Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005630.1 Kokia drynarioides strain JFW-HI SEQ_119789, 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: 8028
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Found at i:954 original size:46 final size:46
Alignment explanation
Indices: 895--995 Score: 148
Period size: 46 Copynumber: 2.2 Consensus size: 46
885 TCCTATGGTC
* * * * * *
895 GGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTTCTTGACTTA
1 GGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCTCTCGACTTA
941 GGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCTCTCGACTTA
1 GGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCTCTCGACTTA
987 GGGGTAAAA
1 GGGGTAAAA
996 AACTTAATGA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (46 bp):
GGGGTAAAAGATTGGATGATGGCTTCAATCTACCCCTCTCGACTTA
Found at i:1006 original size:46 final size:46
Alignment explanation
Indices: 917--1006 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
907 TGGATGGTGT
* * * * *
917 CTTCAATCTGCCCTTCTTGACTTAGGGGTAAAAGATTGGATGATGG
1 CTTCAATCTACCCCTCTCGACTTAGGGGTAAAAAATTGAATGATGG
963 CTTCAATCTACCCCTCTCGACTTAGGGGTAAAAAACTT-AATGAT
1 CTTCAATCTACCCCTCTCGACTTAGGGGTAAAAAA-TTGAATGAT
1007 AATGTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
46 36 0.95
47 2 0.05
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (46 bp):
CTTCAATCTACCCCTCTCGACTTAGGGGTAAAAAATTGAATGATGG
Found at i:1247 original size:75 final size:76
Alignment explanation
Indices: 1069--1249 Score: 231
Period size: 76 Copynumber: 2.4 Consensus size: 76
1059 CTTATTTGAC
* * ***
1069 CCACTTCACTATATCTCATCAGAAAGATGAGGTTTGAAGTTTCTCTCACATTGAGCTTTGCTTCA
1 CCACTTCTCTATATCTCATCAGAAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCACTTCA
* *
1134 TTTGTTTTGGT
66 GTTGATTTGGT
** * *
1145 TTACTTCTCTATATCTCATCA-AGAAGATGGGGTTTGAAGTTTCACTCACATTGCGCTCCACTTC
1 CCACTTCTCTATATCTCATCAGA-AAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCACTTC
1209 -GTTGATTTGGT
65 AGTTGATTTGGT
*
1220 CCACTTCTCTGTATCTCATCAGAAAGATGA
1 CCACTTCTCTATATCTCATCAGAAAGATGA
1250 CTCCTTCATT
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
75 34 0.39
76 54 0.61
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (76 bp):
CCACTTCTCTATATCTCATCAGAAAGATGAGGTTTGAAGTTTCACTCACATTGAGCTCCACTTCA
GTTGATTTGGT
Found at i:1372 original size:123 final size:123
Alignment explanation
Indices: 1147--1510 Score: 498
Period size: 123 Copynumber: 3.0 Consensus size: 123
1137 GTTTTGGTTT
* *
1147 ACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGCGCTCCACTTCGTT
1 ACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCATTTCGTT
*
1212 GATTTGGTCCACTTCTCTGTATCTCA-TCAGAAAGATGACTC-CTTCATTATTTAGATCC
66 GATTTGGTCCACTTCTCTGTATCTCATTAAG-AAGATGAC-CGCTTCATTATTTAGATCC
* * * * *
1270 ACTTCTATGTATCTCAGCAAGAAGATGGGGTTTGAAGTTTCACTCATATTGAGCTTCATTTCGTT
1 ACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCATTTCGTT
* * * *
1335 GATTTGGTTCACTTCTCTGTATCTCATTAAGAGGATGACCGCTTCATTGTTTTGATCC
66 GATTTGGTCCACTTCTCTGTATCTCATTAAGAAGATGACCGCTTCATTATTTAGATCC
* * * * * *
1393 ACTTCTCTATATCTTATTAGGAAGATGGGGTTTGAAGTTTCACTTACATTGAGCTCCGTTTTGTT
1 ACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCATTTCGTT
* * *
1458 GATTTGGTCCACTTCTCTGTATCTCATCAAGAAGATAACCGGTTCATTTATTT
66 GATTTGGTCCACTTCTCTGTATCTCATTAAGAAGATGACCGCTTCA-TTATTT
1511 TTATCCGACC
Statistics
Matches: 209, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
122 1 0.00
123 200 0.96
124 8 0.04
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (123 bp):
ACTTCTCTATATCTCATCAAGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTCCATTTCGTT
GATTTGGTCCACTTCTCTGTATCTCATTAAGAAGATGACCGCTTCATTATTTAGATCC
Found at i:1720 original size:42 final size:42
Alignment explanation
Indices: 1625--1721 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
1615 TAGGGACGTA
* *
1625 AGATTCGCCTTTGCAGCTTTAATTTAGCCTTTTACATCTTCG
