 CATAACTTA
*
3234 CAT-A---G
1 CATAACTTA
* *
3239 CATAATTTT
1 CATAACTTA
3248 CATAA--TA
1 CATAACTTA
* *
3255 CACAACTGA
1 CATAACTTA
* *
3264 CATAATTTT
1 CATAACTTA
3273 CATAA--TA
1 CATAACTTA
*
3280 AATAACTTA
1 CATAACTTA
3289 CATAA--TA
1 CATAACTTA
3296 CATAACTTA
1 CATAACTTA
*
3305 CATAGCTTA
1 CATAACTTA
3314 ATTATACTTA
Statistics
Matches: 318, Mismatches: 51, Indels: 88
0.70 0.11 0.19
Matches are distributed among these distances:
5 3 0.01
6 3 0.01
7 45 0.14
8 14 0.04
9 209 0.66
10 19 0.06
11 2 0.01
12 11 0.03
13 12 0.04
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (9 bp):
CATAACTTA
Found at i:2968 original size:65 final size:64
Alignment explanation
Indices: 2864--3108 Score: 255
Period size: 65 Copynumber: 3.8 Consensus size: 64
2854 AACTTACAAC
** * *
2864 TTACATAACTTACTTTTTTTTA-ATTATTCATAAATTACATAACTTACATTAATGCAATACATAA
1 TTACATAACTTA-TTTAATTAATATTATACATAAATTACATAACTTACATTAATGC-ATACATAA
2928 A
64 A
* *
2929 TTACATAACTTATTTAATTAATATTATACATAACTTACATAACTTACA-TAA--CTTACATTAAT
1 TTACATAACTTATTTAATTAATATTATACATAAATTACATAACTTACATTAATGCATACA-TAA-
2991 A
64 A
* ** * *
2992 TTATACATAAATTACATAACTTAATTAATATACATAAATTACATAACTTACATTAATGTTATACA
1 -T-TACATAACTTATTTAA-TTAA-TATTATACATAAATTACATAACTTACATTAATG-CATACA
3057 TAAA
61 TAAA
* * *
3061 TTACATAACTTAGTTAATTCATATTATACATAACTTACATAACTTACA
1 TTACATAACTTATTTAATTAATATTATACATAAATTACATAACTTACA
3109 ACTTACATAA
Statistics
Matches: 150, Mismatches: 19, Indels: 22
0.79 0.10 0.12
Matches are distributed among these distances:
61 4 0.03
62 4 0.03
63 1 0.01
64 10 0.07
65 74 0.49
66 7 0.05
67 38 0.25
68 4 0.03
69 1 0.01
70 3 0.02
71 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (64 bp):
TTACATAACTTATTTAATTAATATTATACATAAATTACATAACTTACATTAATGCATACATAAA
Found at i:2982 original size:74 final size:76
Alignment explanation
Indices: 2892--3044 Score: 222
Period size: 74 Copynumber: 2.0 Consensus size: 76
2882 TTTAATTATT
* * *
2892 CATAAATTACATAACTTACATTAATGCAATACATAAATTACATAACTTATTTAAT-TA-AT-ATT
1 CATAAATTACATAACTTACATTAATACAATACATAAATTACATAACTTAATTAATATACATAAAT
2954 ATACATAACTTA
66 -TACATAACTTA
* **
2966 CATAACTTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAATATACATAAAT
1 CATAAATTACATAACTTACATTAATACAATACATAAATTACATAACTTAATTAATATACATAAAT
3031 TACATAACTTA
66 TACATAACTTA
3042 CAT
1 CAT
3045 TAATGTTATA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
74 50 0.71
75 2 0.03
76 16 0.23
77 2 0.03
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.37
Consensus pattern (76 bp):
CATAAATTACATAACTTACATTAATACAATACATAAATTACATAACTTAATTAATATACATAAAT
TACATAACTTA
Found at i:3000 original size:40 final size:40
Alignment explanation
Indices: 2921--3044 Score: 134
Period size: 40 Copynumber: 3.1 Consensus size: 40
2911 ATTAATGCAA
* *
2921 TACATAAATTACATAACTTATTTAATTAATATTATACATAACT
1 TACATAACTTACATAACTTA---CATTAATATTATACATAACT
*
2964 TACATAACTTACATAACTTACATTAATATTATACATAAAT
