Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001073.1 Kokia drynarioides strain JFW-HI SEQ_112329, 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: 15226
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:2960 original size:28 final size:27
Alignment explanation
Indices: 2912--3095 Score: 73
Period size: 28 Copynumber: 6.4 Consensus size: 27
2902 TTTTTCCTCA
* *
2912 AACTTCTCAAAAA-ATACATTTTGCCCCT
1 AACTT-TCAAAAATA-AAATTTTACCCCT
2940 AACTTTCAAAAATCAAAATTTTACCCCT
1 AACTTTCAAAAAT-AAAATTTTACCCCT
* * * * **
2968 ATATTTCTCAAAAATTATATTTTTGCCTAT
1 A-ACTT-TCAAAAA-TAAAATTTTACCCCT
* * ** *
2998 GAACTTCCAATAATCACATTTTTTACCCCA
1 -AACTTTCAAAAAT-A-AAATTTTACCCCT
* * * *
3028 AATTTCTCAAAAATTATATTTTACCCTCG
1 AACTT-TCAAAAATAAAATTTTACCC-CT
* *
3057 AACTTTCAAAAATAAAATTTTGCCTCT
1 AACTTTCAAAAATAAAATTTTACCCCT
*
3084 AAACTTCCAAAA
1 -AACTTTCAAAA
3096 TTACATTTTT
Statistics
Matches: 115, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
27 8 0.07
28 54 0.47
29 19 0.17
30 32 0.28
31 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (27 bp):
AACTTTCAAAAATAAAATTTTACCCCT
Found at i:3033 original size:59 final size:58
Alignment explanation
Indices: 2889--3049 Score: 173
Period size: 59 Copynumber: 2.8 Consensus size: 58
2879 CTAAAATTTT
* * * * * * * *
2889 CAAAAATTACATTTTTTTCCTCAAACTTCTCAAAAAATACA-TTTTGCCCCTAACTTT
1 CAAAAATCACATTTTTTACCCCAAATTTCTCAAAAATTATATTTTTGCCCATAACTTC
** * *
2946 CAAAAATCA-AAATTTTACCCCTATATTTCTCAAAAATTATATTTTTGCCTATGAACTTC
1 CAAAAATCACATTTTTTACCCC-AAATTTCTCAAAAATTATATTTTTGCCCAT-AACTTC
*
3005 CAATAATCACATTTTTTACCCCAAATTTCTCAAAAATTATATTTT
1 CAAAAATCACATTTTTTACCCCAAATTTCTCAAAAATTATATTTT
3050 ACCCTCGAAC
Statistics
Matches: 84, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
56 8 0.10
57 23 0.27
58 8 0.10
59 35 0.42
60 10 0.12
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.40
Consensus pattern (58 bp):
CAAAAATCACATTTTTTACCCCAAATTTCTCAAAAATTATATTTTTGCCCATAACTTC
Found at i:3089 original size:86 final size:85
Alignment explanation
Indices: 2988--3386 Score: 267
Period size: 86 Copynumber: 4.6 Consensus size: 85
2978 AAAATTATAT
* *
2988 TTTTGCCTATGAACTTCCAATAATCACATTTTTTACCCCAAATTTCTCAAAAATTATATTTTACC
1 TTTTGCCTCTGAACTTCCAA-AATCACA-TTTTTACCCCGAATTTCTCAAAAATTATATTTTACC
*
3053 CTCGAACTTTCAAAAAT-AAAA
64 CTCGAACTTCCAAAAATCAAAA
* * * *
3074 TTTTGCCTCTAAACTTCCAAAATTACATTTTTATCCTCGAATTTCTCAAAAATTACATTTTTACC
