Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006601.1 Kokia drynarioides strain JFW-HI SEQ_121190, 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: 48532
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:52 original size:6 final size:6
Alignment explanation
Indices: 41--67 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31 CTCTTATTTC
41 TTCCTT TTCCTT TTCCTT TTCCTT TTC
1 TTCCTT TTCCTT TTCCTT TTCCTT TTC
68 TCCTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCCTT
Found at i:362 original size:28 final size:28
Alignment explanation
Indices: 331--389 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
321 ATTAATATTA
331 ATTAATATTATTT-CCATTTATTACTGCT
1 ATTAATATTATTTACCATTTATTA-TGCT
* **
359 ATTATTATTATTTATTATTTATTATGCT
1 ATTAATATTATTTACCATTTATTATGCT
387 ATT
1 ATT
390 TTAAAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.59
Consensus pattern (28 bp):
ATTAATATTATTTACCATTTATTATGCT
Found at i:1104 original size:17 final size:17
Alignment explanation
Indices: 1050--1153 Score: 87
Period size: 17 Copynumber: 6.4 Consensus size: 17
1040 CTTTATTTAT
* *
1050 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
*
1067 TTTAAATTTGAAAACAAA
1 TTTAAATTT-AAAATAAA
*
1085 TTTAAA-CT----TAAA
1 TTTAAATTTAAAATAAA
1097 -TTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
1113 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
1131 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
1148 TTTAAA
1 TTTAAA
1154 ATGAGTTTGG
Statistics
Matches: 69, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
11 5 0.07
12 4 0.06
16 5 0.07
17 29 0.42
18 26 0.38
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:1104 original size:46 final size:46
Alignment explanation
Indices: 1051--1155 Score: 165
Period size: 46 Copynumber: 2.3 Consensus size: 46
1041 TTTATTTATT
* *
1051 TTAAATTTATAATAATTTTAAATTTGAAAACAAATTTAAACTTAAA
1 TTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAA
* *
1097 TTAAATTTAAAATAAATTTAAATTTTAAAACAAATTTAATCTTAAA
1 TTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAA
*
1143 ATAAATTTAAAAT
1 TTAAATTTAAAAT
1156 GAGTTTGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (46 bp):
TTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAA
Found at i:1106 original size:11 final size:11
Alignment explanation
Indices: 1086--1120 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1076 GAAAACAAAT
*
1086 TTAAACTTAAA
1 TTAAATTTAAA
1097 TTAAATTTAAA
1 TTAAATTTAAA
*
1108 ATAAATTTAAA
1 TTAAATTTAAA
1119 TT
1 TT
1121 TTAAAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:1131 original size:29 final size:28
Alignment explanation
Indices: 1070--1135 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
1060 TAATAATTTT
**
1070 AAATTTGAAAACAAATTTAAACTTAAATT
1 AAATTT-AAAACAAATTTAAACTTAAAAC
* *
1099 AAATTTAAAATAAATTTAAATTTTAAAAC
1 AAATTTAAAACAAATTTAAA-CTTAAAAC
1128 AAATTTAA
1 AAATTTAA
1136 TCTTAAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATTTAAAACAAATTTAAACTTAAAAC
Found at i:7448 original size:16 final size:16
Alignment explanation
Indices: 7429--7459 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7419 CATTTTAGAA
7429 CATATACATTTGAAAC
1 CATATACATTTGAAAC
*
7445 CATATATATTTGAAA
1 CATATACATTTGAAA
7460 AATTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATACATTTGAAAC
Found at i:7535 original size:15 final size:15
Alignment explanation
Indices: 7515--7552 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
7505 ATTAGCTCCC
7515 AAAATTATT-ATTTTT
1 AAAATT-TTGATTTTT
7530 AAAATTTTGATTTTT
1 AAAATTTTGATTTTT
*
7545 AATATTTT
1 AAAATTTT
7553 TTAAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
AAAATTTTGATTTTT
