Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004671.1 Kokia drynarioides strain JFW-HI SEQ_118219, 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: 38933
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:176 original size:13 final size:14
Alignment explanation
Indices: 144--177 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
134 AACAAAAAAC
144 TTAAAATAATCAAA
1 TTAAAATAATCAAA
158 TT-AAATAA-CAAA
1 TTAAAATAATCAAA
170 TTAAAATA
1 TTAAAATA
178 TTTTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 11 0.58
14 2 0.11
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
TTAAAATAATCAAA
Found at i:415 original size:11 final size:11
Alignment explanation
Indices: 395--430 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
385 CTTCTCCTTC
395 TTCCTTCTTTT
1 TTCCTTCTTTT
*
406 TTCTTTCTTTT
1 TTCCTTCTTTT
*
417 TTCCTTCATTT
1 TTCCTTCTTTT
428 TTC
1 TTC
431 GTTGGTCCCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (11 bp):
TTCCTTCTTTT
Found at i:1391 original size:3 final size:3
Alignment explanation
Indices: 1383--1409 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1373 GTCAGCCCCT
1383 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1410 AAAGTACCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2411 original size:54 final size:54
Alignment explanation
Indices: 2346--2454 Score: 209
Period size: 54 Copynumber: 2.0 Consensus size: 54
2336 GTAATGTCTG
*
2346 TTTTTGTTGTTTACAAAAATTGATTCTTTCAGCATTCTTACTTGTTTATCTTTA
1 TTTTTATTGTTTACAAAAATTGATTCTTTCAGCATTCTTACTTGTTTATCTTTA
2400 TTTTTATTGTTTACAAAAATTGATTCTTTCAGCATTCTTACTTGTTTATCTTTA
1 TTTTTATTGTTTACAAAAATTGATTCTTTCAGCATTCTTACTTGTTTATCTTTA
2454 T
1 T
2455 AATATCATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.23, C:0.13, G:0.08, T:0.56
Consensus pattern (54 bp):
TTTTTATTGTTTACAAAAATTGATTCTTTCAGCATTCTTACTTGTTTATCTTTA
Found at i:4754 original size:13 final size:13
Alignment explanation
Indices: 4736--4761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4726 TATTTCATAT
4736 TTGTTTCGTTCTA
1 TTGTTTCGTTCTA
4749 TTGTTTCGTTCTA
1 TTGTTTCGTTCTA
4762 CTTAGCCCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (13 bp):
TTGTTTCGTTCTA
Found at i:6751 original size:27 final size:27
Alignment explanation
Indices: 6720--6798 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
6710 TTTTTTTCTA
6720 GAAAATCAATACATTTTCTAAACATTG
1 GAAAATCAATACATTTTCTAAACATTG
*
6747 GAAAAT--ATA-ATTTTCT---C--TA
1 GAAAATCAATACATTTTCTAAACATTG
6766 GAAAATCAATACATTTTCTAAACATTG
1 GAAAATCAATACATTTTCTAAACATTG
6793 GAAAAT
1 GAAAAT
6799 ATAATTTTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 16
0.70 0.03 0.27
Matches are distributed among these distances:
19 7 0.17
21 4 0.10
22 7 0.17
24 7 0.17
25 4 0.10
27 13 0.31
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.34
Consensus pattern (27 bp):
GAAAATCAATACATTTTCTAAACATTG
Found at i:6753 original size:23 final size:24
Alignment explanation
Indices: 6732--6808 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
6722 AAATCAATAC
6732 ATTTTCTAAACATTGGAAAATATA
1 ATTTTCTAAACATTGGAAAATATA
*
6756 ATTTTCT---C--TAGAAAATCAATA
1 ATTTTCTAAACATTGGAAAAT--ATA
6777 CATTTTCTAAACATTGGAAAATATA
1 -ATTTTCTAAACATTGGAAAATATA
6802 ATTTTCT
1 ATTTTCT
6809 CTAGAAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
19 7 0.16
21 4 0.09
22 7 0.16
24 14 0.33
25 4 0.09
27 7 0.16
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (24 bp):
ATTTTCTAAACATTGGAAAATATA
Found at i:6783 original size:46 final size:46
Alignment explanation
Indices: 6686--6829 Score: 252
Period size: 46 Copynumber: 3.1 Consensus size: 46
