Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010334.1 Kokia drynarioides strain JFW-HI SEQ_125200, 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: 1793
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:386 original size:175 final size:174
Alignment explanation
Indices: 95--443 Score: 646
Period size: 175 Copynumber: 2.0 Consensus size: 174
85 CGCCACCGCC
95 GACCGTGCGTTCCCAGACTTCCCCTCTGTGGATTCGAACATAGCAAATCAAGACACATCTTCGAA
1 GACCGTGCGTTCCCAGACTTCCCCTCTGTGGATTCGAACATAGCAAATCAAGACACATCTTCGAA
160 CATGCAAAAAAAAAAGGGATACGATTTTGAGAAGTATTTTTTTAAAACAATAGAGTTAGATTTAA
66 CATGCAAAAAAAAAAGGGATACGATTTTGAGAAGTATTTTTTTAAAACAATAGAGTTAGATTTAA
225 AACATGAAACCGAGTCCTTCTGGGTTTTAAAACACAAAGTTTTT
131 AACATGAAACCGAGTCCTTCTGGGTTTTAAAACACAAAGTTTTT
* *
269 NGACCGTGCGTTCCCAGACTTCCCCTCTGTGGATTCGAACATAGCAAATCCAGGCACATCTTCGA
1 -GACCGTGCGTTCCCAGACTTCCCCTCTGTGGATTCGAACATAGCAAATCAAGACACATCTTCGA
334 ACATGC-AAAAAAAAAGGGATACGATTTTGAGAAGTATTTTTTTAAAAACAATAGAGTTAGATTT
65 ACATGCAAAAAAAAAAGGGATACGATTTTGAGAAGTATTTTTTT-AAAACAATAGAGTTAGATTT
*
398 AAAACATGAAACTGAGTCCTTCTGGGTTTTAAAACACAAAGTTTTT
129 AAAACATGAAACCGAGTCCTTCTGGGTTTTAAAACACAAAGTTTTT
444 TTTAAAAAAA
Statistics
Matches: 170, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
174 37 0.22
175 133 0.78
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (174 bp):
GACCGTGCGTTCCCAGACTTCCCCTCTGTGGATTCGAACATAGCAAATCAAGACACATCTTCGAA
CATGCAAAAAAAAAAGGGATACGATTTTGAGAAGTATTTTTTTAAAACAATAGAGTTAGATTTAA
AACATGAAACCGAGTCCTTCTGGGTTTTAAAACACAAAGTTTTT
Found at i:1254 original size:29 final size:29
Alignment explanation
Indices: 1212--1768 Score: 366
Period size: 29 Copynumber: 18.9 Consensus size: 29
1202 TCCTGGAGGT
*
1212 CCCT-AAACTATCCAAAAATTATATTTTTA
1 CCCTCAAACT-TCCAAAAATTACATTTTTA
* * *
1241 CCCTCGAACCTCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
*
1271 -CCTCGAAACTTCTAAAAATTACATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* * * * *
1300 CCCTTAAATTTCTAAAAATTCCATTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
*
1329 CCC-CAAAACTACCAAAAAAATT-CATTTTTGA
1 CCCTC-AAACTTCC--AAAAATTACATTTTT-A
* *
1360 CCCTAAAACTTCCAAAAATCACATTTTT-
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * * *
1388 CCCTCGAACTTACAAAAAATCAAATTTTTA
1 CCCTCAAACTT-CCAAAAATTACATTTTTA
** * * * *
1418 CCCTTGAATTTCAAAAAATTCCATTTTAA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * *
1447 CCCTAAAACTTCCAAAAATCACATGTTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* * *
1476 CCCTCAAATTTTCAAAAATTCCATTTTTTA
1 CCCTCAAACTTCCAAAAATTACA-TTTTTA
* *
1506 -CCTCGAAACTTTCAAAAATTCCATTTTTGA
1 CCCTC-AAACTTCCAAAAATTACATTTTT-A
1536 -CCTCACAACTTCCAAAAATTACATTTTTA
1 CCCTCA-AACTTCCAAAAATTACATTTTTA
* * *
1565 CCCTCGAACTTCCAAAAAATCATATTTTTA
1 CCCTCAAACTTCC-AAAAATTACATTTTTA
* * *
1595 CCCTTAAACATCCAAAAATTCCATTTTTGA
1 CCCTCAAACTTCCAAAAATTACATTTTT-A
* *
1625 CCC-CAAAACTTCCATAAAA-TCCGTTTTTGA
