Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010995.1 Kokia drynarioides strain JFW-HI SEQ_125965, 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: 28456
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1276 original size:20 final size:20
Alignment explanation
Indices: 1225--1276 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 20
1215 CCATAGTCAA
1225 TTCTATATTTTGAAAATAGG
1 TTCTATATTTTGAAAATAGG
1245 TTCTA-A---TGAAAATAGG
1 TTCTATATTTTGAAAATAGG
1261 TTCTATATTTTGAAAA
1 TTCTATATTTTGAAAA
1277 CAGGCAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 15 0.54
17 1 0.04
19 1 0.04
20 11 0.39
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.42
Consensus pattern (20 bp):
TTCTATATTTTGAAAATAGG
Found at i:1375 original size:49 final size:49
Alignment explanation
Indices: 1300--1771 Score: 340
Period size: 49 Copynumber: 9.7 Consensus size: 49
1290 TAAGGTACCG
* *
1300 GGTTCGCCATTGCGACTTAAATCTTTCCCTTCATGTCTCTGAAGTACTA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTA
* *
1349 GGTTCGTCATTGCGACTTAAACCTTTCCC-TCTATGTCT-TCATGGTACTA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTC-ATGTCTCTGA-GGTACTA
* * ** * * * * * *
1398 GATTTGCTGTTGCGGCTTAGATCC-TTCCCTT-GTGTCTTTGTGGTA-TT
1 GGTTCGCCATTGCGACTTA-AACCTTTCCCTTCATGTCTCTGAGGTACTA
* * * * * * * *
1445 GGATCCACCATTACGGCTTAGATCTTTCCC-TCGTGTCT-TCGTGGTACT-
1 GG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACTA
* * * * * *
1493 GGATCCGCCGTTACGGCTTAAATCTTTCCCTTTTATG-CTTCTGAGGTACTA
1 GG-TTCGCCATTGCGACTTAAACCTTTCCC-TTCATGTC-TCTGAGGTACTA
* *
1544 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCTTGTCT-TCGCGGTACTA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACTA
* * * * * *
1593 GATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTA
* * *
1642 GGTTCGCCATTGCGACTTAAACCTTTCTCTT-ATGTCT-TCGTGGTA-TT
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCT-GAGGTACTA
* * * * * * *
1689 GGATCCGCCGTTCCAACTCAGATCTTTCCCTTCATGTCTCTGAGGTACTA
1 GG-TTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTA
1739 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCA
1 GGTTCGCCATTGCGACTTAAACCTTTCCCTTCA
1772 AATCTTCATG
Statistics
Matches: 327, Mismatches: 73, Indels: 46
0.73 0.16 0.10
Matches are distributed among these distances:
47 9 0.03
48 101 0.31
49 171 0.52
50 43 0.13
51 3 0.01
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (49 bp):
GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTCTGAGGTACTA
Found at i:1462 original size:48 final size:48
Alignment explanation
Indices: 1410--1694 Score: 189
Period size: 48 Copynumber: 5.9 Consensus size: 48
1400 TTTGCTGTTG
* * *
1410 CGGCTTAGATCCTTCCCTTGTGTCTTTGTGGTATTGGATCCACCATTA
1 CGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATCCACCATTA
* * *
1458 CGGCTTAGATCTTTCCCTCGTGTCTTCGTGGTACTGGATCCGCCGTTA
1 CGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATCCACCATTA
* * * * * * *
1506 CGGCTTAAATCTTTCCCTTTTATGCTTCTGAGGTACTAGG-TTCGCCATTG
1 CGGCTTAGATCTTTCCCTTGTGT-CTTC-GTGGTACT-GGATCCACCATTA
* * * * * * * * *
1556 CGACTTAAACCTTTCCCTTCTTGTCTTCGCGGTACTAGATCCGCCGTTG
1 CGGCTTAGATCTTTCCCTT-GTGTCTTCGTGGTACTGGATCCACCATTA
* * * * *
1605 CGGCTTAGATCTTTCCCTTCATGTC-TCTGAGGTACTAGG-TTCGCCATTG
