Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002698.1 Kokia drynarioides strain JFW-HI SEQ_114980, 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: 10428
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Found at i:8851 original size:204 final size:205
Alignment explanation
Indices: 8491--9763 Score: 1995
Period size: 205 Copynumber: 6.2 Consensus size: 205
8481 CGATTATCCG
* * *
8491 AACAGCGATGTGATCATCTTCTTGATAAGACACTGAGAAGAAGATCCAAACGAGGCT-CAAAACG
1 AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
* *
8555 AGCGAAATCTTCAAACCCCGCTTTCCTAATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
66 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* *
8620 TAGCTTCCTGATGAGATATTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
131 TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
8685 AATTGAAACA
196 AATTGAAACA
* * *
8695 AACAGCGATGTGATCATCTTCTTGATGAGACACTGAGAAGAAGATCCAAACAAGGCT-CAAAACG
1 AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
* *
8759 AGCGAAATCTTCAAACCCCGCCTTCTTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGT
66 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* * *
8824 TAGCTTCCTGATGAGACACTAAGAAGTGAACCAAATTCATCTTCCTGATGAGGTATAGAGGAGCG
131 TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
8889 AATTGAAACA
196 AATTGAAACA
* * * *
8899 AACAGCGATGTCATCATCTTCTTGATGAGACACTGAGAAGAAGATCCAAACAAGGCT-CAAAACG
1 AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
*
8963 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTAAGAAGCAGGTCGAAGCAATAAAAGGT
66 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
*
9028 TAGCTTCCTGATGAGACACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
131 TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
9093 AATTGAAACA
196 AATTGAAACA
* *
9103 AACAGCGATGTGATCATCTTCCTGATCAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAATG
1 AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
* * * *
9168 AGCGAAATCTTCAAACCTCGCCATCCTGATGAGACACTGAGAAACAGGTCAAAGCAATAAAAGGT
66 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
*
9233 TAACTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
131 TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
*
9298 AATTGAAATA
196 AATTGAAACA
* * *
9308 AACAGCGATGTTATCATCTTCCTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTAAAAAACG
1 AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
** *
9373 AGCGAAATCTTTGAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGTAATAAAAGGT
66 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* * *
9438 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATGAGGTACAGAGGAGTG
131 TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
9503 AATTGAAACA
196 AATTGAAACA
* * *
9513 AACAGCGACGTGATCATCTTCCTGATGAGACACTGAGAAAAAGACCCAAACGAGGCTAAAAAACG
1 AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
* * * *
9578 AGCGAAATCTTCGAACCCCACCTTCCTGATGAGACACTGAGAAACAGGTCGAAGTAATAAAAGGT
66 AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
* * * * *
9643 TAGCTTCCTGATGAGATACTGAGAAGTGAACCAAACTCGTCTTCCTGATGAGATATAGAGAAGCG
131 TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
*
9708 AATCGAAAC-
196 AATTGAAACA
* * *
9717 AA-A-CGATG-CAGTCATCTTCCTGATGTGATACTGAGAAGAAGA-CCAAA
1 AACAGCGATGTGA-TCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAA
9764 TCAGTAAAAC
Statistics
Matches: 1006, Mismatches: 61, Indels: 7
0.94 0.06 0.01
Matches are distributed among these distances:
201 6 0.01
202 32 0.03
203 1 0.00
204 448 0.45
205 519 0.52
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (205 bp):
AACAGCGATGTGATCATCTTCCTGATGAGACACTGAGAAGAAGATCCAAACGAGGCTAAAAAACG
AGCGAAATCTTCAAACCCCGCCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAGGT
TAGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGGTACAGAGGAGCG
AATTGAAACA
Found at i:10026 original size:28 final size:28
Alignment explanation
Indices: 9995--10048 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
9985 GGGCCTTTTT
* *
9995 TTAATTTTAAATTTGATTTAAATTAATC
1 TTAAATTTAAATTTAATTTAAATTAATC
10023 TTAAATTTAAATTTAATTTAAATTAA
1 TTAAATTTAAATTTAATTTAAATTAA
10049 AAGGTCTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TTAAATTTAAATTTAATTTAAATTAATC
Found at i:10030 original size:17 final size:17
Alignment explanation
Indices: 10010--10046 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
10000 TTTAAATTTG
10010 ATTTAAA-TTAATCTTAA
1 ATTTAAATTTAAT-TTAA
10027 ATTTAAATTTAATTTAA
1 ATTTAAATTTAATTTAA
10044 ATT
1 ATT
10047 AAAAGGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTAATTTAA
Found at i:10040 original size:11 final size:11
Alignment explanation
Indices: 9994--10049 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
9984 TGGGCCTTTT
9994 TTTAATTTTAAA
1 TTTAA-TTTAAA
*
10006 TTTGATTTAAA
1 TTTAATTTAAA
10017 -TTAATCTTAAA
1 TTTAAT-TTAAA
10028 TTTAAATTT-AA
1 TTT-AATTTAAA
*
10039 TTTAAATTAAA
1 TTTAATTTAAA
10050 AGGTCTAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 8 0.22
11 18 0.49
12 8 0.22
13 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:10040 original size:22 final size:22
Alignment explanation
Indices: 9995--10043 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9985 GGGCCTTTTT
* *
9995 TTAATTTTAAATTTGATTTAAA
1 TTAATCTTAAATTTAATTTAAA
*
10017 TTAATCTTAAATTTAAATTTAAT
1 TTAATCTTAAATTT-AATTTAAA
10040 TTAA
1 TTAA
10044 ATTAAAAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATCTTAAATTTAATTTAAA
Done.