Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012410.1 Kokia drynarioides strain JFW-HI SEQ_127414, 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: 9334
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Found at i:394 original size:3 final size:3
Alignment explanation
Indices: 386--436 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
376 AATTTAATAT
386 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
434 TTA
1 TTA
437 ATGCTATTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1149 original size:14 final size:15
Alignment explanation
Indices: 1126--1154 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1116 AATTTGGACA
1126 TGTAATTTGGACTTT
1 TGTAATTTGGACTTT
1141 TGTAA-TTGGACTTT
1 TGTAATTTGGACTTT
1155 ATAATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (15 bp):
TGTAATTTGGACTTT
Found at i:1191 original size:6 final size:6
Alignment explanation
Indices: 1180--1263 Score: 95
Period size: 6 Copynumber: 14.7 Consensus size: 6
1170 ATTTTGAAAA
*
1180 TAAATT TAAATT TAAA-T TAAATT TAAATT TAAAAT T-AATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * *
1226 CAAATT TAAA-A TAAATC TAAATT TAAAAT T-AATT TAAA
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA
1264 AGGGGCCCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
5 17 0.26
6 48 0.74
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:1202 original size:17 final size:17
Alignment explanation
Indices: 1165--1263 Score: 87
Period size: 17 Copynumber: 5.7 Consensus size: 17
1155 ATAATAATCT
*
1165 TTTAAATTTTGAAAATAAA
1 TTTAAA-TTT-AAATTAAA
1184 TTTAAATTTAAATTAAA
1 TTTAAATTTAAATTAAA
1201 TTTAAATTTAAAATT-AA
1 TTTAAATTT-AAATTAAA
*
1218 TTTAAATTCAAATTTAAA
1 TTTAAATTTAAA-TTAAA
* *
1236 -ATAAATCTAAATTTAAA
1 TTTAAATTTAAA-TTAAA
*
1253 ATT-AATTTAAA
1 TTTAAATTTAAA
1264 AGGGGCCCGA
Statistics
Matches: 69, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.04
17 49 0.71
18 11 0.16
19 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:1210 original size:23 final size:23
Alignment explanation
Indices: 1180--1263 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
1170 ATTTTGAAAA
1180 TAAATTTAAATTTAAATTAAATT
1 TAAATTTAAATTTAAATTAAATT
* *
1203 TAAATTTAAAATTAATTTAAATT
1 TAAATTTAAATTTAAATTAAATT
* *
1226 CAAATTTAAA-ATAAATCTAAATT
1 TAAATTTAAATTTAAAT-TAAATT
*
1249 TAAAATT-AATTTAAA
1 TAAATTTAAATTTAAA
1264 AGGGGCCCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 6 0.12
23 45 0.88
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTAAATT
Found at i:1942 original size:207 final size:204
Alignment explanation
Indices: 1673--2194 Score: 726
Period size: 207 Copynumber: 2.5 Consensus size: 204
1663 ATTTGGTTCA
* *
1673 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAAATTTGCTCACATTGAGCATGGGTTTGATT
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG-TTGGGTTTGATT
* *
1738 TGGTCCTCTTCTCAGTATCTCATCAGGAAGATGATAGTATTACC-TGTTTCAATCCACTTCTC-A
65 TGGTCCTCTTCTCAGTATCTCATCAAGAAGATGATAGCA-T-CCATGTTTCAATCCACTTCTCTA
*
1801 GTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGTTAACCTTTTTA
128 -TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTA
1866 TTGCTTCGACCTG
192 TTGCTTCGACCTG
*
1879 CTTCTCAGTATCTCATCAGGAAGCTGGGGGTTCGAAGATTTGCTCACATCGAGTGTGGGTTTGAT
1 CTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTCACATTGAGT-TGGGTTTGAT
* * * * *
1944 TCGATCTTCTTCTCAGTATCTCATCAAGAAGATGATAGCATCCATTGTTTCAATTCGCTTCTCTA
64 TTGGTCCTCTTCTCAGTATCTCATCAAGAAGATGATAGCATCCA-TGTTTCAATCCACTTCTCTA
* *
2009 TATCTCATCAGGAAGATGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTAT
128 TATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTAT
*
2074 TGCTTCGCCCTG
193 TGCTTCGACCTG
* * * * **
2086 CTTCTTATTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTGAGCCTTGTTTCATTG
1 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAG--TTGGGT--TTG
*
2151 ATTTGGT-CTACTTCTCAGTATCTCATCAAGAAGATGATCGCATC
62 ATTTGGTCCT-CTTCTCAGTATCTCATCAAGAAGATGATAGCATC
2195 ACTGTTTGTG
Statistics
Matches: 281, Mismatches: 25, Indels: 17
0.87 0.08 0.05
Matches are distributed among these distances:
205 2 0.01
206 50 0.18
207 185 0.66
208 3 0.01
209 41 0.15
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (204 bp):
CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGTTGGGTTTGATTT
GGTCCTCTTCTCAGTATCTCATCAAGAAGATGATAGCATCCATGTTTCAATCCACTTCTCTATAT
CTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGC
TTCGACCTG
Found at i:2743 original size:50 final size:49
Alignment explanation
Indices: 2689--3075 Score: 225
Period size: 50 Copynumber: 7.7 Consensus size: 49
2679 TACTAGATTT
2689 GCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACATGGTTC
1 GCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TGGTTC
* * * * *
2739 GCCGTTACGACTTAAACCTTTCCCTT-TTGTATCTT-TGTGGTACTGGATCC
1 GCCGTTGCGGCTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTGG-TTC
* * * * *
2789 ACCGTTACGGTCTTAGATCTTTCCCTTCATGTCTTC--ATGGTACTAGATTC
1 GCCGTTGCGG-CTTAAATCTTTCCCTTCTTGTCTTCTGA-GGTACT-GGTTC
* * * ** *
2839 GTCATTAG-GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTCTT
1 GCCGTT-GCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TGGT-TC
* * * * *
2890 GCCGTTGCGACTTAGACCTTT-CCTTTTTGTATCTT-TGTGGTACTGGATTC
1 GCCGTTGCGGCTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTGG-TTC
* * *
2940 GCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACATGATCC
1 GCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTAC-TGGTTC
** * * * * *
2990 TGCTATTGCGACTTAGATCTTTCCCTT-TTGTATCTT-TGTGGTATTGGATC
1 -GCCGTTGCGGCTTAAATCTTTCCCTTCTTG--TCTTCTGAGGTACTGGTTC
* * * * *
3040 TGTCGTTGCGACTTAGACCTTTCCCTTCATGTCTTC
1 -GCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTC
3076 ATGGTACTAA
Statistics
Matches: 255, Mismatches: 57, Indels: 50
0.70 0.16 0.14
Matches are distributed among these distances:
49 37 0.15
50 127 0.50
51 81 0.32
52 10 0.04
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.41
Consensus pattern (49 bp):
GCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACTGGTTC
Found at i:2915 original size:150 final size:150
Alignment explanation
Indices: 2697--2974 Score: 425
Period size: 150 Copynumber: 1.9 Consensus size: 150
2687 TTGCCGTTGC
* **
2697 GGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACATGGTTCGCCGTTACGACTTAAACCTTTCC
1 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTTCGCCGTTACGACTTAAACCTTTCC
*
2762 C-TTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGTCTTAGATCTTTCCCTTCATGTCTTCA
66 CTTTTTGTATCTTTGTGGTACTGGATCCACCGTTACGG-CTTAAATCTTTCCCTTCATGTCTTCA
2826 TGGTACTAGATTCGTCATTAG
130 TGGTACTAGATTCGTCATTAG
* * *
2847 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTCTTGCCGTTGCGACTTAGACCTTT-
1 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGT-TCGCCGTTACGACTTAAACCTTTC
* * * *
2911 CCTTTTTGTATCTTTGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCGTGTCTTC
65 CCTTTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGCTTAAATCTTTCCCTTCATGTCTTC
2975 TGAGGTACAT
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
