Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009069.1 Kokia drynarioides strain JFW-HI SEQ_123769, 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: 1845
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Found at i:429 original size:216 final size:213
Alignment explanation
Indices: 1--1630 Score: 1782
Period size: 216 Copynumber: 7.6 Consensus size: 213
* * *
1 GTGAGAATTGTTTTTCTCTTGGTTCTTGGTCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCA
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCT
** * * * * * *
66 TTTATAACTTTGGTTCTTTAAAGTACTCAAAATGATCAATTCCTTTGAGCAATTTTCCAAACATT
66 TTTATAACTTCAGTTCCTTAAAGTATTCAAGACGATC-ATTCCTTCGAGCAATTTTTCAAACATT
* * *
131 CCATACTCGGGAAATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAAATTTCGGTCT
130 CCATGCTCGAGAAATCGCATCATTTGGTCCAAATAG-TTGTCCTTTTGT-AAAAACTTTCGGTCT
*
196 TTGAATTAAATACTTATTTAC
193 TTGAATTAAAAACTTATTTAC
** * * *
217 GTGAGAATTGTTTCTCTCTTATTTCTTAGCCGAACTTTCGAATTTGTCAAACTTTTTACGACTTC
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAAC-TTTTACGAGTTC
* * * ** * * *
282 TTTTATAACTTCAGTTTCTTAATGTATTCAAGACAACTCATTCCTTTTAGAAAATTTCCAAACAT
65 TTTTATAACTTCAGTTCCTTAAAGTATTCAAGACGA-TCATTCCTTCGAGCAATTTTTCAAACAT
* * * ** * *
347 TCCATGCTTGGGAAATCGTATCATTTGGTCCAAATAGTTGTCAGTTTGTAAAGAAATTTTGGTCT
129 TCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTGTCCTTTTGTAAA-AACTTTCGGTCT
*
412 TTAAATTAAAAACTTATTTAC
193 TTGAATTAAAAACTTATTTAC
* * * *
433 GTG-GAATTGTTTCTCTCTTGGTTCTTGGCTGAAC-ATCTAAACTTGTCAAACTTTTACAAGTTC
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACTTGTCAAACTTTTACGAGTTC
* * * * **
496 TTTTATAACTTCTA-TTCCTTAAGGTATTCAATACGATCCATTCATTCGAGTAATTTTTTGAACA
65 TTTTATAACTTC-AGTTCCTTAAAGTATTCAAGACGAT-CATTCCTTCGAGCAATTTTTCAAACA
* * * * * *
560 TTCCTTGCTCGAGAAATCGCATCATTTCGTCCAAATAATTTGTCATTTTGT-AATACTTTTGGTC
128 TTCCATGCTCGAGAAATCGCATCATTTGGTCCAAAT-AGTTGTCCTTTTGTAAAAACTTTCGGTC
** *
624 TTAAAATTAAAAACTTATTTTC
192 TTTGAATTAAAAACTTATTTAC
* * * * *
646 GTGGGAATGGTTTCTC-CATTGGTTCTTGACTGAACTTTCGAACTTGTCAATCTTTTACGAGTTC
1 GTGAGAATTGTTTCTCTC-TTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGAGTTC
* * * * *
710 TTTTGTAACTTCAGTTTCTTAAAGTATTCAAGACGATTCATTCCTTTGAGCAATTTTCCAATCAT
65 TTTTATAACTTCAGTTCCTTAAAGTATTCAAGACGA-TCATTCCTTCGAGCAATTTTTCAAACAT
* * *
775 TCCATGCTCGAGAAATCGCATCATTTGGTCCAAATATTTTGTCCTTTTGTATACAACTTTCGATC
129 TCCATGCTCGAGAAATCGCATCATTTGGTCCAAATA-GTTGTCCTTTTGTA-AAAACTTTCGGTC
*
840 TTTGAATTAAAAACTTATTTAT
192 TTTGAATTAAAAACTTATTTAC
* * * ** *
862 GTGAGAATTGTTTCTTTCTTGGTTCTTCGCCGAAC-TTCTAAACTTGTCAAACTTTTTGGAGCTC
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACTTGTCAAACTTTTACGAGTTC
* * * *
