Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003689.1 Kokia drynarioides strain JFW-HI SEQ_116619, 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: 7502
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:946 original size:12 final size:12
Alignment explanation
Indices: 928--999 Score: 67
Period size: 11 Copynumber: 6.0 Consensus size: 12
918 GTTTAAATTG
*
928 ATTTAAATTTAT
1 ATTTAAATTTAA
*
940 TTTTAAATTTAA
1 ATTTAAATTTAA
*
952 ATTTATA-TTAA
1 ATTTAAATTTAA
*
963 ATTTAAATTTATCT
1 ATTTAAATTTA--A
*
977 TTTTAAATTTAA
1 ATTTAAATTTAA
989 A-TTAAATTTAA
1 ATTTAAATTTAA
1000 TTTGATTTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
11 20 0.42
12 18 0.38
14 10 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:950 original size:6 final size:6
Alignment explanation
Indices: 928--999 Score: 67
Period size: 6 Copynumber: 12.0 Consensus size: 6
918 GTTTAAATTG
* * * *
928 ATTTAA ATTTAT TTTTAA ATTTAA ATTTAT A-TTAA ATTTAA ATTTATCT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA--A
*
977 TTTTAA ATTTAA A-TTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA
1000 TTTGATTTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
5 9 0.17
6 39 0.75
8 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTAA
Found at i:964 original size:11 final size:11
Alignment explanation
Indices: 919--999 Score: 53
Period size: 11 Copynumber: 7.5 Consensus size: 11
909 TTAAGTTGGG
*
919 TTTAAATT-GA
1 TTTAAATTAAA
**
929 TTTAAATTTATT
1 TTTAAA-TTAAA
941 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
953 TTTATATTAAA
1 TTTAAATTAAA
*
964 TTTAAATT-TA
1 TTTAAATTAAA
*
974 TCTT--TTTAAA
1 T-TTAAATTAAA
984 TTTAAATTAAA
1 TTTAAATTAAA
995 TTTAA
1 TTTAA
1000 TTTGATTTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
9 4 0.07
10 10 0.18
11 26 0.47
12 15 0.27
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:2956 original size:29 final size:29
Alignment explanation
Indices: 2926--3192 Score: 108
Period size: 29 Copynumber: 9.1 Consensus size: 29
2916 TCTTGACATT
*
2926 GATTTCCCAAAAATTACATTTTTACCCTT
1 GATTTCCCAAAAATTACATTTTTACCCTC
* ** * *
2955 GAACTT-GTAAAAATTCCAATTTTAACCC-C
1 G-ATTTCCCAAAAATTAC-ATTTTTACCCTC
* *
2984 AATTATCCTAAAAATTACATTTTTACCCTC
1 GATT-TCCCAAAAATTACATTTTTACCCTC
* *
3014 AAACTTT-CC-AAAATTCCATTTTTAGCCC-C
1 -GA-TTTCCCAAAAATTACATTTTTA-CCCTC
*
3043 AATTTCACCAAAAATTACCA-TTTTACCCTC
1 GATTTC-CCAAAAATTA-CATTTTTACCCTC
* **
3073 GAACTTCCC-AAAATTTTATTTTTGA-CCTC
1 G-ATTTCCCAAAAATTACATTTTT-ACCCTC
* *
3102 GATTTCACCAAAAAATACCA-TTTTACCCTT
1 GATTTC-CCAAAAATTA-CATTTTTACCCTC
* * *
3132 GAAGTT-CCTAAAATTCCATTTTTCACCCT-
1 G-ATTTCCCAAAAATTACATTTTT-ACCCTC
* * *
3161 AATTTTTCC-AAAATTACCATTCTTACCCTC
1 GA-TTTCCCAAAAATTA-CATTTTTACCCTC