1 TACATAACTTACATAACTTACATTAATATTATACATAACT
3004 TACATAACTTA-ATTAA-TATACA-TAA-A-T-TACATAACT
1 TACATAACTTACA-TAACT-TACATTAATATTATACATAACT
3040 TACAT
1 TACAT
3045 TAATGTTATA
Statistics
Matches: 75, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
36 13 0.17
37 1 0.01
38 1 0.01
39 5 0.07
40 36 0.48
43 19 0.25
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.39
Consensus pattern (40 bp):
TACATAACTTACATAACTTACATTAATATTATACATAACT
Found at i:3034 original size:58 final size:57
Alignment explanation
Indices: 2963--3215 Score: 211
Period size: 58 Copynumber: 4.4 Consensus size: 57
2953 TATACATAAC
*
2963 TTACATAACTTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAA
1 TTACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAA
* *
3020 TATACATAAATTACATAACTTACATTAATGTTATACATAAATTACATAACTTAGTTAA
1 T-TACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAA
* ** * ***
3078 TT-CAT-ATTATACATAACTTACA-TAACTTACAACTTACATAACTTACATGTTTTTAATT-A
1 TTACATAAAT-TACATAACTTACATTAA--TATTA--TACATAAATTACAT-AACTTAATTAA
*
3137 TT-CATAAATTACATAACTTAC-TTAATTTTCATA-ATAAATAACTTACATAACTTACA-TAA
1 TTACATAAATTACATAACTTACATTAATATT-ATACAT--A-AA-TTACATAACTTA-ATTAA
3196 CTTACAT-AA-TACATAACTTA
1 -TTACATAAATTACATAACTTA
3216 TATGACTTAC
Statistics
Matches: 158, Mismatches: 20, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
55 7 0.04
56 18 0.11
57 6 0.04
58 60 0.38
59 53 0.34
60 11 0.07
61 3 0.02
ACGTcount: A:0.45, C:0.15, G:0.01, T:0.39
Consensus pattern (57 bp):
TTACATAAATTACATAACTTACATTAATATTATACATAAATTACATAACTTAATTAA
Found at i:3113 original size:16 final size:16
Alignment explanation
Indices: 3092--3124 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3082 TATTATACAT
3092 AACTTACATAACTTAC
1 AACTTACATAACTTAC
3108 AACTTACATAACTTAC
1 AACTTACATAACTTAC
3124 A
1 A
3125 TGTTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (16 bp):
AACTTACATAACTTAC
Found at i:3125 original size:34 final size:33
Alignment explanation
Indices: 3087--3237 Score: 117
Period size: 34 Copynumber: 4.5 Consensus size: 33
3077 ATTCATATTA
3087 TACATAACTTACATAACTTACAACTTACATAACT
1 TACATAACTTACATAA-TTACAACTTACATAACT
*** * * *
3121 TACATGTTTTTA-ATTATTCATAAATTACATAACT
1 TACAT-AACTTACATAATT-ACAACTTACATAACT
* * * * *
3155 TACTTAATTTTCATAATAAATAACTTACATAACT
1 TACATAACTTACATAAT-TACAACTTACATAACT
* *
3189 TACATAACTTACATAA-TACATAACTTATATGACT
1 TACATAACTTACATAATTAC--AACTTACATAACT
3223 TACATAACTTACATA
1 TACATAACTTACATA
3238 GCATAATTTT
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
32 1 0.01
33 5 0.05
34 82 0.90
35 3 0.03
ACGTcount: A:0.43, C:0.17, G:0.01, T:0.38
Consensus pattern (33 bp):
TACATAACTTACATAATTACAACTTACATAACT
Found at i:3180 original size:25 final size:28
Alignment explanation
Indices: 2966--3182 Score: 87
Period size: 31 Copynumber: 7.7 Consensus size: 28
2956 ACATAACTTA
* * *
2966 CATAACTTACATAACTTACATTAATATTATA
1 CATAAATTAAATAACTTAC-TT-A-ATTATT
* * *