1 AGATTCGCCTTTGCAGCTTCAATTTAGCCTTTTACAGCTTCG
** * ** * *
1667 AGATTTACCTTTGCGGCTTCAATTTA-TTTTTCTACAGGTTTG
1 AGATTCGCCTTTGCAGCTTCAATTTAGCCTTT-TACAGCTTCG
1709 AGATTCGCCTTTG
1 AGATTCGCCTTTG
1722 TGACTTTAGT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
41 3 0.07
42 40 0.93
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (42 bp):
AGATTCGCCTTTGCAGCTTCAATTTAGCCTTTTACAGCTTCG
Found at i:1800 original size:49 final size:49
Alignment explanation
Indices: 1747--1977 Score: 153
Period size: 49 Copynumber: 4.7 Consensus size: 49
1737 TCATCTTCAA
*
1747 GGTATAAGATTCGTCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTGG
1 GGTATAAGATTCGTCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTAG
* * *** * * * * *
1796 GGTATAAGGTTCGCCGTTATGGCATCGACCTTTCCTTTCACATCTTTAG
1 GGTATAAGATTCGTCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTAG
* * * * ** * ** * *
1845 GGT-TCAAGATTC-ACTGTTACGGCTTCAATC-TGACTTTCTTATTTCTAA
1 GGTAT-AAGATTCGTC-GTTGCAGCCTCAATCTTTCCCTTCACATCTCTAG
* * * *
1893 GGTATAAGGTTCGTCATTGTAGCCTCAATCTTTCCCTTCACATCTGTAG
1 GGTATAAGATTCGTCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTAG
* * * *
1942 GGTATAAGATTCGTTGTCGCAGCTTCAATTTTTCCC
1 GGTATAAGATTCGTCGTTGCAGCCTCAATCTTTCCC
1978 ATCTCGTCTT
Statistics
Matches: 131, Mismatches: 46, Indels: 10
0.70 0.25 0.05
Matches are distributed among these distances:
48 32 0.24
49 99 0.76
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (49 bp):
GGTATAAGATTCGTCGTTGCAGCCTCAATCTTTCCCTTCACATCTCTAG
Found at i:2849 original size:3 final size:3
Alignment explanation
Indices: 2836--2887 Score: 51
Period size: 3 Copynumber: 18.7 Consensus size: 3
2826 CCTCTCATTT
*
2836 TTC TT- TTC TTC TTC TTC TTC TTC TTC TT- TT- TTCC TTT TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT-C TTC TTC TTC
2878 TTC TT- TTC TT
1 TTC TTC TTC TT
2888 TTTTCTCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
2 10 0.24
3 30 0.71
4 2 0.05
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (3 bp):
TTC
Found at i:2890 original size:6 final size:6
Alignment explanation
Indices: 2833--2890 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
2823 TGACCTCTCA
* * *
2833 TTTTTC -TTTTC TTCTTC TTCTTC TTCTTC TTTTTTCC TTTTTC -TTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC -TTTTT-C TTTTTC TTTTTC
2881 -TTTTC TTTTT
1 TTTTTC TTTTT
2891 TCTCTCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
5 15 0.33
6 21 0.46
7 9 0.20
8 1 0.02
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:2891 original size:12 final size:12
Alignment explanation
Indices: 2839--2902 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
2829 CTCATTTTTC
2839 TTTTCTTCTTC-T
1 TTTTCTT-TTCTT
*
2851 TCTTCTTCTTCTT
1 TTTTCTT-TTCTT
*
2864 TTTTCCTTTT-TC
1 TTTT-CTTTTCTT
2876 TTTTCTTTTCTT
1 TTTTCTTTTCTT
*
2888 TTTTC-TCTCTT
1 TTTTCTTTTCTT
2899 TTTT
1 TTTT
2903 GGGGTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 14 0.32
12 21 0.48
13 6 0.14
14 3 0.07
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:2901 original size:17 final size:15
Alignment explanation
Indices: 2833--2901 Score: 59
Period size: 17 Copynumber: 4.3 Consensus size: 15
2823 TGACCTCTCA
2833 TTTTTC-TTTTCTTC
1 TTTTTCTTTTTCTTC
* *
2847 TTCTTCTTCTTCTTC
1 TTTTTCTTTTTCTTC
*
2862 TTTTTTCCTTTTTCTTT
1 -TTTTT-CTTTTTCTTC
2879 TCTTTTCTTTTTTCTCTC
1 T-TTTTC-TTTTTCT-TC
2897 TTTTT
1 TTTTT
2902 TGGGGTAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
14 5 0.12
15 7 0.16
16 6 0.14
17 23 0.53
18 2 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTTTTCTTC
Found at i:3774 original size:24 final size:23
Alignment explanation
Indices: 3746--3791 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3736 TTCATCATAA
3746 CTTTTCTTTCTT-TTCTTTTCTTTG
1 CTTTTCTTT-TTCTT-TTTTCTTTG
3770 CTTTTCTTTTTCTTTTTTCTTT
1 CTTTTCTTTTTCTTTTTTCTTT