926 TTTTTTAACTTCGGTTCCTTAAAGTATTCATGATGATCGATTCCTTCGAGCAA-TTTTCAGAACA
65 TTTTATAACTTCAGTTCCTTAAAGTATTCAAGACGATC-ATTCCTTCGAGCAATTTTTCA-AACA
* * **
990 TTCCATTCTTGAGAAATCATATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAGACTTTCGGT
128 TTCCATGCTCGAGAAATCGCATCATTTGGTCCAAATAG-TTGTCCTTTTGTAAAA-ACTTTCGGT
* *
1055 CTATGAATTAAAAACTTATATAC
191 CTTTGAATTAAAAACTTATTTAC
* * * * * *
1078 GTGAGAATTATTTATCTCTTGGTTCATGGCCGAACTTTTGAACTTTTCAAACTTTTTCGAGTTCT
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCT
* ** * * * * * * *
1143 TTTACAACTTTGGTTCCTTAAAGTGTTCATGATGATCCTTCCTTCAAGCAAATTTTCGAACATTC
66 TTTATAACTTCAGTTCCTTAAAGTATTCAAGACGATCATTCCTTCGAGCAATTTTTCAAACATTC
* * * * *
1208 CTTGTTCAAGAAATCGCATCATTTGGTCCAAATAATTTGTCCTTTTGTAAAAAAACTTTCGATCT
131 CATGCTCGAGAAATCGCATCATTTGGTCCAAAT-AGTTGTCCTTTTGT--AAAAACTTTCGGTCT
**
1273 TTGGTTTAAAAACTTATTTAC
193 TTGAATTAAAAACTTATTTAC
* * * * * *
1294 GTGAAAATTATTTATCTCTTGGTTCTTAGCCGAACTTTCAAACTTGTCAAACTTTTACAAGTTCT
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCT
* * * *
1359 TTTATAACTTCAGTTCCTTAAAGTATTCAAGATGACTCATTCCTTCTAGTAATTTTTCGAACATT
66 TTTATAACTTCAGTTCCTTAAAGTATTCAAGACGA-TCATTCCTTCGAGCAATTTTTCAAACATT
* * * * *
1424 CCATGCTCGAGAAATGGCATCACTTGGTCCAAATAGTTTGTCATTTCGTAAAGAACTTTTGGTCT
130 CCATGCTCGAGAAATCGCATCATTTGGTCCAAATAG-TTGTCCTTTTGTAAA-AACTTTCGGTCT
**
1489 TTGAATTAAAAACTTAAGTAC
193 TTGAATTAAAAACTTATTTAC
* * **
1510 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCTGAAC-ATCTGAACTTGTCAAACTTTTACTTGTTC
1 GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTC-GAACTTGTCAAACTTTTACGAGTTC
* *
1574 TTTTATAACTTCGGTTTCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT
65 TTTTATAACTTCAGTTCCTTAAAGTATTCAAGACGAT-CATTCCTTCGAGCAATTTT
1631 CTGAACATTT
Statistics
Matches: 1191, Mismatches: 192, Indels: 62
0.82 0.13 0.04
Matches are distributed among these distances:
213 36 0.03
214 237 0.20
215 132 0.11
216 619 0.52
217 165 0.14
218 2 0.00
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (213 bp):
GTGAGAATTGTTTCTCTCTTGGTTCTTGGCCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCT
TTTATAACTTCAGTTCCTTAAAGTATTCAAGACGATCATTCCTTCGAGCAATTTTTCAAACATTC
CATGCTCGAGAAATCGCATCATTTGGTCCAAATAGTTGTCCTTTTGTAAAAACTTTCGGTCTTTG
AATTAAAAACTTATTTAC
Found at i:1256 original size:645 final size:642
Alignment explanation
Indices: 15--1639 Score: 1989
Period size: 645 Copynumber: 2.5 Consensus size: 642
5 GAATTGTTTT
* * *
15 TCTCTTGGTTCTTG-GTCGAACTTTCGAACTTGTCAAACTTTTACGAGTTCATTTATAACTT-TG
1 TCTCTTGGTTCTTGACT-GAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAG
* * * * *
78 GTTCTTTAAAGTACTCAAAATGATCAATTCCTTTGAGCAATTTTCCAAACATTCCATACTCGGGA
65 TTTC-TTAAAGTATTCAAGATGATC-ATTCCTTTGAGCAATTTTCC-AACATTCCATGCTCGAGA