3191 GA
1 GA
3193 GTGTCTAAAA
Statistics
Matches: 179, Mismatches: 32, Indels: 53
0.68 0.12 0.20
Matches are distributed among these distances:
27 3 0.02
28 12 0.07
29 81 0.45
30 68 0.38
31 13 0.07
32 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (29 bp):
GATTTCCCAAAAATTACATTTTTACCCTC
Found at i:2996 original size:30 final size:28
Alignment explanation
Indices: 2962--3067 Score: 90
Period size: 30 Copynumber: 3.6 Consensus size: 28
2952 CTTGAACTTG
2962 TAAAAATTCCAATTTTAACCCCAATTATCC
1 TAAAAATTCC-ATTTTAACCCCAATT-TCC
* *
2992 TAAAAATTACATTTTTACCCTCAAACTTTCC
1 TAAAAATTCCATTTTAACCC-C-AA-TTTCC
*
3023 --AAAATTCCATTTTTAGCCCCAATTTCAC
1 TAAAAATTCCA-TTTTAACCCCAATTTC-C
*
3051 CAAAAATTACCATTTTA
1 TAAAAATT-CCATTTTA
3068 CCCTCGAACT
Statistics
Matches: 63, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
27 4 0.06
28 3 0.05
29 18 0.29
30 28 0.44
31 8 0.13
32 2 0.03
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (28 bp):
TAAAAATTCCATTTTAACCCCAATTTCC
Found at i:3010 original size:59 final size:59
Alignment explanation
Indices: 2880--3192 Score: 221
Period size: 59 Copynumber: 5.3 Consensus size: 59
2870 ACTTTTTGAG
* * ****
2880 AATTACA-TTTTACCC-CTGAACTTTCCAAAATTCC-ATTCTTGACATTGATTTC-CCAAA
1 AATTACATTTTTACCCTC-GAACTTTCAAAAATTCCAATT-TTAACCCCAATTTCACCAAA
* *
2937 AATTACATTTTTACCCTTGAACTTGT-AAAAATTCCAATTTTAACCCCAATTATC-CTAAA
1 AATTACATTTTTACCCTCGAACTT-TCAAAAATTCCAATTTTAACCCCAATT-TCACCAAA
* * * *
2996 AATTACATTTTTACCCTCAAACTTTCCAAAATTCCATTTTTAGCCCCAATTTCACCAAA
1 AATTACATTTTTACCCTCGAACTTTCAAAAATTCCAATTTTAACCCCAATTTCACCAAA
* * ** * * * *
3055 AATTACCA-TTTTACCCTCGAACTTCCCAAAATTTTATTTTTGACCTCGATTTCACCAAA
1 AATTA-CATTTTTACCCTCGAACTTTCAAAAATTCCAATTTTAACCCCAATTTCACCAAA
* * * * * * * * **
3114 AAATACCA-TTTTACCCTTGAAGTTCCTAAAATTCCATTTTTCACCCTAATTTTTCC-AA
1 AATTA-CATTTTTACCCTCGAACTTTCAAAAATTCCAATTTTAACCCCAATTTCACCAAA
*
3172 AATTACCATTCTTACCCTCGA
1 AATTA-CATTTTTACCCTCGA
3193 GTGTCTAAAA
Statistics
Matches: 210, Mismatches: 37, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
57 7 0.03
58 41 0.20
59 160 0.76
60 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (59 bp):
AATTACATTTTTACCCTCGAACTTTCAAAAATTCCAATTTTAACCCCAATTTCACCAAA
Found at i:3150 original size:28 final size:29
Alignment explanation
Indices: 3112--3216 Score: 87
Period size: 29 Copynumber: 3.6 Consensus size: 29
3102 GATTTCACCA
*
3112 AAAAATACCATTTTACCCTTGAAGTTCCT
1 AAAATTACCATTTTACCCTTGAAGTTCCT
*
3141 AAAATT-CCATTTTTCACCC-T-AATTTTTCC-
1 AAAATTACCA-TTTT-ACCCTTGAA--GTTCCT
*
3170 AAAATTACCATTCTTACCCTCG-AGTGT-CT
1 AAAATTACCATT-TTACCCTTGAAGT-TCCT
3199 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
3217 CCGGGTACCC
Statistics