1 CCCTC-AAACTTCCA-AAAATTACATTTTT-A
* * *
1655 -TCTCGAAACTTCCAAGAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATTACATTTTTA
* * * *
1684 -CCTCCGAAC-TCTAAAAAATTACACTTTTC
1 CCCT-CAAACTTC-CAAAAATTACATTTTTA
* * *
1713 CCCT-AAACCTCCAAAAATTCCATATTTA
1 CCCTCAAACTTCCAAAAATTACATTTTTA
* *
1741 ACCTCGAAACTTTCAAAAATTACTATTT
1 CCCTC-AAACTTCCAAAAATTAC-ATTT
1769 CACCCCCGAA
Statistics
Matches: 417, Mismatches: 81, Indels: 58
0.75 0.15 0.10
Matches are distributed among these distances:
28 29 0.07
29 182 0.44
30 181 0.43
31 25 0.06
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATTACATTTTTA
Found at i:1290 original size:30 final size:29
Alignment explanation
Indices: 1216--1761 Score: 343
Period size: 30 Copynumber: 18.5 Consensus size: 29
1206 GGAGGTCCCT
**
1216 AAACTATCCAAAAATTATATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCG
*
1247 -AACCTCCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* * *
1276 AAACTTCTAAAAATTACATTTTTACC-CTT
1 AAACTTCCAAAAATTCCATTTTTACCTC-G
* * * * *
1305 AAATTTCTAAAAATTCCATTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCTCG
* *
1334 AAACTACCAAAAAAATT-CATTTTTGACC-CTA
1 AAACTTCC--AAAAATTCCATTTTT-ACCTC-G
*
1365 AAACTTCCAAAAA-TCACATTTTTCCCTCG
1 AAACTTCCAAAAATTC-CATTTTTACCTCG
* * * *
1394 -AACTTACAAAAAATCAAATTTTTACCCTTG
1 AAACTTCCAAAAATTC-CATTTTTA-CCTCG
* * * *
1424 -AATTTCAAAAAATTCCATTTTAACC-CTA
1 AAACTTCCAAAAATTCCATTTTTACCTC-G
*
1452 AAACTTCCAAAAA-TCACATGTTTACCCTC-
1 AAACTTCCAAAAATTC-CATTTTTA-CCTCG
* *
1481 AAATTTTCAAAAATTCCATTTTTTACCTCG
1 AAACTTCCAAAAATTCCA-TTTTTACCTCG
*
1511 AAACTTTCAAAAATTCCATTTTTGACCTC-
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
*
1540 ACAACTTCCAAAAATTACATTTTTACCCTCG
1 A-AACTTCCAAAAATTCCATTTTTA-CCTCG
* * *
1571 -AACTTCCAAAAAATCATATTTTTACC-CTT
1 AAACTTCCAAAAATTC-CATTTTTACCTC-G
* * *
1600 AAACATCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCTCG
* *
1630 AAACTTCCATAAAA-TCCGTTTTTGATCTCG
1 AAACTTCCA-AAAATTCCATTTTT-ACCTCG
*
1660 AAACTTCCAAGAATTCCATTTTTACCTCCG
1 AAACTTCCAAAAATTCCATTTTTACCT-CG
* * * * *
1690 -AAC-TCTAAAAAATTACACTTTT-CCCCT
1 AAACTTC-CAAAAATTCCATTTTTACCTCG
* *
1717 AAACCTCCAAAAATTCCATATTTAACCTCG
1 AAACTTCCAAAAATTCCAT-TTTTACCTCG
*
1747 AAACTTTCAAAAATT
1 AAACTTCCAAAAATT
1762 ACTATTTCAC
Statistics
Matches: 407, Mismatches: 70, Indels: 77
0.73 0.13 0.14
Matches are distributed among these distances:
27 1 0.00
28 34 0.08
29 161 0.40
30 187 0.46
31 24 0.06
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:1317 original size:59 final size:58
Alignment explanation
Indices: 1216--1768 Score: 385
Period size: 59 Copynumber: 9.4 Consensus size: 58
1206 GGAGGTCCCT
* * ** *
1216 AAACTATCCAAAAATTATATTTTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCTCG
1 AAACT-TCTAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTT-ACCTCG
* * * * *
1276 AAACTTCTAAAAATTACATTTTTACCCTTAAATTTCTAAAAATTCCATTTTGACCCCA