* *
143 AATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAAATTTCGGTCTTTGAATTAAATA
127 AATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGGTCTTTGAATTAAAAA
** *
208 CTTATTTACGTGAGAATTGTTTCTCTCTTATTTCTTAGCCGAACTT-TCGAATTTGTCAAACTTT
192 CTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCCGAACTTCT-GAACTTGTCAAACTTT
* * * ** *
272 TTACGA-CTTCTTTTATAACTTCAGTTTCTTAATGTATTCAAGACAACTCATTCCTTTTAGAAAA
256 TT-CGAGC-TCTTTTATAACTTCGGTTTCTTAAAGTATTCAAGACGA-TCATTCCTTCGAG-CAA
* * *
336 TTTCCA-AACATTCCATGCTTGGGAAATCGTATCATTTGGTCCAAATAGTTGTCAGTTTGTAAAG
317 TTTTCAGAACATTCCATGCTTGAGAAATCATATCATTTGGTCCAAATAGTTGTCAGTTTGTAAAG
* * * * * * *
400 AAATTTTGGTCTTTAAATTAAAAACTTATTTACGTGGAATTGTTTCTCTCTTGGTTCTTGGCTGA
382 AAATTTCGGTCTATAAATTAAAAACTTATATACGTGGAATTATTTATCTCTTGGTTCATGGCCGA
* *
465 ACATCTAAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCTATTCCTTAAGGTATTCAATAC
447 ACATCTAAACTTGTCAAACTTTTACAAGTTCTTTTACAACTTCTATTCCTTAAAGTATTCAATAC
* * * * *
530 GATCCATTCATTCGAGTAATTTTTTGAACATTCCTTGCTCGAGAAATCGCATCATTTCGTCCAAA
512 GATCCATTCATTCAAGCAAATTTTCGAACATTCCTTGCTCAAGAAATCGCATCATTTCGTCCAAA
* * * * ** *
595 TAATTTGTCATTTTGT-AATACTTTTGGTCTTAAAATTAAAAACTTATTTTCGTGGGAATGGTTT
577 TAATTTGTCATTTTGTAAAAACTTTCGATCTTAAAATTAAAAACTTATTTACGTGAAAATGATTT
*
659 C
642 A
* *
660 TC-CATTGGTTCTTGACTGAACTTTCGAACTTGTCAATCTTTTACGAGTTCTTTTGTAACTTCAG
1 TCTC-TTGGTTCTTGACTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAG
*
724 TTTCTTAAAGTATTCAAGACGATTCATTCCTTTGAGCAATTTTCCAATCATTCCATGCTCGAGAA
65 TTTCTTAAAGTATTCAAGATGA-TCATTCCTTTGAGCAATTTTCCAA-CATTCCATGCTCGAGAA
* * * *
789 ATCGCATCATTTGGTCCAAATATTTTGTCCTTTTGTATACAACTTTCGATCTTTGAATTAAAAAC
128 ATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGGTCTTTGAATTAAAAAC
* * * *
854 TTATTTATGTGAGAATTGTTTCTTTCTTGGTTCTTCGCCGAACTTCTAAACTTGTCAAACTTTTT
193 TTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCCGAACTTCTGAACTTGTCAAACTTTTT
* * * * *
919 GGAGCTCTTTTTTAACTTCGGTTCCTTAAAGTATTCATGATGATCGATTCCTTCGAGCAATTTTC
258 CGAGCTCTTTTATAACTTCGGTTTCTTAAAGTATTCAAGACGATC-ATTCCTTCGAGCAATTTTC
* ** *
984 AGAACATTCCATTCTTGAGAAATCATATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAA-AGAC
322 AGAACATTCCATGCTTGAGAAATCATATCATTTGGTCCAAATAG-TTGTCAGTTTGTAAAGA-AA
*
1048 TTTCGGTCTATGAATTAAAAACTTATATACGTGAGAATTATTTATCTCTTGGTTCATGGCCGAAC
385 TTTCGGTCTATAAATTAAAAACTTATATACGTG-GAATTATTTATCTCTTGGTTCATGGCCGAAC
* * * * * * * * *
1113 TTTTGAACTTTTCAAACTTTTTCGAGTTCTTTTACAACTT-TGGTTCCTTAAAGTGTTC-ATGAT
449 ATCTAAACTTGTCAAACTTTTACAAGTTCTTTTACAACTTCT-ATTCCTTAAAGTATTCAAT-AC
* * *
1176 GATCC-TTCCTTCAAGCAAATTTTCGAACATTCCTTGTTCAAGAAATCGCATCATTTGGTCCAAA
512 GATCCATTCATTCAAGCAAATTTTCGAACATTCCTTGCTCAAGAAATCGCATCATTTCGTCCAAA