2997 CATAAATTACATAACTTAATTAA-TATA
1 CATAAATTAAATAACTTACTTAATTATT
* *
3024 CATAAATTACATAACTTACATTAATGTTATA
1 CATAAATTAAATAACTTAC-TTAA--TTATT
* *
3055 CATAAATTACATAACTTAGTTAATTCATATTAT
1 CATAAATTAAATAACTTACTTAA-T--TA-T-T
* *
3088 ACATAACTTACATAACTTAC--AACTTA--
1 -CATAAATTAAATAACTTACTTAA-TTATT
* * * *
3114 CATAACTTACAT--GTT-TTTAATTATT
1 CATAAATTAAATAACTTACTTAATTATT
*
3139 CATAAATTACATAACTTACTTAATT-TT
1 CATAAATTAAATAACTTACTTAATTATT
3166 CAT-AA-TAAATAACTTAC
1 CATAAATTAAATAACTTAC
3183 ATAACTTACA
Statistics
Matches: 155, Mismatches: 15, Indels: 38
0.75 0.07 0.18
Matches are distributed among these distances:
23 5 0.03
24 2 0.01
25 34 0.22
26 2 0.01
27 29 0.19
28 11 0.07
29 2 0.01
30 8 0.05
31 41 0.26
32 4 0.03
34 17 0.11
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (28 bp):
CATAAATTAAATAACTTACTTAATTATT
Found at i:3194 original size:25 final size:25
Alignment explanation
Indices: 3146--3294 Score: 95
Period size: 25 Copynumber: 5.7 Consensus size: 25
3136 ATTCATAAAT
* *
3146 TACATAACTTACTTAATTTTCATAA
1 TACATAACTTACATAATTTACATAA
* *
3171 TAAATAACTTACATAACTTACATAA
1 TACATAACTTACATAATTTACATAA
* * *
3196 CTTACATAA--TACATAACTTATATGACT
1 --TACATAACTTACATAATTTACAT-A-A
*
3223 TACATAACTTACATAGCATAATTTTCATAA
1 TACATAAC-T---TA-CATAATTTACATAA
* * *
3253 TACACAACTGACATAATTTTCATAA
1 TACATAACTTACATAATTTACATAA
*
3278 TAAATAACTTACATAAT
1 TACATAACTTACATAAT
3295 ACATAACTTA
Statistics
Matches: 97, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
25 69 0.71
26 2 0.02
27 6 0.06
29 1 0.01
30 7 0.07
31 3 0.03
32 9 0.09
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (25 bp):
TACATAACTTACATAATTTACATAA
Found at i:9001 original size:66 final size:65
Alignment explanation
Indices: 8893--9058 Score: 174
Period size: 66 Copynumber: 2.5 Consensus size: 65
8883 GAGCAAATTA
* * * ** * *
8893 CACAACTTAAAGCGGAGGCATCATCGAGAGAAGCTGATGTTCAA-AAAAGATATGAAGAACTCCA
1 CACAACTTAAAGCAGATGCAGCAGAGAGAGAAGCTAAGGTTCAACAAAAG-TATGAAGAACTCCA
8957 G
65 G
* *
8958 CTACAACTTAAAGCAGATGCAGCAGAGAGAGAAGCTAAGGTTCAACGAAAGTATGAAGAACTCTA
1 C-ACAACTTAAAGCAGATGCAGCAGAGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCA
9023 G
65 G
* * *
9024 CAGCAGCTTAAAGTAGATGCGGCAGCA-AGAGAAGC
1 CA-CAACTTAAAGCAGATGCAGCAG-AGAGAGAAGC
9059 AGAGGCAGCA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
65 2 0.02
66 78 0.92
67 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCAGCAGAGAGAGAAGCTAAGGTTCAACAAAAGTATGAAGAACTCCAG
Found at i:9075 original size:21 final size:21
Alignment explanation
Indices: 9045--9150 Score: 117
Period size: 21 Copynumber: 5.1 Consensus size: 21
9035 AGTAGATGCG
*
9045 GCAGCAAGAGAAGCAGAGGCA
1 GCAGCGAGAGAAGCAGAGGCA
* * *
9066 GCAGCGAGAGAAGTACAGGCT
1 GCAGCGAGAGAAGCAGAGGCA
9087 GCAGCGAGAGAAGCAGAGGCTA
1 GCAGCGAGAGAAGCAGAGGC-A
* * *
9109 -AAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCA
*
9129 GCAGCGAGGGAAGCAGA-GCA
1 GCAGCGAGAGAAGCAGAGGCA
9149 GC
1 GC