1 TTTTGCCTCTGAACTTCCAAAATCACATTTTTA-CCCCGAATTTCTCAAAAATTATA-TTTTACC
* *
3139 CTCGAACTTCCAAAAATCACAT
64 CTCGAACTTCCAAAAATCAAAA
* * ** * *
3161 TTTTG-CTCCCGAACCTCCAAAAATCACACCTTTACCCTCGAACTTCTCAAAAATTATATTTTTG
1 TTTTGCCT-CTGAACTTCC-AAAATCACATTTTTACCC-CGAATTTCTCAAAAATTATA-TTTTA
* * **
3225 CCCCCGAA-TATCCAAAAATTATCA
62 CCCTCGAACT-TCCAAAAATCAAAA
* * * * * * * * * *
3249 -TTTCCCCCCGAGCATCCAAAATTACCA-TTTTACCCCCAAATATC-CAAAAAATACATTTTGA-
1 TTTTGCCTCTGAACTTCCAAAATCA-CATTTTTA-CCCCGAATTTCTCAAAAATTATATTTT-AC
*
3310 CCTCGAACTTTTCCAAAAAT-TAAA
63 CCTCGAAC--TTCCAAAAATCAAAA
* * * ** *
3334 TTTTGCCCCTGAACATCCAAAAATTACCATTTTGCCCCCAAATTTC-CAAAAAT
1 TTTTGCCTCTGAACTTCC-AAAATCA-CATTTTTACCCCGAATTTCTCAAAAAT
3387 CACTTTTTCA
Statistics
Matches: 249, Mismatches: 47, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
84 16 0.06
85 36 0.14
86 81 0.33
87 60 0.24
88 56 0.22
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (85 bp):
TTTTGCCTCTGAACTTCCAAAATCACATTTTTACCCCGAATTTCTCAAAAATTATATTTTACCCT
CGAACTTCCAAAAATCAAAA
Found at i:3173 original size:29 final size:29
Alignment explanation
Indices: 2889--3366 Score: 245
Period size: 30 Copynumber: 16.5 Consensus size: 29
2879 CTAAAATTTT
** *
2889 CAAAAATTACATTTTTTTCCTCAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * * *
2918 TCAAAAAATACA-TTTTGCCC-CTAACTTT
1 -CAAAAATTACATTTTTACCCTCGAACTTC
* * * * *
2946 CAAAAATCAAAATTTTACCC-CTATATTTC
1 CAAAAATTACATTTTTACCCTCGA-ACTTC
* * *
2975 TCAAAAATTATATTTTT-GCCTATGAACTTC
1 -CAAAAATTACATTTTTACCCT-CGAACTTC
* * * *
3005 CAATAATCACATTTTTTACCC-CAAATTTC
1 CAAAAATTACA-TTTTTACCCTCGAACTTC
* *
3034 TCAAAAATTATA-TTTTACCCTCGAACTTT
1 -CAAAAATTACATTTTTACCCTCGAACTTC
* * * *
3063 CAAAAA-TAAAATTTT-GCCTCTAAACTTC
1 CAAAAATTACATTTTTACCCTC-GAACTTC
* *
3091 C-AAAATTACATTTTTATCCTCGAATTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
3119 TCAAAAATTACATTTTTACCCTCGAACTTC
1 -CAAAAATTACATTTTTACCCTCGAACTTC
* * *
3149 CAAAAATCACATTTTTGCTCC-CGAACCTC
1 CAAAAATTACATTTTTAC-CCTCGAACTTC
* **
3178 CAAAAATCACACCTTTACCCTCGAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTC
* * *
3207 TCAAAAATTATATTTTTGCCCCCGAA-TATC
1 -CAAAAATTACATTTTTACCCTCGAACT-TC
* * * *
3237 CAAAAATTATCA--TTTCCCCCCGAGCATC
1 CAAAAATTA-CATTTTTACCCTCGAACTTC
* *
3265 C-AAAATTACCA-TTTTACCC-CCAAATATC
1 CAAAAATTA-CATTTTTACCCTCGAACT-TC
* *
3293 CAAAAAATACATTTTGA-CCTCGAACTTTTC
1 CAAAAATTACATTTTTACCCTCGAAC--TTC
* ** *
3323 CAAAAATTAAATTTTGCCCCT-GAACATC