1 CGGCTTAGATCTTTCCCTT-GTGTCTTC-GTGGTACT-GGATCCACCATTA
* * * * * *
1654 CGACTTAAACCTTTCTCTTATGTCTTCGTGGTATTGGATCC
1 CGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATCC
1695 GCCGTTCCAA
Statistics
Matches: 192, Mismatches: 36, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
47 2 0.01
48 77 0.40
49 72 0.38
50 36 0.19
51 5 0.03
ACGTcount: A:0.14, C:0.27, G:0.21, T:0.38
Consensus pattern (48 bp):
CGGCTTAGATCTTTCCCTTGTGTCTTCGTGGTACTGGATCCACCATTA
Found at i:1727 original size:97 final size:97
Alignment explanation
Indices: 1304--1769 Score: 551
Period size: 97 Copynumber: 4.8 Consensus size: 97
1294 GTACCGGGTT
* * * * *
1304 CGCCATTGCGACTTAAATCTTTCCCTTCATGTCTCTGAAGTACTAGGTTCGTCATTGCGACTTAA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAA
* *
1369 ACCTTTCCCTCTATGTCTTCATGGTACTAGATT
66 ACCTTTCCCT-TATGTCTTCGTGGTACTAGATC
* * * * * * * * * * *
1402 TGCTGTTGCGGCTTAGATCCTTCCCTT-GTGTCTTTGTGGTA-TTGGATCCACCATTACGGCTTA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGG-TTCGCCATTGCGACTTA
* * ** *
1465 GATCTTTCCCTCGTGTCTTCGTGGTACTGGATC
65 AACCTTTCCCTTATGTCTTCGTGGTACTAGATC
* * *
1498 CGCCGTTACGGCTTAAATCTTTCCCTTTTATG-CTTCTGAGGTACTAGGTTCGCCATTGCGACTT
1 CGCCGTTGCGGCTTAGATCTTTCCC-TTCATGTC-TCTGAGGTACTAGGTTCGCCATTGCGACTT
* *
1562 AAACCTTTCCCTTCTTGTCTTCGCGGTACTAGATC
64 AAACCTTTCCCTT-ATGTCTTCGTGGTACTAGATC
1597 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAA
* * *
1662 ACCTTTCTCTTATGTCTTCGTGGTATTGGATC
66 ACCTTTCCCTTATGTCTTCGTGGTACTAGATC
* ** *
1694 CGCCGTTCCAACTCAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAA
1 CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAA
1759 ACCTTTCCCTT
66 ACCTTTCCCTT
1770 CAAATCTTCA
Statistics
Matches: 306, Mismatches: 55, Indels: 15
0.81 0.15 0.04
Matches are distributed among these distances:
96 40 0.13
97 122 0.40
98 99 0.32
99 45 0.15
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (97 bp):
CGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAA
ACCTTTCCCTTATGTCTTCGTGGTACTAGATC
Found at i:1733 original size:195 final size:195
Alignment explanation
Indices: 1318--1770 Score: 590
Period size: 195 Copynumber: 2.3 Consensus size: 195
1308 ATTGCGACTT
* *
1318 AAATCTTTCCCTTCATGTCTCTGAAGTACTAGGTTCGTCATTGCGACTTAAACCTTTCCC-TCTA
1 AAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCTA
* ** * * * * *
1382 TGTCTTCATGGTACTAGATTTGCTGTTGCGGCTTAGATCCTTCCCTTGTGTCTTTGTGGTATTGG
66 TGTCTTCACGGTACTAGATCCGCCGTTGCGGCTTAGATCCTTCCCTTATGTCTCTGAGGTATAGG
* * * * ** *
1447 ATCCACCATTACGGCTTAGATCTTTCCCTCGTGTCTTCGTGGTACTGGATCCGCCGTTACGGCTT
131 ATCCACCATTACGACTTAAACCTTTCCCTCATGTCTTCGTGGTACTGGATCCGCCGTTACAACTC
*
1512 AAATCTTTCCCTTTTATG-CTTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTC
1 AAATCTTTCCC-TTCATGTC-TCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTC
* *
1576 T-TGTCTTCGCGGTACTAGATCCGCCGTTGCGGCTTAGATCTTTCCCTTCATGTCTCTGAGGTAC
64 TATGTCTTCACGGTACTAGATCCGCCGTTGCGGCTTAGATCCTTCCCTT-ATGTCTCTGAGGTA-
* * * * * * *
1640 TAGG-TTCGCCATTGCGACTTAAACCTTTCTCTTATGTCTTCGTGGTATTGGATCCGCCGTTCCA
127 TAGGATCCACCATTACGACTTAAACCTTTCCCTCATGTCTTCGTGGTACTGGATCCGCCGTTACA
1704 ACTC
192 ACTC
*
1708 AGATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTC
1 AAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTC
1771 AAATCTTCAT
Statistics
Matches: 224, Mismatches: 29, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
194 12 0.05
195 134 0.60
196 75 0.33
197 3 0.01
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (195 bp):
AAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTCTA
TGTCTTCACGGTACTAGATCCGCCGTTGCGGCTTAGATCCTTCCCTTATGTCTCTGAGGTATAGG
ATCCACCATTACGACTTAAACCTTTCCCTCATGTCTTCGTGGTACTGGATCCGCCGTTACAACTC
Found at i:3005 original size:5 final size:6
Alignment explanation
Indices: 2978--3012 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2968 CCTTTTTCTA
* *
2978 TTTTTG TTTTTC TTATTG TTTTTG TTTTTG TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
3013 TCTTTCTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.03, G:0.11, T:0.83
Consensus pattern (6 bp):
TTTTTG
Found at i:3880 original size:16 final size:16
Alignment explanation
Indices: 3857--3896 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3847 TTCATCTTGA
3857 CTTT-TTTTTCCTTTT
1 CTTTCTTTTTCCTTTT
3872 CTTTCTTTTTCCTTTT
1 CTTTCTTTTTCCTTTT
*
3888 -TTACTTTTT
1 CTTTCTTTTT
3897 TATTGGGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTTCTTTTTCCTTTT
Found at i:3897 original size:16 final size:17
Alignment explanation
Indices: 3860--3897 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3850 ATCTTGACTT
*
3860 TTTTTTCCTTTTCTTTC
1 TTTTTTCCTTTTCTTAC
3877 -TTTTTCCTTTT-TTAC
1 TTTTTTCCTTTTCTTAC
3892 TTTTTT
1 TTTTTT
3898 ATTGGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTCCTTTTCTTAC
Found at i:8807 original size:30 final size:30
Alignment explanation
Indices: 8720--8811 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 30
8710 AATCAAGATC
* *
8720 AAAAAT-GGAATTTTTGAAAGTTTAGGGGT
1 AAAAATAGAAATTTTGGAAAGTTTAGGGGT
* * * ** *
8749 -AAAATAGTAATTGTGGGAAGAATCGGGGTT
1 AAAAATAGAAATTTTGGAAAGTTTAGGGG-T
8779 AAAAATA-AAATTTTGGAAAGTTTAGGGGT
1 AAAAATAGAAATTTTGGAAAGTTTAGGGGT
8808 AAAA
1 AAAA
8812 TGGTATTTTT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
28 5 0.11
29 20 0.43
30 16 0.34
31 6 0.13
ACGTcount: A:0.42, C:0.01, G:0.27, T:0.29
Consensus pattern (30 bp):
AAAAATAGAAATTTTGGAAAGTTTAGGGGT
Found at i:8878 original size:28 final size:28
Alignment explanation
Indices: 8839--8939 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 28
8829 ATGAAAGTAA
*
8839 AAAATGGAAATTTTTGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGAAGTTTGGGGGT
* ** * *
8867 AAAATGGTAATTTTGGAA-AATCGAGGT
1 AAAATGGTAATTTTTGAAGTTTGGGGGT
* *
8894 CAAAAATGG-AATTTTTAAAAGTTTGAGGGT
1 --AAAATGGTAATTTTT-GAAGTTTGGGGGT
8924 AAAATGGTAATTTTTG
1 AAAATGGTAATTTTTG
8940 GAAAATCGAG
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
27 5 0.09
28 29 0.54
29 16 0.30
30 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAATGGTAATTTTTGAAGTTTGGGGGT
Found at i:8982 original size:58 final size:58
Alignment explanation
Indices: 8694--9001 Score: 302
Period size: 59 Copynumber: 5.3 Consensus size: 58
8684 AGCATCCGAG
* *
8694 GGTAATTTTTGGAAATAATCAAGATCAAAAATGGAATTTTTGAAAGTTTAGGGGTAAAAT
1 GGTAATTTTTGG-AA-AATCGAGATCAAAAATGGAATTTTTGAAAGTTTGGGGGTAAAAT
* * * * * * ** * *
8754 AGTAATTGTGGGAAGAATCGGGGTTAAAAATAAAATTTTGGAAAGTTTAGGGGTAAAAT
