Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006611.1 Kokia drynarioides strain JFW-HI SEQ_121201, 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, 997
Length: 1663
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:510 original size:11 final size:11
Alignment explanation
Indices: 496--530 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
486 CTTTTAATAA
496 TTTTTTGAATT
1 TTTTTTGAATT
*
507 TTTTTTGCATT
1 TTTTTTGAATT
*
518 TTTTTTAAATT
1 TTTTTTGAATT
529 TT
1 TT
531 AAAAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.74
Consensus pattern (11 bp):
TTTTTTGAATT
Found at i:737 original size:13 final size:13
Alignment explanation
Indices: 699--740 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
689 ATTAACTACC
699 AATTAAATTAAAA
1 AATTAAATTAAAA
* *
712 AATTTACA-CAAAA
1 AA-TTAAATTAAAA
725 AATTAAATTAAAA
1 AATTAAATTAAAA
738 AAT
1 AAT
741 AATCATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 4 0.17
13 15 0.65
14 4 0.17
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAATTAAAA
Found at i:1056 original size:118 final size:118
Alignment explanation
Indices: 913--1150 Score: 460
Period size: 119 Copynumber: 2.0 Consensus size: 118
903 TTTTTTACTC
913 AATTGGGTATTTAAATTTTTAACATAGATAAAAAAGACTCTCAAACTTTTTTTT-AAAAAAATTA
1 AATTGGGTATTTAAATTTTTAACATAGATAAAAAAGACTCTCAAACTTTTTTTTAAAAAAAATTA
977 AGCCATTTTTTTACATTCAATCGGGTACTTGAATTGTCAAAATGTATAAAAAA
66 AGCCATTTTTTTACATTCAATCGGGTACTTGAATTGTCAAAATGTATAAAAAA
1030 NAATTGGGTATTTAAATTTTTAACATAGATAAAAAAGACTCTCAAACTTTTTTTTAAAAAAAATT
1 -AATTGGGTATTTAAATTTTTAACATAGATAAAAAAGACTCTCAAACTTTTTTTTAAAAAAAATT
1095 AAGCCATTTTTTTACATTCAATCGGGTACTTGAATTGTCAAAATGTATAAAAAA
65 AAGCCATTTTTTTACATTCAATCGGGTACTTGAATTGTCAAAATGTATAAAAAA
1149 AA
1 AA
1151 AAAAGATCCT
Statistics
Matches: 119, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
118 56 0.47
119 63 0.53
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.37
Consensus pattern (118 bp):
AATTGGGTATTTAAATTTTTAACATAGATAAAAAAGACTCTCAAACTTTTTTTTAAAAAAAATTA
AGCCATTTTTTTACATTCAATCGGGTACTTGAATTGTCAAAATGTATAAAAAA
Found at i:1273 original size:10 final size:10
Alignment explanation
Indices: 1258--1383 Score: 59
Period size: 10 Copynumber: 12.7 Consensus size: 10
1248 TGGCATATGG
1258 TAAAAAATTA
1 TAAAAAATTA
**
1268 TAAAAATAAAA
1 TAAAAA-ATTA
*
1279 TAAAATAA-AA
1 TAAAA-AATTA
1289 TCAATAAAAGTTA
1 T-AA-AAAA-TTA
1302 T-AAAAATTA
1 TAAAAAATTA
* *
1311 T-TAAATTTAA
1 TAAAAAATT-A
1321 TAAAAAATTA
1 TAAAAAATTA
1331 TAAAAAA--A
1 TAAAAAATTA
* *
1339 TTAAAATTTA
1 TAAAAAATTA
*
1349 TTAAAAATTA
1 TAAAAAATTA
*
1359 GAAAAAA-TA
1 TAAAAAATTA
*
1368 T-AAAAATTG
1 TAAAAAATTA
1377 TAAAAAA
1 TAAAAAA
1384 ATTACGAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
8 11 0.12
9 13 0.14
10 43 0.48
11 18 0.20
12 3 0.03
13 2 0.02
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:1274 original size:9 final size:9
Alignment explanation
Indices: 1260--1454 Score: 68