1 AAACTTCTAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCTCG
* * * *
1334 AAACTACCAAAAAAATT-CATTTTTGACCCTAAAACTTCCAAAAA-TCACATTTTTCCCTCG
1 AAACT-TC-TAAAAATTACATTTTT-ACCCTTAAACTTCCAAAAATTC-CATTTTTACCTCG
* * * * * * * *
1394 -AACTTACAAAAAATCAAATTTTTACCCTTGAATTTCAAAAAATTCCATTTTAACC-CTA
1 AAACTT-CTAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCTC-G
* * * * * *
1452 AAACTTCCAAAAATCACATGTTTACCCTCAAATTTTCAAAAATTCCATTTTTTACCTCG
1 AAACTTCTAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCA-TTTTTACCTCG
* * *
1511 AAACTT-TCAAAAATTCCATTTTTGA-CCTCACAACTTCCAAAAATTACATTTTTACCCTCG
1 AAACTTCT-AAAAATTACATTTTT-ACCCTTA-AACTTCCAAAAATTCCATTTTTA-CCTCG
* * * * * *
1571 -AACTTCCAAAAAATCATATTTTTACCCTTAAACATCCAAAAATTCCATTTTTGACCCCA
1 AAACTT-CTAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTT-ACCTCG
* * * * * *
1630 AAACTTCCATAAAA-TCCGTTTTTGA-TCTCGAAACTTCCAAGAATTCCATTTTTACCTCCG
1 AAACTTCTA-AAAATTACATTTTT-ACCCT-TAAACTTCCAAAAATTCCATTTTTACCT-CG
* * * *
1690 -AAC-TCTAAAAAATTACACTTTT-CCCCTAAACCTCCAAAAATTCCATATTTAACCTCG
1 AAACTTCT-AAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCAT-TTTTACCTCG
1747 AAACTT-TCAAAAATTACTATTT
1 AAACTTCT-AAAAATTAC-ATTT
1769 CACCCCCGAA
Statistics
Matches: 385, Mismatches: 77, Indels: 63
0.73 0.15 0.12
Matches are distributed among these distances:
57 20 0.05
58 100 0.26
59 158 0.41
60 107 0.28
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (58 bp):
AAACTTCTAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTACCTCG
Found at i:1351 original size:31 final size:31
Alignment explanation
Indices: 1313--1377 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1303 TTAAATTTCT
1313 AAAAATTCCA-TTTTGACCCCAAAACTACCAA
1 AAAAATT-CATTTTTGACCCCAAAACTACCAA
* *
1344 AAAAATTCATTTTTGACCCTAAAACTTCCAA
1 AAAAATTCATTTTTGACCCCAAAACTACCAA
1375 AAA
1 AAA
1378 TCACATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.46, C:0.25, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAATTCATTTTTGACCCCAAAACTACCAA
Found at i:1428 original size:118 final size:119
Alignment explanation
Indices: 1225--1759 Score: 368
Period size: 119 Copynumber: 4.5 Consensus size: 119
1215 TAAACTATCC
* ** *
1225 AAAAATTATATTTTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCTCGAAACTTCTAAAAAT
1 AAAAATTATATTTTGACCCTAAAACCTCCAAAAATTCCATTTTTGACCTCGAAACTTCAAAAAAT
* * * *
1290 TACATTTTTACCCTTAAATTTCTAAAAATTCCATTTTGACCCCAAAACTACCAA
66 CAAATTTTTACCCTTAAATTTCAAAAAATTCCATTTTAACCCCAAAACTACCAA
* *
1344 AAAAATTCAT-TTTTGACCCTAAAACTTCCAAAAA-TCACATTTTT-CCCTCG-AACTTACAAAA
1 AAAAATT-ATATTTTGACCCTAAAACCTCCAAAAATTC-CATTTTTGACCTCGAAACTT-CAAAA
* * *
1405 AATCAAATTTTTACCCTTGAATTTCAAAAAATTCCATTTTAACCCTAAAACTTCC--
63 AATCAAATTTTTACCCTTAAATTTCAAAAAATTCCATTTTAACCCCAAAACTACCAA
* * * ** * *
1460 AAAAATCACATGTTT-ACCCTCAAATTTTCAAAAATTCCATTTTTTACCTCGAAACTTTCAAAAA
1 AAAAATTATAT-TTTGACCCTAAAACCTCCAAAAATTCCATTTTTGACCTCGAAAC-TTCAAAAA