Found at i:8523 original size:19 final size:19
Alignment explanation
Indices: 8499--8541 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
8489 AAAAATAAAT
8499 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
8518 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
8537 TAAAT
1 TAAAT
8542 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:9532 original size:25 final size:26
Alignment explanation
Indices: 9488--9537 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
9478 ATTTTGATTT
9488 AACTATAAAAAATTATAAAT-ATATG
1 AACTATAAAAAATTATAAATCATATG
9513 AACTATTAAAATAA-TA-AAATCATAT
1 AACTA-TAAAA-AATTATAAATCATAT
9538 TTTAACTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 9 0.41
26 11 0.50
27 2 0.09
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (26 bp):
AACTATAAAAAATTATAAATCATATG
Found at i:11466 original size:32 final size:32
Alignment explanation
Indices: 11430--11522 Score: 141
Period size: 32 Copynumber: 2.9 Consensus size: 32
11420 AGATTCCGAG
* *
11430 GTTTAAGTTTGGGTTTAATATCGTGGTTCGAA
1 GTTTAGGTTTGGATTTAATATCGTGGTTCGAA
* * *
11462 GTTTAGGTTTGGATTTAGTATGGTGGTTCGAG
1 GTTTAGGTTTGGATTTAATATCGTGGTTCGAA
11494 GTTTAGGTTTGGATTTAATATCGTGGTTC
1 GTTTAGGTTTGGATTTAATATCGTGGTTC
11523 AAGGTTCAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.18, C:0.05, G:0.31, T:0.45
Consensus pattern (32 bp):
GTTTAGGTTTGGATTTAATATCGTGGTTCGAA
Found at i:15173 original size:21 final size:23
Alignment explanation
Indices: 15143--15191 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
15133 AATTTTGATA
15143 TTTTAGCTTAA-T-TTTTAATTT
1 TTTTAGCTTAATTATTTTAATTT
*
15164 TTTTATCTTAATTATTTTAATTT
1 TTTTAGCTTAATTATTTTAATTT
15187 TTTTA
1 TTTTA
15192 ATAATTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 14 0.56
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTAGCTTAATTATTTTAATTT
Found at i:15203 original size:23 final size:22
Alignment explanation
Indices: 15155--15197 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
15145 TTAGCTTAAT
*
15155 TTTTAATTTTTTTATCTTAATTA
1 TTTTAATTTTTTTA-CATAATTA
15178 TTTTAATTTTTTTA-ATAATT
1 TTTTAATTTTTTTACATAATT
15198 TCATTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
23 14 0.74
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAATTTTTTTACATAATTA
Found at i:23394 original size:21 final size:21
Alignment explanation
Indices: 23370--23417 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
23360 AAATATATTT
23370 TAAATACTTTTT-AA-TAATTAA
1 TAAATA-TTTTTAAATTAATT-A
23391 TAAATTATTTTTAAATTAATTA
1 TAAA-TATTTTTAAATTAATTA
23413 TAAAT
1 TAAAT
23418 GAAATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
21 10 0.42
22 9 0.38
23 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATATTTTTAAATTAATTA
Found at i:23409 original size:26 final size:26
Alignment explanation
Indices: 23380--23433 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
23370 TAAATACTTT
* *
23380 TTAATAATTAAT-AAATTATTTTTAAA
1 TTAATAATAAATGAAA-TATTTTAAAA
*
23406 TTAATTATAAATGAAATATTTTAAAA
1 TTAATAATAAATGAAATATTTTAAAA
23432 TT
1 TT
23434 TTAAATGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (26 bp):
TTAATAATAAATGAAATATTTTAAAA
Found at i:23415 original size:22 final size:21
Alignment explanation
Indices: 23377--23417 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
23367 TTTTAAATAC
23377 TTTTTAATAATTAATAAATTA
1 TTTTTAATAATTAATAAATTA
23398 TTTTTAAATTAATT-ATAAAT
1 TTTTT-AA-TAATTAATAAAT
23418 GAAATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTTAATAATTAATAAATTA
Found at i:27194 original size:12 final size:12
Alignment explanation
Indices: 27177--27207 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27167 TATGCTAAAA
27177 GAGAGAGAGAGC
