Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010071.1 Kokia drynarioides strain JFW-HI SEQ_124849, 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: 3971
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.32
Found at i:158 original size:30 final size:28
Alignment explanation
Indices: 71--159 Score: 108
Period size: 30 Copynumber: 3.1 Consensus size: 28
61 TCCTTTTCCT
* *
71 TTTTAAATTTAATTTATAATTT-TTTTA
1 TTTTAAATTTAATTTCTAATTTCTTATA
98 TTTTAAATTTAATTTCTAATTTCCTATATA
1 TTTTAAATTTAATTTCTAATTT-CT-TATA
*
128 TTTTAATTTTAATTTCTAATTGTCTGTATA
1 TTTTAAATTTAATTTCTAATT-TCT-TATA
158 TT
1 TT
160 CTAATTATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 21 0.39
29 1 0.02
30 31 0.57
31 1 0.02
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (28 bp):
TTTTAAATTTAATTTCTAATTTCTTATA
Found at i:1101 original size:62 final size:61
Alignment explanation
Indices: 1010--1224 Score: 195
Period size: 62 Copynumber: 3.5 Consensus size: 61
1000 GGCCACACCC
* * * * *
1010 AAAAATTTG-ATTTTTTTTATTTAATAAATAGGGTTGTCGGCCATGGCATGACCAACACAAA
1 AAAAATTGGAATTTTTTTAATCTGATAAATAGGG-TGTCGACCATGGCATGACCAACACAAA
* * * **
1071 AAAAAATGGAATTTTTTTAATCTGATAAATAAGAGTGTCGACTATGGCATGACCAACAC-CC
1 AAAAATTGGAATTTTTTTAATCTGATAAAT-AGGGTGTCGACCATGGCATGACCAACACAAA
* * * * * *
1132 AAAAATTTGATTTTTTTTATTCAGATCAAA-AGGGGGTGTCCACCATGGCATGGCCAACACAAA
1 AAAAATTGGAATTTTTTTAATCTGAT-AAATA--GGGTGTCGACCATGGCATGACCAACACAAA
* *
1195 AAAAATTGAAAATTTTTT-ATCTGATAAATA
1 AAAAATTGGAATTTTTTTAATCTGATAAATA
1225 AACATTGCCA
Statistics
Matches: 120, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
60 1 0.01
61 31 0.26
62 71 0.59
63 17 0.14
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (61 bp):
AAAAATTGGAATTTTTTTAATCTGATAAATAGGGTGTCGACCATGGCATGACCAACACAAA
Found at i:1330 original size:107 final size:107
Alignment explanation
Indices: 1123--1331 Score: 314
Period size: 105 Copynumber: 1.9 Consensus size: 107
1113 TATGGCATGA
* * *
1123 CCAACACCCAAAAATTTGATTTTTTTTATTCAGATCAAAAGGGGGTGTCCACCATGGCATGGCCA
1 CCAACACCCAAAAATTTGA--TTTTTTATTCAGATAAAAAAGGGGTGTCCACCATGGCATGACCA
1188 ACACAAAAAAAATTGAAAATTTTTTATCTGATAAATAAACATTG
64 ACACAAAAAAAATTGAAAATTTTTTATCTGATAAATAAACATTG
** *
1232 CCAACACCCAAAAATTTGA-TTTTT-TTCAGATAAAAAAGGGGTGTTGATCATGGCATGACCAAC
1 CCAACACCCAAAAATTTGATTTTTTATTCAGATAAAAAAGGGGTGTCCACCATGGCATGACCAAC
1295 ACAAAAAAAAAATTGAAAATTTTTTATCTGATAAATA
66 AC--AAAAAAAATTGAAAATTTTTTATCTGATAAATA
1332 GGGGTGTCGA
Statistics