* **** *
1240 TAATTTGTCCTTTTGTAAAAAAACTTTCGATCTTTGGTTTAAAAACTTATTTACGTGAAAATTAT
577 TAATTTGTCATTTTGT--AAAAACTTTCGATCTTAAAATTAAAAACTTATTTACGTGAAAATGAT
1305 TTA
640 TTA
* * *
1308 TCTCTTGGTTCTT-AGCCGAACTTTCAAACTTGTCAAACTTTTACAAGTTCTTTTATAACTTCAG
1 TCTCTTGGTTCTTGA-CTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAG
* * *
1372 TTCCTTAAAGTATTCAAGATGACTCATTCCTTCT-AGTAATTTTTCGAACATTCCATGCTCGAGA
65 TTTCTTAAAGTATTCAAGATGA-TCATTCCTT-TGAGCAA-TTTTCCAACATTCCATGCTCGAGA
* * * * * *
1436 AATGGCATCACTTGGTCCAAATAGTTTGTCATTTCGTAAAGAACTTTTGGTCTTTGAATTAAAAA
127 AATCGCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGGTCTTTGAATTAAAAA
** * * *
1501 CTTAAGTACGTGAGAATTGTTTCTCTCTTGGTTCTTGGCTGAACATCTGAACTTGTCAAACTTTT
192 CTTATTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCCGAACTTCTGAACTTGTCAAACTTTT
* ** *
1566 ACTTGTTCTTTTATAACTTCGGTTTCTTAAAGTATTCAAGACGATCCATTCCTTCGAGCAATTTT
257 TCGAGCTCTTTTATAACTTCGGTTTCTTAAAGTATTCAAGACGAT-CATTCCTTCGAGCAATTTT
*
1631 CTGAACATT
321 CAGAACATT
1640 TCATACTCAG
Statistics
Matches: 838, Mismatches: 120, Indels: 41
0.84 0.12 0.04
Matches are distributed among these distances:
643 9 0.01
644 85 0.10
645 331 0.39
646 87 0.10
647 1 0.00
648 315 0.38
649 10 0.01
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (642 bp):
TCTCTTGGTTCTTGACTGAACTTTCGAACTTGTCAAACTTTTACGAGTTCTTTTATAACTTCAGT
TTCTTAAAGTATTCAAGATGATCATTCCTTTGAGCAATTTTCCAACATTCCATGCTCGAGAAATC
GCATCATTTGGTCCAAATAGTTTGTCCTTTTGTAAAAAACTTTCGGTCTTTGAATTAAAAACTTA
TTTACGTGAGAATTGTTTCTCTCTTGGTTCTTAGCCGAACTTCTGAACTTGTCAAACTTTTTCGA
GCTCTTTTATAACTTCGGTTTCTTAAAGTATTCAAGACGATCATTCCTTCGAGCAATTTTCAGAA
CATTCCATGCTTGAGAAATCATATCATTTGGTCCAAATAGTTGTCAGTTTGTAAAGAAATTTCGG
TCTATAAATTAAAAACTTATATACGTGGAATTATTTATCTCTTGGTTCATGGCCGAACATCTAAA
CTTGTCAAACTTTTACAAGTTCTTTTACAACTTCTATTCCTTAAAGTATTCAATACGATCCATTC
ATTCAAGCAAATTTTCGAACATTCCTTGCTCAAGAAATCGCATCATTTCGTCCAAATAATTTGTC
ATTTTGTAAAAACTTTCGATCTTAAAATTAAAAACTTATTTACGTGAAAATGATTTA
Found at i:1708 original size:69 final size:69
Alignment explanation
Indices: 1597--1735 Score: 242
Period size: 69 Copynumber: 2.0 Consensus size: 69
1587 GTTTCTTAAA
* * *
1597 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTTCATACTCAGGAAATCACATCT
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATACACAGGAAATCACATCA
1662 TTTG
66 TTTG
*
1666 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATGCACAGGAAATCACATCA
1 GTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATACACAGGAAATCACATCA
1731 TTTG
66 TTTG
1735 G
1 G
1736 ACCAAGTTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.32
Consensus pattern (69 bp):
GTATTCAAGACGATCCATTCCTTCGAGCAATTTTCTGAACATTCCATACACAGGAAATCACATCA
TTTG
Done.