150 62 0.54
151 53 0.46
ACGTcount: A:0.15, C:0.25, G:0.19, T:0.41
Consensus pattern (150 bp):
GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTTCGCCGTTACGACTTAAACCTTTCC
CTTTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGCTTAAATCTTTCCCTTCATGTCTTCAT
GGTACTAGATTCGTCATTAG
Found at i:2955 original size:101 final size:101
Alignment explanation
Indices: 2847--3075 Score: 318
Period size: 101 Copynumber: 2.3 Consensus size: 101
2837 TCGTCATTAG
* *
2847 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAG-TCTTGCCGTTGCGACTTAGACCTTT
1 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACA-AGATCCTGCCATTGCGACTTAGACCTTT
*
2911 CCTTTTTGTATCTTTGTGGTACTGGAT-TCGCCGTTGC
65 CCCTTTTGTATCTTTGTGGTACTGGATCT-GCCGTTGC
* * *
2948 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACATGATCCTGCTATTGCGACTTAGATCTTTC
1 GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACAAGATCCTGCCATTGCGACTTAGACCTTTC
* *
3013 CCTTTTGTATCTTTGTGGTATTGGATCTGTCGTTGC
66 CCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGC
* * * *
3049 GACTTAGACCTTTCCCTTCATGTCTTC
1 GGCTTAAATCTTTCCCTTCGTGTCTTC
3076 ATGGTACTAA
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
100 1 0.01
101 112 0.98
102 1 0.01
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (101 bp):
GGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACAAGATCCTGCCATTGCGACTTAGACCTTTC
CCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGC
Found at i:3047 original size:151 final size:151
Alignment explanation
Indices: 2699--3066 Score: 394
Period size: 151 Copynumber: 2.4 Consensus size: 151
2689 GCCGTTGCGG
* * ** * * *
2699 CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACATGGT-TCGCCGTTACGACTTAAACCTTTCCC
1 CTTAAATCTTTCCCTTCGTATCTTCTGAGGTACACAGTCTTGCCGTTGCGACTTAGACCTTTCCC
*
2763 TTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGTCTTAGATCTTTCCCTTCATGTCTTCATG
66 TTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGTCTTAAATCTTTCCCTTCATGTCTTCATG
* *
2828 GTACTAGATTCGTCATTAGGG
131 GTACTAGATCCGTCATTAGGA
* *
2849 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTCTTGCCGTTGCGACTTAGACCTTTCCT
1 CTTAAATCTTTCCCTTCGTATCTTCTGAGGTACACAGTCTTGCCGTTGCGACTTAGACCTTTCCC
* * * *
2914 TTTTGTATCTTTGTGGTACTGGATTCGCCGTTGCGG-CTTAAATCTTTCCCTTCGTGTCTTC-TG
66 TTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGTCTTAAATCTTTCCCTTCATGTCTTCAT-
2977 AGGTAC-ATGATCC-TGCTATT-GCGA
130 -GGTACTA-GATCCGT-C-ATTAG-GA
* * * *** *
3001 CTTAGATCTTTCCCTTTTGTATCTT-TGTGGTA-TTGGATC-TGTCGTTGCGACTTAGACCTTTC
1 CTTAAATCTTTCCC-TTCGTATCTTCTGAGGTACACAG-TCTTGCCGTTGCGACTTAGACCTTTC
3063 CCTT
64 CCTT
3067 CATGTCTTCA
Statistics
Matches: 186, Mismatches: 23, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
149 1 0.01
150 60 0.32
151 92 0.49
152 25 0.13
153 8 0.04
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (151 bp):
CTTAAATCTTTCCCTTCGTATCTTCTGAGGTACACAGTCTTGCCGTTGCGACTTAGACCTTTCCC
TTTTGTATCTTTGTGGTACTGGATCCACCGTTACGGTCTTAAATCTTTCCCTTCATGTCTTCATG
GTACTAGATCCGTCATTAGGA
Found at i:4299 original size:1 final size:1
Alignment explanation
Indices: 4288--4361 Score: 58
Period size: 1 Copynumber: 74.0 Consensus size: 1
4278 CAACCCCTCC
* * * * * * * * * *
4288 TTTTCTTTTTTTTTTCTTTTTTTTTTATTTTTATTTTTGTTTTTTCTTTTTCTTCTTCTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4353 TTTTTTTTT
1 TTTTTTTTT
4362 AATCATTGAA
Statistics
Matches: 53, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.03, C:0.09, G:0.01, T:0.86
Consensus pattern (1 bp):
T
Done.