1 GAGAGAGAGAGC
27189 GAGAGAGAGAGC
1 GAGAGAGAGAGC
*
27201 AAGAGAG
1 GAGAGAG
27208 CGAGAGTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.06, G:0.48, T:0.00
Consensus pattern (12 bp):
GAGAGAGAGAGC
Found at i:33683 original size:17 final size:17
Alignment explanation
Indices: 33661--33700 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
33651 TGGATTATTA
33661 GTTTCTCTTATTGCTTT
1 GTTTCTCTTATTGCTTT
33678 GTTTCTCTTATTGCTTT
1 GTTTCTCTTATTGCTTT
33695 GTTTCT
1 GTTTCT
33701 GAAGATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.17, G:0.12, T:0.65
Consensus pattern (17 bp):
GTTTCTCTTATTGCTTT
Found at i:40395 original size:261 final size:255
Alignment explanation
Indices: 39931--40677 Score: 942
Period size: 246 Copynumber: 2.9 Consensus size: 255
39921 GGATCTGTTG
* * *
39931 AAGATTCTGAACATAAATCCAAAAGATTAGCCAAAGCCGAAGCCAATGCTAGCCTATCAACTTCA
1 AAGATTCTGAACACAAATCCAAAAGATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCA
* *
39996 GCAGGAGAAACTAACAGCTTGAATTACATAAAAAATGGTGAACAGATACAAAATATGCCTCT-AC
66 GCAGGAGAAACTAACAGCTTGAA-TACATAAAAAATGGTGAACAGATACAAAATATGTCT-TGTC
*
40060 AAGAAGGTATCATGGACACATTACAATCAATGGAAGATAAT-TGCAAGGCCATTGATAGCATCCC
129 AAGAAGGTATCATGGACACATCACAATCAATGGAAGATAATCT-CAAGGCCATTGATAGCATCCC
* * *
40124 AGATGTTGATAATGCTACAAAGGGTACATCTATCGACCATGACATTGCTGTGAAAGCATCAAAGC
193 AGATGTTGATAACGCTACAAAGGGTACATCTATC-ACCATGACATTGC----AAAGAATCAAAAC
40189 CAA
253 CAA
*
40192 AAGATTCTGAACACAAATCCAAAAGATTAGCCGAAGTTGAAGCCAATGCTAGCCTATCAACTTCA
1 AAGATTCTGAACACAAATCCAAAAGATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCA
* * *
40257 GCAGGAGAAACTAACAGCTTGAATAGCATAAAAAATGGTCAACAGATGCAGAATATGTCTTGTCA
66 GCAGGAGAAACTAACAGCTTGAATA-CATAAAAAATGGTGAACAGATACAAAATATGTCTTGTCA
* *
40322 AGAAGGTATCATGGACACGTCACTATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAG
130 AGAAGGTATCATGGACACATCACAATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAG
40387 ATGTTGATAACGCTACAAAGGGTACATCTAT---C---A-A---CAAAGAATCAAAACCAA
195 ATGTTGATAACGCTACAAAGGGTACATCTATCACCATGACATTGCAAAGAATCAAAACCAA
* * ** * * * *
40438 ACGATTCTGAACACAAGTCCAAAATTTTAGCTGAAGCTGAAGCCAACGCTGGCTTATCAACTTCA
1 AAGATTCTGAACACAAATCCAAAAGATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCA
* ** * * * *
40503 GCAGGAGAAGCTAAGGGCTTGAATAACATAAAAAATGGTGAAAAAATACAAAATACGTCTCGTCA
66 GCAGGAGAAACTAACAGCTTGAAT-ACATAAAAAATGGTGAACAGATACAAAATATGTCTTGTCA
** * ** * * *
40568 AGAAGGTATCATGGATGCATCACCATCAGGGGAAGATAATCTTAAGGCCATTGATGGCATCCTAG
130 AGAAGGTATCATGGACACATCACAATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAG
* * *
40633 GTGTTAATACCGCTACAAAGGGTACATCTATCAACCATGACATTG
195 ATGTTGATAACGCTACAAAGGGTACATCTATC-ACCATGACATTG
40678 TGGTGAGAGC
Statistics
Matches: 425, Mismatches: 46, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
246 207 0.49
247 1 0.00
250 2 0.00
253 2 0.00
254 2 0.00
257 1 0.00
260 3 0.01
261 206 0.48
262 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (255 bp):
AAGATTCTGAACACAAATCCAAAAGATTAGCCGAAGCTGAAGCCAATGCTAGCCTATCAACTTCA
GCAGGAGAAACTAACAGCTTGAATACATAAAAAATGGTGAACAGATACAAAATATGTCTTGTCAA
GAAGGTATCATGGACACATCACAATCAATGGAAGATAATCTCAAGGCCATTGATAGCATCCCAGA
TGTTGATAACGCTACAAAGGGTACATCTATCACCATGACATTGCAAAGAATCAAAACCAA
Found at i:48015 original size:11 final size:10
Alignment explanation
Indices: 47999--48041 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
47989 TATGTTTTCC
47999 ATAATATATTA
1 ATAATAT-TTA
*
48010 ATAATATTTT
1 ATAATATTTA
48020 ATAATATTTA
1 ATAATATTTA
*
48030 ATGA-ATTTA
1 ATAATATTTA
48039 ATA
1 ATA
48042 CATTTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.25
10 14 0.50
11 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
ATAATATTTA
Done.