Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006153.1 Kokia drynarioides strain JFW-HI SEQ_120698, 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: 17166
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Warning! 158 characters in sequence are not A, C, G, or T
Found at i:536 original size:16 final size:18
Alignment explanation
Indices: 515--553 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
505 AAATTTCAAC
515 TAAATATATT-ATTT-AT
1 TAAATATATTAATTTGAT
*
531 TAAATATTTTAATTTGAT
1 TAAATATATTAATTTGAT
549 TAAAT
1 TAAAT
554 TGTAATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 4 0.20
18 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
TAAATATATTAATTTGAT
Found at i:5293 original size:27 final size:27
Alignment explanation
Indices: 5263--5314 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
5253 AATGGTTAAA
5263 GTCAAACTCAACT-ATCAACGATCAATT
1 GTCAAACTCAA-TGATCAACGATCAATT
* *
5290 GTCAAAGTCAATGATCAACGGTCAA
1 GTCAAACTCAATGATCAACGATCAA
5315 CTATCAACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.05
27 21 0.95
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (27 bp):
GTCAAACTCAATGATCAACGATCAATT
Found at i:7093 original size:26 final size:26
Alignment explanation
Indices: 7056--7155 Score: 82
Period size: 25 Copynumber: 4.0 Consensus size: 26
7046 CAAGTCTTCT
*
7056 AGAAT-TTAGCTCTAATGAGCCCAGAC
1 AGAATATTAGCTCTAACGAG-CCAGAC
*
7082 AGAATATT-GCTCTTACGAGCCAGAC
1 AGAATATTAGCTCTAACGAGCCAGAC
* * * *
7107 AAAATATCA-CTCTTACGAGCCAGAT
1 AGAATATTAGCTCTAACGAGCCAGAC
* * *
7132 AGAATATCA-CTCTCACAAGCCAGA
1 AGAATATTAGCTCTAACGAGCCAGA
7156 ATTCAAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
25 48 0.75
26 14 0.22
27 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (26 bp):
AGAATATTAGCTCTAACGAGCCAGAC
Found at i:7112 original size:25 final size:25
Alignment explanation
Indices: 7076--7155 Score: 97
Period size: 25 Copynumber: 3.2 Consensus size: 25
7066 TCTAATGAGC
* **
7076 CCAGACAGAATATTGCTCTTACGAG
1 CCAGACAAAATATCACTCTTACGAG
7101 CCAGACAAAATATCACTCTTACGAG
1 CCAGACAAAATATCACTCTTACGAG
* * * *
7126 CCAGATAGAATATCACTCTCACAAG
1 CCAGACAAAATATCACTCTTACGAG
7151 CCAGA
1 CCAGA
7156 ATTCAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.38, C:0.28, G:0.15, T:0.20
Consensus pattern (25 bp):
CCAGACAAAATATCACTCTTACGAG
Found at i:8076 original size:100 final size:100
Alignment explanation
Indices: 7903--8102 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
7893 ATGAAAATGA
7903 TGAATTTTCATCTTAATTTCCTTTAATTTAATATATATAATAATGACAATTTTGTAATTTTTAAG
1 TGAATTTTCATCTTAATTTCCTTTAATTTAATATATATAATAATGACAATTTTGTAATTTTTAAG
7968 ACTTTCTTCATTATGTTTTAATTAACCCTTTTTAG
66 ACTTTCTTCATTATGTTTTAATTAACCCTTTTTAG
8003 TGAATTTTCATCTTAATTTCCTTTAATTTAATATATATAATAATGACAATTTTGTAATTTTTAAG
1 TGAATTTTCATCTTAATTTCCTTTAATTTAATATATATAATAATGACAATTTTGTAATTTTTAAG
8068 ACTTTCTTCATTATGTTTTAATTAACCCTTTTTAG
66 ACTTTCTTCATTATGTTTTAATTAACCCTTTTTAG
