Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011090.1 Kokia drynarioides strain JFW-HI SEQ_126063, 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: 4171
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:1826 original size:97 final size:97
Alignment explanation
Indices: 1651--1844 Score: 243
Period size: 97 Copynumber: 2.0 Consensus size: 97
1641 AACTTTGGAA
*
1651 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTAGCACCTAGTAAGTTAATGCACAAACTTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAACTTTCA
* *
1716 GAATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTCGATTT
* * * *
1748 AAGGGTATTCGATTAT-TACGATTTGAGGAAAAATTA-CACCTAGTAAGTTAAGGCACAAATTTT
1 AAGGATATTCGATTATCT-CGATTTGAAG-AAAAGTAGCACCTAGTAAGTTAAGGCACAAACTTT
* *
1811 CAAAA-CTTGAAATAAAAGAATATTGCCTCGATTT
64 CAAAATC-AGAAATAAAAGAACATTGCCTCGATTT
1845 TAAAGTTTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
96 2 0.02
97 72 0.86
98 10 0.12
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAACTTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:2093 original size:28 final size:28
Alignment explanation
Indices: 2062--2123 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
2052 AAAATGAGAT
2062 TTTTGGATACCCGGGAGCAAAATGGTAA
1 TTTTGGATACCCGGGAGCAAAATGGTAA
* *
2090 TTTTGGATACTCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGGGAGCAAAATGGTAA
2118 TTTTGG
1 TTTTGG
2124 GAAATTGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (28 bp):
TTTTGGATACCCGGGAGCAAAATGGTAA
Found at i:2144 original size:30 final size:30
Alignment explanation
Indices: 2108--2423 Score: 143
Period size: 29 Copynumber: 10.7 Consensus size: 30
2098 ACTCGGGGGC
*
2108 AAAATGGTAATTTTGGGAAATTGAGGGGTA
1 AAAATGGTAATTTTTGGAAATTGAGGGGTA
* * *
2138 AAAATGG-AATTTTTAGACATTCGGGGGGGT-
1 AAAATGGTAATTTTTGGAAATT--GAGGGGTA
* **
2168 AAAATGTTAATTTTTAAAAAATTGA--GGTCA
1 AAAATGGTAATTTTT-GGAAATTGAGGGGT-A
*
2198 AAAATGG-AATTTTTGGAAGTTCGA-GGGT-
1 AAAATGGTAATTTTTGGAAATT-GAGGGGTA
2226 AAAATGGTAA-TTTTGGAAAAATT--GGGGTCA
1 AAAATGGTAATTTTTGG--AAATTGAGGGGT-A
* *
2256 ATAATGG-AATTTTTGGAAAGTT-TGGGGTA
1 AAAATGGTAATTTTTGGAAA-TTGAGGGGTA
*
2285 AAAAT-GTAATTTTTGGAAAAAATT-AGGGTTAA
1 AAAATGGTAATTTTTGG---AAATTGAGGGGT-A
** * *
2317 AAAATGG-AA-TTTTAAAAAGTTTAGGGATA
1 AAAATGGTAATTTTTGGAAA-TTGAGGGGTA
* *
2346 AAAAT-GTAATTTTTGGAGAAATCGA-GGTTA
1 AAAATGGTAATTTTT-G-GAAATTGAGGGGTA
* * * *
2376 AAAATAGAAATTTTT-GAAGTTCGA-GGGTT
1 AAAATGGTAATTTTTGGAAATT-GAGGGGTA
2405 AAAATGGT-ATTTTTGGAAA
1 AAAATGGTAATTTTTGGAAA
2424 AATCGAGGTT
Statistics