Matches: 92, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
105 35 0.38
106 5 0.05
107 33 0.36
109 19 0.21
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (107 bp):
CCAACACCCAAAAATTTGATTTTTTATTCAGATAAAAAAGGGGTGTCCACCATGGCATGACCAAC
ACAAAAAAAATTGAAAATTTTTTATCTGATAAATAAACATTG
Found at i:1410 original size:59 final size:57
Alignment explanation
Indices: 1231--1554 Score: 256
Period size: 58 Copynumber: 5.5 Consensus size: 57
1221 AATAAACATT
** * * * *
1231 GCCAACACCCAAAAATTTGATTTTTT-TCAGATAAAAAAGGGGTGTTGATCATGGCATG
1 GCCAACACAAAAAAAATTGATTTTTTATCA-A-CAAAAAGGGGTGTCGACCATGGCATG
* * * *
1289 ACCAACACAAAAAAAAAATTGAAAATTTTTTATCTGATAAATAGGGGTGTCGACCATGGCATG
1 GCCAACAC--AAAAAAAATTG---ATTTTTTATC-AACAAAAAGGGGTGTCGACCATGGCATG
* * *
1352 GCCAACAC-TAAAAAATTGGATTTTTTATCTAACAAAAAGAGGGTGTCGGCCATTGCATG
1 GCCAACACAAAAAAAATT-GATTTTTTATC-AACAAAAAG-GGGTGTCGACCATGGCATG
** * *
1411 GCCAACACAAAAAAAATTGATTTTTTTATCAGTAAATAGGGGTGTCGAACATGGCATG
1 GCCAACACAAAAAAAATTGA-TTTTTTATCAACAAAAAGGGGTGTCGACCATGGCATG
* * * ** *
1469 GGCAACACAAAAAAAATTAAAATTTTCCTCAGACAAAAAGGGGGTGTCGACCATTGCATG
1 GCCAACACAAAAAAAATT-GATTTTTTATCA-ACAAAAA-GGGGTGTCGACCATGGCATG
* ** *
1529 ACCAACACCCAAAAATTTGATTTTTT
1 GCCAACACAAAAAAAATTGATTTTTT
1555 TTTATCAGAT
Statistics
Matches: 211, Mismatches: 41, Indels: 27
0.76 0.15 0.10
Matches are distributed among these distances:
58 64 0.30
59 43 0.20
60 64 0.30
61 1 0.00
63 36 0.17
64 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.27
Consensus pattern (57 bp):
GCCAACACAAAAAAAATTGATTTTTTATCAACAAAAAGGGGTGTCGACCATGGCATG
Found at i:1516 original size:60 final size:59
Alignment explanation
Indices: 1250--1597 Score: 272
Period size: 60 Copynumber: 5.8 Consensus size: 59
1240 CAAAAATTTG
* * * *
1250 ATTTTTTTCAGATAAAAAAGGGGTGTTGATCATGGCATGACCAACACAAAAAAAAAATTGAAA
1 ATTTTTATCAGAT-AAAAAGGGGTGTCGACCATGGCATGGCCAACAC--AAAAAAAATT-AAA
* * * **
1313 ATTTTTTATCTGATAAATAGGGGTGTCGACCATGGCATGGCCAACAC-TAAAAAATTGGA
1 A-TTTTTATCAGATAAAAAGGGGTGTCGACCATGGCATGGCCAACACAAAAAAAATTAAA
* * * * * *
1372 TTTTTTATCTA-ACAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTGAT
1 ATTTTTATC-AGATAAAAAG-GGGTGTCGACCATGGCATGGCCAACACAAAAAAAATTAAA
* * * *
1432 TTTTTTATCAG-TAAATAGGGGTGTCGAACATGGCATGGGCAACACAAAAAAAATTAAA
1 ATTTTTATCAGATAAAAAGGGGTGTCGACCATGGCATGGCCAACACAAAAAAAATTAAA
** * * * ** * **
1490 ATTTTCCTCAGACAAAAAGGGGGTGTCGACCATTGCATGACCAACACCCAAAAATTTGATTT
1 ATTTTTATCAGATAAAAA-GGGGTGTCGACCATGGCATGGCCAACACAAAAAAAATT-A-AA
* * * *