Matches: 62, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
28 13 0.21
29 35 0.56
30 14 0.23
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTTGAAGTTCCT
Found at i:3230 original size:28 final size:29
Alignment explanation
Indices: 3168--3230 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
3158 CCTAATTTTT
* **
3168 CCAAAATTACCATTCTTACCCTCGAGTGT
1 CCAAAATTACCATTCTTACCCCCGAGTAC
* *
3197 CTAAAATTACCATT-TTACCCCCGGGTAC
1 CCAAAATTACCATTCTTACCCCCGAGTAC
3225 CCAAAA
1 CCAAAA
3231 ATCACATTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.27
Consensus pattern (29 bp):
CCAAAATTACCATTCTTACCCCCGAGTAC
Found at i:5923 original size:78 final size:78
Alignment explanation
Indices: 5822--5996 Score: 176
Period size: 78 Copynumber: 2.2 Consensus size: 78
5812 ATCATTAACC
* * * * * * *
5822 AATCTCTTAGCCCGAGCCTGGGGCAGA-TAGTAGCCATTCGATCTATTACCCCGAGCTTGGGGTA
1 AATCTCTTAGCCCGAGCCTGGGGCAAATTA-CAGCCATACGATATAGTACCCCGAGCCTGGGCTA
5886 GATCAAAACCAATA
65 GATCAAAACCAATA
*
5900 AATCTCTTA-CACCGAG-CTGGGGGCAAATTACAGCCATACGATATCGTACCCCGAGCCTGGGCT
1 AATCTCTTAGC-CCGAGCCT-GGGGCAAATTACAGCCATACGATATAGTACCCCGAGCCTGGGCT
** * *
5963 AGATCATCATCAGTA
64 AGATCAAAACCAATA
* *
5978 AATCTCCTACCCCGAGCCT
1 AATCTCTTAGCCCGAGCCT
5997 AAGGAAGATC
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
77 3 0.04
78 71 0.90
79 5 0.06
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.22
Consensus pattern (78 bp):
AATCTCTTAGCCCGAGCCTGGGGCAAATTACAGCCATACGATATAGTACCCCGAGCCTGGGCTAG
ATCAAAACCAATA
Found at i:5989 original size:39 final size:39
Alignment explanation
Indices: 5946--6763 Score: 178
Period size: 39 Copynumber: 21.1 Consensus size: 39
5936 TACGATATCG
* *
5946 TACCCCGAGCCTGGGCTAGATCATCATCAGTAAATCTCC
1 TACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCT
* * *
5985 TACCCCGAGCCTAAGG-AAGATCATCATTAGCAAATCTCT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* * * *
6024 TACCCCGAGCTTGGGGTAGATTGCAGCCATC--C-GATCTCT
1 TACCCCGAGCCTGGGCTAGA-T-CA-TCATCAGCAAATCTCT
* * *
6063 TACCTCGAGCCTAGGGC-AGATCATCATTAGCCAATCTCT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* * **
6102 TACCCCGAGCCTGGGGTAGATTGCAACCATTTG---ATCTCT
1 TACCCCGAGCCTGGGCTAGA-T-C-ATCATCAGCAAATCTCT
* * ** *
6141 TACCTCGAACCTGGGGAAGATCATCATCAGCCAATCTCT
1 TACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCT
***
6180 TACCTATAGCCTGGGAC-AGATTGCAGTCACTC-G---ATCTCT
1 TACCCCGAGCCTGGG-CTAGA-T-CA-TCA-TCAGCAAATCTCT
* * * * * * *
6219 TACCTCAAGCTTGGGGC-AGATCACCATCAACCAATCTTT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* * * ****
6258 TACCTCGAGCCTGGGGTAGATTAT-AGTCATTTGATCTCT
1 TACCCCGAGCCTGGGCTAGATCATCA-TCAGCAAATCTCT
* * * *