Matches: 221, Mismatches: 33, Indels: 65
0.69 0.10 0.20
Matches are distributed among these distances:
28 42 0.19
29 64 0.29
30 62 0.28
31 33 0.15
32 19 0.09
33 1 0.00
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAATTGAGGGGTA
Found at i:2148 original size:29 final size:29
Alignment explanation
Indices: 2108--2329 Score: 93
Period size: 30 Copynumber: 7.4 Consensus size: 29
2098 ACTCGGGGGC
2108 AAAATGGTAATTTTGGGAAATTGAGGGGTA
1 AAAATGG-AATTTTGGGAAATTGAGGGGTA
** * *
2138 AAAATGGAATTTTTAGACATTCGGGGGGGT-
1 AAAATGGAATTTTGGGAAATT--GAGGGGTA
* ***
2168 AAAATGTTAATTTTTAAAAAATTGA--GGTCA
1 AAAATG-GAA-TTTTGGGAAATTGAGGGGT-A
* *
2198 AAAATGGAATTTTTGGAAGTTCGA-GGGT-
1 AAAATGGAATTTTGGGAAATT-GAGGGGTA
*
2226 AAAATGGTAATTTTGGAAAAATT--GGGGTCA
1 AAAATGG-AATTTTGG-GAAATTGAGGGGT-A
* * *
2256 ATAATGGAATTTTTGGAAAGTT-TGGGGTA
1 AAAATGGAATTTTGGGAAA-TTGAGGGGTA
* * *
2285 AAAATGTAATTTTTGGAAAAAATT-AGGGTTAA
1 AAAATGGAA-TTTTGG--GAAATTGAGGGGT-A
2317 AAAATGGAATTTT
1 AAAATGGAATTTT
2330 AAAAAGTTTA
Statistics
Matches: 146, Mismatches: 27, Indels: 37
0.70 0.13 0.18
Matches are distributed among these distances:
28 25 0.17
29 39 0.27
30 43 0.29
31 18 0.12
32 21 0.14
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGGAAATTGAGGGGTA
Found at i:2179 original size:60 final size:59
Alignment explanation
Indices: 2100--2449 Score: 226
Period size: 60 Copynumber: 5.9 Consensus size: 59
2090 TTTTGGATAC
* *
2100 TCGGGGGCAAAATGGTAATTTTGGGAAATTGAGGGGT-AAAAATGGAATTTTTAGACA-T
1 TCGGGGGTAAAATGGTAATTTTGGAAAATTGAGGGGTCAAAAATGGAATTTTTAGA-AGT
* ** *
2158 TCGGGGGGGTAAAATGTTAATTTTTAAAAAATTGA--GGTCAAAAATGGAATTTTTGGAAGT
1 TC--GGGGGTAAAATGGTAA-TTTTGGAAAATTGAGGGGTCAAAAATGGAATTTTTAGAAGT
* * *
2218 TCGAGGGTAAAATGGTAATTTTGGAAAAATT--GGGGTCAATAATGGAATTTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTGG-AAAATTGAGGGGTCAAAAATGGAATTTTTAG-AAGT
* * * * *
2277 T-TGGGGTAAAAAT-GTAATTTTTGGAAAAAATT-AGGGTTAAAAAATGGAATTTTAAAAAGT
1 TCGGGGGT-AAAATGGTAA-TTTTGG--AAAATTGAGGGGTCAAAAATGGAATTTTTAGAAGT
** * * * *
2337 TTAGGGATAAAAAT-GTAATTTTTGGAGAAATCGA--GGTTAAAAATAGAAATTTTT-GAAGT
1 TCGGGGGT-AAAATGGTAA-TTTTGGA-AAATTGAGGGGTCAAAAAT-GGAATTTTTAGAAGT
* * * * *
2396 TCGAGGGTTAAAATGGTATTTTTGGAAAAATCGA--GGTTAAAAATAGAATTTTTA
1 TCG-GGGGTAAAATGGTAATTTTGG-AAAATTGAGGGGTCAAAAATGGAATTTTTA
2450 AAAATGTAAT
Statistics
Matches: 238, Mismatches: 33, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
57 4 0.02
58 57 0.24
59 62 0.26
60 65 0.27
61 50 0.21
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (59 bp):
TCGGGGGTAAAATGGTAATTTTGGAAAATTGAGGGGTCAAAAATGGAATTTTTAGAAGT
