Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009569.1 Kokia drynarioides strain JFW-HI SEQ_124283, 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: 20674
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9767 original size:29 final size:28
Alignment explanation
Indices: 9564--9956 Score: 176
Period size: 29 Copynumber: 13.6 Consensus size: 28
9554 CTTAGACCAC
* *
9564 CCACGAAGGCGTTCCTTTAACATG-GATCA
1 CCACAAAGGC-TTCCTTTAACA-GAGATTA
* * *
9593 CCACCAAGGGCTTACCTTTAACAGAAATTG
1 CCA-CAAAGGCTT-CCTTTAACAGAGATTA
* * * * *
9623 CCGCAAAGGCTTGTCCATTAAAAG-GTTTG
1 CCACAAAGGC-T-TCCTTTAACAGAGATTA
** *
9652 CCACAAAGGCTTACCTTT-TTAGAGTTTTA
1 CCACAAAGGCTT-CCTTTAACAGAG-ATTA
* *
9681 CCACGAAGGCTTCCTTTAACAGAGGTCT-
1 CCACAAAGGCTTCCTTTAACAGAGAT-TA
* *
9709 CCACAAAGGCTTCATTT-ACAGAGATTG
1 CCACAAAGGCTTCCTTTAACAGAGATTA
**
9736 CCACAAAGGCGTTCCTTTAACAGAGATCG
1 CCACAAAGGC-TTCCTTTAACAGAGATTA
* * *
9765 CCATAAAGGATTATCCTTT-A-AGAGGTTCA
1 CCACAAAGG-CT-TCCTTTAACAGAGATT-A
* * **
9794 CCACAAAGGCTTACATTT-ATAGATTTTTA
1 CCACAAAGGCTT-CCTTTAACAGA-GATTA
* * *
9823 CCACAAAGGCTTCTCTTTAATAAAGATTG
1 CCACAAAGGCTTC-CTTTAACAGAGATTA
* * *
9852 TCACAAAGGCTTCCTTTAACAGAAATCA
1 CCACAAAGGCTTCCTTTAACAGAGATTA
* * * *
9880 CCATAAAGACTTGTCCTTTAACAG-GTTTG
1 CCACAAAGGC-T-TCCTTTAACAGAGATTA
* * *
9909 CCATAAAGGCTTACCTTT-TCAGAGTTTTA
1 CCACAAAGGCTT-CCTTTAACAGAG-ATTA
9938 CCACAAAGGCTTCTCTTTA
1 CCACAAAGGCTTC-CTTTA
9957 TTGGTGTTTT
Statistics
Matches: 279, Mismatches: 57, Indels: 55
0.71 0.15 0.14
Matches are distributed among these distances:
26 1 0.00
27 25 0.09
28 70 0.25
29 132 0.47
30 50 0.18
31 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.30
Consensus pattern (28 bp):
CCACAAAGGCTTCCTTTAACAGAGATTA
Found at i:9860 original size:87 final size:86
Alignment explanation
Indices: 9692--9874 Score: 196
Period size: 87 Copynumber: 2.1 Consensus size: 86
9682 CACGAAGGCT
* *
9692 TCCTTTAACAGAGGTCTCCACAAAGGCTTCATTTACAGAGATTGCCACAAAGGCGTTCCTTTAAC
1 TCCTTTAACAGAGGTCACCACAAAGGCTTCATTTACAGAGATTACCACAAAGGCGTTCCTTTAAC
* *
9757 AGAGATCGCCATAAAGGATTA
66 AAAGATCGCCACAAAGGATTA
* **
9778 TCCTTT-A-AGAGGTTCACCACAAAGGCTTACATTTATAGATTTTTACCACAAAGGC-TTCTCTT
1 TCCTTTAACAGAGG-TCACCACAAAGGCTT-CATTTACAGA-GATTACCACAAAGGCGTTC-CTT
* * * *
9840 TAATAAAGATTGTCACAAAGG-CT-
62 TAACAAAGATCGCCACAAAGGATTA
9863 TCCTTTAACAGA
1 TCCTTTAACAGA
9875 AATCACCATA
Statistics
Matches: 80, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
84 5 0.06
85 21 0.26
86 20 0.25
87 34 0.43
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (86 bp):
TCCTTTAACAGAGGTCACCACAAAGGCTTCATTTACAGAGATTACCACAAAGGCGTTCCTTTAAC
AAAGATCGCCACAAAGGATTA
Found at i:9884 original size:115 final size:116
Alignment explanation
Indices: 9709--9956 Score: 326