1 CAAAAATTACATTTTTACCCTCGAACTTC
3351 CAAAAATTACCATTTT
1 CAAAAATTA-CATTTT
3367 GCCCCCAAAT
Statistics
Matches: 344, Mismatches: 74, Indels: 61
0.72 0.15 0.13
Matches are distributed among these distances:
27 30 0.09
28 91 0.26
29 107 0.31
30 109 0.32
31 7 0.02
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTC
Found at i:3182 original size:58 final size:57
Alignment explanation
Indices: 3085--3394 Score: 247
Period size: 59 Copynumber: 5.4 Consensus size: 57
3075 TTTGCCTCTA
** * *
3085 AACTTCC-AAAATTACATTTTTATCCTCGAATTTCTCAAAAATTACATTTTTACCCTCG
1 AACTTCCAAAAATTACATTTTTGCCCCCGAATATC-CAAAAATTACA-TTTTACCCTCG
* * ** * *
3143 AACTTCCAAAAATCACATTTTTGCTCCCGAACCTCCAAAAATCACACCTTTACCCTCG
1 AACTTCCAAAAATTACATTTTTGCCCCCGAATATCCAAAAATTACA-TTTTACCCTCG
* * *
3201 AACTTCTCAAAAATTATATTTTTGCCCCCGAATATCCAAAAATTATCA-TTTCCCCCCG
1 AACTTC-CAAAAATTACATTTTTGCCCCCGAATATCCAAAAATTA-CATTTTACCCTCG
* * * * *
3259 AGCATCC-AAAATTACCA-TTTTACCCCCAAATATCCAAAAAATACATTTTGA-CCTCG
1 AACTTCCAAAAATTA-CATTTTTGCCCCCGAATATCCAAAAATTACATTTT-ACCCTCG
* * * * * *
3315 AACTTTTCCAAAAATTA-AATTTTGCCCCTGAACATCCAAAAATTACCATTTTGCCCCCA
1 AAC--TTCCAAAAATTACATTTTTGCCCCCGAATATCCAAAAATTA-CATTTTACCCTCG
* *
3374 AATTTCCAAAAATCAC-TTTTT
1 AACTTCCAAAAATTACATTTTT
3395 CAACTTCAAA
Statistics
Matches: 200, Mismatches: 39, Indels: 27
0.75 0.15 0.10
Matches are distributed among these distances:
55 2 0.01
56 39 0.19
57 18 0.09
58 69 0.34
59 70 0.35
60 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.32
Consensus pattern (57 bp):
AACTTCCAAAAATTACATTTTTGCCCCCGAATATCCAAAAATTACATTTTACCCTCG
Found at i:3257 original size:28 final size:28
Alignment explanation
Indices: 3092--3386 Score: 175
Period size: 29 Copynumber: 10.2 Consensus size: 28
3082 CTAAACTTCC
** * *
3092 AAAATTACATTTTTATCCTCGAATTTCTCA
1 AAAATTACA-TTTTGCCCCCGAATATC-CA
* *
3122 AAAATTACATTTTTACCCTCGAACT-TCCA
1 AAAATTACA-TTTTGCCCCCGAA-TATCCA
* * **
3151 AAAATCACATTTTTGCTCCCGAACCTCCA
1 AAAATTACA-TTTTGCCCCCGAATATCCA
* * * *
3180 AAAATCACACCTTTACCCTCGAACT-TCTCA
1 AAAATTACA-TTTTGCCCCCGAA-TATC-CA
*
3210 AAAATTATATTTTTGCCCCCGAATATCCA
1 AAAATTACA-TTTTGCCCCCGAATATCCA
* **
3239 AAAATTATCA-TTTCCCCCCGAGCATCC-
1 AAAATTA-CATTTTGCCCCCGAATATCCA
* *
3266 AAAATTACCATTTTACCCCCAAATATCCA
1 AAAATTA-CATTTTGCCCCCGAATATCCA
* * * *
3295 AAAAATACATTTTGACCTCGAACTTTTCCA
1 AAAATTACATTTTGCCCCCGAA--TATCCA
* * *
3325 AAAATTAAATTTTGCCCCTGAACATCCA
1 AAAATTACATTTTGCCCCCGAATATCCA