Found at i:2299 original size:59 final size:57
Alignment explanation
Indices: 2103--2448 Score: 260
Period size: 59 Copynumber: 5.9 Consensus size: 57
2093 TGGATACTCG
* * *
2103 GGGGCAAAATGGTAA-TTTTGG-GAAATTGAGGGGT-AAAAATGGAATTTTTAGACA-TTC
1 GGGGTAAAAT-GTAATTTTTGGAAAAATTGA--GGTCAAAAATGGAATTTTTGGA-AGTTC
*
2160 GGGGGGGTAAAATGTTAATTTTT-AAAAAATTGAGGTCAAAAATGGAATTTTTGGAAGTTC
1 ---GGGGTAAAATG-TAATTTTTGGAAAAATTGAGGTCAAAAATGGAATTTTTGGAAGTTC
* * *
2220 GAGGGTAAAATGGTAA-TTTTGGAAAAATTGGGGTCAATAATGGAATTTTTGGAAAGTTT
1 G-GGGTAAAAT-GTAATTTTTGGAAAAATTGAGGTCAAAAATGGAATTTTTGG-AAGTTC
* *** *
2279 GGGGTAAAAATGTAATTTTTGGAAAAAATT-AGGGTTAAAAAATGGAATTTTAAAAAGTTTA
1 GGGGT-AAAATGTAATTTTTGG-AAAAATTGA-GG-TCAAAAATGGAATTTTTGGAAG-TTC
* * * * *
2340 GGGATAAAAATGTAATTTTTGGAGAAATCGAGGTTAAAAATAGAAATTTTT-GAAGTTC
1 GGGGT-AAAATGTAATTTTTGGAAAAATTGAGGTCAAAAAT-GGAATTTTTGGAAGTTC
* * *
2398 GAGGGTTAAAATGGT-ATTTTTGGAAAAATCGAGGTTAAAAATAGAATTTTT
1 G-GGG-TAAAAT-GTAATTTTTGGAAAAATTGAGGTCAAAAATGGAATTTTT
2449 AAAAATGTAA
Statistics
Matches: 239, Mismatches: 27, Indels: 42
0.78 0.09 0.14
Matches are distributed among these distances:
57 5 0.02
58 58 0.24
59 66 0.28
60 61 0.26
61 49 0.21
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (57 bp):
GGGGTAAAATGTAATTTTTGGAAAAATTGAGGTCAAAAATGGAATTTTTGGAAGTTC
Found at i:2378 original size:29 final size:29
Alignment explanation
Indices: 2346--2448 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 29
2336 TTTAGGGATA
2346 AAAAT-GTAATTTTTGGAGAAATCGAGGTT
1 AAAATAGTAATTTTTGGA-AAATCGAGGTT
* **
2375 AAAAATAGAAATTTTT-GAAGTTCGAGGGTT
1 -AAAATAGTAATTTTTGGAAAATCGA-GGTT
*
2405 AAAATGGT-ATTTTTGGAAAAATCGAGGTT
1 AAAATAGTAATTTTTGG-AAAATCGAGGTT
2434 AAAAATAG-AATTTTT
1 -AAAATAGTAATTTTT
2449 AAAAATGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
28 6 0.10
29 16 0.27
30 29 0.49
31 8 0.14
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (29 bp):
AAAATAGTAATTTTTGGAAAATCGAGGTT
Found at i:2430 original size:30 final size:30
Alignment explanation
Indices: 2198--2437 Score: 103
Period size: 30 Copynumber: 8.1 Consensus size: 30
2188 ATTGAGGTCA
* **
2198 AAAATGGAATTTTTGG-AAGTTCGAGGG-T
1 AAAATGGTATTTTTGGAAAAATCGAGGGTT
* * *
2226 AAAATGGTAATTTTGGAAAAATTG-GGGTC
1 AAAATGGTATTTTTGGAAAAATCGAGGGTT
* ** * *
2255 AATAATGGAATTTTTGGAAAGTTTG-GGGTA
1 AA-AATGGTATTTTTGGAAAAATCGAGGGTT
*
2285 AAAAT-GTAATTTTTGGAAAAAAT-TAGGGTT
1 AAAATGGT-ATTTTTGG-AAAAATCGAGGGTT
* ** *
2315 AAAAAATGG-AATTTT--AAAAAGTTTAGGGATA
1 --AAAATGGTATTTTTGGAAAAA-TCGAGGG-TT
*