6297 TATCCCGAACTTGGGGC-AGATCACCATCAGCAAATCTCT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* *
6336 TACCCCGAGCCTGGGGC-AGAT--TGCAGCCATTC-AATCTCT
1 TACCCCGAGCCT-GGGCTAGATCAT-CA-TCA-GCAAATCTCT
* * * * * *
6375 TACCCTGAGCTTCGGGC-AAATCACCATTAGCCAA-----
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* * *
6409 -NCCCCGAGCCTGGGGC-AGAT--TGCTGTC-GTTC-GATCTCT
1 TACCCCGAGCCT-GGGCTAGATCAT-C-ATCAG--CAAATCTCT
* * *
6447 TACCTCGAGCTTGGGGC-AGATCATCATCAGCCAATCTCT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* ** * * * *
6486 TACCCTGAGCCTGGGGC-AGATTGT-AGCCGTTC-GATCTTT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAG--CAAATCTCT
* * * * *
6525 TACCTCGAGCTTGGGGTAGATCACCATCAATC-AATCTCT
1 TACCCCGAGCCTGGGCTAGATCATCATC-AGCAAATCTCT
* * *
6564 TACCCCGAGCCTGTGGC-AGATTAT-AGTCATTC-GATCTCT
1 TACCCCGAGCCTG-GGCTAGATCATCA-TCA-GCAAATCTCT
* *
6603 TACCCCGAGCTTGGGGC-AGATAATCATCAGCAAATCTCT
1 TACCCCGAGCCT-GGGCTAGATCATCATCAGCAAATCTCT
* * * * *
6642 TACCCTGAGCCTGAGGC-AGATCACCATCAACCAATCTTT
1 TACCCCGAGCCTG-GGCTAGATCATCATCAGCAAATCTCT
* * * **
6681 TACCCTGAGCCTGGGCCAGATTA-CAGTCA-CTCGATCTCT
1 TACCCCGAGCCTGGGCTAGATCATCA-TCAGC-AAATCTCT
** * *
6720 TGTCTCGAGCCTGAGG-TAGATCATCATCAGCCAATCTCT
1 TACCCCGAGCCTG-GGCTAGATCATCATCAGCAAATCTCT
*
6759 CACCC
1 TACCC
6764 GATCATGGGG
Statistics
Matches: 573, Mismatches: 138, Indels: 136
0.68 0.16 0.16
Matches are distributed among these distances:
32 2 0.00
33 17 0.03
34 1 0.00
35 2 0.00
36 10 0.02
37 5 0.01
38 33 0.06
39 449 0.78
40 33 0.06
41 6 0.01
42 13 0.02
43 2 0.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
TACCCCGAGCCTGGGCTAGATCATCATCAGCAAATCTCT
Found at i:5994 original size:117 final size:117
Alignment explanation
Indices: 5868--6122 Score: 287
Period size: 117 Copynumber: 2.2 Consensus size: 117
5858 TTCGATCTAT
* *
5868 TACCCCGAGCTTGGGGTAGATCAAAACCAATAAATCTCTTACACCGAGCTGGGGGCAAATTACAG
1 TACCCCGAGCCTGGGGTAGATCAAAACCAACAAATCTCTTACACCGAGCTGGGGGCAAATTACAG
*
5933 CCATACGATATCGTACCCCGAGCCT-GGGCTAGATCATCATCAGTAAATCTCC
66 CCATACGATATCGTACCCCGAGCCTAGGGC-AGATCATCATCAGCAAATCTCC
** * ** ** * * * * * *
5985 TACCCCGAGCCTAAGGAAGATCATCATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTGCAG
1 TACCCCGAGCCTGGGGTAGATCAAAACCAACAAATCTCTTACACCGAGCTGGGGGCAAATTACAG
* * * * * * *
6050 CCATCCGATCTCTTACCTCGAGCCTAGGGCAGATCATCATTAGCCAATCTCT
66 CCATACGATATCGTACCCCGAGCCTAGGGCAGATCATCATCAGCAAATCTCC
6102 TACCCCGAGCCTGGGGTAGAT
1 TACCCCGAGCCTGGGGTAGAT
6123 TGCAACCATT
Statistics
Matches: 111, Mismatches: 26, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
117 107 0.96
118 4 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (117 bp):
TACCCCGAGCCTGGGGTAGATCAAAACCAACAAATCTCTTACACCGAGCTGGGGGCAAATTACAG
CCATACGATATCGTACCCCGAGCCTAGGGCAGATCATCATCAGCAAATCTCC