* *
3353 AAAATTACCATTTTGCCCCCAAATTTCCA
1 AAAATTA-CATTTTGCCCCCGAATATCCA
3382 AAAAT
1 AAAAT
3387 CACTTTTTCA
Statistics
Matches: 209, Mismatches: 45, Indels: 23
0.75 0.16 0.08
Matches are distributed among these distances:
27 9 0.04
28 49 0.23
29 82 0.39
30 68 0.33
31 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (28 bp):
AAAATTACATTTTGCCCCCGAATATCCA
Found at i:3367 original size:29 final size:28
Alignment explanation
Indices: 3035--3371 Score: 148
Period size: 28 Copynumber: 11.7 Consensus size: 28
3025 CCAAATTTCT
* * * *
3035 CAAAAATTATATTTT-ACCCTCGAACTTT
1 CAAAAATTACATTTTGCCCCT-GAACATC
* * * * *
3063 CAAAAATAAAATTTTGCCTCTAAACTTC
1 CAAAAATTACATTTTGCCCCTGAACATC
*** **
3091 C-AAAATTACATTTTTATCCTCGAATTTC
1 CAAAAATTACATTTTGCCCCT-GAACATC
** *
3119 TCAAAAATTACATTTTTACCCTCGAACTTC
1 -CAAAAATTACATTTTGCCCCT-GAACATC
* *
3149 CAAAAATCACATTTTTGCTCCC-GAACCTC
1 CAAAAATTACA-TTTTGC-CCCTGAACATC
* * * *
3178 CAAAAATCACACCTTT-ACCCTCGAACTTC
1 CAAAAATTACA-TTTTGCCCCT-GAACATC
* * *
3207 TCAAAAATTATATTTTTGCCCCCGAATATC
1 -CAAAAATTACA-TTTTGCCCCTGAACATC
* * *
3237 CAAAAATTATCA-TTTCCCCCCGAGCATC
1 CAAAAATTA-CATTTTGCCCCTGAACATC
* ** *
3265 C-AAAATTACCATTTTACCCCCAAATATC
1 CAAAAATTA-CATTTTGCCCCTGAACATC
* * *
3293 CAAAAAATACATTTTG-ACCTCGAACTTTTC
1 CAAAAATTACATTTTGCCCCT-GAAC--ATC
*
3323 CAAAAATTAAATTTTGCCCCTGAACATC
1 CAAAAATTACATTTTGCCCCTGAACATC
3351 CAAAAATTACCATTTTGCCCC
1 CAAAAATTA-CATTTTGCCCC
3372 CAAATTTCCA
Statistics
Matches: 238, Mismatches: 53, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
27 27 0.11
28 70 0.29
29 65 0.27
30 67 0.28
31 9 0.04
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (28 bp):
CAAAAATTACATTTTGCCCCTGAACATC
Found at i:3424 original size:87 final size:86
Alignment explanation
Indices: 3235--3414 Score: 213
Period size: 87 Copynumber: 2.1 Consensus size: 86
3225 CCCCCGAATA
* * * *
3235 TCCAAAAATTATCA-TTTCCCCCCGAGCATCCAAAATTACCATTTTACCCCCAAATATCCAAAAA
1 TCCAAAAATTA-AATTTTGCCCCTGAACATCCAAAATTACCATTTTACCCCCAAATATCCAAAAA
* *
3299 ATACATTTTGACCTCGAACTTT
65 ATACATTTTAACCTCGAAATTT
* *
3321 TCCAAAAATTAAATTTTGCCCCTGAACATCCAAAAATTACCATTTTGCCCCCAAATTTCC-AAAA
1 TCCAAAAATTAAATTTTGCCCCTGAACATCC-AAAATTACCATTTTACCCCCAAATATCCAAAAA
* *
3385 ATCACTTTTTCAACTTC-AAATTT
65 AT-ACATTTT-AACCTCGAAATTT
3408 TCCAAAA
1 TCCAAAA
3415 GTTCGATTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
85 1 0.01
86 31 0.39
87 44 0.55
88 4 0.05