1552 TTTTTTATCAGATTAAAAGGGGTATCGGCCAT-GCAATGGCCAACAC
1 ATTTTTATCAGATAAAAAGGGGTGTCGACCATGGC-ATGGCCAACAC
1598 CAATTTTTTT
Statistics
Matches: 227, Mismatches: 48, Indels: 22
0.76 0.16 0.07
Matches are distributed among these distances:
58 56 0.25
59 36 0.16
60 59 0.26
61 23 0.10
62 13 0.06
63 30 0.13
64 10 0.04
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (59 bp):
ATTTTTATCAGATAAAAAGGGGTGTCGACCATGGCATGGCCAACACAAAAAAAATTAAA
Found at i:1527 original size:118 final size:118
Alignment explanation
Indices: 1257--1597 Score: 348
Period size: 118 Copynumber: 2.8 Consensus size: 118
1247 TTGATTTTTT
* * * * * *
1257 TCAGATAAAAAAGGGGTGTTGATCATGGCATGACCAACACAAAAAAAAAATTGAAAATTTTTTAT
1 TCAGACAAAAAGGGGGTGTCGACCATTGCATGACCAACAC--AAAAAAAATTG--ATTTTTTTAT
* * * ** * *
1322 CTGATAAATAGGGGTGTCGACCATGGCATGGCCAACACTAAAAAATTGGATTTTTTA
62 CAGATAAATAGGGGTGTCGAACATGGCATGGCCAACACAAAAAAATTAAAATTTTCA
* * *
1379 TCTA-ACAAAAAGAGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTGATTTTTTTATCAG
1 TC-AGACAAAAAGGGGGTGTCGACCATTGCATGACCAACACAAAAAAAATTGATTTTTTTATCAG
* *
1443 -TAAATAGGGGTGTCGAACATGGCATGGGCAACACAAAAAAAATTAAAATTTTCC
65 ATAAATAGGGGTGTCGAACATGGCATGGCCAACAC-AAAAAAATTAAAATTTTCA
** *
1497 TCAGACAAAAAGGGGGTGTCGACCATTGCATGACCAACACCCAAAAATTTGATTTTTTTTTATCA
1 TCAGACAAAAAGGGGGTGTCGACCATTGCATGACCAACACAAAAAAAATTGA--TTTTTTTATCA
* **
1562 GATTAAA-AGGGGTATCGGCCAT-GCAATGGCCAACAC
64 GA-TAAATAGGGGTGTCGAACATGGC-ATGGCCAACAC
1598 CAATTTTTTT
Statistics
Matches: 183, Mismatches: 28, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
117 33 0.18
118 68 0.37
120 25 0.14
121 22 0.12
122 34 0.19
123 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (118 bp):
TCAGACAAAAAGGGGGTGTCGACCATTGCATGACCAACACAAAAAAAATTGATTTTTTTATCAGA
TAAATAGGGGTGTCGAACATGGCATGGCCAACACAAAAAAATTAAAATTTTCA
Found at i:3154 original size:29 final size:29
Alignment explanation
Indices: 3041--3286 Score: 189
Period size: 29 Copynumber: 8.4 Consensus size: 29
3031 AAAGAATATG
* *
3041 GGGTTAAAACGTAATTTT-GAAAGAGTTTGA
1 GGGTTAAAATGTAATTTTAGGAA-AGTTT-A
* * *
3071 GGGTCAAAATGCAATTTT-GGAAAATTTTAA
1 GGGTTAAAATGTAATTTTAGG-AAAGTTT-A
* *
3101 GGGCTAAAATGTAACTTTT-GAAAAGTTTA
1 GGGTTAAAATGTAA-TTTTAGGAAAGTTTA
* * *
3130 GGGTTAAAATATAATGTTAGGAAAGTTTG
1 GGGTTAAAATGTAATTTTAGGAAAGTTTA
* *
3159 GGGTCAAAA-GTAATTTTGGGAAAGTTTA
1 GGGTTAAAATGTAATTTTAGGAAAGTTTA
** * *
3187 GGGGCCAAAATGCAATTTT-GGAAAATTTTA
1 -GGGTTAAAATGTAATTTTAGG-AAAGTTTA
* * * *
3217 GGCTTAAAATTTAATTTTTA-AAAAGATTA
1 GGGTTAAAATGTAA-TTTTAGGAAAGTTTA