1 GGTAATTTTTGGAA-AATCGAGATCAAAAATGGAATTTTTGAAAGTTTGGGGGTAAAAT
* * *
8813 GGTATTTTTTGGAAAAAT-GAAAGTAAAAAATGGAAATTTTTG-AAGTTTGGGGGTAAAAT
1 GGTAATTTTTGG-AAAATCGAGA-TCAAAAATGG-AATTTTTGAAAGTTTGGGGGTAAAAT
* * *
8872 GGTAA-TTTTGGAAAATCGAGGTCAAAAATGGAATTTTTAAAAGTTTGAGGGTAAAAT
1 GGTAATTTTTGGAAAATCGAGATCAAAAATGGAATTTTTGAAAGTTTGGGGGTAAAAT
* ** * *
8929 GGTAATTTTTGGAAAATCGAGATTAAAAATGGAATTTAGGAATGTTCGGGGGTAAAAAT
1 GGTAATTTTTGGAAAATCGAGATCAAAAATGGAATTTTTGAAAGTTTGGGGGT-AAAAT
*
8988 -GTTATTTTT-GAAAA
1 GGTAATTTTTGGAAAA
9002 GTTTAGGTGT
Statistics
Matches: 203, Mismatches: 38, Indels: 17
0.79 0.15 0.07
Matches are distributed among these distances:
56 7 0.03
57 40 0.20
58 56 0.28
59 82 0.40
60 18 0.09
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.32
Consensus pattern (58 bp):
GGTAATTTTTGGAAAATCGAGATCAAAAATGGAATTTTTGAAAGTTTGGGGGTAAAAT
Found at i:9065 original size:30 final size:30
Alignment explanation
Indices: 8977--9069 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
8967 GGAATGTTCG
* * *
8977 GGGGTAAAAATGTTATTTTTGAAAAGTTTA
1 GGGGTAAAAATATAATTTTTGGAAAGTTTA
* * *
9007 GGTGTTAAAATATAA-TTATGGAGAAGTTTA
1 GGGGTAAAAATATAATTTTTGGA-AAGTTTA
* *
9037 GGGGTCAAAATATAATTTTTGGATAGTTTA
1 GGGGTAAAAATATAATTTTTGGAAAGTTTA
9067 GGG
1 GGG
9070 ACCTTCGAGG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
29 5 0.10
30 40 0.78
31 6 0.12
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38
Consensus pattern (30 bp):
GGGGTAAAAATATAATTTTTGGAAAGTTTA
Found at i:10254 original size:3 final size:3
Alignment explanation
Indices: 10232--10279 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
10222 TGGTTTAATG
* * * *
10232 ATT AAT ATT ATT ACT GTT ATT ATT ATT ATC ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10280 GTTAAACTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:15282 original size:17 final size:17
Alignment explanation
Indices: 15249--15293 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
15239 CATTAAATTT
*
15249 CAATGACAAATGGAAATG
1 CAATGAC-AATGCAAATG
15267 CAATGACAATGCAAATG
1 CAATGACAATGCAAATG
*
15284 CAGTGACAAT
1 CAATGACAAT
15294 TAAAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.47, C:0.16, G:0.20, T:0.18
Consensus pattern (17 bp):
CAATGACAATGCAAATG
Found at i:15299 original size:17 final size:17
Alignment explanation
Indices: 15249--15328 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 17
15239 CATTAAATTT
*
15249 CAATGACAAATGGAAATG
1 CAATGAC-AATGAAAATG
*
15267 CAATGACAATGCAAATG
1 CAATGACAATGAAAATG
* * *
15284 CAGTGACAATTAAAATA
1 CAATGACAATGAAAATG
* * *
15301 TAATGAAAATGAGAATG
1 CAATGACAATGAAAATG
**
15318 TGATGACAATG
1 CAATGACAATG
15329 CTTACTAACA
Statistics
Matches: 49, Mismatches: 13, Indels: 1
0.78 0.21 0.02
Matches are distributed among these distances:
17 42 0.86
18 7 0.14
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (17 bp):
CAATGACAATGAAAATG
Found at i:15794 original size:12 final size:12
Alignment explanation
Indices: 15777--15801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15767 GCTTCATTTC
15777 CTTCCTCTTCTT
1 CTTCCTCTTCTT
15789 CTTCCTCTTCTT
1 CTTCCTCTTCTT
15801 C
1 C
15802 CATGGGTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCCTCTTCTT
Done.