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (86 bp):
TCCAAAAATTAAATTTTGCCCCTGAACATCCAAAATTACCATTTTACCCCCAAATATCCAAAAAA
TACATTTTAACCTCGAAATTT
Found at i:3434 original size:29 final size:31
Alignment explanation
Indices: 3402--3466 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
3392 TTTCAACTTC
*
3402 AAATTTTCC-AAAAGTTCGATTTTAAT-CCT
1 AAATTTTCCAAAAAGTTCAATTTTAATCCCT
* *
3431 AAATTTTCCAAAAATTTCAATTTTGATCCCT
1 AAATTTTCCAAAAAGTTCAATTTTAATCCCT
3462 AAATT
1 AAATT
3467 CCTTGAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.29
30 14 0.45
31 8 0.26
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.42
Consensus pattern (31 bp):
AAATTTTCCAAAAAGTTCAATTTTAATCCCT
Found at i:6055 original size:95 final size:95
Alignment explanation
Indices: 5892--6177 Score: 554
Period size: 95 Copynumber: 3.0 Consensus size: 95
5882 CAAAGAGAAT
*
5892 CAAACTCAAGTCTCTAAGTGAATTACACTATATTCTTATTTACCACTAAATTAATTACTCAATGT
1 CAAACTCAAGTCTCTAAGTGAATTACACTGTATTCTTATTTACCACTAAATTAATTACTCAATGT
5957 TGCTATAATTTTACTAATTTTTAACTGAAA
66 TGCTATAATTTTACTAATTTTTAACTGAAA
5987 CAAACTCAAGTCTCTAAGTGAATTACACTGTATTCTTATTTACCACTAAATTAATTACTCAATGT
1 CAAACTCAAGTCTCTAAGTGAATTACACTGTATTCTTATTTACCACTAAATTAATTACTCAATGT
6052 TGCTATAATTTTACTAATTTTTAACTGAAA
66 TGCTATAATTTTACTAATTTTTAACTGAAA
6082 CAAACTCAAGTCTCTAAGTGAATTACACTGTATTCTTATTTACCACTAAATTAATTACTCAATGT
1 CAAACTCAAGTCTCTAAGTGAATTACACTGTATTCTTATTTACCACTAAATTAATTACTCAATGT
*
6147 TGCTATAATTTTACTAATTTTTAACTAAAA
66 TGCTATAATTTTACTAATTTTTAACTGAAA
6177 C
1 C
6178 TCACAGTGTG
Statistics
Matches: 189, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 189 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (95 bp):
CAAACTCAAGTCTCTAAGTGAATTACACTGTATTCTTATTTACCACTAAATTAATTACTCAATGT
TGCTATAATTTTACTAATTTTTAACTGAAA
Found at i:7662 original size:43 final size:43
Alignment explanation
Indices: 7611--7748 Score: 170
Period size: 43 Copynumber: 3.2 Consensus size: 43
7601 ATGTAGAAAC
*
7611 ACGCCGCTATATAACATGGTCTTTAGCGGTGCTTTTCCAACAA
1 ACGCCGCTATAGAACATGGTCTTTAGCGGTGCTTTTCCAACAA
* * ** *
7654 ACACCGCTAAAGAATGTGGTCTTTAGCGGCGCTTTTCCAACAA
1 ACGCCGCTATAGAACATGGTCTTTAGCGGTGCTTTTCCAACAA
* * * *
7697 ACGCCACTATAGAACATGTTCTTTAGCGGCT-TTTTTCCCACAA
1 ACGCCGCTATAGAACATGGTCTTTAGCGG-TGCTTTTCCAACAA
7740 ACGCCGCTA
1 ACGCCGCTA
7749 ACATTAACAG
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (43 bp):
ACGCCGCTATAGAACATGGTCTTTAGCGGTGCTTTTCCAACAA
Found at i:10695 original size:58 final size:58