2346 AAAAT-GTAATTTTTGGAGAAATCGA-GGTT
1 AAAATGGT-ATTTTTGGAAAAATCGAGGGTT
** **
2375 AAAAATAGAAATTTTT-G-AAGTTCGAGGGTT
1 -AAAAT-GGTATTTTTGGAAAAATCGAGGGTT
2405 AAAATGGTATTTTTGGAAAAATCGA-GGTT
1 AAAATGGTATTTTTGGAAAAATCGAGGGTT
2434 AAAA
1 AAAA
2438 ATAGAATTTT
Statistics
Matches: 158, Mismatches: 32, Indels: 43
0.68 0.14 0.18
Matches are distributed among these distances:
28 31 0.20
29 43 0.27
30 60 0.38
31 14 0.09
32 9 0.06
33 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAATGGTATTTTTGGAAAAATCGAGGGTT
Found at i:2439 original size:30 final size:30
Alignment explanation
Indices: 2176--2448 Score: 156
Period size: 29 Copynumber: 9.2 Consensus size: 30
2166 GTAAAATGTT
* * *
2176 AATTTTT-AAAAAATTGAGGTCAAAAATGG
1 AATTTTTGGAAAAATCGAGGTTAAAAATGG
** *
2205 AATTTTTGG-AAGTTCGAGGGT-AAAATGG
1 AATTTTTGGAAAAATCGAGGTTAAAAATGG
* * * *
2233 TAA-TTTTGGAAAAATTGGGGTCAATAATGG
1 -AATTTTTGGAAAAATCGAGGTTAAAAATGG
** * * *
2263 AATTTTTGGAAAGTTTG-GGGTAAAAATGT
1 AATTTTTGGAAAAATCGAGGTTAAAAATGG
*
2292 AATTTTTGGAAAAAAT-TAGGGTTAAAAAATGG
1 AATTTTTGG-AAAAATCGA-GGTT-AAAAATGG
** * *
2324 AA-TTTT--AAAAAGTTTAGGGATAAAAATGT
1 AATTTTTGGAAAAA-TCGA-GGTTAAAAATGG
* *
2353 AATTTTTGGAGAAATCGAGGTTAAAAATAGA
1 AATTTTTGGAAAAATCGAGGTTAAAAAT-GG
**
2384 AATTTTT-G-AAGTTCGAGGGTT-AAAATGG
1 AATTTTTGGAAAAATCGA-GGTTAAAAATGG
* *
2412 TATTTTTGGAAAAATCGAGGTTAAAAATAG
1 AATTTTTGGAAAAATCGAGGTTAAAAATGG
2442 AATTTTT
1 AATTTTT
2449 AAAAATGTAA
Statistics
Matches: 185, Mismatches: 40, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
28 25 0.14
29 66 0.36
30 64 0.35
31 17 0.09
32 13 0.07
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (30 bp):
AATTTTTGGAAAAATCGAGGTTAAAAATGG
Found at i:3019 original size:30 final size:29
Alignment explanation
Indices: 2984--3195 Score: 130
Period size: 30 Copynumber: 7.1 Consensus size: 29
2974 NNNNNNNNNN
*
2984 TTTTGGAAAAATTGGGGTCAAGAATGGAAT
1 TTTTGGAAAAATTGGGGT-AAAAATGGAAT
** *
3014 TTTTGGAAAGTTTGGGGTAAAAATGTAAT
1 TTTTGGAAAAATTGGGGTAAAAATGGAAT
*
3043 TTTTGGAAAAAATTAGGGTTAAAAATGGAA-
1 TTTTGG-AAAAATT-GGGGTAAAAATGGAAT
* *
3073 TTTT--AAAAAGTTTAGGGATAAAAATGTAAT
1 TTTTGGAAAAA--TT-GGGGTAAAAATGGAAT
* * * * *
3103 TTTTGGAGAAATCGAGGTTAAAAATAGAAAA
1 TTTTGGAAAAATTG-GGGTAAAAAT-GGAAT
* * *
3134 TTTT-G--AAGTTCGAGGGTTAAAATGGTAT
1 TTTTGGAAAAATT-G-GGGTAAAAATGGAAT
* *
3162 TTTTGGAAAAATCGAGGTTAAAAATGGAAT
1 TTTTGGAAAAATTG-GGGTAAAAATGGAAT
3192 TTTT
1 TTTT
3196 AAAAATGTAA
Statistics
Matches: 142, Mismatches: 27, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
27 5 0.04
28 9 0.06
29 43 0.30
30 58 0.41