Period size: 9 Copynumber: 21.4 Consensus size: 9
1250 GCATATGGTA
1260 AAAAATTAT
1 AAAAATTAT
1269 AAAAA-TA-
1 AAAAATTAT
*
1276 AAATAA-AAT
1 AAA-AATTAT
*
1285 -AAAATCAAT
1 AAAAATTA-T
*
1294 AAAAGTTAT
1 AAAAATTAT
1303 AAAAATTAT
1 AAAAATTAT
* *
1312 TAAATTTAAT
1 AAAAATT-AT
1322 AAAAAATTAT
1 -AAAAATTAT
*
1332 AAAAA-AATT
1 AAAAATTA-T
*
1341 AAAATTTATT
1 AAAAATTA-T
*
1351 AAAAATTAG
1 AAAAATTAT
*
1360 AAAAAATAT
1 AAAAATTAT
*
1369 AAAAATTGTAA
1 AAAAA-T-TAT
*
1380 AAAAATTACG
1 AAAAATTA-T
*
1390 AAAATTTTAT
1 AAAA-ATTAT
**
1400 AAAAATCGT
1 AAAAATTAT
1409 AAAAA-TAT
1 AAAAATTAT
1417 ATAAAATATAT
1 A-AAAAT-TAT
*
1428 AGAAA-TAT
1 AAAAATTAT
*
1436 AGAAA--A-
1 AAAAATTAT
1442 AAAAATTAT
1 AAAAATTAT
1451 AAAA
1 AAAA
1455 TTTTATAAAG
Statistics
Matches: 139, Mismatches: 28, Indels: 38
0.68 0.14 0.19
Matches are distributed among these distances:
6 4 0.03
7 6 0.04
8 20 0.14
9 59 0.42
10 31 0.22
11 19 0.14
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:1315 original size:28 final size:28
Alignment explanation
Indices: 1273--1374 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
1263 AATTATAAAA
* *
1273 ATAAAATAAAATAAAATCAAT-AAAAGTT
1 ATAAAA-AAATTAAAATCAATAAAAAATT
* * *
1301 ATAAAAATTATTAAATTTAATAAAAAATT
1 ATAAAAA-AATTAAAATCAATAAAAAATT
** *
1330 ATAAAAAAATTAAAATTTATTAAAAATT
1 ATAAAAAAATTAAAATCAATAAAAAATT
* *
1358 AGAAAAAATATAAAAAT
1 ATAAAAAA-ATTAAAAT
1375 TGTAAAAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 1 0.02
28 39 0.65
29 20 0.33
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.30
Consensus pattern (28 bp):
ATAAAAAAATTAAAATCAATAAAAAATT
Found at i:1326 original size:29 final size:28
Alignment explanation
Indices: 1273--1387 Score: 101
Period size: 29 Copynumber: 4.0 Consensus size: 28
1263 AATTATAAAA
* * *
1273 ATAAAATAAAATAAAA-TCAATAAAAGTT
1 ATAAAA-AAATTAAAATTTAATAAAAATT
*
1301 ATAAAAATTATT-AAATTTAATAAAAAATT
1 ATAAAAA-AATTAAAATTTAAT-AAAAATT
*
1330 ATAAAAAAATTAAAATTTATTAAAAATT
1 ATAAAAAAATTAAAATTTAATAAAAATT
* *
1358 AGAAAAAATATAAAAATTGTAA-AAAAATT
1 ATAAAAAA-ATTAAAATT-TAATAAAAATT
1387 A
1 A
1388 CGAAAATTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
27 4 0.06
28 29 0.40
29 37 0.51
30 2 0.03
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
ATAAAAAAATTAAAATTTAATAAAAATT
Found at i:1459 original size:61 final size:64
Alignment explanation
Indices: 1378--1499 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 64
1368 TAAAAATTGT
* *
1378 AAAAAAATTACGAAAATTTTATAAAAATCGT-A-AAAAT-ATATAAAATATATAGAAATATAGAA
1 AAAAAAATTACGAAAATTTTAT-AAAATCATAAGAAAATAATATAAAATATAAAGAAATATAGAA
* * *
1440 AAAAAAATTA-TAAAATTTTATAAAGTCATAAGAAAATAATATAAAATGTAAAGAAATATA
1 AAAAAAATTACGAAAATTTTATAAAATCATAAGAAAATAATATAAAATATAAAGAAATATA
1500 AAATTCGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
60 6 0.12
61 11 0.21
62 15 0.29
63 20 0.38
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (64 bp):
AAAAAAATTACGAAAATTTTATAAAATCATAAGAAAATAATATAAAATATAAAGAAATATAGAA
Done.