* * * * * * * * *
1524 TTC-CATTTTTGA-CCTCACAACTTCCAAAAATTACATTTTTACCCTC-GAACTTCC-A
64 ATCAAATTTTT-ACCCTTA-AATTTCAAAAAATTCCATTTTAACCC-CAAAACTACCAA
* * * * * * *
1579 AAAAATCATATTTTTACCCTTAAACATCCAAAAATTCCATTTTTGACCCCAAAACTTCCATAAAA
1 AAAAATTATATTTTGACCCTAAAACCTCCAAAAATTCCATTTTTGACCTCGAAACTT-CAAAAAA
** * * * * * * * *
1644 TC-CGTTTTTGA-TCTCGAAACTTCCAAGAATTCCATTTTTACCTCC-GAACT--CTA
65 TCAAATTTTT-ACCCT-TAAATTTCAAAAAATTCCATTTTAACC-CCAAAACTACCAA
* * * *
1697 AAAAATTACACTTTT-CCCCT-AAACCTCCAAAAATTCCATATTTAACCTCGAAACTTTCAAAAA
1 AAAAATTATA-TTTTGACCCTAAAACCTCCAAAAATTCCATTTTTGACCTCGAAAC-TTCAAAAA
1760 TTACTATTTC
Statistics
Matches: 343, Mismatches: 53, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
115 1 0.00
116 30 0.09
117 59 0.17
118 120 0.35
119 129 0.38
120 4 0.01
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (119 bp):
AAAAATTATATTTTGACCCTAAAACCTCCAAAAATTCCATTTTTGACCTCGAAACTTCAAAAAAT
CAAATTTTTACCCTTAAATTTCAAAAAATTCCATTTTAACCCCAAAACTACCAA
Found at i:1681 original size:89 final size:87
Alignment explanation
Indices: 1216--1761 Score: 394
Period size: 89 Copynumber: 6.2 Consensus size: 87
1206 GGAGGTCCCT
** ** * * *
1216 AAACTATCCAAAAATTATATTTTTACCCTCGAACCTCCAAAAATTCCATTTTTGACCTCGAAACT
1 AAACT-TCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACT
* * *
1281 TCTAAAAATTACATTTTTACC-CTT
65 TCCAAAAA-TCCATTTTTACCTC-G
* * * ** * *
1305 AAATTTCTAAAAATTCCATTTTGACCCCAAAACTACCAAAAAAATT-CATTTTTGACCCTAAAAC
1 AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCC--AAAAATTCCATTTTTGACCCCAAAAC
*
1369 TTCCAAAAATCACATTTTTCCCTCG
64 TTCCAAAAATC-CATTTTTACCTCG
* * * * * * * *
1394 -AACTTACAAAAAATCAAATTTTTACCCTTGAATTTCAAAAAATTCCA-TTTTAACCCTAAAACT
1 AAACTTCCAAAAATTC-CATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACT
*
1457 TCCAAAAATCACATGTTTACCCTC-
65 TCCAAAAATC-CATTTTTA-CCTCG
* * * * * *
1481 AAATTTTCAAAAATTCCATTTTTTA-CCTCGAAACTTTCAAAAATTCCATTTTTGACCTCACAAC
1 AAACTTCCAAAAATTCCA-TTTTTACCCT-TAAACTTCCAAAAATTCCATTTTTGACCCCAAAAC
*
1545 TTCCAAAAATTACATTTTTACCCTCG
64 TTCCAAAAA-TCCATTTTTA-CCTCG
* * *
1571 -AACTTCCAAAAAATCATATTTTTACCCTTAAACATCCAAAAATTCCATTTTTGACCCCAAAACT
1 AAACTTCCAAAAATTC-CATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACT
* *
1635 TCCATAAAATCCGTTTTTGATCTCG
65 TCCA-AAAATCCATTTTT-ACCTCG
* ** * * * *
1660 AAACTTCCAAGAATTCCATTTTTA-CCTCCGAAC-TCTAAAAAATTACACTTTT--CCCCTAAAC
1 AAACTTCCAAAAATTCCATTTTTACCCT-TAAACTTC-CAAAAATTCCATTTTTGACCCCAAAAC
* *
1721 CTCCAAAAATTCCATATTTAACCTCG
64 TTCCAAAAA-TCCAT-TTTTACCTCG
*
1747 AAACTTTCAAAAATT
1 AAACTTCCAAAAATT
1762 ACTATTTCAC
Statistics
Matches: 361, Mismatches: 74, Indels: 46
0.75 0.15 0.10
Matches are distributed among these distances:
86 4 0.01
87 77 0.21
88 81 0.22
89 168 0.47
90 31 0.09
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (87 bp):
AAACTTCCAAAAATTCCATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTT
CCAAAAATCCATTTTTACCTCG
Done.