31 23 0.16
32 4 0.03
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAAATTGGGGTAAAAATGGAAT
Found at i:3076 original size:60 final size:58
Alignment explanation
Indices: 2984--3195 Score: 223
Period size: 59 Copynumber: 3.6 Consensus size: 58
2974 NNNNNNNNNN
* * * *
2984 TTTTGGAAAAATTGGGGTCAAGAATGGAATTTTTGGAAAGTTTGGGGTAAAAATGTAAT
1 TTTTGGAAAAATCGAGGTTAAAAATGGAATTTTT-GAAAGTTTGGGGTAAAAATGTAAT
* ** *
3043 TTTTGGAAAAAAT-TAGGGTTAAAAATGGAATTTTAAAAAGTTTAGGGATAAAAATGTAAT
1 TTTTGG-AAAAATCGA-GGTTAAAAATGGAATTTTTGAAAGTTT-GGGGTAAAAATGTAAT
* * * * *
3103 TTTTGGAGAAATCGAGGTTAAAAATAGAAAATTTTG-AAGTTCGAGGGTTAAAATGGT-AT
1 TTTTGGAAAAATCGAGGTTAAAAAT-GGAATTTTTGAAAGTTTG-GGGTAAAAAT-GTAAT
3162 TTTTGGAAAAATCGAGGTTAAAAATGGAATTTTT
1 TTTTGGAAAAATCGAGGTTAAAAATGGAATTTTT
3196 AAAAATGTAA
Statistics
Matches: 127, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
58 8 0.06
59 67 0.53
60 52 0.41
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (58 bp):
TTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGAAAGTTTGGGGTAAAAATGTAAT
Found at i:3199 original size:15 final size:15
Alignment explanation
Indices: 3179--3210 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3169 AAAATCGAGG
3179 TTAAAAATGGAATTT
1 TTAAAAATGGAATTT
*
3194 TTAAAAATGTAATTT
1 TTAAAAATGGAATTT
3209 TT
1 TT
3211 GGAGAAATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (15 bp):
TTAAAAATGGAATTT
Found at i:3202 original size:45 final size:44
Alignment explanation
Indices: 3152--3238 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 44
3142 TTCGAGGGTT
*
3152 AAAATGGT-ATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTA
1 AAAAT-GTAATTTTTGGAAAAATCG-GGGTAAAAATGGAATTTTTA
* *
3197 AAAATGTAATTTTTGGAGAAATCGGGGTCAAAATGGAATTTT
1 AAAATGTAATTTTTGGAAAAATCGGGGTAAAAATGGAATTTT
3239 GGAAGTTTGG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 18 0.47
45 20 0.53
ACGTcount: A:0.40, C:0.03, G:0.22, T:0.34
Consensus pattern (44 bp):
AAAATGTAATTTTTGGAAAAATCGGGGTAAAAATGGAATTTTTA
Found at i:3284 original size:30 final size:28
Alignment explanation
Indices: 3220--3288 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
3210 TGGAGAAATC
* *
3220 GGGGTCAAAATGGAATTTTGGAAGTTTG
1 GGGGTCAAAATGGAATTTTGAAAATTTG
* *
3248 GGGGTCAAAATGGTATTTTAGAAAAATTTT
1 GGGGTCAAAATGGAATTTT-G-AAAATTTG
3278 GGGGTCAAAAT
1 GGGGTCAAAAT
3289 ATGATTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 18 0.51
29 1 0.03
30 16 0.46
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.32
Consensus pattern (28 bp):
GGGGTCAAAATGGAATTTTGAAAATTTG
Done.