*
3246 GGGTTAAAATGTAATTTTAGGAAAGTTTG
1 GGGTTAAAATGTAATTTTAGGAAAGTTTA
3275 GGGTTAAAATGT
1 GGGTTAAAATGT
3287 GACTTTTAAA
Statistics
Matches: 170, Mismatches: 37, Indels: 19
0.75 0.16 0.08
Matches are distributed among these distances:
28 23 0.14
29 84 0.49
30 56 0.33
31 7 0.04
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTAGGAAAGTTTA
Found at i:3276 original size:116 final size:118
Alignment explanation
Indices: 3039--3283 Score: 347
Period size: 116 Copynumber: 2.1 Consensus size: 118
3029 TCAAAGAATA
*
3039 TGGGGTTAAAACGTAATTTTGAAAGAGTTTGAGGGTCAAAATGCAATTTTGGAAAATTTTAAGGG
1 TGGGGTTAAAACGTAATTTTGAAAGAGTTTGAGGGCCAAAATGCAATTTTGGAAAATTTTAAGGG
* *
3104 CTAAAATGTAACTTTTGAAAAGTTTAGGGTTAAAATATAATGTTAGGAAAGTT
66 CTAAAATGTAACTTTTAAAAAGATTAGGGTTAAAATATAATGTTAGGAAAGTT
* *
3157 TGGGGTCAAAA-GTAATTTTGGGAA-AGTTT-AGGGGCCAAAATGCAATTTTGGAAAATTTT-A-
1 TGGGGTTAAAACGTAATTTT-GAAAGAGTTTGA-GGGCCAAAATGCAATTTTGGAAAATTTTAAG
* * * *
3217 GGCTTAAAATTTAATTTTTAAAAAGATTAGGGTTAAAATGTAATTTTAGGAAAGTT
64 GGC-TAAAATGTAACTTTTAAAAAGATTAGGGTTAAAATATAATGTTAGGAAAGTT
3273 TGGGGTTAAAA
1 TGGGGTTAAAA
3284 TGTGACTTTT
Statistics
Matches: 114, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
115 3 0.03
116 58 0.51
117 40 0.35
118 13 0.11
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (118 bp):
TGGGGTTAAAACGTAATTTTGAAAGAGTTTGAGGGCCAAAATGCAATTTTGGAAAATTTTAAGGG
CTAAAATGTAACTTTTAAAAAGATTAGGGTTAAAATATAATGTTAGGAAAGTT
Found at i:3284 original size:87 final size:87
Alignment explanation
Indices: 3052--3285 Score: 242
Period size: 87 Copynumber: 2.7 Consensus size: 87
3042 GGTTAAAACG
* * * * * *
3052 TAATTTTGAAAGAGTTTGAGGGTCAAAATGCAATTTTGGAAAATTTTAAGGGCTAAAATGTAACT
1 TAATTTTTAAAAAGTTT-AGGGTCAAAATGTAATTTTGG-AAAGTTTAGGGGCTAAAATGCAACT
*
3117 TTTGAAAAGTTTAGGGTTAAAATA
64 TTTGAAAAGTTTAGGCTTAAAATA
* * * *
3141 TAA-TGTTAGGAAAGTTTGGGGTCAAAA-GTAATTTTGGGAAAGTTTAGGGGCCAAAATGCAA-T
1 TAATTTTTA-AAAAGTTTAGGGTCAAAATGTAATTTT-GGAAAGTTTAGGGGCTAAAATGCAACT
* *
3203 TTTGGAAAATTTTAGGCTTAAAATT
64 TTT-GAAAAGTTTAGGCTTAAAATA
* * *
3228 TAATTTTTAAAAAGATTAGGGTTAAAATGTAATTTTAGGAAAGTTT-GGGGTTAAAATG
1 TAATTTTTAAAAAGTTTAGGGTCAAAATGTAATTTT-GGAAAGTTTAGGGGCTAAAATG
3286 TGACTTTTAA
Statistics
Matches: 119, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
86 4 0.03
87 71 0.60
88 35 0.29
89 9 0.08
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (87 bp):
TAATTTTTAAAAAGTTTAGGGTCAAAATGTAATTTTGGAAAGTTTAGGGGCTAAAATGCAACTTT
TGAAAAGTTTAGGCTTAAAATA
Done.