Found at i:6392 original size:78 final size:78
Alignment explanation
Indices: 6002--6662 Score: 717
Period size: 78 Copynumber: 8.6 Consensus size: 78
5992 AGCCTAAGGA
* * * * *
6002 AGATCATCATTAGCAAATCTCTTACCCCGAGCTTGGGGTAGATTGCAGCCATCCGATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
* *
6067 TCGAGCCTAGGGC
66 TCGAGCTTGGGGC
* * * *
6080 AGATCATCATTAGCCAATCTCTTACCCCGAGCCTGGGGTAGATTGCAACCATTTGATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
* * *
6145 TCGAACCTGGGGA
66 TCGAGCTTGGGGC
*** * * *
6158 AGATCATCATCAGCCAATCTCTTACCTATAGCCTGGGACAGATTGCAGTCACTCGATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
*
6223 TCAAGCTTGGGGC
66 TCGAGCTTGGGGC
* * * * * ** * *
6236 AGATCACCATCAACCAATCTTTTACCTCGAGCCTGGGGTAGATTATAGTCATTTGATCTCTTATC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTA-C
*
6301 C-CGAACTTGGGGC
65 CTCGAGCTTGGGGC
* * *
6314 AGATCACCATCAGCAAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCAATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
*
6379 -CTGAGCTTCGGGC
66 TC-GAGCTTGGGGC
* * * * * * *
6392 AAATCACCATTAGCCAA------NCCCCGAGCCTGGGGCAGATTGCTGTCGTTCGATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
6451 TCGAGCTTGGGGC
66 TCGAGCTTGGGGC
* * * *
6464 AGATCATCATCAGCCAATCTCTTACCCTGAGCCTGGGGCAGATTGTAGCCGTTCGATCTTTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
*
6529 TCGAGCTTGGGGT
66 TCGAGCTTGGGGC
* ** * ** *
6542 AGATCACCATCAATCAATCTCTTACCCCGAGCCTGTGGCAGATTATAGTCATTCGATCTCTTACC
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
*
6607 CCGAGCTTGGGGC
66 TCGAGCTTGGGGC
* * * *
6620 AGATAATCATCAGCAAATCTCTTACCCTGAGCCTGAGGCAGAT
1 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGAT
6663 CACCATCAAC
Statistics
Matches: 490, Mismatches: 84, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
72 61 0.12
73 1 0.00
77 3 0.01
78 423 0.86
79 2 0.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (78 bp):
AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATTCGATCTCTTACC
TCGAGCTTGGGGC
Found at i:6645 original size:117 final size:116
Alignment explanation
Indices: 6519--6778 Score: 306
Period size: 117 Copynumber: 2.2 Consensus size: 116
6509 TAGCCGTTCG
* * *
6519 ATCTTTTACCTCGAGCTTGGGGTAGATCACCATCAATCAATCTCTTACCCCGAGCCTGTGG-CAG
1 ATCTCTTACC-CGAGCATGGGGTAGATCACCATCAACCAATCTCTTACCCCGAGCCTG-GGCCAG
* * * *
6583 ATTATAGTCATTCGATCTCTTACCCCGAGCTTGGGGCAGATAATCATCAGCAA
64 ATTACAGTCACTCGATCTCTTACCCCGAGCCTGAGGCAGATAATCATCAGCAA
* * * * *
6636 ATCTCTTACCCTGAGCCTGAGGCAGATCACCATCAACCAATCTTTTACCCTGAGCCTGGGCCAGA
1 ATCTCTTACCC-GAGCATGGGGTAGATCACCATCAACCAATCTCTTACCCCGAGCCTGGGCCAGA
** * * * *
6701 TTACAGTCACTCGATCTCTTGTCTCGAGCCTGAGGTAGATCATCATCAGCCA