Alignment explanation
Indices: 10611--10758 Score: 158
Period size: 58 Copynumber: 2.5 Consensus size: 58
10601 TTTTGGATGC
* **
10611 CCGGGGGCAAAATGG-AATTTTGGGAAAGTTCAGGG-TCAAAAATAGAATTTTTAGACA-T
1 CCGGGGGAAAAATGGTAATTTT-GGAAAAATCAGGGTTC-AAAATAGAATTTTTAGA-AGT
* * * *
10669 CCGGGGGTAAAATGGTAATTTTGGAAAAATCGGGGTTCAAAATGGAATTTTTGGAAGT
1 CCGGGGGAAAAATGGTAATTTTGGAAAAATCAGGGTTCAAAATAGAATTTTTAGAAGT
**
10727 TTGGGGGAAAAATGGTAATTTTTGGAAAAATC
1 CCGGGGGAAAAATGGTAA-TTTTGGAAAAATC
10759 GAGGTAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
57 1 0.01
58 55 0.71
59 21 0.27
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.28
Consensus pattern (58 bp):
CCGGGGGAAAAATGGTAATTTTGGAAAAATCAGGGTTCAAAATAGAATTTTTAGAAGT
Found at i:10702 original size:29 final size:30
Alignment explanation
Indices: 10670--10767 Score: 105
Period size: 29 Copynumber: 3.4 Consensus size: 30
10660 TTTAGACATC
10670 CGGGGGTAAAATGGTAA-TTTTGGAAAAAT
1 CGGGGGTAAAATGGTAATTTTTGGAAAAAT
* **
10699 CGGGGTTCAAAATGG-AATTTTTGG-AAGTT
1 CGGGGGT-AAAATGGTAATTTTTGGAAAAAT
* *
10728 TGGGGGAAAAATGGTAATTTTTGGAAAAAT
1 CGGGGGTAAAATGGTAATTTTTGGAAAAAT
*
10758 C-GAGGTAAAA
1 CGGGGGTAAAA
10768 AATGGAACTT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
28 7 0.13
29 31 0.57
30 16 0.30
ACGTcount: A:0.37, C:0.04, G:0.31, T:0.29
Consensus pattern (30 bp):
CGGGGGTAAAATGGTAATTTTTGGAAAAAT
Found at i:10713 original size:30 final size:30
Alignment explanation
Indices: 10670--10768 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
10660 TTTAGACATC
*
10670 CGGGGGTAAAATGGTAA-TTTTGGAAAAAT
1 CGGGGGAAAAATGGTAATTTTTGGAAAAAT
** **
10699 CGGGGTTCAAAATGG-AATTTTTGG-AAGTT
1 CGGGG-GAAAAATGGTAATTTTTGGAAAAAT
*
10728 TGGGGGAAAAATGGTAATTTTTGGAAAAAT
1 CGGGGGAAAAATGGTAATTTTTGGAAAAAT
* *
10758 CGAGGTAAAAA
1 CGGGGGAAAAA
10769 ATGGAACTTT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
28 7 0.13
29 23 0.43
30 24 0.44
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.28
Consensus pattern (30 bp):
CGGGGGAAAAATGGTAATTTTTGGAAAAAT
Found at i:10785 original size:59 final size:58
Alignment explanation
Indices: 10671--10786 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 58
10661 TTAGACATCC
* * ** * **
10671 GGGGGTAAAATGGTAATTTTGGAAAAATCGGGGTTCAAAATGGAATTTTTGGAAGTTT
1 GGGGGAAAAATGGTAATTTTGGAAAAATCGAGGTAAAAAATGGAACTTTAAGAAGTTT
10729 GGGGGAAAAATGGTAATTTTTGGAAAAATCGAGGTAAAAAATGGAACTTTAAGAAGTT
