Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000095.1 Kokia drynarioides strain JFW-HI SEQ_110723, 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: 2921
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Found at i:1328 original size:97 final size:96
Alignment explanation
Indices: 1142--1316 Score: 235
Period size: 97 Copynumber: 1.8 Consensus size: 96
1132 AACCTTGGAA
* * * * *
1142 AAGGATGTTCGATTATCTAGTTTTGAAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTCAA
1 AAGGATATTCGATTATCTAGATTTGAAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAA
*
1207 AATCAGAGATAAAGAAACATTGCCTCGTTTT
66 AATCAGAAATAAAGAAACATTGCCTCGTTTT
* * **
1238 AAGGATATTCGATTATTTCGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTAGATTTGAA-AAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
1303 AAACTC-GAAATAAA
65 AAA-TCAGAAATAAA
1317 AGAATATTGC
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
96 23 0.34
97 42 0.63
98 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTAGATTTGAAAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAA
AATCAGAAATAAAGAAACATTGCCTCGTTTT
Found at i:1583 original size:28 final size:28
Alignment explanation
Indices: 1552--1612 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1542 AAAATGTGAT
* *
1552 TTTTGGATACCC-AGGGGCAAAATGGTAA
1 TTTTGGACACCCGA-GGGCAAAATAGTAA
*
1580 TTTTGGACACTCGAGGGCAAAATAGTAA
1 TTTTGGACACCCGAGGGCAAAATAGTAA
1608 TTTTG
1 TTTTG
1613 TGAAGTTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGCAAAATAGTAA
Found at i:1652 original size:58 final size:57
Alignment explanation
Indices: 1565--1869 Score: 172
Period size: 60 Copynumber: 5.3 Consensus size: 57
1555 TGGATACCCA
* * * * *
1565 GGGGCAAAATGGTAATTTTGGACACTCGAGGGC-AAAATAGTAA-TTTTGTGAAGTTTG
1 GGGGTAAAATGGTAATTTTGGAAAATCGAGGGCAAAAAT-GGAATTTTTG-GAAGTTCG
*
1622 GGGGTAAAAATGG-AATTTCTGGAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCG
1 GGGGT-AAAATGGTAATTT-TGGAAAATCGAGGGCAAAAATGGAATTTTTGGAAGTTCG
**
1680 GGGGTAAAATGGTAATTTTTTGGAAAAATC-ATGGTTAAAAATGGAA---TT-----TT-G
1 GGGGTAAAATGGTAA--TTTTGG-AAAATCGA-GGGCAAAAATGGAATTTTTGGAAGTTCG
** * * * * *
1731 GGGGTAAAATGGTTTTTTTTTTGGAAAAATCAAGGTCAAAAATGAAATTTTTGAAAGTTTG
1 GGGGTAAAATGG---TAATTTTGG-AAAATCGAGGGCAAAAATGGAATTTTTGGAAGTTCG
* * ** *
1792 AGGGTAAAATGGTAATTTTTTGAAAAATCG-GGGTCAAAAATAAAATTTTTTTGAAGTTCG
1 GGGGTAAAATGGTAA--TTTTGGAAAATCGAGGG-CAAAAATGGAA-TTTTTGGAAGTTCG
*
1852 GAGGT-AAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
1870 TAGAAAAAAA
Statistics
Matches: 199, Mismatches: 23, Indels: 52
0.73 0.08 0.19
Matches are distributed among these distances:
51 13 0.07
52 27 0.14
53 1 0.01
54 1 0.01
55 2 0.01
57 22 0.11
58 39 0.20
59 39 0.20
60 43 0.22
61 12 0.06
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGAAAATCGAGGGCAAAAATGGAATTTTTGGAAGTTCG
Found at i:1698 original size:28 final size:28
Alignment explanation
Indices: 1565--1698 Score: 96
Period size: 29 Copynumber: 4.7 Consensus size: 28
1555 TGGATACCCA
* *
1565 GGGGCAAAATGGTAATTTTGGACA-CTCG
1 GGGGTAAAATGGTAATTTTGGA-AGTTCG
* * * *
1593 AGGGCAAAATAGTAATTTTGTGAAGTTTG
1 GGGGTAAAATGGTAATTTTG-GAAGTTCG
**
1622 GGGGTAAAAATGG-AATTTCTGGAAAATC-
1 GGGGT-AAAATGGTAATTT-TGGAAGTTCG
*
1650 GAGGTCAAAAATGG-AATTTTTGGAAGTTCG
1 GGGGT--AAAATGGTAA-TTTTGGAAGTTCG
1680 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
1699 TTGGAAAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
28 34 0.40
29 35 0.42
30 15 0.18
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.30
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGAAGTTCG
Found at i:1734 original size:51 final size:52
Alignment explanation
Indices: 1670--1781 Score: 154
Period size: 52 Copynumber: 2.2 Consensus size: 52
1660 ATGGAATTTT
* * * *
1670 TGGAAGTTCGGGGGTAAAATGG-TAATTTTTTGGAAAAATCATGGTTAAAAA
1 TGGAATTTTGGGGGTAAAATGGTTAATTTTTTGGAAAAATCAAGGTCAAAAA
**
1721 TGGAATTTTGGGGGTAAAATGGTTTTTTTTTTGGAAAAATCAAGGTCAAAAA
1 TGGAATTTTGGGGGTAAAATGGTTAATTTTTTGGAAAAATCAAGGTCAAAAA
*
1773 TGAAATTTT
1 TGGAATTTT
1782 TGAAAGTTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 20 0.38
52 33 0.62
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (52 bp):
TGGAATTTTGGGGGTAAAATGGTTAATTTTTTGGAAAAATCAAGGTCAAAAA
Found at i:1827 original size:59 final size:59
Alignment explanation
Indices: 1727--1920 Score: 180
Period size: 59 Copynumber: 3.2 Consensus size: 59
1717 AAAATGGAAT
* ** *
1727 TTTGGGGGTAAAATGGTTTTTTTTTTGGAAAAATCAAGGTCAAAAATGAAATTTTTGAAAG
1 TTTGAGGGTAAAATGG-TAATTTTTT-GAAAAATCGAGGTCAAAAATGAAATTTTTGAAAG
* *
1788 TTTGAGGGTAAAATGGTAATTTTTTGAAAAATCGGGGTCAAAAATAAAATTTTTTTG-AAG
1 TTTGAGGGTAAAATGGTAATTTTTTGAAAAATCGAGGTCAAAAATGAAA--TTTTTGAAAG
* * * * *
1848 TTCG-GAGGT-AAATGGTAATTTTTAGAAAAAAACGAGGTC-AAAATGGAATTTTGGAGAAG
1 TTTGAG-GGTAAAATGGTAATTTTTTG-AAAAATCGAGGTCAAAAATGAAATTTTTGA-AAG
*
1907 TTTAAGGGTCAAAA
1 TTTGAGGGT-AAAA
1921 AATAATTTCT
Statistics
Matches: 109, Mismatches: 15, Indels: 18
0.77 0.11 0.13
Matches are distributed among these distances:
57 5 0.05
59 52 0.48
60 28 0.26
61 24 0.22
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.34
Consensus pattern (59 bp):
TTTGAGGGTAAAATGGTAATTTTTTGAAAAATCGAGGTCAAAAATGAAATTTTTGAAAG
Done.