Period size: 115 Copynumber: 2.2 Consensus size: 116
9699 ACAGAGGTCT
* * * *
9709 CCACAAAGGCTTC-ATTT-ACAGAGATTGCCACAAAGGCGTTCCTTTAACAGAGATCGCCATAAA
1 CCACAAAGGCTTCTCTTTAACAAAGATTGCCACAAAGGCGTTCCTTTAACAGAAATCACCATAAA
* *
9772 GGA-TTATCCTTTAAGAGGTTCACCACAAAGGCTTACATTTAT-AGATTTTTA
66 -GACTTATCCTTTAACAGGTTCACCACAAAGGCTTACATTT-TCAGAGTTTTA
* *
9823 CCACAAAGGCTTCTCTTTAATAAAGATTGTCACAAAGGC-TTCCTTTAACAGAAATCACCATAAA
1 CCACAAAGGCTTCTCTTTAACAAAGATTGCCACAAAGGCGTTCCTTTAACAGAAATCACCATAAA
* ** * *
9887 GACTTGTCCTTTAACAGGTTTGCCATAAAGGCTTACCTTTTCAGAGTTTTA
66 GACTTATCCTTTAACAGGTTCACCACAAAGGCTTACATTTTCAGAGTTTTA
9938 CCACAAAGGCTTCTCTTTA
1 CCACAAAGGCTTCTCTTTA
9957 TTGGTGTTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
114 16 0.14
115 84 0.72
116 17 0.15
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (116 bp):
CCACAAAGGCTTCTCTTTAACAAAGATTGCCACAAAGGCGTTCCTTTAACAGAAATCACCATAAA
GACTTATCCTTTAACAGGTTCACCACAAAGGCTTACATTTTCAGAGTTTTA
Found at i:10236 original size:15 final size:15
Alignment explanation
Indices: 10203--10247 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
10193 CTCACCATTC
*
10203 ATAGACTCATTTATA
1 ATAGACTCATTCATA
* *
10218 ATAGACTCGTTCATG
1 ATAGACTCATTCATA
*
10233 ATAGATTCATTCATA
1 ATAGACTCATTCATA
10248 CTTTTAGGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (15 bp):
ATAGACTCATTCATA
Found at i:14575 original size:30 final size:30
Alignment explanation
Indices: 14539--14639 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
14529 TTTTACCCTG
14539 AACTTCCAAAAATCCCATTTTTGACCCCAA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
* **
14569 AACTTCCTAAAAATACCA-TTTT-ACCCCTG
1 AACTTCC-AAAAATCCCATTTTTGACCCCAA
*
14598 AACTTCCAAAAATCCCATTTTTGACCCCGA
1 AACTTCCAAAAATCCCATTTTTGACCCCAA
*
14628 CACTTCCAAAAA
1 AACTTCCAAAAA
14640 AAATTATCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
28 9 0.15
29 16 0.26
30 27 0.44
31 9 0.15
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.27
Consensus pattern (30 bp):
AACTTCCAAAAATCCCATTTTTGACCCCAA
Found at i:14610 original size:59 final size:59
Alignment explanation
Indices: 14518--14654 Score: 204
Period size: 59 Copynumber: 2.3 Consensus size: 59
14508 TAAATTGTCC
*
14518 AAAAATTACCATTTTACCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCT
1 AAAAATTACCATTTTACCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
* *
14577 AAAAA-TACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCCCGACACTTCCAAA
1 AAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCC--A
*
14638 AAAAATTATCATTTTAC
1 AAAAATTACCATTTTAC
14655 TCCCGGATGT
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
58 10 0.14
59 45 0.64
61 6 0.09
62 9 0.13
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTGAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCCA
Done.