9151 GTCAAAAGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.06
21 67 0.94
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.04
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCA
Found at i:9091 original size:42 final size:42
Alignment explanation
Indices: 9045--9150 Score: 135
Period size: 42 Copynumber: 2.5 Consensus size: 42
9035 AGTAGATGCG
* *
9045 GCAGCAAGAGAAGCAGAGGCAGCAGCGAGAGAAGTACAGGCT
1 GCAGCGAGAGAAGCAGAGGCAGCAGCGAGAGAAGCACAGGCT
* * *
9087 GCAGCGAGAGAAGCAGAGGCTA-AAGCGAGGGAAGCAGAGGCT
1 GCAGCGAGAGAAGCAGAGGC-AGCAGCGAGAGAAGCACAGGCT
*
9129 GCAGCGAGGGAAGCAGA-GCAGC
1 GCAGCGAGAGAAGCAGAGGCAGC
9151 GTCAAAAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 51 0.93
43 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.42, T:0.04
Consensus pattern (42 bp):
GCAGCGAGAGAAGCAGAGGCAGCAGCGAGAGAAGCACAGGCT
Found at i:9554 original size:43 final size:43
Alignment explanation
Indices: 9474--9769 Score: 152
Period size: 43 Copynumber: 6.9 Consensus size: 43
9464 GTTTTTCAAA
* * ** * *
9474 AAAAAAACGCCACTAAAGGTGTTGGCCTTTAGTGGCGTTTTCG
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
*
9517 AAAAAAGCGCCACTAAAGATCATGGTCTTTCGCGGCGTTTGT-G
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTT-TCG
*** * * * * * *
9560 GGGACAGCGCCGCTATAGATCAGGGTCTTTTGCGGCGTTTTAG
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
** * * * *
9603 GGAAAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGCTTGTCG
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCG-TTTTCG
* * * * *
9647 CAAAAAA--GCCACTAAAGACCCTGATCTTTAGCGACG-TTTCC
1 -AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
** * * ** * *
9688 ACTAAAGCGCCGCTAAAGACCATTATCTTTAGCGGCG-CTTCC
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
** * * * * *
9730 ACTAAAGCGCCGCTAAAGGTCTTAGTCTTCAGCGGCGTTT
1 AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTT
9770 GTGCTAGAAG
Statistics
Matches: 201, Mismatches: 45, Indels: 14
0.77 0.17 0.05
Matches are distributed among these distances:
40 4 0.02
41 3 0.01
42 61 0.30
43 124 0.62
44 5 0.02
45 4 0.02
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (43 bp):
AAAAAAGCGCCACTAAAGATCATGGTCTTTAGCGGCGTTTTCG
Found at i:9717 original size:42 final size:42
Alignment explanation
Indices: 9606--9747 Score: 171
Period size: 42 Copynumber: 3.4 Consensus size: 42
9596 GTTTTAGGGA
9606 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGCTTGTCGCA--
1 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCG-TT-TC-CACT
** *
9649 AAAAAGCCACTAAAGACCCTGATCTTTAGCGACGTTTCCACT
1 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGTTTCCACT
* * * *
9691 AAAGCGCCGCTAAAGACCATTATCTTTAGCGGCGCTTCCACT
1 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGTTTCCACT
*
9733 AAAGCGCCGCTAAAG
1 AAAGCGCCACTAAAG
9748 GTCTTAGTCT
Statistics
Matches: 87, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
42 52 0.60
43 31 0.36