1 GGGGGAAAAATGGTAA-TTTTGGAAAAATCGAGGTAAAAAATGGAACTTTAAGAAGTT
10787 CGAGGGTAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 15 0.30
59 35 0.70
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.29
Consensus pattern (58 bp):
GGGGGAAAAATGGTAATTTTGGAAAAATCGAGGTAAAAAATGGAACTTTAAGAAGTTT
Found at i:10859 original size:59 final size:59
Alignment explanation
Indices: 10796--10920 Score: 171
Period size: 59 Copynumber: 2.1 Consensus size: 59
10786 TCGAGGGTAG
* * *
10796 AAATGTAA-ATTTCAAAATGTTCGGGGTCAAAAATGTAATTTTGGAAAAGTGTAGGGTTA
1 AAATGTAATATTTCAAAA-GTTCGAGGTCAAAAATATAATTTTGGAAAAGTGCAGGGTTA
* ** *
10855 AAATGTAATTTTTGGAAAGTTTGAGGTCAAAAATATAATTTTGGAAAAGTGCAGGGTTA
1 AAATGTAATATTTCAAAAGTTCGAGGTCAAAAATATAATTTTGGAAAAGTGCAGGGTTA
10914 AAATGTA
1 AAATGTA
10921 CTTAATAGGC
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 52 0.90
60 6 0.10
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (59 bp):
AAATGTAATATTTCAAAAGTTCGAGGTCAAAAATATAATTTTGGAAAAGTGCAGGGTTA
Found at i:10870 original size:30 final size:29
Alignment explanation
Indices: 10825--10920 Score: 115
Period size: 29 Copynumber: 3.3 Consensus size: 29
10815 TTCGGGGTCA
10825 AAAATGTAATTTTGGAAAAGTGTAGGGTT
1 AAAATGTAATTTTGGAAAAGTGTAGGGTT
* *
10854 AAAATGTAATTTTTGG-AAAGT-TTGAGGTCA
1 AAAATGTAA-TTTTGGAAAAGTGTAG-GGT-T
* *
10884 AAAATATAATTTTGGAAAAGTGCAGGGTT
1 AAAATGTAATTTTGGAAAAGTGTAGGGTT
10913 AAAATGTA
1 AAAATGTA
10921 CTTAATAGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.04
29 30 0.55
30 22 0.40
31 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTGTAGGGTT
Found at i:11601 original size:17 final size:17
Alignment explanation
Indices: 11579--11635 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
11569 TATTTCAAAT
11579 TTTAAATTTTAAATAAA
1 TTTAAATTTTAAATAAA
*
11596 TTTAAATTTAAAAT-AA
1 TTTAAATTTTAAATAAA
11612 TTCTAAA-TTTAGAATAAA
1 TT-TAAATTTTA-AATAAA
11630 TTTAAA
1 TTTAAA
11636 ATAAAGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
16 7 0.20
17 24 0.69
18 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TTTAAATTTTAAATAAA
Found at i:14133 original size:18 final size:19
Alignment explanation
Indices: 14110--14146 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
14100 AATTAATTGA
14110 AGGCATAT-TTTTTTTAAT
1 AGGCATATGTTTTTTTAAT
14128 AGGCATATGTTTTTTTAAT
1 AGGCATATGTTTTTTTAAT
14147 CGGGAGCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (19 bp):
AGGCATATGTTTTTTTAAT
Done.