8103 CCCAAATTAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (100 bp):
TGAATTTTCATCTTAATTTCCTTTAATTTAATATATATAATAATGACAATTTTGTAATTTTTAAG
ACTTTCTTCATTATGTTTTAATTAACCCTTTTTAG
Found at i:8988 original size:31 final size:31
Alignment explanation
Indices: 8871--8988 Score: 98
Period size: 31 Copynumber: 3.9 Consensus size: 31
8861 TTAATATAAC
* ** * *
8871 ATTTGGTACTTGAACTTGACACTTTTTCTTA
1 ATTTGGTACTTAAACTTTTCATTTTTTCCTA
*
8902 ATTTGGTACCTAAACTTTT--TTTTTGTCC-A
1 ATTTGGTACTTAAACTTTTCATTTTT-TCCTA
* * ** *
8931 ATTTGATACTCAAACTTGGCACTTTTTCCTA
1 ATTTGGTACTTAAACTTTTCATTTTTTCCTA
*
8962 ATTTGGTGCTTAAACTTTTCATTTTTT
1 ATTTGGTACTTAAACTTTTCATTTTTT
8989 TTTAGTTGAT
Statistics
Matches: 65, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
29 19 0.29
30 5 0.08
31 41 0.63
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTTTCATTTTTTCCTA
Found at i:9370 original size:28 final size:28
Alignment explanation
Indices: 9278--9430 Score: 135
Period size: 28 Copynumber: 5.2 Consensus size: 28
9268 TTCACGTATA
* *
9278 AAATTGGGTCCAAAAAAAGTTTTGGTATC
1 AAATTGGGT-CAAAAAAAGTTTAGGTACC
*** *
9307 AAATTCGGAAAAAAATGACAAATTTAGGTACC
1 AAATT-GGGTCAAAA--A-AAGTTTAGGTACC
*
9339 AAATTGGGTCAAAAAAAGATTAGGTACC
1 AAATTGGGTCAAAAAAAGTTTAGGTACC
* **
9367 AAATTAGGAAAAAATATCAAGTTTAGGTACC
1 AAATTGGGTCAAAA-A--AAGTTTAGGTACC
*
9398 AAATTGGGTCAAAAAAAGTTTAAGTACC
1 AAATTGGGTCAAAAAAAGTTTAGGTACC
9426 AAATT
1 AAATT
9431 AAGAAAAAAT
Statistics
Matches: 98, Mismatches: 19, Indels: 15
0.74 0.14 0.11
Matches are distributed among these distances:
28 39 0.40
29 11 0.11
30 3 0.03
31 30 0.31
32 15 0.15
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (28 bp):
AAATTGGGTCAAAAAAAGTTTAGGTACC
Found at i:9457 original size:59 final size:59
Alignment explanation
Indices: 9229--9460 Score: 266
Period size: 59 Copynumber: 3.9 Consensus size: 59
9219 ATTGAATTTA
* * * * * **
9229 AAAAAAAGCTTAGGTACCAAATTAGGAAATAATGCCAAGTTCACGTATAAAATTGGGTCC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTACCAAATTGGGT-C
* * * * *
9289 AAAAAAAGTTTTGGTATCAAATTCGGAAAAAAATGACAAATTTAGGTACCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGG-AAAAAATGTCAAATTCAGGTACCAAATTGGGTC
* * * *
9349 AAAAAAAGATTAGGTACCAAATTAGGAAAAAATATCAAGTTTAGGTACCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTACCAAATTGGGTC
* * **
9408 AAAAAAAGTTTAAGTACCAAATTAAGAAAAAATGTCAAATTCAAATACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTACCAAAT
9461 ATTATATTAA
Statistics
Matches: 145, Mismatches: 26, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
59 75 0.52
60 45 0.31
61 25 0.17
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTACCAAATTGGGTC
Found at i:12954 original size:31 final size:31
Alignment explanation
Indices: 12915--13019 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 31
12905 TAAAAAAAGC
12915 TTAGGTACCAAATTAGAAAAAAATGATAAGT
1 TTAGGTACCAAATTAGAAAAAAATGATAAGT
* * * * **