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (42 bp):
AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGTTTCCACT
Found at i:9764 original size:42 final size:42
Alignment explanation
Indices: 9606--9766 Score: 135
Period size: 42 Copynumber: 3.8 Consensus size: 42
9596 GTTTTAGGGA
* * * * * * *
9606 AAAGCGCCACTAAAGACCCTGATCTTTAGCGGCGCTTGTCGCA
1 AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTT-CCACT
** * * * * * *
9649 AAAAAGCCACTAAAGACCCTGATCTTTAGCGACGTTTCCACT
1 AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTTCCACT
*
9691 AAAGCGCCGCTAAAGACCATTATCTTTAGCGGCGCTTCCACT
1 AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTTCCACT
**
9733 AAAGCGCCGCTAAAGGTC-TTAGTCTTCAGCGGCG
1 AAAGCGCCGCTAAAGACCATTA-TCTTCAGCGGCG
9767 TTTGTGCTAG
Statistics
Matches: 100, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
41 3 0.03
42 64 0.64
43 33 0.33
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGACCATTATCTTCAGCGGCGCTTCCACT
Found at i:9933 original size:22 final size:22
Alignment explanation
Indices: 9906--9948 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9896 TTGCGGCGTT
*
9906 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
9928 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
9949 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:10599 original size:44 final size:43
Alignment explanation
Indices: 10455--10616 Score: 209
Period size: 43 Copynumber: 3.7 Consensus size: 43
10445 TCGTCGCAAA
* * *
10455 CTTTTGCGGCGCTTTTACCACAAACGCCGCTATAGATCAGGAT
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATCAAGAC
* *
10498 CTTTAGCGGCGCTTTT-CTAACAAACGCCGCTATAGCTCAAGAC
1 CTTTAGCGGCGCTTTTAC-CACAAACGCCGCTATAGATCAAGAC
*
10541 CTTTAGCGGCGCTTTTACCACAAACGCCACTATAGATCAAAGAC
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATC-AAGAC
* * **
10585 CTTTAGCGACGCTTTGATTACAAACGCCGCTA
1 CTTTAGCGGCGCTTTTACCACAAACGCCGCTA
10617 AAAACACCAC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
42 1 0.01
43 69 0.67
44 33 0.32
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGATCAAGAC
Found at i:10662 original size:23 final size:24
Alignment explanation
Indices: 10636--10691 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
10626 CATTTAGAAA
* *
10636 TATTAAATAT-TAAAATTAAACAT
1 TATTAAATATCAAAAATTAAACAG
**
10659 TATT-AATATCAAAAATTAATTAG
1 TATTAAATATCAAAAATTAAACAG
10682 TATTAAATAT
1 TATTAAATAT
10692 ATACTTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 17 0.63
24 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.41
Consensus pattern (24 bp):
TATTAAATATCAAAAATTAAACAG
Found at i:10930 original size:15 final size:15
Alignment explanation
Indices: 10910--10939 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10900 TGGATCATCT
10910 TCATCTTCATCTTCA
1 TCATCTTCATCTTCA
*
10925 TCATCTTCTTCTTCA
1 TCATCTTCATCTTCA
10940 CTTTCAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (15 bp):
TCATCTTCATCTTCA
Done.