3792 TCTTGGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (23 bp):
CTTTTCTTTTTCTTTTTTCTTTG
Found at i:3782 original size:6 final size:5
Alignment explanation
Indices: 3746--3795 Score: 61
Period size: 5 Copynumber: 10.6 Consensus size: 5
3736 TTCATCATAA
* *
3746 CTTTT C-TTT CTTTT CTTTT CTTTG CTTTT CTTTT -TCTT -TTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3793 CTT
1 CTT
3796 GGGTTTTAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 10 0.26
5 29 0.74
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
CTTTT
Found at i:3802 original size:28 final size:30
Alignment explanation
Indices: 3747--3802 Score: 80
Period size: 28 Copynumber: 1.9 Consensus size: 30
3737 TCATCATAAC
*
3747 TTTTCTTTCTTTTCTTTTCTTTGCTTTTCT
1 TTTTCTTTCTTTTCTTTTCTTGGCTTTTCT
*
3777 TTTTC-TT-TTTTCTTTTCTTGGGTTTT
1 TTTTCTTTCTTTTCTTTTCTTGGCTTTT
3803 AAGATACCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.71
29 2 0.08
30 5 0.21
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (30 bp):
TTTTCTTTCTTTTCTTTTCTTGGCTTTTCT
Found at i:3858 original size:16 final size:14
Alignment explanation
Indices: 3839--3900 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 14
3829 TCATCTCGAC
3839 CTTTTTCTTTTCTTTT
1 CTTTTTC-TTTC-TTT
3855 CTTTTTCTTTCTTT
1 CTTTTTCTTTCTTT
3869 C--TTTCTTTCTTT
1 CTTTTTCTTTCTTT
3881 CTTTTTCCTCTT-TTT
1 CTTTTT-CT-TTCTTT
3896 CTTTT
1 CTTTT
3901 GACCTCTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.29
14 7 0.17
15 14 0.33
16 9 0.21
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
CTTTTTCTTTCTTT
Found at i:3867 original size:4 final size:4
Alignment explanation
Indices: 3858--3884 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3848 TTCTTTTCTT
3858 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
3885 TTCCTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:3910 original size:15 final size:15
Alignment explanation
Indices: 3878--3911 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3868 TCTTTCTTTC
*
3878 TTTCTTTTTCCTCTT
1 TTTCTTTTACCTCTT
3893 TTTCTTTTGACCTCTT
1 TTTCTTTT-ACCTCTT
3909 TTT
1 TTT
3912 GATAACATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTCTTTTACCTCTT
Found at i:7248 original size:30 final size:29
Alignment explanation
Indices: 7214--7344 Score: 158
Period size: 29 Copynumber: 4.4 Consensus size: 29
7204 AATGGGGTCA
* *
7214 AAAATG-AAGTTTTGGAGAATTTTAGGGGTT
1 AAAATGTAA-TTTTGGAAAAGTTTA-GGGTT
*
7244 AAAATATAATTTTGGAAAAGTTTAGGGTT
1 AAAATGTAATTTTGGAAAAGTTTAGGGTT
* *
7273 AAAAAGTAATTTTGGAAAAGTTTAAGGGTA
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT
*
7303 AAAATGTAATTTTTGG-AAAGTTTAGAGTT
1 AAAATGTAA-TTTTGGAAAAGTTTAGGGTT
7332 AAAATGTAATTTT
1 AAAATGTAATTTT
7345 AAGAAAGTTT
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
28 4 0.04
29 39 0.44
30 38 0.43
31 8 0.09
ACGTcount: A:0.40, C:0.00, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTT
Found at i:7307 original size:59 final size:59
Alignment explanation
Indices: 7223--7344 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 59
7213 AAAAATGAAG
* * * * *
7223 TTTTGGAGAATTTTAGGGGTTAAAATATAA-TTTTGGAAAAGTTTAGGGTTAAAAAGTAA
1 TTTTGGAAAAGTTTAAGGGTAAAAATATAATTTTTGG-AAAGTTTAGAGTTAAAAAGTAA
* *
7282 TTTTGGAAAAGTTTAAGGGTAAAAATGTAATTTTTGGAAAGTTTAGAGTTAAAATGTAA
1 TTTTGGAAAAGTTTAAGGGTAAAAATATAATTTTTGGAAAGTTTAGAGTTAAAAAGTAA
7341 TTTT
1 TTTT
7345 AAGAAAGTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
59 49 0.89
60 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.22, T:0.39
Consensus pattern (59 bp):
TTTTGGAAAAGTTTAAGGGTAAAAATATAATTTTTGGAAAGTTTAGAGTTAAAAAGTAA
Found at i:7973 original size:2 final size:2
Alignment explanation
Indices: 7966--8000 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7956 ACCAGAGTAA
*
7966 AT AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
8001 AATGCTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Done.