65 TTACAGTCACTCGATCTCTTACCCCGAGCCTGAGGCAGATAATCATCAGCAA
* *
6753 ATCTCTCACCCGATCATGGGGTAGAT
1 ATCTCTTACCCGAGCATGGGGTAGAT
6779 GATAATCATT
Statistics
Matches: 119, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
116 14 0.12
117 105 0.88
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (116 bp):
ATCTCTTACCCGAGCATGGGGTAGATCACCATCAACCAATCTCTTACCCCGAGCCTGGGCCAGAT
TACAGTCACTCGATCTCTTACCCCGAGCCTGAGGCAGATAATCATCAGCAA
Found at i:7256 original size:29 final size:28
Alignment explanation
Indices: 7217--7316 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 28
7207 TAAAATTATA
*
7217 TTAAGTTTAAATAGGTTTTAAATTTATTT
1 TTAAATTTAAAT-GGTTTTAAATTTATTT
* *
7246 TTAAATTTAAATTTGTTGTAAATTTAAATTTAGT
1 TTAAATTTAAA-TGGTTTTAAATTT--A-TT--T
* *
7280 TTAAATTTGAAATGGTTTTAAACTTAATT
1 TTAAATTT-AAATGGTTTTAAATTTATTT
7309 TTAAATTT
1 TTAAATTT
7317 TAATTTAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
29 29 0.51
30 1 0.02
31 2 0.04
32 3 0.05
34 19 0.33
35 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (28 bp):
TTAAATTTAAATGGTTTTAAATTTATTT
Found at i:7269 original size:17 final size:17
Alignment explanation
Indices: 7233--7292 Score: 77
Period size: 17 Copynumber: 3.4 Consensus size: 17
7223 TTAAATAGGT
*
7233 TTTAAATTTATTTTTAAA
1 TTTAAATTTA-GTTTAAA
7251 TTTAAATTT-GTTGTAAA
1 TTTAAATTTAGTT-TAAA
7268 TTTAAATTTAGTTTAAA
1 TTTAAATTTAGTTTAAA
7285 TTTGAAAT
1 TTT-AAAT
7293 GGTTTTAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
16 2 0.05
17 20 0.53
18 16 0.42
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TTTAAATTTAGTTTAAA
Found at i:7311 original size:63 final size:63
Alignment explanation
Indices: 7204--7322 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
7194 GAAACTTTTG
* * *
7204 ATTTAAAATTATATTAAGTTTAAATAGGTTTTAAATTTATTTTTAAATTTAAATTTGTTGTAA
1 ATTTAAAATTATATTAAATTTAAATAGGTTTTAAACTTAATTTTAAATTTAAATTTGTTGTAA
* *
7267 ATTTAAATTTAGT-TTAAATTTGAAAT-GGTTTTAAACTTAATTTTAAATTTTAATTT
1 ATTTAAAATTA-TATTAAATTT-AAATAGGTTTTAAACTTAATTTTAAATTTAAATTT
7323 AAAAAGTCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
63 44 0.90
64 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.08, T:0.53
Consensus pattern (63 bp):
ATTTAAAATTATATTAAATTTAAATAGGTTTTAAACTTAATTTTAAATTTAAATTTGTTGTAA
Found at i:7400 original size:40 final size:40
Alignment explanation
Indices: 7342--7417 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
7332 AAAATACAAA
* *
7342 AAGGCCTAACTACGAGTTTAACTAGACAAACCCAAACACT
1 AAGGCCCAACTACAAGTTTAACTAGACAAACCCAAACACT
* *
7382 AAGGCCCAATTACAAGTTTAACTAGACAGACCCAAA
1 AAGGCCCAACTACAAGTTTAACTAGACAAACCCAAA
7418 ACCTAACCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (40 bp):
AAGGCCCAACTACAAGTTTAACTAGACAAACCCAAACACT
Done.