6676 ACATGGAATC
*
6686 TTCTAAACATTGGAAAATATAATTTTTTTTTCTAGAAAATCAATACATT
1 TTCTAAACATTGGAAAATATAA---TTTTCTCTAGAAAATCAATACATT
6735 TTCTAAACATTGGAAAATATAATTTTCTCTAGAAAATCAATACATT
1 TTCTAAACATTGGAAAATATAATTTTCTCTAGAAAATCAATACATT
6781 TTCTAAACATTGGAAAATATAATTTTCTCTAGAAAATCAATACATT
1 TTCTAAACATTGGAAAATATAATTTTCTCTAGAAAATCAATACATT
6827 TTC
1 TTC
6830 CATAAAAGAT
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
46 72 0.77
49 22 0.23
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (46 bp):
TTCTAAACATTGGAAAATATAATTTTCTCTAGAAAATCAATACATT
Found at i:12429 original size:16 final size:17
Alignment explanation
Indices: 12408--12442 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12398 ATAAACATTA
12408 TAATTAAT-TTAAATAT
1 TAATTAATATTAAATAT
*
12424 TAATTAATATTAACTAT
1 TAATTAATATTAAATAT
12441 TA
1 TA
12443 TAAATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTAATATTAAATAT
Found at i:26878 original size:59 final size:59
Alignment explanation
Indices: 26783--26972 Score: 238
Period size: 59 Copynumber: 3.2 Consensus size: 59
26773 ATTTAATAAA
* * *
26783 TTTAGGTACCAAATTGAATCTAAAAAAAA-CTTAGGTACCAAATTAGAAAAAATGTCAAG
1 TTTAGGTACCAACTTGGATC-AAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAG
* * * * * * *
26842 TTCAGGTACCAATTTGGGTCCAAAAAAGGTTTAGGTACCAAAATAGGAAAAATGTCAAG
1 TTTAGGTACCAACTTGGATCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAG
* * *
26901 TTTAGGTACCAACTTGGATCAAAAAAAAGTTTAGGCACCAAATTAGGAAAAAGTGTTAAG
1 TTTAGGTACCAACTTGGATCAAAAAAAAGTTTAGGTACCAAATTA-GAAAAAATGTCAAG
26961 TTTAGGTACCAA
1 TTTAGGTACCAA
26973 AAGTTATATT
Statistics
Matches: 110, Mismatches: 19, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
58 6 0.05
59 81 0.74
60 23 0.21
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (59 bp):
TTTAGGTACCAACTTGGATCAAAAAAAAGTTTAGGTACCAAATTAGAAAAAATGTCAAG
Found at i:26906 original size:30 final size:30
Alignment explanation
Indices: 26870--26974 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 30
26860 TCCAAAAAAG
*
26870 GTTTAGGTACCAAAATAGGAAAAATGTCAA
1 GTTTAGGTACCAAAATAGGAAAAATGTAAA
* * *
26900 GTTTAGGTACC-AACTTGGATCAAAA--AAAA
1 GTTTAGGTACCAAAATAGGA--AAAATGTAAA
* * *
26929 GTTTAGGCACCAAATTAGGAAAAAGTGTTAA
1 GTTTAGGTACCAAAATAGGAAAAA-TGTAAA
26960 GTTTAGGTACCAAAA
1 GTTTAGGTACCAAAA
26975 GTTATATTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
28 4 0.07
29 18 0.31
30 17 0.29
31 19 0.33
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.25
Consensus pattern (30 bp):
GTTTAGGTACCAAAATAGGAAAAATGTAAA
Found at i:27272 original size:14 final size:15
Alignment explanation
Indices: 27253--27317 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
27243 TATATATTTA
27253 TTAAATATAAA-TAT
1 TTAAATATAAATTAT
* **
27267 TTAAATTTAAACAAT
1 TTAAATATAAATTAT
* *
27282 TAATAATATAAATTGT
1 TTA-AATATAAATTAT
*
27298 TTTAAT-TAAATTAT
1 TTAAATATAAATTAT
27312 TTAAAT
1 TTAAAT
27318 GGATATCAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 4
0.72 0.21 0.08
Matches are distributed among these distances:
14 22 0.58
15 7 0.18
16 9 0.24
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAAATATAAATTAT
Found at i:29972 original size:40 final size:40
Alignment explanation
Indices: 29917--29998 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
29907 GAGAGTAAGA
29917 ATCTTCTTGTGCTTTTTCTACGTCTCAGTAGCATTATCAT
1 ATCTTCTTGTGCTTTTTCTACGTCTCAGTAGCATTATCAT
29957 ATCTTCTTGTGCTTTTTCTACGTCTCAGTAGCATTATCAT
1 ATCTTCTTGTGCTTTTTCTACGTCTCAGTAGCATTATCAT
29997 AT
1 AT
29999 ATTGTTTGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (40 bp):
ATCTTCTTGTGCTTTTTCTACGTCTCAGTAGCATTATCAT
Done.