12946 TCATGTACCGAATTGGGTCAAAAA--A-AAGT
1 TTAGGTACCAAATT-AGAAAAAAATGATAAGT
* * *
12975 TTAGGTATCAAATTAGGAAAAAATGTTAAGT
1 TTAGGTACCAAATTAGAAAAAAATGATAAGT
13006 TTAGGTACCAAATT
1 TTAGGTACCAAATT
13020 GAGTCAAAAA
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
28 6 0.11
29 14 0.25
30 1 0.02
31 28 0.51
32 6 0.11
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.29
Consensus pattern (31 bp):
TTAGGTACCAAATTAGAAAAAAATGATAAGT
Found at i:12970 original size:60 final size:60
Alignment explanation
Indices: 12888--13030 Score: 178
Period size: 60 Copynumber: 2.4 Consensus size: 60
12878 TAATAATTAT
* * **
12888 AGGTACTAAATTGAATTTAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGATAAGTTC
1 AGGTACCAAATTGAGTCAAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGATAAGTTC
* * * * * * * *
12948 ATGTACCGAATTGGGTCAAAAAAAAGTTTAGGTATCAAATTAGGAAAAAATGTTAAGTTT
1 AGGTACCAAATTGAGTCAAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGATAAGTTC
13008 AGGTACCAAATTGAGTCAAAAAA
1 AGGTACCAAATTGAGTCAAAAAA
13031 GTCTAAATTC
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 68 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (60 bp):
AGGTACCAAATTGAGTCAAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGATAAGTTC
Found at i:13587 original size:19 final size:19
Alignment explanation
Indices: 13536--13605 Score: 79
Period size: 19 Copynumber: 3.6 Consensus size: 19
13526 CTCTCAACAT
*
13536 AAATTGCAAAATAATTTTCA
1 AAATT-CAAAATAATTTTTA
13556 AAACTTCAAAATAATTTTTA
1 AAA-TTCAAAATAATTTTTA
* *
13576 AAATTTAAAAT-ATTTGTAA
1 AAATTCAAAATAATTT-TTA
13595 AAATTCAAAAT
1 AAATTCAAAAT
13606 TTATATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
18 4 0.09
19 19 0.43
20 19 0.43
21 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (19 bp):
AAATTCAAAATAATTTTTA
Found at i:14398 original size:20 final size:20
Alignment explanation
Indices: 14353--14401 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
14343 TAAAAATTAC
14353 AAAACAATTCAAAACAATTTT
1 AAAA-AATTCAAAACAATTTT
* *
14374 CAAAAATTCAAAA-TATTTAT
1 AAAAAATTCAAAACAATTT-T
14394 AAAAAATT
1 AAAAAATT
14402 TTAATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 17 0.71
21 3 0.12
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATTCAAAACAATTTT
Found at i:17017 original size:52 final size:54
Alignment explanation
Indices: 16951--17059 Score: 125
Period size: 52 Copynumber: 2.0 Consensus size: 54
16941 AATGAATTGA
* * * *
16951 TGATTAATCGATTTGATCATCGAA-TCGATTCTAAAAA-CTT-TTATATAAAAGT
1 TGATTAATCAATTTGACCATC-AATTCAATTCTAAAAACCTTAATATATAAAAGT
* *
17003 TGATTAATTAATTTGACCATCAATTCAATTTTAAAAACCTTAAATATATAAAAGT
1 TGATTAATCAATTTGACCATCAATTCAATTCTAAAAACCTT-AATATATAAAAGT
17058 TG
1 TG
17060 GAGCTTGTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
51 2 0.04
52 29 0.62
53 3 0.06
55 13 0.28
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (54 bp):
TGATTAATCAATTTGACCATCAATTCAATTCTAAAAACCTTAATATATAAAAGT
Done.